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Search Results: 1 - 10 of 1648 matches for " Yumi Yamaguchi-Kabata "
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Distribution and Effects of Nonsense Polymorphisms in Human Genes
Yumi Yamaguchi-Kabata, Makoto K. Shimada, Yosuke Hayakawa, Shinsei Minoshima, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003393
Abstract: Background A great amount of data has been accumulated on genetic variations in the human genome, but we still do not know much about how the genetic variations affect gene function. In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products. Methodology/Principal Findings To detect polymorphisms affecting gene function, we analyzed all publicly available polymorphisms in a database for single nucleotide polymorphisms (dbSNP build 125) located in the exons of 36,712 known and predicted protein-coding genes that were defined in an annotation project of all human genes and transcripts (H-InvDB ver3.8). We found a total of 252,555 single nucleotide polymorphisms (SNPs) and 8,479 insertion and deletions in the representative transcripts in these genes. The SNPs located in ORFs include 40,484 synonymous and 53,754 nonsynonymous SNPs, and 1,258 SNPs that were predicted to be nonsense SNPs or read-through SNPs. We estimated the density of nonsense SNPs to be 0.85×10?3 per site, which is lower than that of nonsynonymous SNPs (2.1×10?3 per site). On average, nonsense SNPs were located 250 codons upstream of the original termination codon, with the substitution occurring most frequently at the first codon position. Of the nonsense SNPs, 581 were predicted to cause nonsense-mediated decay (NMD) of transcripts that would prevent translation. We found that nonsense SNPs causing NMD were more common in genes involving kinase activity and transport. The remaining 602 nonsense SNPs are predicted to produce truncated polypeptides, with an average truncation of 75 amino acids. In addition, 110 read-through SNPs at termination codons were detected. Conclusion/Significance Our comprehensive exploration of nonsense polymorphisms showed that nonsense SNPs exist at a lower density than nonsynonymous SNPs, suggesting that nonsense mutations have more severe effects than amino acid changes. The correspondence of nonsense SNPs to known pathological variants suggests that phenotypic effects of nonsense SNPs have been reported for only a small fraction of nonsense SNPs, and that nonsense SNPs causing NMD are more likely to be involved in phenotypic variations. These nonsense SNPs may include pathological variants that have not yet been reported. These data are available from Transcript View of H-InvDB and VarySysDB (http://h-invitational.jp/varygene/).
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Tadashi Imanishi,Takeshi Itoh,Yutaka Suzuki,Claire O'Donovan,Satoshi Fukuchi,Kanako O. Koyanagi,Roberto A. Barrero,Takuro Tamura,Yumi Yamaguchi-Kabata,Motohiko Tanino
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0020162
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.
Prediction of Protein-Destabilizing Polymorphisms by Manual Curation with Protein Structure
Craig Alan Gough, Keiichi Homma, Yumi Yamaguchi-Kabata, Makoto K. Shimada, Ranajit Chakraborty, Yasuyuki Fujii, Hisakazu Iwama, Shinsei Minoshima, Shigetaka Sakamoto, Yoshiharu Sato, Yoshiyuki Suzuki, Masahito Tada-Umezaki, Ken Nishikawa, Tadashi Imanishi, Takashi Gojobori
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050445
Abstract: The relationship between sequence polymorphisms and human disease has been studied mostly in terms of effects of single nucleotide polymorphisms (SNPs) leading to single amino acid substitutions that change protein structure and function. However, less attention has been paid to more drastic sequence polymorphisms which cause premature termination of a protein’s sequence or large changes, insertions, or deletions in the sequence. We have analyzed a large set (n = 512) of insertions and deletions (indels) and single nucleotide polymorphisms causing premature termination of translation in disease-related genes. Prediction of protein-destabilization effects was performed by graphical presentation of the locations of polymorphisms in the protein structure, using the Genomes TO Protein (GTOP) database, and manual annotation with a set of specific criteria. Protein-destabilization was predicted for 44.4% of the nonsense SNPs, 32.4% of the frameshifting indels, and 9.1% of the non-frameshifting indels. A prediction of nonsense-mediated decay allowed to infer which truncated proteins would actually be translated as defective proteins. These cases included the proteins linked to diseases inherited dominantly, suggesting a relation between these diseases and toxic aggregation. Our approach would be useful in identifying potentially aggregation-inducing polymorphisms that may have pathological effects.
