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Sample records for deltasup 18osub pdb

  1. Isotopic variations ({delta}{sup 13} C and {delta}{sup 18} O) in Siderastrea stellata (Cnidaria-Anthozoa), Itamaraca island, State of Pernambuco, Northeastern Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Valderez P.; Sial, Alcides N. [Pernambuco Univ., Recife, PE (Brazil). Dept. de Geologia. Lab. de Isotopos Estaveis; Mayeal, Elga M.; Exner, Marco Antonio [Pernambuco Univ., Recife, PE (Brazil). Dept. de Zoologia. Lab. de Macro e Megabentos

    1998-12-01

    Isotopic determinations for O and C were performed in coral skeletons collected in beach rocks from two localities (Orange and Catuama), Itamaraca Island, north littoral of the State of pernambuco, northeastern Brazil. Large variations of {delta}{sup 18} O and {delta}{sup 13} C in corals from both localities are found, the largest ones being observed at the Orange locality {delta}{sup 13} C in this locality varies from -0.8 to +1.8% PDB and {delta}{sup 1.8} O from -5.3 to -1.8% PDB, while at the Catuama locality, they vary from -1.8 to 0.1% PDB and -3.8 to -2.7% PDB, respectively. Large variations in {delta}{sup 18} O (up to 2.5%) coupled with weakly defined positive correlation between {delta}{sup 18} O and {delta}{sup 13} C, can be attributed to temperature variations as consequence of climatic perturbations. Temperature estimates, calculated from {delta}{sup 18} O values, assuming isotopic equilibrium with seawater, yield values between 24.9 deg C and 43.1 deg C at Orange, and from 28.4 deg C to 35 deg C at Catuama, all of them (expect one growth band from one sample) are high enough for the full development of the coral colony. Temperature average is 31.4 deg C at Orange, which is a little bit higher than that at Catuama, but both of them indicate thermal stress conditions. In all analyzed specimens, expect for one, at Orange, T increases was accompanied by decreasing in the organic activity, as suggested by corresponding negative {delta}{sup 13} C anomaly. Therefore, the observed bleaching is possibly related to thermal stress and the high T may be related to the El Nino-Southern Oscillation (ENSO) warning event. On the other hand, anthropogenic action at Orange, local of intense tourism throughout the year, coupled with high rate of sedimentation in the region, may contribute to the observed coral bleaching. (author)

  2. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  3. PDBCOP: PDB comparison program

    Czech Academy of Sciences Publication Activity Database

    Fejfarová, Karla; Dohnálek, Jan; Hašek, Jindřich

    2015-01-01

    Roč. 22, č. 1 (2015), s. 35 ISSN 1211-5894. [Discussions in Structural Molecular Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] R&D Projects: GA MŠk(CZ) EE2.3.30.0029; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 ; RVO:86652036 Keywords : crystal structure * protein * PDB Subject RIV: CE - Biochemistry

  4. Unexpected {delta}{sup 18}O and {delta}{sup 2}H Variability of Groundwater in the Eastern Paris Basin

    Energy Technology Data Exchange (ETDEWEB)

    Gourcy, L.; Petelet-Giraud, E. [BRGM Service EAU, Orleans (France)

    2013-07-15

    The Paris Basin covers about one-third of the total surface area of France. In 2009, two campaigns sampling 25 boreholes tapping Tertiary aquifers were carried out in the Basin. These aquifers are recharged at a similar altitude and the groundwater age is too young to have registered climate change. In the past, regional studies included the use of isotopes to understand groundwater origin and dynamics. Both {delta}{sup 18}O and {delta}{sup 2}H as well as ages (CFC/SF{sub 6)} and chemical components were determined in all collected samples. A noticeable stable isotope 'anomaly' appears in the south-western part of the Basin, where the average {delta}{sup 18}O and {delta}{sup 2}H values are more depleted and do not fit the pattern given by the continental effect in this area. A regional particularity of the spatial distribution of such isotopes in precipitation may be possible, but should be confirmed by additional work. (author)

  5. PDBsum: Structural summaries of PDB entries

    OpenAIRE

    Laskowski, Roman A.; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M.

    2017-01-01

    Abstract PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image‐based and include protein secondary structure, protein‐ligand and protein‐DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password‐protected PDBsum analyses for e...

  6. PDBsum: Structural summaries of PDB entries.

    Science.gov (United States)

    Laskowski, Roman A; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M

    2018-01-01

    PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum. © 2017 The Protein Society.

  7. PDB: CBRC-HSAP-10-0036 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-HSAP-10-0036 1HLL,1HO9,1HOD,1HOF, Region:118-149(Identity=100%) PDB:1HLL Chain...:A (NMR),Region:118-149(Identity=100%) PDB:1HO9 Chain:A (NMR),Region:118-149(Identity=100%) PDB:1HOD Chain:A (NMR),Region:118-149(Identity=100%) PDB:1HOF Chain:A (NMR), ...

  8. PDB: CBRC-MMUS-19-0098 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUS-19-0098 1HLL,1HO9,1HOD,1HOF, Region:133-164(Identity=100%) PDB:1HLL Chain...:A (NMR),Region:133-164(Identity=100%) PDB:1HO9 Chain:A (NMR),Region:133-164(Identity=100%) PDB:1HOD Chain:A (NMR),Region:133-164(Identity=100%) PDB:1HOF Chain:A (NMR), ...

  9. PDB: CBRC-BTAU-01-1941 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-BTAU-01-1941 1HLL,1HO9,1HOD,1HOF, Region:118-149(Identity=100%) PDB:1HLL Chain...:A (NMR),Region:118-149(Identity=100%) PDB:1HO9 Chain:A (NMR),Region:118-149(Identity=100%) PDB:1HOD Chain:A (NMR),Region:118-149(Identity=100%) PDB:1HOF Chain:A (NMR), ...

  10. PDB: CBRC-BTAU-01-2619 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-BTAU-01-2619 1U34,2JNC,2JND, Region:43-137(Identity=85%) PDB:1U34 Chain:A (NMR),Region:43-137(Identity...=85%) PDB:2JNC Chain:A (NMR),Region:43-137(Identity=85%) PDB:2JND Chain:A (NMR), ...

  11. PDB: CBRC-PABE-08-0030 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PABE-08-0030 1U34,2JNC,2JND, Region:45-139(Identity=85%) PDB:1U34 Chain:A (NMR),Region:45-139(Identity...=85%) PDB:2JNC Chain:A (NMR),Region:45-139(Identity=85%) PDB:2JND Chain:A (NMR), ...

  12. PDB: CBRC-PCAP-01-1657 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PCAP-01-1657 1U34,2JNC,2JND, Region:43-137(Identity=80%) PDB:1U34 Chain:A (NMR),Region:43-137(Identity...=80%) PDB:2JNC Chain:A (NMR),Region:43-137(Identity=80%) PDB:2JND Chain:A (NMR), ...

  13. Controls of {delta}{sup 34}S and {delta}{sup 18}O in dissolved sulphate: Learning from a detailed survey in the Llobregat River (Spain)

    Energy Technology Data Exchange (ETDEWEB)

    Otero, Neus [Departament Cristal . lografia, Mineralogia i Diposits Minerals, Facultat de Geologia, Universitat de Barcelona, Marti i Franques, s/n, 08028 Barcelona (Spain); Grup d' Hidrogeoquimica, Departament de Geologia Ambiental, Institut de Ciencies de la Terra ' Jaume Almera' , CSIC, Lluis Sole i Sabaris, s/n, 08028 Barcelona (Spain)], E-mail: notero@ub.edu; Soler, Albert; Canals, Angels [Departament Cristal . lografia, Mineralogia i Diposits Minerals, Facultat de Geologia, Universitat de Barcelona, Marti i Franques, s/n, 08028 Barcelona (Spain)

    2008-05-15

    The S and O isotopic composition of dissolved SO{sub 4}, used as a tracer for SO{sub 4} sources, was applied to the water of the Llobregat River system (NE Spain). The survey was carried out at 30 sites where surface water was sampled on a monthly basis over a period of 2a. The concentration of dissolved SO{sub 4} varied from 20 to 1575 mg L{sup -1}. Sulphur isotopic compositions clustered in two populations: one - 93% of the samples - had positive values with a mode of +9 per mille ; the other had negative values and a mode of -5 per mille . Data for {delta}{sup 18}O{sub SO{sub 4}} showed a mean value of +11 per mille , with no bi-modal distribution, though lower values of {delta}{sup 18}O corresponded to samples with negative {delta}{sup 34}S. These values can not be explained solely by the contribution of bedrock SO{sub 4} sources: that is, sulphide oxidation and the weathering of outcrops of sulphates, though numerous chemical sediments exist in the basin. Even in a river with a high concentration of natural sources of dissolved SO{sub 4}, such as the Llobregat River, the {delta}{sup 34}S values suggest that dissolved SO{sub 4} is controlled by a complex mix of both natural and anthropogenic sources. The main anthropogenic sources in this basin are fertilizers, sewage, potash mine effluent and power plant emissions. Detailed river water sampling, together with the chemical and isotopic characterisation of the main anthropogenic inputs, allowed determination of the influence of redox processes, as well as identification of the contribution of natural and anthropogenic SO{sub 4} sources and detection of spatial variations and seasonal changes among these sources. For instance, in the Llobregat River the input of fertilisers is well marked seasonally. Minimum values of {delta}{sup 34}S are reported during fertilization periods - from January to March - indicating a higher contribution of this source. The dual isotope approach, {delta}{sup 34}S and {delta}{sup 18}O

  14. The young person's guide to the PDB.

    Science.gov (United States)

    Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

  15. PDB: CBRC-TNIG-22-0159 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2WBE,3DU7,2E4H, Region:346-770(Identity=93%) PDB:3E22 Chain:A (X-ray Resolution=3.80),Region:346-770(Identity...=95%) PDB:3DCO Chain:A (EM Resolution=1.90),Region:346-770(Identity=95%) PDB:3EDL Chain:A (EM Resolution=28.00),Region:346-770(Ident...ity=94%) PDB:1FFX Chain:A (X-ray Resolution=3.95),Region:346-770(Identity...=94%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:346-770(Identity=94%) PDB:1JFF Chain:A ...(EM Resolution=3.50),Region:346-770(Identity=94%) PDB:1SA0 Chain:A (X-ray Resolution=3.58),Region:346-770(Identity

  16. PDB@: an offline toolkit for exploration and analysis of PDB files.

    Science.gov (United States)

    Mani, Udayakumar; Ravisankar, Sadhana; Ramakrishnan, Sai Mukund

    2013-12-01

    Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

  17. Coral skeletal {delta}{sup 15}N reveals isotopic traces of an agricultural revolution

    Energy Technology Data Exchange (ETDEWEB)

    Marion, Guy S. [Department of Biological Sciences, Stanford University, Stanford, CA 94305 (United States)]. E-mail: g.marion@uq.edu.au; Dunbar, Robert B. [Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305 (United States); Mucciarone, David A. [Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305 (United States); Kremer, James N. [Department of Marine Sciences, University of Connecticut at Avery Point, Groton, CT 06340 (United States); Lansing, J. Stephen [Department of Anthropology, University of Arizona, Tucson, AZ 85721 (United States); Arthawiguna, Alit [Installation for Agricultural Research (IP 2TP), Kotak Pos 3480, Denpasar, Bali (Indonesia)

    2005-09-01

    This study introduces a new method of tracing the history of nutrient loading in coastal oceans via {delta}{sup 15}N analysis of organic nitrogen preserved in the skeleton of the massive Porites coral. Four coral cores were collected in Bali, Indonesia, from reefs exposed to high levels of fertilizers in agricultural run-off, from lagoonal corals impacted by sewage, and from a reef located 30 km offshore. Skeletal {delta}{sup 15}N in the agriculturally exposed coral declined from 10.7 {+-} 0.4 per mille in 1970-1971, when synthetic fertilizers (-0.8 per mille {+-} 0.2 per mille ) were introduced to Bali, to a depleted 'anthropogenic' baseline of 3.5 per mille {+-} 0.4% in the mid-1990s. {delta}{sup 15}N values were negatively correlated with rainfall, suggesting that marine {delta}{sup 15}N lowers during flood-born influxes of waste fertilizers. Reef cores exposed to untreated sewage in terrestrial discharge were enriched (7.8 and 7.3 {+-} 0.4 per mille ), while the offshore core reflected background oceanic signals (6.2 {+-} 0.4 per mille). {delta}{sup 15}N, N concentration, and C:N systematics indicate that the N isotopic composition of skeletal organic matter was generally well preserved over 30 years. We suggest that skeletal organic {delta}{sup 15}N can serve as a recorder of past nitrogen sources. In Bali, this tracer suggests that the intensification of Western style agricultural practices since 1970 are contributing to the degradation of coastal coral reefs.

  18. PDB: CBRC-CJAC-01-0391 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CJAC-01-0391 1FFX,1IA0,1JFF,1SA0,1SA1,1TUB,1TVK,2WBE,1Z2B,3DCO,3DU7,3E22, Region:421-804(Identity...=82%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:421-804(Identity=82%) PDB:1IA0 Chai...n:B (EM Resolution=15.00),Region:421-804(Identity=82%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:421-804(Identity...=82%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:421-804(Identity=82...%) PDB:1SA1 Chain:B (X-ray Resolution=4.20),Region:421-788(Identity=82%) PDB:1TUB Chain:B (EM Resolution=3.70),Region:421-788(Identit

  19. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

    Science.gov (United States)

    Burley, Stephen K; Berman, Helen M; Kleywegt, Gerard J; Markley, John L; Nakamura, Haruki; Velankar, Sameer

    2017-01-01

    The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

  20. PDB: CBRC-CJAC-01-1334 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CJAC-01-1334 2R4R,2RH1,3D4S,2R4S, Region:32-398(Identity=96%) PDB:2R4R Chain:A... (X-ray Resolution=3.40),Region:32-398(Identity=96%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:32-398(Identity...=96%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:55-398(Identity=96%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  1. PDB: CBRC-HSAP-05-0044 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-HSAP-05-0044 2R4R,2RH1,3D4S,2R4S, Region:1-365(Identity=99%) PDB:2R4R Chain:A ...(X-ray Resolution=3.40),Region:1-365(Identity=99%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:1-365(Identity...=99%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:24-365(Identity=99%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  2. PDB: CBRC-RMAC-06-0031 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-RMAC-06-0031 2R4R,2RH1,3D4S,2R4S, Region:1-367(Identity=98%) PDB:2R4R Chain:A ...(X-ray Resolution=3.40),Region:1-367(Identity=98%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:1-367(Identity...=98%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:24-367(Identity=97%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  3. PDB: CBRC-PTRO-06-0041 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-06-0041 2R4R,2RH1,3D4S,2R4S, Region:85-449(Identity=99%) PDB:2R4R Chain:A... (X-ray Resolution=3.40),Region:85-449(Identity=99%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:85-449(Identity...=99%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:108-449(Identity=99%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  4. Three New Offset {delta}{sup 11}B Isotope Reference Materials for Environmental Boron Isotope Studies

    Energy Technology Data Exchange (ETDEWEB)

    Rosner, M. [BAM Federal Institute for Materials Research and Testing, Berlin (Germany); IsoAnalysis UG, Berlin (Germany); Vogl, J. [BAM Federal Institute for Materials Research and Testing, Berlin (Germany)

    2013-07-15

    The isotopic composition of boron is a well established tool in various areas of science and industry. Boron isotope compositions are typically reported as {delta}{sup 11}B values which indicate the isotopic difference of a sample relative to the isotope reference material NIST SRM 951. A significant drawback of all of the available boron isotope reference materials is that none of them covers a natural boron isotope composition apart from NIST SRM 951. To fill this gap of required {delta}{sup 11}B reference materials three new solution boric acid reference materials were produced, which cover 60 per mille of the natural boron isotope variation (-20 to 40 per mille {delta}{sup 11}B) of about 100 per mille . The new reference materials are certified for their {delta}{sup 11}B values and are commercially available through European Reference Materials (http://www.erm-crm.org). The newly produced and certified boron isotope reference materials will allow straightforward method validation and quality control of boron isotope data. (author)

  5. Spatio-temporal distributions of delta>18O, delta D and salinity in the Arabian Sea: Identifying processes and controls

    Digital Repository Service at National Institute of Oceanography (India)

    Deshpande, R.D; Muraleedharan, P.M.; Singh, R.L.; Kumar, B.; Rao, M.S.; Dave, M.; Sivakumar, K.U.; Gupta, S.K.

    the geographic distributions of the delta>18O and S; (2) in spite of a large scatter, a statistically significant delta>18O–S relationship can be identified in much of the investigated part of the AS; (3) the delta>18O– delta...

  6. {delta}{sup 15}N of seagrass leaves for monitoring anthropogenic nutrient increases in coral reef ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Yamamuro, M.; Kayanne, H.; Yamano, H

    2003-04-01

    In a coral reef environment, a slight increase in dissolved inorganic nitrogen (DIN;{>=}1.0 {mu}M) can alter the ecosystem via macroalgal blooms. We collected seagrass leaves from the tropical and subtropical Pacific Ocean in five countries and examined the interactions between nutrient concentrations (C, N, P), molar ratios of nutrients, and {delta}{sup 15}N to find a possible indicator of the DIN conditions. Within most sites, the concentrations of nutrients and their molar ratios showed large variations owing to species-specific values. On the other hand, almost identical {delta}{sup 15}N values were found in seagrass leaves of several species at each site. The correlations between {delta}{sup 15}N and nutrient concentrations and between {delta}{sup 15}N and molar ratios of nutrients suggested that nutrient availability did not affect the {delta}{sup 15}N value of seagrass leaves by altering the physiological condition of the plants. Increases in {delta}{sup 15}N of seagrass leaves mostly matched increases in DIN concentrations in the bottom water. We suggest that {delta}{sup 15}N in seagrass leaves can be a good tool to monitor time-integrated decrease/increase of DIN concentrations at a site, both in the water column and the interstitial water.

  7. PDB: CBRC-PTRO-04-0067 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=93%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=93%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=95%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=93%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=93%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=93%) PDB:1GZM Chain:A (X-ray Resolut

  8. PDB: CBRC-PABE-04-0004 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=93%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=93%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=95%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=93%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=93%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=93%) PDB:1GZM Chain:A (X-ray Resolut

  9. PDB: CBRC-TTRU-01-1321 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2G87,2HPY,2I35,2I36,3C9M,2J4Y,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=92%) PDB:2I37 Chain:...A (X-ray Resolution=4.15),Region:1-348(Identity=92%) PDB:2PED Chain:A (X-ray Resolution=2.95),Region:1-348(Identity...=92%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity=92%) ...PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=92%) PDB:1EDX Chain:A (NMR),Region:1-348(Identity...=92%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity=92%) PDB:3DQB Chain:A (X-ray Resolut

  10. PDB: CBRC-HSAP-03-0075 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=93%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=93%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=95%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=93%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=93%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=93%) PDB:1GZM Chain:A (X-ray Resolut

  11. PDB: CBRC-CPOR-01-1479 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2G87,2HPY,2I35,2I36,3C9M,2J4Y,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-354(Identity=88%) PDB:2I37 Chain:...A (X-ray Resolution=4.15),Region:1-354(Identity=88%) PDB:2PED Chain:A (X-ray Resolution=2.95),Region:1-354(Identity...=88%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-354(Identity=88%) ...PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=87%) PDB:1EDX Chain:A (NMR),Region:1-354(Identity...=88%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-354(Identity=88%) PDB:3DQB Chain:A (X-ray Resolut

  12. PDB: CBRC-RMAC-11-0073 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=93%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=93%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=95%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=93%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=93%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=93%) PDB:1GZM Chain:A (X-ray Resolut

  13. PDB: CBRC-CFAM-20-0004 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=94%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=94%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=94%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=97%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=94%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=94%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=94%) PDB:1GZM Chain:A (X-ray Resolut

  14. PDB: CBRC-OANA-01-1800 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2G87,2HPY,2I35,2I36,3C9M,2J4Y,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-353(Identity=89%) PDB:2I37 Chain:...A (X-ray Resolution=4.15),Region:1-353(Identity=89%) PDB:2PED Chain:A (X-ray Resolution=2.95),Region:1-353(Identity...=89%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-353(Identity=89%) ...PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=82%) PDB:1EDX Chain:A (NMR),Region:1-353(Identity...=89%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-353(Identity=89%) PDB:3DQB Chain:A (X-ray Resolut

  15. PDB: CBRC-PVAM-01-0804 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=94%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=94%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=94%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=97%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=94%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=94%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=94%) PDB:1GZM Chain:A (X-ray Resolut

  16. PDB: CBRC-GGOR-01-1431 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=93%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=93%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=95%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=93%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=93%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=93%) PDB:1GZM Chain:A (X-ray Resolut

  17. PDB: CBRC-FCAT-01-1134 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available 2HPY,2I35,2I36,2I37,2J4Y,3C9M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity=95%) PDB:2PED Chain:...A (X-ray Resolution=2.95),Region:1-348(Identity=95%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Region:1-348(Identity...=95%) PDB:3CAP Chain:A (X-ray Resolution=2.90),Region:1-40(Identity=97%) P...DB:1EDX Chain:A (NMR),Region:1-348(Identity=95%) PDB:1F88 Chain:A (X-ray Resolution=2.80),Region:1-348(Identity...=95%) PDB:3DQB Chain:A (X-ray Resolution=3.20),Region:1-348(Identity=95%) PDB:1GZM Chain:A (X-ray Resolut

  18. Representation of viruses in the remediated PDB archive

    International Nuclear Information System (INIS)

    Lawson, Catherine L.; Dutta, Shuchismita; Westbrook, John D.; Henrick, Kim; Berman, Helen M.

    2008-01-01

    A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described. A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive

  19. The PDB_REDO server for macromolecular structure model optimization

    Directory of Open Access Journals (Sweden)

    Robbie P. Joosten

    2014-07-01

    Full Text Available The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB. The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011, Structure, 19, 1395–1412]. The PDB_REDO procedure aims for `constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallographers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.

  20. BLOCKS - PDB ATOM matching - DB-SPIRE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us DB-SPIRE BLOCKS - PDB ATOM matching Data detail Data name BLOCKS - PDB ATOM matching DOI 10....18908/lsdba.nbdc00411-008 Description of data contents Sequence numbers of PDB entries/chains whose ATOM mat...ches a BLOCKS entry Data file File name: dbspire_blocks_pdb_atom.zip File URL: ftp://ftp.biosciencedbc.jp/ar...chive/dbspire/LATEST/dbspire_blocks_pdb_atom.zip File size: 6.2 MB Simple search ...URL http://togodb.biosciencedbc.jp/togodb/view/dbspire_blocks_pdb_atom#en Data acquisition method BLOCKS, PD

  1. {delta}{sup 13}C in Tibetan juniper trees - climate trends through the past 1600 years; {delta}{sup 13}C in tibetischen Wacholdern - Klimaentwicklung der letzten 1600 Jahre

    Energy Technology Data Exchange (ETDEWEB)

    Zimmermann, B.

    1998-09-01

    A {delta}{sup 13}C{sub Zell}-chronology of juniper tree cellulose from the upper treeline covering the last 1600 years was set up. The tree site is situated close to Qamdo in southeast Tibet at an altitude of 4350 m a.s.l. The southwest slope gets rain during the Indian summer monsoon. Ten trees have been sampled either by coring or by cutting of trunc-sections in pentad sampling interval. Three trees were analysed in two different radial directions. The very positive {delta}{sup 13}C{sub Zell}-data generally varying around -18,75 permille show the typical low fractionation of high mountain plants. Different interpretations are suggested for data before and after 1800 A.D. (orig.) [Deutsch] An Zellulose von Wacholdern der oberen Waldgrenze in Suedost-Tibet wurde eine 1600-jaehrige {delta}{sup 13}C{sub Zell}-Chronologie aufgestellt. Der Standort liegt in 4350 m ue.M. in der Naehe von Qamdo, ist nach Suedwest geneigt und erhaelt Niederschlaege in den Sommermonaten durch den Indischen-Suedwest-Monsun. Zehn Baeume wurden anhand von Kernen und Stammscheiben in Abschnitten von fuenf Jahren beprobt. An drei Baeumen konnten zwei Segmente desselben Baumes untersucht werden. Die im Mittel sehr positiven {delta}{sup 13}C{sub Zell}-Daten um -18,75 permille deuten auf eine fuer Hochgebirgspflanzen typische geringere Fraktionierung hin. Unterschiedliche Interpretationswege werden fuer die Daten vor und nach 1800 verfolgt. (orig.)

  2. Multivariate analysis of calcareous nanno fossils and stable isotopic ({delta}{sup 18}O and {delta}{sup 13}C) in the upper Campanian - lower Maastrichtian of the Campos Basin, Brazil; Analise multivariada em nanofosseis calcarios e isotopos estaveis ({delta}{sup 18}O e {delta}{sup 13}C) do Campaniano superior - Maastrichtiano inferior na Bacia de Campos

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Luiz Carlos Veiga de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas. Gerencia de Bioestratigrafia e Paleoecologia]. E-mail: lcveiga@petrobras.com.br; Rodrigues, Rene; Lemos, Valesca Brasil

    2005-05-01

    Qualitative analysis in calcareous nanno fossils is a powerful tool for bio stratigraphic uses, principally in identification of bio zones and determination of relative age. But quantitative studies must be applied for pale oceanographic applications and high resolution bio stratigraphy. In order to better understand the relationships between the different species of nanno fossils, new methodologies and non-traditional correlation tools were tested on a 18 m upper Campanian - lower Maastrichtian core from Campos Basin. Multiple regression helped to determine the best counting method. Watznaueria barnesae and Micula decussata dominate the fossil assemblage and have inverse abundances to each other. Both were opportunist species in competition for nutrients. Q mode factorial analysis (57 samples, 19 variables) was applied to the same core and shows that two factors explain 99.2% of the total variance of the micro fossil assemblage. The first factor represents 83.6% and the second factor only 15.6% of the total variance. The former is associated with Watznaueria barnesae, Cribrosphaerella ehrenbergii and Stradneria crenulata, which represent the original population of nano plankton. The latter factor is associated with Micula decussata, which is believed to represent the effect of solution at the sediment water interface. Both factors were used to develop a dissolution-sea level curve for nanno fossils. When combined with oxygen and carbon isotopes, this curve clearly shows that higher dissolution occurred during the late Campanian - early Maastrichtian time when {delta}{sup 18}O, {delta}{sup 13} C and TOC all had lower values. These correlations indicate a strong link between high sea levels, high temperatures and lower amount of continental organic debris. (author)

  3. Recommendations of the wwPDB NMR Validation Task Force

    Science.gov (United States)

    Montelione, Gaetano T.; Nilges, Michael; Bax, Ad; Güntert, Peter; Herrmann, Torsten; Richardson, Jane S.; Schwieters, Charles; Vranken, Wim F.; Vuister, Geerten W.; Wishart, David S.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.

    2013-01-01

    As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with the wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment. PMID:24010715

  4. Using Whole Stream {delta}{sup 15}N Additions to Understand the Effects of Land Use Change on Stream Function

    Energy Technology Data Exchange (ETDEWEB)

    Deegan, L. A.; Neill, C.; Thomas, S.; Haupert, C. [Marine Biological Laboratory, Woods Hole, MA (United States); Victoria, R. L.; Krusche, A. V.; Ballester, M. V.R. [Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Sao Paulo (Brazil)

    2013-05-15

    In this paper we introduce an emerging new technique; the use of {delta}{sup 15}N stable isotope tracers to understand both short term and long term alterations in stream ecosystem nitrogen biogeochemistry and food web dynamics. The use of {delta}{sup 15}N isotopes to determine stream nitrogen cycling was developed in small tundra streams in Alaska (USA), but a network of researchers using similar technique has rapidly grown to answer questions about nitrogen cycling and stream food webs in a variety of ecosystem types and subject to human modifications. Here we provide an overview of some of the information that can be provided using stable isotope additions and describe the general approach of an isotope addition experiment. To illustrate the scope of isotope applicability some examples are provided of work undertaken in the Brazilian Amazon. (author)

  5. Metabolic origin of the {delta}{sup 13}C of respired CO{sub 2} in roots of Phaseolus vulgaris

    Energy Technology Data Exchange (ETDEWEB)

    Bathellier, C.; Tcherkez, G.; Cornic, G.; Ghashghaie, J. [Laboratoire d' Ecologie, Systematique et Evolution - ESE, CNRS-UMR 8079 - IFR 87, Batiment 362, Universite Paris-Sud, 91405-Orsay Cedex (France); Tcherkez, G. [Plateforme Metabolisme-Metabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Batiment 630, Universite Paris-Sud, 91405-Orsay Cedex (France); Bligny, R.; Gout, E. [Laboratoire de Physiologie Cellulaire Vegetale CEA-Grenoble 17, rue des Martyrs, 38054 Grenoble Cedex 9 (France)

    2009-07-01

    - Root respiration is a major contributor to soil CO{sub 2} efflux, and thus an important component of ecosystem respiration. But its metabolic origin, in relation to the carbon isotope composition ({delta}{sup 13}C), remains poorly understood. - Here, {sup 13}C analysis was conducted on CO{sub 2} and metabolites under typical conditions or under continuous darkness in French bean (Phaseolus vulgaris) roots. {sup 13}C contents were measured either under natural abundance or following pulse-chase labeling with {sup 13}C-enriched glucose or pyruvate, using isotope ratio mass spectrometer (IRMS) and nuclear magnetic resonance (NMR) techniques. - In contrast to leaves, no relationship was found between the respiratory quotient and the {delta}{sup 13}C of respired CO{sub 2}, which stayed constant at a low value (c. -27.5 per thousand) under continuous darkness. With labeling experiments, it is shown that such a pattern is explained by the {sup 13}C-depleting effect of the pentose phosphate pathway; and the involvement of the Krebs cycle fueled by either the glycolytic input or the lipid/protein recycling. The anaplerotic phosphoenolpyruvate carboxylase (PEPc) activity sustained glutamic acid (Glu) synthesis, with no net effect on respired CO{sub 2}. - These results indicate that the root {delta}{sup 13}C signal does not depend on the availability of root respiratory substrates and it is thus plausible that, unless the {sup 13}C photosynthetic fractionation varies at the leaf level, the root {delta}{sup 13}C signal hardly changes under a range of natural environmental conditions. (authors)

  6. A global analysis of NMR distance constraints from the PDB

    International Nuclear Information System (INIS)

    Vranken, Wim

    2007-01-01

    Information obtained from Nuclear Magnetic Resonance (NMR) experiments is encoded as a set of constraint lists when calculating three-dimensional structures for a protein. With the amount of constraint data from the world wide Protein Data Bank (wwPDB) that is now available, it is possible to do a global, large-scale analysis using only information from the constraints, without taking the coordinate information into account. This article describes such an analysis of distance constraints from NOE data based on a set of 1834 NMR PDB entries containing 1909 protein chains. In order to best represent the quality and extent of the data that is currently deposited at the wwPDB, only the original data as deposited by the authors was used, and no attempt was made to 'clean up' and further interpret this information. Because the constraint lists provide a single set of data, and not an ensemble of structural solutions, they are easier to analyse and provide a reduced form of structural information that is relevant for NMR analysis only. The online resource resulting from this analysis makes it possible to check, for example, how often a particular contact occurs when assigning NOESY spectra, or to find out whether a particular sequence fragment is likely to be difficult to assign. In this respect it formalises information that scientists with experience in spectrum analysis are aware of but cannot necessarily quantify. The analysis described here illustrates the importance of depositing constraints (and all other possible NMR derived information) along with the structure coordinates, as this type of information can greatly assist the NMR community

  7. ccPDB: compilation and creation of data sets from Protein Data Bank.

    Science.gov (United States)

    Singh, Harinder; Chauhan, Jagat Singh; Gromiha, M Michael; Raghava, Gajendra P S

    2012-01-01

    ccPDB (http://crdd.osdd.net/raghava/ccpdb/) is a database of data sets compiled from the literature and Protein Data Bank (PDB). First, we collected and compiled data sets from the literature used for developing bioinformatics methods to annotate the structure and function of proteins. Second, data sets were derived from the latest release of PDB using standard protocols. Third, we developed a powerful module for creating a wide range of customized data sets from the current release of PDB. This is a flexible module that allows users to create data sets using a simple six step procedure. In addition, a number of web services have been integrated in ccPDB, which include submission of jobs on PDB-based servers, annotation of protein structures and generation of patterns. This database maintains >30 types of data sets such as secondary structure, tight-turns, nucleotide interacting residues, metals interacting residues, DNA/RNA binding residues and so on.

  8. C{sub 4} plant isotopic composition ({delta}{sup 13}C) evidence for urban CO{sub 2} pollution in the city of Cotonou, Benin (West Africa)

    Energy Technology Data Exchange (ETDEWEB)

    Kelome, Nelly C.; Leveque, Jean; Andreux, Francis; Milloux, Marie-Jeanne [UMR Microbiologie et Geochimie des Sols INRA, Universite de Bourgogne, Centre des Sciences de la Terre, 6 Bd Gabriel, 21000 Dijon (France); Oyede, Lucien-Marc [Departement des Sciences de la Terre, Universite d' Abomey-Calavi, 01 B.P. 526, Cotonou (Benin)

    2006-08-01

    The carbon isotopic composition ({delta}{sup 13}C) of plants can reveal the isotopic carbon content of the atmosphere in which they develop. The {delta}{sup 13}C values of air and plants depend on the amount of atmospheric fossil fuel CO{sub 2}, which is chiefly emitted in urban areas. A new indicator of CO{sub 2} pollution is tested using the {delta}{sup 13}C variation in a C{sub 4} grass: Eleusine indica. A range of about 4%% delta units was observed at different sites in Cotonou, the largest city in the Republic of Benin. The highest {delta}{sup 13}C values, from -12%% to -14%%, were found in low traffic zones; low {delta}{sup 13}C values, from -14%% to -16%%, were found in high traffic zones. The amount of fossil fuel carbon assimilated by plants represented about 20% of the total plant carbon content. An overall decrease in plant {delta}{sup 13}C values was observed over a four-year monitoring period. This decrease was correlated with increasing vehicle traffic. The {delta}{sup 13}C dataset and the corresponding geographical database were used to map and define zones of high and low {sup 13}C-depleted CO{sub 2} emissions in urban and sub-urban areas. The spatial distribution follows dominant wind directions, with the lowest emission zones found in the southwest of Cotonou. High CO{sub 2} emissions occurred in the north, the east and the center, providing evidence of intense anthropogenic activity related to industry and transportation. (author)

  9. C{sub 4} plant isotopic composition ((delta){sup 13}C) evidence for urban CO{sub 2} pollution in the city of Cotonou, Benin (West Africa)

    Energy Technology Data Exchange (ETDEWEB)

    Kelome, Nelly C.; Leveque, Jean; Andreux, Francis; Milloux, Marie-Jeanne [UMR Microbiologie et Geochimie des Sols INRA, Universite de Bourgogne, Centre des Sciences de la Terre, 6 Bd Gabriel, 21000 Dijon (France); Oyede, Lucien-Marc [Departement des Sciences de la Terre, Universite d' Abomey-Calavi, 01 B.P. 526, Cotonou (Benin)

    2006-08-01

    The carbon isotopic composition ((delta){sup 13}C) of plants can reveal the isotopic carbon content of the atmosphere in which they develop. The (delta){sup 13}C values of air and plants depend on the amount of atmospheric fossil fuel CO{sub 2}, which is chiefly emitted in urban areas. A new indicator of CO{sub 2} pollution is tested using the (delta){sup 13}C variation in a C{sub 4} grass: Eleusine indica. A range of about 4%% delta units was observed at different sites in Cotonou, the largest city in the Republic of Benin. The highest (delta){sup 13}C values, from -12%% to -14%%, were found in low traffic zones; low (delta){sup 13}C values, from -14%% to -16%%, were found in high traffic zones. The amount of fossil fuel carbon assimilated by plants represented about 20% of the total plant carbon content. An overall decrease in plant (delta){sup 13}C values was observed over a four-year monitoring period. This decrease was correlated with increasing vehicle traffic. The (delta){sup 13}C dataset and the corresponding geographical database were used to map and define zones of high and low {sup 13}C-depleted CO{sub 2} emissions in urban and sub-urban areas. The spatial distribution follows dominant wind directions, with the lowest emission zones found in the southwest of Cotonou. High CO{sub 2} emissions occurred in the north, the east and the center, providing evidence of intense anthropogenic activity related to industry and transportation. (author)

  10. Seasonal mercury concentrations and {delta}{sup 15}N and {delta}{sup 13}C values of benthic macroinvertebrates and sediments from a historically polluted estuary in south central Chile

    Energy Technology Data Exchange (ETDEWEB)

    Diaz-Jaramillo, Mauricio, E-mail: mdiazjaramillo@conicet.gov.ar [Aquatic Systems Research Unit, EULA Chile Environmental Sciences Centre, Universidad de Concepcion (Chile); Munoz, Claudia; Rudolph, Ignacio [Aquatic Systems Research Unit, EULA Chile Environmental Sciences Centre, Universidad de Concepcion (Chile); Servos, Mark [Department of Biology, University of Waterloo, ON (Canada); Barra, Ricardo [Aquatic Systems Research Unit, EULA Chile Environmental Sciences Centre, Universidad de Concepcion (Chile)

    2013-01-01

    The Lenga Estuary is one of the most industrialized sites in south central Chile where the historic operation of chlor-alkali plants resulted in large quantities of mercury (Hg) being deposited into the estuary. This historical contamination may still represent a risk to the biota in the estuary. To investigate this four macroinvertebrates, Neotrypaea uncinata (ghostshrimp), Elminius kingii (barnacle), Hemigrapsus crenulatus (shore crab) and Perinereis gualpensis (ragworm) were collected seasonally from three different sites in the Lenga Estuary and one in a reference estuary (Tubul Estuary), and analyzed for Hg and stable isotopes ({delta}{sup 15}N and {delta}{sup 13}C). Mercury concentrations in Lenga sediments ranged from 0.4 {+-} 0.1 to 13 {+-} 3 mg/kg, while those in Tubul sediments ranged from 0.02 {+-} 0.01 to 0.07 {+-} 0.09 mg/kg. Total Hg concentrations of invertebrates were significantly different between estuaries (p < 0.05), but not by species or season for each estuary (p > 0.05). In contrast, organic Hg concentrations were different by species and season with shore crab muscle tissues exhibiting the greatest percent difference. Site-specific relationships demonstrated that total Hg concentrations in ragworm best reflected the total Hg sediment mercury concentrations. Signatures of {delta}{sup 13}C were correlated to the organic Hg % rather than total Hg. This suggests that organic Hg concentrations in these species were related to the carbon sources. -- Highlights: Black-Right-Pointing-Pointer Hg in sediments and biota from Lenga Estuary were elevated compared to nearby estuary. Black-Right-Pointing-Pointer Invertebrates showed interspecific and seasonal differences in terms of organic Hg %. Black-Right-Pointing-Pointer Total Hg levels in the ragworm best reflect Hg sediment gradient in Lenga Estuary. Black-Right-Pointing-Pointer Interspecific variation in {delta}{sup 13}C signatures indicated different feeding modes. Black

  11. The Use of {delta}{sup 37}CL to Explain Origin and Production of Salt from the Saline Spring 'Fonte da Pipa' in Rio Maior (Central Portugal)

    Energy Technology Data Exchange (ETDEWEB)

    Eggenkamp, H. G.M.; Marques, J. M. [Centro de Petrologia e Geoquimica, Instituto Superior Tecnico, Lisbon (Portugal); Graca, H. [Centro Hospitalar das Caldas da Rainha, Caldas da Rainha (Portugal)

    2013-07-15

    Salt extraction in Rio Maior (Central Portugal) is unique in the sense that salt is exploited from a very saline (134 g/L NaCl) terrestrial spring. This spring receives its salt through meteoric water circulation from nearby hills along a shallow salt diapir. This is shown using {delta}{sup 37}Cl, as the composition in dug wells between the mountains and the saline spring is comparable, while {delta}{sup 37}Cl in a well to the east is significantly different. Unlike seawater this spring contains nearly pure NaCl, giving us the opportunity to determine {delta}{sup 37}Cl values in a natural salt precipitating system beyond the point where (in seawater) potassium and magnesium chlorides start to precipitate. {delta}{sup 37}Cl values were determined from brines and by precipitating salt in salt pans with different evaporation stages. Fractionation of up to 1 per mille was found. To complement these natural data, evaporation/precipitation experiments are currently being conducted under controlled laboratory conditions. First results of these experiments indicate that during continued evaporation and precipitation {delta}{sup 37}Cl continues to decrease. (author)

  12. Effects of elevated ozone on leaf {delta}{sup 13}C and leaf conductance of plant species grown in semi-natural grassland with or without irrigation

    Energy Technology Data Exchange (ETDEWEB)

    Jaeggi, M. [Agroscope FAL Reckenholz, Swiss Federal Research Station for Agroecology and Agriculture, Air Pollution/Climate Group, CH-8046 Zurich (Switzerland)]. E-mail: maya.jaeggi@psi.ch; Saurer, M. [Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Volk, M. [Agroscope FAL Reckenholz, Swiss Federal Research Station for Agroecology and Agriculture, Air Pollution/Climate Group, CH-8046 Zurich (Switzerland); Fuhrer, J. [Agroscope FAL Reckenholz, Swiss Federal Research Station for Agroecology and Agriculture, Air Pollution/Climate Group, CH-8046 Zurich (Switzerland)

    2005-03-01

    Stable carbon isotope ratios ({delta}{sup 13}C) and leaf conductance (g{sub s}) were measured (2002, 2003) in Holcus lanatus L., Plantago lanceolata L. Ranunculus friesianus (Jord.), and Trifolium pratense L. at two levels of ozone (O{sub 3}) with or without irrigation. In non-irrigated control plots, R. friesianus showed the least negative {delta}{sup 13}C, and the smallest response to the treatments. Irrigation caused more negative {delta}{sup 13}C, especially in H. lanatus. Irrespective of irrigation, O{sub 3} increased {delta}{sup 13}C in relationship to a decrease in g{sub s} in P. lanceolata and T. pratense. The strongest effect of O{sub 3} on {delta}{sup 13}C occurred in the absence of irrigation, suggesting that under field conditions lack of moisture in the top soil does not always lead to protection from O{sub 3} uptake. It is concluded that in species such as T. pratense plants can maintain stomatal O{sub 3} uptake during dry periods when roots can reach deeper soil layers where water is not limiting. - Under natural field conditions, lack of precipitation may not protect semi-natural vegetation from O{sub 3} effects on leaf gas exchange.

  13. SEQATOMS: a web tool for identifying missing regions in PDB in sequence context

    NARCIS (Netherlands)

    Brandt, B.W.; Heringa, J.; Leunissen, J.A.M.

    2008-01-01

    With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files contain sequence and coordinate information. Residues present in the sequence can be absent from the coordinate section, which means their

  14. PDB2CD visualises dynamics within protein structures.

    Science.gov (United States)

    Janes, Robert W

    2017-10-01

    Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

  15. hpvPDB: An Online Proteome Reserve for Human Papillomavirus

    Directory of Open Access Journals (Sweden)

    Satish Kumar

    2013-12-01

    Full Text Available Human papillomavirus (HPV infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

  16. Sediment features, macrozoobenthic assemblages and trophic relationships ({delta}{sup 13}C and {delta}{sup 15}N analysis) following a dystrophic event with anoxia and sulphide development in the Santa Giusta lagoon (western Sardinia, Italy)

    Energy Technology Data Exchange (ETDEWEB)

    Magni, P. [CNR-IAMC National Research Council - Institute for Coastal Marine Environment c/o IMC - International Marine Centre, Loc. Sa Mardini, Torregrande, 09072 Oristano (Italy); IMC - International Marine Centre, Loc. Sa Mardini, Torregrande, 09072 Oristano (Italy)], E-mail: paolo.magni@iamc.cnr.it; Rajagopal, S. [Department of Animal Ecology and Ecophysiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Toernooiveld, 6525 ED Nijmegen (Netherlands); Velde, G. van der [Department of Animal Ecology and Ecophysiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Toernooiveld, 6525 ED Nijmegen (Netherlands); National Museum of Natural History Naturalis, P.O. Box 9517, 2300 RA Leiden (Netherlands); Fenzi, G. [IMC - International Marine Centre, Loc. Sa Mardini, Torregrande, 09072 Oristano (Italy); Kassenberg, J. [Department of Animal Ecology and Ecophysiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Toernooiveld, 6525 ED Nijmegen (Netherlands); Vizzini, S.; Mazzola, A. [Dipartimento di Biologia Animale, Universita di Palermo, via Archirafi 18, 90123 Palermo (Italy); Giordani, G. [Dipartimento di Scienze Ambientali, Universita di Parma, Via Usberti 33/A, 43100 Parma (Italy)

    2008-07-01

    Macrozoobenthic assemblages and stable carbon ({delta}{sup 13}C) and nitrogen ({delta}{sup 15}N) isotope values of various primary producers (macroalgae and angiosperms) and consumers (macroinvertebrate filter/suspension feeders, deposit feeders, detritivores/omnivores and carnivores and fishes) were studied in the Santa Giusta lagoon (Sardinia, Italy) before (spring) and after (autumn) a dystrophic event which occurred in the summer of 2004. A few days after the dystrophy, the physico-chemical characteristics of sediments and macrozoobenthic assemblages were also investigated. In the latter occasion, high total organic carbon (3.9%) and organic matter (15.9%) contents of surface sediments went together with peaks in acid-volatile sulphide concentrations. Certain immediate effects were quite extreme, such as the drastic reduction in macrozoobenthos and the massive fish kill in August 2004. Among the macrozoobenthos, there were few individuals of chironomid larvae and Capitella cf. capitata left. However, by October, chironomid larvae were numerous, indicating a lack of predators (e.g. fish) and competitors. In addition, some bivalve species and polychaetes which were absent, or present in small numbers before the event, became relatively numerous. The results are discussed based on a knowledge of the sulphide tolerance of these species. Stable isotope analysis clearly showed that the basal level of the food web for most consumers consisted mainly of macroalgae and sedimentary organic matter, and that the values before and after the dystrophic event were not significantly different from one another. This indicates that the relations among different trophic levels were quickly restored following the dystrophic event.

  17. PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

    Science.gov (United States)

    Delage, E.; Pham, Q. T.; Karamitros, M.; Payno, H.; Stepan, V.; Incerti, S.; Maigne, L.; Perrot, Y.

    2015-07-01

    This paper describes PDB4DNA, a new Geant4 user application, based on an independent, cross-platform, free and open source C++ library, so-called PDBlib, which enables use of atomic level description of DNA molecule in Geant4 Monte Carlo particle transport simulations. For the evaluation of direct damage induced on the DNA molecule by ionizing particles, the application makes use of an algorithm able to determine the closest atom in the DNA molecule to energy depositions. Both the PDB4DNA application and the PDBlib library are available as free and open source under the Geant4 license.

