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  • Copernicus  (23)
  • Oxford University Press  (16)
  • Blackwell Publishing Ltd  (3)
  • Cambridge University Press  (3)
  • American Geophysical Union (AGU)
  • 2010-2014  (39)
  • 1985-1989  (6)
  • 1950-1954
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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Plant pathology 35 (1986), S. 0 
    ISSN: 1365-3059
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Multiplication and spread of respresentative strains of three pathovars of Xanthomonas campestris were monitored by maceration and plating from inoculated leaves of the host and non-host plant species Oryza sativa, Poa trivialis, Brassica oleracea and Phleum pratense.Homologous interactions were characterized by higher multiplication rates and larger population increases than heterologous interactions, except for pv. oryzae which increased as much as pv. poae in leaves of Poa. Spread of heterologous pathovars was limited, but homologous pathovars were distributed throughout host leaves soon after inoculation. Pvs poae and oryzae (from Poaceae) demonstrated considerably greater population increases and higher initial multiplication rates than pv. campestris in leaves of all non-host Poaceae. Pv. poae spread further into leaves of Oryza and pv. oryzae further into leaves of Poa and Phleum than did pv. campestris. Numbers of pv. poae declined in Brassica as did those of pv. oryzae, which was localized within 2 mm of the point of inoculation.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 458 (1985), S. 0 
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Physiologia plantarum 72 (1988), S. 0 
    ISSN: 1399-3054
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Robinson, J. M. 1988. Does O2 photoreduction occur within chloroplasts in vivo? -Physiol. Plant. 72: 666–680.This discussion reviews evidence supporting the hypothesis that within intact chloroplasts in vivo, molecular O2 may serve as an alternative Hill oxidant (electron acceptor) on the reducing side of Photosystem I. Depending upon the availability of Hill oxidants such as NADP+ and NO−2, there is the potential within intact plastids in vivo, for photolytically derived reducing equivalents to reduce O2 to O−2 and H2O2 (the Mehler reaction). In chloroplasts of healthy tissues, the products of photosyn-thetic O2 reduction O−2 and H2O2) are rapidly removed by superoxide dismutase (EC 1.15.1.1) and L-ascorbate peroxidase (EC 1.11.1.11) to prevent toxicity. The presence of these two enzymes within chloroplasts in vivo reflects the potential for linear (non-cyclic) photosynthetic electron transport systems to draw upon molecular O2 as a terminal oxidant. In the intact plastid, O2 may act as an electron acceptor in the place of any other physiological Hill oxidant, e.g., NADP+, NO−2, and, presumably, oxidized thioredoxin. Under aerobic, physiological conditions, photo reduced ferre-doxin (Fdred), and/or reduced flavoprotein enzymes, e.g., ferredoxin:NADP+ oxidoreductase (EC 1.18.1.2), can donate electrons to O2; this reductive reaction appears to be non-enzymatic, but it is rapid. Stated from another viewpoint, O2 may serve as a Hill oxidant to support some linear electron flow when reductant supplies are in excess of reductant demands. For example, there are nitrogen assimilatory sites in the chloroplast, i.e., ferredoxin-nitrite reductase (NiR; EC 1.7.7.1) and glutamate synthase (ferredoxin) (GOGAT; EC 1.4.7.1), to which Fdred is allocated as reductant. Because NADH:nitrate reductase (NR; EC 1.6.6.1) is the rate limiting step of nitrogen assimilation, and, because NiR and GOGAT activities are in excess of NR activities by a factor of 2 or more, then an excess of unreacted Fdred could accumulate. Alternatively, the allocated Fdred would reduce the excess NiR and GOGAT sites, but the excess of reduced enzymes would not have substrates (e.g., NO−2, glutamine, and α-ketoglutarate) with which to react. Therefore, if ‘excess’ NiR and GOGAT binding sites were not employed, the available excess Fdred, and/or the reduced NiR and GOGAT proteins, would be susceptible to oxidation by O2. The resulting O2 photoreduction could account for nearly all of the observed in vivo Mehler type reactions. In vivo, apparent foliar O2 photoreduction occurs simultaneously with maximal CO2 photoassimilation, and, in high light, average rates have been determined by direct measurement to range from 10 to 40 μmol O2 consumed (mg Chl)−1 h−1. Therefore O2 reduction would support a low rate of linear (non-cyclic) electron flow which, in turn, could maintain a low, but significant rate of ATP production. However, there is not total agreement among researchers that the physiological role of O2 is that of serving as an alternative Hill oxidant in order to recycle unutilized Fdred or other photoreduced proteins. Also, there continues to be considerable controversy on whether or not O2 reduction supports significant photosynthetic phosphorylation. The total process of O2 photoreduction, and its physiological role(s), requires much more study before absolute functions can be assigned to O2 terminated, linear electron transport.