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Träfflista för sökning "WFRF:(Graham Richard) srt2:(2005-2009)"

Sökning: WFRF:(Graham Richard) > (2005-2009)

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1.
  • Clark, Andrew G., et al. (författare)
  • Evolution of genes and genomes on the Drosophila phylogeny
  • 2007
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
  • Tidskriftsartikel (refereegranskat)abstract
    • Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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2.
  • Brown, Kevin M., et al. (författare)
  • Common sequence variants on 20q11.22 confer melanoma susceptibility
  • 2008
  • Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 40:7, s. 838-840
  • Tidskriftsartikel (refereegranskat)abstract
    • We conducted a genome-wide association pooling study for cutaneous melanoma and performed validation in samples totaling 2,019 cases and 2,105 controls. Using pooling, we identified a new melanoma risk locus on chromosome 20 (rs910873 and rs1885120), with replication in two further samples (combined P < 1 x 10(-15)). The per allele odds ratio was 1.75 (1.53, 2.01), with evidence for stronger association in early-onset cases.
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3.
  • Lindblad-Toh, Kerstin, et al. (författare)
  • Genome sequence, comparative analysis and haplotype structure of the domestic dog.
  • 2005
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
  • Tidskriftsartikel (refereegranskat)abstract
    • Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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4.
  • Zeggini, Eleftheria, et al. (författare)
  • Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes
  • 2008
  • Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 40:5, s. 638-645
  • Tidskriftsartikel (refereegranskat)abstract
    • Genome-wide association (GWA) studies have identified multiple loci at which common variants modestly but reproducibly influence risk of type 2 diabetes (T2D)(1-11). Established associations to common and rare variants explain only a small proportion of the heritability of T2D. As previously published analyses had limited power to identify variants with modest effects, we carried out meta-analysis of three T2D GWA scans comprising 10,128 individuals of European descent and similar to 2.2 million SNPs (directly genotyped and imputed), followed by replication testing in an independent sample with an effective sample size of up to 53,975. We detected at least six previously unknown loci with robust evidence for association, including the JAZF1 (P=5.0 x 10(-14)), CDC123-CAMK1D (P=1.2 x 10(-10)), TSPAN8-LGR5 (P=1.1 x 10(-9)), THADA (P=1.1 x 10(-9)), ADAMTS9 (P=1.2 x 10(-8)) and NOTCH2 (P=4.1 x 10(-8)) gene regions. Our results illustrate the value of large discovery and follow-up samples for gaining further insights into the inherited basis of T2D.
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5.
  • Ainsworth, Elizabeth A., et al. (författare)
  • Next generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world
  • 2008
  • Ingår i: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 31:9, s. 1317-1324
  • Tidskriftsartikel (refereegranskat)abstract
    • A rising global population and demand for protein-rich diets are increasing pressure to maximize agricultural productivity. Rising atmospheric [CO2] is altering global temperature and precipitation patterns, which challenges agricultural productivity. While rising [CO2] provides a unique opportunity to increase the productivity of C-3 crops, average yield stimulation observed to date is well below potential gains. Thus, there is room for improving productivity. However, only a fraction of available germplasm of crops has been tested for CO2 responsiveness. Yield is a complex phenotypic trait determined by the interactions of a genotype with the environment. Selection of promising genotypes and characterization of response mechanisms will only be effective if crop improvement and systems biology approaches are closely linked to production environments, that is, on the farm within major growing regions. Free air CO2 enrichment (FACE) experiments can provide the platform upon which to conduct genetic screening and elucidate the inheritance and mechanisms that underlie genotypic differences in productivity under elevated [CO2]. We propose a new generation of large-scale, low-cost per unit area FACE experiments to identify the most CO2-responsive genotypes and provide starting lines for future breeding programmes. This is necessary if we are to realize the potential for yield gains in the future.
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6.
  • Allan, Ian J., et al. (författare)
  • Evaluation of the Chemcatcher and DGT passive samplers for monitoring metals with highly fluctuating water concentrations
  • 2007
  • Ingår i: Journal of Environmental Monitoring. ; 9:7, s. 672-681
  • Tidskriftsartikel (refereegranskat)abstract
    • Passive sampling devices accumulate chems. continuously from water and can provide time weighted av. (TWA) concns. of pollutants over the exposure period. Hence, they offer a no. of advantages over other conventional monitoring techniques such as spot or grab sampling. The diffusive gradient in thin film (DGT) and the Chemcatcher passive samplers can be used to provide TWA concns. of labile metals, but the approaches to their calibration differ. DGT uses diffusion coeffs. of metals in the hydrogel layer, whereas Chemcatcher uses metal specific uptake rates, with both sets of values obtained under controlled lab. conditions with const. aq. metal concns. However, little is known of how such samplers respond to fluctuating concns. We evaluated the responsiveness of these two passive sampling devices to rapidly changing concns. of Cd, Cu, Ni, Pb and Zn in natural freshwater, over a relatively short deployment time. Maximum metal concns. in water were varied between 70 and 140 mg L-1. Expts. were carried out in a tank with a rotating carousel system and filled with Meuse River water, allowing a degree of control over exptl. conditions while using natural river water. Fluctuating concns. were obtained by stepwise addn. of std. solns. of the metals. The reliability and accuracy of the TWA concns. measured by the samplers were assessed by comparison with concns. of the metals in spot samples of water taken regularly over the deployment period. The spot samples of water were either unfiltered (total), filtered (0.45 mm) or ultrafiltered (5 kDa). Predictive speciation modeling using the visual MINTEQ program was also undertaken. There was reasonable agreement between the TWA concns. of Cd and Ni obtained with Chemcatcher and DGT and the total Cd and Ni concns. measured in repeated unfiltered spot samples. For elements (i.e. Cu, Pb, Zn) that assoc. to a significant degree with suspended solids, colloids or dissolved org. carbon, or form complexes with large org. ligands, optimum agreement was with the filtered or ultrafiltered fractions and with the predicted inorg. and inorg.-fulvic acid assocd. fractions. While Chemcatcher-based TWA concn. ranges for Cu and Zn were in best agreement with the total filtered fraction, there was lack of agreement for Pb. The combined use of DGT devices with open pore (OP) and restricted pore (RP) gels allowed the labile fraction of metal assocd. with large org. ligands or DOC to be differentiated and quantified, since this is available to DGT OP but unable to diffuse into the DGT RP. This evaluation of the two sampling devices clearly demonstrated their ability to react reliably to transient peaks in concn. of metal pollutants in water and indicated where future efforts are needed to improve calibration data. Such samplers may prove valuable in responding to the monitoring requirements of the European Union's Water Framework Directive. [on SciFinder (R)]
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7.