  18. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

    Science.gov (United States)

    Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel

    2009-06-01

    LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

  19. PDB-Explorer: a web-based interactive map of the protein data bank in shape space.

    Science.gov (United States)

    Jin, Xian; Awale, Mahendra; Zasso, Michaël; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis

    2015-10-23

    The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3

  20. Growth and {delta}{sup 13}C responses to increasing atmospheric carbon dioxide concentrations for several crop species

    Energy Technology Data Exchange (ETDEWEB)

    Hanba, Y.T.; Wada, E. [Center for Ecological Research, Kyoto University, Kyoto (Japan); Osaki, M.; Nakamura, T. [Faculty of Agriculture, Hokkaido University, Hokkaido (Japan)

    1996-04-01

    The responses of plant growth and carbon isotope discrimination ({Delta}) to elevated atmospheric CO{sub 2} concentrations for several crop species (lettuce: Lactuca sativa L.; corn: Zea Mays L. var. P3540, wheat: Triticum aestivum L. var Haruyutaka; and soybean: Glycine Max (L). Merr. var. Kitamusume) were investigated. Shoot relative growth rate was used to indicate plant growth, and {delta}{sup 13}C value of leaf materials in corn (C4 species) was used to calculate {Delta} for C3 species. Plant growth was stimulated by enriched CO{sub 2}, while {Delta} remained almost constant as CO{sub 2} concentration changed. {Delta} showed interspecific difference, and the plant species of larger {Delta} had larger relative growth rates. Relative growth rates of the plants of larger {Delta} were stimulated by CO{sub 2} enrichment more than those of the plants of smaller {Delta}. We propose that plant {Delta} could be a possible parameter to assess the interspecific difference of plant response to the increasing atmospheric CO{sub 2} concentrations. 3 figs., 2 tabs., 25 refs.

  1. Impact of carbohydrate supply on stem growth, wood and respired CO{sub 2} {delta}{sup 13}C : assessment by experimental girdling

    Energy Technology Data Exchange (ETDEWEB)

    Maunoury-Danger, F. [Paris-Sud Univ., Orsay Cedex (France). Laboratoire Ecologie, Systematique et Evolution; Centre National de la Recherche Scientifique, Orsay CEDEX (France); AgroParisTech, Paris (France); Paul Verlaine-Metz Univ., Metz (France). Laboratoire des Interactions Ecotoxicologie Biodiversite Ecosystemes; Fresneau, C.; Eglin, T.; Berveiller, D.; Francois, C.; Damesin, C. [Paris-Sud Univ., Orsay Cedex (France). Laboratoire Ecologie, Systematique et Evolution; Centre National de la Recherche Scientifique, Orsay CEDEX (France); AgroParisTech, Paris (France); Lelarge-Trouverie, C. [Paris-Sud Univ., Orsay Cedex (France). Inst. de Biotechnologie des Plantes, Plateforme Metabolisme-Metabolome

    2010-07-15

    In trees, carbohydrate storage and remobilization may affect the carbon isotope signals of sugars exported from leaves, tree organic matter and respired carbon dioxide (CO{sub 2}). This study characterized the impact of a change in the carbon (C) source used for stem functioning on the {delta}{sup 13} C of stem organic matter and respired CO{sub 2}. Girdling experiments were carried out on 2-year old oaks that consisted in removing the bark and phloem around the stem so that the sap would cease to flow. The stem was therefore forced to use its own C reserves to maintain metabolic activity. Trees were girdled at 3 different periods, notably just after budburst, during stem growth, and just after cessation of stem radial growth. Stem radial growth and respiration rate were measured throughout the year. Other measured variables included {delta}{sup 13} C of respired CO{sub 2} and contents of starch and water-soluble fraction in stems and leaves. The study showed that girdling stopped growth, even early in the growing season, leading to a decrease in stem CO{sub 2} efflux. The study demonstrated that leaf carbohydrate supply versus reserve use could be an important factor controlling stem growth and {delta}{sup 13} C of both ring and stem CO{sub 2} efflux. 69 refs., 3 tabs., 5 figs.

  2. {Delta}{sup 14}C level of annual plants and fossil fuel derived CO{sub 2} distribution across different regions of China

    Energy Technology Data Exchange (ETDEWEB)

    Xi, X.T.; Ding, X.F.; Fu, D.P. [State Key Laboratory of Nuclear Physics and Technology and Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing 100871 (China); Zhou, L.P. [Laboratory for Earth Surface Processes, Department of Geography, Peking University, Beijing 100871 (China); Liu, K.X., E-mail: kxliu@pku.edu.cn [State Key Laboratory of Nuclear Physics and Technology and Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing 100871 (China)

    2013-01-15

    The {sup 14}C level in annual plants is a sensitive tracer for monitoring fossil fuel derived CO{sub 2} in the atmosphere. Corn leave samples were selected from different regions of China, including high mountains in the Tibetan Plateau, grassland in Inner Mongolia, and inland and coastal cities during the summer of 2010. The {sup 14}C/{sup 12}C ratio of the samples was measured with the NEC compact AMS system at the Institute of Heavy Ion Physics, Peking University. The fossil fuel derived CO{sub 2} was estimated by comparing the measured {Delta}{sup 14}C values of corn leave samples to background atmospheric {Delta}{sup 14}C level. The influences of topography, meteorological conditions and carbon cycling processes on the fossil fuel derived CO{sub 2} concentration are considered when interpreting the data. Our results show a clear association of the low {Delta}{sup 14}C values with regions where human activities are intensive.

  3. Macroalgal bioindicators (growth, tissue N, {delta}{sup 15}N) detect nutrient enrichment from shrimp farm effluent entering Opunohu Bay, Moorea, French Polynesia

    Energy Technology Data Exchange (ETDEWEB)

    Lin, David T. [Department of Zoology, University of Hawaii at Manoa, 2538 McCarthy Mall, Edmondson 152, Honolulu, HI 96822 (United States)], E-mail: david.t.lin@ucla.edu; Fong, Peggy [Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Young Drive South, Los Angeles, CA 90095 (United States)

    2008-02-15

    Nutrient enrichment from shrimp aquaculture poses an increasing environmental threat due to the industry's projected rapid growth and unsustainable management practices. Traditional methods to monitor impacts emphasize water quality sampling; however, there are many advantages to bioindicators, especially in developing countries. We investigated the usefulness of three bioindicators-growth, tissue nitrogen content and nitrogen stable isotope signature ({delta}{sup 15}N)-in the tropical red macroalga Acanthophora spicifera. Algae were collected, cultured, and deployed in a spatial array around the outflow from a shrimp farm in Moorea, French Polynesia, to detect nitrogenous wastes. All three parameters were highest adjacent to the shrimp farm indicating nutrient enrichment, and {delta}{sup 15}N values confirmed the shrimp farm as the dominant nutrient source (5.63-5.96 per mille ). Isotope ratios proved the most sensitive indicator, as {delta}{sup 15}N signatures were detected at the most distant sites tested, confirming their usefulness in tracing nutrients and mapping the spatial extent of enrichment.

  4. The dynamics of central Main Ethiopian Rift waters: Evidence from {delta}D, {delta}{sup 18}O and {sup 87}Sr/{sup 86}Sr ratios

    Energy Technology Data Exchange (ETDEWEB)

    Rango, Tewodros, E-mail: tewodros.godebo@duke.edu [Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC 27708 (United States)] [Addis Ababa University, Department of Earth Sciences, P.O. Box 1176, Addis Ababa (Ethiopia); Petrini, Riccardo; Stenni, Barbara [University of Trieste, Department of Geosciences, Via Weiss 1, I-34100 Trieste (Italy); Bianchini, Gianluca [Istituto di Geoscienze e Georisorse-CNR, Pisa (Italy)] [Department of Earth Sciences, University of Ferrara, Via Saragat 1, 44100 Ferrara (Italy); Slejko, Francesca [University of Trieste, Department of Geosciences, Via Weiss 1, I-34100 Trieste (Italy); Beccaluva, Luigi [Department of Earth Sciences, University of Ferrara, Via Saragat 1, 44100 Ferrara (Italy); Ayenew, Tenalem [Addis Ababa University, Department of Earth Sciences, P.O. Box 1176, Addis Ababa (Ethiopia)

    2010-12-15

    Research highlights: {yields} Chemical and isotope ({delta}D, {delta}{sup 18}O and {sup 87}Sr/{sup 86}Sr) techniques are applied to understand various hydrological processes in the Main Ethiopian Rift. {yields} Some of the studied groundwaters display a depleted {delta}D-{delta}{sup 18}O composition when compared to the present-day average precipitation, thus suggesting that the rift floor aquifers also contains paleo-meteoric waters recharge associated with deep flow system. {yields} The pristine waters coming from the highlands display isotopic compositions characterized by less radiogenic {sup 87}Sr/{sup 86}Sr (and more depleted {delta}D, {delta}{sup 18}O). This isotopic signature subsequently evolves towards higher {sup 87}Sr/{sup 86}Sr by an interaction with the more radiogenic rhyolites of the rift and their weathered and redeposited products. - Abstract: Water samples from cold and geothermal boreholes, hot springs, lakes and rivers were analyzed for {delta}D, {delta}{sup 18}O and {sup 87}Sr/{sup 86}Sr compositions in order to investigate lake water-groundwater mixing processes, water-rock interactions, and to evaluate groundwater flow paths in the central Main Ethiopian Rift (MER) of the Ziway-Shala basin. Different ranges of isotopic values were recorded for different water types: hot springs show {delta}{sup 18}O -3.36 to +3.69 and {delta}D -15.85 to +24.23, deep Aluto-Langano geothermal wells show {delta}{sup 18}O -4.65 to -1.24 and {delta}D -12.39 to -9.31, groundwater wells show {delta}{sup 18}O -3.99 to +5.14 and {delta}D -19.69 to +32.27, whereas the lakes show {delta}{sup 18}O and {delta}D in the range +3.98 to +7.92 and +26.19 to +45.71, respectively. The intersection of the Local Meteoric Water Line (LMWL: {delta}D = 7 {delta}{sup 18}O + 11.2, R{sup 2} = 0.94, n = 42) and the Local Evaporation Line (LEL: {delta}D = 5.63{delta}{sup 18}O + 8, n = 14, R{sup 2} = 0.82) was used to estimate the average isotopic composition of recharge water into the

  5. The Use of PDB database as a Tool for Biochemistry Active Learning of Undergraduate Students

    Directory of Open Access Journals (Sweden)

    T.M.F. Günther et al.

    2017-07-01

    Full Text Available Traditional Biochemistry teaching-learning is still an ongoing practice at UFSC. There are few published reports about innovative pedagogical practices of this discipline at this University. To ensure motivation through active learning of Basic Biochemistry we started to apply new methodologies back to 2005. This approach intended to stimulate undergraduate students in learning Biochemistry proactively. Objectives: Use PDB as a tool to improve skills related to Biochemistry education, while using specific information available; provide virtual data in order to stimulate student autonomy in active teaching-learning processes through methodologies based on the use of safe and suitable scientific information. Material and Methods: At the beginning, students were exposed to Biochemistry of Proteins content through traditional lectures. On the following stage, an introduction to PDB was made at the digital environment (http://www.rcsb.org/pdb/home/home.do depicting scientific information. Students received a model-instruction describing myoglobin characteristics at PDB (https://pdb101.rcsb.org/motm/1. This Powerpoint™ presentation gave clues on how the work was to be done. A lottery was made and each pair of students was allowed to select a protein and then developed Powerpoint™ presentations. Proteins were chosen from the PDB categories and obtained from the academic educational plan for Basic Biochemistry related to the Nutrition-Course. The Moodle plataform provided virtual materials, allowing full interactivity to all student presentations. Results and Discussion: There was total adherence to the pedagogical proposal. The student presentations in Powerpoint™ were adequate and made available to the attendees in the Moodle platform. Items surveyed in the presented script with the highest hit rates (grade ten were: biological importance (100%, amino acid composition (92.30%, structural information (89.75%, occurrence (89.74%, URL cited (79

  6. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    Science.gov (United States)

    Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

    2011-01-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

  7. PyPDB: a Python API for the Protein Data Bank.

    Science.gov (United States)

    Gilpin, William

    2016-01-01

    We have created a Python programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval for a wide range of result types, including BLAST and sequence motif queries. The API relies on the existing XML-based API and operates by creating custom XML requests from native Python types, allowing extensibility and straightforward modification. The package has the ability to perform many types of advanced search of the PDB that are otherwise only available through the PDB website. PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibility. The most up-to-date version, including iPython notebooks containing usage tutorials, is available free-of-charge under an open-source MIT license via GitHub at https://github.com/williamgilpin/pypdb, and the full API reference is at http://williamgilpin.github.io/pypdb_docs/html/. The latest stable release is also available on PyPI. wgilpin@stanford.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. {delta}{sup 13}C of Tree-Ring Lignin as an Indirect Measure of Climate Change

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, I. [CSIR Environmentek, Quaternary Dating Research Unit (South Africa)], E-mail: i.robertson@swansea.ac.uk; Loader, N. J.; McCarroll, D. [University of Wales Swansea, Department of Geography (United Kingdom); Carter, A. H. C. [University of Cambridge, Godwin Institute for Quaternary Research (United Kingdom); Cheng, L.; Leavitt, S. W. [University of Arizona, Laboratory of Tree-Ring Research (United States)

    2004-06-15

    High-resolution paleoclimatic data are an essential requirement for testing numerical models of climate change and the global carbon cycle. If the long tree-ring chronologies, originally established for the purpose of dendrochronology, are to be fully exploited as an indirect measure of past climatic variability, additional techniques are required to obtain this information. The determination of the {delta}{sup 13}C value of tree-ring cellulose has been used successfully to reconstruct past climates. However, under both aerobic and anaerobic conditions, the polysaccharide components of vascular plants (mainly cellulose and hemicelluloses) are more prone to rapid degradation than lignin. This has serious implications for the use of carbon isotope values of tree-ring cellulose as an indirect measure of past climates. An absolutely dated ring-width chronology was established for oaks (Quercus robur L.) growing at Sandringham Park in eastern England. Carbon isotope values were determined on {alpha}-cellulose and 'Klason' lignin isolated from annual latewood samples over the period AD 1895-1999. The carbon isotope values of earlywood lignin are correlated with the latewood carbon isotope values of the previous year, supporting the theory that some of the carbon utilised in earlywood synthesis is assimilated in the previous year. The high-frequency variance in the carbon isotope indices of latewood lignin and cellulose is highly correlated with combined July and August environmental variables, indicating that they were formed at similar times. There was no evidence of secondary lignification. These results demonstrate that the determination of carbon isotope values of latewood lignin offers the potential to obtain unambiguous proxy climatic data covering several millennia.

  9. Novel time-dependent vascular actions of {delta}{sup 9}-tetrahydrocannabinol mediated by peroxisome proliferator-activated receptor gamma

    Energy Technology Data Exchange (ETDEWEB)

    O' Sullivan, Saoirse E [School of Biomedical Sciences, E Floor, Queen' s Medical Centre, University of Nottingham, Nottingham NG7 2UH (United Kingdom); Tarling, Elizabeth J [School of Biomedical Sciences, E Floor, Queen' s Medical Centre, University of Nottingham, Nottingham NG7 2UH (United Kingdom); Bennett, Andrew J [School of Biomedical Sciences, E Floor, Queen' s Medical Centre, University of Nottingham, Nottingham NG7 2UH (United Kingdom); Kendall, David A [School of Biomedical Sciences, E Floor, Queen' s Medical Centre, University of Nottingham, Nottingham NG7 2UH (United Kingdom); Randall, Michael D [School of Biomedical Sciences, E Floor, Queen' s Medical Centre, University of Nottingham, Nottingham NG7 2UH (United Kingdom)

    2005-11-25

    Cannabinoids have widespread effects on the cardiovascular system, only some of which are mediated via G-protein-coupled cell surface receptors. The active ingredient of cannabis, {delta}{sup 9}-tetrahydrocannabinol (THC), causes acute vasorelaxation in various arteries. Here we show for the first time that THC also causes slowly developing vasorelaxation through activation of peroxisome proliferator-activated receptors gamma (PPAR{gamma}). In vitro, THC (10 {mu}M) caused time-dependent vasorelaxation of rat isolated arteries. Time-dependent vasorelaxation to THC was similar to that produced by the PPAR{gamma} agonist rosiglitazone and was inhibited by the PPAR{gamma} antagonist GW9662 (1 {mu}M), but not the cannabinoid CB{sub 1} receptor antagonist AM251 (1 {mu}M). Time-dependent vasorelaxation to THC requires an intact endothelium, nitric oxide, production of hydrogen peroxide, and de novo protein synthesis. In transactivation assays in cultured HEK293 cells, THC-activated PPAR{gamma}, transiently expressed in combination with retinoid X receptor {alpha} and a luciferase reporter gene, in a concentration-dependent manner (100 nM-10 {mu}M). In vitro incubation with THC (1 or 10 {mu}M, 8 days) stimulated adipocyte differentiation in cultured 3T3L1 cells, a well-accepted property of PPAR{gamma} ligands. The present results provide strong evidence that THC is a PPAR{gamma} ligand, stimulation of which causes time-dependent vasorelaxation, implying some of the pleiotropic effects of cannabis may be mediated by nuclear receptors.

  10. PDB-NMA of a protein homodimer reproduces distinct experimental motility asymmetry

    Science.gov (United States)

    Tirion, Monique M.; ben-Avraham, Daniel

    2018-03-01

    We have extended our analytically derived PDB-NMA formulation, Atomic Torsional Modal Analysis or ATMAN (Tirion and ben-Avraham 2015 Phys. Rev. E 91 032712), to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3 {\\mathringA} resolution model of a small homodimer, ActVA-ORF6, consisting of two 112-residue subunits identically folded in a compact 50 {\\mathringA} sphere, reproduces the distinct experimental Debye-Waller motility asymmetry for the two chains, demonstrating that structure sensitively selects vibrational signatures. The vibrational analysis of this PDB entry, together with biochemical and crystallographic data, demonstrates the cooperative nature of the dimeric interaction of the two subunits and suggests a mechanical model for subunit interconversion during the catalytic cycle.

  11. A tool for calculating binding-site residues on proteins from PDB structures

    Directory of Open Access Journals (Sweden)

    Hu Jing

    2009-08-01

    Full Text Available Abstract Background In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB that consists of the protein of interest and its interacting partner(s and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. Results In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. Conclusion The developed tool is very useful for the research on protein binding site analysis and prediction.

  12. Variability of {sup 10}Be and {delta}{sup 18}O in snow pits from Greenland and a surface traverse from Antarctica

    Energy Technology Data Exchange (ETDEWEB)

    Berggren, A.-M. [Dept. of Earth Sciences, Uppsala University, Villav. 16, 752 36 Uppsala (Sweden); Aldahan, A., E-mail: ala.aldahan@geo.uu.se [Dept. of Earth Sciences, Uppsala University, Villav. 16, 752 36 Uppsala (Sweden); Dept. of Geology, United Arab Emirates University, P.O. Box 17551 Al Ain (United Arab Emirates); Possnert, G. [Tandem Laboratory, Uppsala University, P.O. Box 529, 751 20 Uppsala (Sweden); Hansson, M. [Dept. of Physical Geography and Quaternary Geology, Stockholm University, 106 91 Stockholm (Sweden); Steen-Larsen, H.C. [Centre for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej, 30,2100 Copenhagen (Denmark); Sturevik Storm, A. [Dept. of Earth Sciences, Uppsala University, Villav. 16, 752 36 Uppsala (Sweden); Moerth, C.-M. [Dept. of Geology and Geochemistry, Stockholm University, 106 91 Stockholm (Sweden); Murad, A. [Dept. of Geology, United Arab Emirates University, P.O. Box 17551 Al Ain (United Arab Emirates)

    2013-01-15

    To examine temporal variability of {sup 10}Be in glacial ice, we sampled snow to a depth of 160 cm at the NEEM (North Greenland Eemian Ice Drilling) drilling site in Greenland. The samples span three years between the summers of 2006 and 2009. At the same time, spatial variability of {sup 10}Be in glacial ice was explored through collection of the upper {approx}5 cm of surface snow in Antarctica during part of the Swedish-Japanese traverse from Svea to Syowa station during the austral summer in 2007-2008. The results of the Greenlandic {sup 10}Be snow suggested variable concentrations that apparently do not clearly reflect the seasonal change as indicated by the {delta}{sup 18}O data. The {sup 10}Be concentration variability most likely reflects also effects of aerosol loading and deposition pathways, possibly in combination with post-depositional processes. The Antarctic traverse data expose a negative correlation between {sup 10}Be and {delta}{sup 18}O, while there are weaker but still significant correlations to altitude and distance to the coast (approximated by the distance to the 70th latitude). These relationships indicate that geographical factors, mainly the proximity to the coast, may strongly affect {sup 10}Be concentrations in snow in Queen Maud Land, Antarctica.

  13. PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

    Science.gov (United States)

    Lee, Jonas; Kim, Sung Hou

    2009-04-01

    The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

  14. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

    Science.gov (United States)

    Quinn, Gregory B; Bi, Chunxiao; Christie, Cole H; Pang, Kyle; Prlić, Andreas; Nakane, Takanori; Zardecki, Christine; Voigt, Maria; Berman, Helen M; Bourne, Philip E; Rose, Peter W

    2015-01-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service. RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org). © The Author 2014. Published by Oxford University Press.

  15. A urinary metabolite of {Delta}{sup 1}-tetrahydrocannabinol. The first synthesis of 4``-hydroxy-{Delta}{sup 1}-tetrahydrocannabinol-7-oic acid labelled with deuterium

    Energy Technology Data Exchange (ETDEWEB)

    Szirmai, Maria; Odqvist, Helena [Uppsala Univ. (Sweden). Dept. of Pharmacognosy; Halldin, M.M. [Karolinska Inst., Stockholm (Sweden). Dept. of Pharmacology

    1996-04-01

    The first synthesis of 4``-hydroxy-{Delta}-{sup 1}-THC-7-oic acid, one of the three major metabolites of {Delta}{sup 1}-THC identified in human urine is discussed. Methyl 4-(3,5-dihydroxyphenyl)butanoate was prepared from 3,5-diydroxybenzoic acid in an overall yield of 15% was condensed with a terpene synthon under acidic conditions followed by hydrolysis and conversion of the 4``-carboxylic acid function to the corresponding methyl ketone using methyllithium. Reduction with NaBH{sub 4} afforded the secondary alcohol in the side-chain. Acetylation and removal of the 1,3-dithiane masking group gave the aldehyde in C-7-position which was further oxidized using NaClO{sub 2} followed by deacetylation to give the desired metabolite. The same procedure may be used for the synthesis of unlabelled 4``-hydroxy-{Delta}{sup 1}-THC-7-oic acid. (author).

  16. Pharmacophore searching: A potential solution for correcting unknown ligands (UNK) labelling errors in Protein Data Bank (PDB'S).

    Science.gov (United States)

    Ibrahim, Musadiq; Lapthorn, Adrian Jonathan; Ibrahim, Mohammad

    2017-08-01

    The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, error-free as much as possible. In this study, we have critically examined PDB structures of 292 protein molecules which have been deposited in the repository along with potentially incorrect ligands labelled as Unknown ligands (UNK). Pharmacophores were generated for all the protein structures by using Discovery Studio Visualizer (DSV) and Accelrys, Catalyst ® . The generated pharmacophores were subjected to the database search containing the reported ligand. Ligands obtained through Pharmacophore searching were then checked for fitting the observed electron density map by using Coot ® . The predicted ligands obtained via Pharmacophore searching fitted well with the observed electron density map, in comparison to the ligands reported in the PDB's. Based on our study we have learned that till may 2016, among 292 submitted structures in the PDB, at least 20 structures have ligands with a clear electron density but have been incorrectly labelled as unknown ligands (UNK). We have demonstrated that Pharmacophore searching and Coot ® can provide potential help to find suitable known ligands for these protein structures, the former for ligand search and the latter for electron density analysis. The use of these two techniques can facilitate the quick and reliable labelling of ligands where the electron density map serves as a reference. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree.

    Science.gov (United States)

    DeForte, Shelly; Uversky, Vladimir N

    2016-03-01

    Missing regions in X-ray crystal structures in the Protein Data Bank (PDB) have played a foundational role in the study of intrinsically disordered protein regions (IDPRs), especially in the development of in silico predictors of intrinsic disorder. However, a missing region is only a weak indication of intrinsic disorder, and this uncertainty is compounded by the presence of ambiguous regions, where more than one structure of the same protein sequence "disagrees" in terms of the presence or absence of missing residues. The question is this: are these ambiguous regions intrinsically disordered, or are they the result of static disorder that arises from experimental conditions, ensembles of structures, or domain wobbling? A novel way of looking at ambiguous regions in terms of the pattern between multiple PDB structures has been demonstrated. It was found that the propensity for intrinsic disorder increases as the level of ambiguity decreases. However, it is also shown that ambiguity is more likely to occur as the protein region is placed within different environmental conditions, and even the most ambiguous regions as a set display compositional bias that suggests flexibility. The results suggested that ambiguity is a natural result for many IDPRs crystallized under different conditions and that static disorder and wobbling domains are relatively rare. Instead, it is more likely that ambiguity arises because many of these regions were conditionally or partially disordered. © 2016 The Protein Society.

  18. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

    Science.gov (United States)

    Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

    2013-01-01

    Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures.

  19. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

    Directory of Open Access Journals (Sweden)

    Sunhwan Jo

    Full Text Available Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures.

  20. Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

    Science.gov (United States)

    Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

    2013-01-01

    We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc. PMID:23180575

  1. Nearest-cell: a fast and easy tool for locating crystal matches in the PDB

    International Nuclear Information System (INIS)

    Ramraj, V.; Evans, G.; Diprose, J. M.; Esnouf, R. M.

    2012-01-01

    A fast and easy tool to locate unit-cell matches in the PDB is described. When embarking upon X-ray diffraction data collection from a potentially novel macromolecular crystal form, it can be useful to ascertain whether the measured data reflect a crystal form that is already recorded in the Protein Data Bank and, if so, whether it is part of a large family of related structures. Providing such information to crystallographers conveniently and quickly, as soon as the first images have been recorded and the unit cell characterized at an X-ray beamline, has the potential to save time and effort as well as pointing to possible search models for molecular replacement. Given an input unit cell, and optionally a space group, Nearest-cell rapidly scans the Protein Data Bank and retrieves near-matches

  2. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

    Science.gov (United States)

    Sali, Andrej; Berman, Helen M.; Schwede, Torsten; Trewhella, Jill; Kleywegt, Gerard; Burley, Stephen K.; Markley, John; Nakamura, Haruki; Adams, Paul; Bonvin, Alexandre M.J.J.; Chiu, Wah; Dal Peraro, Matteo; Di Maio, Frank; Ferrin, Thomas E.; Grünewald, Kay; Gutmanas, Aleksandras; Henderson, Richard; Hummer, Gerhard; Iwasaki, Kenji; Johnson, Graham; Lawson, Catherine L.; Meiler, Jens; Marti-Renom, Marc A.; Montelione, Gaetano T.; Nilges, Michael; Nussinov, Ruth; Patwardhan, Ardan; Rappsilber, Juri; Read, Randy J.; Saibil, Helen; Schröder, Gunnar F.; Schwieters, Charles D.; Seidel, Claus A. M.; Svergun, Dmitri; Topf, Maya; Ulrich, Eldon L.; Velankar, Sameer; Westbrook, John D.

    2016-01-01

    Summary Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models? PMID:26095030

  3. Simulating dynamics of {delta}{sup 13}C of CO{sub 2} in the planetary boundary layer a boreal forest region: covariation between surface fluxes and atmospheric mixing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Baozhang; Chen, Jing M. [Univ. of Toronto, ON (Canada). Dept. of Geography; Tans, Pieter P. [National Oceanic and Atmospheric Administration, Boulder, CO (United States). Earth System Research Lab.; Huang, Lin [Environment Canada, Toronto, ON (Canada). Atmospheric Science and Technology Directorate

    2006-11-15

    Stable isotopes of CO{sub 2} contain unique information on the biological and physical processes that exchange CO{sub 2} between terrestrial ecosystems and the atmosphere. Ecosystem exchange of carbon isotopes with the atmosphere is correlated diurnally and seasonally with the planetary boundary layer (PBL) dynamics. The strength of this kind of covariation affects the vertical gradient of {delta}{sup 13}C and thus the global {delta}{sup 13}C distribution pattern. We need to understand the various processes involved in transport/diffusion of carbon isotope ratio in the PBL and between the PBL and the biosphere and the troposphere. In this study, we employ a one-dimensional vertical diffusion/transport atmospheric model (VDS), coupled to an ecosystem isotope model (BEPS-EASS) to simulate dynamics of {sup 13}CO{sub 2} in the PBL over a boreal forest region in the vicinity of the Fraserdale (FRD) tower (49 deg 52 min 29.9 sec N, 81 deg 34 min 12.3 sec W) in northern Ontario, Canada. The data from intensive campaigns during the growing season in 1999 at this site are used for model validation in the surface layer. The model performance, overall, is satisfactory in simulating the measured data over the whole course of the growing season. We examine the interaction of the biosphere and the atmosphere through the PBL with respect to {delta}{sup 13}C on diurnal and seasonal scales. The simulated annual mean vertical gradient of {delta}{sup 13}C in the PBL in the vicinity of the FRD tower was about 0.025% in 1999. The {delta}{sup 13}C vertical gradient exhibited strong diurnal (29%) and seasonal (71%) variations that do not exactly mimic those of CO{sub 2}. Most of the vertical gradient (96.5% {+-}) resulted from covariation between ecosystem exchange of carbon isotopes and the PBL dynamics, while the rest (3.5%{+-}) was contributed by isotopic disequilibrium between respiration and photosynthesis. This disequilibrium effect on {delta}{sup 13}C of CO{sub 2} dynamics in PBL

  4. Simulating dynamics of (delta){sup 13}C of CO{sub 2} in the planetary boundary layer a boreal forest region: covariation between surface fluxes and atmospheric mixing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Baozhang; Chen, Jing M. [Univ. of Toronto, ON (Canada). Dept. of Geography; Tans, Pieter P. [National Oceanic and Atmospheric Administration, Boulder, CO (United States). Earth System Research Lab.; Huang, Lin [Environment Canada, Toronto, ON (Canada). Atmospheric Science and Technology Directorate

    2006-11-15

    Stable isotopes of CO{sub 2} contain unique information on the biological and physical processes that exchange CO{sub 2} between terrestrial ecosystems and the atmosphere. Ecosystem exchange of carbon isotopes with the atmosphere is correlated diurnally and seasonally with the planetary boundary layer (PBL) dynamics. The strength of this kind of covariation affects the vertical gradient of (delta){sup 13}C and thus the global (delta){sup 13}C distribution pattern. We need to understand the various processes involved in transport/diffusion of carbon isotope ratio in the PBL and between the PBL and the biosphere and the troposphere. In this study, we employ a one-dimensional vertical diffusion/transport atmospheric model (VDS), coupled to an ecosystem isotope model (BEPS-EASS) to simulate dynamics of {sup 13}CO{sub 2} in the PBL over a boreal forest region in the vicinity of the Fraserdale (FRD) tower (49 deg 52 min 29.9 sec N, 81 deg 34 min 12.3 sec W) in northern Ontario, Canada. The data from intensive campaigns during the growing season in 1999 at this site are used for model validation in the surface layer. The model performance, overall, is satisfactory in simulating the measured data over the whole course of the growing season. We examine the interaction of the biosphere and the atmosphere through the PBL with respect to (delta){sup 13}C on diurnal and seasonal scales. The simulated annual mean vertical gradient of (delta){sup 13}C in the PBL in the vicinity of the FRD tower was about 0.025% in 1999. The (delta){sup 13}C vertical gradient exhibited strong diurnal (29%) and seasonal (71%) variations that do not exactly mimic those of CO{sub 2}. Most of the vertical gradient (96.5% {+-}) resulted from covariation between ecosystem exchange of carbon isotopes and the PBL dynamics, while the rest (3.5%{+-}) was contributed by isotopic disequilibrium between respiration and photosynthesis. This disequilibrium effect on (delta){sup 13}C of CO{sub 2} dynamics in PBL

  5. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) f...

  6. Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis.

    Science.gov (United States)

    Nadzirin, Nurul; Firdaus-Raih, Mohd

    2012-10-08

    Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under "unknown function" are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

  7. Proteins of Unknown Function in the Protein Data Bank (PDB: An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis

    Directory of Open Access Journals (Sweden)

    Nurul Nadzirin

    2012-10-01

    Full Text Available Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB. Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files that were categorized under “unknown function” are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

  8. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

    Science.gov (United States)

    Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

    2016-05-01

    The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Outcome of the first wwPDB/CCDC/D3R Ligand Validation Workshop

    Science.gov (United States)

    Adams, Paul D.; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A.; Berman, Helen M.; Bhat, Talapady N.; Blaney, Jeff; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K.; Case, David A.; Clark, Kirk L.; Darden, Tom; Emsley, Paul; Feher, Victoria A.; Feng, Zukang; Groom, Colin R.; Harris, Seth F.; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J.; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E.; Markley, John L.; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T.; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T.; Padyana, Anil K.; Peishoff, Catherine E.; Pieniazek, Susan; Read, Randy J.; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C.; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna; Warren, Gregory L.; Westbrook, John D.; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-01-01

    Summary Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. PMID:27050687

  10. Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

    Science.gov (United States)

    Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

    2018-04-01

    The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

  11. Oxygen isotope variations in phosphate of biogenic apatites. Pt. 2. Phosphorite rocks

    Energy Technology Data Exchange (ETDEWEB)

    Kolodny, Y; Luz, B; Shemesh, A [Hebrew Univ., Jerusalem (Israel). Dept. of Geology

    1983-09-01

    Phosphorites from sedimentary sequences ranging in age from Archaen to Recent were analysed for delta/sup 18/O in both the PO/sub 4/ (delta/sup 18/Osub(p)) and CO/sub 3/ (delta/sup 18/Osub(c)) in the apatite lattice. The oxygen isotope record is considerably better preserved in phosphates than in either carbonates or cherts. The use of the Longinelli and Nuti temperature equation yields temperatures for Recent phosphorites that are in good agreement with those measured in the field. The delta/sup 18/Osub(p) values of ancient phosphorites decrease with increasing age. These changes with time are not likely to be due to post-depositional exchange. Changes in delta/sup 18/O values of seawater and variations of temperatures with time can account for the delta/sup 18/Osub(p) time trend, but the latter explanation is preferred. In Ancient phosphorites delta/sup 18/Osub(c) in structurally bound carbonate in apatite is not a reliable geochemical indicator.

  12. Measurement of the reaction {gamma}d {yields}pn{pi}{sup +}{pi}{sup -} at SAPHIR and investigation of the decay angular distribution of the {Delta}{sup ++}(1232) resonance; Messung der Reaktion {gamma}d {yields}pn{pi}{sup +}{pi}{sup -} an SAPHIR und Untersuchung der Zerfallswinkelverteilung der {Delta}{sup ++}(1232)-Resonanz

    Energy Technology Data Exchange (ETDEWEB)

    Schuetz, P.

    1993-03-01

    SAPHIR, a new experiment at the Bonn electron stretcher ring ELSA, started taking data in spring 1992. It was set up for the investigation of photon induced reactions with multiparticle final states. In the first part of this paper the special design of the target is described. It can be operated with liquefied hydrogen or deuterium and is placed in the middle of the central drift chamber. To project the surrounding chamber in case of a fracture of the target cell as safety system is installed. In addition two independent methods of monitoring the cell are procided. The first measurement was performed with a deuterium target at a photon energy range of E{sub {gamma}} = 500-700 MeV. In the second part of this paper first results of an analysis of the decay angular distribution of the {Delta}{sup ++}(1232) in the reaction {gamma}d {yields} n{Delta}{sup ++}{pi}{sup -} are presented. They are compared to old data from a hydrogen bubble chamber experiment and are discussed on the basis of a spectator model. (orig.) [Deutsch] Im Rahmen dieser Arbeit ist der Aufbau eines Fluessiggas-Targets beschrieben worden, das speziell fuer den Einsatz im SAPHIR-Detektor entwickelt worden ist. Es wurden Funktionen zur Ueberwachung der Targetzelle vorgestellt und ein Sicherheitssystem zum Schutz der zentralen Driftkammer, die das Target unmittelbar umgibt. Weiterhin ist in Simulationsrechnungen untersucht worden, welchen Einfluss die Konstruktion des Targetstreutopfes auf die Messung unterschiedlicher Reaktionen haben kann. Dabei sind bei 50% bis 70% der Ereignisse Treffer in den Aluminiumstuetzen des Targetstreutopfes aufgetreten. Diese starke Beeintraechtigung kann durch eine Neukonstruktion des Streutopfes und der Verwendung von z.B. Rohazell als Streutopffenster vermieden werden. Rohazell zeichnet sich durch eine hohe Festigkeit und grosse Strahlungslaenge aus. An der Neukonstruktion des Streutopfes wird z.Z. gearbeitet. Der zweite Teil der Arbeit beschreibt eine der ersten

  13. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2015-09-15

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

  14. Using nitrogen stable isotope ratios ({delta}{sup 15}N) of macroalgae to determine the effectiveness of sewage upgrades: changes in the extent of sewage plumes over four years in Moreton Bay, Australia

    Energy Technology Data Exchange (ETDEWEB)

    Costanzo, Simon D. [National Research Centre for Environmental Toxicology, University of Queensland, 39 Kessels Road, Coopers Plains, QLD 4108 (Australia)]. E-mail: s.costanzo@uq.edu.au; Udy, James [Marine Botany, Centre for Marine Studies, University of Queensland, 4072 (Australia); Longstaff, Ben [Environmental Protection Agency, 80 Meiers Road, Indooroopilly, QLD 4058 (Australia); Jones, Adrian [University of Maryland Center for Environmental Science, P.O. Box 775, Cambridge, MD 21613, USA (United States)

    2005-07-01

    Nitrogen loading to aquatic ecosystems from sewage is recognised worldwide as a growing problem. The use of nitrogen stable isotopes as a means of discerning sewage nitrogen in the environment has been used annually by the Ecosystem Health Monitoring Program in Moreton Bay (Australia) since 1997 when the technique was first developed. This ('sewage plume mapping') technique, which measures the {delta}{sup 15}N isotopic signature of the red macroalga Catenella nipae after incubation in situ, has demonstrated a large reduction in the magnitude and spatial extent of sewage nitrogen within Moreton Bay over the past 5 years. This observed reduction coincides with considerable upgrades to the nitrogen removal efficacy at several sewage treatment plants within the region. This paper describes the observed changes and evaluates whether they can be attributed to the treatment upgrades.

  15. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-01-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  16. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  17. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

    Science.gov (United States)

    Terwilliger, Thomas C; Bricogne, Gerard

    2014-10-01

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  18. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    Energy Technology Data Exchange (ETDEWEB)

    Rimsa, Vadim; Eadsforth, Thomas C. [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

    2014-02-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.

  19. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    International Nuclear Information System (INIS)

    Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.; Hunter, William N.

    2014-01-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn 2+ -containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn 2+ , where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate

  20. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    Science.gov (United States)

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

  1. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

    International Nuclear Information System (INIS)

    Markley, John L.; Ulrich, Eldon L.; Berman, Helen M.; Henrick, Kim; Nakamura, Haruki; Akutsu, Hideo

    2008-01-01

    We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems

  2. PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

    Science.gov (United States)

    Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

    2004-04-01

    We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

  3. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

    Energy Technology Data Exchange (ETDEWEB)

    Doreleijers, Jurgen F. [University of Wisconsin-Madison, BioMagResBank, Department of Biochemistry (United States); Nederveen, Aart J. [Utrecht University, Bijvoet Center for Biomolecular Research (Netherlands); Vranken, Wim [European Bioinformatics Institute, Macromolecular Structure Database group (United Kingdom); Lin Jundong [University of Wisconsin-Madison, BioMagResBank, Department of Biochemistry (United States); Bonvin, Alexandre M.J.J.; Kaptein, Robert [Utrecht University, Bijvoet Center for Biomolecular Research (Netherlands); Markley, John L.; Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Department of Biochemistry (United States)], E-mail: elu@bmrb.wisc.edu

    2005-05-15

    We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA.

  4. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

    International Nuclear Information System (INIS)

    Doreleijers, Jurgen F.; Nederveen, Aart J.; Vranken, Wim; Lin Jundong; Bonvin, Alexandre M.J.J.; Kaptein, Robert; Markley, John L.; Ulrich, Eldon L.

    2005-01-01

    We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA

  5. The adsorption of Tl(I), Au(III), Cu(II) and the separation of 199Tl from alpha bombardment of gold target with PDB-18C6

    International Nuclear Information System (INIS)

    Zhou Dehai; Zhou Jimeng

    1989-01-01

    The adsorptive behavior of polymer of methyl aldehyde of dibenzo-18-crown-6 (PDB-18C6) in hydrochloric acid medium is studied and it is shown that the adsorption of T1(I), Au(III), and Cu(II) depends on the particle size of the crown ether resins, hydrochloric acid concentration and amount of the crown ether resins used. The difference in the adsorption behavior of different particle sizes of crown ether resins may be used for separating Tl(I), Au(III), and Cu(II) ions. The best eluant of Tl(I) and Au(III) is 0.4 mol/l perchloric acid and 2-ethoxy-ethanol. The recovery for Tl(I) is 82-98.8%. The gold target is bombarded in a 1.2 m cyclotron with 25-27 MeV α-particle with a cumulative beam intensities of 27μA·h, and 199 Tl is separated from the gold target with PDB-18C6. γ-spectrometry has shown that the Tl obtained is 199 Tl of high purity containing only about 0.50% 200 Tl

  6. The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens [version 2; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2015-06-01

    Full Text Available The therapeutic potential of α-helical anti-microbial peptides (AH-AMP to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL, we elucidate a search methodology (SCALPEL that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens (Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens by identifying AH-AMPs that mirror the function and properties of cecropin B, a well-studied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20, and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25. The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar approach to target Ebola epitopes, enumerated using PAGAL recently, by selecting suitable peptides from the human proteome, especially in wake of recent reports of cationic amphiphiles inhibiting virus entry and infection.

  7. Chemical and isotopic composition of high-temperature gases from the new Andesitic lava dome in the Soufriere of Saint-Vincent (Lesser Antilles)

    Energy Technology Data Exchange (ETDEWEB)

    Allard, P. (Centre des Faibles radioactivites, Gif-sur-Yvette (France))

    1981-11-09

    High-temperature gases emitted by the new lava dome built within the crater of the Soufriere of Saint-Vincent, in 1979, were collected. Their chemical composition and a possible deep-seated origin for carbon (mean delta/sup 13/C=-5.5 0/00 vs PDB) are discussed here.

  8. {delta}{sup 13}C and {delta}{sup 15}N shifts in benthic invertebrates exposed to sewage from McMurdo Station, Antarctica

    Energy Technology Data Exchange (ETDEWEB)

    Conlan, Kathleen E. [Canadian Musem of Nature, P.O. Box 3443 Station D, Ottawa, Ont., K1P 6P4 (Canada)]. E-mail kconlan@mus-nature.ca; Rau, Greg H. [Institute of Marine Sciences, University of California, Santa Cruz, CA 95064 (United States); Kvitek, Rikk G. [Earth Systems Science and Policy, California State University Monterey Bay, 100 Campus Center, Seaside, CA 93955 (United States)

    2006-12-15

    In an effort to identify biomonitors for contamination of Antarctic marine benthos by sewage, this study determines whether the US Antarctic Program's McMurdo Station produces a benthic sewage footprint and whether resident megafauna are assimilating sewage-derived material. We identified strong C and N isotopic gradients in benthic sediment as a function of downstream distance from McMurdo Station's point-source sewage addition. Sediment C and N isotope ratios approached marine background levels at the sampling end-point 612 m downcurrent. Based on isotope abundances in their tissues, at least some sewage C and N were assimilated by the sedentary, suspension feeding soft coral Alcyonium antarcticum, ascidian Cnemidocarpa verrucosa and bivalve Laternula elliptica. However, as inferred by tissue-sediment differences in downstream isotope trends, such assimilation was not in proportion to sewage exposure and input, therefore implying non-generalist feeding behavior by these species. In contrast, the motile, generalist feeding sea urchin Sterechinus neumayeri, sea star Odontaster validus and ribbon worm Parborlasia corrugatus showed isotopic evidence of sewage C and N assimilation roughly in proportion to sewage input. We recommend these generalist feeders for further use as biomonitors at this site now that sewage treatment has been implemented. As these species are circumpolar in distribution, they may also prove useful elsewhere in the Antarctic.

  9. Disposition of smoked cannabis with high {Delta}{sup 9}-tetrahydrocannabinol content: A kinetic model

    Energy Technology Data Exchange (ETDEWEB)

    Hunault, Claudine C., E-mail: claudine.hunault@rivm.n [National Poisons Information Center, National Institute for Public Health and the Environment, Bilthoven (Netherlands); Eijkeren, Jan C.H. van [Expertise Center for Methodology and Information Services, National Institute for Public Health and the Environment, Bilthoven (Netherlands); Mensinga, Tjeert T [National Poisons Information Center, National Institute for Public Health and the Environment, Bilthoven (Netherlands); Clinic for treatment of drug addiction in Northern, Vondellaan 71-73, 9721 LB, Groningen (Netherlands); Vries, Irma de [National Poisons Information Center, National Institute for Public Health and the Environment, Bilthoven (Netherlands); Leenders, Marianne E.C. [National Poisons Information Center, National Institute for Public Health and the Environment, Bilthoven (Netherlands); Division of Perioperative and Emergency Care, University Medical Center Utrecht, 3584 CX (Netherlands); Meulenbelt, Jan [National Poisons Information Center, National Institute for Public Health and the Environment, Bilthoven (Netherlands); Division Intensive Care Center, University Medical Center Utrecht, 3584 CX, Utrecht (Netherlands); Institute for Risk Assessment Sciences, Utrecht University, Utrecht (Netherlands)

    2010-08-01

    Introduction: No model exists to describe the disposition and kinetics of inhaled cannabis containing a high THC dose. We aimed to develop a kinetic model providing estimates of the THC serum concentrations after smoking cannabis cigarettes containing high THC doses (up to 69 mg THC). Methods: Twenty-four male non-daily cannabis users smoked cannabis cigarettes containing 29.3 mg, 49.1 mg, and 69.4 mg THC. Blood samples were collected over a period of 0-8 h and serum THC concentrations were measured. A two-compartment open model was fitted on the individual observed data. Results: Large inter-individual variability was observed in the pharmacokinetic parameters. The median pharmacokinetic parameters generated by the model were C{sub max} = 175 ng/mL, T{sub max} = 14 min, and AUC{sub 0-8h} = 8150 ng x min/mL for the 69.4 mg THC dose. Median model results show an almost linear dose response relation for C{sub max}/Dose = 2.8 x 10{sup -6}/mL and AUC{sub 0-8h}/Dose = 136 x 10{sup -6} min/mL. However, for increasing dose level, there was a clear decreasing trend: C{sub max}/Dose = 3.4, 2.6 and 2.5 x 10{sup -6}/mL and AUC{sub 0-8h}/Dose = 157, 133 and 117 x 10{sup -6} min/mL for the 29.3, 49.1 and 69.4 mg dose, respectively. Within the restriction of 8 h of observation, the apparent terminal half life of THC was 150 min. Conclusion: The model offers insight into the pharmacokinetics of THC in recreational cannabis users smoking cannabis containing high doses of THC mixed with tobacco. The model is an objective method for providing serum THC concentrations up to 8 h after smoking cannabis with a high THC content (up to 23%).

