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Sökning: WFRF:(Lee Andrew) > (2005-2009)

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  • Clark, Andrew G., et al. (författare)
  • Evolution of genes and genomes on the Drosophila phylogeny.
  • 2007
  • Ingår i: Nature. - 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.
  • Birney, Ewan, et al. (författare)
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  • 2007
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
  • Tidskriftsartikel (refereegranskat)abstract
    • We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
  • Beers, Timothy C., et al. (författare)
  • Broadband UBVRCIC photometry of horizontal-branch and metal-poor candidates from the HK and Hamburg/ESO surveys. I.
  • 2007
  • Ingår i: The Astrophysical Journal Supplement Series. - University of Chicago Press. - 0067-0049. ; 168:1, s. 128-139
  • Tidskriftsartikel (refereegranskat)abstract
    • We report broadband UBV and/or BVRCIC CCD photometry for a total of 1857 stars in the thick-disk and halo populations of the Galaxy. The majority of our targets were selected as candidate field horizontal-branch or other A-type stars (FHB/ A, N = 576), or candidate low-metallicity stars (N = 1221), from the HK and Hamburg/ESO objective-prism surveys. Similar data for a small number of additional stars from other samples are also reported. These data are being used for several purposes. In the case of the FHB/ A candidates they are used to accurately separate the lower gravity FHB stars from various higher gravity A-type stars, a subsample that includes the so-called blue metal poor stars, halo and thick-disk blue stragglers, main-sequence A-type dwarfs, and Am and Ap stars. These data are also being used to derive photometric distance estimates to high-velocity hydrogen clouds in the Galaxy and for improved measurements of the mass of the Galaxy. Photometric data for the metal-poor candidates are being used to refine estimates of stellar metallicity for objects with available medium-resolution spectroscopy, to obtain distance estimates for kinematic analyses, and to establish initial estimates of effective temperature for analysis of high-resolution spectroscopy of the stars for which this information now exists.
  • Lindblad-Toh, Kerstin, et al. (författare)
  • Genome sequence, comparative analysis and haplotype structure of the domestic dog.
  • 2005
  • Ingår i: Nature. - 1476-4687. ; 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.
  • Almany, Glenn R., et al. (författare)
  • Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009
  • 2009
  • Ingår i: Molecular Ecology Resources. - Wiley-Blackwell. - 1755-098X. ; 9:6, s. 1460-1466
  • Tidskriftsartikel (refereegranskat)abstract
    • This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
  • El-Sayed, Ashraf, et al. (författare)
  • Attraction and Antennal Response of the Common Wasp, Vespula vulgaris (L.), to Selected Synthetic Chemicals in New Zealand Beech Forests
  • 2009
  • Ingår i: Pest Management Science. - 1526-498X. ; 65:9, s. 975-981
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The common wasp, Vespula vulgaris (L.), and the German wasp, Vespula germanica (F.), are significant problems in New Zealand beech forests (Nothofagus spp.), adversely affecting native birds and invertebrate biodiversity. This work was undertaken to develop synthetic attractants for these species to enable more efficient monitoring and management. RESULTS: Seven known wasp attractants (acetic acid, butyl butyrate, isobutanol, heptyl butyrate, octyl butyrate and 2,4-hexadienyl butyrate) were field tested, and only heptyl butyrate and octyl butyrate attracted significantly higher numbers of wasps than a non-baited trap. Accordingly, a series of straight-chain esters from methyl to decyl butyrate were prepared and field tested for attraction of social wasps. Peak biological activity occurred with hexyl butyrate, heptyl butyrate, octyl butyrate and nonyl butyrate. Polyethylene bags emitting approximately 18.4-22.6 mg day(-1) of heptyl butyrate were more attractive than polyethylene bags emitting approximately 14.7-16.8 mg day(-1) of heptyl butyrate in the field. Electroantennogram (EAG) studies indicated that queens and workers of V. vulgaris had olfactory receptor neurons responding to various aliphatic butyrates. CONCLUSION: These results are the first to be reported on the EAG response and the attraction of social wasps to synthetic chemicals in New Zealand beech forests and will enable monitoring of social wasp activity in beech forests. (C) 2009 Society of Chemical industry
  • Gruber, Jan, et al. (författare)
  • Allantoin in human plasma, serum, and nasal-lining fluids as a biomarker of oxidative stress : avoiding artifacts and establishing real in vivo concentrations.
  • 2009
  • Ingår i: Antioxidants and Redox Signaling. - 1523-0864. ; 11:8, s. 1767-1776
  • Tidskriftsartikel (refereegranskat)abstract
    • Urate is the terminal product of purine metabolism in primates, including humans. Urate is also an efficient scavenger of oxidizing species and is thought to be an important antioxidant in human body fluids. Allantoin, the major oxidation product of urate, has been suggested as a candidate biomarker of oxidative stress because it is not produced metabolically. Although urate is converted to allantoin under strongly alkaline pH, such conditions have been used in the past to facilitate extraction of allantoin. We evolved a method for the determination of allantoin concentrations in human plasma and serum by gas chromatography-mass spectrometry without such artifact. With this method, we show that alkaline conditions do indeed cause breakdown of urate, leading to significant overestimation of allantoin concentration in human samples. By using our alternative method, serum samples from 98 volunteers were analyzed, and allantoin levels were found to be significantly lower than was previously reported. The in vivo utility and sensitivity of our method was further evaluated in human nasal-lining fluids. We were able to demonstrate an ozone-induced increase in allantoin, in the absence of increases in either ascorbate or glutathione oxidation products.
  • Mikkelsen, Tarjei S, et al. (författare)
  • Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
  • 2007
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
  • Tidskriftsartikel (refereegranskat)abstract
    • We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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