Identification of Nine Novel Loci Associated with White Blood Cell Subtypes in a Japanese Population
Yukinori Okada ,Tomomitsu Hirota,Yoichiro Kamatani,Atsushi Takahashi,Hiroko Ohmiya,Natsuhiko Kumasaka,Koichiro Higasa,Yumi Yamaguchi-Kabata,Naoya Hosono,Michael A. Nalls,Ming Huei Chen,Frank J. A. van Rooij,Albert V. Smith,Toshiko Tanaka,David J. Couper,Neil A. Zakai,Luigi Ferrucci,Dan L. Longo,Dena G. Hernandez,Jacqueline C. M. Witteman,Tamara B. Harris,Christopher J. O'Donnell,Santhi K. Ganesh,Koichi Matsuda,Tatsuhiko Tsunoda,Toshihiro Tanaka,Michiaki Kubo,Yusuke Nakamura,Mayumi Tamari,Kazuhiko Yamamoto,Naoyuki Kamatani
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002067
Abstract: White blood cells (WBCs) mediate immune systems and consist of various subtypes with distinct roles. Elucidation of the mechanism that regulates the counts of the WBC subtypes would provide useful insights into both the etiology of the immune system and disease pathogenesis. In this study, we report results of genome-wide association studies (GWAS) and a replication study for the counts of the 5 main WBC subtypes (neutrophils, lymphocytes, monocytes, basophils, and eosinophils) using 14,792 Japanese subjects enrolled in the BioBank Japan Project. We identified 12 significantly associated loci that satisfied the genome-wide significance threshold of P<5.0×10?8, of which 9 loci were novel (the CDK6 locus for the neutrophil count; the ITGA4, MLZE, STXBP6 loci, and the MHC region for the monocyte count; the SLC45A3-NUCKS1, GATA2, NAALAD2, ERG loci for the basophil count). We further evaluated associations in the identified loci using 15,600 subjects from Caucasian populations. These WBC subtype-related loci demonstrated a variety of patterns of pleiotropic associations within the WBC subtypes, or with total WBC count, platelet count, or red blood cell-related traits (n = 30,454), which suggests unique and common functional roles of these loci in the processes of hematopoiesis. This study should contribute to the understanding of the genetic backgrounds of the WBC subtypes and hematological traits.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Tadashi Imanishi,Takeshi Itoh,Yutaka Suzuki,Claire O'Donovan,Satoshi Fukuchi,Kanako O Koyanagi,Roberto A Barrero,Takuro Tamura,Yumi Yamaguchi-Kabata,Motohiko Tanino,Kei Yura,Satoru Miyazaki,Kazuho Ikeo,Keiichi Homma,Arek Kasprzyk,Tetsuo Nishikawa,Mika Hirakawa,Jean Thierry-Mieg,Danielle Thierry-Mieg,Jennifer Ashurst,Libin Jia,Mitsuteru Nakao,Michael A Thomas,Nicola Mulder,Youla Karavidopoulou,Lihua Jin,Sangsoo Kim,Tomohiro Yasuda,Boris Lenhard,Eric Eveno,Yoshiyuki Suzuki,Chisato Yamasaki,Jun-ichi Takeda,Craig Gough,Phillip Hilton,Yasuyuki Fujii,Hiroaki Sakai,Susumu Tanaka,Clara Amid,Matthew Bellgard,Maria de Fatima Bonaldo,Hidemasa Bono,Susan K Bromberg,Anthony J Brookes,Elspeth Bruford,Piero Carninci,Claude Chelala,Christine Couillault,Sandro J. de Souza,Marie-Anne Debily,Marie-Dominique Devignes,Inna Dubchak,Toshinori Endo,Anne Estreicher,Eduardo Eyras,Kaoru Fukami-Kobayashi,Gopal R. Gopinath,Esther Graudens,Yoonsoo Hahn,Michael Han,Ze-Guang Han,Kousuke Hanada,Hideki Hanaoka,Erimi Harada,Katsuyuki Hashimoto,Ursula Hinz,Momoki Hirai,Teruyoshi Hishiki,Ian Hopkinson,Sandrine Imbeaud,Hidetoshi Inoko,Alexander Kanapin,Yayoi Kaneko,Takeya Kasukawa,Janet Kelso,Paul Kersey,Reiko Kikuno,Kouichi Kimura,Bernhard Korn,Vladimir Kuryshev,Izabela Makalowska,Takashi Makino,Shuhei Mano,Regine Mariage-Samson,Jun Mashima,Hideo Matsuda,Hans-Werner Mewes,Shinsei Minoshima,Keiichi Nagai,Hideki Nagasaki,Naoki Nagata,Rajni Nigam,Osamu Ogasawara,Osamu Ohara,Masafumi Ohtsubo,Norihiro Okada
PLOS Biology , 2004, DOI: 10.1371/journal.pbio.0020162
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.