  10. Molmil: a molecular viewer for the PDB and beyond.

    Science.gov (United States)

    Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R

    2016-01-01

    We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

  11. Stable isotopes and heavy metal distribution in Dreissena polymorpha (Zebra Mussels) from western basin of Lake Erie, Canada

    Energy Technology Data Exchange (ETDEWEB)

    Al-Aasm, I.S.; Clarke, J.D.; Fryer, B.J. [Windsor Univ., ON (Canada). Dept. of Earth Sciences

    1998-02-01

    Dreissena polymorpha is an exotic freshwater bivalve species which was introduced into the Great Lakes system in the fall of 1985 through the release of ballast water from European freighters. Utilizing individual growth rings of the shells, the stable isotope distribution ({delta}{sup 18}O and {delta}{sup 13}C) was determined for the life history of selected samples which were collected from the western basin of Lake Erie. These bivalves deposit their shell in near equilibrium with the ambient water and thus reflect any annual variation of the system in the isotopic records held within their shells. Observed values for {delta}{sup 18}O range from -6.64 to -9.46 permille with an average value of -7.69 permille PDB, while carbon values ranged from -0.80 to -4.67 permille with an average value of -1.76 permille PDB. Dreissena polymorpha shells incorporate metals into their shells during growth. Individual shell growth increments were analyzed for Pb, Fe, Mg, Mn, Cd, Cu, and V concentrations. The shells show increased uptake of certain metals during periods of isotopic enrichment which correspond with warmer water temperatures. Since metals are incorporated into the shells, the organism may be useful as a biomonitor of metal pollution within aquatic environments. (orig.)

  12. On the Sources of Salinity in Groundwater under Plain Areas. Insights from {delta}{sup 18}O, {delta}{sup 2}H and Hydrochemistry in the Azul River Basin, Argentina

    Energy Technology Data Exchange (ETDEWEB)

    Zabala, M. E.; Varni, M.; Weinzettel, P. [Instituto de Hidrologia de llanuras, Azul (Argentina); Manzano, M. [Technical University of Cartagena (Spain)

    2013-07-15

    The Azul River basin, with some 6200 km{sup 2}, is located in the plains of Buenos Aires Province, Argentina. The Azul River flows along 160 km from the Tandilia Range, in the SW, to the Channel 11, in the NE. Average annual precipitation is 1005 mm (1988-2000); mean reference evapotranspiration is 1090 mm. The geology consists of Miocene to recent sediments, mostly sands and silts with some clay and calcrete layers, overlying crystalline rocks and marine sediments. The water table is shallow and groundwater in the aquifer upper 30 m displays an increasing salinity from SW to NE. The previous hypothesis to explain the salinity was infiltration of evapo-concentrated surface water, as the small soil slope in the northern basin (< 0.2%) induces rainfall accumulation in lowlands, where water evaporates prior to infiltration. But recent chemical and isotopic data reveal two salinity sources: evaporation of recent recharge water, and mixing with old saline groundwater of yet unknown origin. (author)

  13. Investigation of changes in {delta}{sup 13}C of PAHs during phytoremediation of coal tar-contaminated soils

    Energy Technology Data Exchange (ETDEWEB)

    Mick Cooper; Cheng-Gong Sun; Margaret Smith; Harry Duncan; Colin Snape [University of Nottingham, Nottingham (United Kingdom). School of Chemical Environmental and Mining Engineering

    2007-07-01

    It has been shown that phytoremediation of polyaromatic hydrocarbon (PAH) contaminated land is a useful, low cost, low maintenance method of cleaning up land at former gas and coking works. However, PAH degradation in the soil and sediment is slow, but PAHs may be degraded through properly stimulated soil micro-organisms. Here we describe a laboratory trial, employing the clover Trifolium pretense (L.)(TP), which was grown in samples of soil contaminated by fresh coal tar, and in soil heavily contaminated by PAHs, obtained from a former coking works. As the latter substrate was 'naturally' contaminated, it contained both pure PAHs and their derivatives, and was thus considered fully 'weathered', and contained recalcitrant PAH species. Conventional analytical techniques (for example, GC-MS) generally provide little information on the source of pollutants such as PAHs. Previous work has established, however, that significant differences existed in the {sup 13}C/{sup 12}C isotopic ratios between PAHs from various sources. Source apportionment of PAH contamination by stable isotope analysis is a powerful technique, but one which assumes that isotopic fractionation is not a significant factor in aged or bioaltered matrices. Phytoremediation trials described here have been utilised in order to determine whether or not any such fractionation of {sup 13}C occurs during the process. Although PAH distributions can be markedly altered by biodegradation, it has been demonstrated that, for low temperature coal tar, the carbon stable isotopic values of the parent PAHs remain fairly constant. 22 refs., 2 figs., 5 tabs.

  14. Diagenesis and reservoir quality evolution of palaeocene deep-water, marine sandstones, the Shetland-Faroes Basin, British continental shelf

    Energy Technology Data Exchange (ETDEWEB)

    Mansurbeg, H. [Department of Earth Sciences, Uppsala University, Villavaegen 16, SE 752 36 Uppsala (Sweden); Morad, S. [Department of Earth Sciences, Uppsala University, Villavaegen 16, SE 752 36 Uppsala (Sweden); Department of Petroleum Geosciences, The Petroleum Institute, P.O. Box 2533, Abu Dhabi (United Arab Emirates); Salem, A. [Faculty of Education at Kafr El-Sheikh, Tanta University, Kafr El-Sheikh (Egypt); Marfil, R.; Caja, M.A. [Departmento Petrologia y Geoquimica, Facultad de Geologia, UCM, 28040 Madrid (Spain); El-ghali, M.A.K. (Geology Department, Al-Fateh University, P.O. Box 13696, Libya); Nystuen, J.P. [Department of Geosciences, University of Oslo, P.O. Box 1047 Blindern, NO-0316 Oslo (Norway); Amorosi, A. [Department of Earth Sciences, University of Bologna, Via Zamboni 67, 40127 Bologna (Italy); Garcia, D. [Centre SPIN, Department GENERIC, Ecole Nationale Superieure des Mines de Saint Etienne 158, Cours Fauriel 42023, Saint-Etienne (France); La Iglesia, A. [Instituto de Geologia Economica (CSIC-UCM), Facultad de Geologia, UCM, 28040 Madrid (Spain)

    2008-06-15

    The Palaeocene, deep-water marine sandstones recovered from six wells in the Shetland-Faroes Basin represent lowstand, transgressive and highstand systems tract turbiditic sediments. Mineralogic, petrographic, and geochemical analyses of these siliciclastics are used to decipher and discuss the diagenetic alterations and subsequent reservoir quality evolution. The Middle-Upper Palaeocene sandstones (subarkoses to arkoses) from the Shetland-Faroes Basin, British continental shelf are submarine turbiditic deposits that are cemented predominantly by carbonates, quartz and clay minerals. Carbonate cements (intergranular and grain replacive calcite, siderite, ferroan dolomite and ankerite) are of eogenetic and mesogenetic origins. The eogenetic alterations have been mediated by marine, meteoric and mixed marine/meteoric porewaters and resulted mainly in the precipitation of calcite ({delta}{sup 18}O{sub V-PDB}=-10.9 permille and -3.8 permille), trace amounts of non-ferroan dolomite, siderite ({delta}{sup 18}O{sub V-PDB}=-14.4 permille to -0.6 permille), as well as smectite and kaolinite in the lowstand systems tract (LST) and highstand systems tract (HST) turbiditic sandstone below the sequence boundary. Minor eogenetic siderite has precipitated between expanded and kaolinitized micas, primarily biotite. The mesogenetic alterations are interpreted to have been mediated by evolved marine porewaters and resulted in the precipitation of calcite ({delta}{sup 18}O{sub V-PDB}=-12.9 permille to -7.8 permille) and Fe-dolomite/ankerite ({delta}{sup 18}O{sub V-PDB}=-12.1 permille to -6.3 permille) at temperatures of 50-140 and 60-140 C, respectively. Quartz overgrowths and outgrowth, which post- and pre-date the mesogenetic carbonate cements is more common in the LST and TST of distal turbiditic sandstone. Discrete quartz cement, which is closely associated with illite and chlorite, is the final diagenetic phase. The clay minerals include intergranular and grain replacive

  15. A study of the process of joint formation of methane gas-hydrate and authigenic carbonates in bottom sediments in the Sea of Okhotsk

    Energy Technology Data Exchange (ETDEWEB)

    Esikov, A D [AN SSSR, Moscow (USSR). Water Problems Inst.; Pashkina, V I [AN SSSR, Moscow (USSR). Inst. Okeanologii

    1990-01-01

    The discovery of gas-hydrates in bottom sediments in the Sea of Okhotsk has allowed isotope fractionation of oxygen and hydrogen to be determined in the formation of the crystal lattice. It was established that the structure of gas-hydrate selectively included the heavier isotopes of oxygen and hydrogen, so that the gas-hydrate water had values of {delta}{sup 18}O = +1.9 per mille and {delta}D = +23 per mille, whereas the interstitial water was ''lighter'' in isotopes, with the values of {delta}{sup 18}O = -0.5 per mille and {delta}D = -5 per mille (relative to SMOW (standard mean ocean water)). The formation of gas-hydrates under the conditions of underwater discharge of methane alters the chemical composition of interstitial water, so that the carbonate equilibrium is shifted, and carbonates of authigenic origin are formed. The isotope composition of the carbonates is characterized by a low content of {sup 13}C({delta}{sup 13}C from -39.3 to -51.8 per mille PDB) and a high content of {sup 18}O({delta}{sup 18}O from + 2.7 to +6.3 per mille PDB) in comparison with carbonates of sea origin. These characteristics of the isotope composition suggest the participation of methane in the formation of authigenic carbonates, due to its anaerobic oxidation and the involvement of sulfate in the silt water. (author).

  16. hPDB – Haskell library for processing atomic biomolecular structures in protein data bank format

    OpenAIRE

    Gajda, Michał Jan

    2013-01-01

    Background Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. Findings I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The propo...

  17. FAKTOR-FAKTOR YANG MEMENGARUHI PDB INDONESIA DENGAN PERSAMAAN SIMULTAN 2SLS

    Directory of Open Access Journals (Sweden)

    NI MADE SRI KUSUMAWARDHANI

    2012-09-01

    Full Text Available Economic growth is indicated by an increase in the value of Gross Domestic Product (GDP. The size of GDP is influenced by various factors, including the Household Consumption, Investment, Government Spending, and Net Exports. One of the components that contribute to determine the amount of GDP is investment. According to the concept of macroeconomics, investment is also influenced by the GDP, tax revenue, and Currency. The reciprocal relationship between GDP and the investment is called a simultaneous relationship, therefore this study uses simultaneous equation Two Stage Least Squares (2SLS. 2SLS is one of the statistical methods used to replace the OLS method that can not be used to estimate an equation in a system of simultaneous equations. After analysis, the result shows the variables that influence the investment equation are GDP, tax, and revenue.

  18. Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

    Science.gov (United States)

    Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

    2013-01-01

    The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

  19. Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

    Directory of Open Access Journals (Sweden)

    Carugo Oliviero

    2011-10-01

    Full Text Available Abstract Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.

  20. PENGARUH PDB RIIL DAN VARIABEL FISKAL TERHADAP PENANAMAN MODAL ASING LANGSUNG DI INDONESIA

    Directory of Open Access Journals (Sweden)

    Yosi Eka Putri

    2012-10-01

    Full Text Available This study aims to determine the influence of Real GDP and fiscal variables for foreign direct investment in Indonesia in period 1980 to 2006, and also to determine the level of sensitivity (elasticity of foreign direct investment to GDP Real and fiscal variables in Indonesia in 1980 to 2006. The data used in this study is time series data or annual data for 27 years secondary. Data obtained from Statistics Economics and Finance Indonesia (SEKI BI. The research method used a model with a Multiple Linear Regression analysis: analysis of correlation (R, the analysis of the coefficient of determination (R2, the elasticity analysis, and test the stability of the model, while the tests performed were F test, t test, and test autocorrelation with Durbin Watson and multicollinearity test using Eviews program. From the results of this study showed that 96.16% of foreign direct investment in Indonesia is influenced by real GDP, income tax, property tax, sales tax, economic development spending, government spending on transport and communications, government spending on education, as well as the economic crisis while the rest of 3.84 % influenced by other factors outside the model. Effect of Real GDP, PBB, government spending on transport and communications and in partial dummy variable is not significant while the Income Tax, sales tax, government spending for education and development are significant on direct foreign investment in Indonesia from 1980 to 2006.

  1. CH4 fluxes across the seafloor at three district gas hydrate fields: Impacts on ocean and atmosphere chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Kastner, M.; Bartlett, D.; MacDonald, I.; Solomon, E.

    2005-07-01

    The role of methane hydrate in the global methane budget is poorly documented because relatively little is known about the transport of methane through the seafloor into the ocean and atmosphere, and the extent of en route water-column methanotrophy. Pore fluids and water column samples within and adjacent to methane plumes were analyzed for methane, dissolved inorganic C (DIC), sulfide/sulfate, alkalinity, and major element concentrations, and for delta{sup 13}C-CH4 and DIC, at three distinct gas hydrate environments. The three environments are: Bush Hill (BH) in the northern Gulf of Mexico (GOM), Eel River (ER) offshore Northern California, and North and South Hydrate Ridges (HR), Cascadia, Oregon margin. The methane source at these sites ranges from mostly thermogenic at GOM to primarily biogenic at HR. At these three distinct gas hydrate environments, at all the sites a significant enrichment in {sup 13}C-CH4 along isopycnals away from the methane plumes is observed, indicating extensive aerobic bacterial methane oxidation in the water column, and correspondingly of oxygen consumption. This is principally pronounced in the mostly biogenic methane setting. The delta{sup 13}C-CH4 values range from approx. 12 to -67 , PDB, at the Hydrate Ridges, from approx. 34 to -52 at Eel River, and from approx. 41 to -67 at Bush Hill. The large variation in methane C isotope ranges between the sites suggests that major differences exist in both the rates of aerobic methane oxidation and system openness at the studied locations. Methane fluxes across the sediment/seawater interface were measured, with a flux meter, MOSQUITO (Multiple Orifice Sampler and Quantitative Injection Tracer Observers) only at BH (Solomon et al., 2005). Water column methane concentrations are on average lower at HR than at ER and GOM. Preliminary estimates suggests that aerobic oxidation is nearly complete, consumes most to all of the water column methane at HR, but at the GOM only approx. 80% to a

  2. Water circulation control on carbonate-{delta}{sup 18}O records in a low permeability clay formation and surrounding limestones: The Upper Dogger-Oxfordian sequence from the eastern Paris basin, France

    Energy Technology Data Exchange (ETDEWEB)

    Lavastre, Veronique, E-mail: veronique.lavastre@univ-st-etienne.fr [Universite de Lyon, Universite Jean Monnet, F-42023 Saint Etienne (France)] [CNRS, UMR 6524, LMV, F-42023 Saint Etienne (France)] [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France); Ader, Magali [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France); Buschaert, Stephane [Andra, Parc de la Croix Blanche, 7-8 rue Jean Monnet, 92 298 Chatenay-Malabry Cedex (France); Petit, Eddy; Javoy, Marc [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France)

    2011-05-15

    Research Highlights: > Up. Dog./Oxf. sequence is investigated for radioactive waste disposal feasibilities. > Marine carbonates suffered isotopic exchanges with meteoric water. > Modelling shows that very low W/R ratio can explain isotopic changes in clay layer. > Higher W/R ratio are needed to reach isotopic changes in carbonated layers. > Confirmed barrier property of clay layer was probably reached during early burial. - Abstract: Upper Dogger to Oxfordian Formations in the eastern part of the Paris basin (France) are currently being investigated by the French nuclear waste management agency (Andra), testing the feasibility of long-term deep nuclear waste disposal in the Callovo-Oxfordian claystones. Characterising the hydrogeological behaviour of the Callovo-Oxfordian claystones is, therefore, essential in evaluating its potential as a geological barrier. In order to evaluate and quantify water/rock interactions experienced over geological time by these Formations, bulk carbonate {delta}{sup 13}C and {delta}{sup 18}O were measured and calculations of water-rock ratios were used to explain carbonate-{delta}{sup 18}O changes. Meteoric porewater and a maximum temperature reached of about 40 deg. C were considered. The Jurassic marine carbonate {delta}{sup 13}C was preserved in the Callovo-Oxfordian claystones and in the overlying limestones (-0.28 per mille to 3.39 per mille/PDB), while the {delta}{sup 18}O values are lower by 0-5 per mille (-6.25 per mille to -1.32 per mille/PDB). Calculations show that Upper Dogger and Oxfordian Limestone {delta}{sup 18}O data: (i)have random-like distribution through theoretical {delta}{sup 18}O-W/R curves and (ii)suggest that water/rock ratios (0.08-0.4) needed to explain {delta}{sup 18}O changes are higher by a factor of about 2-20 compared to the present-day water/rock ratio. These features indicate advection in both aquifers. According to the history of the Paris basin, this hydrogeological behaviour could have been

  3. Radiocarbon dating of VIRI bone samples using ultrafiltration

    Energy Technology Data Exchange (ETDEWEB)

    Minami, Masayo, E-mail: minami@nendai.nagoya-u.ac.jp [Center for Chronological Research, Nagoya University, Nagoya 464-8602 (Japan); Yamazaki, Kana [Faculty of Science, Nagoya University, Nagoya 464-8602 (Japan); Omori, Takayuki [University Museum, University of Tokyo, Tokyo 113-0033 (Japan); Nakamura, Toshio [Center for Chronological Research, Nagoya University, Nagoya 464-8602 (Japan)

    2013-01-15

    Ultrafiltration can effectively remove low-molecular-weight (LMW) contaminants from bone gelatin to extract high-molecular-weight (HMW) proteins that are derived from original bone collagen, though it cannot remove HMW collagen crosslinked with humic acids. Therefore, ultrafiltration is often used to obtain more accurate {sup 14}C dates of bones. However, ultrafiltration may introduce new contaminants to bone gelatins, mainly from ultrafilters used. To study the effects of ultrafiltration on {sup 14}C age, we analyzed the C/N ratio, {delta}{sup 13}C{sub PDB} and {delta}{sup 15}N{sub AIR} values, and {sup 14}C ages of acid-soluble bone collagen obtained by decalcification, gelatin extracted from acid-insoluble bone collagen, and the HMW gelatin and LMW fractions produced during ultrafiltration of the extracted gelatin. Bone samples from the Fifth International Radiocarbon Intercomparison (VIRI) were used: VIRI-E (mammoth), -F (horse), -G (human), and -I (whale). In this study, carbon and nitrogen content and gelatin yields were used to evaluate collagen preservation in the VIRI bone samples. Radiocarbon ages, {delta}{sup 13}C{sub PDB} and {delta}{sup 15}N{sub AIR} values of unfiltered and HMW gelatins were obtained and compared with the published consensus values. The LMW fraction was found to exhibit different values from those of the other fractions, indicating the possible presence of extraneous contamination. The Vivaspin Trade-Mark-Sign 6 ultrafilters used in this study were analyzed and radiocarbon dated both before and after cleaning. We present evidence to suggest that LMW fraction contaminants could be derived from the ultrafilters rather than humic substances. Excessively long ultrafiltration time was suspected to have contaminated the bone samples with material from the ultrafilter, because those samples exhibited older {sup 14}C ages than did those filtered for shorter durations. The results in this study indicate that {sup 14}C ages of unfiltered

  4. Delta.sup.15 ./sup.N as an indicator of N.sub.2./sub.-fixation by cyanobacterial mats in tropical marshes

    Czech Academy of Sciences Publication Activity Database

    Rejmánková, E.; Komárková, Jaroslava; Rejmánek, M.

    2004-01-01

    Roč. 67, č. 3 (2004), s. 353-368 ISSN 0168-2563 Grant - others:UC Davis Faculty(US) Research Grants Institutional research plan: CEZ:AV0Z6017912 Keywords : delta 15N * cyanobacteria * nitrogen fixation * wetlands Subject RIV: CE - Biochemistry Impact factor: 2.125, year: 2004

  5. Isotopic and chemical characterization of coal in Pakistan

    International Nuclear Information System (INIS)

    Qureshi, R.M.; Hasany, S.M.; Javed, T.; Sajjad, M.I.; Shah, Z.; Rehman, H.

    1993-11-01

    Stable carbon isotope ratios (delta/sup 13/C PDB) and toxic/trace element concentration levels are determined for Tertiary coal samples collected from seven coal fields in Pakistan. No systematic isotope effects are found in the process of coal liquefaction from peat to Tertiary lignites and sub bituminous coal. Similarly, no age effects are observed during the Tertiary regime. The observed variations in the carbon isotopic composition of coal obtained from 'Sharigh coal field' and the 'Sor-Range/Degari coal field' in Baluchistan are attributed to the depositional environments. More sampling of stable carbon isotope analysis are required to validate these observations. Significant concentrations of toxic elements such as S, Cr, Cd and Pb in Makarwal coal may pose environmental and engineering/operational problems for thermal power plants. (author)

  6. Study of groundwater in the Chicu River basin, Sabana de Bogota, Colombia; Estudio de las aguas subterraneas de la cuenca del Rio Chicu, Sabana de Bogota, Colombia

    Energy Technology Data Exchange (ETDEWEB)

    Obando G, E; Jimenez B, G; Torres Q, E; Alayon C, E; Garavito B, F [Instituto de Ciencias Nucleares y Energias Alternativas, INEA, Bogota (Colombia)

    1995-10-01

    The Rio Chicu Valley aquifer system represents one of the many sub-systems constituting the hydrogeological system of the Sabana de Bogota. The valley has a structure of a graben, covered by a quaternary alluvial formation, which has a low permeability and therefore is an aquifer of poor characteristics. Due to the thickness of this aquifer (around 300 m), the tertiary aquifers are only exploited by few deep wells. The isotopic composition of water collected from the tertiary aquifer is depleted by 1 per mille in {delta}{sup 18}O and 8 per mille in {delta}D. This difference is due to the altitude effect of recharge, because the tertiary aquifers outcrop on the top of the surrounding hills. In some places, the stable isotope content of water sampled in wells tapping water from the quaternary aquifer is similar to the values found in the tertiary aquifer. This fact indicates the ascending leakage from deep horizons. A rather unique characteristics of the quaternary aquifer is that in the central part of the basin the dissolved inorganic carbon DIC is very high and shows a {delta}{sup 13}C values around +10 per mille vs PDB and {sup 14}C around 5-10 pmc. The positive values are probably related to decomposition of organic matter in anaerobic conditions. These values reflect a very low flow in the system and limited recharge. (author). 1 ref., 5 figs, 2 tabs.

  7. Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids.

    Science.gov (United States)

    Annavarapu, Srinivas; Nanda, Vikas

    2009-09-22

    Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids. Propensities for amino acids to occur in contiguous alpha(L) helices correlate with published thermodynamic scales for incorporation of D-amino acids into alpha(R) helices. Two backbone rules for terminating a left-handed helix are found: an alpha(R) conformation is disfavored at the amino terminus, and a beta(R) conformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to alpha(L) helices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus. By examining left-handed alpha-turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed alpha-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds.

  8. Mirrors in the PDB: left-handed α-turns guide design with D-amino acids

    Directory of Open Access Journals (Sweden)

    Nanda Vikas

    2009-09-01

    Full Text Available Abstract Background Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids. Results Propensities for amino acids to occur in contiguous αL helices correlate with published thermodynamic scales for incorporation of D-amino acids into αR helices. Two backbone rules for terminating a left-handed helix are found: an αR conformation is disfavored at the amino terminus, and a βR conformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to αL helices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus. Conclusion By examining left-handed α-turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed α-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds.

  9. Studies of base pair sequence effects on DNA solvation based on all ...

    Indian Academy of Sciences (India)

    pdb1. 2.00. CATGGCCATG. 158d.pdb1. 1.90. CCAAGCTTGG. 167d.pdb1. 2.30. CCATTAATGG. 194d.pdb1. 2.30. CGCGTTAACGCG. 196d.pdb1. 1.70. CTCTCGAGAG. 1bd1.pdb1. 1.60. CCAGGCCTGG. 1bdn.pdb1. 2.60. CGCAAAAATGCG.

  10. Geological setting, isotope studies (C, O and Pb) and associated metals in the Tocantinzinho gold deposit, Tapajos domain, Tapajos-Parima Province; Contexto geologico, estudos isotopicos (C, O e Pb) e associacao metalica do deposito aurifero Tocantinzinho, dominio Tapajos, Provincia Tapajos-Parima

    Energy Technology Data Exchange (ETDEWEB)

    Villas, Raimundo Netuno Nobre [Universidade Federal do Para (UFPA), Belem, PA (Brazil); Santiago, Erika Suellen Barbosa; Castilho, Marilia Portela, E-mail: netuno@ufpa.br, E-mail: esbsantiago@gmail.com, E-mail: castilho.marilia@hotmail.com [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Geociencias. Programa de Pos-graduacao em Geologia e Geoquimica

    2013-03-15

    The Tocantinzinho ore deposit is located along a NW-SE-trending lineament, southwestern of Itaituba (Para, Brazil), and is the largest known gold deposit of the Tapajos Province. The host Tocantinzinho granite is essentially isotropic and dominated by syenogranites and monzogranites that have been weakly to moderately altered by hydrothermal fluids. Microclinization (earliest), chloritization, sericitization, silicification and carbonatization (latest) are the main types of alteration. Most mineralization was contemporaneous with the sericitization/silicification and is represented by sulfide- and gold-bearing veinlets which locally occur as stockwork. Pyrite, chalcopyrite, sphalerite and galena are the most common sulfides. Among the ore metals, Cu, Pb and Zn present the highest contents, but Mo, As and Bi locally show anomalous concentrations. The relationship of Au with Cu, Pb or Zn is at random and the Au/Ag ratios range from 0.05 to 0.5. The higher the sulfide contents, the higher the Au concentrations, though it occurs mainly included in pyrite. Zircon monocrystals from the Tocantinzinho granite yielded an average Pb-Pb age of 1982 {+-}8Ma and may represent an earlier event of the Creporizao magmatic arc. {delta}{sup 13}C{sub PDB} values for calcite from the carbonatization stage fall dominantly between -3.45 and -2.29 Per-Mille-Sign , being compatible with a deep crustal source that may include carbonatite reservoirs. In turn, {delta}{sup 18}O{sub SMOW} values vary from +5.97 to +14.10 Per-Mille-Sign , being indicative of magmatic derivation, although the less positive values suggest contribution from surficial waters. Unpublished fluid inclusion study reveals the presence of aquo-carbonic fluids, whose CO{sub 2} could have been dissolved in the granitic magma rather than being related to the shear zone. The available data allow the Tocantinzinho deposit to be classified as a granite-hosted, intrusion-related gold deposit. (author)

  11. Late production of hydrocarbon gases in sedimentary basins: kinetic and isotopic study; Genese tardive des gaz hydrocarbures dans les bassins sedimentaires: etude cinetique et isotopique

    Energy Technology Data Exchange (ETDEWEB)

    Lorant, F.

    1999-06-23

    to describe more precisely these reactions, additional pyrolysis experiments were performed on an aromatic compound, representative of the chemical structure of mature kerogens: the 1-methyl-pyrene. The data show that the methane is mainly produced during secondary and tertiary mechanisms, following to global succeeding stages: E{sub 1} = 56.7 kcal/mol and A{sub 1} = 8.52 x 10{sup 12} s{sup -1}, E{sub 2} = 49.5 kcal/mol and A{sub 2} 2.48 x 10{sup 9} s{sup -1}. By analogy, it was established that the three reactions of late methane generation, as observed by pyrolyzing mature kerogens, are respectively related to beta-scission, demethylation and cokefaction processes. In other respects, the late methane is characterized by {delta}{sup 13}C values between -36 and -24 0/00{sub PDB} (experimental conditions), and for the Type II kerogen by a reversal of the isotopic fractionation between the gas and its source at the high maturity levels: {delta}{sup 13}C{sub CH4/kerogene} = -10 to +2 0/00{sub PDB}. Such an uncommon {delta}{sup 13}C evolution was not observed during the pyrolysis of the I-methyl-pyrene, the generated methane being, on the contrary, strongly {sup 12}C-enriched compared to its source ({delta}{sup 13}C{sub CH4/1-MPy} = -35 to -19 0/00{sub PDB}). Nevertheless, by coupling a model of isotopic fractionation, based on the assumption of strictly kinetically-controlled effects, to the kinetic scheme previously generated, it was shown that the differences of isotopic signature between the model compound and the kerogens are mainly due to highly contrasted precursor effects (i.e. {delta}{sup 13}C of the functional groups from which the methane originates) specific to demethylation processes. Besides the elaboration of a methodology for the acquisition of kinetic, stoichiometric and isotopic parameters specific to the generation of late methane, this work has allowed the validation of a model of isotopic fractionation, especially by emphasizing the synergy between

  12. Determination of the positions and residues of the. delta. /sup + +/ and. delta. /sup 0/ poles. [Phase shifts,coulomb corrections

    Energy Technology Data Exchange (ETDEWEB)

    Vasan, S S [Carnegie-Mellon Univ., Pittsburgh, Pa. (USA). Dept. of Physics

    1976-04-19

    The poles and the associated residues in the ..pi..N P/sub 33/ amplitude corresponding to the resonances ..delta../sup + +/ and ..delta../sup 0/ are determined by fitting the ..pi../sup +/p and ..pi../sup -/p hadronic phase shifts from the Carter 73 analysis. The ..delta../sup + +/ and ..delta../sup 0/ pole positions are determined also from the nuclear phase shifts, these being the phase shifts made up of the hadronic phase shifts plus the Coulomb corrections. The pole positions obtained from the two sets of phase shifts are different, the differences being larger in the case of the ..delta../sup + +/.

  13. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 7:H7] pdb|2REC|F Chain F, Reca ... Hexamer Model, Electron Microscopy pdb|2REC|E Chain E, ... ...Reca Hexamer Model, Electron Microscopy pdb|2REC|D Chain ... D, Reca Hexamer Model, Electron Microscopy... pdb|2REC|C ... Chain C, Reca Hexamer Model, Electron Microscopy ... ... ... pdb|2REC|B Chain B, Reca Hexamer Model, Electron ... Microscopy pdb|2REC|A Chain A, Reca Hexamer ...Model, ... Electron Microscopy ... Length = 326 ... Query: 7 ... KQKALAAALGQIEKQFGKGSIMRLGEDRSMDVET

  14. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 7:H7] pdb|2REC|F Chain F, Reca ... Hexamer Model, Electron Microscopy pdb|2REC|E Chain E, ... ...Reca Hexamer Model, Electron Microscopy pdb|2REC|D Chain ... D, Reca Hexamer Model, Electron Microscopy... pdb|2REC|C ... Chain C, Reca Hexamer Model, Electron Microscopy ... ... ... pdb|2REC|B Chain B, Reca Hexamer Model, Electron ... Microscopy pdb|2REC|A Chain A, Reca Hexamer ...Model, ... Electron Microscopy ... Length = 326 ... Query: 7 ... KQKALAAALGQIEKQFGKGSIMRLGEDRSMDVET

  15. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 7:H7] pdb|2REC|F Chain F, Reca ... Hexamer Model, Electron Microscopy pdb|2REC|E Chain E, ... ...Reca Hexamer Model, Electron Microscopy pdb|2REC|D Chain ... D, Reca Hexamer Model, Electron Microscopy... pdb|2REC|C ... Chain C, Reca Hexamer Model, Electron Microscopy ... ... ... pdb|2REC|B Chain B, Reca Hexamer Model, Electron ... Microscopy pdb|2REC|A Chain A, Reca Hexamer ...Model, ... Electron Microscopy ... Length = 326 ... Query: 7 ... KQKALAAALGQIEKQFGKGSIMRLGEDRSMDVET

  16. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 7:H7] pdb|2REC|F Chain F, Reca ... Hexamer Model, Electron Microscopy pdb|2REC|E Chain E, ... ...Reca Hexamer Model, Electron Microscopy pdb|2REC|D Chain ... D, Reca Hexamer Model, Electron Microscopy... pdb|2REC|C ... Chain C, Reca Hexamer Model, Electron Microscopy ... ... ... pdb|2REC|B Chain B, Reca Hexamer Model, Electron ... Microscopy pdb|2REC|A Chain A, Reca Hexamer ...Model, ... Electron Microscopy ... Length = 326 ... Query: 7 ... KQKALAAALGQIEKQFGKGSIMRLGEDRSMDVET

  17. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 7:H7] pdb|2REC|F Chain F, Reca ... Hexamer Model, Electron Microscopy pdb|2REC|E Chain E, ... ...Reca Hexamer Model, Electron Microscopy pdb|2REC|D Chain ... D, Reca Hexamer Model, Electron Microscopy... pdb|2REC|C ... Chain C, Reca Hexamer Model, Electron Microscopy ... ... ... pdb|2REC|B Chain B, Reca Hexamer Model, Electron ... Microscopy pdb|2REC|A Chain A, Reca Hexamer ...Model, ... Electron Microscopy ... Length = 326 ... Query: 7 ... KQKALAAALGQIEKQFGKGSIMRLGEDRSMDVET

  18. PDBML: the representation of archival macromolecular structure data in XML.

    Science.gov (United States)

    Westbrook, John; Ito, Nobutoshi; Nakamura, Haruki; Henrick, Kim; Berman, Helen M

    2005-04-01

    The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.

  19. Palynological and bulk geochemical constraints on the paleoceanographic conditions across the Frasnian-Famennian boundary, New Albany Shale, Indiana

    Energy Technology Data Exchange (ETDEWEB)

    Rue, Sarah R. de la [Department of Geology and Geophysics, Louisiana State University, Baton Rouge, Louisiana 70803-4101 (United States); Rowe, Harold D.; Rimmer, Susan M. [Department of Earth and Environmental Sciences, Slone Research Building, University of Kentucky, Lexington KY 40506-0053 (United States)

    2007-06-01

    A down-core record of stable isotope and geochemical results is integrated with palynofacies (kerogen) data from the New Albany Shale (Indiana) to reconstruct environmental changes that occurred across the Frasnian-Famennian boundary. Preliminary interpretations are focused on developing several multiproxy linkages that will potentially lead toward a more robust understanding of the occurrence and significance of phytoplankton assemblage variations during the Late Devonian, a time of widespread black shale formation. Development of such linkages will potentially provide a more comprehensive assessment of the various controls on 1) primary production, and 2) carbon sequestration in a large, low-paleolatitude intracratonic basin. An abrupt change in the geochemical and biotic proxies for particulate organic matter across the Frasnian-Famennian boundary coincides with a distinct lithological change, characterized by laminated, brownish-black Famennian mudstones unconformably overlying alternating bioturbated, greenish-gray and non-bioturbated, dark-gray Frasnian mudstones. Elemental and isotopic profiles reflect different patterns of production, degradation, and removal of organic carbon in the two shale facies. A shift from acritarch- to prasinophyte-dominated waters across the boundary indicates the overall importance of bathymetric fluctuations, chemico-physical conditions, and nutrient availability related to eustatic sea-level change. A positive {delta}{sup 13}C{sub V-PDB} shift of 1.1 permille across the boundary is interpreted to be correlative with the global Upper Kellwasser Event. A preliminary model is proposed to explain the sustainable primary production during times of maximum flooding, thereby enhancing organic preservation during black shale formation. (author)

  20. Preparation data of the bromodomains BRD3(1, BRD3(2, BRD4(1, and BRPF1B and crystallization of BRD4(1-inhibitor complexes

    Directory of Open Access Journals (Sweden)

    Martin Hügle

    2016-06-01

    Full Text Available This article presents detailed purification procedures for the bromodomains BRD3(1, BRD3(2, BRD4(1, and BRPF1B. In addition we provide crystallization protocols for apo BRD4(1 and BRD4(1 in complex with numerous inhibitors. The protocols described here were successfully applied to obtain affinity data by isothermal titration calorimetry (ITC and by differential scanning fluorimetry (DSF as well as structural characterizations of BRD4(1 inhibitor complexes (PDB codes: PDB: 4LYI, PDB: 4LZS, PDB: 4LYW, PDB: 4LZR, PDB: 4LYS, PDB: 5D24, PDB: 5D25, PDB: 5D26, PDB: 5D3H, PDB: 5D3J, PDB: 5D3L, PDB: 5D3N, PDB: 5D3P, PDB: 5D3R, PDB: 5D3S, PDB: 5D3T. These data have been reported previously and are discussed in more detail elsewhere [1,2].

  1. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available inase (EC 2.7.4.6) - Mycobacterium tuberculosis (strain ... H37RV) pdb|1K44|F Chain F, Mycobacterium Tuberculosis...losis Nucleoside Diphosphate Kinase ... pdb|1K44|D Chain D, Mycobacterium Tuberculosis... ... Nucleoside Diphosphate Kinase pdb|1K44|C Chain C, ... Mycobacterium Tuberculosis... Nucleoside Diphosphate Kinase ... pdb|1K44|B Chain B, Mycobacterium Tuberculosis ... Nucleos...ide Diphosphate Kinase pdb|1K44|A Chain A, ... Mycobacterium Tuberculosis

  2. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available inase (EC 2.7.4.6) - Mycobacterium tuberculosis (strain ... H37RV) pdb|1K44|F Chain F, Mycobacterium Tuberculosis...losis Nucleoside Diphosphate Kinase ... pdb|1K44|D Chain D, Mycobacterium Tuberculosis... ... Nucleoside Diphosphate Kinase pdb|1K44|C Chain C, ... Mycobacterium Tuberculosis... Nucleoside Diphosphate Kinase ... pdb|1K44|B Chain B, Mycobacterium Tuberculosis ... Nucleos...ide Diphosphate Kinase pdb|1K44|A Chain A, ... Mycobacterium Tuberculosis

  3. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available inase (EC 2.7.4.6) - Mycobacterium tuberculosis (strain ... H37RV) pdb|1K44|F Chain F, Mycobacterium Tuberculosis...losis Nucleoside Diphosphate Kinase ... pdb|1K44|D Chain D, Mycobacterium Tuberculosis... ... Nucleoside Diphosphate Kinase pdb|1K44|C Chain C, ... Mycobacterium Tuberculosis... Nucleoside Diphosphate Kinase ... pdb|1K44|B Chain B, Mycobacterium Tuberculosis ... Nucleos...ide Diphosphate Kinase pdb|1K44|A Chain A, ... Mycobacterium Tuberculosis

  4. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... glutamine [Escherichia coli K12] pdb|1WXI|A Chain A, ... E.Coli Nad Synthetase, Amp.Pp pdb|1WXH|A Chain A, E.Coli... ... Nad Synthetase, Nad pdb|1WXG|A Chain A, E.Coli... Nad ... Synthetase, Dnd pdb|1WXF|A Chain A, E.Coli Nad ... Synthetase pdb|1WXE|A Chain A, E.Coli

  5. Carbon and oxygen isotopes in carbonatites from Puna, Jujuy and Salta, Argentina; Isotopos de carbono y oxigeno en carbonatitas en la Puna Oriental, Provincias de Jujuy y Salta, Republica Argentina

    Energy Technology Data Exchange (ETDEWEB)

    Zappettini, Eduardo O; Rubiolo, Daniel [Servicio Geologico Minero Argentino (SEGEMAR), Buenos Aires (Argentina). Instituto de Geologia y Recursos Naturales; Hubberten, Hans W [Alfred-Wegener-Institut fuer Polar- und Meeresforschung, Bremerhaven (Germany)

    1998-07-01

    {delta}{sup 13} and {delta}{sup 18}O data from carbonatites indicate that bodies formed by crystallization of carbonate magma with subsequent formation of metasomatic and hydrothermal carbonatitic veins. The isotopic data are consistent with the available geochemical and petrologic information. (author)

  6. Pion content of the nucleon in polarized semi-inclusive DIS

    Energy Technology Data Exchange (ETDEWEB)

    Melnitchouk, W. [Univ. of Regensburg (Germany); Thomas, A.W. [Univ. of Adelaide (Australia)

    1994-04-01

    An explicit pionic component of the nucleon may be identified by measuring polarized {Delta}{sup ++} fragments produced in deep-inelastic scattering (DIS) off polarized protons. The pion-exchange model predicts highly correlated polarizations of the {Delta}{sup ++} and target proton, in marked contrast with the competing diquark fragmentation process.

  7. Role of crude oil in the genesis of Mississippi Valley-type deposits. Evidence from the Cincinnati arch

    Energy Technology Data Exchange (ETDEWEB)

    Kesler, S.E.; Jones, H.D. (Univ. of Michigan, Ann Arbor, MI (United States)); Furman, F.C. (Univ. of Missouri, Rolla, MO (United States)); Sassen, R. (Texas A M Univ., College Station, TX (United States)); Anderson, W.H. (Univ. of Kentucky, Lexington, KY (United States)); Kyle, J.R. (Univ. of Texas, Austin, TX (United States))

    1994-07-01

    Mississippi Valley-type (MVT) sulfide minerals and oil from deposits along the Cincinnati arch have almost identical [delta][sup 34]S values (-9% to +9% for MVT sulfides, -12% to +9% for oils). These values are very similar to those for MVT sulfides and oil in the Illinois-Kentucky district and support their proposed inclusion in a regional hydrothermal system. Many MVT deposits with low [delta][sup 34]S values are closely associated with oil, whereas MVT deposits with high [delta][sup 34]S values often contain bitumen. Reduced sulfur in MVT deposits with high [delta][sup 34]S values probably came from thermochemical sulfate reduction, whereas that in MVT deposits with low [delta][sup 34]S values probably came from oil and related organic matter. Oil-related sulfur could have been derived from oil fields or disseminated oil and other organic matter in regional wallrocks. 44 refs., 3 figs., 2 tabs.

  8. Environmental isotopes (N, S, C, O, D) to determine natural attenuation processes in nitrate contaminated waters: Example of Osona (NE Spain)

    Energy Technology Data Exchange (ETDEWEB)

    Vitoria, Laura [Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristal.lografia, Mineralogia i Diposits Minerals, Facultat de Geologia, Universitat de Barcelona, Marti i Franques, s/n, 08028, Barcelona (Spain)], E-mail: lvitoria@ub.edu; Soler, Albert; Canals, Angels [Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristal.lografia, Mineralogia i Diposits Minerals, Facultat de Geologia, Universitat de Barcelona, Marti i Franques, s/n, 08028, Barcelona (Spain); Otero, Neus [Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristal.lografia, Mineralogia i Diposits Minerals, Facultat de Geologia, Universitat de Barcelona, Marti i Franques, s/n, 08028, Barcelona (Spain); Departament de Geologia Ambiental, Institut de Ciencies de la Terra ' Jaume Almera' , CSIC C/Lluis Sole i Sabaris s/n, Barcelona 08028 (Spain)

    2008-12-15

    Nitrate-contaminated groundwater from an aquifer in the Osona region (NE Spain) was chemically and isotopically ({delta}{sup 15}N{sub NO{sub 3}},{delta}{sup 18}O{sub NO{sub 3}},{delta}{sup 34}S{sub SO{sub 4}},{delta}{sup 18}O{sub SO{sub 4}}, {delta}D, {delta}{sup 18}O{sub H{sub 2}}{sub O} and {delta}{sup 13}C{sub DIC}) characterized. Diffuse- NO{sub 3}{sup -} contamination reached values of 366 mg/L. Nearly 75% of the 37 sampled sites had higher concentrations than the 50 mg/L in NO{sub 3}{sup -} limit for drinking water. To identify the source of pollution {delta}{sup 15}N{sub NO{sub 3}} and {delta}{sup 18}O{sub NO{sub 3}} were used with results, for most samples, in the range of pig manure NO{sub 3}{sup -}. Nitrification processes were evaluated by means of the {delta}{sup 18}O of NO{sub 3}{sup -} and water. Isotopic data suggested that natural attenuation of NO{sub 3}{sup -} was taking place. This process was confirmed using the {delta}{sup 18}O{sub NO{sub 3}} coupled with the NO{sub 3}{sup -}/Cl{sup -} ratio, avoiding the influence of continuous NO{sub 3}{sup -} inputs. A further insight on denitrification processes was obtained by analyzing the ions involved in denitrification reactions. Although the role of organic matter oxidation could neither be confirmed nor discarded, this approach showed a link between denitrification and pyrite oxidation. Therefore, in areas with no adequate infrastructure (e.g. multipiezometers), such as the one studied, this approach could be useful for implementing better water management.

