Genome Sequence of Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shōchū.

Here, we report a draft genome sequence of strain Kagoshima no. 2, which is used for brewing shōchū, a traditional distilled spirit in Japan. The genome data will facilitate an understanding of the evolutional traits and genetic background related to the characteristic features of strain Kagoshima no.

Toward Network Biology in E. coli Cell.

E. coli has been a critically important model research organism for more than 50 years, particularly in molecular biology. In 1997, the E.

Development and mining of a volatile organic compound database.

Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases.

GenoBase: comprehensive resource database of Escherichia coli K-12.

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12.

PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list.

Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies.

Colony-live--a high-throughput method for measuring microbial colony growth kinetics--reveals diverse growth effects of gene knockouts in Escherichia coli.

Background: Precise quantitative growth measurements and detection of small growth changes in high-throughput manner is essential for fundamental studies of bacterial cell. However, an inherent tradeoff for measurement quality in high-throughput methods sacrifices some measurement quality. A key challenge has been how to enhance measurement quality without sacrificing throughput.

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach.

Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale.

Modular architecture of metabolic pathways revealed by conserved sequences of reactions.

The metabolic network is both a network of chemical reactions and a network of enzymes that catalyze reactions. Toward better understanding of this duality in the evolution of the metabolic network, we developed a method to extract conserved sequences of reactions called reaction modules from the analysis of chemical compound structure transformation patterns in all known metabolic pathways stored in the KEGG PATHWAY database. The extracted reaction modules are repeatedly used as if they are building blocks of the metabolic network and contain chemical logic of organic reactions.

Analysis of common substructures of metabolic compounds within the different organism groups.

With the increase in available post-genomic data and metabolic pathway information, we have been focusing on revealing the biological meaning of higher phenomena such as relationships of metabolic systems in different organisms. Metabolism plays an essential role in all cellular organisms, e.g.