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Biomedical subjects

Naoto Tanaka

Publications and source records attributed to Naoto Tanaka.

7 recordsLinked to original sources
PubMed2006

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

Bacteria↗
PubMed2006

Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes.

Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at http://gib-v.genes.nig.ac.jp/.

Databases, Nucleic Acid↗
PubMed2006

G-InforBIO: integrated system for microbial genomics.

BACKGROUND: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. RESULTS: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. CONCLUSION: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.

Algorithms↗
PubMed2004

The PDGF B-chain is involved in the ontogenic susceptibility of the developing rat brain to NMDA toxicity.

Hypoxic-ischemic (H-I) injury to neonatal brains can cause a life-long neuronal deficit because of increased susceptibility in the neonatal period. Excitotoxicity due to overstimulation of the N-methyl-d-aspartate receptor (NMDAR) is assumed to be the basis of the injury. However, the ontogenic profile of the susceptibility does not directly correlate with the levels of NMDAR expression. Platelet-derived growth factor B-chain (PDGF-B) has been reported to protect neurons by suppressing the NMDA-evoked current and translocating the glutamate transporter to the cell membrane. Thus, we assessed the relationship between the susceptibility to H-I injury and the expression of PDGF-B in neonatal rat brain. PDGF-B infusion before and after an intrastriatal NMDA injection significantly reduced the size of the lesions in 7-day-old rats, when they are most susceptible and the neuronal expression of PDGF-B is low. Fourteen-day-old neonatal rats were found to be resistant to NMDA injury, even though NMDARs are expressed at high levels in the brain at this age. Inhibition of PDGF-B protein synthesis by antisense oligodeoxynucleotides increased the size of the NMDA-induced lesions up to 6-fold at postnatal day 14, when PDGF-B is expressed at high levels in neurons. These data suggest that PDGF-B is an important physiological modulator of NMDAR excitability in the developing brain, and that the balance between the expression of NMDAR and PDGF-B partly determines the ontogenic susceptibility to brain injury. Enhancement of the PDGF-B/receptor signal pathway might rescue neonatal brains at risk of H-I injury.

Aging↗
PubMed2001

The formation and structures of cystites of Arthrobacter ureafaciens NRIC 0157T induced by antibiotics.

The cystite formation of Arthrobacter ureafaciens NRIC 0157(T) was induced by some antibiotics, and the addition of tetracycline at a lag phase was effective for cystite formation in YPM liquid medium. Cystites differed from vegetative cells in the cell wall structure, protein content, and water content. Furthermore, the characteristics and structures of cystites induced by tetracycline were similar to those of cystites produced by nutritional imbalance in CT medium. Consequently, various triggers would induce cystite formation. It is interesting that cystite formation was found in part of the Arthrobacter strains and seemed to correlate with the type of peptidoglycan.

Journal Article↗
PubMed2000

Cystite formation of Arthrobacter ureafaciens NRIC 0157(T).

The cystite formation of Arthrobacter ureafaciens NRIC 0157(T) was studied by the use of a newly designed CT medium composed of 2.0% D-glucose, 0.28% NH(4)H(2)PO(4), 0.136% K(2)HPO(4) 0.136% KH(2)PO(4), 0.0005% MgSO(4).7H(2)O, and 0.0007% CaCl(2).2H(2)O. Cystites are drumstick-shaped and oval cells and are larger than vegetative cells. Cystites are Gram-negative, whereas vegetative cells are Gram-positive by the KOH reaction. The concentration and ratio of K(+) and Mg(2+) in CT medium mainly affected the cystite formation. Cystites are considered aberrant forms produced by nutritional imbalance.

Journal Article↗