| 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. |
- Banerjee, Mitali, et al.
(författare)
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Magnetism in FeNiW disordered alloys : Experiment and theory
- 2010
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Ingår i: Journal of Magnetism and Magnetic Materials. - : Elsevier BV. - 0304-8853 .- 1873-4766. ; 322:21, s. 3558-3564
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Tidskriftsartikel (refereegranskat)abstract
- We report here an experimental study of magnetization of FeNiW alloys at different compositions. We have studied variation of magnetization with temperature (at low external fields) and magnetic field (at low temperatures). The alloy shows para to ferromagnetic transitions across the composition range. We do not find any indication of the spin-glass phase. We have supplemented the experimental work with theoretical analysis using the first-principles tight-binding linear muffin-tin orbitals based augmented space recursion method. Our theoretical estimates of magnetic moment and Curie temperatures agree well with experiment. Our mean-field phase analysis also does not indicate the possibility of a spin-glass.
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| 3. |
- Banerjee, Mitali, et al.
(författare)
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Magnetism in NiFeMo disordered alloys : Experiment and theory
- 2010
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Ingår i: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 405:20, s. 4287-4293
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Tidskriftsartikel (refereegranskat)abstract
- In this communication we carry out experimental investigation of the behavior of magnetization with temperature and magnetic field of six samples at different compositions of the disordered ternary alloy NiFeMo. We analyze the data using a fist-principles density functional based electronic structure method and a mean-field phase diagram study.
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| 4. |
- Banerjee, Rudra, et al.
(författare)
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Fe3.3Ni83.2Mo13.5 : a likely candidate to show spin-glass behaviour at low temperatures
- 2011
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Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 23:10, s. 106002-
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Tidskriftsartikel (refereegranskat)abstract
- Unlike other transition metals alloyed with a non-magnetic metal, alloys of Ni behave rather differently. This is because of the fragility of the local magnetic moment on Ni. NiMo and NiW do not show any spin-glass phase. However, addition of Fe can bolster the moment on Ni. We wish to study whether the alloy Fe3.3Ni83.2Mo13.5, chosen near a composition where mean-field estimates suggest there could be a spin-glass phase, shows such a phase or not.
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| 5. |
- Pal, Pampa, et al.
(författare)
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Magnetic ordering in Ni-rich NiMn alloys around the multicritical point : Experiment and theory
- 2012
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 85:17, s. 174405-
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Tidskriftsartikel (refereegranskat)abstract
- We have carried out an experimental study of Ni-rich NiMn alloys in a series of compositions across the multicritical point and determined the phase diagram within that range. We have observed ferromagnetic long-range order with reentrant spin-glass/ferro-spin-glass phase for x <= 25, an antiferromagnetic long-range order around x similar to 37, and a gradual change from a canonical spin-glass state to a long-range antiferromagnetic phase in the intermediate composition region. In order to explain the experimental observations, we have examined the physical properties from a density functional based first-principals theoretical analysis and used it to understand the experimental results. Using atomic spin dynamics simulations based on the Landau-Lifshitz-Gilbert equation, we have found the aging behavior and anomalously slow relaxation of magnetization in the composition range where experiment observes spin-glassy behavior.
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| 6. |
- Rozenblum, E, et al.
(författare)
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A genomic map of a 6-Mb region at 13q21-q22 implicated in cancer development: identification and characterization of candidate genes
- 2002
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Ingår i: Human Genetics. - : Springer Science and Business Media LLC. - 1432-1203 .- 0340-6717. ; 110:2, s. 111-121
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Tidskriftsartikel (refereegranskat)abstract
- Chromosomal region 13q21-q22 harbors a putative breast cancer susceptibility gene and has been implicated as a common site for somatic deletions in a variety of malignant tumors. We have built a complete physical clone contig for a region between D13S1308 and AFM220YE9 based on 18 yeast artificial chromosome and 81 bacterial artificial chromosome (BAC) clones linked together by 22 genetic markers and 61 other sequence tagged sites. Combining data from 47 sequenced BACs (as of June 2001), we have assembled in silico an integrated 5.7-Mb genomic map with 90% sequence coverage. This area contains eight known genes, two hypothetical proteins, 24 additional Unigene clusters, and approximately 100 predicted genes and exons. We have determined the cDNA and genomic sequence, and tissue expression profiles for the KIAA1008 protein (homologous to the yeast mitotic control protein dis3+), KLF12 (AP-2 repressor), progesterone induced blocking factor 1, zinc finger transcription factor KLF5, and LIM domain only-7, and for the hypothetical proteins FLJ22624 and FLJ21869. Mutation screening of the five known genes in 19 breast cancer families has revealed numerous polymorphisms, but no deleterious mutations. These data provide a basis and resources for further analyses of this chromosomal region in the development of cancer.