〈section xml:id="abs1-1"〉〈title type="main"〉SummaryMolecular O2 possesses the physico-chemical properties that permit this molecule to serve as an alternative Hill oxidant within chloroplasts in vivo. Additionally, the physical and physiological properties within the chloroplast in vivo favor the potential for O2 to serve as an electron acceptor on the reducing side of Photosystem I. This may reflect an important ‘fail-safe mechanism’ which prevents over-reduction of linear photosynthetic electron transport chain proteins. This review has focused on the possibility that unutilized Fdred and/or other non-utilized, reduced plastid enzymes (e.g., NiR) may be electron donors to O2. It is hypothesized that this oxidation ultimately would be reflected as an in vivo Mehler reaction. However, it remains for future studies to establish without doubt, that in vivo, photoreduced chloroplast enzyme proteins can utilize O2 as a terminal electron acceptor.Further, that O2 photoreduction supports a significant level of photophosphorylation in vivo remains to be firmly established. Certainly, considerable evidence, gained with experiments utilizing isolates of intact chlo-roplasts and reconstituted chloroplast systems, supports the hypothesis that O2-terminated linear electron transport has the potential to support high rates of ATP production. However, in vivo studies e.g., with intact leaf tissues, which actually quantitate the relationship between O2 photoreduction and associated ATP production have not been conducted. These will be difficult experiments to perform, because, in vivo, it will be difficult to separate photosynthetic ATP production mediated by O2 from ATP production mediated by those other, more predominant Hill oxidants (e.g., NADP+, NO−2). Also, it continues to be a possibility that it is cyclic, and not pseudocyclic photophosphorylation that provides additional ATP to support photosynthetic cell metabolism. To establish beyond doubt that an in vivo role of the Mehler reaction is that of supplying ‘additional ATP’, remains for considerable future study.
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  • 4
    Publication Date: 2013-10-19
    Description: : Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3–11.4% for coding variants with minor allele frequency 〈1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2’s two-panel combination. Contact: yunli@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2014-03-20
    Description: The study of genetic influences on drug response and efficacy (‘pharmacogenetics’) has existed for over 50 years. Yet, we still lack a complete picture of how genetic variation, both common and rare, affects each individual's responses to medications. Exome sequencing is a promising alternative method for pharmacogenetic discovery as it provides information on both common and rare variation in large numbers of individuals. Using exome data from 2203 AA and 4300 Caucasian individuals through the NHLBI Exome Sequencing Project, we conducted a survey of coding variation within 12 Cytochrome P450 ( CYP ) genes that are collectively responsible for catalyzing nearly 75% of all known Phase I drug oxidation reactions. In addition to identifying many polymorphisms with known pharmacogenetic effects, we discovered over 730 novel nonsynonymous alleles across the 12 CYP genes of interest. These alleles include many with diverse functional effects such as premature stop codons, aberrant splicesites and mutations at conserved active site residues. Our analysis considering both novel, predicted functional alleles as well as known, actionable CYP alleles reveals that rare, deleterious variation contributes markedly to the overall burden of pharmacogenetic alleles within the populations considered, and that the contribution of rare variation to this burden is over three times greater in AA individuals as compared with Caucasians. While most of these impactful alleles are individually rare, 7.6–11.7% of individuals interrogated in the study carry at least one newly described potentially deleterious alleles in a major drug-metabolizing CYP .
