Genetic relationships of char distributed in the watershed border between three river basins in the eastern Chugoku Region, Japan.

Genetic relationships among a subspecies of white-spotted char, Salvelinus leucomaenis pluvius, distributed in the border area of three river basins in the eastern Chugoku region of Japan (the Sendai River, flowing into the Sea of Japan, and the Yoshii and Chigusa rivers, both flowing into the Seto Inland Sea), were investigated based on mitochondrial DNA cytochrome-b gene sequences. A total of 7 haplotypes were recognized and there were 8 polymorphic sites in a 447 bp fragment. Some haplotypes were shared by fish in two adjacent basins across passes, and some were confined to restricted basins. One haplotype estimated to be the oldest could be connected to ‘Gogi’, S. leucomaenis imbrius. Another haplotype, estimated to have derived in the most recent period, was observed in more than half the samples. There was a significant positive correlation between the geographic and genetic distances. These results suggest that genetic distance was more strongly determined by geographic distance than by river-basin location, and may support the possibility of range expansion of char by taking advantage of geologic events

Influences of riverside vegetation on the health of ‘Gogi’ char <Article>

Relationships between the riverside vegetation and the health of a subspecies of Japanese common char, Salvelinus leucomaenis imbrius (‘Gogi’) were studied in the Chugoku Mountains. The densities of riverside vegetation comprising deciduous broad-leaf and evergreen coniferous trees, food environments comprising benthic and flowing aquatic animals and falling terrestrial animals, and the relative liver weight of char were examined. It is suggested that a high density of deciduous broad-leaf trees provides a good food environment, resulting in sound health of Gogi char

Seasonal Occurrence of Large-sized Black Porgy, Acanthopagrus schlegelii in an Intertidal Short-neck Clam Fishery Ground in Hiroshima Bay, Japan

広島湾最大のアサリ漁獲量のある漁場である広島県廿日市市の前潟干潟において，2003年2月から2004年1月の1年間にわたり刺網による調査を行い，アサリ食害魚種である大型のクロダイAcanthopagrus schlegeliiの出現状況を明らかにした。9種73個体の魚類が採集され，クロダイ（23.6～48.5cm TL）が全個体数の79％を占める優占種であった。クロダイの月別CPUE（個体数/300m/回）は0～18.8の範囲であり，6月末に急上昇し，7月末には最高値の18.8を示し，8月末，9月末も高値を示した。本種は，初夏から秋季の6月末～10月末の5ヶ月間に多く出現すること，この間は，体サイズにかかわらず干潟域を利用することが明らかになった。Black porgy, Acanthopagrus schlegelii (Family: Sparidae), is a commercially important fish in Japan. This species is known as a major predator of the short-neck clam Ruditapes philippinarum in tidal flats. Seasonal occurrence of large fishes such as the porgy was investigated from February 2003 to January 2004 at the Maegata tidal flat, which has the largest catch of short-neck clam in Hiroshima Bay, western Seto Inland Sea. As a result, 73 individuals from nine species were collected by monthly gill net sampling. A. schlegelii, 23.6-48.5 cm total length was the dominant species and accounted for 79% of the total individuals. The catch per unit effort (CPUE: number of fish caught/300 m of netting) of the porgy was 0–18.8. The CPUE rapidly increased in late June. In late July, it reached 18.8, the highest annual value, after which the CPUE maintained high values during late August and late September. From late November values were low (0-3.0) again. These results indicate that large-sized A. schlegelii occur seasonally in the tidal flats from late June to late October

Characterization of Catalase from Psychrotolerant Psychrobacter piscatorii T-3 Exhibiting High Catalase Activity

A psychrotolerant bacterium, strain T-3 (identified as Psychrobacter piscatorii), that exhibited an extraordinarily high catalase activity was isolated from the drain pool of a plant that uses H2O2 as a bleaching agent. Its cell extract exhibited a catalase activity (19,700 U·mg protein−1) that was higher than that of Micrococcus luteus used for industrial catalase production. Catalase was approximately 10% of the total proteins in the cell extract of the strain. The catalase (PktA) was purified homogeneously by only two purification steps, anion exchange and hydrophobic chromatographies. The purified catalase exhibited higher catalytic efficiency and higher sensitivity of activity at high temperatures than M. luteus catalase. The deduced amino acid sequence showed the highest homology with catalase of Psycrobacter cryohalolentis, a psychrotolelant bacterium obtained from Siberian permafrost. These findings suggest that the characteristics of the PktA molecule reflected the taxonomic relationship of the isolate as well as the environmental conditions (low temperatures and high concentrations of H2O2) under which the bacterium survives. Strain T-3 efficiently produces a catalase (PktA) at a higher rate than Exiguobacterium oxidotolerans, which produces a very strong activity of catalase (EktA) at a moderate rate, in order to adapt to high concentration of H2O2

Reports of studies supported by Grant-in-Aid for Research from the Graduate School of Biosphere Science, Hiroshima University

プロジェクト研究 Grant-in-Aid for Project Research ・ミャンマー沿岸における有害・有毒植物プランクトンの発生・増殖機構に関する調査研究...Su MYAT, Maung Saw Htoo THAW, 藤瀬里紗, Khin Ko LAY, 小池一彦 ・東日本大震災における水産業・漁村の復興戦略に向けた提言作り : 東アジア海域社会の地震・津波復興に関する比較研究を通じて...山尾政博 基盤研究サポート Grant-in-Aid for Fundamental Research ・大脳によらない恐怖学習 : 魚類小脳に注目して...吉田将之 ・チョコレートモデル油脂結晶の分子レベルその場観察...本同宏成 ・広島市近郊における伝統的青果物流通主体の形成・展開と産地維持機能に関する研究...細野賢治，矢野泉，高梨子文恵 ・釣り餌として海外から流通される水生動物の移入と定着に関する基礎的研究...斉藤英俊 ・低い割合で給与するイタリアンライグラスサイレージの栽培時施肥方法の違いが泌乳中・後期牛の乳生産に及ぼす影響...黒川勇

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

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