| 1. |
- Imanishi, T., et al.
(författare)
-
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
-
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.
|
|
| 2. |
- Steeneken, P. G., et al.
(författare)
-
Crossing the gap from p- to n-type doping : Nature of the states near the chemical potential in La2-xSrxCuO4 and Nd2-xCexCuO4-delta
- 2003
-
Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 90:24
-
Tidskriftsartikel (refereegranskat)abstract
- We report on an x-ray absorption and resonant photoemission study on single crystals of the high-T-c cuprates La2-xSrxCuO4 and Nd2-xCexCuO4-delta. Using an intrinsic energy reference, we find that the chemical potential of La2-xSrxCuO4 lies near the top of the La2CuO4 valence band whereas in Nd2-xCexCuO4-delta it is situated near the bottom of the Nd2CuO4 conduction band. The data clearly establish that the introduction of Ce in Nd2CuO4 results in electrons being doped into the CuO2 planes. We infer that the states closest to the chemical potential have a Cu 3d(10) singlet origin in Nd2-xCexCuO4-delta and a 3d(9) (L) under bar singlet origin in La2-xSrxCuO4.
|
|
| 3. |
- Tjernberg, Oscar, et al.
(författare)
-
Electrons, holes, and spin in Nd2-xCexCuO4-delta
- 2003
-
Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 67:10
-
Tidskriftsartikel (refereegranskat)abstract
- The spin nature of the states at the top of the valence band in Nd2CuO4 and Nd1.85Ce0.15CuO4-delta has been investigated with spin polarized resonant photoemission. A clear Zhang-Rice singlet state is observed at the top of the valence band in the undoped compound showing that the parent compound of this electron doped superconductor is similar to the parent compounds of hole doped cuprate superconductors. Upon doping, the stability of the singlet is destroyed and the optimum doped compound Nd1.85Ce0.15CuO4-delta does not display any well-separated singlet state. These results indicate that hole contribution to the superconductivity in this system is not important in contrast to what has previously been suggested on the bases of transport measurements.
|
|
| 4. |
|
|
| 5. |
- Prince, J.A., et al.
(författare)
-
Lack of replication of association findings in complex disease : An analysis of 15 polymorphisms in prior candidate genes for sporadic Alzheimer's disease
- 2001
-
Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 9:6, s. 437-444
-
Tidskriftsartikel (refereegranskat)abstract
- There is considerable enthusiasm for the prospect of using common polymorphisms (primarily single nucleotide polymorphisms, SNPs) in candidate genes to unravel the genetics of complex disease. This approach has generated a number of findings of loci which are significantly associated with sporadic Alzheimer's disease (AD). In the present study, a total of 15 genes of interest were chosen from among the previously published reports of significant association in AD. Genotyping was performed on polymorphisms within those genes (14 SNPs and one deletion) using Dynamic Allele Specific Hybridization (DASH) in 204 Swedish patients with sporadic late-onset AD and 186 Swedish control subjects. The genes chosen for analysis were, low-density lipoprotein receptor-related protein (LRP1), angiotensin converting enzyme (DCP1), alpha-2-macroglobulin (A2M), bleomycin hydrolase (BLMH), dihydrolipoyl S-succinyltransferase (DLST), tumour necrosis factor receptor superfamily member 6 (TNFRSF6), nitric oxide synthase (NOS3), presenilin 1 (PSEN1), presenilin 2 (PSEN2), butyrylcholinesterase (BCHE), Fe65 (APBB1), oestrogen receptor alpha (ESR1), cathepsin D (CTSD), methylenetetrahydrofolate reductase (MTHFR), and interleukin 1A (IL1A). We found no strong evidence of association for any of these loci with AD in this population. While the possibility exists that the genes analysed are involved in AD (ie they have weak effects and/or are population specific), results reinforce the need for extensive replication studies if we are to be successful in defining true risk factors in complex diseases.
|
|
| 6. |
- Blennow, Kaj, 1958, et al.