  9. Palaeohydrological implications in the Baltic area and its relation to the groundwater at Aespoe, south-eastern Sweden - A literature study

    Energy Technology Data Exchange (ETDEWEB)

    Wallin, B [Geokema AB, Lidingoe (Sweden)

    1995-03-01

    A literature study of different groundwaters in the circum Baltic region is presented in this work. The study is mainly focused on the isotopic signatures observed in different groundwaters in Sweden and Finland. Several saline groundwaters in the Baltic region at depth of 150 to 500m depth show stable ({delta}D, {delta}{sup 13}C, {delta}{sup 18}O) and radiogenic ({delta}{sup 87}Sr) isotope assembly which is suggestive of a marine origin. However, a discrepancy is sometimes observed between the stable as well as radiogenic isotopes of the intermediate groundwater, which suggest a mixture of fossil marine water and a post-glacial runoff of melt water. In order to explain this phenomenon, the initial setting in {delta}{sup 18}O may have been depleted due to large input of high latitude marine water or cold melt waters. A solution to the contradiction between the strontium ({delta}{sup 87}Sr) and stable isotope ({delta}D, {delta}{sup 13}C, {delta}{sup 18}O) signatures of the groundwater and of the calcite fracture fillings at Aespoe and other places is attained, if it is assumed that the strontium in Baltic Sea water has undergone a significant decrease in {delta}{sup 87}Sr since the last glaciation. A scenario can be constructed to suggest that the Baltic Sea during the initial stage of the Litorina sea (8000 to 5000 Y B.P.) contained strontium with much larger {delta}{sup 87}Sr values. Another explanation for the positive {delta}{sup 87}Sr values may be due to water/rock interaction between the groundwater and the abundant fracture clay minerals, which are observed at Aespoe. Typically most of the saline groundwaters occur both in Sweden and Finland below the highest marine shore line during the Holocene. Almost all inland groundwaters show a totally different pattern which is typically non marine, meteoric in origin. (Abstract Truncated)

  10. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... I pdb|1GTP|A Chain A, Gtp Cyclohydrolase I pdb|1FBX|O ... Chain O, Crystal Structure Of Zinc-Containing E.Coli... Gtp ... Cyclohydrolase I pdb|1FBX|N Chain N, Crystal Structure ... Of Zinc-Containing E.Coli... Gtp Cyclohydrolase I ... pdb|1FBX|M Chain M, Crystal Structure Of Zinc-Containing ... E.Coli...oli Gtp Cyclohydrolase I ... pdb|1FBX|K Chain K, Crystal Structure Of Zinc-Containing ... E.Co...li Gtp Cyclohydrolase I pdb|1FBX|J Chain J, Crystal ... Structure Of Zinc-Containing E.Coli

  11. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... I pdb|1GTP|A Chain A, Gtp Cyclohydrolase I pdb|1FBX|O ... Chain O, Crystal Structure Of Zinc-Containing E.Coli... Gtp ... Cyclohydrolase I pdb|1FBX|N Chain N, Crystal Structure ... Of Zinc-Containing E.Coli... Gtp Cyclohydrolase I ... pdb|1FBX|M Chain M, Crystal Structure Of Zinc-Containing ... E.Coli...oli Gtp Cyclohydrolase I ... pdb|1FBX|K Chain K, Crystal Structure Of Zinc-Containing ... E.Co...li Gtp Cyclohydrolase I pdb|1FBX|J Chain J, Crystal ... Structure Of Zinc-Containing E.Coli

  12. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... I pdb|1GTP|A Chain A, Gtp Cyclohydrolase I pdb|1FBX|O ... Chain O, Crystal Structure Of Zinc-Containing E.Coli... Gtp ... Cyclohydrolase I pdb|1FBX|N Chain N, Crystal Structure ... Of Zinc-Containing E.Coli... Gtp Cyclohydrolase I ... pdb|1FBX|M Chain M, Crystal Structure Of Zinc-Containing ... E.Coli...oli Gtp Cyclohydrolase I ... pdb|1FBX|K Chain K, Crystal Structure Of Zinc-Containing ... E.Co...li Gtp Cyclohydrolase I pdb|1FBX|J Chain J, Crystal ... Structure Of Zinc-Containing E.Coli

  13. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... I pdb|1GTP|A Chain A, Gtp Cyclohydrolase I pdb|1FBX|O ... Chain O, Crystal Structure Of Zinc-Containing E.Coli... Gtp ... Cyclohydrolase I pdb|1FBX|N Chain N, Crystal Structure ... Of Zinc-Containing E.Coli... Gtp Cyclohydrolase I ... pdb|1FBX|M Chain M, Crystal Structure Of Zinc-Containing ... E.Coli...oli Gtp Cyclohydrolase I ... pdb|1FBX|K Chain K, Crystal Structure Of Zinc-Containing ... E.Co...li Gtp Cyclohydrolase I pdb|1FBX|J Chain J, Crystal ... Structure Of Zinc-Containing E.Coli

  14. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... I pdb|1GTP|A Chain A, Gtp Cyclohydrolase I pdb|1FBX|O ... Chain O, Crystal Structure Of Zinc-Containing E.Coli... Gtp ... Cyclohydrolase I pdb|1FBX|N Chain N, Crystal Structure ... Of Zinc-Containing E.Coli... Gtp Cyclohydrolase I ... pdb|1FBX|M Chain M, Crystal Structure Of Zinc-Containing ... E.Coli...oli Gtp Cyclohydrolase I ... pdb|1FBX|K Chain K, Crystal Structure Of Zinc-Containing ... E.Co...li Gtp Cyclohydrolase I pdb|1FBX|J Chain J, Crystal ... Structure Of Zinc-Containing E.Coli

  15. Discrimination between ginseng from Korea and China by light stable isotope analysis

    Energy Technology Data Exchange (ETDEWEB)

    Horacek, Micha, E-mail: micha.horacek@ait.ac.at [Department of Environmental Resources and Technology, Austrian Institute of Technology, 2444 Seibersdorf (Austria); Min, Ji-Sook; Heo, Sang-Cheol [National Institute of Scientific Investigation, 331-1 Shinwol-7dong, Yangcheon-ku, Seoul 158-707 (Korea, Republic of); Soja, Gerhard [Department of Environmental Resources and Technology, Austrian Institute of Technology, 2444 Seibersdorf (Austria)

    2010-12-03

    Ginseng is a health food and traditional medicine highly valued in Asia. Ginseng from certain origins is higher valued than from other origins, so that a reliable method for differentiation of geographical origin is important for the economics of ginseng production. To discriminate between ginseng samples from South Korea and PR China, 29 samples have been analyzed for the isotopic composition of the elements H, C and N. The results showed {delta}{sup 2}H values between -94 and -79 per mille , for {delta}{sup 13}C -27.9 to -23.7 per mille and for {delta}{sup 15}N 1.3-5.4 per mille for Chinese ginseng. Korean ginseng gave {delta}{sup 2}H ratios between -91 and -69 per mille , {delta}{sup 13}C ratios between -31.2 and -22.4 per mille and {delta}{sup 15}N ratios between -2.4 and +7 per mille . Despite the overlap between the values for individual isotopes, a combination of the isotope systems gave a reasonable differentiation between the two geographic origins. Especially the statistically significant difference in {delta}{sup 2}H ratios facilitated the differentiation between Korean and Chinese ginseng samples.

  16. Alteration of /sup 15/N//sup 14/N and /sup 13/C//sup 12/C ratios of plant matter during the initial stages of diagenesis: studies utilizing archaeological specimens from Peru

    Energy Technology Data Exchange (ETDEWEB)

    DeNiro, M J [California Univ., Los Angeles (USA). Dept. of Earth and Space Sciences; Hastorf, C A [California Univ., Los Angeles (USA). Dept. of Anthropology

    1985-01-01

    The stable carbon and nitrogen isotope ratios of plants extracted from Peruvian archaeological sites, ranging in age from 400 to 4000 years B.P., have been measured. The delta/sup 13/C and delta/sup 15/N values of prehistoric plants that were carbonized prior to deposition are similar to those of modern plants which have the same carbon dioxide fixation or nitrogen assimilation mechanisms. In contrast, the delta/sup 15/N values of prehistoric plants that were not carbonized are generally 10 to 20 per mille and as much as 35 per mille more positive than those of their modern counterparts. The delta/sup 13/C and delta/sup 15/N values of different parts of prehistoric uncarbonized plants differ by as much as 8 per mille and 21 per mille respectively, whereas the same parts of modern plants have delta/sup 13/C or delta/sup 15/N values that lie within 2 per mille of one another. SEM analysis eliminated the possibility that diagenetic alteration of the isotope ratios of the prehistoric uncarbonized plants was caused by the adsorption of particulate soil matter. The results are discussed.

  17. Effect of resonance production and diffraction on the inclusive spectra of pions and protons in 19 GeV/c pn interactions

    Energy Technology Data Exchange (ETDEWEB)

    Baken, V.; Breivik, F.O.; Jacobsen, T. (Oslo Univ. (Norway). Fysisk Inst.)

    1984-01-01

    Bubble chamber data on pn interactions at 19 GeV/c are used to investigate the effects of nucleon diffraction and resonance production on the inclusive x- and psub(T)/sup 2/-distributions of protons and pions. We determine the differential distributions of p, ..pi../sup -/ and ..pi../sup +/ due to neutron and proton diffraction and similarly the distributions from the decay of the strong resonances ..delta../sup + +/(1232) and ..delta../sup -/(1232) and from rho/sup 0/(770). The x-distributions of the protons in the two c.m. hemispheres become quite similar when the effect of diffraction and ..delta../sup + +/ is subtracted. The psub(T)/sup 2/-distributions can then be described by a single exponential in the whole kinematic region. The net effect on the shapes of the x-distributions of the pions due to diffraction, ..delta../sup + +//..delta../sup -/ and rho/sup 0/ production is rather small. The separate effects of these processes on the particle ratio ..pi../sup -//..pi../sup +/ is investigated. By excluding the diffraction and ..delta../sup + +//..delta../sup -/ production, the strength of the low-psub(T)/sup 2/ component of the psub(T)/sup 2/-distributions of the pions is reduced, but it seems that diffraction and resonance production cannot account for all of this low-psub(T)/sup 2/ enhancement.

  18. Geochemistry of the stable isotopes of silicon

    Energy Technology Data Exchange (ETDEWEB)

    Douthitt, C B [California Inst. of Tech., Pasadena (USA). Div. of Geological and Planetary Sciences

    1982-08-01

    One hundred thirty two new measurements of the relative abundances of the stable isotopes of silicon in terrestrial materials are presented. The total variation of delta/sup 30/Si found is 6.2 parts per thousand, centered on the mean of terrestrial mafic and ultramafic igneous rocks, delta/sup 30/Si = -0.4 parts per thousand. Igneous rocks show limited variation; coexisting minerals exhibit small, systematic silicon isotopic fractionations that are roughly 1/3 the magnitude of concomitant oxygen isotopic fractionations at 1150/sup 0/C. In both igneous minerals and rocks, delta/sup 30/Si shows a positive correlation with silicon content, as does delta/sup 18/O. Opal from both sponge spicules and sinters is light, with delta/sup 30/Si = -2.3 and -1.4 parts per thousand respectively. Large delta/sup 30/Si values of both positive and negative sign are reported for the first time from clay minerals, opaline phytoliths, and authigenic quartz. All highly fractionated samples were precipitated from solution at low temperatures; however, aqueous silicon is not measurably fractionated relative to quartz at equilibrium. A kinetic isotope fractionation of approximately 3.5 parts per thousand is postulated to occur during the low temperature precipitation of opal and, possibly, poorly ordered phyllosilicates, with the silicate phase being enriched in /sup 28/Si. This fractionation, coupled with a Rayleigh precipitation model, is capable of explaining most non-magmatic delta/sup 30/Si variations.

  19. Nitrogen isotope variations in camphor (Cinnamomum Camphora) leaves of different ages in upper and lower canopies as an indicator of atmospheric nitrogen sources

    Energy Technology Data Exchange (ETDEWEB)

    Xiao Huayun, E-mail: xiaohuayun@vip.skleg.c [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, No. 46, Guanshui Road, Guiyang 550002 (China); Wu Lianghong; Zhu Renguo; Wang Yanli; Liu Congqiang [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, No. 46, Guanshui Road, Guiyang 550002 (China)

    2011-02-15

    Nitrogen isotopic composition of new, middle-aged and old camphor leaves in upper and lower canopies has been determined in a living area, near a motorway and near an industrial area (Jiangan Chemical Fertilizer Plant). We found that at sites near roads, more positive {delta}{sup 15}N values were observed in the camphor leaves, especially in old leaves of upper canopies, and {Delta}{delta}{sup 15}N = {delta}{sup 15}N{sub upper} - {delta}{sup 15}N{sub lower} > 0, while those near the industrial area had more negative {delta}{sup 15}N values and {Delta}{delta}{sup 15}N < 0. These could be explained by two isotopically different atmospheric N sources: greater uptake from isotopically heavy pools of atmospheric NO{sub x} by old leaves in upper canopies at sites adjacent to roads, and greater uptake of {sup 15}N-depleted NH{sub y} in atmospheric deposition by leaves at sites near the industrial area. This study presents novel evidence that {sup 15}N natural abundance of camphor leaves can be used as a robust indicator of atmospheric N sources. - Research highlights: Camphor leaves showed high {delta}{sup 15}N values near roads and low values near the industrial area. The {delta}{sup 15}N values of camphor leaves near roads increased with time of exposure. The {delta}{sup 15}N values of camphor leaves near the industrial area decreased with time of exposure. More positive foliage {delta}{sup 15}N values were found in the upper canopies near roads. Near the industrial area, the upper canopies showed more negative foliage {delta}{sup 15}N values. - Nitrogen isotope in camphor leaves indicating atmospheric nitrogen sources.

  20. Validation of an O-18 leaf water enrichment model

    Energy Technology Data Exchange (ETDEWEB)

    Jaeggi, M.; Saurer, M.; Siegwolf, R.

    2002-03-01

    The seasonal trend in {delta}{sup 18}O{sub ol} in leaf organic matter of spruce needles of mature trees could be modelled for two years. The seasonality was mainly explained by the {delta}{sup 18}O of top-soil water, whereas between years differences were due to variation in air humidity. Application of a third year's data set improved the correlation between modelled and measured {delta}{sup 18}O{sub ol} and thus validated our extended Dongmann model. (author)

  1. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

    Science.gov (United States)

    Kinjo, Akira R; Suzuki, Hirofumi; Yamashita, Reiko; Ikegawa, Yasuyo; Kudou, Takahiro; Igarashi, Reiko; Kengaku, Yumiko; Cho, Hasumi; Standley, Daron M; Nakagawa, Atsushi; Nakamura, Haruki

    2012-01-01

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

  2. The RCSB Protein Data Bank: new resources for research and education.

    Science.gov (United States)

    Rose, Peter W; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dimitropoulos, Dimitris; Dutta, Shuchismita; Green, Rachel K; Goodsell, David S; Prlic, Andreas; Quesada, Martha; Quinn, Gregory B; Ramos, Alexander G; Westbrook, John D; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E

    2013-01-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.

  3. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available K-12) pdb|1PV2|H ... Chain H, Native Form 2 E.Coli Chaperone Hsp31 pdb|1PV...2|G ... Chain G, Native Form 2 E.Coli Chaperone Hsp31 pdb|1PV2|F ... Chain F, Native Form 2 E.Coli... Chaperone Hsp31 pdb|1PV2|E ... Chain E, Native Form 2 E.Coli Chaperone Hsp31 pdb|1PV2|D ... ... ... Chain D, Native Form 2 E.Coli Chaperone Hsp31 pdb|1PV2|C ... Chain C, Native Form 2 E.Coli... Chaperone Hsp31 pdb|1PV2|B ... Chain B, Native Form 2 E.Coli Chaperone Hsp31 pdb|

  4. ORF Alignment: NC_002977 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available xylase) pdb|1FZI|D Chain D, Methane Monooxygenase ... Hydroxylase, Form I Pressurized With Xenon Gas ... ... pdb|1FZI|C Chain C, Methane Monooxygenase Hydroxylase, ... Form I Pressurized With Xenon G...as pdb|1FZH|D Chain D, ... Methane Monooxygenase Hydroxylase, Form Ii Press...urized ... With Xenon Gas pdb|1FZH|C Chain C, Methane Monooxygenase ... Hydroxylase, Form Ii Press

  5. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Crystallographic Structure Of Mycobacterium Tuberculosis ... Hemoglobin O pdb|1NGK|K Chain K..., Crystallographic ... Structure Of Mycobacterium Tuberculosis Hemoglobin ...O ... pdb|1NGK|J Chain J, Crystallographic Structure Of ... Mycobacterium Tuberculosis Hemoglo...bin O pdb|1NGK|I Chain ... I, Crystallographic Structure Of Mycobacterium ... Tuberculosis Hem...oglobin O pdb|1NGK|H Chain H, ... Crystallographic Structure Of Mycobacterium Tuberculosis

  6. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Crystallographic Structure Of Mycobacterium Tuberculosis ... Hemoglobin O pdb|1NGK|K Chain K..., Crystallographic ... Structure Of Mycobacterium Tuberculosis Hemoglobin ...O ... pdb|1NGK|J Chain J, Crystallographic Structure Of ... Mycobacterium Tuberculosis Hemoglo...bin O pdb|1NGK|I Chain ... I, Crystallographic Structure Of Mycobacterium ... Tuberculosis Hem...oglobin O pdb|1NGK|H Chain H, ... Crystallographic Structure Of Mycobacterium Tuberculosis

  7. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tase) pdb|1XXU|D Chain D, Crystal Structure Of Ahpe ... From Mycrobacterium Tuberculosis...pe From ... Mycrobacterium Tuberculosis, A 1-Cys Peroxiredoxin ... ...pdb|1XXU|A Chain A, Crystal Structure Of Ahpe From ... Mycrobacterium Tuberculosis, A 1-Cys Peroxired..., A 1-Cys Peroxiredoxin ... pdb|1XXU|C Chain C, Crystal Structure Of Ahpe From ... Mycrobacterium Tubercu...losis, A 1-Cys Peroxiredoxin ... pdb|1XXU|B Chain B, Crystal Structure Of Ah

  8. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tase) pdb|1XXU|D Chain D, Crystal Structure Of Ahpe ... From Mycrobacterium Tuberculosis...pe From ... Mycrobacterium Tuberculosis, A 1-Cys Peroxiredoxin ... ...pdb|1XXU|A Chain A, Crystal Structure Of Ahpe From ... Mycrobacterium Tuberculosis, A 1-Cys Peroxired..., A 1-Cys Peroxiredoxin ... pdb|1XXU|C Chain C, Crystal Structure Of Ahpe From ... Mycrobacterium Tubercu...losis, A 1-Cys Peroxiredoxin ... pdb|1XXU|B Chain B, Crystal Structure Of Ah

  9. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available pterin Aldolase Complexed With Product From ... Mycobacterium Tuberculosis pdb|1NBU|G Chain G, ... ... ... 7,8-Dihydroneopterin Aldolase Complexed With Product ... From Mycobacterium Tuberculosis pdb|1NB... ... From Mycobacterium Tuberculosis pdb|1NBU|E Chain E, ... 7,8-Dihydroneopterin Aldolase Complexe...d With Product ... From Mycobacterium Tuberculosis pdb|1NBU|A Chain A, ... 7,8-Dihydroneopteri...n Aldolase Complexed With Product ... From Mycobacterium Tuberculosis ...

  10. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Crystallographic Structure Of Mycobacterium Tuberculosis ... Hemoglobin O pdb|1NGK|K Chain K..., Crystallographic ... Structure Of Mycobacterium Tuberculosis Hemoglobin ...O ... pdb|1NGK|J Chain J, Crystallographic Structure Of ... Mycobacterium Tuberculosis Hemoglo...bin O pdb|1NGK|I Chain ... I, Crystallographic Structure Of Mycobacterium ... Tuberculosis Hem...oglobin O pdb|1NGK|H Chain H, ... Crystallographic Structure Of Mycobacterium Tuberculosis

  11. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available pterin Aldolase Complexed With Product From ... Mycobacterium Tuberculosis pdb|1NBU|G Chain G, ... ... ... 7,8-Dihydroneopterin Aldolase Complexed With Product ... From Mycobacterium Tuberculosis pdb|1NB... ... From Mycobacterium Tuberculosis pdb|1NBU|E Chain E, ... 7,8-Dihydroneopterin Aldolase Complexe...d With Product ... From Mycobacterium Tuberculosis pdb|1NBU|A Chain A, ... 7,8-Dihydroneopteri...n Aldolase Complexed With Product ... From Mycobacterium Tuberculosis ...

  12. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available pterin Aldolase Complexed With Product From ... Mycobacterium Tuberculosis pdb|1NBU|G Chain G, ... ... ... 7,8-Dihydroneopterin Aldolase Complexed With Product ... From Mycobacterium Tuberculosis pdb|1NB... ... From Mycobacterium Tuberculosis pdb|1NBU|E Chain E, ... 7,8-Dihydroneopterin Aldolase Complexe...d With Product ... From Mycobacterium Tuberculosis pdb|1NBU|A Chain A, ... 7,8-Dihydroneopteri...n Aldolase Complexed With Product ... From Mycobacterium Tuberculosis ...

  13. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tase) pdb|1XXU|D Chain D, Crystal Structure Of Ahpe ... From Mycrobacterium Tuberculosis...pe From ... Mycrobacterium Tuberculosis, A 1-Cys Peroxiredoxin ... ...pdb|1XXU|A Chain A, Crystal Structure Of Ahpe From ... Mycrobacterium Tuberculosis, A 1-Cys Peroxired..., A 1-Cys Peroxiredoxin ... pdb|1XXU|C Chain C, Crystal Structure Of Ahpe From ... Mycrobacterium Tubercu...losis, A 1-Cys Peroxiredoxin ... pdb|1XXU|B Chain B, Crystal Structure Of Ah

  14. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HQY|E Chain E, Nucleotide-...Dependent ... Conformational Changes In A Protease- Associated Atpase ... ... ... Hslu pdb|1HT1|I Chain I, Nucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase...ent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HT1|E Chain E, N...ucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1

  15. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HQY|E Chain E, Nucleotide-...Dependent ... Conformational Changes In A Protease- Associated Atpase ... ... ... Hslu pdb|1HT1|I Chain I, Nucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase...ent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HT1|E Chain E, N...ucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1

  16. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HQY|E Chain E, Nucleotide-...Dependent ... Conformational Changes In A Protease- Associated Atpase ... ... ... Hslu pdb|1HT1|I Chain I, Nucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase...ent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HT1|E Chain E, N...ucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1

  17. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HQY|E Chain E, Nucleotide-...Dependent ... Conformational Changes In A Protease- Associated Atpase ... ... ... Hslu pdb|1HT1|I Chain I, Nucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase...ent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HT1|E Chain E, N...ucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1

  18. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HQY|E Chain E, Nucleotide-...Dependent ... Conformational Changes In A Protease- Associated Atpase ... ... ... Hslu pdb|1HT1|I Chain I, Nucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase...ent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1HT1|E Chain E, N...ucleotide-Dependent ... Conformational Changes In A Protease- Associated Atpase ... Hslu pdb|1

  19. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ctase ... pdb|1P45|B Chain B, Targeting Tuberculosis And Malaria ... Through Inhibition Of Eno...yl Reductase: Compound Activity ... And Structural Data pdb|1P45|A Chain A, Targeting ... Tuberculosis And Malaria...ctivity And Structural Data ... pdb|1P44|F Chain F, Targeting Tuberculosis And Malaria ... Thr...geting ... Tuberculosis And Malaria Through Inhibition Of Enoyl ... ... Reductase: Compound Activity And Structural Data ... pdb|1P44|D Chain D, Targeting Tuberculosis And Malaria

  20. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ctase ... pdb|1P45|B Chain B, Targeting Tuberculosis And Malaria ... Through Inhibition Of Eno...yl Reductase: Compound Activity ... And Structural Data pdb|1P45|A Chain A, Targeting ... Tuberculosis And Malaria...ctivity And Structural Data ... pdb|1P44|F Chain F, Targeting Tuberculosis And Malaria ... Thr...geting ... Tuberculosis And Malaria Through Inhibition Of Enoyl ... ... Reductase: Compound Activity And Structural Data ... pdb|1P44|D Chain D, Targeting Tuberculosis And Malaria

  1. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ctase ... pdb|1P45|B Chain B, Targeting Tuberculosis And Malaria ... Through Inhibition Of Eno...yl Reductase: Compound Activity ... And Structural Data pdb|1P45|A Chain A, Targeting ... Tuberculosis And Malaria...ctivity And Structural Data ... pdb|1P44|F Chain F, Targeting Tuberculosis And Malaria ... Thr...geting ... Tuberculosis And Malaria Through Inhibition Of Enoyl ... ... Reductase: Compound Activity And Structural Data ... pdb|1P44|D Chain D, Targeting Tuberculosis And Malaria

  2. Chemical and isotopic study of thermal springs and gas discharges from Sierra de Chiapas, Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Nencetti, A; Tassi, F; Vaselli, O [Department of Earth Sciences, Florence (Italy); Macias, J. L [Instituto de Geofisica, Universidad Nacional Autonoma de Mexico, D.F. (Mexico); Magro, G [CNR-Institute of Geosciences and Earth Resources, Pisa (Italy); Capaccioni, B [Institute of Volcanology and Geochemistry, Urbino (Italy); Minissale, A [CNR-Institute of Geosciences and Earth Resources, Florence (Italy); Mora, J. C [Instituto de Geofisica, Universidad Nacional Autonoma de Mexico, D.F. (Mexico)

    2005-01-15

    (SDT <250mg/L). La mayoria de estas aguas estan asociadas con descargas de gas compuestas por N{sub 2} (hasta 93 % en vol.), CO{sub 2} (2.4-31.2 % en vol.) y Ar (hasta 1.25 % en vol.) con origen predominantemente meteorico. H{sub 2}S aparece unicamente en las muestras de gas colectadas en El Azufre (hasta 1.1 % en vol.). Los valores de {delta}{sup 1}3C-CO{sub 2} comunmente inferiores a -9.7% (PDB) sugieren un origen parcialmente biogenico del CO{sub 2}. Los parametros quimicos e isotopicos de los manantiales indican que la circulacion de fluidos en la Sierra de Chiapas se regula principalmente por la infiltracion de aguas meteoricas en rocas carbonatadas del Cretacico medio-tardio hasta las formaciones evaporiticas del Jurasico tardio-Cretacico temprano. Estas ultimas representan la fuente principal de las especies en solucion de las aguas. No se encontraron evidencias de la presencia de sistemas con entalpias medias a altas por debajo de la Sierra de Chiapas.

  3. Remediation of the protein data bank archive.

    NARCIS (Netherlands)

    Henrick, K.; Feng, Z.; Bluhm, W.F.; Dimitropoulos, D.; Doreleijers, J.; Dutta, S.; Flippen-Anderson, J.L.; Ionides, J.; Kamada, C.; Krissinel, E.; Lawson, C.L.; Markley, J.L.; Nakamura, H.; Newman, R.; Shimizu, Y.; Swaminathan, J.; Velankar, S.; Ory, J.; Ulrich, E.L.; Vranken, W; Westbrook, J.; Yamashita, R.; Yang, H.; Young, J.; Yousufuddin, M.; Berman, H.M.

    2008-01-01

    The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000

  4. ORF Alignment: NC_002977 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available (Methane ... hydroxylase) pdb|1FZI|F Chain F, Methane Monooxygenase ... Hydroxylase, Form I Press...roxylase, ... Form I Pressurized With Xenon Gas pdb|1FZH|F Chain F, ... Methane Monooxygenase Hydroxylase, Form Ii Pres... ... Hydroxylase, Form Ii Pressurized With Xenon Gas ... pdb|1FZ9|F Chain F

  5. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tallographic Structure Of A Relaxed ... Glutamine Synthetase From Mycobacterium Tuberculosis ... ...m Mycobacterium ... Tuberculosis pdb|1HTQ|V Chain V, Multicopy ... ...Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis pdb|... From Mycobacterium ... Tuberculosis pdb|1HTQ|T Chain T, Multicopy ... ... ... Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis

  6. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tallographic Structure Of A Relaxed ... Glutamine Synthetase From Mycobacterium Tuberculosis ... ...m Mycobacterium ... Tuberculosis pdb|1HTQ|V Chain V, Multicopy ... ...Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis pdb|... From Mycobacterium ... Tuberculosis pdb|1HTQ|T Chain T, Multicopy ... ... ... Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis

  7. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tallographic Structure Of A Relaxed ... Glutamine Synthetase From Mycobacterium Tuberculosis ... ...m Mycobacterium ... Tuberculosis pdb|1HTQ|V Chain V, Multicopy ... ...Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis pdb|... From Mycobacterium ... Tuberculosis pdb|1HTQ|T Chain T, Multicopy ... ... ... Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis

  8. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004337 gi|24115225 >1e94E 1 443 7 449 e-162 ... pdb|1E94|F Chain F, Hslv-Hslu From E.Coli... pdb|1E94|E Chain E, Hslv-Hslu From ... E.Coli pdb|1HQY|F Chain F, Nucleotide-Dependent ...

  9. ORF Alignment: NC_000917 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Template pdb|1SZ1|B Chain B, Mechanism Of Cca-Adding ... Enzymes Specificity Revealed By Cryst...al Structures Of ... Ternary Complexes pdb|1SZ1|A Chain A, Mechanism Of ... Cca-Adding Enzym...es Specificity Revealed By Crystal ... Structures Of Ternary Complexes pdb|1

  10. ORF Alignment: NC_000964 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available lus ... Subtilis Cota After 8h Soaking With Abts pdb|1UVW|A ... Chain A, Bacillus Subtilis Cot...Cota After 6h Soaking With Abts pdb|1OF0|A ... Chain A, Crystal Structure ...ure Of Bacillus Subtilis Cota After20h Soaking ... With Abts pdb|1HL0|A Chain A, Crystal Structure Of

  11. Investigations of the ratios of stable carbon isotopes in atmospheric relevant VOC using simulation and field experiments; Untersuchungen der Verhaeltnisse stabiler Kohlenstoffisotope in atmosphaerisch relevanten VOC in Simulations- und Feldexperimenten

    Energy Technology Data Exchange (ETDEWEB)

    Spahn, Holger

    2010-07-01

    Volatile organic compounds (VOC) play an important role in the regional and global atmospheric chemistry. The author of the contribution under consideration reports on the analysis of the ratios of stable carbon isotopes ({delta}({sup 13}C) analysis) in atmospheric VOCs. At first, the state of the art of this analytical technique is described. For the first time {delta}({sup 13}C) values of different monoterpenes have been determined in the investigation of vegetable emissions at a plant chamber. By means of the oxidation of {beta}-pinene by ozone in an aerosol chamber, the kinetic isotope effect of this reaction was determined. In southern Germany, air samples for the {delta}({sup 13}C) analysis were collected using a zeppelin. This enables a height-resolved measurement of {delta}({sup 13}C) values. Based on these measurements, the average photochemical age for methanol, toluene and p-xylene at different heights was calculated.

  12. Estimation of precipitation rates by measurements of {sup 36}Cl in the GRIP ice core with the PSI/ETH tandem accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, G.; Baumgartner, S.; Beer, J. [EAWAG, Duebendorf (Switzerland); Synal, H.A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Suter, M. [Eidgenoessische Technische Hochschule, Zurich (Switzerland)

    1997-09-01

    Within the European Greenland ice core project (GRIP) {sup 36}Cl AMS measurements have been performed on ice core samples from Summit (Greenland, 73{sup o}N, 37{sup o}W). Most data analysed so far are from the lower part of the ice core. The {sup 36}Cl concentration is well correlated with {delta}{sup 18}O, which is considered as a proxy for paleotemperatures. Assuming that the deposition rate of radionuclides is independent of {delta}{sup 18}O, {sup 36}Cl is used to estimate the relationship between accumulation and {delta}{sup 18}O. The results confirm that the rapid changes of {delta}{sup 18}O, the so-called Dansgaard-Oeschger events, are also reflected in the precipitation rate. (author) 1 fig., 3 refs.

  13. Fish Movement and Dietary History Derived from Otolith (delta)13C

    Energy Technology Data Exchange (ETDEWEB)

    Weber, P K; Finlay, J C; Power, M E; Phillis, C C; Ramon, C E; Eaton, G F; Ingram, B L

    2005-09-08

    Habitat use and food web linkages are critical data for fish conservation and habitat restoration efforts, particularly for threatened salmonids species. Otolith microchemistry has been shown to be a powerful tool for reconstructing fish movement, but over small distances (kilometers), geology-derived differences in otolith chemistry are rare. Here, we demonstrate that otolith {sup 13}C/{sup 12}C ratio (i.e. {delta}{sup 13}C) of anadromous steelhead trout can be used to distinguish residence in small streams from residence in larger streams and rivers. While previous research has shown that water dissolved inorganic carbon {delta}{sup 13}C is the primary source of carbon in otoliths, the downstream change in food {delta}{sup 13}C in this watershed appears to be the primary control on otolith {delta}{sup 13}C. As a result, this method can also be applied to the problem of reconstructing feeding history at a location.

  14. Carbon-13 isotope effects on 199Hg nuclear shielding

    International Nuclear Information System (INIS)

    Sebald, Angelika; Wrackmeyer, Bernd

    1985-01-01

    Secondary 13 C/ 12 C isotope effects on 199 Hg nuclear shielding (Δdeltasup(i)( 199 Hg)) are of interest because of the unusual shift to high frequency which has been observed for a few alkyl mercury compounds. Continuing interest in the NMR parameters of mercury compounds prompted a search for the values Δdeltasup(i)( 199 Hg) in a greater variety of organomercurials. This should help to find out about the range of Δdeltasup(i)( 199 Hg) and to obtain a firmer basis for the discussion of the high-frequency shifts. The data and experimental conditions are given for chemical shifts delta 199 Hg, coupling constants sup(n)J( 199 Hg 13 C) and 13 C/ 12 C isotope shifts Δdeltasup(i)( 199 Hg) of fourteen 199 Hg organomercury compounds. The results are discussed. (author)

  15. Backward production of mesons associated with. Delta. sup ++ (1232) in. pi. sup + p interactions at 20 GeV/c

    Energy Technology Data Exchange (ETDEWEB)

    Perepelitsa, V.F.; Mikhailichenko, V.I.; Nikitin, S.Ya.; Zhokin, A.S. (Institut Teoreticheskoj i Ehksperimental' noj Fiziki, Moscow (USSR)); Akopov, N.Z.; Grigoryan, A.A.; Karapetyan, V.V. (Erevanskij Fizicheskij Inst., Erevan (USSR)); Dorsaz, L.; Sonderegger, P. (European Organization for Nuclear Research, Geneva (Switzerland)); Ferrer, A. (Centro Mixto Valencia Univ./CSIC, Valencia (Spain). Inst. de Fisica Corpuscular)

    1991-05-01

    We have analyzed backward meson production in {pi}{sup +}p reactions at 20 GeV/c, which were measured in the CERN {Omega} spectrometer triggered by a fast proton (p{sub f}), in experiment WA 56. Production via baryon exchange of quasi-two-body final states {Delta}{sup ++}(1232) rho{sup 0}(770), {Delta}{sup ++}(1232) f{sub 2}(1270) and {Delta}{sup ++}(1232) rho{sub 3}{sup 0}(1690) is clearly identified. The density matrix elements of meson resonances and of {Delta}{sup ++}(1232) are analyzed. We have observed also the reactions {pi}{sup +}p->{Delta}{sup ++}(1232){pi}{sup 0} and {pi}{sup +}p->{Delta}{sup ++}(1232){omega} in the p{sub f}{pi}{sup +}{pi}{sup 0} and p{sub f}{pi}{sup +}{pi}{sup +}{pi}{sup -}{pi}{sup 0} final states. (orig.).

  16. Influence of diet on the distribution of nitrogen isotopes in animals

    Energy Technology Data Exchange (ETDEWEB)

    DeNiro, M J; Epstein, S [California Inst. of Tech., Pasadena (USA). Div. of Geological Sciences

    1981-03-01

    The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The delta/sup 15/N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different delta/sup 15/N values. The variability of the relationship between the delta/sup 15/N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in /sup 15/N relative to the diet, with the difference between the delta/sup 15/N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The delta/sup 15/N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the delta/sup 15/N value of the diet. The dependence of the delta/sup 15/N values of whole animals and their tissues and biochemical components on the delta/sup 15/N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different delta/sup 15/N values. The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the delta/sup 13/C and delta/sup 15/N values of bone collagen suggest that C/sub 4/ and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

  17. Temperature and vital effect controls on Bamboo coral (Isididae) isotopegeochemistry: A test of the "lines method"

    Energy Technology Data Exchange (ETDEWEB)

    Hill, T M; Spero, H J; Guilderson, T P; LaVigne, M; Clague, D; Macalello, S; Jang, N

    2011-03-01

    Deep-sea bamboo corals hold promise as long-term climatic archives, yet little information exists linking bamboo coral geochemistry to measured environmental parameters. This study focuses on a suite of 10 bamboo corals collected from the Pacific and Atlantic basins (250-2136 m water depth) to investigate coral longevity, growth rates, and isotopic signatures. Calcite samples for stable isotopes and radiocarbon were collected from the base the corals, where the entire history of growth is recorded. In three of the coral specimens, samples were also taken from an upper branch for comparison. Radiocarbon and growth band width analyses indicate that the skeletal calcite precipitates from ambient dissolved inorganic carbon and that the corals live for 150-300 years, with extension rates of 9-128 {micro}m/yr. A linear relationship between coral calcite {delta}{sup 18}O and {delta}{sup 13}C indicates that the isotopic composition is influenced by vital effects ({delta}{sup 18}O:{delta}{sup 13}C slope of 0.17-0.47). As with scleractinian deep-sea corals, the intercept from a linear regression of {delta}{sup 18}O versus {delta}{sup 13}C is a function of temperature, such that a reliable paleotemperature proxy can be obtained, using the 'lines method.' Although the coral calcite {delta}{sup 18}O:{delta}{sup 13}C slope is maintained throughout the coral base ontogeny, the branches and central cores of the bases exhibit {delta}{sup 18}O:{delta}{sup 13}C values that are shifted far from equilibrium. We find that a reliable intercept value can be derived from the {delta}{sup 18}O:{delta}{sup 13}C regression of multiple samples distributed throughout one specimen or from multiple samples within individual growth bands.

  18. Stable isotope geochemistry of deep sea cherts

    Energy Technology Data Exchange (ETDEWEB)

    Kolodny, Y; Epstein, S [California Inst. of Tech., Pasadena (USA). Div. of Geological Sciences

    1976-10-01

    Seventy four samples of DSDP (Deep Sea Drilling Project) recovered cherts of Jurassic to Miocene age from varying locations, and 27 samples of on-land exposed cherts were analyzed for the isotopic composition of their oxygen and hydrogen. These studies were accompanied by mineralogical analyses and some isotopic analyses of the coexisting carbonates. delta/sup 18/0 of chert ranges between 27 and 39 parts per thousand relative to SMOW, delta/sup 18/0 of porcellanite - between 30 and 42 parts per thousand. The consistent enrichment of opal-CT in porcellanites in /sup 18/0 with respect to coexisting microcrystalline quartz in chert is probably a reflection of a different temperature (depth) of diagenesis of the two phases. delta/sup 18/0 of deep sea cherts generally decrease with increasing age, indicating an overall cooling of the ocean bottom during the last 150 m.y. A comparison of this trend with that recorded by benthonic foraminifera (Douglas et al., Initial Reports of the Deep Sea Drilling Project; 32:509(1975)) indicates the possibility of delta/sup 18/0 in deep sea cherts not being frozen in until several tens of millions of years after deposition. Cherts of any Age show a spread of delta/sup 18/0 values, increasing diagenesis being reflected in a lowering of delta/sup 18/0. Drusy quartz has the lowest delta/sup 18/0 values. On land exposed cherts are consistently depleted in /sup 18/0 in comparison to their deep sea time equivalent cherts. Water extracted from deep sea cherts ranges between 0.5 and 1.4 wt%. deltaD of this water ranges between -78 and -95 parts per thousand and is not a function of delta/sup 18/0 of the cherts (or the temperature of their formation).

  19. Simultaneous Measurement of Nitrogen and Oxygen Isotopes of Nitrate to Evaluate Nitrate Sources and Processes in Catchments

    Energy Technology Data Exchange (ETDEWEB)

    Ohte, Nobuhito [Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo (Japan); Nagata, Toshi; Tayasu, Ichiro [Center for Ecological Research, Kyoto University, Ohtsu (Japan); Kyozu, Ayato; Yoshimizu, Chikage [CREST, Japan Science and Technology Agency, Center for Ecological Research, Kyoto University, Ohtsu (Japan); Osaka, Ken' ichi [Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental Sciences, Tsukuba, (Japan)

    2013-05-15

    We review studies on applied isotope analytical techniques for identifying sources and transformations of river nitrate (NO{sub 3}{sup -}) to examine the influences of water pollution, excess nutrient (nitrogen) loads and ecosystem disturbances in river systems. We also discuss the current status and future perspectives of the application of NO{sub 3}{sup -} isotope measurements to the assessment of river nutrients. Our review shows that in recent years simultaneous measurements of nitrogen and oxygen isotopes ({delta}{sup 15}N and {delta}{sup 18}O) of NO{sub 3}{sup -} have been increasingly used to identify the sources and pathways of nitrogen in river systems. The {delta}{sup 15}N value of NO{sub 3}{sup -} is a useful indicator to evaluate the contributions of sewage and/or animal waste to NO{sub 3}{sup -} load, and the {delta}{sup 18}O value can be used for estimation of the contribution of NO{sub 3}{sup -} derived through atmospheric deposition. The microbial denitrification method is currently a most useful tool to measure the {delta}{sup 15}N and {delta}{sup 18}O values of NO{sub 3}{sup -} simultaneously, because of its capability for high throughput of samples. This method allows us to conduct a comprehensive investigation of spatial and temporal variations and mechanisms of nitrogen transport and transformation in rivers and catchments in more precise and effective manner. (author)

  20. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2010-09-15

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  1. A 50-year record of NOx and SO{sub 2} sources in precipitation in the Northern Rocky Mountains, USA - article no. 4

    Energy Technology Data Exchange (ETDEWEB)

    Naftz, D.L.; Schuster, P.F.; Johnson, C.A. [US Geological Survey, Salt Lake City, UT (United States)

    2011-03-07

    Ice-core samples from Upper Fremont Glacier (UFG), Wyoming, were used as proxy records for the chemical composition of atmospheric deposition. Results of analysis of the ice-core samples for stable isotopes of nitrogen ({delta}{sup 15}, NO{sub 3}{sup -}) and sulfur ({delta}{sup 34}S, SO{sub 4}{sup 2}), as well as NO{sub 3}{sup -} and SO{sub 4}{sup 2} deposition rates from the late-1940s through the early-1990s, were used to enhance and extend existing National Atmospheric Deposition Program/National Trends Network (NADP/NTN) data in western Wyoming. The most enriched {delta}{sup 34}S value in the UFG ice-core samples coincided with snow deposited during the 1980 eruption of Mt. St. Helens, Washington. The remaining {delta}{sup 34}S values were similar to the isotopic composition of coal from southern Wyoming. The {delta}{sup 15}N values in ice-core samples representing a similar period of snow deposition were negative, ranging from -5.9 to -3.2 parts per thousand and all fall within the {delta}{sup 15}N values expected from vehicle emissions. Ice-core nitrate and sulfate deposition data reflect the sharply increasing U.S. emissions data from 1950 to the mid-1970s.

