| 1. |
- 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. |
- Popat, S, et al.
(författare)
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Variation in the CTLA4/CD28 gene region confers an increased risk of coeliac disease.
- 2002
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Ingår i: Annals of human genetics. - 0003-4800 .- 1469-1809. ; 66:Pt 2, s. 125-37
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Tidskriftsartikel (refereegranskat)abstract
- Susceptibility to coeliac disease involves HLA and non-HLA-linked genes. The CTLA4/CD28 gene region encodes immune regulatory T-cell surface molecules and is a strong candidate as a susceptibility locus. We evaluated CTLA4/CD28 in coeliac disease by genetic linkage and association and combined our findings with published studies through a meta-analysis. 116 multiplex families were genotyped across CTLA4/CD28 using eight markers. The contribution of CTLA4/CD28 to coeliac disease was assessed by non-parametric linkage and association analyses. Seven studies were identified that had evaluated the relationship between CTLA4/CD28 and coeliac disease and a pooled analysis of data undertaken. In our study there was evidence for a relationship between variation in the CTLA4/CD28 region and coeliac disease by linkage and association analyses. However, the findings did not attain formal statistical significance (p = 0.004 and 0.039, respectively). Pooling findings with published results showed significant evidence for linkage (504 families) and association (940 families): p values, 0.0001 and 0.0014 at D2S2214, respectively, and 0.0008 and 0.0006 at D2S116, respectively. These findings suggest that variation in the CD28/CTLA4 gene region is a determinant of coeliac disease susceptibility. Dissecting the sequence variation underlying this relationship will depend on further analyses utilising denser sets of markers.
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| 3. |
- Popat, S, et al.
(författare)
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Genome screening of coeliac disease
- 2002
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Ingår i: Journal of Medical Genetics. - : BMJ. - 0022-2593 .- 1468-6244. ; 39:5, s. 328-331
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Ristow, M, et al.
(författare)
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Frataxin deficiency in pancreatic islets causes diabetes due to loss of beta cell mass
- 2003
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Ingår i: Journal of Clinical Investigation. - 0021-9738. ; 112:4, s. 527-534
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Tidskriftsartikel (refereegranskat)abstract
- Diabetes is caused by an absolute (type 1) or relative (type 2) deficiency of insulin-producing beta cells. We have disrupted expression of the mitochondrial protein frataxin selectively in pancreatic beta cells. Mice were born healthy but subsequently developed impaired glucose tolerance progressing to overt diabetes mellitus. These observations were explained by impairment of insulin secretion due to a loss of beta cell mass in knockout animals. This phenotype was preceded by elevated levels of reactive oxygen species in knockout islets, an increased frequency of apoptosis, and a decreased number of proliferating beta cells. Hence, disruption of the frataxin gene in pancreatic beta cells causes diabetes following cellular growth arrest and apoptosis, paralleled by an increase in reactive oxygen species in islets. These observations might provide insight into the deterioration of beta cell function observed in different subtypes of diabetes in humans.
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| 5. |
- Popat, S, et al.
(författare)
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Genome screening of coeliac disease.
- 2001
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Ingår i: Journal of Medical Genetics. - 0022-2593 .- 1468-6244. ; 39, s. 328-331
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Tidskriftsartikel (refereegranskat)
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| 6. |
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| 7. |
- Gustafsson, Jon Petter, et al.
(författare)
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Aluminium solubility mechanisms in moderately acid Bs horizons of podzolized soils
- 2001
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Ingår i: European Journal of Soil Science. - : Wiley. - 1351-0754 .- 1365-2389. ; 52:4, s. 655-665
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Tidskriftsartikel (refereegranskat)abstract
- The processes controlling the retention and release of aluminium in acid forest soils are still subject to controversy, and therefore a universal hypothesis as to what mechanisms are operating has not been firmly established. By studying the Bs horizons of Swedish and Swiss podzolized soils, and by analysing data in the literature, we have found that aluminium hydroxide, and in some cases also poorly ordered imogolite, may control Al solubility in moderately acid (pH>4.2-4.3) Bs horizons. The strongest evidence in support of the presence of a quickly reacting Al(OH)(3) pool came from the temperature dependence of Al solubility in a Bs horizon, which was consistent with the reaction enthalpy of an Al(OH)3 phase such as gibbsite, and from the observation that the eon activity product for Al(OH)3 was the same regardless of whether equilibrium was reached from over- or undersaturation. The pool of Al(OH)3 is commonly small and may be completely dissolved after large additions of acid. This may be explained by the continuing redissolution of reactive Al(OH)(3) to form less soluble imogolite-type phases. By using the same methods it was found that soil suspensions did not reach equilibrium with poorly ordered imogolite even after 17 days. Thus, imogolite probably does not control Al solubility in the short term in many soils despite the common occurrence of this mineral. This is due to the relatively slow kinetics of imogolite formation and dissolution, especially at low temperatures and at small solution H4SiO4 concentrations.
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| 8. |
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| 9. |
- Rotticci, D., et al.
(författare)
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Improved enantioselectivity of a lipase by rational protein engineering
- 2001
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Ingår i: ChemBioChem. - 1439-4227 .- 1439-7633. ; 2:10, s. 766-770
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Tidskriftsartikel (refereegranskat)abstract
- A model based on two different binding modes for alcohol enantiomers in the active site of a lipase allowed rational redesign of its enantioselectivity, 1-Halo-2-octanols were poorly resolved by Candida antarctica lipase B. Interactions between the substrates and the lipase were investigated with molecular modeling. Unfavorable interactions were found between the halogen moiety of the fast-reacting S enantiomer and a region situated at the bottom of the active site (stereoselectivity pocket). The lipase was virtually mutated in this region and energy contour maps of some variants displayed better interactions for the target substrates. Four selected variants of the lipase were produced and kinetic resolution experiments were undertaken with these mutants. Single point mutants gave rise to one variant with doubled enantioselectivity as well as one variant with annihilated enantioselectivity towards the target halohydrins. An increased volume of the stereoselectivity pocket caused a decrease in enantioselectivity, while changes in electrostatic potential increased enantioselectivity, The enantioselectivity of these new lipase variants towards other types of alcohols was also investigated. The changes in enantioselectivity caused by the mutations were well in agreement with the proposed model concerning the chiral recognition of alcohol enantiomers by this lipase.
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| 10. |
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