Search

International audience; Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

Introduction 76Br is of interest for in vivo PET imaging applications. Its relatively long half-life (16.1 h) allows use not only on small molecules but also proteins which have slow excretion as carrier molecules. Irradiation using a low energy proton beam (~ 20 MeV) on an enriched Cu276Se target, followed by dry distillation with thermal chromatography, is one of the best methods to obtain sufficient amounts of 76Br for clinical applications1,2. However, the thermal chromatography is plagued by poor reproducibility and appears unsuitable for automation of its production, leading us to remove the thermal chroma-tography from the dry distillation. In this investigation we employed H2O solution to collect 76Br and optimized the distillation condition using a small amount of 77Br (57.0 h). We also produced large amount of 76Br under the optimized conditions to evaluate the dry distillation method. Material and Methods Target preparation and dry distillation were conducted based on the methods described in previous reports1,2. To produce 77Br, Cu2natSe target was irradiated with 20 MeV proton beams (5 µA) accelerated by AVF cyclotron in the Japan Atomic Energy Agency. The following two systems were used in the dry distillation optimization studies; (1) an initial system was composed of two furnaces, a main and an auxiliary furnace. Temperature of each furnace was set at 1050 °C (main) and 200 °C (auxiliary) respectively; (2) the second system was made of one large furnace composed of heating and cooling area. Temperature of the heating area was varied from 1050 to 1120 °C. In both systems PTFE tubing, leading to a H2O solution (15 mL), was inserted into the apparatus. The irradiated target was heated under streaming Ar gas (30 mL/min.). An enriched Cu276Se target (76Se enrichment: 99.67%) was used for 76Br production. Radioactivity was measured on a high-purity germanium (HPGe) detector coupled to a multichannel analyzer. TLC analyses were conducted on Al2O3 plates (Merck) using 7:1 acetone:H2O as the eluting solvent. Results and Conclusion Low efficiency (33 %) of 77Br recovery was ob-served in the initial system. Distribution of radioactivity inside the apparatus showed that 35 % was trapped in the PTFE tube and the quartz tube. The recovery yield was increased up to 54 % when the auxiliary furnace was turned off, indicating that the temperature gradient inside the quartz tube is suitable to carry 77Br effectively to the H2O trap. We initially used a quartz boat to place the irradiated target in the furnace, but found that using a reusable tungsten backing was better. However, we found that recovery yield was dramatically reduced to 18 %. The studies where the temperature was varied showed that releasing efficiency was increased up to 100 % at the temperature of 1120 °C. Good recovery yield (~ 77 %) was achieved after optimizing the temperature gradient (FIG. 1b). Using the optimized setup, 76Br production runs (n = 6) have been conducted, allowing us to recover up to 39.8 MBq/µAh (EOB) of 76Br. High specific activity (~4400 GBq/µmol) was obtained in the final solution. TLC analysis showed that chemical form obtained was bromide. We concluded that the dry distillation using H2O trap is capable of providing enough high purity 76Br for clinical applications.

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein\ud requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of\ud investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene\ud prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus\ud performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as\ud complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level.\ud Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length\ud cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also\ud manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene\ud database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following:\ud integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms,\ud non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein\ud three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic\ud microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB\ud analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information\ud build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates\ud (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for nonprotein-coding\ud RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within\ud human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together\ud with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing\ud phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources\ud needed for the exploration of human biology and pathology

For the purpose of clarifying the histogenesis of clear cell sarcoma of tendons and aponeuroses (CCS) as well as the problem of whether or not CCS is a heterogeneous group of neoplasms, studies based on various methods were performed. Analysis of glycosaminoglycans gave the same results for amelanotic CCS and synovial sarcoma, and the DOPA reaction gave the same negative results for amelanotic CCS and synovial sarcoma. However, the DOPA reaction was also negative in an amelanotic recurrent tumor of a melanotic CCS, and electron-microscopic studies revealed a close resemblance between amelanotic CCS and melanotic CCS. Further, enzyme histochemical studies showed definite differences between synovial sarcoma and amelanotic CCS but gave identical results for amelanotic and melanotic CCS. Immunohistochemical studies revealed the presence of S-100 protein in all CCS cases, both amelanotic and melanotic. These results indicate that CCS is not a heterogeneous group of neoplasms, and that both amelanotic and melanotic CCS are of neural crest origin.

As an initial step to elucidate the nature of the unique characteristics of the crystalloids of alveolar soft part sarcoma, a three-dimensional model of the crystalloids was prepared by digital image analysis of electron micrographs by computer. It was revealed that occult periodicities are present at two intervals, 60 A and 380 A, in the filamentous structure of the crystalloid; and it was also revealed by the observation of each cross-section that two globular substances with a diameter of 60 A are arranged in a dumbbell pattern in each filamentous structure. The model prepared based on these data showed the double strands crossing each other at intervals of 380 A, each of which consists of successive arrangement of the globular substances with a diameter of 60 A. This structure is clearly similar to that of actin. The similarities and differences between these results and the well-known studies of the organization of naturally occurring actin bundles are discussed.

Skeletal lesions are not uncommon in von Recklinghausen neurofibromatosis. Most of them are considered to be dysplastic in nature. Association of osteomalacia or rickets with neurofibromatosis has been documented only rarely. Reported herein is a 40-year-old woman with known von Recklinghausen neurofibromatosis who presented with bone pain, multiple pseudofractures, marked increase in osteoid by bone biopsy, and hypophosphatemia with renal phosphate wasting. Treatment with oral phosphate and vitamin D was effective. A survey of the literature revealed that 34 similar cases have been reported in the past. Although the exact pathogenetic mechanism remains to be determined, osteomalacia in neurofibromatosis appears to be distinct from more common dysplastic skeletal affections of this disease, being characterized by later onset in adulthood as a rule, renal phosphate loss with hypophosphatemia, multiple pseudofractures in typical cases, and response to treatment with pharmacological dose of vitamin D with or without phosphate supplement.