Homology modeling and structural analysis of human γ-glutamylcysteine ligase catalytic subunit for antitumor drug development  [PDF]
Hideaki Yamaguchi, Tatsuo Akitaya, Yumi Kidachi, Katsuyoshi Kamiie, Hironori Umetsu
Journal of Biophysical Chemistry (JBPC) , 2012, DOI: 10.4236/jbpc.2012.33028
Abstract: Homology modeling and structural analysis of human glutamate cysteine ligase catalytic subunit (hGCLC) were performed with a software package the Molecular Operating Environment. A yeast GCLC (yGCLC; PDB code: 3LVV) was selected as a template for the 3D structure modeling of hGCLC. The modeled hGCLC showed significant 3D similarities at the ligand biding site (LBS) to the yGCLC structure. The contact energy profiles of the hGCLC model were in good agreement with those of the yGCLC structure. Ramachandran plots revealed that only 1.4% of the amino acid residues were in the disfavored region for hGCLC. The molecular electrostatic potential (MEP) map of the hGCLC model exhibited that the model was slightly different from the yGCLC model electrostatically at the LBS. Further, docking simulations revealed the similarity of the ligand-receptor bound location between the hGCLC and yGCLC models. The different binding orientations between the glutathione (GSH)-hGCLC and GSH-yGCLC complexes reflected the different MEP maps at the LBSs between the hGCLC and yGCLC models. These results indicate that the hGCLC model was successfully modeled and analyzed. To the best of our knowledge, this is the first report of a hGCLC model with detailed analyses, and our data verify that the model can be utilized for application to target hGCLC for the development of anticancer drugs.
Mouse 11β-Hydroxysteroid Dehydrogenase Type 2 for Human Application: Homology Modeling, Structural Analysis and Ligand-Receptor Interaction
Hideaki Yamaguchi,Tatsuo Akitaya,Yumi Kidachi,Katsuyoshi Kamiie
Cancer Informatics , 2011,
Abstract:
Recognition of plane-to-plane map-germs
Yutaro Kabata
Mathematics , 2015,
Abstract: We present a complete set of criteria for determining A-types of plane-to-plane map-germs of corank one with A-codimension <7, which provides a new insight into the A-classification theory from the viewpoint of recognition problem. As an application to generic differential geometry, we discuss about projections of smooth surfaces in 3-space.
Coastal Planning Strategies for Adaptation to Sea Level Rise: A Case Study of Mokpo, Korea  [PDF]
Yumi Lee
Journal of Building Construction and Planning Research (JBCPR) , 2014, DOI: 10.4236/jbcpr.2014.21007
Abstract: Climate change and sea level rise necessitate adaptation strategies for coastal areas. This paper showcases five strategies for sea level rise adaptation: hard protection, soft protection, accommodation, retreat, and attack. This study proposes adaptation measures and a phased development strategy for coastal areas of Mokpo, an old port city on the southwestern tip of the Korean Peninsula that has been expanded by land reclamation. Mokpo presently experiences frequent flooding during high-water and storm events; due to their low elevation and land subsidence, most of the reclaimed areas are susceptible to future inundation via sea level rise. The fundamental adaptation strategies for the impact areas are: hard protection of important infrastructures via multi-tiered terraces; the retreat of coastal developments accompanied by green buffer zones such as wetlands and parks to accommodate temporary inundation; and up-leveling the ground for new development and phased relocation of existing development. Through the case study of Mokpo, the paper emphasizes the importance of resilient planning strategies for urban development, and highlights both the challenges and opportunities for sea level rise adaptation.
Protecting the Coastline from the Effects of Climate Change: Adaptive Design for the Coastal Areas of Gangneung, Korea  [PDF]
Yumi Lee
Journal of Building Construction and Planning Research (JBCPR) , 2015, DOI: 10.4236/jbcpr.2015.32011
Abstract: The purpose of this research is to present design strategies to enable coastal areas to adapt to climate change and maintain the coastlines by addressing the environmental and urban issues. Gangneung is a tourist attraction situated on South Korea’s east coast, and there is an urgent need for integrated research on strategies to prevent the loss of sandy beaches and the damage caused by storm surges and high swell. This research has two objectives: The first is to offer an overview and describe the characteristics of exemplary projects carried out to manage the storm damage while maintaining the coastlines. The second is to propose a design model that can be applied to coastal areas susceptible to climate change by analyzing the design strategies and the current conditions of the Gangneung coastal area. In the case of Gangneung, the damage caused by the storm surges and high swells are more severe compared to inundation caused by sea level rise because of the steep slope and deep water. Therefore, adaptive design strategies are mainly focused on accommodation and retreat strategies that consider these characteristics by moving the coastal roads behind the pine forest and raising the coastal buildings to connect the coast to the forest and to prevent coastal erosion. This research has the potential to be used as an exemplary design adaptation for coastal erosion as well as a basis for regulating the land use policy in areas susceptible to flood by establishing guidelines for publicly funded developments, and preparing long-term relocation plans for the existing coastal developments to create a sustainable and resilient future for the coastal areas.
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