  • Allan, Ian J., et al. (författare)
  • Strategic monitoring for the European Water Framework Directive
  • 2006
  • Ingår i: TrAC - Trends in Analytical Chemistry. - : Elsevier BV. - 0165-9936. ; 25:7, s. 704-715
  • Tidskriftsartikel (refereegranskat)abstract
    • This article first reviews the principal monitoring requirements of the Water Framework Directive (WFD) of the European Union (EU) and assesses how contaminant monitoring may fit into a risk-assessment approach. In this context, we show the limited ability of conventional trace-contaminant-monitoring methods to fulfil all of the WFD requirements. We then clearly define and exemplify the roles and the functions of a new set of monitoring tools, using three case studies based on datasets that we obtained during a field trial in the River Meuse as part of the Screening methods for Water data InFormaTion (SWIFT-WFD) project in support of implementing the WFD.
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8.
  • Bailey, Richard, et al. (författare)
  • Host Niches and Defensive Extended Phenotypes Structure Parasitoid Wasp Communities
  • 2009
  • Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 7:8, s. e1000179-
  • Tidskriftsartikel (refereegranskat)abstract
    • Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies. Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the "Enemy Hypothesis,'' which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness), supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed). The combined explanatory power of structural and spatiotemporal traits on community structure can be high, reaching 62% in one analysis. The observed patterns derive mainly from partial niche specialisation of highly generalist parasitoids with broad host ranges (>20 hosts), rather than strict separation of enemies with narrower host ranges, and so may contribute to maintenance of the richness of generalist parasitoids in gallwasp communities. Though evolutionary escape from parasitoids might most effectively be achieved via changes in host oak taxon, extreme conservatism in this trait for gallwasps suggests that selection is more likely to have acted on gall morphology and location. Any escape from parasitoids associated with evolutionary shifts in these traits has probably only been transient, however, due to subsequent recruitment of parasitoid species already attacking other host galls with similar trait combinations.
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9.
  • Bishop, D. Timothy, et al. (författare)
  • Genome-wide association study identifies three loci associated with melanoma risk
  • 2009
  • Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:8, s. 920-925
  • Tidskriftsartikel (refereegranskat)abstract
    • We report a genome-wide association study of melanoma conducted by the GenoMEL consortium based on 317K tagging SNPs for 1,650 selected cases and 4,336 controls, with replication in an additional two cohorts (1,149 selected cases and 964 controls from GenoMEL, and a population-based case-control study in Leeds of 1,163 cases and 903 controls). The genome-wide screen identified five loci with genotyped or imputed SNPs reaching P < 5 x 10(-7). Three of these loci were replicated: 16q24 encompassing MC1R (combined P = 2.54 x 10(-27) for rs258322), 11q14-q21 encompassing TYR (P = 2.41 x 10(-14) for rs1393350) and 9p21 adjacent to MTAP and flanking CDKN2A (P = 4.03 x 10(-7) for rs7023329). MC1R and TYR are associated with pigmentation, freckling and cutaneous sun sensitivity, well-recognized melanoma risk factors. Common variants within the 9p21 locus have not previously been associated with melanoma. Despite wide variation in allele frequency, these genetic variants show notable homogeneity of effect across populations of European ancestry living at different latitudes and show independent association to disease risk.
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10.
  • Dalrymple, Annette, et al. (författare)
  • Proteomic profiling of plasma in Huntington's disease reveals neuroinflammatory activation and biomarker candidates
  • 2007
  • Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:7, s. 2833-2840
  • Tidskriftsartikel (refereegranskat)abstract
    • Huntington's disease (HD) causes widespread CNS changes and systemic abnormalities including endocrine and immune dysfunction. HD biomarkers are needed to power clinical trials of potential treatments. We used multiplatform proteomic profiling to reveal plasma changes with HD progression. Proteins of interest were evaluated using immunoblotting and ELISA in plasma from 2 populations, CSF and R6/2 mice. The identified proteins demonstrate neuroinflammation in HD and warrant further investigation as possible biomarkers.
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