  2. ORF Alignment: NC_003106 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003106 gi|15922724 >1jzgA 8 127 23 138 1e-23 ... pdb|1OV8|D Chain D, Auracyanin B Structure In Space... Group, P65 pdb|1OV8|C ... Chain C, Auracyanin B Structure In Space Group, P65 ... ... ... pdb|1OV8|B Chain B, Auracyanin B Structure In Space ... Group, P65 pdb|1OV8|A Chain A, Auracya...nin B Structure In ... Space Group, P65 pdb|1QHQ|A Chain A, Auracyanin, A

  3. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Mycobacterium ... Tuberculosis pdb|1YK3|G Chain G, Crystal Structure Of ... ... ... Rv1347c From Mycobacterium Tuberculosis pdb|1YK3|F Chain ... F, Crystal Structure Of Rv1347...c From Mycobacterium ... Tuberculosis pdb|1YK3|E Chain E, Crystal Structure Of ... Rv1347c From Mycobacterium Tuberculo...Rv1347c From Mycobacterium ... Tuberculosis pdb|1YK3|C Chain C, Crystal Structure Of ... Rv1347c From Mycobacterium Tub...erculosis pdb|1YK3|B Chain ... B, Crystal Structure Of Rv1347c From Mycobacterium ... Tubercul

  4. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ructure Of The Single-Stranded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE7|C Cha...Protein From Mycobacterium Tuberculosis pdb|1UE7|B Chain ... B, Crystal Structure Of The Single-Stran...ded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE7|A Chain ... A, Crystal St...ructure Of The Single-Stranded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE6|D Cha...Protein From Mycobacterium Tuberculosis pdb|1UE6|C Chain ... C, Crystal Structure Of The Single-Stran

  5. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ructure Of The Single-Stranded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE7|C Cha...Protein From Mycobacterium Tuberculosis pdb|1UE7|B Chain ... B, Crystal Structure Of The Single-Stran...ded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE7|A Chain ... A, Crystal St...ructure Of The Single-Stranded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE6|D Cha...Protein From Mycobacterium Tuberculosis pdb|1UE6|C Chain ... C, Crystal Structure Of The Single-Stran

  6. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ] pdb|1U0T|B Chain B, ... Crystal Structure Of Mycobacterium Tuberculosis ...Nad ... Kinase pdb|1U0T|A Chain A, Crystal Structure Of ... Mycobacterium Tuberculosis Nad Kin...ase pdb|1U0R|D Chain ... D, Crystal Structure Of Mycobacterium Tuberculosis Nad ... Kinase pdb...|1U0R|C Chain C, Crystal Structure Of ... Mycobacterium Tuberculosis Nad Kinase pdb|1U0R|B Chain ... ... ... B, Crystal Structure Of Mycobacterium Tuberculosis Nad ... Kinase p

  7. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ] pdb|1U0T|B Chain B, ... Crystal Structure Of Mycobacterium Tuberculosis ...Nad ... Kinase pdb|1U0T|A Chain A, Crystal Structure Of ... Mycobacterium Tuberculosis Nad Kin...ase pdb|1U0R|D Chain ... D, Crystal Structure Of Mycobacterium Tuberculosis Nad ... Kinase pdb...|1U0R|C Chain C, Crystal Structure Of ... Mycobacterium Tuberculosis Nad Kinase pdb|1U0R|B Chain ... ... ... B, Crystal Structure Of Mycobacterium Tuberculosis Nad ... Kinase p

  8. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ructure Of The Single-Stranded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE7|C Cha...Protein From Mycobacterium Tuberculosis pdb|1UE7|B Chain ... B, Crystal Structure Of The Single-Stran...ded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE7|A Chain ... A, Crystal St...ructure Of The Single-Stranded Dna-Binding ... Protein From Mycobacterium Tuberculosis pdb|1UE6|D Cha...Protein From Mycobacterium Tuberculosis pdb|1UE6|C Chain ... C, Crystal Structure Of The Single-Stran

  9. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Mycobacterium ... Tuberculosis pdb|1YK3|G Chain G, Crystal Structure Of ... ... ... Rv1347c From Mycobacterium Tuberculosis pdb|1YK3|F Chain ... F, Crystal Structure Of Rv1347...c From Mycobacterium ... Tuberculosis pdb|1YK3|E Chain E, Crystal Structure Of ... Rv1347c From Mycobacterium Tuberculo...Rv1347c From Mycobacterium ... Tuberculosis pdb|1YK3|C Chain C, Crystal Structure Of ... Rv1347c From Mycobacterium Tub...erculosis pdb|1YK3|B Chain ... B, Crystal Structure Of Rv1347c From Mycobacterium ... Tubercul

  10. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Mycobacterium ... Tuberculosis pdb|1YK3|G Chain G, Crystal Structure Of ... ... ... Rv1347c From Mycobacterium Tuberculosis pdb|1YK3|F Chain ... F, Crystal Structure Of Rv1347...c From Mycobacterium ... Tuberculosis pdb|1YK3|E Chain E, Crystal Structure Of ... Rv1347c From Mycobacterium Tuberculo...Rv1347c From Mycobacterium ... Tuberculosis pdb|1YK3|C Chain C, Crystal Structure Of ... Rv1347c From Mycobacterium Tub...erculosis pdb|1YK3|B Chain ... B, Crystal Structure Of Rv1347c From Mycobacterium ... Tubercul

  11. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ] pdb|1U0T|B Chain B, ... Crystal Structure Of Mycobacterium Tuberculosis ...Nad ... Kinase pdb|1U0T|A Chain A, Crystal Structure Of ... Mycobacterium Tuberculosis Nad Kin...ase pdb|1U0R|D Chain ... D, Crystal Structure Of Mycobacterium Tuberculosis Nad ... Kinase pdb...|1U0R|C Chain C, Crystal Structure Of ... Mycobacterium Tuberculosis Nad Kinase pdb|1U0R|B Chain ... ... ... B, Crystal Structure Of Mycobacterium Tuberculosis Nad ... Kinase p

  12. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available UM|F Chain F, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1EUM|E Chain E, Crystal Structure Of ... The E.Co...li Ferritin Ecftna pdb|1EUM|D Chain D, Crystal ... Structure Of The E.Coli... Ferritin Ecftna pdb|1EUM|C Chain ... C, Crystal Structure Of The E.Coli Fer...ritin Ecftna ... pdb|1EUM|B Chain B, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1...EUM|A Chain A, Crystal Structure Of ... The E.Coli Ferritin Ecftna dbj|BAA

  13. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004741 gi|30064775 >1g3kA 24 172 24 171 2e-58 ... pdb|1E94|D Chain D, Hslv-Hslu From E.Coli... pdb|1E94|C Chain C, Hslv-Hslu From ... E.Coli pdb|1E94|B Chain B, Hslv-Hslu From E.Coli ... ... ... pdb|1E94|A Chain A, Hslv-Hslu From E.Coli pdb|1HQY|D ... Chain D, Nucleotide-Dependent Confor

  14. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available UM|F Chain F, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1EUM|E Chain E, Crystal Structure Of ... The E.Co...li Ferritin Ecftna pdb|1EUM|D Chain D, Crystal ... Structure Of The E.Coli... Ferritin Ecftna pdb|1EUM|C Chain ... C, Crystal Structure Of The E.Coli Fer...ritin Ecftna ... pdb|1EUM|B Chain B, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1...EUM|A Chain A, Crystal Structure Of ... The E.Coli Ferritin Ecftna dbj|BAA

  15. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available UM|F Chain F, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1EUM|E Chain E, Crystal Structure Of ... The E.Co...li Ferritin Ecftna pdb|1EUM|D Chain D, Crystal ... Structure Of The E.Coli... Ferritin Ecftna pdb|1EUM|C Chain ... C, Crystal Structure Of The E.Coli Fer...ritin Ecftna ... pdb|1EUM|B Chain B, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1...EUM|A Chain A, Crystal Structure Of ... The E.Coli Ferritin Ecftna dbj|BAA

  16. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Formate-Lyase With Pyruvate pdb|1H18|B Chain B, Pyruvate ... Formate-Lyase (E.Coli) In Complex ...With Pyruvate ... pdb|1H18|A Chain A, Pyruvate Formate-Lyase (E.Coli) In ... ... ... Complex With Pyruvate pdb|1H17|A Chain A, Pyruvate ... Formate-Lyase (E.Coli) In Complex Wi...th Coa And The ... Substrate Analog Oxamate pdb|1H16|A Chain A, Pyruvate ... Formate-Lyase (E.Coli...) In Complex With Pyruvate And Coa ... pdb|3PFL|B Chain B, Crystal Structure Of Pfl From E.Coli

  17. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available UM|F Chain F, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1EUM|E Chain E, Crystal Structure Of ... The E.Co...li Ferritin Ecftna pdb|1EUM|D Chain D, Crystal ... Structure Of The E.Coli... Ferritin Ecftna pdb|1EUM|C Chain ... C, Crystal Structure Of The E.Coli Fer...ritin Ecftna ... pdb|1EUM|B Chain B, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1...EUM|A Chain A, Crystal Structure Of ... The E.Coli Ferritin Ecftna dbj|BAA

  18. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available UM|F Chain F, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1EUM|E Chain E, Crystal Structure Of ... The E.Co...li Ferritin Ecftna pdb|1EUM|D Chain D, Crystal ... Structure Of The E.Coli... Ferritin Ecftna pdb|1EUM|C Chain ... C, Crystal Structure Of The E.Coli Fer...ritin Ecftna ... pdb|1EUM|B Chain B, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1...EUM|A Chain A, Crystal Structure Of ... The E.Coli Ferritin Ecftna dbj|BAA

  19. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available UM|F Chain F, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1EUM|E Chain E, Crystal Structure Of ... The E.Co...li Ferritin Ecftna pdb|1EUM|D Chain D, Crystal ... Structure Of The E.Coli... Ferritin Ecftna pdb|1EUM|C Chain ... C, Crystal Structure Of The E.Coli Fer...ritin Ecftna ... pdb|1EUM|B Chain B, Crystal Structure Of The E.Coli ... Ferritin Ecftna pdb|1...EUM|A Chain A, Crystal Structure Of ... The E.Coli Ferritin Ecftna dbj|BAA

  20. ORF Alignment: NC_000912 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available CC ... 29342) pdb|1KNX|F Chain F, Hpr KinasePHOSPHATASE FROM ... MYCOPLASMA PNEUMONIAE pdb|1KN...X|E Chain E, Hpr ... KinasePHOSPHATASE FROM MYCOPLASMA PNEUMONIAE pdb|1KNX...|D ... Chain D, Hpr KinasePHOSPHATASE FROM MYCOPLASMA ... PNEUMONIAE pdb|1KNX|C Chain C, Hpr K...inasePHOSPHATASE ... FROM MYCOPLASMA PNEUMONIAE pdb|1KNX|B Chain B, Hpr ... KinasePHOSPHATASE FROM MYCOPLASMA PNEUMONIA...ROM MYCOPLASMA ... PNEUMONIAE ref|NP_109911.1| HPr(Ser) kinase [Mycoplasma ... pneumoniae M129

  1. ORF Alignment: NC_003106 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003106 gi|15922725 >1jzgA 8 127 23 138 1e-23 ... pdb|1OV8|D Chain D, Auracyanin B Structure In Space... Group, P65 pdb|1OV8|C ... Chain C, Auracyanin B Structure In Space Group, P65 ... ... ... pdb|1OV8|B Chain B, Auracyanin B Structure In Space ... Group, P65 pdb|1OV8|A Chain A, Auracya...nin B Structure In ... Space Group, P65 pdb|1QHQ|A Chain A, Auracyanin, A

  2. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

    Science.gov (United States)

    Westbrook, John D; Feng, Zukang; Persikova, Irina; Sala, Raul; Sen, Sanchayita; Berrisford, John M; Swaminathan, G Jawahar; Oldfield, Thomas J; Gutmanas, Aleksandras; Igarashi, Reiko; Armstrong, David R; Baskaran, Kumaran; Chen, Li; Chen, Minyu; Clark, Alice R; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M S; Hudson, Brian P; Ikegawa, Yasuyo; Kengaku, Yumiko; Lawson, Catherine L; Liang, Yuhe; Mak, Lora; Mukhopadhyay, Abhik; Narayanan, Buvaneswari; Nishiyama, Kayoko; Patwardhan, Ardan; Sahni, Gaurav; Sanz-García, Eduardo; Sato, Junko; Sekharan, Monica R; Shao, Chenghua; Smart, Oliver S; Tan, Lihua; van Ginkel, Glen; Yang, Huanwang; Zhuravleva, Marina A; Markley, John L; Nakamura, Haruki; Kurisu, Genji; Kleywegt, Gerard J; Velankar, Sameer; Berman, Helen M; Burley, Stephen K

    2018-01-01

    Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/ PMID:29688351

  3. Spatial Distribution of Stable Isotopes of Precipitation in Kumamoto, Japan

    Energy Technology Data Exchange (ETDEWEB)

    Anoue, M. T.; Shimada, J. [Graduate School of Science and Technology, Kumamoto University (Japan); Ichiyanagi, K. [Graduate School of Science and Technology, Kumamoto University and Japan Agency for Marine-Earth Science and Technology (Japan)

    2013-07-15

    To understand the spatial distribution of stable isotopic compositions in precipitation, precipitation samples were collected every two weeks from november 2009 to december 2010 at 6 points in Kumamoto, Japan. The {delta}{sup 18}O and {delta}{sup 2}H of precipitation samples were measured by isotope ratio mass spectrometry (Delta-S) with CO{sub 2}/H2{sub O} equivalent method for {delta}{sup 18}O and the chromium reduction method for {delta}2H. The range of {delta}{sup 18}O and d-excess (= {delta}{sup 2}H - 8 {delta}{sup 18}O) in precipitation is from -13.4 per mille to -3.5 per mille and from 2.6 per mille to 35.6 per mille , respectively. Seasonal variability of {delta}{sup 18}O (d-excess) in precipitation was low (high) in winter and high (low) in summer. The seasonal wind of this study area was dominated by south-westerly in summer (from June to August) and north-westerly in winter (from December to February). These wind regimes indicate seasonal variabilities of the water vapour pathway from the origin. In this paper the trend of inland effect to the {delta}{sup 18}O for both south-westerly and north-westerly are also considered. As a result, significant correlation between distances from the coastal line at south-westerly or north-westerly and {delta}{sup 18}O in precipitation was recognized, particularly from 18 February to 7 March and from 29 September to 19 October in 2010 (statistically significant with 5% level). Furthermore, in order to evaluate the course of precipitation, the column total of water vapour flux was considered in the whole period by using JRA-25 and JCDAS. It is interesting that the inland effect corresponded to the column total of water vapour flux at south-westerly (north-westerly). Hence, it is conceivable that the spatial distribution of {delta}{sup 18}O in precipitation was controlled by a column total of water vapour flux in this area. (author)

  4. Pooled versus separate measurements of tree-ring stable isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Dorado Linan, Isabel, E-mail: isabel@gfz-potsdam.de [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Gutierrez, Emilia, E-mail: emgutierrez@ub.edu [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); Helle, Gerhard, E-mail: ghelle@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Heinrich, Ingo, E-mail: heinrich@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Andreu-Hayles, Laia, E-mail: laiandreu@ub.edu [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); Tree-Ring Laboratory, Lamont-Doherty Earth Observatory of Columbia University, Palisades NY (United States); Planells, Octavi, E-mail: leocarpus@hotmail.com [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); Leuenberger, Markus, E-mail: leuenberger@climate.unibe.ch [Climate and Environmental Physics, Physics Institute, University of Bern, Sidlerstrasse 5, 3012 Bern (Switzerland); Oeschger Centre of Climate Change Research, University of Bern, Zaehringerstrasse 25, 3012 Bern (Switzerland); Buerger, Carmen, E-mail: buerger@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Schleser, Gerhard, E-mail: schleser@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany)

    2011-05-01

    {delta}{sup 13}C and {delta}{sup 18}O of tree rings contain time integrated information about the environmental conditions weighted by seasonal growth dynamics and are well established as sources of palaeoclimatic and ecophysiological data. Annually resolved isotope chronologies are frequently produced by pooling dated growth rings from several trees prior to the isotopic analyses. This procedure has the advantage of saving time and resources, but precludes from defining the isotopic error or statistical uncertainty related to the inter-tree variability. Up to now only a few studies have compared isotope series from pooled tree rings with isotopic measurements from individual trees. We tested whether or not the {delta}{sup 13}C and the {delta}{sup 18}O chronologies derived from pooled and from individual tree rings display significant differences at two locations from the Iberian Peninsula to assess advantages and constraints of both methodologies. The comparisons along the period 1900-2003 reveal a good agreement between pooled chronologies and the two mean master series which were created by averaging raw individual values (Mean) or by generating a mass calibrated mean (MassC). In most of the cases, pooled chronologies show high synchronicity with averaged individual samples at interannual scale but some differences also show up especially when comparing {delta}{sup 18}O decadal to multi-decadal variations. Moreover, differences in the first order autocorrelation among individuals may be obscured by pooling strategies. The lack of replication of pooled chronologies prevents detection of a bias due to a higher mass contribution of one sample but uncertainties associated with the analytical process itself, as sample inhomogeneity, seems to account for the observed differences. - Research Highlights: {yields} Pooled {delta}{sup 13}C and {delta}{sup 18}O chronologies are expected to be similar to the mean. {yields} Empirical pooled chronologies {delta}{sup 13}C and

  5. RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

    Science.gov (United States)

    Burley, Stephen K; Berman, Helen M; Christie, Cole; Duarte, Jose M; Feng, Zukang; Westbrook, John; Young, Jasmine; Zardecki, Christine

    2018-01-01

    The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  6. A stable isotope study of serpentinization in the Fengtien ophiolite, Taiwan

    Energy Technology Data Exchange (ETDEWEB)

    Tzen-Fu Yui; Hsueh-Wen Yeh (Univ. of Hawaii, Honolulu (USA)); Chihming Wang Lee (National Taiwan Univ. (Taiwan))

    1990-05-01

    Detailed H- and O-isotopic studies of serpentinites of Fengtien ophiolite have been made in order to enhance our knowledge on the process of serpentinization. Pseudomorphic lizardites have {delta}{sup 18}O = +3.6{per thousand} and {delta}D = {minus}48 to {minus}49{per thousand}; bladed-mat and foliated antigorites have {delta}{sup 18}O = +3.5 to +5.8{per thousand} and {delta}D = {minus}45 to {minus}69{per thousand}; slickensided antigorites have {delta}{sup 18}O = +4.1 to +4.9{per thousand} and {delta}D = {minus}46 to {minus}50{per thousand}; picrolites have {delta}{sup 18}O = +4.2 to +4.3{per thousand} and {delta}D = {minus}65 to {minus}67{per thousand}; and slickensided chrysotiles have {delta}{sup 18}O = +4.1 to +4.5{per thousand} and {delta}D = {minus}80{per thousand}. It is suggested that lizardite might have formed in an oceanic environment, whereas antigorite and chrysotile have formed in continental environments. These results depict complicated multiple serpentinization processes. Isotopic temperatures calculated using {delta}{sup 18}O values of coexisting fissure-filling minerals range from 325 to 370{degree}C, which are consistent with those derived from phase equilibria involving serpentines. The narrow range of {delta}{sup 18}O and wide range of {delta}D values for antigorite and chrysotile also demonstrate that water/rock ratios during these serpentinizations should not have been high. These Fengtien serpentines fall outside either of the continental domains described by Wenner and Taylor (1973, 1974); and fall within their oceanic domain. We suggest that the domains proposed by Wenner and Taylor (1973, 1974) should be extended and that the terms, especially the continental antigorite and the continental lizardite-chrysotile, should be purely occurrence-descriptive.

  7. Radiological features of Paget disease of bone associated with VCP myopathy

    Energy Technology Data Exchange (ETDEWEB)

    Farpour, Farzin [University of California, Department of Radiology, VA Long Beach Health Care, Irvine, CA (United States); Queens Hospital Center, Mount Sinai School of Medicine, New York, NY (United States); Tehranzadeh, Jamshid [University of California, Department of Radiology, VA Long Beach Health Care, Irvine, CA (United States); Donkervoort, Sandra; Vanjara, Pari [University of California, Division of Genetics and Metabolism, Department of Pediatrics, Irvine, CA (United States); Smith, Charles [University of Kentucky, Department of Neurology and Sanders-Brown Center on Aging, Lexington, KY (United States); Martin, Barbara [University of Kentucky, Lexington, KY (United States); Osann, Kathryn [University of California, Department of Medicine, Division of Hematology/Oncology, Irvine, CA (United States); Kimonis, Virginia E. [University of California, Division of Genetics and Metabolism, Department of Pediatrics, Irvine, CA (United States); UC Irvine Medical Center, Division of Genetics and Metabolism, Orange, CA (United States)

    2012-03-15

    Mutations in the Valosin-containing protein (VCP) gene cause a unique disorder characterized by classic Paget disease of bone (PDB), inclusion body myopathy, and frontotemporal dementia (IBMPFD). Our objective was to analyze the radiographic features of PDB associated with VCP mutations since there is a dearth of literature on the PDB component of VCP disease. Radiographic bone surveys were examined in 23 individuals with VCP mutation and compared with their unaffected relatives. Laboratory testing relevant for VCP disease was performed in all individuals. Of the 17 affected individuals with clinical manifestations of VCP disease, 16 of whom had myopathy, radiographic analysis revealed classic PDB in 11 individuals (65%). The mean age of diagnosis for myopathy was 43.8 years and for PDB was 38.1 years of age. Radiological evidence of PDB was seen in one individual (16%) amongst six clinically asymptomatic VCP mutation carriers. Alkaline phosphatase was a useful marker for diagnosing PDB in VCP disease. Radiographic findings of classic PDB are seen in 52% of individuals carrying VCP mutations at a significantly younger age than conventional PDB. Screening for PDB is warranted in at-risk individuals because of the benefit of early treatment with the new powerful bisphosphonates that hold the potential for prevention of disease. (orig.)

  8. The origins and behaviour of carbon in a major semi-arid river, the Murray River, Australia, as constrained by carbon isotopes and hydrochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Cartwright, Ian, E-mail: ian.cartwright@monash.edu [School of Geosciences, Monash University, Clayton, Vic. 3800 (Australia)] [National Centre for Groundwater Research and Training, Flinders University, Adelaide SA 5001 (Australia)

    2010-11-15

    Research highlights: {yields} {delta}{sup 13}C and concentrations of DIC in Murray River controlled by mineralisation of organic carbon and evasion. {yields} Murray River is source of atmospheric CO{sub 2}. {yields} In-river processing of carbon results in difficulties in determining carbon sources. - Abstract: {delta}{sup 13}C values of dissolved inorganic C (DIC), dissolved organic C (DOC), and particulate organic C (POC) together with {delta}{sup 18}O and {delta}{sup 2}H values of water, {delta}{sup 34}S values of dissolved SO{sub 4}, and major ion concentrations were measured in the Murray River and its tributaries between November 2005 and April 2007 to constrain the origins and behaviour of riverine C. {delta}{sup 13}C{sub DIC} values in the Murray River vary between -9.5 and -4.7 per mille with a range of <3 per mille within any sampling round. {delta}{sup 13}C{sub DIC} values of the tributaries are -11.0 per mille to -5.1 per mille. DIC concentrations of the Murray River increase from {approx}25 mg/L in the middle and upper reaches of the river to 45-55 mg/L in the lower reaches. However, the mass ratio of DIC as a proportion of the total dissolved solids (TDS) decreases from {approx}0.6-0.7 in the headwaters to {approx}0.2-0.3 in the lower reaches of the river, with similar downstream changes in DIC/Cl ratios. This precludes simple evaporative concentration of DIC and is interpreted as the river evading CO{sub 2}; this interpretation is consistent with pCO{sub 2} values that are in the range 550-11,200 ppm volume (ppmv), which are far higher than those in equilibrium with the atmosphere ({approx}360 ppmv). The {delta}{sup 13}C{sub DIC} values are similar to those that would be produced by the weathering of marine limestone ({delta}{sup 13}C {approx} 0 per mille). However, the lack of marine limestones cropping out in the Murray-Darling Basin and the relatively uniform {delta}{sup 13}C{sub DIC} values of the Murray River (even in upland reaches where the

  9. Using variation in the chemical and stable isotopic composition of Zostera noltii to assess nutrient dynamics in a temperate seagrass meadow

    Energy Technology Data Exchange (ETDEWEB)

    Papadimitriou, S.; Kennedy, H.; Rodrigues, R.M.N.V.; Kennedy, D.P. [University of Wales, Bangor (United Kingdom). School of Ocean Sciences; Heaton, T.H.E. [British Geological Survey, Nottingham (United Kingdom). NERC Isotope Geosciences Laboratory

    2006-10-15

    The influence of seasonality in growth and benthic organic matter remineralization on the chemical and isotopic composition of the seagrass Zostera noltii was investigated from March to November over the course of two years in a temperate meadow in North Wales, UK. The carbon (C{sub org}) and nitrogen (N{sub org}) concentrations in new {sub leaf} tissue ranged from 25 to 35 mmol C g{sup -1} and 2 to 5 mmol N g{sup -1}. Their stable isotopic composition ranged from -11.0 per thousand to -6.9 per thousand ({delta}{sup 13}C{sub leaf}) and +3.3 per thousand to +7.5 per thousand ({delta}{sup 15}N{sub leaf}), while the stable isotopic composition of sulphur in the new {sub leaf} ({delta}{sup 34}S{sub leaf}) ranged from -3.0 per thousand to +6.4 per thousand. The young seagrass tissues had lowest Norg, highest C:N, most depleted {delta}{sup 13}C{sub leaf}, and most enriched {delta}{sup 15}N{sub leaf} at the standing biomass maximum (approximately 150-200 g dry weight m{sup -2}) in the summer, reflecting the temporal imbalance between inorganic nutrient supply and plant demand imposed by seasonality in the growth rate. The most depleted {delta}{sup 34}S{sub leaf} was recorded in the same season. The isotopic composition of the seagrass tissues reflected that of the external inorganic source. The {delta}{sup 13}C{sub leaf} correlated (r{sup 2} {approx} 0.4) with the {delta}{sup 13}C of total dissolved inorganic carbon (DIC) in the surface waters ({delta}{sup 13}C{sub DIC} range: -0.4 per thousand to +1.2 per thousand).The apparent carbon isotope enrichment factor of new leaf relative to the bulk seawater DIC ({epsilon} {sub seagrass-DIC} range: -11.2 to -8.1 per thousand) indicated reliance on direct HCO{sub 3}{sup -} uptake, especially early in the growing season (spring). The {delta}{sup 15}N{sub leaf} reflected the {delta}{sup 15}N of pore water ammonium ({delta}{sup 15}NH{sub 4}{sup +} range: +6 per thousand to +10 per thousand; average: +7.4 {+-} 0.8 per thousand) as

  10. Sulfur isotope composition of orogenic spinel lherzolite massifs from Ariege (north-eastern pyrenees, France): An ion microprobe study

    Energy Technology Data Exchange (ETDEWEB)

    Chaussidon, M. (Centre de Recherches Petrographiques et Geochimiques, Vandoeuvre-les-Nancy (France)); Lorand, J. (Unite associee au CNRS, Paris (France))

    1990-10-01

    The orogenic spinel lherzolite massifs from Ariege, which represent tectonically emplaced fragments of the sub-continental upper mantle, are composed mainly of variously depleted peridotites. These rocks are crosscut by two generations of pyroxenites. The first is made up of layered pyroxenites, which are interpreted either as crystal segregates from Triassic continental tholeiites or as subducted parts of the oceanic crust re-injected within the upper mantle. The second consists of amphibole-rich dikes separated from Cretaceous alkali basalts. Forty sulfide grains, occurring either as inclusions within silicates or as interstitial grains, were investigated by ion microprobe for their sulfur isotopic compositions. Comparison between sulfide inclusions in silicates and interstitial sulfide grains strongly suggests that serpentinization and pyrenean metamorphism had no significant effect don the {delta}{sup 34}S values. Likewise, these values are broadly independent of the degree of partial melting. The negative {delta}{sup 34}S values of the massive peridotites could represent an ancient depletion event in the upper mantle. By contrast, the positive {delta}{sup 34}S values observed in the layered pryoxenites and the amphibole-rich dikes indicate that the two parent magmas had in common a mantle source variously enriched in {sup 34}S. Therefore, the present study reveals two extreme reservoirs characterized by different {delta}{sup 34}S values in the upper mantle. This range of variations can explain most {delta}{sup 34}S values found in MORB, continental tholeiites, and alkali basalts.

  11. Use of N stable isotope and microbial analyses to define wastewater influence in Mobile Bay, AL

    Energy Technology Data Exchange (ETDEWEB)

    Daskin, Joshua H. [MB 0193 Brandeis University, Waltham, MA 02454 (United States); Calci, Kevin R.; Burkhardt, William [1 Iberville Road, US Food and Drug Administration Gulf Coast Seafood Laboratory, Dauphin Island, AL 36528 (United States); Carmichael, Ruth H. [101 Bienville Boulevard, Dauphin Island Sea Lab, Dauphin Island, AL 36528 (United States); University of South Alabama, Mobile, AL, 36688 (United States)], E-mail: rcarmichael@disl.org

    2008-05-15

    We assessed short-term ecological and potential human health effects of wastewater treatment plant (WTP) effluent by measuring {delta}{sup 15}N per mille and microbial concentrations in oysters and suspended particulate matter (SPM). We also tested male-specific bacteriophage (MSB) as an alternative to fecal coliforms, to assess potential influence of wastewater contamination on shellfish. WTP effluent did not affect oyster growth or survival, but SPM and oysters acquired wastewater-specific {delta}{sup 15}N per mille . {delta}{sup 15}N values were depleted near the WTP, typical of low-level processed wastewater. Fecal coliform and MSB concentrations were higher in samples taken closest to the WTP, and MSB values were significantly correlated with {delta}{sup 15}N per mille in oyster tissues. Overall, oysters demonstrated relatively rapid integration and accumulation of wastewater-specific {delta}{sup 15}N per mille and indicator microorganisms compared to water samples. These data suggest oysters were superior sentinels compared to water, and MSB was a more reliable indicator of wastewater influence on shellfish than fecal coliforms.

  12. Environmental controls on the carbon isotope composition of ecosystem-respired CO{sub 2} in contrasting forest ecosystems in Canada and the USA

    Energy Technology Data Exchange (ETDEWEB)

    Alstad, K.P. [Lethbridge Univ., Lethbridge, AB (Canada). Dept. of Biological Sciences; Toledo Univ., Toledo, OH (United States). Dept. of Environmental Sciences; Flanagan, L.B. [Lethbridge Univ., Lethbridge, AB (Canada). Dept. of Biological Sciences; Lai, C.T. [Utah Univ., Salt Lake City, UT (United States); San Diego State Univ., San Diego, CA (United States); Ehleringer, J.R. [Utah Univ., Salt Lake City, UT (United States)

    2007-10-15

    Eleven forest ecosystems in Canada and the United States were compared in order to test for differences among forest {delta}{sup 13} carbon (C) responses to seasonal variations in environmental conditions from May to October 2004. Carbon isotope composition of ecosystem-respired carbon dioxide (CO{sub 2}) was considered as a proxy for short-term changes in photosynthetic discrimination. The study compared coniferous and deciduous forests, as well as forests in boreal and coastal environments. It was hypothesized that the carbon isotope composition of ecosystem-respired CO{sub 2} varied in a manner consistent with results obtained in leaf-level studies. Results of the study showed that higher R{sup 2} values were obtained for coastal ecosystems. The relationships between {delta}{sup 13}C{sub R} and environmental conditions were consistent with results obtained from leaf-level studies. Vapour pressure deficits and soil temperatures were significant determinants of variations in {delta}{sup 13}C{sub R} in the boreal forest ecosystem. Variations in {delta}{sup 13}C{sub R} in the coastal forest ecosystem correlated with changes in photosynthetic photon flux (PPF). It was concluded that {delta}{sup 13}C{sub R} measurements can be used to assess yearly variations in ecosystem physiological responses to changing environmental conditions. 59 refs., 7 tabs., 6 figs.

  13. Aquatic subsidies transport anthropogenic nitrogen to riparian spiders

    Energy Technology Data Exchange (ETDEWEB)

    Akamatsu, Fumikazu, E-mail: f-akamt55@pwri.go.jp [Department of Environmental Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan); Toda, Hideshige [Department of Environmental Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan)

    2011-05-15

    Stable nitrogen isotopic composition ({delta}{sup 15}N) of aquatic biota increases with anthropogenic N inputs such as sewage and livestock waste downstream. Increase in {delta}{sup 15}N of riparian spiders downstream may reflect the anthropogenic pollution exposure through predation on aquatic insects. A two-source mixing model based on stable carbon isotopic composition showed the greatest dependence on aquatic insects (84%) by horizontal web-building spiders, followed by intermediate (48%) and low (31%) dependence by cursorial and vertical web-building spiders, respectively. The spider body size was negatively correlated with the dietary proportion of aquatic insects and spider {delta}{sup 15}N. The aquatic subsidies transported anthropogenic N to smaller riparian spiders downstream. This transport of anthropogenic N was regulated by spider's guild designation and body size. - Highlights: > {delta}{sup 15}N of aquatic insects increases downstream with anthropogenic nitrogen inputs. > {delta}{sup 15}N of riparian spiders increases with a high dietary proportion of aquatic insects and smaller spider body size. > The aquatic subsidies transport anthropogenic nitrogen to smaller riparian spiders downstream. - Smaller spiders assimilate anthropogenic nitrogen through the predation on aquatic subsides.

  14. Late Holocene Radiocarbon Variability in Northwest Atlantic Slope Waters

    Energy Technology Data Exchange (ETDEWEB)

    Sherwood, O; Edinger, E; Guilderson, T P; Ghaleb, B; Risk, M J; Scott, D B

    2008-08-15

    Deep-sea gorgonian corals secrete a 2-part skeleton of calcite, derived from dissolved inorganic carbon at depth, and gorgonin, derived from recently fixed and exported particulate organic matter. Radiocarbon contents of the calcite and gorgonin provide direct measures of seawater radiocarbon at depth and in the overlying surface waters, respectively. Using specimens collected from Northwest Atlantic slope waters, we generated radiocarbon records for surface and upper intermediate water layers spanning the pre- and post bomb-{sup 14}C eras. In Labrador Slope Water (LSW), convective mixing homogenizes the pre-bomb {Delta}{sup 14}C signature (-67 {+-} 4{per_thousand}) to at least 1000 m depth. Surface water bomb-{sup 14}C signals were lagged and damped (peaking at {approx} +45{per_thousand} in the early 1980s) relative to other regions of the northwest Atlantic, and intermediate water signals were damped further. Off southwest Nova Scotia, the vertical gradient in {Delta}{sup 14}C is much stronger. In surface water, pre-bomb {Delta}{sup 14}C averaged -75 {+-} 5{per_thousand}. At 250-475 m depth, prebomb {Delta}{sup 14}C oscillated quasi-decadally between -80 and -100{per_thousand}, likely reflecting interannual variability in the presence of Labrador Slope Water vs. Warm Slope Water (WSW). Finally, subfossil corals reveal no systematic changes in vertical {Delta}{sup 14}C gradients over the last 1200 years.

  15. Annual Growth Bands in Hymenaea courbaril

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, J A; Guilderson, T P; Colinvaux, P A

    2004-02-09

    One significant source of annual temperature and precipitation data arises from the regular annual secondary growth rings of trees. Several tropical tree species are observed to form regular growth bands that may or may not form annually. Such growth was observed in one stem disk of the tropical legume Hymenaea courbaril near the area of David, Panama. In comparison to annual reference {Delta}{sup 14}C values from wood and air, the {Delta}{sup 14}C values from the secondary growth rings formed by H. courbaril were determined to be annual in nature in this one stem disk specimen. During this study, H. courbaril was also observed to translocate recently produced photosynthate into older growth rings as sapwood is converted to heartwood. This process alters the overall {Delta}{sup 14}C values of these transitional growth rings as cellulose with a higher {Delta}{sup 14}C content is translocated into growth rings with a relatively lower {Delta}{sup 14}C content. Once the annual nature of these growth rings is established, further stable isotope analyses on H. courbaril material in other studies may help to complete gaps in the understanding of short and of long term global climate patterns.

  16. Development and application of the mollusc Arctica islandica as a paleoceanographic tool for the North Atlantic Ocean

    Energy Technology Data Exchange (ETDEWEB)

    Weidman, C.R.

    1995-09-01

    Until now there has been no tool comparable to corals for reconstructing long term high-resolution geochemical time-series for the colder, higher-latitude oceans. In this thesis, the long-lived (+100 years) boreal mollusc (Bivalvia) Arctica islandica is shown to be practical for this purpose in the northern North Atlantic Ocean. The evidence, compiled here, demonstrates that the carbonate shell of this species faithfully records the ambient dissolved inorganic carbon`s (DIC) radiocarbon ({Delta}{sup 14}C) concentration and accurately reflects the ambient temperature in its stable oxygen isotope ({delta}{sup 18}O) composition. However, the stable carbon isotope ({delta}{sup 13}C) composition of the A. islandica shell likely is not a good recorder of ambient DIC {delta}{sup 13}C, and likely responds to physiological controls. Four {Delta}{sup 14}C time histories are reconstructed from the annual bands of A. islandica shells for the higher-latitudes of the northern North Atlantic Ocean (from 41{degree}N to 70{degree}N).

  17. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 2|D Chain D, ... E. Coli Ribokinase Complexed With Ribose And Adp, Solved ... In Space Group P...d Adp, Solved In ... Space Group P212121 pdb|1RK2|B Chain B, E. Coli ... Ribokinase Complexed ...With Ribose And Adp, Solved In ... Space Group P212121 pdb|1RK2|A Chain A, E. Coli ... Ribokin...ase Complexed With Ribose And Adp, Solved In ... Space Group P212121 pdb|1

  18. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 2|D Chain D, ... E. Coli Ribokinase Complexed With Ribose And Adp, Solved ... In Space Group P...d Adp, Solved In ... Space Group P212121 pdb|1RK2|B Chain B, E. Coli ... Ribokinase Complexed ...With Ribose And Adp, Solved In ... Space Group P212121 pdb|1RK2|A Chain A, E. Coli ... Ribokin...ase Complexed With Ribose And Adp, Solved In ... Space Group P212121 pdb|1

  19. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 2|D Chain D, ... E. Coli Ribokinase Complexed With Ribose And Adp, Solved ... In Space Group P...d Adp, Solved In ... Space Group P212121 pdb|1RK2|B Chain B, E. Coli ... Ribokinase Complexed ...With Ribose And Adp, Solved In ... Space Group P212121 pdb|1RK2|A Chain A, E. Coli ... Ribokin...ase Complexed With Ribose And Adp, Solved In ... Space Group P212121 pdb|1

  20. ORF Alignment: NC_002754 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available , ... 5'-Deoxy-5'-Methylthioadenosine Phosphorylase Complex ... With Phosphate (Space Group P2...1) pdb|1JDS|E Chain E, ... 5'-Deoxy-5'-Methylthioadenosine Phosphorylase Complex ... With Phosphate (Space... ... With Phosphate (Space Group P21) pdb|1JDS|C Chain C, ... 5'-De...oxy-5'-Methylthioadenosine Phosphorylase Complex ... With Phosphate (Space Group P21) pdb|1JDS|B Chai...n B, ... 5'-Deoxy-5'-Methylthioadenosine Phosphorylase Complex ... With Phosphate (Space Group

  1. ORF Alignment: NC_002754 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ure Of The Complete Core Of Archaeal Srp And ... Implications For Inter-Domain Communication pdb|1QZX...r Inter-Domain ... Communication pdb|1QZW|G Chain G, Crystal Structure Of ... ... The Complete Core Of Archaeal Srp And Implications For ... Inter-Domain Communication pdb|... Of The Complete Core Of ... Archaeal Srp And Implications For Inter-Domain ... Communication ... ... Inter-Domain Communication ... Length = 295 ... Query: 1 ... MLENIRDA

  2. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis... Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis pdb|1TED|A Chain ... A..., Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis emb|C... pdb|1TED|C Chain ... C, Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculos...is pdb|1TED|B Chain ... B, Crystal Structure Of A

  3. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002755 gi|15841371 >1wc3A 2 197 10 178 6e-16 ... pdb|1YBU|D Chain D, Mycobacterium Tuberculosis...C, ... Mycobacterium Tuberculosis Adenylyl Cyclase Rv1900c Chd, ... In Complex With A Substrat...e Analog. pdb|1YBU|B Chain B, ... Mycobacterium Tuberculosis Adenylyl Cycl...ase Rv1900c Chd, ... In Complex With A Substrate Analog. pdb|1YBU|A Chain A, ... Mycobacterium Tuberculosis

  4. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Udp-Galactopyranose Mutase From Mycobacterium ... Tuberculosis pdb|1V0J|C... Chain C, Udp-Galactopyranose ... Mutase From Mycobacterium Tuberculosis pdb|1V0J|B Chain ... ...B, Udp-Galactopyranose Mutase From Mycobacterium ... Tuberculosis pdb|1V0J|A Chain A, Udp-Galactopyra...nose ... Mutase From Mycobacterium Tuberculosis emb|CAA17873.1| ... UDP-GALACTOPYRANOSE MUTASE

  5. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available reductase pdb|1P9L|B Chain B, Structure Of M. ... Tuberculosis Dihydrodipicolinate Reductase In Comp...lex ... With Nadh And 2,6 Pdc pdb|1P9L|A Chain A, Structure Of ... M. Tuberculosis Dihydrodipi..., ... Dihydrodipicolinate Reductase From Mycobacterium ... Tuberculosis Complexed With Nadph A...nd Pdc pdb|1C3V|A ... Chain A, Dihydrodipicolinate Reductase From ... Mycobacterium Tuberculosis

  6. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis... Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis pdb|1TED|A Chain ... A..., Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis emb|C... pdb|1TED|C Chain ... C, Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculos...is pdb|1TED|B Chain ... B, Crystal Structure Of A

  7. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Udp-Galactopyranose Mutase From Mycobacterium ... Tuberculosis pdb|1V0J|C... Chain C, Udp-Galactopyranose ... Mutase From Mycobacterium Tuberculosis pdb|1V0J|B Chain ... ...B, Udp-Galactopyranose Mutase From Mycobacterium ... Tuberculosis pdb|1V0J|A Chain A, Udp-Galactopyra...nose ... Mutase From Mycobacterium Tuberculosis emb|CAA17873.1| ... UDP-GALACTOPYRANOSE MUTASE

  8. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available b|AAB38113.1| unknown gb|AAA86657.1| AhpD ... pdb|1KNC|C Chain C, Structure Of Ahpd From Mycobacterium ... Tuberculosis...ty. pdb|1KNC|B Chain B, Structure Of Ahpd From ... Mycobacterium Tuberculosis, A Novel Enzyme With ... ... ... Thioredoxin-Like Activity. pdb|1KNC|A Chain A, Structure ... Of Ahpd From Mycobacterium Tuberculosis

  9. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available b|AAB38113.1| unknown gb|AAA86657.1| AhpD ... pdb|1KNC|C Chain C, Structure Of Ahpd From Mycobacterium ... Tuberculosis...ty. pdb|1KNC|B Chain B, Structure Of Ahpd From ... Mycobacterium Tuberculosis, A Novel Enzyme With ... ... ... Thioredoxin-Like Activity. pdb|1KNC|A Chain A, Structure ... Of Ahpd From Mycobacterium Tuberculosis

  10. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_000962 gi|15609037 >1wc3A 2 197 10 178 6e-16 ... pdb|1YBU|D Chain D, Mycobacterium Tuberculosis...C, ... Mycobacterium Tuberculosis Adenylyl Cyclase Rv1900c Chd, ... In Complex With A Substrat...e Analog. pdb|1YBU|B Chain B, ... Mycobacterium Tuberculosis Adenylyl Cycl...ase Rv1900c Chd, ... In Complex With A Substrate Analog. pdb|1YBU|A Chain A, ... Mycobacterium Tuberculosis

  11. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available reductase pdb|1P9L|B Chain B, Structure Of M. ... Tuberculosis Dihydrodipicolinate Reductase In Comp...lex ... With Nadh And 2,6 Pdc pdb|1P9L|A Chain A, Structure Of ... M. Tuberculosis Dihydrodipi..., ... Dihydrodipicolinate Reductase From Mycobacterium ... Tuberculosis Complexed With Nadph A...nd Pdc pdb|1C3V|A ... Chain A, Dihydrodipicolinate Reductase From ... Mycobacterium Tuberculosis

  12. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002945 gi|31793093 >1wc3A 2 197 10 178 6e-16 ... pdb|1YBU|D Chain D, Mycobacterium Tuberculosis...C, ... Mycobacterium Tuberculosis Adenylyl Cyclase Rv1900c Chd, ... In Complex With A Substrat...e Analog. pdb|1YBU|B Chain B, ... Mycobacterium Tuberculosis Adenylyl Cycl...ase Rv1900c Chd, ... In Complex With A Substrate Analog. pdb|1YBU|A Chain A, ... Mycobacterium Tuberculosis

  13. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Udp-Galactopyranose Mutase From Mycobacterium ... Tuberculosis pdb|1V0J|C... Chain C, Udp-Galactopyranose ... Mutase From Mycobacterium Tuberculosis pdb|1V0J|B Chain ... ...B, Udp-Galactopyranose Mutase From Mycobacterium ... Tuberculosis pdb|1V0J|A Chain A, Udp-Galactopyra...nose ... Mutase From Mycobacterium Tuberculosis emb|CAA17873.1| ... UDP-GALACTOPYRANOSE MUTASE

  14. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available b|AAB38113.1| unknown gb|AAA86657.1| AhpD ... pdb|1KNC|C Chain C, Structure Of Ahpd From Mycobacterium ... Tuberculosis...ty. pdb|1KNC|B Chain B, Structure Of Ahpd From ... Mycobacterium Tuberculosis, A Novel Enzyme With ... ... ... Thioredoxin-Like Activity. pdb|1KNC|A Chain A, Structure ... Of Ahpd From Mycobacterium Tuberculosis

  15. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis... Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis pdb|1TED|A Chain ... A..., Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis emb|C... pdb|1TED|C Chain ... C, Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculos...is pdb|1TED|B Chain ... B, Crystal Structure Of A

  16. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available EDL933] pdb|1KDT|B Chain B, ... Cytidine Monophosphate Kinase From E.Coli In Complex ... With... 2',3'-Dideoxy-Cytidine Monophosphate pdb|1KDT|A ... Chain A, Cytidine Monophosphate Kinase From E.Coli...|1KDR|B Chain B, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara-Cytidine Monophosp...hate ... pdb|1KDR|A Chain A, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara

  17. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available EDL933] pdb|1KDT|B Chain B, ... Cytidine Monophosphate Kinase From E.Coli In Complex ... With... 2',3'-Dideoxy-Cytidine Monophosphate pdb|1KDT|A ... Chain A, Cytidine Monophosphate Kinase From E.Coli...|1KDR|B Chain B, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara-Cytidine Monophosp...hate ... pdb|1KDR|A Chain A, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara

  18. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available EDL933] pdb|1KDT|B Chain B, ... Cytidine Monophosphate Kinase From E.Coli In Complex ... With... 2',3'-Dideoxy-Cytidine Monophosphate pdb|1KDT|A ... Chain A, Cytidine Monophosphate Kinase From E.Coli...|1KDR|B Chain B, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara-Cytidine Monophosp...hate ... pdb|1KDR|A Chain A, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara

  19. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available EDL933] pdb|1KDT|B Chain B, ... Cytidine Monophosphate Kinase From E.Coli In Complex ... With... 2',3'-Dideoxy-Cytidine Monophosphate pdb|1KDT|A ... Chain A, Cytidine Monophosphate Kinase From E.Coli...|1KDR|B Chain B, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara-Cytidine Monophosp...hate ... pdb|1KDR|A Chain A, Cytidine Monophosphate Kinase From ... E.Coli In Complex With Ara

  20. Paget's disease of jaw bones as primary manifestation: A case report of a proper diagnosis made by general dentist.

    Science.gov (United States)

    Campolongo, Martin G; Cabras, Marco; Bava, Luca; Arduino, Paolo G; Carbone, Mario

    2018-06-01

    To present a case of early diagnosis mandibular Paget's disease of bone (PDB), recognised by a general dentist. PDB is responsible of rapid bone resorption and disorganised bone formation. The patient was a 72-year-old female patient complaining of dental malposition and blatant prognathism. Clinicians should consider PDB in differential diagnosis for an elderly patient undergoing unexplained alteration in face profile and occlusion. © 2018 John Wiley & Sons A/S and The Gerodontology Association. Published by John Wiley & Sons Ltd.

  1. ORF Alignment: NC_001148 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available e Of A Heptameric Ring Complex Of Yeast ... Smf In Spacegroup P4122 pdb|1N9R|F Chain F, Crystal ... ... ... Structure Of A Heptameric Ring Complex Of Yeast Smf In ... Spacegroup P4122 pdb|1N9R|E Chain E, Cr...ystal Structure ... Of A Heptameric Ring Complex Of Yeast Smf In Spacegroup... ... P4122 pdb|1N9R|D Chain D, Crystal Structure Of A ... Heptameric Ring Complex Of Yeast Smf In Space...group ... P4122 pdb|1N9R|C Chain C, Crystal Structure Of A ... Heptameric Ring Complex Of Yeast Smf In Space

  2. ORF Alignment: NC_001136 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Ypd1 And Sln1 Response Regulator Domain In ... Space Group P3(2) pdb|1OXK|I Chain I, Complex Between... ... Ypd1 And Sln1 Response Regulator Domain In Space Group ... P3(2) pdb|1OXK|G Chain G, Comp...lex Between Ypd1 And Sln1 ... Response Regulator Domain In Space Group P3(...2) ... pdb|1OXK|E Chain E, Complex Between Ypd1 And Sln1 ... Response Regulator Domain In Space... Group P3(2) ... pdb|1OXK|C Chain C, Complex Between Ypd1 And Sln1 ... Response Regulator Domain In Space

  3. Main: 1E1E [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available Mays Molecule: Beta-Glucosidase; Chain: A, B; Engineered: Yes Glycoside Hydrolase 3.2.1.21 (Beta-Glucosidas..., B.Henrissat, A.Esen Crystal Structure Of A Monocotyledon (Maize Zmglu1) Beta-Gl...55-566.|PDB; 1E55; X-ray; A/B=55-566.|PDB; 1E56; X-ray; A/B=55-566.|PDB; 1H49; X-ray; A/B=55-566.|PDB; 1HXJ; X-ray; A/B=60-566.|Mai...ze-2DPAGE; P49235; COLEOPTILE.|MaizeDB; 13870; -.|InterPro

  4. Citing a Data Repository: A Case Study of the Protein Data Bank.

    Science.gov (United States)

    Huang, Yi-Hung; Rose, Peter W; Hsu, Chun-Nan

    2015-01-01

    The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB's large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.

  5. Cysteine and tryptophan anomalies found when scanning all the binding sites in the Protein Data Bank.

    Science.gov (United States)

    Iván, Gábor; Szabadka, Zoltán; Grolmusz, Vince

    2010-01-01

    The Protein Data Bank (PDB) is one of the richest sources of structural biological information in the World. It started to exist as the computer-readable depository of crystallographic data complementing printed papers. The proper interpretation of the content of the individual files in the PDB still needs the detailed information found in the citing publication. An advanced graph theoretical method is presented here for automatically repairing, re-organising and re-structuring PDB data yielding the identification of all the protein-ligand complexes and all the binding sites in the PDB. As an application, we identified strong cysteine and tryptophan irregularities in the data.