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| 7. |
- Bhardwaj, Vishal, et al.
(författare)
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Observation of surface dominated topological transport in strained semimetallic ErPdBi thin films
- 2020
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 117:13
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Tidskriftsartikel (refereegranskat)abstract
- In this Letter, we present experimental observation of surface-dominated transport properties in [110]-oriented strained (∼1.6%) ErPdBi thin films. The resistivity data show typical semi-metallic behavior in the temperature range of 3 K ≤ T ≤ 350 K with a transition from semiconductor- to metal-like behavior below 3 K. The metallic behavior at low temperature disappears entirely in the presence of an external magnetic field >1 T. The weak-antilocalization (WAL) effect is observed in magneto-conductance data in the low magnetic field region and follows the Hikami-Larkin-Nagaoka (HLN) model. HLN fitting estimated single coherent channel, i.e., α ∼-0.51 at 1.9 K, and the phase coherence length (Lφ) shows the Lφ ∼T-0.52 power law dependence on temperature in the range of 1.9 K-10 K, indicating the observation of 2D WAL. Shubnikov-de Haas (SdH) oscillations are observed in magneto-resistance data below 10 K and are fitted to standard Lifhsitz Kosevich theory. Fitting reveals the effective mass of charge carriers ∼0.15 me and a finite Berry phase of 0.86π± 0.16. The sheet carrier concentration and mobility of carriers estimated using SdH data are ns ∼1.35 × 1012 cm-2 and μs = 1210 cm2 V-1 s-1, respectively, and match well with the data measured using the Hall measurement at 1.9 K to be n ∼1.22 × 1012 cm-2, μ = 1035 cm2 V-1 s-1. These findings indicate the non-trivial nature and surface-dominated transport properties of strained (110) ErPdBi thin films at low temperatures.
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| 8. |
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| 9. |
- Liang, Y., et al.
(författare)
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Desmosomal COP9 regulates proteome degradation in arrhythmogenic right ventricular dysplasia/cardiomyopathy
- 2021
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Ingår i: Journal of Clinical Investigation. - : American Society for Clinical Investigation. - 0021-9738 .- 1558-8238. ; 131:11
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Tidskriftsartikel (refereegranskat)abstract
- Dysregulated protein degradative pathways are increasingly recognized as mediators of human disease. This mechanism may have particular relevance to desmosomal proteins that play critical structural roles in both tissue architecture and cell-cell communication, as destabilization/breakdown of the desmosomal proteome is a hallmark of genetic-based desmosomal-targeted diseases, such as the cardiac disease arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C). However, no information exists on whether there are resident proteins that regulate desmosomal proteome homeostasis. Here, we uncovered a cardiac constitutive photomorphogenesis 9 (COP9) desmosomal resident protein complex, composed of subunit 6 of the COP9 signalosome (CSN6), that enzymatically restricted neddylation and targeted desmosomal proteome degradation. CSN6 binding, localization, levels, and function were affected in hearts of classic mouse and human models of ARVD/C affected by desmosomal loss and mutations, respectively. Loss of desmosomal proteome degradation control due to junctional reduction/loss of CSN6 and human desmosomal mutations destabilizing junctional CSN6 were also sufficient to trigger ARVD/C in mice. We identified a desmosomal resident regulatory complex that restricted desmosomal proteome degradation and disease.
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