Identification of 45 New Neutron-Rich Isotopes Produced by In-Flight Fission of a 238U Beam at 345 MeV/nucleon

A search for new isotopes using in-flight fission of a 345 MeV/nucleon 238U beam has been carried out at the RI Beam Factory at the RIKEN Nishina Center. Fission fragments were analyzed and identified by using the superconducting in-flight separator BigRIPS. We observed 45 new neutron-rich isotopes: 71Mn, 73,74Fe, 76Co, 79Ni, 81,82Cu, 84,85Zn, 87Ga, 90Ge, 95Se, 98Br, 101Kr, 103Rb, 106,107Sr, 108,109Y, 111,112Zr, 114,115Nb, 115,116,117Mo, 119,120Tc, 121,122,123,124Ru, 123,124,125,126Rh, 127,128Pd, 133Cd, 138Sn, 140Sb, 143Te, 145I, 148Xe, and 152Ba

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

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

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.National audienceThe 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

Oligomerization of optineurin and its oxidative stress- or E50K mutation-driven covalent cross-linking: possible relationship with glaucoma pathology.

The optineurin gene, OPTN, is one of the causative genes of primary open-angle glaucoma. Although oligomerization of optineurin in cultured cells was previously observed by gel filtration analysis and blue native gel electrophoresis (BNE), little is known about the characteristics of optineurin oligomers. Here, we aimed to analyze the oligomeric state of optineurin and factors affecting oligomerization, such as environmental stimuli or mutations in OPTN. Using BNE or immunoprecipitation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), we demonstrated that both endogenous and transfected optineurin exist as oligomers, rather than monomers, in NIH3T3 cells. We also applied an in situ proximity ligation assay to visualize the self-interaction of optineurin in fixed HeLaS3 cells and found that the optineurin oligomers were localized diffusely in the cytoplasm. Optineurin oligomers were usually detected as a single band of a size equal to that of the optineurin monomer upon SDS-PAGE, while an additional protein band of a larger size was observed when cells were treated with H2O2. We showed that larger protein complex is optineurin oligomers by immunoprecipitation and termed it covalent optineurin oligomers. In cells expressing OPTN bearing the most common glaucoma-associated mutation, E50K, covalent oligomers were formed even without H2O2 stimulation. Antioxidants inhibited the formation of E50K-induced covalent oligomers to various degrees. A series of truncated constructs of OPTN was used to reveal that covalent oligomers may be optineurin trimers and that the ubiquitin-binding domain is essential for formation of these trimers. Our results indicated that optineurin trimers may be the basic unit of these oligomers. The oligomeric state can be affected by many factors that induce covalent bonds, such as H2O2 or E50K, as demonstrated here; this provides novel insights into the pathogenicity of E50K. Furthermore, regulation of the oligomeric state should be studied in the future

Association of Objectively Measured Physical Activity with Physical Function in Patients with Sarcopenia during Hospitalized Rehabilitation

This study aimed to investigate the association between objectively measured physical activity and functional improvement in hospitalized patients with sarcopenia. In this retrospective cohort study, physical activity (light-intensity physical activity [LIPA]; moderate-to-physical activity [MVPA]) was measured using a triaxial accelerometer in patients with sarcopenia undergoing rehabilitation on hospital admission. The primary outcome was physical function measured with the SPPB and activity of daily living (ADL) measured with the functional independence measure scores for motor function (FIM-M) at hospital discharge. Multiple regression analysis was per-formed to investigate the relationship between the objectively measured physical activity and functional outcomes. A total of 182 patients with sarcopenia (aged 81; interquartile range (IQR) 13 years) were included in this study. In the multiple regression analysis, LIPA was associated with the SPPB score at discharge (β = 0.180, p = 0.015) but not with FIM-M at discharge. MVPA was not associated with SPPB or FIM-M scores at discharge. In conclusion, LIPA on admission is independently associated with physical function, but not ADL, in patients with sarcopenia undergoing hospitalized rehabilitation

Predicted and estimated molecular weights of monomers and covalent oligomers of optineurin and its mutants.

<p>OPTN, optineurin; WT, wild-type; Lc1st, lacking the first OPTN region; L2nd, lacking the second OPTN region; Lc3rd, lacking the third OPTN region; Lc4th, lacking the fourth OPTN region.</p

Covalently bonded oligomers of optineurin are induced by oxidative stress.

<p><b>A.</b> NIH3T3 cells transfected with FLAG-OPTN were incubated without or with 25 mM H₂O₂ for 20 min and then analyzed by SDS-PAGE and western blotting with anti-FLAG antibody. A protein complex (right lane, arrow) was observed in the H₂O₂-treated sample. Other high molecular weight bands (asterisk) were seen at low density in both untreated and H₂O₂-treated samples. The optineurin (OPTN) monomer was observed at the expected position (arrowhead) <b>B</b>. After standard transfection into NIH3T3 or HeLaS3 cells and treatment without or with FLAG-OPTN and H₂O₂, lysates were immunoprecipitated with anti-OPTN antibody for detection of endogenous OPTN (left panel), or anti-FLAG antibody for detection of transfected OPTN. The H₂O₂-induced protein band was detected by anti-OPTN antibody in all cases (arrow). Both endogenous and transfected OPTN monomer band was observed at an expected position (arrowhead). Another band was seen above the monomer in the lane of transfected OPTN, but it was not analyzed in this study because it was not present in the case of endogenous OPTN. <b>C</b>. NIH3T3 cells expressing GFP-OPTN and FLAG-OPTN, or both, were treated without or with H₂O₂. Cell lysates were immunoprecipitated with anti-FLAG antibody and analyzed by western blotting with antibodies against FLAG (lanes 1–6) or GFP (lanes 7–12). The H₂O₂-induced bands were detected in co-transfected and FLAG-transfected samples (lanes 2, 4, and 8, arrows). OPTN monomer bands were shown as arrowheads. IB: immunoblotting; IP: immunoprecipitation.</p

Ubiquitin binding is not involved in the formation of covalent optineurin trimers.

<p><b>A.</b> Covalent trimers were observed in NIH3T3 cells expressing the D474N mutant (arrow) using SDS-PAGE followed by western blotting (WB). Monomers were shown as arrowhead. <b>B</b>. HeLa cells transfected with wild-type (WT) or one of the mutants of optineurin (OPTN; D474N, LcZF, or LcUBD) along with firefly and <i>Renilla</i> luciferase reporters were incubated with 10 ng/ml TNFα for 5 h and examined using a Dual-Luciferase Reporter Assay System (DLRAS). Cells expressing WT OPTN or empty vector were used as controls. The ratios of firefly luminescence to <i>Renilla</i> luminescence represented the relative luciferase activity (n = 3). There were statistically significant differences between WT and mutants of OPTN (<i>P</i><0.05). <b>C</b>. Confirmation of the expression of WT and OPTN mutants in HeLaS3 cells before DLRAS, shown by WB. <b>D</b>. Expression of double point mutations of OPTN (E50K–D474N) induced the formation of covalent trimers in NIH3T3 cells, without H₂O₂ treatment. IB: immunoblotting; IP: immunoprecipitation.</p