  6. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Structure Of The Mycobacterium Tuberculosis Chaperonin ... 10 Tetradecamer pdb|1P3H|L Chain L, C...rystal Structure Of ... The Mycobacterium Tuberculosis Chaperonin 10 ... ... ... Tetradecamer pdb|1P3H|K Chain K, Crystal Structure Of ... The Mycobacterium Tuberculosis Chaper...onin 10 ... Tetradecamer pdb|1P3H|J Chain J, Crystal Structure Of ... The Mycobacterium Tuberculosis...e Of ... The Mycobacterium Tuberculosis Chaperonin 10 ... Tetradecamer pdb|1P3H|H Chain H, Cry

  7. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|G Chain G, S123c ... ... ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|F Chain F,... S123c ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis...se From ... Mycobacterium Tuberculosis. pdb|1GN2|C Chain C, S123c ... ... ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|B Chain B, S

  8. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Structure Of The Mycobacterium Tuberculosis Chaperonin ... 10 Tetradecamer pdb|1P3H|L Chain L, C...rystal Structure Of ... The Mycobacterium Tuberculosis Chaperonin 10 ... ... ... Tetradecamer pdb|1P3H|K Chain K, Crystal Structure Of ... The Mycobacterium Tuberculosis Chaper...onin 10 ... Tetradecamer pdb|1P3H|J Chain J, Crystal Structure Of ... The Mycobacterium Tuberculosis...e Of ... The Mycobacterium Tuberculosis Chaperonin 10 ... Tetradecamer pdb|1P3H|H Chain H, Cry

  9. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|G Chain G, S123c ... ... ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|F Chain F,... S123c ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis...se From ... Mycobacterium Tuberculosis. pdb|1GN2|C Chain C, S123c ... ... ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|B Chain B, S

  10. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|G Chain G, S123c ... ... ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|F Chain F,... S123c ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis...se From ... Mycobacterium Tuberculosis. pdb|1GN2|C Chain C, S123c ... ... ... Mutant Of The Iron-Superoxide Dismutase From ... Mycobacterium Tuberculosis. pdb|1GN2|B Chain B, S

  11. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Structure Of The Mycobacterium Tuberculosis Chaperonin ... 10 Tetradecamer pdb|1P3H|L Chain L, C...rystal Structure Of ... The Mycobacterium Tuberculosis Chaperonin 10 ... ... ... Tetradecamer pdb|1P3H|K Chain K, Crystal Structure Of ... The Mycobacterium Tuberculosis Chaper...onin 10 ... Tetradecamer pdb|1P3H|J Chain J, Crystal Structure Of ... The Mycobacterium Tuberculosis...e Of ... The Mycobacterium Tuberculosis Chaperonin 10 ... Tetradecamer pdb|1P3H|H Chain H, Cry

  12. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004741 gi|30064608 >1xeoA 1 165 1 165 2e-58 ... pdb|1LRU|C Chain C, Crystal Structure Of E.Coli... ... Structure Of E.Coli Peptide Deformylase Complexed With ... Antibiotic Actinonin pdb|1LRU|...A Chain A, Crystal ... Structure Of E.Coli Peptide Deformylase Complexed W...ith ... Antibiotic Actinonin pdb|1G2A|C Chain C, The Crystal ... Structure Of E.Coli Peptide D...eformylase Complexed With ... Actinonin pdb|1G2A|B Chain B, The Crystal Structure Of ... E.Coli

  13. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002695 gi|15833406 >1xeoA 1 165 1 165 2e-58 ... pdb|1LRU|C Chain C, Crystal Structure Of E.Coli... ... Structure Of E.Coli Peptide Deformylase Complexed With ... Antibiotic Actinonin pdb|1LRU|...A Chain A, Crystal ... Structure Of E.Coli Peptide Deformylase Complexed W...ith ... Antibiotic Actinonin pdb|1G2A|C Chain C, The Crystal ... Structure Of E.Coli Peptide D...eformylase Complexed With ... Actinonin pdb|1G2A|B Chain B, The Crystal Structure Of ... E.Coli

  14. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002655 gi|15803814 >1xeoA 1 165 1 165 2e-58 ... pdb|1LRU|C Chain C, Crystal Structure Of E.Coli... ... Structure Of E.Coli Peptide Deformylase Complexed With ... Antibiotic Actinonin pdb|1LRU|...A Chain A, Crystal ... Structure Of E.Coli Peptide Deformylase Complexed W...ith ... Antibiotic Actinonin pdb|1G2A|C Chain C, The Crystal ... Structure Of E.Coli Peptide D...eformylase Complexed With ... Actinonin pdb|1G2A|B Chain B, The Crystal Structure Of ... E.Coli

  15. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004337 gi|24114564 >1xeoA 1 165 1 165 2e-58 ... pdb|1LRU|C Chain C, Crystal Structure Of E.Coli... ... Structure Of E.Coli Peptide Deformylase Complexed With ... Antibiotic Actinonin pdb|1LRU|...A Chain A, Crystal ... Structure Of E.Coli Peptide Deformylase Complexed W...ith ... Antibiotic Actinonin pdb|1G2A|C Chain C, The Crystal ... Structure Of E.Coli Peptide D...eformylase Complexed With ... Actinonin pdb|1G2A|B Chain B, The Crystal Structure Of ... E.Coli

  16. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_000913 gi|16131166 >1xeoA 1 165 1 165 2e-58 ... pdb|1LRU|C Chain C, Crystal Structure Of E.Coli... ... Structure Of E.Coli Peptide Deformylase Complexed With ... Antibiotic Actinonin pdb|1LRU|...A Chain A, Crystal ... Structure Of E.Coli Peptide Deformylase Complexed W...ith ... Antibiotic Actinonin pdb|1G2A|C Chain C, The Crystal ... Structure Of E.Coli Peptide D...eformylase Complexed With ... Actinonin pdb|1G2A|B Chain B, The Crystal Structure Of ... E.Coli

  17. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available amine-6-Phosphate ... Deaminase From E.Coli, T Conformer, At 1.9a Resolution ... pdb|1FS6|A Ch...ain A, Glucosamine-6-Phosphate Deaminase ... From E.Coli, T Conformer, At ...phate Isomerase pdb|1FRZ|B Chain B, ... Glucosamine-6-Phosphate Deaminase From E.Coli, R ... C...lution ... pdb|1FRZ|A Chain A, Glucosamine-6-Phosphate Deaminase ... From E.Coli, R Conformer....hate At 2.2 A ... Resolution pdb|1CD5|A Chain A, Glucosamine-6-Phosphate ... Deaminase From E.Coli

  18. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004431 gi|26249871 >1xeoA 1 165 1 165 2e-58 ... pdb|1LRU|C Chain C, Crystal Structure Of E.Coli... ... Structure Of E.Coli Peptide Deformylase Complexed With ... Antibiotic Actinonin pdb|1LRU|...A Chain A, Crystal ... Structure Of E.Coli Peptide Deformylase Complexed W...ith ... Antibiotic Actinonin pdb|1G2A|C Chain C, The Crystal ... Structure Of E.Coli Peptide D...eformylase Complexed With ... Actinonin pdb|1G2A|B Chain B, The Crystal Structure Of ... E.Coli

  19. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available mational Changes In ... A Protease- Associated Atpase Hslu pdb|1HQY|C Chai...n C, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase Hslu... pdb|1HQY|B Chain B, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase...al Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Y Chain Y, ... Nucleotide-Depend...ent Conformational Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Z Chain Z, ... N

  20. ORF Alignment: NC_005835 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available thermophilus HB8] pdb|1V9M|A Chain A, Crystal Structure ... Of The C Subunit Of V-Type Atpase From Th...ermus ... Thermophilus pdb|1R5Z|C Chain C, Crystal Structure Of ... Subunit C Of V-Atpase pdb|...1R5Z|B Chain B, Crystal ... Structure Of Subunit C Of V-Atpase pdb|1R5Z|A ...Chain A, ... Crystal Structure Of Subunit C Of V-Atpase ... Length = 319 ... Query: 5 ... FAYLNARVR

  1. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available mational Changes In ... A Protease- Associated Atpase Hslu pdb|1HQY|C Chai...n C, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase Hslu... pdb|1HQY|B Chain B, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase...al Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Y Chain Y, ... Nucleotide-Depend...ent Conformational Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Z Chain Z, ... N

  2. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available mational Changes In ... A Protease- Associated Atpase Hslu pdb|1HQY|C Chai...n C, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase Hslu... pdb|1HQY|B Chain B, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase...al Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Y Chain Y, ... Nucleotide-Depend...ent Conformational Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Z Chain Z, ... N

  3. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available mational Changes In ... A Protease- Associated Atpase Hslu pdb|1HQY|C Chai...n C, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase Hslu... pdb|1HQY|B Chain B, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase...al Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Y Chain Y, ... Nucleotide-Depend...ent Conformational Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Z Chain Z, ... N

  4. ORF Alignment: NC_006461 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available thermophilus HB8] pdb|1V9M|A Chain A, Crystal Structure ... Of The C Subunit Of V-Type Atpase From Th...ermus ... Thermophilus pdb|1R5Z|C Chain C, Crystal Structure Of ... Subunit C Of V-Atpase pdb|...1R5Z|B Chain B, Crystal ... Structure Of Subunit C Of V-Atpase pdb|1R5Z|A ...Chain A, ... Crystal Structure Of Subunit C Of V-Atpase ... Length = 319 ... Query: 5 ... FAYLNARVR

  5. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available mational Changes In ... A Protease- Associated Atpase Hslu pdb|1HQY|C Chai...n C, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase Hslu... pdb|1HQY|B Chain B, ... Nucleotide-Dependent Conformational Changes In A ... Protease- Associated Atpase...al Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Y Chain Y, ... Nucleotide-Depend...ent Conformational Changes In A ... Protease- Associated Atpase Hslu pdb|1HT1|Z Chain Z, ... N

  6. ORF Alignment: NC_000917 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available Chain ... E, Structural Basis For The Mechanism And Regulation Of ... Sir2 Enzymes pdb|1S7G|D... Chain D, Structural Basis For ... The Mechanism And Regulation Of Sir2 Enzymes pdb|1S7G|C ... ... Chain C, Structural Basis For The Mechanism And ... Regulation Of Sir2 Enzymes... pdb|1S7G|B Chain B, ... Structural Basis For The Mechanism And Regulation Of ... Sir2 Enzymes... pdb|1S7G|A Chain A, Structural Basis For ... The Mechanism And Regulation Of Sir2 Enzymes ...

  7. Perfusion of the isolated rat brain with (/sup 14/C)-. delta. /sup 1/-tetrahydrocannabinol

    Energy Technology Data Exchange (ETDEWEB)

    Martin, B; Agurell, S [Dept. of Pharmacognosy, Faculty of Pharmacy, BMC, Uppsala (Sweden); Krieglstein, J; Rieger, H

    1977-12-01

    There is controversy over whether ..delta../sup 1/-tetrahydrocannabinol (..delta../sup 1/-THC) or its metabolites is responsible for the behavioural and cardiovascular effects of cannabis. It has been shown that, even in the absence of metabolism, ..delta../sup 1/-THC was capable of altering the EEG of isolated perfused rat brain, and must therefore contribute to the psychoactivity of cannabis. TLC studies showed no evidence for brain metabolism of (/sup 14/C)-..delta../sup 1/-THC, and in particular the 7-hydroxylated metabolite (7-OH-..delta../sup 1/-THC) could not be detected. A disproportionate amount of CNS activity in the rat cannot therefore be attributed to 7-OH-..delta../sup 1/-THC on the basis that it is formed at or near its locus of action.

  8. Determination of strontium isotopic composition in natural waters: examples of application in subsurface waters of the coastal zone of Bragantina region, Para, BR; Determinacao da composicao isotopica de estroncio em aguas naturais: exemplos de sua aplicacao em aguas subsuperficiais da zona costeira na regiao Bragantina-PA

    Energy Technology Data Exchange (ETDEWEB)

    Bordalo, Adriana Oliveira; Moura, Candido Augusto Veloso; Scheller, Thomas [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Centro de Geociencias]. E-mail: adriana@ufpa.br

    2007-07-15

    Analytical procedures used for determining the concentrations and isotope composition of strontium in subsurface waters, by mass spectrometry, are described. Sampling was performed in coastal plateaus, salt marsh and mangrove environments in the coastal region of Para. Coastal plateau waters have {delta}{sup 87}Sr between 1.51 and 6.26 per mille and Sr concentration bellow 58 ppb. Salt marsh waters show {delta}{sup 87}Sr between 0.55 and 0.90 per mille and Sr concentration between 93 and 114 ppm, while mangrove waters have {delta}{sup 87}Sr per mille around zero and Sr concentration above 15 ppm. Differences in the {sup 87}Sr/{sup 86}Sr ratio in these subsurface waters are detected, as well as seasonal variations in the coastal plateau waters. (author)

  9. Proxy Records of the Indonesian Low and the El Ni{tilde n}o-Southern Oscillation (ENSO) from Stable Isotope Measurements of Indonesian Reef Corals

    Energy Technology Data Exchange (ETDEWEB)

    Moore, M.D.

    1995-12-31

    The Earth`s largest atmospheric convective center is the Indonesian Low. It generates the Australasian monsoon, drives the zonal tropospheric Walker Circulation, and is implicated in the genesis of the El Nino-Southern Oscillation (ENSO). The long-term variability of the Indonesian Low is poorly characterized, yet such information is crucial for evaluating whether changes in the strength and frequency of ENSO events are a possible manifestation of global warming. Stable oxygen isotope ratios ({delta}{sup 18}O) in shallow-water reef coral skeletons track topical convective activity over hundreds of years because the input of isotopically-depleted rainwater dilutes seawater {delta}{sup 18}O. Corals also impose a temperature-dependent fractionation on {delta}{sup 18}O, but where annual rainfall is high and sea surface temperature (SST) variability is low the freshwater flux effect dominates.

  10. Variations of sulfur isotope ratios in a single lichen thallus: A potential historical archive for sulfur pollution

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Misuk, E-mail: yun@cc.umanitoba.c [Department of Earth Sciences and Environmental Science Program, Memorial University, St. John' s, NL, A1B 3X5 (Canada); Wadleigh, Moire A. [Department of Earth Sciences and Environmental Science Program, Memorial University, St. John' s, NL, A1B 3X5 (Canada); Mayer, Bernhard [Department of Geoscience, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4 (Canada)

    2010-12-15

    Utilizing the analytical capability to measure S isotope ratios of small quantities of S in biological material without any chemical pretreatment, the variation of {delta}{sup 34}S within a lichen thallus was investigated using old and young segments of fruticose lichen thalli (Alectoria sarmentosa) from an oil refinery area in Come-By-Chance and two coastal areas, Newfoundland, Canada. Old segments of lichen samples from the oil refinery area showed significantly higher {delta}{sup 34}S values (1.0-2.5 per mille) than their corresponding young segments. Lichen samples from two coastal areas showed no noticeable differences in {delta}{sup 34}S values between old and young segments. These results demonstrate that lichen thalli record temporal changes in the isotopic composition of atmospheric S and hence constitute a historical archive of atmospheric S pollution. - Lichen thalli record temporal changes in the isotopic composition of atmospheric S and hence constitute a suitable historical archive for biomonitoring.

  11. Study of K. pi. scattering using the reactions K/sup + -/p. -->. K/sup + -/. pi. /sup +/n and K/sup + -/p. -->. K/sup + -/. pi. /sup -/. delta. /sup + +/ at 13 GeV/c

    Energy Technology Data Exchange (ETDEWEB)

    Estabrooks, P [McGill Univ., Montreal, Quebec (Canada); Carnegie, R K [Carleton Univ., Ottawa, Ontario (Canada); Martin, A D [Durham Univ. (UK); Dunwoodie, W M; Lasinski, T A; Leith, D W.G.S. [Stanford Linear Accelerator Center, Calif. (USA)

    1978-02-27

    An elastic K..pi.. partial-wave analysis is presented. It is based on high-statistics data for the reactions K/sup + -/p ..-->.. K/sup + -/..pi../sup +/n and K/sup + -/p ..-->.. K/sup + -/..pi../sup -/..delta../sup + +/ at 13 GeV obtained in a spectrometer experiment performed at SLAC. For each reaction, a t-dependent parametrization of the production amplitudes provides information on both the K..pi.. mass dependence of the production mechanisms and on K..pi.. scattering. Knowledge of the t-dependence then allows a calculation of the K..pi.. partial-wave amplitudes for K..pi.. masses from 0.7 to 1.9 GeV. The results of such analyses using data for (i) the neutral recoil reactions, (ii) the ..delta../sup + +/ recoil reactions, and (iii) both neutron and ..delta../sup + +/ recoil reactions simultaneously are presented.

  12. Growth Rates, Stable Oxygen Isotopes (18O), and Strontium (Sr/Ca) Composition in Two Species of Pacific Sclerosponges (Acanthocheatetes wellsi and Astrosclera willeyana) with 18O Calibration and Application to Paleoceanography

    Energy Technology Data Exchange (ETDEWEB)

    Grottoli, A.; Adkins, J; Panero, W; Reaman, D; Moots, K

    2010-01-01

    The isotopic and elemental composition of sclerosponge skeletons is used to reconstruct paleoceanographic records. Yet few studies have systematically examined the natural variability in sclerosponge skeletal {delta}{sup 18}O, growth, and Sr/Ca, and how that may influence the interpretation of sclerosponge proxy records. Here, we analyzed short records in seven specimens of Acanthocheatetes wellsi (high-Mg calcite, 21 mol% Mg) from Palau, four A. wellsi (high-Mg calcite, 21 mol% Mg) from Saipan, and three Astrosclera willeyana (aragonite) sclerosponges from Saipan, as well as one long record in an A. wellsi specimen from Palau spanning 1945-2001.5. In Saipan, species-specific and mineralogical effects appear to have a negligible effect on sclerosponge {delta}{sup 18}O, facilitating the direct comparison of {delta}{sup 18}O records between species at a given location. At both sites, A. wellsi {delta}{sup 18}O and growth rates were sensitive to environmental conditions, but Sr/Ca was not sensitive to the same conditions. High-resolution {delta}{sup 18}O analyses confirmed this finding as both A. wellsi and A. willeyana deposited their skeleton in accordance with the trends in isotopic equilibrium with seawater, though with a 0.27{per_thousand} offset in the case of A. willeyana. In the high-Mg-calcite species A. wellsi, Mg may be interfering with Sr incorporation into the skeleton. On multidecadal timescales, A. wellsi sclerosponge {delta}{sup 18}O in Palau tracked the Southern Oscillation Index variability post-1977, but not pre-1977, coincident with the switch in the Pacific Decadal Oscillation (PDO) at {approx}1976. This suggests that water mass circulation in the region is influenced by El Nino-Southern Oscillation variability during positive PDO phases, but not during negative ones.

  13. Human impacts on groundwater flow and contamination deduced by multiple isotopes in Seoul City, South Korea

    Energy Technology Data Exchange (ETDEWEB)

    Hosono, Takahiro, E-mail: hosono@chikyu.ac.jp [Research Institute for Humanity and Nature, 457-4 Motoyama Kamigamo, Kita-ku, Kyoto 603-8047 (Japan); Ikawa, Reo, E-mail: r_ikawa@es.sci.kumamoto-u.ac.jp [Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Shimada, Jun, E-mail: jshimada@sci.kumamoto-u.ac.jp [Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Nakano, Takanori, E-mail: nakanot@chikyu.ac.jp [Research Institute for Humanity and Nature, 457-4 Motoyama Kamigamo, Kita-ku, Kyoto 603-8047 (Japan); Saito, Mitsuyo, E-mail: misaito@hiroshima-u.ac.jp [Graduate School of Biosphere Science, Hiroshima University, 1-7-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521 (Japan); Onodera, Shin-ichi, E-mail: sonodera@hiroshima-u.ac.jp [Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521 (Japan); Lee, Kang-Kun, E-mail: kklee@snu.ac.kr [School of Earth and Environmental Science, Seoul National University, San 56-1, Shinrim-dong, Kwanak-gu, Seoul 151-747 (Korea, Republic of); Taniguchi, Makoto, E-mail: makoto@chikyu.ac.jp [Research Institute for Humanity and Nature, 457-4 Motoyama Kamigamo, Kita-ku, Kyoto 603-8047 (Japan)

    2009-04-15

    The influence of human activities on the flow system and contamination of groundwater were investigated in Seoul City, South Korea, one of the largest Asian cities, using a combination of isotopes ({delta}D, T, {delta}{sup 15}N, {delta}{sup 18}O, {delta}{sup 34}S, and {sup 87}Sr/{sup 86}Sr). Eighteen representative groundwater and river water samples, which were collected over a wide area of the city, were compared with previously reported data. The distribution of stable isotopes ({delta}D and {delta}{sup 18}O) with groundwater potential data shows that recharged groundwater from either the surrounding mountainous area as well as the Han River and other surface streams discharged towards the northern-central part of the city, where a subway tunnel pumping station is located. It is suggested from T values (3.3 to 5.8 T.U.) that groundwater was recharged in the last 30 to 40 years. The {delta}{sup 34}S and {delta}{sup 15}N of SO{sub 4}{sup 2-} and NO{sub 3}{sup -} data were efficiently used as indicators of contamination by human activities. These isotopes clarified that the contribution of anthropogenic contaminants i.e., industrial and household effluents, waste landfills, and fertilizers, are responsible for the enrichment by SO{sub 4}{sup 2-} (> 30 ppm as SO{sub 4}{sup 2-}) and NO{sub 3}{sup -} (> 20 ppm as NO{sub 3}{sup -}) of groundwater. The {sup 87}Sr/{sup 86}Sr values of groundwater vary (0.71326 to 0.75058) in accordance with the host rocks of different origins. Mineral elements such as Ca are also suggested to be derived naturally from rocks. The groundwater under Seoul City is greatly affected by transportation of pollutants along the groundwater flow controlled by subway tunnel pumping, contributing to the degradation of water quality in urbanized areas.

  14. Oxygen isotopic ratios of quartz from wind-erosive soils of southwestern United States in relation to aerosol dust

    Energy Technology Data Exchange (ETDEWEB)

    Sridhar, K.; Jackson, M.L.; Clayton, R.N.; Gillette, D.A.; Hawley, J.W.

    1978-01-01

    The oxygen isotopic ratios (expressed as parts per thousand relative to mean ocean water, SMOW, delta/sup 18/O) of the quartz from 13 soils undergoing much wind erosion during the study period of 1972-1975 in four southwestern states and from comparison areas were determined. The delta/sup 18/O for quartz from eight Texas (TX) and Arizona (AZ) soils range from 13.0 to 15.9 /sup 0///sub 00/. The quartz of the sands and silts coarser than 20 ..mu..m from three of the soils had delta/sup 18/O values ranging from 13.1 to 15.1 /sup 0///sub 00/, characteristic of an ultimate igneous-metamorphic origin. The delta/sup 18/O values increase greatly with decreasing particle size of quartz from three soils ranging from loamy fine sand to loam to clay in texture. The delta/sup 18/O of the 1-10 ..mu..m quartz fraction (aerosol size) ranged from 19.2 to 20.2 /sup 0///sub 00/ (19.55 +- 0.28 /sup 0///sub 00/; +- sigma) for the thirteen soils most affected by dust storms. The oxygen isotopic ratios of 1-10 ..mu..m quartz from three Hawaiian soils and two sediments from Lake Waiau occurring at 3,970 m altitude on the Mauna Kea summit on the Island of Hawaii give a delta/sup 18/O mean of 18.3 +- 0.2 /sup 0///sub 00/.

  15. Supersymmetric regulators and supercurrent anomalies

    International Nuclear Information System (INIS)

    Majumdar, P.; Poggio, E.C.; Schnitzer, H.J.

    1980-01-01

    The supercurrent anomalies of the supercurrent deltasub(μ) of the supersymmetric Yang-Mills theory in Wess-Zumino gauge are computed using the supersymmetric dimensional regulator of Siegel. It is shown that γsub(μ)deltasup(μ) = 0 and deltasub(μ)deltasup(μ) unequal 0 in agreement with an earlier calculation based on the Adler-Rosenberg method. The problem of exhibiting the chiral anomaly and a regulator for local supersymmetry suggests that the interpretation of dimensional reduction in component language is incomplete. (orig.)

  16. SU-F-T-238: Analyzing the Performance of MapCHECK2 and Delta4 Quality Assurance Phantoms in IMRT and VMAT Plans

    Energy Technology Data Exchange (ETDEWEB)

    Lu, SH; Tsai, YC; Lan, HT; Wen, SY; Chen, LH; Kuo, SH; Wang, CW [National Taiwan University Hospital, Taipei City, Taiwan (China)

    2016-06-15

    Purpose: Intensity-modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT) have been widely investigated for use in radiotherapy and found to have a highly conformal dose distribution. Delta{sup 4} is a novel cylindrical phantom consisting of 1069 p-type diodes with true treatments measured in the 3D target volume. The goal of this study was to compare the performance of a Delta{sup 4} diode array for IMRT and VMAT planning with ion chamber and MapCHECK2. Methods: Fifty-four IMRT (n=9) and VMAT (n=45) plans were imported to Philips Pinnacle Planning System 9.2 for recalculation with a solid water phantom, MapCHECK2, and the Delta4 phantom. To evaluate the difference between the measured and calculated dose, we used MapCHECK2 and Delta{sup 4} for a dose-map comparison and an ion chamber (PTW 31010 Semiflex 0.125 cc) for a point-dose comparison. Results: All 54 plans met the criteria of <3% difference for the point dose (at least two points) by ion chamber. The mean difference was 0.784% with a standard deviation of 1.962%. With a criteria of 3 mm/3% in a gamma analysis, the average passing rates were 96.86%±2.19% and 98.42%±1.97% for MapCHECK2 and Delta{sup 4}, respectively. The student t-test of MapCHECK2/Delta{sup 4}, ion chamber/Delta{sup 4}, and ion chamber/MapCHECK2 were 0.0008, 0.2944, and 0.0002, respectively. There was no significant difference in passing rates between MapCHECK2 and Delta{sup 4} for the IMRT plan (p = 0.25). However, a higher pass rate was observed in Delta{sup 4} (98.36%) as compared to MapCHECK2 (96.64%, p < 0.0001) for the VMAT plan. Conclusion: The Pinnacle planning system can accurately calculate doses for VMAT and IMRT plans. The Delta{sup 4} shows a similar result when compared to ion chamber and MapCHECK2, and is an efficient tool for patient-specific quality assurance, especially for rotation therapy.

  17. Stable isotopes and mercury in a model estuarine fish: Multibasin comparisons with water quality, community structure, and available prey base

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Douglas H., E-mail: Doug.Adams@MyFWC.com; Paperno, Richard

    2012-01-01

    Stable-isotope ratios ({delta}{sup 13}C and {delta}{sup 15}N) and mercury in a model predator, and associated prey community assessments were used to make inferences regarding food web relationships and how these relationships are influenced by habitat variability and anthropogenic factors. Although interconnected, the three major basins of the Indian River Lagoon system on the Atlantic coast of Florida comprise noticeably different available habitat types with spatially distinct faunal communities and available prey for spotted seatrout, Cynoscion nebulosus, a model predatory fish species. Water quality, degree of urbanization, human population density, and levels of nitrogen enrichment clearly differ between these representative estuarine basins. The differences can influence feeding ecology and therefore result in different mercury concentrations and different stable-isotope signatures of spotted seatrout between basins. Mercury concentrations in spotted seatrout were greatest in Mosquito Lagoon (ML) and least in the Indian River Lagoon proper (IRL), although concentrations were low for all basins. Spotted seatrout from IRL were carbon-depleted and nitrogen-enriched compared with those from the other basins; this suggests either that the fish's primary source of carbon in IRL is an algae- or phytoplankton-based food web or that the pathway through the food web is shorter there. The {delta}{sup 15}N values of IRL spotted seatrout were greater than those in the Banana River Lagoon or ML, suggesting slightly different trophic positioning of fish in these basins. The greater {delta}{sup 15}N values in IRL spotted seatrout may also reflect the greater human population density and resultant anthropogenic inputs (e.g., observed higher total nitrogen levels) in IRL compared with the other more pristine basins examined. Understanding species' responses to broad-scale habitat heterogeneity in estuaries and knowing basin-specific differences in stable isotopes

  18. Oxygen isotope effect in 55Mn and 95Mo NMR spectra of the permanganate and molybdate ion

    International Nuclear Information System (INIS)

    Buckler, K.U.; Haase, A.R.; Lutz, O.; Mueller, M.; Nolle, A.

    1977-01-01

    By Fourier transform NMR spectroscopy the 55 Mn and 95 Mo resonance lines in the different permanganate and molybdate species Mn 16 Osub(4-n) 18 Osub(n) - and Mo 16 Osub(4-n) 18 Osub(n) 2- (n = 0,1,2,3,4) have been resolved in aqueous solutions of potassium permanganate and sodium molybdate. An isotopic effect on the Larmor frequency for 55 Mn of (0.59+-0.02)ppm and for 95 Mo of (0.25+-0.01)ppm to lower frequency has been found for the substitution of one 16 O atom by one 18 O atom. The relaxation rates 1/T 1 of 55 Mn in the different lines of the permanganate solution are equal within the limits of error. The oxygen exchange rate for the water-permanganate system has been evaluated. (orig.) [de

  19. Secondary biological coalbed gas in the Xinji area, Anhui province, China: Evidence from the geochemical features and secondary changes

    Energy Technology Data Exchange (ETDEWEB)

    Tao, Mingxin [Key Laboratory of Environmental Change and Natural Disaster of Ministry of Education, College of Resources Sciences and Technology, Beijing Normal University, Beijing 100875 (China); Key Laboratory of Gas Geochemistry, Institute of Geology and Geophysics, Chinese Academy of Sciences, Lanzhou 730000 (China); Shi, Baoguang; Wang, Wanchun; Li, Xiaobin; Gao, Bo [Key Laboratory of Gas Geochemistry, Institute of Geology and Geophysics, Chinese Academy of Sciences, Lanzhou 730000 (China); Li, Jinying [Material and Environment College, Qindao University of Science and Technology, Qindao 266042 (China)

    2007-07-02

    In order to ascertain the origin of the coalbed gas in the Xinji area, Anhui Province of China, the paper examined the geochemical features and secondary changes of CH{sub 4}, C{sub 2}H{sub 6}, CO{sub 2} and N{sub 2} from the coalbed gas. The related gas composition, carbon isotope and tracer geochemical data are as follows: 0.993 to 1.0 for C{sub 1}/C{sub 1-n}, 188.6 to 2993.7 for C{sub 1}/C{sub 2}, < 2% for CO{sub 2}, 0.64 to 3.06% for [CO{sub 2}/(CO{sub 2} + CH{sub 4})]100%, - 50.7 permille to - 61.3 permille for {delta}{sup 13}C{sub 1} with the average value of - 56.6 permille, - 15.9 permille to - 26.7 permille for {delta}{sup 13}C{sub 2}, - 10.8 permille to - 25.3 permille for {delta}{sup 13}C{sub 3}, - 6.0 permille to - 39.0 permille for {delta}{sup 13}C{sub CO2} with the average value of - 17.9 permille, 30.7 permille to 43.9 permille for {delta}{delta}{sup 13}C{sub C2-C1}, and 17.2 permille to 50 permille for {delta}{delta}{sup 13}C{sub CO2-C1}, - 1 permille to + 1 permille for {delta}{sup 15}N{sub N2}, 1.13 x 10{sup -7} to 3.20 x 10{sup -7} for {sup 3}He/{sup 4}He with R/Ra ratios range from 0.08 to 0.23. The Ro values of the coal range from 0.88% to 0.91%. The trends of the {delta}{sup 13}C{sub 1} values and {delta}{sup 13}C{sub CO2} values downward in the stratigraphic profile are opposite: the former appears as a slight light-heavy-light trend, but the latter appears as a heavy-light-heavy trend. The {delta}{sup 13}C{sub 1} values have a negative correlation with the {delta}{sup 13}C{sub CO2} values. However, the {delta}{sup 13}C{sub 2} values have no correlation with the {delta}{sup 13}C{sub 1} values due to its complicated variation. The thermal evolution of the coal in the Xinji area is in the phase of a lot of wet gas generation, but most of the CO{sub 2} and heavy hydrocarbons have been reduced or degraded by microbes and have changed into biogenic methane. The coalbed gas is comprised of secondary biogenic methane, thermogenic methane, the

  20. OXYGEN ISOTOPIC COMPOSITIONS OF THE ALLENDE TYPE C CAIs: EVIDENCE FOR ISOTOPIC EXCHANGE DURING NEBULAR MELTING AND ASTEROIDAL THERMAL METAMORPHISM

    Energy Technology Data Exchange (ETDEWEB)

    Krot, A N; Chaussidon, M; Yurimoto, H; Sakamoto, N; Nagashima, K; Hutcheon, I D; MacPherson, G J

    2008-02-21

    Based on the mineralogy and petrography, coarse-grained, igneous, anorthite-rich (Type C) calcium-aluminum-rich inclusions (CAIs) in the CV3 carbonaceous chondrite Allende have been recently divided into three groups: (i) CAIs with melilite and Al,Ti-diopside of massive and lacy textures (coarse grains with numerous rounded inclusions of anorthite) in a fine-grained anorthite groundmass (6-1-72, 100, 160), (ii) CAI CG5 with massive melilite, Al,Ti-diopside and anorthite, and (iii) CAIs associated with chondrule material: either containing chondrule fragments in their peripheries (ABC, TS26) or surrounded by chondrule-like, igneous rims (93) (Krot et al., 2007a,b). Here, we report in situ oxygen isotopic measurements of primary (melilite, spinel, Al,Ti-diopside, anorthite) and secondary (grossular, monticellite, forsterite) minerals in these CAIs. Spinel ({Delta}{sup 17}O = -25{per_thousand} to -20{per_thousand}), massive and lacy Al,Ti-diopside ({Delta}{sup 17}O = -20{per_thousand} to -5{per_thousand}) and fine-grained anorthite ({Delta}{sup 17}O = -15{per_thousand} to -2{per_thousand}) in 100, 160 and 6-1-72 are {sup 16}O-enriched relative spinel and coarse-grained Al,Ti-diopside and anorthite in ABC, 93 and TS26 ({Delta}{sup 17}O ranges from -20{per_thousand} to -15{per_thousand}, from -15{per_thousand} to -5{per_thousand}, and from -5{per_thousand} to 0{per_thousand}, respectively). In 6-1-72, massive and lacy Al,Ti-diopside grains are {sup 16}O-depleted ({Delta}{sup 17}O {approx} -13{per_thousand}) relative to spinel ({Delta}{sup 17}O = -23{per_thousand}). Melilite is the most {sup 16}O-depleted mineral in all Allende Type C CAIs. In CAI 100, melilite and secondary grossular, monticellite and forsterite (minerals replacing melilite) are similarly {sup 16}O-depleted, whereas grossular in CAI 160 is {sup 16}O-enriched ({Delta}{sup 17}O = -10{per_thousand} to -6{per_thousand}) relative to melilite ({Delta}{sup 17}O = -5{per_thousand} to -3{per_thousand}). We infer

  1. Data of evolutionary structure change: 1ADEA-1DJ3B [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1ADEA-1DJ3B 1ADE 1DJ3 A B -------GNNVVVLGTQWGDEGKGKIVDLLTERAKYVVR.../pdbID> A 1ADEA LVING...pdbChain>A 1ADEA ALDNA-REKAR A 1ADEA RGAKAIGTTGR A 1ADEA HNFQLVNYYKA

  2. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  3. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  4. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available bosomal subunit protein L13 ... [Escherichia coli O157:H7] pdb|1P86|H Chain H, Real ... Space ...Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|H Chain H, Real ... Space

  5. ORF Alignment: NC_005126 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  6. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  7. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  8. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available bosomal subunit protein L13 ... [Escherichia coli O157:H7] pdb|1P86|H Chain H, Real ... Space ...Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|H Chain H, Real ... Space

  9. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  10. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312210.1| 50S ribosomal subunit protein L23 ... [Escherichia coli O157:H7] pdb|1P86|R Chain R, Real ... Space...he Low Resolution Cryo-Em Map Of The ... Initiation-Like State Of E. Coli 70s Ribosome ... pdb|1P85|R Chain R, Real Space

  11. Probing the Role of Loops & Domains in Regulating Coagulation Factor VIIa Allostery and Specificity

    DEFF Research Database (Denmark)

    Sørensen, Anders Bundgård

    2016-01-01

    The front-page illustrates the protease domain of factor VII in complex with tissue factor, the structure was solved during this dissertation (pdb id 5feo).......The front-page illustrates the protease domain of factor VII in complex with tissue factor, the structure was solved during this dissertation (pdb id 5feo)....

  12. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

    Science.gov (United States)

    Kinjo, Akira R; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

    2017-01-04

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future

    OpenAIRE

    Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki; Markley, John L.

    2012-01-01

    A symposium celebrating the 40th anniversary of the Protein Data Bank archive (PDB), organized by the Worldwide Protein Data Bank, was held at Cold Spring Harbor Laboratory (CSHL) October 28–30, 2011. PDB40’s distinguished speakers highlighted four decades of innovation in structural biology, from the early era of structural determination to future directions for the field.

  14. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

    NARCIS (Netherlands)

    Joosten, R.P.; Joosten, K.; Cohen, S.X.; Vriend, G.; Perrakis, A.

    2011-01-01

    MOTIVATION: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better

  15. ORF Alignment: NC_000917 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_000917 gi|11498546 >1yozA 1 116 1 116 6e-47 ... pdb|1YOZ|B Chain B, Predicted Coding... Region Af0941 From Archaeoglobus Fulgidus ... pdb|1YOZ|A Chain A, Predicted Coding Region Af0941 F

  16. Data of evolutionary structure change: 1AQ7A-2FODA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1AQ7A-2FODA 1AQ7 2FOD A A IVGGYTCGANTVPYQVSLNSG-----YHFCGGSLINSQW...pdbChain>A 2FODA SLQYRSGSSWAHTCG 2FOD A 2FODA PLHCLVNGQYAVHG 2FOD A 2FODA...pdbChain> 2FODA TRTNG-QLAQT -

  17. Houtman Abrolhos Isotope (delta 18O, delta 13C) Data for 1795 to 1994

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — DESCRIPTION: VARIABLES AND UNITS: Column #1: core depth in mm Column #2: delta C-13 vs V-PDB Column #3: delta O-18 vs V-PDB Column #4: assigned date in years A.D....

  18. NCBI nr-aa BLAST: CBRC-EEUR-01-0952 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-0952 pdb|1CI4|A Chain A, The Crystal Structure Of Human Barrier-To-Autointegration... Factor (Baf) pdb|1CI4|B Chain B, The Crystal Structure Of Human Barrier-To-Autointegration Factor (Baf) 1CI4 3e-07 52% ...

  19. Stemcell Information: SKIP000968 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000968 ... Diseased PDB1lox-21Puro-12 PDB1lox-21Puro-12 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  20. Stemcell Information: SKIP000974 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000974 ... Diseased PDB1lox-21GFP-41 PDB1lox-21GFP-41 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  1. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available hain A, Dihydrofolate ... Reductase Of Mycobacterium Tuberculosis Complexed With ... Nadph And... Methotrexate pdb|1DG8|A Chain A, Dihydrofolate ... Reductase Of Mycobacterium Tuberculosis... Complexed With ... Nadph pdb|1DG7|A Chain A, Dihydrofolate Reductase Of ... Mycobacterium Tuberculosi...late ... Reductase Of Mycobacterium Tuberculosis Complexed With ... Nadph And Trimethoprim emb

  2. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available - Mycobacterium tuberculosis (strain H37RV) ... pdb|1LQU|B Chain B, Mycobacterium Tuberculosis... Fpra In ... Complex With Nadph pdb|1LQU|A Chain A, Mycobacterium ... Tuberculosis... By The ... Atomic Resolution Structure Of Fpra, A Mycobacterium ... Tuberculosis...e Atomic ... Resolution Structure Of Fpra, A Mycobacterium ... Tuberculosis Oxidoreductase sp|

  3. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available hain A, Dihydrofolate ... Reductase Of Mycobacterium Tuberculosis Complexed With ... Nadph And... Methotrexate pdb|1DG8|A Chain A, Dihydrofolate ... Reductase Of Mycobacterium Tuberculosis... Complexed With ... Nadph pdb|1DG7|A Chain A, Dihydrofolate Reductase Of ... Mycobacterium Tuberculosi...late ... Reductase Of Mycobacterium Tuberculosis Complexed With ... Nadph And Trimethoprim emb

  4. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 1551] ... pdb|1N8W|B Chain B, Biochemical And Structural Studies ... Of Malate Synthase From Mycobacterium Tuberculosis...al Studies ... Of Malate Synthase From Mycobacterium Tuberculosis ... pdb|1N8I|A Chain A, Bioc...hemical And Structural Studies ... Of Malate Synthase From Mycobacterium Tuberculosis ... emb|

  5. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 1551] ... pdb|1N8W|B Chain B, Biochemical And Structural Studies ... Of Malate Synthase From Mycobacterium Tuberculosis...al Studies ... Of Malate Synthase From Mycobacterium Tuberculosis ... pdb|1N8I|A Chain A, Bioc...hemical And Structural Studies ... Of Malate Synthase From Mycobacterium Tuberculosis ... emb|

  6. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available From ... Mycobacterium Tuberculosis pdb|1WQG|A Chain A, Crystal ... Structure Of Ribosome Rec...ycling Factor From ... Mycobacterium Tuberculosis pdb|1WQF|A Chain A, Crys...tal ... Structure Of Ribosome Recycling Factor From ... Mycobacterium Tuberculosis ref|NP_3374

  7. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available 1551] ... pdb|1N8W|B Chain B, Biochemical And Structural Studies ... Of Malate Synthase From Mycobacterium Tuberculosis...al Studies ... Of Malate Synthase From Mycobacterium Tuberculosis ... pdb|1N8I|A Chain A, Bioc...hemical And Structural Studies ... Of Malate Synthase From Mycobacterium Tuberculosis ... emb|

  8. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available hain A, Dihydrofolate ... Reductase Of Mycobacterium Tuberculosis Complexed With ... Nadph And... Methotrexate pdb|1DG8|A Chain A, Dihydrofolate ... Reductase Of Mycobacterium Tuberculosis... Complexed With ... Nadph pdb|1DG7|A Chain A, Dihydrofolate Reductase Of ... Mycobacterium Tuberculosi...late ... Reductase Of Mycobacterium Tuberculosis Complexed With ... Nadph And Trimethoprim emb

  9. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available - Mycobacterium tuberculosis (strain H37RV) ... pdb|1LQU|B Chain B, Mycobacterium Tuberculosis... Fpra In ... Complex With Nadph pdb|1LQU|A Chain A, Mycobacterium ... Tuberculosis... By The ... Atomic Resolution Structure Of Fpra, A Mycobacterium ... Tuberculosis...e Atomic ... Resolution Structure Of Fpra, A Mycobacterium ... Tuberculosis Oxidoreductase sp|

  10. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available From ... Mycobacterium Tuberculosis pdb|1WQG|A Chain A, Crystal ... Structure Of Ribosome Rec...ycling Factor From ... Mycobacterium Tuberculosis pdb|1WQF|A Chain A, Crys...tal ... Structure Of Ribosome Recycling Factor From ... Mycobacterium Tuberculosis ref|NP_3374

  11. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available From ... Mycobacterium Tuberculosis pdb|1WQG|A Chain A, Crystal ... Structure Of Ribosome Rec...ycling Factor From ... Mycobacterium Tuberculosis pdb|1WQF|A Chain A, Crys...tal ... Structure Of Ribosome Recycling Factor From ... Mycobacterium Tuberculosis ref|NP_3374

  12. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002655 gi|15800390 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

  13. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004741 gi|30062138 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

  14. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004431 gi|26246664 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

  15. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002695 gi|15829972 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

  16. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004337 gi|56479698 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

  17. NCBI nr-aa BLAST: CBRC-PHAM-01-0774 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available ced As A Secretion Protein In E.Coli pdb|3BSQ|B Chain B, Crystal Structure Of Human Kallikrein 7 Produced As... A Secretion Protein In E.Coli pdb|3BSQ|C Chain C, Crystal Structure Of Human Kallikrein 7 Produced As A Secretion Protein In E.Coli 3BSQ 2e-12 89% ...

  18. NCBI nr-aa BLAST: CBRC-MLUC-01-0889 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available neurons protein 2 pdb|3HAJ|A Chain A, Crystal Structure Of Human Pacsin2 F-Bar Domain (P212121 Lattice) pdb...|3HAJ|B Chain B, Crystal Structure Of Human Pacsin2 F-Bar Domain (P212121 Lattice

  19. NCBI nr-aa BLAST: CBRC-OPRI-01-0218 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available neurons protein 2 pdb|3HAJ|A Chain A, Crystal Structure Of Human Pacsin2 F-Bar Domain (P212121 Lattice) pdb...|3HAJ|B Chain B, Crystal Structure Of Human Pacsin2 F-Bar Domain (P212121 Lattice

  20. NCBI nr-aa BLAST: CBRC-PHAM-01-1678 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available neurons protein 2 pdb|3HAJ|A Chain A, Crystal Structure Of Human Pacsin2 F-Bar Domain (P212121 Lattice) pdb...|3HAJ|B Chain B, Crystal Structure Of Human Pacsin2 F-Bar Domain (P212121 Lattice

  1. Stemcell Information: SKIP000593 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000593 ... Diseased PDB3F-9 PDB3F-9 ... パーキンソン病 G20 Parkinson disease 168600 ... ... ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induc

  2. Stemcell Information: SKIP000594 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000594 ... Diseased PDB3F-d12 PDB3F-d12 ... パーキンソン病 G20 Parkinson disease 1686...he Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced

  3. Stemcell Information: SKIP000596 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000596 ... Diseased PDB4F-2 PDB4F-2 ... パーキンソン病 G20 Parkinson disease 168600 ... ...f Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkins...on's disease patient-derived induced pluripotent stem ce

  4. Stemcell Information: SKIP000960 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000960 ... Diseased PDB1lox-17GFP-55 PDB1lox-17GFP-55 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  5. Stemcell Information: SKIP000598 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000598 ... Diseased PDB4F-4 PDB4F-4 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

  6. Stemcell Information: SKIP000763 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000763 ... Diseased PDB2lox-17 PDB2lox-17 ... パーキンソン病 G20 Parkinson disease 16...9371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of v

  7. Stemcell Information: SKIP000973 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000973 ... Diseased PDB1lox-21Puro-28 PDB1lox-21Puro-28 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  8. Stemcell Information: SKIP000969 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000969 ... Diseased PDB1lox-21Puro-13 PDB1lox-21Puro-13 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  9. Stemcell Information: SKIP000962 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000962 ... Diseased PDB1lox-17Puro-10 PDB1lox-17Puro-10 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  10. Stemcell Information: SKIP000971 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000971 ... Diseased PDB1lox-21Puro-20 PDB1lox-21Puro-20 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  11. Stemcell Information: SKIP000967 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000967 ... Diseased PDB1lox-21Puro-5 PDB1lox-21Puro-5 ... パーキンソン病 G20 Parkinson... Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  12. Stemcell Information: SKIP000765 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000765 ... Diseased PDB2lox-22 PDB2lox-22 ... パーキンソン病 G20 Parkinson disease 16...9371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of v

  13. Stemcell Information: SKIP000966 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000966 ... Diseased PDB1lox-21GFP-19 PDB1lox-21GFP-19 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  14. Stemcell Information: SKIP000595 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000595 ... Diseased PDB4F-1 PDB4F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

  15. Stemcell Information: SKIP000599 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000599 ... Diseased PDB4F-5 PDB4F-5 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

  16. Stemcell Information: SKIP000959 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000959 ... Diseased PDB1lox-17GFP-29 PDB1lox-17GFP-29 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  17. Stemcell Information: SKIP000972 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000972 ... Diseased PDB1lox-21Puro-26 PDB1lox-21Puro-26 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  18. Stemcell Information: SKIP000590 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000590 ... Diseased PDB3F-1 PDB3F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...e ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived in

  19. Stemcell Information: SKIP000597 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000597 ... Diseased PDB4F-3 PDB4F-3 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

  20. Stemcell Information: SKIP000970 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000970 ... Diseased PDB1lox-21Puro-18 PDB1lox-21Puro-18 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  1. Stemcell Information: SKIP000964 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000964 ... Diseased PDB1lox-17Puro-31 PDB1lox-17Puro-31 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  2. Stemcell Information: SKIP000963 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000963 ... Diseased PDB1lox-17Puro-12 PDB1lox-17Puro-12 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  3. Stemcell Information: SKIP000591 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000591 ... Diseased PDB3F-5 PDB3F-5 ... パーキンソン病 G20 Parkinson disease 168600 ... ...dolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  4. Stemcell Information: SKIP000762 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000762 ... Diseased PDB2lox-5 PDB2lox-5 ... パーキンソン病 G20 Parkinson disease 1686...71 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of vir

  5. Stemcell Information: SKIP000592 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000592 ... Diseased PDB3F-8 PDB3F-8 ... パーキンソン病 G20 Parkinson disease 168600 ... ...ute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived

  6. ORF Alignment: NC_002607 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002607 gi|15790649 >1b22A 10 70 5 63 2e-10 ... pdb|1XU4|A Chain A, Atpase In Compl...ex With Amp-Pnp, Magnesium And Potassium ... Co-F pdb|1T4G|A Chain A, Atpase In Complex With Amp-Pnp ...

