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- Imanishi, T., et al.
(author)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Journal article (peer-reviewed)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 2. |
- Christlieb, N., et al.
(author)
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The Hamburg/ESO R-process Enhanced Star survey (HERES). I. Project description, and discovery of two stars with strong enhancements of neutron-capture elements
- 2004
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In: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 428:3, s. 1027-1037
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Journal article (peer-reviewed)abstract
- We report on a dedicated effort to identify and study metal-poor stars strongly enhanced in r-process elements ([r/Fe]>1 dex; hereafter r-IIstars), the Hamburg/ESO R-process Enhanced Star survey (HERES).Moderate-resolution (∼2 Å) follow-up spectroscopy has been obtained for metal-poor giant candidates selected from the Hamburg/ESO objective-prism survey (HES) as well as the HK survey to identify sharp-lined stars with [Fe/H]<-2.5 dex. For several hundred confirmed metal-poor giants brighter than B∼ 16.5 mag (most of them from theHES), ``snapshot'' spectra (R∼ 20 000; S/N ∼ 30 per pixel) are being obtained with VLT/UVES, with the main aim of finding the 2-3% r-II stars expected to be among them. These are studied in detail by means of higher resolution and higher S/N spectra. In this paper we describe a pilot study based on a set of 35 stars, including 23 from the HK survey,eight from the HES, and four comparison stars. We discovered two new r-II stars, CS 29497-004 ([Eu/Fe]=1.64± 0.22) and CS 29491-069([Eu/Fe]=1.08± 0.23). A first abundance analysis of CS 29497-004 yields that its abundances of Ba to Dy are on average enhanced by 1.5 dex with respect to iron and the Sun and match a scaled solar r-process pattern well, while Th is underabundant relative to that pattern by 0.3dex, which we attribute to radioactive decay. That is, CS 29497-004 seems not to belong to the class of r-process enhanced stars displaying an ``actinide boost'', like CS 31082-001 (Hill et al. 2002), or CS30306-132 (Honda et al. 2004b). The abundance pattern agrees well with predictions of the phenomenological model of Qian & Wasserburg.Based in large part on observations collected at the European Southern Observatory, Paranal, Chile (proposal number 68.B-0320).}
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