Biological Networks Laboratory

Arita Group

Biological Systems as a Network

Faculty

ARITA, Masanori　Professor

arita@nig.ac.jp

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KOSHIMIZU, Shizuka
Assistant Professor

skoshimizu@nig.ac.jp

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 Lab HP

Research Summary

1. Analysis of Metabolic Networks

Enzymes transform the molecular structure of metabolites to constitute the metabolic network. We analyze the network at the atomic scale. Comprehensive analysis of small molecules inside cells is called metabolomics, the third omics approach following genomics and proteomics. We develop foundational software platforms to support metabolomics such as databases and spectral matching algorithms.

2. Web Portal of Phytochemicals

Plants provide various compounds that enrich our daily life. Such metabolites are called phytochemicals and include flavonoids, vitamins, phytosterols and polysaccharides. We accumulate phytochemical information and create a wiki-style repository to feedback useful knowledge to the public. The system is more like a portal or cyber-infrastructure rather than a database. We also plan to use this resource to analyze biosynthetic pathways in plants.

Trace or nitrogen atom in a pathway
Plant species （□）and their flavonoids （○）in Lamiaceae (mint family)

Selected Publications

  • Maryenti T, Koshimizu S, Onda N, Ishii T, Yano K, Okamoto T. Wheat Cybrid Plants, OryzaWheat, Regenerated from Wheat-Rice Hybrid Zygotes via in Vitro Fertilization System Possess Wheat-Rice Hybrid Mitochondria. Plant Cell Physiol. 2024 Sep 3;65(8):1344-1357.
  • Arita M, Pulverer B, Uemura T, Sakuma C, Hayashi S. Publishing in the Open Access and Open Science era. Genes Cells. 2024 Apr;29(4):275-281.
  • Moseley HNB, Rocca-Serra P, Salek RM, Arita M, Schymanski EL. InChI isotopologue and isotopomer specifications. J Cheminform. 2024 May 14;16(1):54.
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