  7. ORF Alignment: cds [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available cds gnl|CMER >1e79I 1 47 1 47 1e-07 ... pdb|1E79|I Chain I, Bovine F1-Atpase Inhibite...d By Dccd ... (Dicyclohexylcarbodiimide) pdb|1H8E|I Chain I, ... (Adp.Alf4)2(Adp.So4) Bovine F1-Atpase

  8. ORF Alignment: NC_003551 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003551 gi|20094872 >1b22A 10 70 5 63 2e-10 ... pdb|1XU4|A Chain A, Atpase In Compl...ex With Amp-Pnp, Magnesium And Potassium ... Co-F pdb|1T4G|A Chain A, Atpase In Complex With Amp-Pnp

  9. [5-(aralkyl/aryl)-1,3,4-oxadiazol-2- yl]sulfanyl

    African Journals Online (AJOL)

    3 in an aprotic polar solvent. The structures of these bi-heterocycles were elucidated by infrared (IR), .... cold distilled water (40 mL) was added, and the precipitate formed was .... glucosidase (PDB ID: 3NO4) and urease (PDB. ID: 4UBP).

  10. Download this PDF file

    African Journals Online (AJOL)

    2017-09-28

    Sep 28, 2017 ... made by blending fresh J. gendarussa leaves in cold water. Then the ... The structure of the HIV-1 reverse transcriptase receptor is obtained from Protein Data Bank (http://www.pdb.org/pdb/home/home.do) with 3V4I code.

  11. ORF Alignment: NC_006905 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available bosomal subunit protein L13 ... [Escherichia coli O157:H7] pdb|1P86|H Chain H, Real ... Space ...Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|H Chain H, Real ... Space

  12. ORF Alignment: NC_001148 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tive Proteinase A In The Space Group P21 ... pdb|1FMX|A Chain A, Structure Of Native Proteinase A In ... The Space... Group P21 pdb|1FMU|A Chain A, Structure Of ... Native Proteinase A In P3221 Space

  13. ORF Alignment: NC_006511 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available bosomal subunit protein L13 ... [Escherichia coli O157:H7] pdb|1P86|H Chain H, Real ... Space ...Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|H Chain H, Real ... Space

  14. Stemcell Information: SKIP000961 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000961 ... Diseased PDB1lox-17Puro-5 PDB1lox-17Puro-5 ... パーキンソン病 G20 Parkinson... Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  15. Stemcell Information: SKIP000965 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000965 ... Diseased PDB1lox-17Puro-33 PDB1lox-17Puro-33 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

  16. Stemcell Information: SKIP000764 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available SKIP000764 ... Diseased PDB2lox-21 PDB2lox-21 ... パーキンソン病 G20 Parkinson disease 16...9371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of v

  17. How community has shaped the Protein Data Bank.

    Science.gov (United States)

    Berman, Helen M; Kleywegt, Gerard J; Nakamura, Haruki; Markley, John L

    2013-09-03

    Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. EST Table: AV404143 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available ructure Of The Tail Terminator Protein From Phage Lambda (Gpu-Wt) pdb|3FZB|B Chain B, Crystal Structure Of T...he Tail Terminator Protein From Phage Lambda (Gpu-Wt) pdb|3FZB|C Chain C, Crystal Structure Of The Tail Term...inator Protein From Phage Lambda (Gpu-Wt) pdb|3FZB|D Chain D, Crystal Structure O...f The Tail Terminator Protein From Phage Lambda (Gpu-Wt) pdb|3FZB|E Chain E, Crystal Structure Of The Tail T...erminator Protein From Phage Lambda (Gpu-Wt) pdb|3FZB|F Chain F, Crystal Structure Of The Tail Terminator Protein From Phage Lambda

  19. Late Pleistocene Vegetation, Climate and Relative Sea Level Changes in the Southeastern Brazilian Coast, Based on C and N Isotopes and Bio Indicator Analysis of Mangrove Organic Matter

    Energy Technology Data Exchange (ETDEWEB)

    Pessenda, L. C.R.; Vidotto, E.; Buso, Jr., A. A.; Assarini, Jr., J. P.; Bendassollia, J. A. [Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Sao Paulo (Brazil); De Oliveira, P. E. [University of Guarulhos (UNG), Guarulhos, Sao Paulo (Brazil); Macias, F. [' ' Luiz de Queiroz' ' College of Agriculture/USP, Piracicaba, Sao Paulo (Brazil); Ricardi-Branco, F. [University of Campinas - Geosciences Institute, Campinas, Sao Paulo (Brazil)

    2013-07-15

    On the southeastern Brazilian coast, mangrove organic matter records have been studied by C and N isotopes, pollen and diatom analysis to reconstruct 40 ka of vegetation and climatic history. The {delta}{sup 13}C and {delta}{sup 15}N presented more depleted values from 40 to 19 ka BP. The high C/N ratios and depleted isotopic values indicate the predominance of C3 land plants in the location presently occupied by the mangrove vegetation, and a lower sea level than today. The presence of pollen of Ilex, Weinmannia, Symplocos, Drimys and Podocarpus suggest a colder and more humid climate than present. From 19 to 2.2 ka BP a sedimentary hiatus is associated with a sea level rise. The presence of mangrove in its present position since at least 2.200 a BP and the return of the marine coastline are associated with the lowest C/N ratio, more enriched {delta}{sup 13}C and {delta}{sup 15}N values and the presence of marine diatoms. (author)

  20. Isotopic Characterization of Snow, Ice and Glacial Melt in the Western Himalayas, India

    Energy Technology Data Exchange (ETDEWEB)

    Rai, S. P.; Kumar, B.; Arora, M.; Singh, R. D. [National Institute of Hydrology, Roorkee, 247 667 (India)

    2013-07-15

    Precipitation and glacial melt samples were collected at the snout of the Gangotri Glacier, popularly known as Gaumukh, located in the western Himalayas, India. Snow and ice samples were collected from different sites of the Gangotri Glacier. The local meteoric water line (LMWL) developed for the ablation period (May to October) is {delta}{sup 2}H = 8.2 {delta}{sup 18}O + 17.1 (r{sup 2} = 0.99), which shows a slightly higher slope and intercept than GMWL. This may be due to local summer connective precipitation occurring under dry climatic conditions and mountainous region moisture recycling with the south-west monsoon. The meltwater line, {delta}{sup 2}H =9.4 {delta}{sup 18}O + 37.5 (r{sup 2}= 0.96), having a significantly higher slope and intercept than the GMWL and LMWL. The main reasons for the higher slope and intercept of meltwater line may be due to the recycling of local vapour with moisture derived from the Western disturbance moisture whose source is the Mediterranean sea. The high d-exess values of snow, ice and meltwater indicate that the source of moisture is the Western disturbances. (author)

  1. Natural Tracers and Isotope Techniques to Define Groundwater Recharge and Salinization in the Bou Areg Coastal Aquifer (North Morocco)

    Energy Technology Data Exchange (ETDEWEB)

    Re, V. [Department of Molecular Sciences and Nanosystems, University Ca' Foscari, Venice (Italy); Allais, E. [ISO4 s.n.c., Torino (Italy); El Hamouti, N. [Multidisciplinary Faculty of Nador, University of Oujda, Nador (Morocco); Bouchnan, R. [Laboratory of Physical Phenomena and Natural Risk Modelling, University of Tangier, Tangier (Morocco); Sacchi, E. [Department of Earth Sciences, University of Pavia, Pavia (Italy); Rizzo, F. [UNESCO International Hydrological Programme, Paris (France); Zuppi, G. M. [Department of Molecular Sciences and Nanosystems, University Ca' Foscari, Venice and Institute of Environmental Geology and Geoengineering, National Research Council, Monterotondo (Italy)

    2013-07-15

    The geochemical and isotopic ({delta}{sup 2}H, {delta}{sup 18}O, {delta}{sup 13}C, {delta}{sup 15}N{sub NO3},{delta} {sup 18}O{sub NO3}) characterization of the Bou Areg aquifer (North Morocco) based on samples collected during two surveys in November 2009 and June 2010 allowed the identification of run-off from the mountain regions and agricultural return flows as the main sources of aquifer recharge. The high salinization of the aquifer is not only due to the intensive agricultural activities but it is also associated with the natural quality of the catchment. The isotopic signal of dissolved nitrates allowed for the identification of two main sources of nitrogen in the system: (i) fertilizers and (ii) manure and septic effluents. The study, framed within the UNESCO-IHP sub component of the Strategic Partnership for the Mediterranean Large Marine Ecosystem, represents the first isotopic investigation of the area and will serve as a basis for the promotion of robust science based management practices in the region. (author)

  2. Toward a Mechanistic Understanding of Deuterium Excess as a Tracer for Evapotranspiration

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Chun-Ta [Department of Biology, San Diego State University, San Diego, CA (United States)

    2013-07-15

    An understanding of atmospheric water vapour and its isotopic composition is useful for modelling effects of terrestrial evapotranspiration on regional hydrologic cycles. Previous studies showed diurnal and vertical patterns of water vapour isotope ratios ({delta}{sup 2}H{sub v} and {delta}{sup 18}O{sub v}) consistently observed in an old growth coniferous forest. Using a box model and a mass balance approach to simulate 'isoflux of d-excess', the effect of evapotranspiration on the d-excess in atmospheric water vapour is quantitatively demonstrated. The results suggest that d-excess can be mechanistically utilized to identify processes that contribute to the diurnal variation in atmospheric moisture. These new findings have implications for larger-scale predictions of precipitation across the terrestrial landscape. In this paper, I report the initial results of the {delta}{sup 2}H{sub v} and {delta}{sup 18}O{sub v} measurements using a cavity enhanced spectroscopy instrument. These recent data are consistent with the pattern observed by the conventional sampling method, providing new opportunities for studying d-excess as a tracer for evapotranspiration. (author)

  3. Use of Isotopic Techniques for the Assessment of Hydrological Processes in Wetlands (Cienaga Colombia)

    Energy Technology Data Exchange (ETDEWEB)

    Betancur, T.; Santa, D.; Palacio, P.; Palacio, C.; Wills, B.; Hoyos, D. A. [Universidad de Antioquia, Medellin (Colombia)

    2013-07-15

    The Cienaga Colombia wetland is located in the Bajo Cauca Antioqueno region where the 'Man' river flows into the Cauca River. Hydrological processes on the Cienaga Colombia wetland are complex because of the interactive effects of both local and regional elements, associated with a typical tropical wet climatic regime. In this groundwater dependent wetland hydrological studies have been conducted, including hydrochemical analyses and isotope tracers, to describe and understand the interactions between groundwater and surface water, not only for the wetland itself but also for the entire catchment area. Rain samples (five year record) were used to obtain the LML: {delta}{sup 2}H = 8.03 {delta}{sup 18}O +9.9. The evaporation line is: {delta}{sup 2}H = 5.9 {delta}{sup 18}O - 7.3. According to the analyses, both groundwater and surface waters have the same isotopic signatures. Unsustainable land use practices along with current and predicted global environmental changes may cause negative impacts on the hydrological functioning of the region, affecting primarily, but not exclusively, evapotranspiration-recharge processes and the sustainability of the entire system. (author)

  4. Hydrogeochemical and Isotopic Characteristics of Tufa Precipitating Wates: A Case Study of the River Krka (Slovenia)

    Energy Technology Data Exchange (ETDEWEB)

    Zavadlav, S.; Lojen, S. [Jozef Stefan Institute, Department of Environmental Sciences, Ljubljana (Slovenia)

    2013-07-15

    The geochemical and stable isotope composition of tufa precipitating water in the River Krka in the Slovenian karst area were studied. Surface water chemistry in the River Krka is controlled by groundwater interactions with carbonate rocks, soil CO{sub 2} and meteoric water in the aquifer. Major element chemistry of water is controlled by dissolution of dolomite and calcite. The aquifer is the main source of cations, since concentrations of Mg{sup 2+}, Sr{sup 2+} and Ba{sup 2+} in water are highest at the spring. Ca{sup 2+} concentrations are slightly increasing due to the additional mixing of surface and groundwater downstream. Oxygen isotope composition of water indicates homogenization of meteoric water in the aquifer, while {delta}{sup 13}C values of dissolved inorganic carbon in water are affected by biological activity in the soil. {delta}{sup 18}O and {delta}{sup 13}C of bulk tufa show that deposition of tufa precipitates in the River Krka is kinetically controlled resulting in enrichment with heavier isotopes. Calculated equilibrium temperature of tufa precipitation based on the oxygen isotope composition of water and tufa fit with measured water temperature when average {delta}{sup 18}O values of water and tufa are considered. (author)

  5. Isotopic Composition and Age of Surface Water as Indicators of Groundwater Sustainability in a Semiarid Area: Case of the Souss Basin (Morocco)

    Energy Technology Data Exchange (ETDEWEB)

    Bouchaou, L.; Tagma, T.; Boutaleb, S.; Hsissou, Y. [LAGAGE Laboratory, Ibn Zohr University, Agadir (Morocco); Nathaniel, W.; Vengosh, A. [Duke University (United States); Michelot, J. L.; Massault, M. [UMR ' IDES' , CNRS - Universite Paris-Sud, Orsay (France); Elfaskaoui, M. [Hydraulic Agency of Souss-Massa-Draa Basins, Agadir (Morocco)

    2013-07-15

    This study aims to determine the surface water and groundwater interconnection in the Souss catchment of western Morocco by applying multiple isotopic tracers such as {delta}{sup 18}O, {delta}{sup 2}H, {sup 3}H, Ra, {sup 14}C, {sup 87}Sr/{sup 86}Sr and CFCs. Stable water isotope data indicate that the High Atlas Mountains, with their high rainfall and low {delta}{sup 18}O and {delta}{sup 2}H values, constitute the major source of recharge to the Souss-Massa aquifer. Carbon-{sup 14} activities (34-94 pMC) and {sup 3}H indicate a long residence time of groundwater in some areas. The high {sup 14}C activities measured in the Ifni spring located at 2158 m a.s.l. and the Tiar spring at 711 m a.s.l. indicate a modern contribution, which is consistent with recharge from the High Atlas tributaries. In the upstream mountainous section, the mass balance mixing model suggest that groundwater contribution to stream flow is about 72% during the wet season and 36% during the dry season. In the downstream plain, 80% of surface flow infiltrates to the aquifer. {sup 226}Ra and {sup 87}Sr/{sup 86}Sr variations were indistinguishable for surface waters and groundwater. (author)

  6. Detection of low momentum protons with the new HERMES recoil detector

    Energy Technology Data Exchange (ETDEWEB)

    Vilardi, Ignazio

    2008-10-15

    In this theis the recoil detector for the HERMES experiment at HERA is described. It consists of a silicon strip detector, a scintillating fiber tracker, and a photon detector for the {delta}{sup +} background rejection, all surrounded by a superconducting 1 Tesla solenoid. Results of cosmic ray tests are presented. (HSI)

  7. Palaeoceanographic controls on geochemical characteristics of organic-rich Exshaw mudrocks: role of enhanced primary production

    Energy Technology Data Exchange (ETDEWEB)

    Caplan, M.L.; Bustin, R.M. [University of British Columbia, Vancouver (Canada). Dept. of Earth and Ocean Sciences

    1999-07-01

    Organic-rich source rocks have generally been attributed to enhanced preservation of organic matter under anoxic bottom waters. Here geochemical analysis of kerogen and whole rock samples of organic-rich (lithofacies B{sub 1}) and organic-lean (lithofacies B{sub 2}) laminated mudrocks of the Devonian-Carboniferous Exshaw Formation, Alberta, highlight the importance of primary production in governing the quantity and quality of organic matter. Lower Si/Al, K/Al, Ti/Al and quartz/clay ratios in lithofacies B{sub 2}, similar maceral types and the laminated fabric of the two lithofacies indicate that the quality and quantity of organic matter are not related to grain size, redox or organic matter source changes. High Total Organic Carbon (TOC) and Hydrogen Index (HI), low Oxidation Index (Ox.I. ratio of oxygen functional groups to aliphatic groups derived by FTIR), lighter {delta}{sup 15}N{sub tot} and heavier {delta}{sup 13}C{sub org} isotopes indicate that kerogen of lithofacies B{sub 1} accumulated during periods of high organic-carbon production and delivery of relatively fresh, labile, well-preserved organic matter to the sea floor. In contrast, low TOC, HI, high Ox.I., heavier {delta}{sup 15}N{sub tot} and lighter {delta}{sup 13}C{sub org} isotopes indicate low primary productivity and delivery, high recycling and poor preservation of organic matter during accumulation of lithofacies B{sub 2}. (author)

  8. Determination of the K*(1800) spin parity

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, G W; Carnegie, R K; Cashmore, R J; Davier, M; Dunwoodie, W M; Lasinski, T A; Leith, D W.G.S.; Matthews, J A.J.; Walden, P; Williams, S H [Stanford Linear Accelerator Center, Calif. (USA)

    1976-02-16

    A spherical harmonic moment analysis of the reactions K/sup -/p..-->..K/sup -/..pi../sup +/n and K/sup +/p..-->..K/sup +/..pi../sup -/..delta../sup + +/ at 13 GeV/c demonstrates the existence of a broad K* state with mass in the vicinity of 1800 MeV and spin parity 3/sup -/.

  9. Natural and anthropogenic nitrogen uptake by bloom-forming macroalgae

    Energy Technology Data Exchange (ETDEWEB)

    Thornber, Carol S. [Department of Biological Sciences, 100 Flagg Road, University of Rhode Island, Kingston, RI 02881 (United States)], E-mail: thornber@uri.edu; DiMilla, Peter; Nixon, Scott W. [Graduate School of Oceanography, University of Rhode Island, South Ferry Road, Narragansett, RI 02881 (United States); McKinney, Richard A. [US Environmental Protection Agency, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882 (United States)

    2008-02-15

    The frequency and duration of macroalgal blooms have increased in many coastal waters over the past several decades. We used field surveys and laboratory culturing experiments to examine the nitrogen content and {delta}{sup 15}N values of Ulva and Gracilaria, two bloom-forming algal genera in Narragansett Bay, RI (USA). The northern end of this bay is densely populated with large sewage treatment plant nitrogen inputs; the southern end is more lightly populated and opens to the Atlantic Ocean. Field-collected Ulva varied in {delta}{sup 15}N among sites, but with two exceptions had {delta}{sup 15}N above 10 per mille , reflecting a significant component of heavy anthropogenic N. This variation was not correlated with a north-south gradient. Both Ulva and Gracilaria cultured in water from across Narragansett Bay also had high signals ({delta}{sup 15}N = {approx}14-17 per mille and 8-12 per mille , respectively). These results indicate that inputs of anthropogenic N can have far-reaching impacts throughout estuaries.

  10. Interference of aldehyde metabolizing enzyme with diamine oxidase/histaminase/activity as determined by /sup 14/C putrescine method

    Energy Technology Data Exchange (ETDEWEB)

    Fogel, W A [Polish Academy of Sciences, Cracow (Poland). Inst. of Pharmacology; Bieganski, T; Wozniak, J; Maslinski, C

    1978-01-01

    The ..delta../sup 1/ pyrroline formation, as an indicator of diamine oxidase activity according to Okuyama and Kobayashi /sup 14/C putrescine test (1961, Archs Biochem. Biophys., vol.95, 242), has been investigated in several tissue homogenates. When guinea pig liver homogenate was used as a source of enzyme in the presence of aldehyde dehydrogenase inhibitors chlorate hydrate and acetaldehyde the level of formation ..delta../sup 1/ pyrroline was strongly increased in a dose-dependent manner. Also inhibition of aldehyde reductase by phenobarbital enhanced ..delta../sup 1/ pyrroline formation, but to a lesser degree. In other tissues, with very high initial diamine oxidase activity (rat intestine, dog kidney) or with very low diamine oxidase activity (guinea pig skin, dog liver) the influence of these inhibitors was only slight. Pyrazole, an inhibitor of alcohol dehydrogenase exerted only a small effect on ..delta../sup 1/ pyrroline formation. All aldehyde-metabolizing enzymes inhibitors, except pyrazole, were without effect on purified pea seddling and hog kidney diamine oxidases. The use of aldehyde-metabolizing enzymes inhibitors may help to reveal the real values of diamine oxidase activity, when tissues homogenates are used as a source of enzyme.

  11. Boron/calcium ratios in Globigerinoides ruber from the Arabian Sea: Implications for controls on boron incorporation

    Digital Repository Service at National Institute of Oceanography (India)

    Naik, S.S.; Naidu, P.D.

    of Globigerinoides ruber from the Ocean Drilling Program (ODP) Site 723A (western Arabian Sea) and Core AAS9/21 (eastern Arabian Sea) from the last 22 kyr were analysed for B/Ca, delta>18O and Mg/Ca. B/Ca was compared to reconstructed salinity and sea...

  12. Mercury and flooding cycles in the Tapajos river basin, Brazilian Amazon: The role of periphyton of a floating macrophyte (Paspalum repens)

    Energy Technology Data Exchange (ETDEWEB)

    Coelho-Souza, Sergio A., E-mail: sacs@biof.ufrj.br [Lab. Tracadores Wolfgang C. Pfeiffer, SL 049, Instituto de Biofisica Carlos Chagas Filho/UFRJ, Bloco G, Centro de Ciencias e Saude, Ilha do Fundao, Rio de Janeiro, RJ, CEP 21949-902 (Brazil); Guimaraes, Jean R.D.; Miranda, Marcio R. [Lab. Tracadores Wolfgang C. Pfeiffer, SL 049, Instituto de Biofisica Carlos Chagas Filho/UFRJ, Bloco G, Centro de Ciencias e Saude, Ilha do Fundao, Rio de Janeiro, RJ, CEP 21949-902 (Brazil); Poirier, Hugo [Chaire de Reserche en Environment, Universite du Quebec a Montreal (UQaM), CP 8888, Montreal, H3C 3P8 (Canada); Mauro, Jane B.N. [Lab. Tracadores Wolfgang C. Pfeiffer, SL 049, Instituto de Biofisica Carlos Chagas Filho/UFRJ, Bloco G, Centro de Ciencias e Saude, Ilha do Fundao, Rio de Janeiro, RJ, CEP 21949-902 (Brazil); Lucotte, Marc [Chaire de Reserche en Environment, Universite du Quebec a Montreal (UQaM), CP 8888, Montreal, H3C 3P8 (Canada); Mergler, Donna [CINBIOSE, UQaM, CP 8888, succ. Centre-ville, Montreal, H3C 3P8 (Canada)

    2011-06-15

    Methylmercury (MeHg) increases mercury (Hg) toxicity and is biomagnified in the trophic chain contaminating riverine Amazon populations. Freshwater macrophyte roots are a main site of Hg methylation in different Brazilian environments. Paspalum repens periphyton was sampled in four floodplain lakes during the dry, rainy and wet seasons for measurement of total Hg (THg), MeHg, Hg methylation potentials, %C, %N, {delta}{sup 13}C, {delta}{sup 15}N and bacterial heterotrophic production as {sup 3}H-leucine incorporation rate. THg concentration varied from 67 to 198 ng/g and the potential of Me{sup 203}Hg formation was expressive (1-23%) showing that periphyton is an important matrix both in the accumulation of Hg and in MeHg production. The concentration of MeHg varied from 1 to 6 ng/g DW and was positively correlated with Me{sup 203}Hg formation. Though methylmercury formation is mainly a bacterial process, no significant correlation was observed between the methylation potentials and bacterial production. The multiple regressions analyses suggested a negative correlation between THg and %C and %N and between methylation potential and {delta}{sup 13}C. The discriminant analysis showed a significant difference in periphyton {delta}{sup 15}N, {delta}{sup 13}C and THg between seasons, where the rainy season presented higher {delta}{sup 15}N and the wet period lighter {delta}{sup 13}C, lower THg values and higher Me{sup 203}Hg formation. This exploratory study indicates that the flooding cycle could influence the periphyton composition, mercury accumulation and methylmercury production. - Research highlights: {yields} During rainy season mercury (Hg{sup 2+}) is carried out from terrestrial to aquatic systems by runoff. {yields} Macrophyte roots accumulates Hg{sup 2+} from suspended particulate matter (SPM). {yields} Hg methylation increases during the wet season. {yields} Flooded forest is a source of labile organic carbon and bioavailable Hg. {yields} Macrophytes

  13. SU-F-T-587: Quality Assurance of Stereotactic Radiosurgery (SRS) and Stereotactic Body Radiation Therapy (SBRT) for Patient Specific Plans: A Comparison Between MATRIXX and Delta4 QA Devices

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, YC; Lu, SH; Chen, LH; Kuo, SH; Wang, CW [National Taiwan University Hospital, Taipei City, Taiwan (China)

    2016-06-15

    Purpose: Patient-specific quality assurance (QA) is necessary to accurately deliver high dose radiation to the target, especially for stereotactic radiosurgery (SRS) and stereotactic body radiation therapy (SBRT). Unlike previous 2 dimensional (D) array QA devices, Delta{sup 4} can verify the dose delivery in 3D. In this study, the difference between calculated and measured dose distribution was compared with two QA devices (MATRIXX and Delta{sup 4}) to evaluate the delivery accuracy. Methods: Twenty-seven SRS/SBRT plans with VMAT were verified with point-dose and dose-map analysis. We use an ion chamber (A1SL, 0.053cc) for point-dose measurement. For verification of the dose map, the differences between the calculated and measured doses were analyzed with a gamma index using MATRIXX and Delta{sup 4} devices. The passing criteria for gamma evaluation were set at 3 mm for distance-to-agreement (DTA) and 3% for dose-difference. A gamma index less than 1 was defined as the verification passing the criteria and satisfying at least 95% of the points. Results: The mean prescribed dose and fraction was 40 ± 14.41 Gy (range: 16–60) and 10 ± 2.35 fractions (range: 1–8), respectively. In point dose analysis, the differences between the calculated and measured doses were all less than 5% (mean: 2.12 ± 1.13%; range: −0.55% to 4.45%). In dose-map analysis, the average passing rates were 99.38 ± 0.96% (range: 95.31–100%) and 100 ± 0.12% (range: 99.5%–100%) for MATRIXX and Delta{sup 4}, respectively. Even using criteria of 2%/2 mm, the passing rate of Delta{sup 4} was still more than 95% (mean: 99 ± 1.08%; range: 95.6%–100%). Conclusion: Both MATRIXX and Delta{sup 4} offer accurate and efficient verification for SRS/SBRT plans. The results measured by MATRIXX and Delta{sup 4} dosimetry systems are similar for SRS/SBRT performed with the VMAT technique.

  14. Organochlorine contaminant and stable isotope profiles in Arctic fox (Alopex lagopus) from the Alaskan and Canadian Arctic

    Energy Technology Data Exchange (ETDEWEB)

    Hoekstra, P.F.; Braune, B.M.; O' Hara, T.M.; Elkin, B.; Solomon, K.R.; Muir, D.C.G

    2003-04-01

    PCBs in Arctic fox are lower than reported in other Arctic populations and unlikely to cause significant impairment of reproductive success. - Arctic fox (Alopex lagopus) is a circumpolar species distributed across northern Canada and Alaska. Arctic fox muscle and liver were collected at Barrow, AK, USA (n=18), Holman, NT, Canada (n=20), and Arviat, NU, Canada (n=20) to elucidate the feeding ecology of this species and relate these findings to body residue patterns of organochlorine contaminants (OCs). Stable carbon ({delta}{sup 13}C) and nitrogen ({delta}{sup 15}N) isotope analyses of Arctic fox muscle indicated that trophic position (estimated by {delta}{sup 15}N) is positively correlated with increasing {delta}{sup 13}C values, suggesting that Arctic fox with a predominately marine-based foraging strategy occupy a higher trophic level than individuals mostly feeding from a terrestrial-based carbon source. At all sites, the rank order for OC groups in muscle was polychlorinated biphenyls ({sigma}PCB) > chlordane-related compounds ({sigma}CHLOR) > hexachlorocyclohexane ({sigma}HCH) > total toxaphene (TOX) {>=}chlorobenzenes ({sigma}ClBz) > DDT-related isomers ({sigma}DDT). In liver, {sigma}CHLOR was the most abundant OC group, followed by {sigma}PCB > TOX > {sigma}HCH > {sigma}ClBz > {sigma}DDT. The most abundant OC analytes detected from Arctic fox muscle and liver were oxychlordane, PCB-153, and PCB-180. The comparison of {delta}{sup 15}N with OC concentrations indicated that relative trophic position might not accurately predict OC bioaccumulation in Arctic fox. The bioaccumulation pattern of OCs in the Arctic fox is similar to the polar bear. While {sigma}PCB concentrations were highly variable, concentrations in the Arctic fox were generally below those associated with the toxicological endpoints for adverse effects on mammalian reproduction. Further research is required to properly elucidate the potential health impacts to this species from exposure to OCs.

  15. Stable isotope compositions of quartz pebbles and their fluid inclusions as tracers of sediment provenance: Implications for gold- and uranium-bearing quartz pebble conglomerates

    Energy Technology Data Exchange (ETDEWEB)

    Vennemann, T.W.; Kesler, S.E.; O' Neil, J.R. (Univ. of Michigan, Ann Arbor (United States))

    1992-09-01

    Oxygen isotope compositions of pebbles from late Archean to paleo-Proterozoic gold- and/or uranium-bearing oligomictic quartz pebble conglomerates of the Witwatersrand district, South Africa, and Huronian Supergroup, Canada, were determined in an attempt to define the nature of the source terrain. The [delta][sup 18]O values of quartz pebbles within any one sample typically vary by [approximately] 4[per thousand] or more, but occasionally by as much as 8[per thousand], even for adjacent pebbles within the same hand specimen. In addition, adjacent quartz pebbles of widely contrasting [delta][sup 18]O values also preserve distinct isotopic signatures of their fluid inclusions. This overall heterogeneity suggests that the pebbles did not undergo significant oxygen isotope exchange after incorporation in the conglomerates. Therefore, oxygen isotope analyses of such quartz pebbles, in combination with a detailed investigation of their mineral and fluid inclusions, can provide a useful method for characterizing pebble populations and hence dominant sediment source modes. Comparison of values found in this study with [delta][sup 18]O values of quartz from Archean granites, pegmatites, and mesothermal greenstone gold veins, i.e., [delta][sup 18]O values of sources commonly proposed for the conglomerate ores, suggests that uranium is derived from a granitic source, whereas gold has a mesothermal greenstone gold source. Low [delta][sup 18]O values of chert pebbles (9[per thousand] to 11.5[per thousand]) relative to those expected for Archean and Proterozoic marine cherts (commonly [ge] 17[per thousand]) effectively exclude marine cherts, and therefore, auriferous iron formations and exhalatives, as likely sources of gold.

  16. Stable Isotopes in Precipitation over Indonesia Maritime Continent

    Energy Technology Data Exchange (ETDEWEB)

    Ichiyanagi, K. [Graduate School of Science and Technology, Kumamoto University, and Japan Agency for Marine-Earth Science and Technology (JAMSTEC) (Japan); Suwarman, R. [Graduate School of Science and Technology, Kumamoto University (Japan); Yamanaka, M. D. [Japan Agency for Marine-Earth Science and Technology (JAMSTEC) (Japan)

    2013-07-15

    Daily variability of stable isotopes in precipitation was observed at 6 stations in the Indonesian Maritime Continent from 2000 to 2006. The annual mean {delta}{sup 18}O at Bukit Kototabang (GAW), Jambi, and Makassar are heavier than those for others. The precipitation amount effect was observed only at Denpasar and Makassar. There are 2 groups resulting from the local Meteoric Water line; (1) slope is nearly 7.0 and high d-excess more than 10 at GAW, Denpasar, and Manado, (2) slope is around 7.4 and low d-excess less than 7.5 per mille at Jambi, Makassar, and Palau. Seasonal variability of {delta}{sup 18}O and d-excess were classified into three patterns. There are no seasonal variations in {delta}{sup 18}O and d-excess at GAW and Jambi, but clear seasonal variations at Denpasar (DPS) and Makassar (MKS). Due to the amount effect, {delta}{sup 18}O in precipitation is high when the precipitation amount is low from May to october. In contrast, the amount effect is not significant and d-excess is constant throughout the year in Manado and Palau. The {delta}{sup 18}O in precipitation at 2 stations located in sumatra Island corresponded with the Madden-Jullian Oscillation index, while those for the other 4 stations in more easterly locations did not. This finding indicates that water vapour evaporated from the Indian Ocean can reach the Island of sumatra, but can't reach more easterly locations. (author)

  17. The Oxygen Isotopic Composition of Phosphate: A Tracer for Phosphate Sources and Cycling

    Energy Technology Data Exchange (ETDEWEB)

    Mclaughlin, K. [Southern California Coastal Water Research Project, Costa Mesa, University of California, CA (United States); Young, M. B.; Paytan, A.; Kendall, C. [U.S. Geological Survey, University of California, CA (United States)

    2013-05-15

    Phosphorus (P) is a limiting macro-nutrient for primary productivity and anthropogenic P-loading to aquatic ecosystems is one of the leading causes of eutrophication in many ecosystems throughout the world. Because P has only one stable isotope, traditional isotope techniques are not possible for tracing sources and cycling of P in aquatic systems. However, much of the P in nature is bonded to four oxygen (O) atoms as orthophosphate (PO{sub 4}{sup 3-}). The P-O bonds in orthophosphate are strongly resistant to inorganic hydrolysis and do not exchange oxygen with water without biological mediation (enzyme-mediated recycling). Thus, the oxygen isotopic composition of dissolved inorganic phosphate ({delta}{sup 18}O{sub p}) may be used as a tracer for phosphate sources and cycling in aquatic ecosystems. Recently, several studies have been conducted utilizing {delta}{sup 18}O{sub p} as a tracer for phosphate sources and cycling in various aquatic environments. Specifically, work to date indicates that {delta}{sup 18}O{sub p} is useful for determining sources of phosphate to aquatic systems if these sources have unique isotopic signatures and phosphate cycling within the system is limited compared to input fluxes. In addition, because various processes imprint specific fractionation effects, the {delta}{sup 18}O{sub p} tracer can be utilized to determine the degree of phosphorous cycling and processing through the biomass. This chapter reviews several of these studies and discusses the potential to utilize the {delta}{sup 18}O{sub p} of phosphate in rivers and streams. (author)

  18. Application of iron and zinc isotopes to track the sources and mechanisms of metal loading in a mountain watershed

    Energy Technology Data Exchange (ETDEWEB)

    Borrok, David M., E-mail: dborrok@utep.edu [Department of Geological Sciences, University of Texas, El Paso, TX 79968 (United States); Wanty, Richard B.; Ian Ridley, W.; Lamothe, Paul J. [US Geological Survey, Denver Federal Center, Denver, CO 80225 (United States); Kimball, Briant A. [US Geological Survey, 2329 W. Orton Cir., Salt Lake City, UT 84119 (United States); Verplanck, Philip L.; Runkel, Robert L. [US Geological Survey, Denver Federal Center, Denver, CO 80225 (United States)

    2009-07-15

    Here the hydrogeochemical constraints of a tracer dilution study are combined with Fe and Zn isotopic measurements to pinpoint metal loading sources and attenuation mechanisms in an alpine watershed impacted by acid mine drainage. In the tested mountain catchment, {delta}{sup 56}Fe and {delta}{sup 66}Zn isotopic signatures of filtered stream water samples varied by {approx}3.5 per mille and 0.4 per mille, respectively. The inherent differences in the aqueous geochemistry of Fe and Zn provided complimentary isotopic information. For example, variations in {delta}{sup 56}Fe were linked to redox and precipitation reactions occurring in the stream, while changes in {delta}{sup 66}Zn were indicative of conservative mixing of different Zn sources. Fen environments contributed distinctively light dissolved Fe (<-2.0 per mille) and isotopically heavy suspended Fe precipitates to the watershed, while Zn from the fen was isotopically heavy (>+0.4 per mille). Acidic drainage from mine wastes contributed heavier dissolved Fe ({approx}+0.5 per mille) and lighter Zn ({approx}+0.2 per mille) isotopes relative to the fen. Upwelling of Fe-rich groundwater near the mouth of the catchment was the major source of Fe ({delta}{sup 56}Fe {approx} 0 per mille) leaving the watershed in surface flow, while runoff from mining wastes was the major source of Zn. The results suggest that given a strong framework for interpretation, Fe and Zn isotopes are useful tools for identifying and tracking metal sources and attenuation mechanisms in mountain watersheds.

  19. Boron isotope ratios of surface waters in Guadeloupe, Lesser Antilles

    Energy Technology Data Exchange (ETDEWEB)

    Louvat, Pascale, E-mail: louvat@ipgp.fr [Geochimie et Cosmochimie, IPGP, Universite Paris Diderot, Sorbonne Paris Cite, UMR 7154 CNRS, 75005 Paris (France); Gaillardet, Jerome; Paris, Guillaume; Dessert, Celine [Geochimie et Cosmochimie, IPGP, Universite Paris Diderot, Sorbonne Paris Cite, UMR 7154 CNRS, 75005 Paris (France)

    2011-06-15

    Highlights: > Rivers outer of hydrothermal areas have d11B around 40 per mille and [B] of 10-31 {mu}g/L. > Thermal springs have d11B of 8-15 per mille and [B] between 250 and 1000 {mu}g/L. > With Na, SO{sub 4} and Cl, boron shows mixing of rain, low and high-T weathering inputs. > Guadeloupe rivers and thermal springs have d11B 20-40 per mille higher than the local rocks. > Solid-solution fractionation during weathering pathways may explain this gap of d11B. - Abstract: Large variations are reported in the B concentrations and isotopic ratios of river and thermal spring waters in Guadeloupe, Lesser Antilles. Rivers have {delta}{sup 11}B values around 40 per mille and B concentrations lower than 30 {mu}g/L, while thermal springs have {delta}{sup 11}B of 8-15 per mille and B concentrations of 250-1000 {mu}g/L. River samples strongly impacted by hydrothermal inputs have intermediate {delta}{sup 11}B and B contents. None of these surface water samples have {delta}{sup 11}B comparable to the local unweathered volcanic rocks (around 0 per mille), implying that a huge isotopic fractionation of 40 per mille takes place during rock weathering, which could be explained by preferential incorporation of {sup 10}B during secondary mineral formation and adsorption on clays, during rock weathering or in the soils. The soil-vegetation B cycle could also be a cause for such a fractionation. Atmospheric B with {delta}{sup 11}B of 45 per mille represents 25-95% of the river B content. The variety of the thermal spring chemical composition renders the understanding of B behavior in Guadeloupe hydrothermal system quite difficult. Complementary geochemical tracers would be helpful.

  20. Spatial distribution of bottlenose dolphins (Tursiops truncatus) inferred from stable isotopes and priority organic pollutants

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Rachel Marie, E-mail: ryounge@ocean.fsu.edu [Department of EOAS-Oceanography, Florida State University, 117 North Woodward Avenue, Tallahassee, Florida, 32306 (United States); Kucklick, John R. [National Institute of Standards and Technology, Hollings Marine Laboratory, Charleston, 331 Fort Johnson Road, Charleston, South Carolina 29412 (United States); Balmer, Brian C.; Wells, Randall S. [Chicago Zoological Society c/o Mote Marine Laboratory, 1600 Ken Thompson Parkway Sarasota, FL, 34236 (United States); Chanton, Jeffrey P. [Department of EOAS-Oceanography, Florida State University, 117 North Woodward Avenue, Tallahassee, Florida, 32306 (United States); Nowacek, Douglas P. [Nicholas School of the Environment and Pratt School of Engineering, Duke University - Marine Laboratory, 135 Duke Marine Lab Rd., Beaufort, NC 28516 (United States)

    2012-05-15

    Differences in priority organic pollutants (POPs), analyzed by gas chromatography-mass spectrometry, and stable isotope ratios ({delta}{sup 13}C, {delta}{sup 34}S, and {delta}{sup 15}N; analyzed by isotope ratio-mass spectrometry), divide 77 bottlenose dolphins (Tursiops truncatus) from the Florida Gulf Coast into three distinct groups. POP levels reflect human population and historical contamination along the coast. In the least disturbed site, concentrations of {Sigma}POP in male dolphins were 18,000 ng g{sup -1} {+-} 6000 (95% confidence interval here and throughout); in the intermediate bay, males had {Sigma}POP concentrations of 19,000 ng g{sup -1} {+-} 10,000. St Andrews Bay was home to dolphins with the highest {Sigma}POP concentrations: 44,000 ng g{sup -1} {+-} 10,300. {delta}{sup 34}S and {delta}{sup 15}N, differed significantly between St. George Sound dolphins and those frequenting each of the other two bays, but not between St. Andrews and St. Joseph Bays. {Sigma}POP concentrations were statistically higher in dolphins frequenting St. Andrews Bay, but were not significantly different between dolphins occupying St. Joseph Bay and St. George Sound. Thus, using either POP or isotope values alone, we would only be able to identify two dolphin groups, but when POP and isotope data are viewed cumulatively, the results clearly define three distinct communities occupying this region. - Highlights: Black-Right-Pointing-Pointer We compare isotopes and POP levels in dolphins occupying three embayments. Black-Right-Pointing-Pointer POP levels varied significantly among two embayments separated by < 50 km. Black-Right-Pointing-Pointer Differentiation correlated with historical contamination from a SuperFund site. Black-Right-Pointing-Pointer Cumulatively, isotopes and POP levels indicate 3 distinct dolphin communities. Black-Right-Pointing-Pointer This data provides the first assessment of dolphin POP contamination in the region.

  1. Response of C3 and C4 plants to middle-Holocene climatic variation near the prairie-forest ecotone of Minnesota, U.S.A.

    Energy Technology Data Exchange (ETDEWEB)

    Tian, J; Brown, T A; Hu, F S; Stefanova, I; Nelson, D M

    2003-12-24

    Paleorecords of the middle Holocene (MH) from the North American midcontinent can offer insights into ecological responses to pervasive drought that may accompany future climatic warming. We analyzed MH sediments from West Olaf Lake (WOL) and Steel Lake (SL) in Minnesota to examine the effects of warm/dry climatic conditions on prairie-woodland ecosystems. Mineral composition and carbonate {delta}{sup 18}O were used to determine climatic variations, whereas pollen assemblages, charcoal {delta}{sup 13}C, and charcoal accumulation rates were used to reconstruct vegetation composition, C{sub 3} and C{sub 4} plant abundance, and fire. The ratio of aragonite:calcite at WOL and {delta}{sup 18}O at SL suggest that pronounced droughts occurred during the MH but that drought severity decreased with time. From charcoal {delta}{sup 13}C data we estimated that the MH abundance of C{sub 4} plants averaged 50% at WOL and 43% at SL. At WOL C{sub 4} abundance was negatively correlated with aragonite:calcite, suggesting that severe moisture deficits suppressed C{sub 4} plants in favor of weedy C{sub 3} plants (e.g., Ambrosia). As climate ameliorated C{sub 4} abundance increased (from {approx}33 to 66%) at the expense of weedy species, enhancing fuel availability and fire occurrence. In contrast, farther east at SL climate was cooler and wetter than at WOL, and C{sub 4} abundance showed no correlation with {delta}{sup 18}O-inferred aridity. Woody C{sub 3} plants (e.g., Quercus) were more abundant, biomass flammability lower, and fires less important at SL than at WOL. Our results suggest that C{sub 4} plants are adapted to warm/dry climatic conditions, but not to extreme droughts, and that the fire regime is controlled by biomass-climate interactions.

  2. Timely deposition of macromolecular structures is necessary for peer review

    International Nuclear Information System (INIS)

    Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

    2013-01-01

    Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature

  3. Timely deposition of macromolecular structures is necessary for peer review

    Energy Technology Data Exchange (ETDEWEB)

    Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

    2013-12-01

    Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

  4. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

    Science.gov (United States)

    Joosten, Robbie P; Joosten, Krista; Cohen, Serge X; Vriend, Gert; Perrakis, Anastassis

    2011-12-15

    Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo. r.joosten@nki.nl; a.perrakis@nki.nl Supplementary data are available at Bioinformatics online.

  5. An approach to creating a more realistic working model from a protein data bank entry.

    Science.gov (United States)

    Brandon, Christopher J; Martin, Benjamin P; McGee, Kelly J; Stewart, James J P; Braun-Sand, Sonja B

    2015-01-01

    An accurate model of three-dimensional protein structure is important in a variety of fields such as structure-based drug design and mechanistic studies of enzymatic reactions. While the entries in the Protein Data Bank ( http://www.pdb.org ) provide valuable information about protein structures, a small fraction of the PDB structures were found to contain anomalies not reported in the PDB file. The semiempirical PM7 method in MOPAC2012 was used for identifying anomalously short hydrogen bonds, C-H⋯O/C-H⋯N interactions, non-bonding close contacts, and unrealistic covalent bond lengths in recently published Protein Data Bank files. It was also used to generate new structures with these faults removed. When the semiempirical models were compared to those of PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/), the clashscores, as defined by MolProbity ( http://molprobity.biochem.duke.edu/), were better in about 50% of the structures. The semiempirical models also had a lower root-mean-square-deviation value in nearly all cases than those from PDB_REDO, indicative of a better conservation of the tertiary structure. Finally, the semiempirical models were found to have lower clashscores than the initial PDB file in all but one case. Because this approach maintains as much of the original tertiary structure as possible while improving anomalous interactions, it should be useful to theoreticians, experimentalists, and crystallographers investigating the structure and function of proteins.

