A5036861980- Biomedical Text Mining and Ontologies
- Molecular Biology Techniques and Applications
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Ion Transport and Channel Regulation
- Semantic Web and Ontologies
- Hepatitis B Virus Studies
- RNA modifications and cancer
- Connexins and lens biology
- Ocular Surface and Contact Lens
- Corneal Surgery and Treatments
- Agriculture, Soil, Plant Science
- RNA Research and Splicing
- Genetics, Bioinformatics, and Biomedical Research
- Ubiquitin and proteasome pathways
- Congenital heart defects research
- Research Data Management Practices
- Plant Pathogens and Fungal Diseases
- Aldose Reductase and Taurine
- Protease and Inhibitor Mechanisms
- Pancreatic function and diabetes
- Environmental Monitoring and Data Management
- Wikis in Education and Collaboration
National Institute of Genetics
2003-2025
The Graduate University for Advanced Studies, SOKENDAI
2021-2025
Research Organization of Information and Systems
2008-2014
Chiba University Hospital
2011
Osaka International Cancer Institute
2007
National Institute of Informatics
2006-2007
Nara Institute of Science and Technology
2005
Kyushu University
2003
Osaka University
1990-2002
Hitachi (Japan)
2000
Formalin-fixed archival samples are known to be poor materials for molecular biological applications. We conducted a series of experiments understand the alterations in RNA fixed tissue. found that formalin-fixed tissue was resistant solubilization by chaotropic agents. However, proteinase K completely solubilized and enabled extraction almost same amount as from fresh sample. The extracted did not show apparent degradation. reported, successful PCR amplification limited short targets....
BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of whole-body model an adult human male. It encompasses morphological and geometrical knowledge complements ontological representation. Moreover, introduces universal coordinate system anatomy, may facilitate management samples biomedical research clinical practice. As today, 382 concepts, sufficient mapping materials most molecular...
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
High endothelial venule (HEV) cells support lymphocyte migration from the peripheral blood into secondary lymphoid tissues. Using gene expression profiling of mucosal addressin cell adhesion molecule-1(+) mesenteric lymph node HEV by quantitative 3'-cDNA collection, we have identified a leucine-rich protein, named glycoprotein (LRHG) that is selectively expressed in these cells. Northern blot analysis revealed LRHG mRNA approximately 1.3 kb and nodes, liver, heart. In situ hybridization...
Abstract Background OryzaGenome ( http://viewer.shigen.info/oryzagenome21detail/index.xhtml ), a feature within Oryzabase https://shigen.nig.ac.jp/rice/oryzabase/ is genomic database for wild Oryza species that provides comparative and evolutionary genomics approaches the rice research community. Results Here we release OryzaGenome2.1, first major update of OryzaGenome. The main in this version inclusion newly sequenced genotypes their meta-information, giving total 217 accessions 19 O....
High endothelial venules (HEV) allow rapid and selective lymphocyte trafficking from the blood into secondary lymphoid tissues. Here we report expression profile of active genes in mouse high cells (HEC). HEC were first purified lymph nodes (LN) by magnetic cell sorting with MECA-79 mAb a 3′-directed cDNA library that faithfully represents composition mRNA was constructed. A total 1495 sequences obtained randomly selected clones. Based on their sequence identity, they grouped 754 different...
BioHackathon 2010 was the third in a series of meetings hosted by Database Center for Life Sciences (DBCLS) Tokyo, Japan. The overall goal is to improve quality and accessibility life science research data on Web bringing together representatives from public databases, analytical tool providers, cyber-infrastructure researchers jointly tackle important challenges area silico biological research. theme 'Semantic Web', all attendees gathered with shared producing Semantic their respective...
Cultivated barley (Hordeum vulgare ssp. vulgare) is used for food, animal feed, and alcoholic beverages widely grown in temperate regions. Both its wild progenitor (H. spontaneum) have large 5.1-Gb genomes. High-quality chromosome-scale assemblies several representative genotypes, both domesticated, been constructed recently to populate the nascent pan-genome infrastructure. Here, we release a assembly of Japanese elite malting cultivar 'Haruna Nijo' using similar methodology as project. The...
BodyMap is a collection of site-directed 3' expressed sequence tags (ESTs) (gene signatures, GSs) that contains the transcript compositions various human tissues and was first systematic effort to acquire gene expression data. For construction BodyMap, cDNA libraries were made, preserving abundance information histologic resolutions tissue mRNAs. By sequencing 164,000 randomly selected clones, 88,587 GSs represent chromosomally coded transcripts have been collected from 51 organs tissues....
The availability of comprehensive sets genes has prompted the researchers to carry out systematic collection gene expression data. RT–PCR highest specificity and sensitivity for transcript detection among all available methods. Low throughput, especially when quantitative data are desired, precluded from genome-wide application. Here we report a PCR-based profiling method, introduced amplified fragment length polymorphism (iAFLP), that same as throughput level comparable DNA–microarray...
During their migration to the periphery, cranial neural crest cells (NCCs) are repulsed by an ErbB4-dependent cue(s) in mesenchyme adjoining rhombomeres (r) 3 and 5, which segmented hindbrain neuromeres. ErbB4 has many ligands, but ligand functions above system not yet been clearly determined. Here we found that a cornichon-like protein/cornichon homolog 2 (CNIL/CNIH2) gene was expressed developing chick r3 r5. In cell culture system, its product facilitated secretion of heparin-binding...
To characterize transcripts abundantly expressed in the human pituitary gland general as well to isolate novel specifically this gland, we generated an expression profile of active genes transcribed it. A total 1015 randomly collected 3prime prime or minute sequence tags (ESTs) (gene signatures, GSs) were grouped into 527GS species. The results showed relative levels gland. comprising more than 1% mRNA prolactin, growth hormone and chromogranin B genes. When known categorized, for hormones...
Abstract: To identify differentially expressed genes which play causal roles in pathogenesis and maintenance for psoriasis, we used BodyMapping introduced amplified fragment length polymorphism approaches. From the BodyMap database, selected 2007 specifically epithelial tissues. Among genes, surveyed involved or uninvolved psoriatic lesional skin samples compared with atopic dermatitis, mycosis fungoides, normal samples. As a result of surveying 241 were only but not other Hierarchical...
Protoplast regeneration of a wild-type and two mutant strains Candida glabrata defective in CHS3 homologues encoding class IV chitin synthase Saccharomyces cerevisiae was examined by scanning negative-staining electron microscopy. In the strain, small particles short filaments appeared on protoplast surface at 10 min, filamentous materials covered entire 1 h, granular started filling interspaces 2 h completed 6 h. The consisted microfibrils various widths ranging from ≤5 to 40 nm, composed...
Abstract Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations ten inbred strains: Mus musculus -derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M . m domesticus PGN2/Ms BFM/Ms; castaneus HMI/Ms; JF1/Ms MSM/Ms, which were a hybrid between These established by Prof. Moriwaki the 1980s collectively named “Mishima Battery”. show large phenotypic body size many physiological traits. We...