Mammalian genome research resources available from the National BioResource Project in Japan.

Mammalian genome research has conventionally involved mice and rats as model organisms for humans. Given the recent advances in life science research, to understand complex and higher-order biological phenomena and to elucidate pathologies and develop therapies to promote human health and overcome diseases, it is necessary to utilize not only mice and rats but also other bioresources such as standardized genetic materials and appropriate cell lines in order to gain deeper molecular and cellular insights. The Japanese bioresource infrastructure program called the National BioResource Project (NBRP) systematically collects, preserves, controls the quality, and provides bioresources for use in life science research worldwide.

Chromosome-scale assembly of barley cv. 'Haruna Nijo' as a resource for barley genetics.

Cultivated barley (Hordeum vulgare ssp. vulgare) is used for food, animal feed, and alcoholic beverages and is widely grown in temperate regions. Both barley and its wild progenitor (H.

MoG+: a database of genomic variations across three mouse subspecies for biomedical research.

Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m.

Collection, preservation and distribution of genetic resources by the National Bioresource Project RICE (NBRP-RICE).

Biological resources are the basic infrastructure of bioscience research. Rice ( L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding.

Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan.

The RIKEN BioResource Research Center (BRC) was established in 2001 as a comprehensive biological resource center in Japan. The Experimental Animal Division, one of the BRC infrastructure divisions, has been designated as the core facility for mouse resources within the National BioResource Project (NBRP) by the Japanese government since FY2002. Our activities regarding the collection, preservation, quality control, and distribution of mouse resources have been supported by the research community, including evaluations and guidance on advancing social and research needs, as well as the operations and future direction of the BRC.

OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species.

Background: OryzaGenome ( http://viewer.shigen.info/oryzagenome21detail/index.

Life science database cross search: A single window system for dispersed biological databases.

A comprehensive search system for the bioscience databases is in progress. We constructed a search service, Life science database cross search system (https://biosciencedbc.jp/dbsearch/index.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research.

Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces.

BodyParts3D: 3D structure database for anatomical concepts.

BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a 3D whole-body model for an adult human male. It encompasses morphological and geometrical knowledge in anatomy and complements ontological representation. Moreover, BodyParts3D introduces a universal coordinate system in human anatomy, which may facilitate management of samples and data in biomedical research and clinical practice.

A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction.

Background: Changes in genomic copy number occur in many human diseases including cancer. Characterization of these changes is important for both basic understanding and diagnosis of these diseases. Microarrays have recently become the standard technique and are commercially available.

Cornichon-like protein facilitates secretion of HB-EGF and regulates proper development of cranial nerves.

During their migration to the periphery, cranial neural crest cells (NCCs) are repulsed by an ErbB4-dependent cue(s) in the mesenchyme adjoining rhombomeres (r) 3 and 5, which are segmented hindbrain neuromeres. ErbB4 has many ligands, but which ligand functions in the above system has not yet been clearly determined. Here we found that a cornichon-like protein/cornichon homolog 2 (CNIL/CNIH2) gene was expressed in the developing chick r3 and r5.

BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression.

BodyMap-Xs (http://bodymap.jp) is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose.

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.

The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein expression data from multiple platforms that has been associated with both manually annotated full-length cDNAs from H-InvDB and RefSeq sequences. Of the H-Inv predicted genes, 18 897 have associated expression data generated by at least one platform.

Zipf's law and human transcriptomes: an explanation with an evolutionary model.

Detailed analysis of human gene expression data reveals several patterns of relationship between transcript frequency and abundance rank. In muscle and liver, organs composed primarily of a homogeneous population of differentiated cells, they obey Zipf's law. In cell lines, epithelial tissue and compiled transcriptome data, only high-rankers deviate from it.

Up-regulated gene expression in the conjunctival epithelium of patients with Sjögren's syndrome.

Purpose: To elucidate the pathogenesis of ocular surface abnormalities in patients with Sjögren's syndrome (SS) by comparing global gene expression patterns in conjunctival epithelial cells from normal individuals and SS patients.

Methods: The study population consisted of 56 subjects (26 SS patients and 30 normal volunteers). RNA extracted from their conjunctival epithelial cells was subjected to introduced amplified fragment length polymorphism (iAFLP), a competitive PCR-based gene expression assay, to measure gene expression in the 56 samples against 931 genes.

Construction of human corneal endothelial cDNA library and identification of novel active genes.

Purpose: To describe genes expressed in human corneal endothelial cells and identify novel genes.

Methods: Sixteen human donor corneas that had no history of corneal disease, infection, or intraocular surgery were used within 7 days of death. Total RNA was extracted from corneal endothelial cells with attached Descemet membranes.

Non-overlapping expression of Olig3 and Olig2 in the embryonic neural tube.

Olig family is a novel sub-family of basic helix-loop-helix transcription factors recently identified. Olig1 and Olig2 were first reported to promote oligodendrocyte differentiation, and later Olig2 was reported to be involved in motoneuron specification as well. Olig3 was isolated as a third member of Olig family, but its precise expression pattern is poorly understood.

Gene expression profiling of mucosal addressin cell adhesion molecule-1+ high endothelial venule cells (HEV) and identification of a leucine-rich HEV glycoprotein as a HEV marker.

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 cells by quantitative 3'-cDNA collection, we have identified a leucine-rich protein, named leucine-rich HEV glycoprotein (LRHG) that is selectively expressed in these cells. Northern blot analysis revealed that LRHG mRNA is approximately 1.