  6. Main: 1LR4 [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 1LR4 トウモロコシ Corn Zea mays L. Casein Kinase Ii, Alpha Chain Name=Ack2; Zea Mays Mole...cule: Protein Kinase Ck2; Chain: A; Synonym: Casein Kinase Ii, Alpha Chain; Engineered: Yes Transferase 2.7....ray; A=2-326.|PDB; 1M2Q; X-ray; A=2-328.|PDB; 1M2R; X-ray; A=2-328.|PDB; 1OM1; X-ray; A=1-332.|Mai

  7. The Protein Data Bank in Europe (PDBe): bringing structure to biology.

    Science.gov (United States)

    Velankar, Sameer; Kleywegt, Gerard J

    2011-04-01

    The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.

  8. Trendspotting in the Protein Data Bank.

    Science.gov (United States)

    Berman, Helen M; Coimbatore Narayanan, Buvaneswari; Di Costanzo, Luigi; Dutta, Shuchismita; Ghosh, Sutapa; Hudson, Brian P; Lawson, Catherine L; Peisach, Ezra; Prlić, Andreas; Rose, Peter W; Shao, Chenghua; Yang, Huanwang; Young, Jasmine; Zardecki, Christine

    2013-04-17

    The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  9. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available terium tuberculosis CDC1551] pdb|1W2H|B Chain B, ... Crystal Structure Of Mycobacterium Tuberculosis ...ate (Azt-Mp) (2.0 A Resolution) pdb|1W2H|A ... Chain A, Crystal Structure Of Mycobacterium Tuberculosis...lution) pdb|1W2G|B ... Chain B, Crystal Structure Of Mycobacterium Tuberculosis ... Thymidylat...G|A Chain A, Crystal Structure ... Of Mycobacterium Tuberculosis Thymidylate Kinase ... Comple...re Of ... Mycobacterium Tuberculosis Thymidylate Kinase ... Crystallized In Sodium Malonate, A

  10. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ulosis CDC1551] pdb|1N3I|C Chain C, ... Crystal Structure Of Mycobacterium Tuberculosis...Structure Of Mycobacterium Tuberculosis Pnp With ... Transition State Analog Dadme-Immh pdb|1N3I|A Ch...ain A, ... Crystal Structure Of Mycobacterium Tuberculosis Pnp With ... Transition State Analo...g Dadme-Immh pdb|1I80|C Chain C, ... Crystal Structure Of M. Tuberculosis ...in B, Crystal Structure Of M. Tuberculosis ... Pnp In Complex With Iminoribitol, 9-Deazahypoxanthine

  11. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_000962 gi|57116993 >1uslC 1 158 13 170 3e-65 ... pdb|2BET|E Chain E, Structure Of Mycobacterium Tuberculosi...-D- ... Erythronate. pdb|2BET|D Chain D, Structure Of ... Mycobacterium Tuberculosis Ribose-5-...ronate. ... pdb|2BET|C Chain C, Structure Of Mycobacterium ... Tuberculosis Ribose-5-Phosphate...B, Structure Of Mycobacterium ... Tuberculosis Ribose-5-Phosphate Isomeras...ure Of Mycobacterium ... Tuberculosis Ribose-5-Phosphate Isomerase, Rpib, ... Rv2465c, In Comp

  12. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002945 gi|31793646 >1uslC 1 158 13 170 3e-65 ... pdb|2BET|E Chain E, Structure Of Mycobacterium Tuberculosi...-D- ... Erythronate. pdb|2BET|D Chain D, Structure Of ... Mycobacterium Tuberculosis Ribose-5-...ronate. ... pdb|2BET|C Chain C, Structure Of Mycobacterium ... Tuberculosis Ribose-5-Phosphate...B, Structure Of Mycobacterium ... Tuberculosis Ribose-5-Phosphate Isomeras...ure Of Mycobacterium ... Tuberculosis Ribose-5-Phosphate Isomerase, Rpib, ... Rv2465c, In Comp

  13. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ulosis CDC1551] pdb|1N3I|C Chain C, ... Crystal Structure Of Mycobacterium Tuberculosis...Structure Of Mycobacterium Tuberculosis Pnp With ... Transition State Analog Dadme-Immh pdb|1N3I|A Ch...ain A, ... Crystal Structure Of Mycobacterium Tuberculosis Pnp With ... Transition State Analo...g Dadme-Immh pdb|1I80|C Chain C, ... Crystal Structure Of M. Tuberculosis ...in B, Crystal Structure Of M. Tuberculosis ... Pnp In Complex With Iminoribitol, 9-Deazahypoxanthine

  14. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available terium tuberculosis CDC1551] pdb|1W2H|B Chain B, ... Crystal Structure Of Mycobacterium Tuberculosis ...ate (Azt-Mp) (2.0 A Resolution) pdb|1W2H|A ... Chain A, Crystal Structure Of Mycobacterium Tuberculosis...lution) pdb|1W2G|B ... Chain B, Crystal Structure Of Mycobacterium Tuberculosis ... Thymidylat...G|A Chain A, Crystal Structure ... Of Mycobacterium Tuberculosis Thymidylate Kinase ... Comple...re Of ... Mycobacterium Tuberculosis Thymidylate Kinase ... Crystallized In Sodium Malonate, A

  15. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ulosis CDC1551] pdb|1N3I|C Chain C, ... Crystal Structure Of Mycobacterium Tuberculosis...Structure Of Mycobacterium Tuberculosis Pnp With ... Transition State Analog Dadme-Immh pdb|1N3I|A Ch...ain A, ... Crystal Structure Of Mycobacterium Tuberculosis Pnp With ... Transition State Analo...g Dadme-Immh pdb|1I80|C Chain C, ... Crystal Structure Of M. Tuberculosis ...in B, Crystal Structure Of M. Tuberculosis ... Pnp In Complex With Iminoribitol, 9-Deazahypoxanthine

  16. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available terium tuberculosis CDC1551] pdb|1W2H|B Chain B, ... Crystal Structure Of Mycobacterium Tuberculosis ...ate (Azt-Mp) (2.0 A Resolution) pdb|1W2H|A ... Chain A, Crystal Structure Of Mycobacterium Tuberculosis...lution) pdb|1W2G|B ... Chain B, Crystal Structure Of Mycobacterium Tuberculosis ... Thymidylat...G|A Chain A, Crystal Structure ... Of Mycobacterium Tuberculosis Thymidylate Kinase ... Comple...re Of ... Mycobacterium Tuberculosis Thymidylate Kinase ... Crystallized In Sodium Malonate, A

  17. ORF Alignment: NC_002754 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of Glcv, The ... Abc-Atpase Of The Glucose Abc Transporter From ... ... ... Sulfolobus Solfataricus pdb|1OXV|B Chain B, Crystal ... Structure Of Glcv, The Abc-Atpase Of Th...folobus Solfataricus ... pdb|1OXU|C Chain C, Crystal Structure Of Glcv, The ... Abc-Atpase Of ...tructure Of Glcv, The Abc-Atpase Of The Glucose Abc ... Transporter From S...ulfolobus Solfataricus pdb|1OXU|A ... Chain A, Crystal Structure Of Glcv, The Abc-Atpase Of ...

  18. ORF Alignment: NC_006348 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of Glcv, The ... Abc-Atpase Of The Glucose Abc Transporter From ... ... ... Sulfolobus Solfataricus pdb|1OXV|B Chain B, Crystal ... Structure Of Glcv, The Abc-Atpase Of Th...folobus Solfataricus ... pdb|1OXU|C Chain C, Crystal Structure Of Glcv, The ... Abc-Atpase Of ...tructure Of Glcv, The Abc-Atpase Of The Glucose Abc ... Transporter From S...ulfolobus Solfataricus pdb|1OXU|A ... Chain A, Crystal Structure Of Glcv, The Abc-Atpase Of ...

  19. ORF Alignment: NC_006350 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of Glcv, The ... Abc-Atpase Of The Glucose Abc Transporter From ... ... ... Sulfolobus Solfataricus pdb|1OXV|B Chain B, Crystal ... Structure Of Glcv, The Abc-Atpase Of Th...folobus Solfataricus ... pdb|1OXU|C Chain C, Crystal Structure Of Glcv, The ... Abc-Atpase Of ...tructure Of Glcv, The Abc-Atpase Of The Glucose Abc ... Transporter From S...ulfolobus Solfataricus pdb|1OXU|A ... Chain A, Crystal Structure Of Glcv, The Abc-Atpase Of ...

  20. Development of a molecular test of Paget's disease of bone.

    Science.gov (United States)

    Guay-Bélanger, Sabrina; Simonyan, David; Bureau, Alexandre; Gagnon, Edith; Albert, Caroline; Morissette, Jean; Siris, Ethel S; Orcel, Philippe; Brown, Jacques P; Michou, Laëtitia

    2016-03-01

    Depending on populations, 15 to 40% of patients have a familial form of Paget's disease of bone (PDB), which is transmitted in an autosomal-dominant mode of inheritance with incomplete penetrance. To date, only SQSTM1 gene mutations have been linked to the disease. Several single nucleotide polymorphisms (SNPs) have been associated with PDB in patient non-carriers of SQSTM1 mutations, but they have minor size effects. The current clinical practice guidelines still recommend to measure total serum alkaline phosphatase (sALP) for PDB screening. However, genetic or bone biomarkers alone may lack sensitivity to detect PDB. Thus, the objective of this study was to develop a molecular test of PDB, combining genetic and bone biomarkers, in order to detect PDB, which is frequently asymptomatic. We genotyped 35 SNPs previously associated with PDB in 305 patients, and 292 healthy controls. In addition, serum levels of 14 bone biomarkers were assayed in 51 patients and 151 healthy controls. Bivariate and multivariate logistic regression models with adjustment for age and sex were fitted to search for a combination of SNPs and/or bone biomarkers that could best detect PDB in patient non-carriers of SQSTM1 mutations. First, a combination of five genetic markers gave rise to the highest area under the ROC curve (AUC) with 95% confidence interval [95% CI] of 0.731 [0.688; 0.773], which allowed us to detect 81.5% of patients with PDB. Second, a combination of two bone biomarkers had an AUC of 0.822 [0.726; 0.918], and was present in 81.5% of patients with PDB. Then, the combination of the five genetic markers and the two bone biomarkers increased the AUC up to 0.892 [0.833; 0.951], and detected 88.5% of patients with PDB. These results suggested that an algorithm integrating first a screen for SQSTM1 gene mutations, followed by either a genetic markers combination or a combined genetic and biochemical markers test in patients non-carrier of any SQSTM1 mutation, may detect the PDB

  1. ORF Alignment: NC_000918 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available n A, Crystal Structure Of Aquifex Aeolicus ... N-Utilization Substance G (Nusg), Space Group I222 ... ... ... pdb|1M1G|D Chain D, Crystal Structure Of Aquifex ... Aeolicus N-Uti...lization Substance G (Nusg), Space Group ... P2(1) pdb|1M1G|C Chain C, Crystal Structure Of Aquifex ... Aeolicus N-Uti...al Structure Of Aquifex ... Aeolicus N-Utilization Substance G (Nusg), Space Group ... P2(1) p...db|1M1G|A Chain A, Crystal Structure Of Aquifex ... Aeolicus N-Utilization

  2. Flow of river water into a Karstic limestone aquifer. 1. Tracing the young fraction in groundwater mixtures in the Upper Floridan Aquifer near Valdosta, Georgia

    Energy Technology Data Exchange (ETDEWEB)

    Plummer, L.N.; Busenberg, E. [U.S. Geological Survey, 432 National Center, Reston, VA (United States); McConnell, J.B. [U.S. Geological Survey, 3039 Amwiler Rd., Atlanta, GA (United States); Drenkard, S.; Schlosser, P. [Lamont-Doherty Earth Observatory of Columbia University, 61 Route 9W, Palisades, NY (United States); Michel, R.L. [U.S. Geological Survey, Mail Stop 434, 345 Middlefield Road, Menlo Park, CA (United States)

    1998-11-01

    he quality of water in the Upper Floridan aquifer near Valdosta, Georgia is affected locally by discharge of Withlacoochee River water through sinkholes in the river bed. Data on transient tracers and other dissolved substances, including Cl{sup -}, {sup 3}H, tritiogenic helium-3 ({sup 3}He), chlorofluorocarbons (CFC-11, CFC-12, CFC-113), organic C (DOC), O{sub 2} (DO), H{sub 2}S, CH{sub 4}, {delta}{sup 18}O, {delta}D, and {sup 14}C were investigated as tracers of Withlacoochee River water in the Upper Floridan aquifer. The concentrations of all tracers were affected by dilution and mixing. Dissolved Cl{sup -}, {delta}{sup 18}O, {delta}D, CFC-12, and the quantity ({sup 3}H+{sup 3}He) are stable in water from the Upper Floridan aquifer, whereas DOC, DO, H{sub 2}S, CH{sub 4}, {sup 14}C, CFC-11, and CFC-113 are affected by microbial degradation and other geochemical processes occurring within the aquifer. Groundwater mixing fractions were determined by using dissolved Cl{sup -} and {delta}{sup 18}O data, recognizing 3 end-member water types in the groundwater mixtures: (1) Withlacoochee River water ({delta}{sup 18}O=-2.5{+-}0.3per thousand, Cl{sup -}=12.2{+-}2 mg/l), (2) regional infiltration water ({delta}{sup 18}O=-4.2{+-}0.1per thousand, Cl{sup -}=2.3{+-}0.1 mg/l), and (3) regional paleowater resident in the Upper Floridan aquifer ({delta}{sup 18}O=-3.4{+-}0.1per thousand, Cl{sup -}=2.6{+-}0.1 mg/l) (uncertainties are {+-}1{sigma}). Error simulation procedures were used to define uncertainties in mixing fractions. Fractions of river water in groundwater range from 0 to 72% and average 10%. The influence of river-water discharge on the quality of water in the Upper Floridan aquifer was traced from the sinkhole area on the Withlacoochee River 25 km SE in the direction of regional groundwater flow. Infiltration of water is most significant to theN and NW of Valdosta, but becomes negligible to the S and SE in the direction of general thickening of post-Eocene confining

  3. Tissue N content and {sup 15}N natural abundance in epilithic mosses for indicating atmospheric N deposition in the Guiyang area, SW China

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xueyan [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002 (China); Graduate University of the Chinese Academy of Sciences, Beijing 100049 (China)], E-mail: liuxueyan@vip.skleg.cn; Xiao Huayun [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002 (China)], E-mail: xiaohuayun@vip.skleg.cn; Liu Congqiang [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002 (China); Li Youyi; Xiao Hongwei [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002 (China); Graduate University of the Chinese Academy of Sciences, Beijing 100049 (China)

    2008-09-15

    Tissue N contents and {delta}{sup 15}N signatures in 175 epilithic mosses were investigated from urban to rural sites in Guiyang (SW China) to determine atmospheric N deposition. Moss N contents (0.85-2.97%) showed a significant decrease from the urban area (mean = 2.24 {+-} 0.32%, 0-5 km) to the rural area (mean = 1.27 {+-} 0.13%, 20-25 km), indicating that the level of N deposition decreased away from the urban environment, while slightly higher N contents re-occurred at sites beyond 30 km, suggesting higher N deposition in more remote rural areas. Moss {delta}{sup 15}N ranged from -12.50 per mille to -1.39 per mille and showed a clear bimodal distribution (-12 per mille to -6 per mille and -5 per mille to -2 per mille ), suggesting that there are two main sources for N deposition in the Guiyang area. More negative {delta}{sup 15}N (mean = -8.87 {+-} 1.65 per mille ) of urban mosses mainly indicated NH{sub 3} released from excretory wastes and sewage, while the less negative {delta}{sup 15}N (from -3.83 {+-} 0.82 per mille to -2.48 {+-} 0.95 per mille ) of rural mosses were mainly influenced by agricultural NH{sub 3}. With more negative values in the urban area than in the rural area, the pattern of moss {delta}{sup 15}N variation in Guiyang was found to be opposite to cities where N deposition is dominated by NO{sub x}-N. Therefore, NH{sub x}-N is the dominant N form deposited in the Guiyang area, which is supported by higher NH{sub x}-N than NO{sub x}-N in local atmospheric deposition. From the data showing that moss is responding to NH{sub x}-N/NO{sub x}-N in deposition it can be further demonstrated that the variation of moss {delta}{sup 15}N from the Guiyang urban to rural area was more likely controlled by the ratio of urban-NH{sub x}/agriculture-NH{sub x} than the ratio of NH{sub x}-N/NO{sub x}-N. The results of this study have extended knowledge of atmospheric N sources in city areas, showing that urban sewage discharge could be important in cities co

  4. Chemistry of fluids from a natural analogue for a geological CO{sub 2} storage site (Montmiral, France): Lessons for CO{sub 2}-water-rock interaction assessment and monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Pauwels, Helene [BRGM - Water Division, 3, av Claude Guillemin, 45060 Orleans Cedex (France)], E-mail: h.pauwels@brgm.fr; Gaus, Irina; Le Nindre, Yves Michel [BRGM - Water Division, 3, av Claude Guillemin, 45060 Orleans Cedex (France); Pearce, Jonathan [British Geological Survey, Kingsley Dunham Centre, Keyworth, Nottingham NG125GG (United Kingdom); Czernichowski-Lauriol, Isabelle [BRGM - Water Division, 3, av Claude Guillemin, 45060 Orleans Cedex (France)

    2007-12-15

    Chemical and isotope studies of natural CO{sub 2} accumulations aid in assessing the chemical effects of CO{sub 2} on rock and thus provide a potential for understanding the long-term geochemical processes involved in CO{sub 2} geological storage. Several natural CO{sub 2} accumulations were discovered during gas and oil exploration in France's carbogaseous peri-Alpine province (south-eastern France) in the 1960s. One of these, the Montmiral accumulation at a depth of more than 2400 m, is currently being exploited. The chemical composition of the water collected at the wellhead has changed in time and the final salinity exceeds 75 g/L. These changes in time can be explained by assuming that the fraction of the reservoir brine in the recovered brine-CO{sub 2}-H{sub 2}O mixture varies, resulting in variable proportions of H{sub 2}O and brine in the sampled water. The proportions can be estimated in selected samples due to the availability of gas and water flowrate data. These data enabled the reconstruction of the chemical and isotope composition of the brine. The proportions of H{sub 2}O and brine can also be estimated from isotope ({delta}{sup 2}H, {delta}{sup 18}O) composition of collected water and {delta}{sup 18}O of the sulfates or CO{sub 2}. The reconstituted brine has a salinity of more than 85 g/L and, according to its Br{sup -} content and isotope ({delta}{sup 2}H, {delta}{sup 18}O, {delta}{sup 34}S) composition, originates from an evaporated Triassic seawater that underwent dilution by meteoric water. The reconstitution of the brine's chemical composition enabled an evaluation of the CO{sub 2}-water-rock interactions based on: (1) mineral saturation indices; and (2) comparison with initial evaporated Triassic seawater. Dissolution of K- and SO{sub 4}-containing minerals such as K-feldspar and anhydrite, and precipitation of Ca and Mg containing minerals that are able to trap CO{sub 2} (carbonates) are highlighted. The changes in concentration of

  5. Data of evolutionary structure change: 1BUCB-3MDEA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1BUCB-3MDEA 1BUC 3MDE B A -MDFNLTDIQQDFLKLAHDFGEKKLAPTVTERDHKGIYD...ENVLTGEGAGFKIAMGTFDKTRPPVAAGAVGLAQRALDEATKYALERKTFGKLLAEHQGISFLLADMAMKVELARLSYQRAAWEIDSGRRNTYYASIAKAYAADIANQ...pdbID> A 3MDEA RSDPDP...in> 3MDE A 3MDEA IEANT-LGQVPA 3MDEA AEKKG-DEYII

  6. Data of evolutionary structure change: 3MDEA-3EOMA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 3MDEA-3EOMA 3MDE 3EOM A A ---------GFSFELTEQQKEFQATARKFAREEIIPVAA...KTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQIGRKEI-NMGQRCSDTRGIVFEDVRVPKENVLTGEGAGFKIAMGTFDKTRPPVAAGAVGLAQRALDEA...EPD----PGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED----GRDEIRGFILEKGCKGLSAP-AIHGKVGLRASITGEIVLDEA.../pdbChain> 3MDEA IEANT-LGQVP

  7. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available W Chain W, Real ... Space Refined Coordinates Of The 50s Subunit Fitted ... Into The Low Resolut... ... pdb|1P85|W Chain W, Real Space Refined Coordinates Of ... The 50s Subunit Fitted Into The Low

  8. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available W Chain W, Real ... Space Refined Coordinates Of The 50s Subunit Fitted ... Into The Low Resolut... ... pdb|1P85|W Chain W, Real Space Refined Coordinates Of ... The 50s Subunit Fitted Into The Low

  9. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available W Chain W, Real ... Space Refined Coordinates Of The 50s Subunit Fitted ... Into The Low Resolut... ... pdb|1P85|W Chain W, Real Space Refined Coordinates Of ... The 50s Subunit Fitted Into The Low

  10. ORF Alignment: NC_005835 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available [Thermus thermophilus HB8] pdb|1FP9|A Chain A, Structure ... Of Amylomaltase From Thermus Thermophilus Hb8 In Space... ... Amylomaltase From Thermus Thermophilus Hb8 In Space ... Group P21212 ... Length = 500 ... Query

  11. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available W Chain W, Real ... Space Refined Coordinates Of The 50s Subunit Fitted ... Into The Low Resolut... ... pdb|1P85|W Chain W, Real Space Refined Coordinates Of ... The 50s Subunit Fitted Into The Low

  12. Validation of Structures in the Protein Data Bank.

    Science.gov (United States)

    Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M S; Gutmanas, Aleksandras; Westbrook, John D; Yang, Huanwang; Feng, Zukang; Baskaran, Kumaran; Berrisford, John M; Hudson, Brian P; Ikegawa, Yasuyo; Kobayashi, Naohiro; Lawson, Catherine L; Mading, Steve; Mak, Lora; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Peisach, Ezra; Sahni, Gaurav; Sekharan, Monica R; Sen, Sanchayita; Shao, Chenghua; Smart, Oliver S; Ulrich, Eldon L; Yamashita, Reiko; Quesada, Martha; Young, Jasmine Y; Nakamura, Haruki; Markley, John L; Berman, Helen M; Burley, Stephen K; Velankar, Sameer; Kleywegt, Gerard J

    2017-12-05

    The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Archaeological skeletons support a northwest European origin for Paget's disease of bone.

    Science.gov (United States)

    Mays, Simon

    2010-08-01

    The strong genetic component in the etiology of Paget's disease of bone (PDB), together with marked geographic variation in its prevalence, with high frequencies in British populations, has led some to suggest that the disease originated in Britain and spread around the world in recent times by the migration and admixture of British populations. This study aims to investigate this hypothesis by studying the world geographic distribution of PDB cases identified in ancient skeletons excavated from archaeological sites. The methodology is a review of PDB cases described in the literature. There were 109 cases that met modern diagnostic criteria. All came from Western Europe, 94% from England. These data support the hypothesis that PDB originated in this geographic region.

  14. The RCSB Protein Data Bank: redesigned web site and web services.

    Science.gov (United States)

    Rose, Peter W; Beran, Bojan; Bi, Chunxiao; Bluhm, Wolfgang F; Dimitropoulos, Dimitris; Goodsell, David S; Prlic, Andreas; Quesada, Martha; Quinn, Gregory B; Westbrook, John D; Young, Jasmine; Yukich, Benjamin; Zardecki, Christine; Berman, Helen M; Bourne, Philip E

    2011-01-01

    The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.

  15. Remediation of the protein data bank archive

    Science.gov (United States)

    Henrick, Kim; Feng, Zukang; Bluhm, Wolfgang F.; Dimitropoulos, Dimitris; Doreleijers, Jurgen F.; Dutta, Shuchismita; Flippen-Anderson, Judith L.; Ionides, John; Kamada, Chisa; Krissinel, Eugene; Lawson, Catherine L.; Markley, John L.; Nakamura, Haruki; Newman, Richard; Shimizu, Yukiko; Swaminathan, Jawahar; Velankar, Sameer; Ory, Jeramia; Ulrich, Eldon L.; Vranken, Wim; Westbrook, John; Yamashita, Reiko; Yang, Huanwang; Young, Jasmine; Yousufuddin, Muhammed; Berman, Helen M.

    2008-01-01

    The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented. PMID:18073189

  16. Bioinformatic analysis of dihydrofolate reductase predicted in the ...

    African Journals Online (AJOL)

    olayemitoyin

    TASSER was used to predict the 3-D model structure of the protein and potential active binding site residues. ..... co-ordinate file model in PDB format was visualized with Jmol molecular .... evolutionary preservation of the protein dynamics to.

  17. The Protein Data Bank in Europe (PDBe): bringing structure to biology

    International Nuclear Information System (INIS)

    Velankar, Sameer; Kleywegt, Gerard J.

    2011-01-01

    Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described. The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described

  18. Cloning of nis gene and Nisin purification from Lactococcus lactis ...

    African Journals Online (AJOL)

    user

    2014-12-31

    Dec 31, 2014 ... dimension structure of the purified Nisin was studied by CPHModels as pdb with chimera program. Key words: ..... tionists the classification of microorganisms, and makes ... towards lipid membrane (Breukink and Kruijff, 1999;.

  19. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Structure Of Mycobacterium Tuberculosis Pyridoxine ... 5'-Phosphate Oxidase At 1.8 A Resolution p...db|1XXO|A ... Chain A, X-Ray Crystal Structure Of Mycobacterium ... Tuberculosis Pyridoxine 5'

  20. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Structure Of Mycobacterium Tuberculosis Pyridoxine ... 5'-Phosphate Oxidase At 1.8 A Resolution p...db|1XXO|A ... Chain A, X-Ray Crystal Structure Of Mycobacterium ... Tuberculosis Pyridoxine 5'

  1. The Protein Data Bank in Europe (PDBe): bringing structure to biology

    Energy Technology Data Exchange (ETDEWEB)

    Velankar, Sameer; Kleywegt, Gerard J., E-mail: gerard@ebi.ac.uk [Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom)

    2011-04-01

    Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described. The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.

  2. ORF Alignment: NC_006814 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available chemistry Of Atp-Driven Dimerization And Dna ... Stimulated Activation Of Smc Atpases. pdb|1XEW|X Cha...in ... X, Structural Biochemistry Of Atp-Driven Dimerization ... And Dna Stimulated Activation Of Smc Atpase

  3. ORF Alignment: NC_003413 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ure Analysis Of Pyrococcus Furiosus Cell ... Division Atpase Mind pdb|1G3Q|A Chain A, Crystal ... ... ... Structure Analysis Of Pyrococcus Furiosus Cell Division ... Atpase Mind ... Length = 231 ...

  4. Data of evolutionary structure change: 1ONAD-2D3RB [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1ONAD-2D3RB 1ONA 2D3R D B ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAK...WNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKT------NALHFMFNQFSKDQKDLILQGDAT...pdbID>1ONA D 1ONAD TRVSSNGSPQG

  5. ORF Alignment: NC_005835 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ine pdb|1FJG|S Chain S, Structure ... Of The Thermus Thermophilus 30s Ribosomal Subunit In ... Complex With The Antibioti...cs Streptomycin, ... Spectinomycin, And Paromomycin ... Length = 84 ... Q

  6. Data of evolutionary structure change: 1EP8B-1FAAA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1EP8B-1FAAA 1EP8 1FAA B A -------------GGSVIVIDSKAAWDAQLAKGKEEHKP...IVVAFTATWCGPCKMIAPLFETLSNDYAGKVIFLKVDVD-AVAAVAEAAGITAMPTFHVYKDGVKADDLVGASQDKLKALVAKHAAA LELALGT.../pdbChain> 1FAAA KLDCNQENKTL EEE HHH 1 1FAA A 1FAAA

  7. 77 FR 21616 - Agency Information Collection Activities: Proposed Request and Comment Request

    Science.gov (United States)

    2012-04-10

    ... disability payments. SSA considers the claimants the primary sources of verification; therefore, if claimants... or private self-insured companies administering WC/PDB benefits to disability claimants. Type of...

  8. Chemical annotation of small and peptide-like molecules at the Protein Data Bank

    Science.gov (United States)

    Young, Jasmine Y.; Feng, Zukang; Dimitropoulos, Dimitris; Sala, Raul; Westbrook, John; Zhuravleva, Marina; Shao, Chenghua; Quesada, Martha; Peisach, Ezra; Berman, Helen M.

    2013-01-01

    Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org PMID:24291661

  9. Effect of temperature on DNA double helix: An insight from ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... We have carried out detailed MD simulations of DNA double ..... Wireframe representation of B-DNA crystal structures with PDB identifier (a) 1EHV, ..... nucleic acid structures, PhD thesis, University of Calcutta, Kolkata.

  10. ORF Alignment: NC_006461 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ine pdb|1FJG|S Chain S, Structure ... Of The Thermus Thermophilus 30s Ribosomal Subunit In ... Complex With The Antibioti...cs Streptomycin, ... Spectinomycin, And Paromomycin ... Length = 84 ... Q

  11. Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect

    NARCIS (Netherlands)

    Helliwell, John R.; Tanley, Simon W. M.; Schreurs, Antoine M. M.; Kroon - Batenburg, Louise

    2016-01-01

    Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses.

  12. Detection and quantification of probiotic bacteria using optimized ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-03-08

    Mar 8, 2010 ... mgml-1 and incubated in water bath (Reciprocal Water. Bakar et al. 1483 .... RefSeq Nucleotides + EMBL + DDBJ + PDB sequences are included and the database of ...... Y, Setoyama H (2000). Structure of the intestinal flora.

  13. In silico characterization of antifreeze proteins using computational ...

    Indian Academy of Sciences (India)

    WINTEC

    structure. SOSUI server predicts one transmembrane region in winter flounder fish and atlantic cod and ..... result in a better interaction with water. The secon- ... structure of antifreeze protein P05140 (using PDB template 2AFP_A). The 10 ...

  14. Standardization of DNA extraction from invasive alien weed ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    due to its great structural and physio-chemical flexibility, vegetative multiplication ... water. Germinated seed (five days old seedlings) were transferred to Soilrite™ (Keltech ..... Protocols 2009(3):pdb-prot 5177. Doyle JJ, Doyle JL (1990) ...

  15. Molecular cloning, expression and computational analysis of a water ...

    African Journals Online (AJOL)

    User

    2012-11-06

    Nov 6, 2012 ... analysis of a water stress inducible copper-containing ... Although, in slico analysis of the protein have indicated its probable structure and functions, further ..... based on protein data bank (PDB) template c1ksiA which.

  16. Sub classification and targeted characterization of prophage ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... structure-function characterization of proteins encoded by cryptic prophages will help understand the contribution of prophage .... distilled water, collected by centrifugation and suspended in. 1 ml of .... Pdb homolog. Acc no.

  17. Determination of low-energy structures of a small RNA hairpin using ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... such as water clusters, Argon clusters and different biomo- lecules. ... Keywords. Energy landscape; Monte Carlo; optimization; RNA; tertiary structure .... tui large ribosomal subunit (Residues 310–321, PDB ID: 1JJ2).

  18. Pharmacologically significant tetraaza macrocyclic metal complexes ...

    Indian Academy of Sciences (India)

    MOHAMMAD SHAKIR

    2017-11-22

    Nov 22, 2017 ... structural biological models.6 Hence, biological prop- erties of ... poor water solubility, exhibits intrinsic resistance and ..... pdb). The metal complex files were drawn using. ChemDraw (MM2) and their energies were minimized.

  19. Novel hydroquinone derivatives alleviate algesia, inflammation and ...

    African Journals Online (AJOL)

    derivatives were synthesized and their structures were confirmed by .... to water. The baseline rectal temperature of all mice was noted by inserting a lubricated digital thermometer ... (PDB) and the binding site residues of the receptors were ...

  20. Characterization of V71M mutation in the aquaporin-2 gene causing ...

    Indian Academy of Sciences (India)

    Introduction. The aquaporin-2 (AQP2) water channel plays an important ... X-ray structure of lens aquaporin-0 open form (Lens Mip) as template (pdb. Keywords. AQP2 gene; nephrogenic diabetes insipidus; mutation; structural modelling.

  1. Effect of different concentrations of red palm olein on antioxidant ...

    African Journals Online (AJOL)

    Administrator

    2011-05-30

    May 30, 2011 ... hydrogen peroxide to water and oxygen per second. (David, 2004). Hydrogen .... David S (2004) PDB Molecules of the Quarter: DNA ligase, capases, & catalase. ... Structures of two superoxide dismutases from Bacillus ...

  2. The potential of Aspergillus fumigatus and Aspergillus niger in ...

    African Journals Online (AJOL)

    SARAH

    2015-10-31

    Oct 31, 2015 ... for the remediation of heavy metals in polluted water bodies. Comparatively A. .... Media amendment: Potato Dextrose Broth (PDB) was amended with filtrate of ... the structure of fungal membrane molecules by forming.

  3. Quaternary association in β-prism I fold plant lectins: Insights from X ...

    Indian Academy of Sciences (India)

    The importance of quaternary association in the structure and function of proteins .... a locally maintained PDB-FTP anonymous server at the. Bioinformatics ... TIP4P water model using the program genbox available in the GROMACS suite.

  4. n-Alkanes in surficial sediments of Visakhapatnam harbour, east ...

    Indian Academy of Sciences (India)

    Visakhapatnam harbour, a semi-enclosed water body is one of the .... PDB − 1. } × 1000. 2.5 Extraction of lipids. Total lipids (TL) were extracted from lyophilized sediments following ..... 2010 Sources of OM and microbial community structure.

  5. Biological and technological effects of some mulberry varieties and ...

    African Journals Online (AJOL)

    egyptian hak

    Agricultural Structures and Environmental Control Division, Central Institute ... beaker with a known quantity of sterilized distilled water and shaken for 45 min in an orbital ... flasks containing potato dextrose broth (PDB) and incubated at 28 ± 2.

  6. Temperature Dependence of the Stability of Ion Pair Interactions ...

    Indian Academy of Sciences (India)

    The occurrence of bridging water molecules between the ions ensures that the ions are not ... The structural features that render this thermostability ..... dehydrogenase single site mutant T198I from Thermus thermophilus with PDB ID 1BDM.

  7. Docking mode of delvardine and its analogues into the p66 domain ...

    Indian Academy of Sciences (India)

    SEARCHU

    Delvardine and its structural derivatives are important non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs). .... [PDB ID:1REV] was taken from the Protein Data Bank ... Water molecules were removed and H atoms were added.

  8. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of The Hypothetical Protein Yggu From ... E. Coli. Northeast Structural Genomics Consortium Targ...et ... Er14. pdb|1YH5|A Chain A, Solution Structure Of The ... Hypothetical Protein Yggu From E. Coli. Northeast

  9. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of The Hypothetical Protein Yggu From ... E. Coli. Northeast Structural Genomics Consortium Targ...et ... Er14. pdb|1YH5|A Chain A, Solution Structure Of The ... Hypothetical Protein Yggu From E. Coli. Northeast

  10. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of The Hypothetical Protein Yggu From ... E. Coli. Northeast Structural Genomics Consortium Targ...et ... Er14. pdb|1YH5|A Chain A, Solution Structure Of The ... Hypothetical Protein Yggu From E. Coli. Northeast

  11. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of The Hypothetical Protein Yggu From ... E. Coli. Northeast Structural Genomics Consortium Targ...et ... Er14. pdb|1YH5|A Chain A, Solution Structure Of The ... Hypothetical Protein Yggu From E. Coli. Northeast

  12. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of The Hypothetical Protein Yggu From ... E. Coli. Northeast Structural Genomics Consortium Targ...et ... Er14. pdb|1YH5|A Chain A, Solution Structure Of The ... Hypothetical Protein Yggu From E. Coli. Northeast

  13. ORF Alignment: NC_000853 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Proteomics Target Tm0979_1_87; Northeast Structural ... Genomics Target Vt98. pdb|1X9A|A Chain... ... Thermotoga Maritima. Ontario Center For Structural ... Proteomics Target Tm0979_1_87; Northeast Stru

  14. Data of evolutionary structure change: 1PVDB-2VBFB [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1PVDB-2VBFB 1PVD 2VBF B B SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEV...ASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLT-AENATYEIDRVLSQLLKERKPVYINLPVD.../ss_2> 0 1PVD B 1PVDB KGYKP-VAVPA - 1 1PVDpdbID

  15. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tructure Of The Outer Membrane Enzyme Pagp ... In Og Micelles pdb|1MM4|A Chain A, Solution Nmr ... ... ... Structure Of The Outer Membrane Enzyme Pagp In Dpc ... Micelles ... Length = 157 ... Query:

  16. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tructure Of The Outer Membrane Enzyme Pagp ... In Og Micelles pdb|1MM4|A Chain A, Solution Nmr ... ... ... Structure Of The Outer Membrane Enzyme Pagp In Dpc ... Micelles ... Length = 157 ... Query:

  17. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available tructure Of The Outer Membrane Enzyme Pagp ... In Og Micelles pdb|1MM4|A Chain A, Solution Nmr ... ... ... Structure Of The Outer Membrane Enzyme Pagp In Dpc ... Micelles ... Length = 157 ... Query:

  18. Download

    African Journals Online (AJOL)

    promoting healing by protecting the surface of the wound when the ... compound interaction with receptors, in this case. COX-2 ... for Structural Bioinformatics Protein Data Bank. (RCSB-PDB) .... hydrogen bond and electrostatic terms. MolDock.

  19. ORF Alignment: NC_006461 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available [Thermus thermophilus HB8] pdb|1FP9|A Chain A, Structure ... Of Amylomaltase From Thermus Thermophilus Hb8 In Space... ... Amylomaltase From Thermus Thermophilus Hb8 In Space ... Group P21212 ... Length = 500 ... Query

  20. Protein Data Bank depositions from synchrotron sources.

    Science.gov (United States)

    Jiang, Jiansheng; Sweet, Robert M

    2004-07-01

    A survey and analysis of Protein Data Bank (PDB) depositions from international synchrotron radiation facilities, based on the latest released PDB entries, are reported. The results (http://asdp.bnl.gov/asda/Libraries/) show that worldwide, every year since 1999, more than 50% of the deposited X-ray structures have used synchrotron facilities, reaching 75% by 2003. In this web-based database, all PDB entries among individual synchrotron beamlines are archived, synchronized with the weekly PDB release. Statistics regarding the quality of experimental data and the refined model for all structures are presented, and these are analysed to reflect the impact of synchrotron sources. The results confirm the common impression that synchrotron sources extend the size of structures that can be solved with equivalent or better quality than home sources.

  1. Protein Data Bank Depositions from Synchrotron Sources

    International Nuclear Information System (INIS)

    Jiang, J.; Sweet, R.

    2004-01-01

    A survey and analysis of Protein Data Bank (PDB) depositions from international synchrotron radiation facilities, based on the latest released PDB entries, are reported. The results ( ) show that worldwide, every year since 1999, more than 50% of the deposited X-ray structures have used synchrotron facilities, reaching 75% by 2003. In this web-based database, all PDB entries among individual synchrotron beamlines are archived, synchronized with the weekly PDB release. Statistics regarding the quality of experimental data and the refined model for all structures are presented, and these are analysed to reflect the impact of synchrotron sources. The results confirm the common impression that synchrotron sources extend the size of structures that can be solved with equivalent or better quality than home sources

  2. Database Description - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available sidue (or mutant) in a protein. The experimental data are collected from the literature both by searching th...the sequence database, UniProt, structural database, PDB, and literature database

  3. Journal of Biosciences | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    bonding dynamics of catalytic Asn 175 in plant thiol protease ... Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures ... Water-mediated ionic interactions in protein structures.

  4. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available |NP_313206.1| 50S ribosomal subunit protein ... L9 [Escherichia coli O157:H7] pdb|1P86|F Chain F, Real ... Space...The Low Resolution Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|F Ch...ain F, Real ... Space Refined Coordinates Of The 50s Subunit Fitted Into ... The Low Resolutio

  5. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available f|NP_312212.1| 50S ribosomal subunit protein ... L3 [Escherichia coli O157:H7] pdb|1P86|B Chain B, Real ... Space...hain B, Real ... Space Refined Coordinates Of The 50s Subunit Fitted Into ... The Low Resoluti... The Low Resolution Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|B C

  6. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available |NP_313206.1| 50S ribosomal subunit protein ... L9 [Escherichia coli O157:H7] pdb|1P86|F Chain F, Real ... Space...The Low Resolution Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|F Ch...ain F, Real ... Space Refined Coordinates Of The 50s Subunit Fitted Into ... The Low Resolutio

  7. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available |NP_313206.1| 50S ribosomal subunit protein ... L9 [Escherichia coli O157:H7] pdb|1P86|F Chain F, Real ... Space...The Low Resolution Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|F Ch...ain F, Real ... Space Refined Coordinates Of The 50s Subunit Fitted Into ... The Low Resolutio

  8. ORF Alignment: NC_004337 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available |NP_313206.1| 50S ribosomal subunit protein ... L9 [Escherichia coli O157:H7] pdb|1P86|F Chain F, Real ... Space...The Low Resolution Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|F Ch...ain F, Real ... Space Refined Coordinates Of The 50s Subunit Fitted Into ... The Low Resolutio

  9. ORF Alignment: NC_004741 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available |NP_313206.1| 50S ribosomal subunit protein ... L9 [Escherichia coli O157:H7] pdb|1P86|F Chain F, Real ... Space...The Low Resolution Cryo-Em Map Of The Initiation-Like ... State Of E. Coli 70s Ribosome pdb|1P85|F Ch...ain F, Real ... Space Refined Coordinates Of The 50s Subunit Fitted Into ... The Low Resolutio

  10. ORF Alignment: NC_002754 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available cture Of The Complete Core Of Archaeal Srp And ... Implications For Inter-Domain Communication pdb|1Q...For Inter-Domain ... Communication pdb|1QZW|G Chain G, Crystal Structure O...f ... The Complete Core Of Archaeal Srp And Implications For ... Inter-Domain Communication pd...re Of The Complete Core Of ... Archaeal Srp And Implications For Inter-Domain ... Communication... ... Inter-Domain Communication ... Length = 104 ... Query: 326 KLTLRD

  11. Main: 1LR5 [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available Aux311; Zea Mays Molecule: Auxin Binding Protein 1; Chain: A, B, C, D; Engineered: Yes; Mutation: Yes Protei...-.|EMBL; L08425; AAA33430.1; -.|PIR; S16262; S16262.|PDB; 1LR5; X-ray; A/B/C/D=39-201.|PDB; 1LRH; X-ray; A/B/C/D=39-201.|Mai

  12. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of Cyanide Derivative Of ... Truncated Hemoglobin N (Trhbn) From Mycobacterium ... Tuberculosis...) ... From Mycobacterium Tuberculosis pdb|1S61|B Chain B, ... Crystal Structure Of truncated H...emoglobin N (Hbn) From ... Mycobacterium Tuberculosis, Soaked With Butyl-I...socyanide ... pdb|1S61|A Chain A, Crystal Structure Of truncated ... Hemoglobin N (Hbn) From Mycobacterium Tuberculosis...ructure Of truncated Hemoglobin N (Hbn) From ... Mycobacterium Tuberculosis

  13. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of Cyanide Derivative Of ... Truncated Hemoglobin N (Trhbn) From Mycobacterium ... Tuberculosis...) ... From Mycobacterium Tuberculosis pdb|1S61|B Chain B, ... Crystal Structure Of truncated H...emoglobin N (Hbn) From ... Mycobacterium Tuberculosis, Soaked With Butyl-I...socyanide ... pdb|1S61|A Chain A, Crystal Structure Of truncated ... Hemoglobin N (Hbn) From Mycobacterium Tuberculosis...ructure Of truncated Hemoglobin N (Hbn) From ... Mycobacterium Tuberculosis

  14. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ] ... pdb|1M4I|B Chain B, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis...ain A, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis-Complex W...se From Mycobacterium ... Tuberculosis-Complex With Coenzyme A And Ribostamycin ... pdb|1M4G|A... Chain A, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis... ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis-Complex With Coenzyme A And Tob

  15. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ] ... pdb|1M4I|B Chain B, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis...ain A, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis-Complex W...se From Mycobacterium ... Tuberculosis-Complex With Coenzyme A And Ribostamycin ... pdb|1M4G|A... Chain A, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis... ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis-Complex With Coenzyme A And Tob

  16. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available al ... Structure Of Mycobacterium Tuberculosis Menb, A Key ... Enzyme In Vitamin K2 Biosynthes...is pdb|1Q52|K Chain K, ... Crystal Structure Of Mycobacterium Tuberculosis Menb, A ... Key Enz... ... I, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key Enzyme In Vitamin K2 Biosynt...hesis pdb|1Q52|H Chain ... H, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key ... ... F, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key Enzyme In Vitamin K2 Bios

  17. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available al ... Structure Of Mycobacterium Tuberculosis Menb, A Key ... Enzyme In Vitamin K2 Biosynthes...is pdb|1Q52|K Chain K, ... Crystal Structure Of Mycobacterium Tuberculosis Menb, A ... Key Enz... ... I, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key Enzyme In Vitamin K2 Biosynt...hesis pdb|1Q52|H Chain ... H, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key ... ... F, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key Enzyme In Vitamin K2 Bios

  18. ORF Alignment: NC_002755 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ] ... pdb|1M4I|B Chain B, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis...ain A, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis-Complex W...se From Mycobacterium ... Tuberculosis-Complex With Coenzyme A And Ribostamycin ... pdb|1M4G|A... Chain A, Aminoglycoside ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis... ... 2'-N-Acetyltransferase From Mycobacterium ... Tuberculosis-Complex With Coenzyme A And Tob

  19. ORF Alignment: NC_000962 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ture Of Cyanide Derivative Of ... Truncated Hemoglobin N (Trhbn) From Mycobacterium ... Tuberculosis...) ... From Mycobacterium Tuberculosis pdb|1S61|B Chain B, ... Crystal Structure Of truncated H...emoglobin N (Hbn) From ... Mycobacterium Tuberculosis, Soaked With Butyl-I...socyanide ... pdb|1S61|A Chain A, Crystal Structure Of truncated ... Hemoglobin N (Hbn) From Mycobacterium Tuberculosis...ructure Of truncated Hemoglobin N (Hbn) From ... Mycobacterium Tuberculosis

  20. ORF Alignment: NC_002945 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available al ... Structure Of Mycobacterium Tuberculosis Menb, A Key ... Enzyme In Vitamin K2 Biosynthes...is pdb|1Q52|K Chain K, ... Crystal Structure Of Mycobacterium Tuberculosis Menb, A ... Key Enz... ... I, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key Enzyme In Vitamin K2 Biosynt...hesis pdb|1Q52|H Chain ... H, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key ... ... F, Crystal Structure Of Mycobacterium Tuberculosis Menb, ... A Key Enzyme In Vitamin K2 Bios