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 6
    Publication Date: 2014-04-18
    Description: Many coral reef fish species form predictable, transient spawning aggregations. Many aggregations are overfished, making them a target for spatial management. Here, we develop a per-recruit model to evaluate the performance of no-take marine reserves protecting transient spawning aggregations. The model consists of only 14 demographic and exploitation-related parameters. We applied the model to a protogynous grouper and a gonochoristic rabbitfish from Seychelles and tested six scenarios regarding the extent of protected areas, the level of fish spawning-site fidelity, and fishing effort redistribution post reserve implementation. Spawning aggregation reserves improve spawning-stock biomass-per-recruit and reduce the sex ratio bias in protogynous populations for all scenarios examined. However, these benefits are often small and vary among the different scenarios and as a function of sexual ontogeny. In all scenarios, increases in yield-per-recruit do not occur or are negligible. The long-term yield increases due to spawning aggregation reserves may still occur, but only if spawning-stock biomass recovery results in a recruitment subsidy. Given these limited benefits, the value of no-take reserves must be weighed against those of other management options, such as fishing effort reduction and seasonal fishery closures. The latter is particularly appropriate when spawning and non-spawning areas overlap in space.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 7
    Publication Date: 2014-09-30
    Description: There is a global trend in the depletion of transient reef fish spawning aggregations ("FSAs"), making them a primary target for management with marine protected areas (MPAs). Here, we review the observed and likely effectiveness of FSA MPAs, discuss how future studies could fill knowledge gaps, and provide recommendations for MPA design based on species' life history and behaviour, enforcement potential, and management goals. Modelling studies indicate that FSA MPAs can increase spawning-stock biomass and normalize sex ratio in protogynous fish populations, unless fishing mortality remains high outside protected FSA sites and spawning times. In the field, observations of no change or continued decline in spawning biomass are more common than population recovery. When empirical studies suggest that FSA MPAs may not benefit fish productivity or recovery, extenuating factors such as insufficient time since MPA creation, poor or lack of enforcement, inadequate design, and poorly defined management objectives are generally blamed rather than failure of the MPA concept. Results from both the empirical and modelling literature indicate that FSA MPAs may not improve exploitable biomass and fisheries yields; however, investigations are currently too limited to draw conclusions on this point. To implement effective FSA MPAs, additional modelling work, long-term monitoring programmes at FSA sites, and collections of fisheries-dependent data are required, with greater attention paid to the design and enforcement of area closures. We recommend a harmonized, adaptive approach that combines FSA MPA design with additional management measures to achieve explicitly stated objectives. Conservation objectives and, therefore, an overall reduction in mortality rates should be targeted first. Fisheries objectives build on conservation objectives, in that they require an overall reduction in mortality rates while maintaining sufficient access to exploitable biomass. Communication among researchers, regulatory agencies, park authorities, and fishers will be paramount for effective action, along with significant funds for implementation and enforcement.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 8
    Publication Date: 2013-03-21
    Description: Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today’s sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv , under a GNU LGPL open-source license.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 9
    Publication Date: 2013-11-22
    Description: This article considers the unwieldy state of UK environmental legislation in 2013, after 25 years of innovation, ad hoc reform and political change. It shows that an appraisal of UK environmental legislation involves considering much more than primary legislation emanating from Westminster—secondary legislation, devolved legislative instruments, policy documents and administrative norms all serve to constitute and inform the legislative picture. Through this wide analytical lens, the article considers legal problems that characterise UK environmental legislation today, from undermining of the rule of law due to its inaccessible complexity, to occupying an awkward place in public law terms. A particular problem is the fragmentation of legislation, and the article examines the case for integrating environmental legislation in a way that does not undermine the flexibility and institutional expertise that more focused legislation allows. The article offers not only a method for analysing the current UK environmental legislative landscape, but suggests routes for reform that might now be considered.
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 10
    Publication Date: 2012-12-20
    Description: The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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