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- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)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. |
- Ma, Zhi, et al.
(författare)
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Enhanced in vitro production of amyloid-like fibrils from mutant (S20G) islet amyloid polypeptide
- 2001
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Ingår i: Amyloid. - : Informa UK Limited. - 1350-6129 .- 1744-2818. ; 8, s. 242-
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Tidskriftsartikel (refereegranskat)abstract
- Islet amyloid polypeptide (IAPP, “amylin”) is the amyloid-fibril-forming polypeptide in the islets of Langerhans associated with type 2 diabetes mellitus. A missense mutation in the IAPP gene associated with early-onset type 2 diabetes has been identified in the Japanese population. This mutation results in a glycine for serine substitution at position 20 of the mature IAPP molecule. Whether or not formation of islet amyloid with resulting destruction of islet tissue is the cause of this diabetes is yet not known. The present in vitro study was performed in order to investigate any influence of the amino acid substitution on the fibril formation capacity. Synthetic full-length wild type (lAPPwt) and mutant (IAPPS20G) as well as corresponding truncated peptides (position 18-29) were dissolved in dimethylsulfoxide (DMSO) or in 10% acetic acid at a concentration of 10 mg/mL and their fibril forming capacity was checked by Congo red staining, electron microscopy, a Congo red affinity assay and Thioflavine T fluorometric assay. It was found that full-length and truncated IAPPS20G both formed more amyloid-like fibrils and did this faster compared to IAPPwt. The fibril morphology differed slightly between the preparations. Conclusion: The amino acid substitution (S20G) is situated close to the region of the IAPP molecule implicated in the IAPP fibrillogenesis. The significantly increased formation of amyloid-like fibrils by IAPPS20G is highly interesting and may be associated with an increased islet amyloid formation in vivo and of fundamental importance in the pathogenesis of this specific form of diabetes.
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| 3. |
- Sakamoto, K., et al.
(författare)
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Interaction of metastable molecular oxygen with the dangling bonds of a Si(111)-(7×7) surface
- 2001
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - 0368-2048 .- 1873-2526. ; 114-116, s. 489-494
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the interaction between metastable molecular oxygen and the adatom dangling bonds modified by the adsorption of atomic oxygen into the back-bonds of a Si(111)-(7×7) surface. Ultraviolet photoelectron spectroscopy shows that the metastable states increase in intensity faster but with a decrease in its saturated intensity as the coverage of atomic oxygen increases. This result suggests that the number of modified dangling bonds is not the only important factor for the adsorption process of metastable oxygen. Taking into account the observation of modified dangling bonds with different density of states in scanning tunneling microscopy, we conclude that the adsorption of the metastable oxygen species correlates closely with the density of states of the dangling bond.
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| 4. |
- Sips, A. C. C., et al.
(författare)
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An international database for the study of the formation of ITBs in tokamaks
- 2002
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Ingår i: Plasma Physics and Controlled Fusion. - 0741-3335 .- 1361-6587. ; 44, s. A391-A398
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Tidskriftsartikel (refereegranskat)abstract
- For the first time, data from eight,different tokamaks have been combined in an international database for internal transport barriers (ITBs). An analysis of the data for the formation of an ITB with dominant ion heating shows a clear dependence of the threshold power on the minor radius and line-averaged electron density for the formation of ion ITBs. The dependence of ITB formation on the toroidal magnetic field is weak. For the formation of ITBs with dominant electron heating, the database is smaller, but for the threshold power a strong increase with plasma size and a weak toroidal field dependence could also be identified. Based on these results, an expression for the power required to form an ITB is given using global variables only. These results give a basis for the analysis of the database using local values (like magnetic shear) and a detailed comparison with theory-based models.
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| 5. |
- Zheng, W.T., et al.
(författare)
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Chemical bonding in carbon nitride films studied by X-ray spectroscopies
- 2001
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Ingår i: Diamond and related materials. - 0925-9635 .- 1879-0062. ; 10:9-10, s. 1897-1900
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Tidskriftsartikel (refereegranskat)abstract
- Carbon nitride films are deposited using dc magnetron sputtering in a N2 discharge. The nature of chemical bonding of the films is investigated using X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure, and X-ray emission spectroscopy. X-Ray photoelectron spectroscopy spectra show that N1s binding states depend on substrate temperature, in which two pronounced peaks can be observed. The near edge X-ray absorption fine structure at C1s and N1s exhibits a similar absorption profile in the p* resonance region, but the s* resonance is sharper in the N1s spectra. Resonant N K-emission spectra show a strong dependence on excitation photo energies. Compared XPS N1s spectra with recent theoretical calculations by Johansson and Stafstrom, two main nitrogen sites are assigned in which N bound to sp3 hybridized C and sp2 hybridized C, respectively. The correlation of X-ray photoelectron, X-ray absorption, and X-ray emission spectra for N in carbon nitride films is also discussed. © 2001 Elsevier Science B.V. All rights reserved.
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