(författare)
-
No association between the alpha2-macroglobulin (A2M) deletion and Alzheimer's disease, and no change in A2M mRNA, protein, or protein expression.
- 2000
-
Ingår i: Journal of neural transmission (Vienna, Austria : 1996). - : Springer Science and Business Media LLC. - 0300-9564 .- 1435-1463. ; 107:8-9, s. 1065-79
-
Tidskriftsartikel (refereegranskat)abstract
- A polymorphism consisting of a deletion near the 5' splice site of exon 18 on the alpha2-macroglobulin (A2M) gene (A2M-2) has been suggested to be associated with Alzheimer's disease (AD) in family-based studies. We studied the A2M-2 allele together with the ApoE alleles in a large series on patients with AD (n = 449) and age-matched controls (n = 349). Neuropathologically confirmed diagnoses were available in 199 cases (94 AD and 107 control cases). We found no increase in A2M-2 genotype or allele frequencies in AD (27.5% and 14.6%) versus controls (26.4% and 14.9%). In contrast, a marked increase (p < 0.0001) in ApoE epsilon4 genotype or allele frequencies was found in AD (66.6% and 41.2%) as compared with controls (29.8% and 16.5%), suggesting sufficient statistical power in our sample. No relation was found between the A2M-2 and the ApoE epsilon4 allele. No change in A2M exon 17-18 mRNA size or sequence or A2M protein size was found in cases carrying the A2M-2 deletion, suggesting that there is no biological consequences of the A2M intronic deletion. No change in A2M protein level in cerebrospinal fluid was found in AD, suggesting that the A2M-2 allele does not effect the A2M protein expression in the brain. The lack of an association between the A2M-2 allele and AD in the present study, and the lack of abnormalities in the A2M mRNA or protein suggest that the A2M-2 allele is not associated with AD.
|
|
| 7. |
|
|
| 8. |
- Brookes, N. B., et al.
(författare)
-
Detection of Zhang-Rice singlets using spin-polarized photoemission
- 2001
-
Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 8723:23
-
Tidskriftsartikel (refereegranskat)abstract
- From a spin-resolved photoemission study on the Bi2Sr2CaCu2O8+delta superconductor, we show experimentally that the first ionization state is of nearly pure singlet character. This is true both above and below the superconducting transition and in the presence of doping and band formation. This provides direct support for the existence and stability of Zhang-Rice singlets in high-temperature superconductors, justifying the ansatz of single-band models. Moreover, we establish this technique as an important probe for a wide range of cuprates and strongly correlated materials.
|
|
| 9. |
- Ghiringhelli, G., et al.
(författare)
-
Probing the singlet character of the two-hole states in cuprate superconductors
- 2002
-
Ingår i: Physica. B, Condensed matter. - 0921-4526 .- 1873-2135. ; 312, s. 34-35
-
Tidskriftsartikel (refereegranskat)abstract
- Using spin-resolved resonant photoemission we have probed the singlet vs. triplet character of the two-hole state in the layered cuprates Bi2Sr2CaCu2O8+delta La2-xSrxCuO4 and Sr2CuO2Cl2. The combination of the photon circular polarization with the photoelectron spin detection gives access to the character of the photoemission final states, which correspond to the two-hole configurations localized at a (CuO4) site. In particular, the lowest energy state is found to have a very high singlet character in all the measured compounds. This can be considered as a strong indication of the existence and stability of the so-called Zhang-Rice singlets in the layered cuprates.
|
|
| 10. |
- J.Lindner, A.Scherz, P.Poulopoulos, C.Rudt, A.N.Anisimov, H.Wende, K.Baberschke, P.Blomquist, R.Wäppling, F.Wilhelm, N.B.Brookes
(författare)
-
Ultrathin Fe-limit in Fe/V(001) superlattices
- 2003
-
Ingår i: Journal of Magnetism and Magnetic Materials. ; 256:1-3, s. 404-411
-
Tidskriftsartikel (refereegranskat)
|
|
