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Biomedical Chemistry

Biomedical ChemistryThe aim of our department is to contribute to global health and welfare through basic research. Our department, formerly called Biochemistry and Nutrition, was renamed the Department of Biomedical Chemistry on April 1, 1996, when it became affiliated with the Biomedical Science Division of International Health, Graduate School of Medicine, The University of Tokyo. Prof. Kita transferred from The Institute of Medical Science, The University of Tokyo on March 1, 1998. All of our members are highly motivated.
Energy metabolism is essential for the survival, continued growth, and reproduction of living organisms. From the standpoint of biological adaptation, we have been studying the molecular mechanisms of energy-transducing systems, such as the mitochondrial and bacterial respiratory chains. As the energy metabolism of pathogenic organisms such as bacteria and parasites is quite different from that of their mammalian hosts, these unique aspects of pathogens make promising targets for chemotherapy.
We have been studying the biological strategy by which they adapt to differences in the availability of oxygen in eukaryotes. This project has several purposes. We would like to identify a common strategy used to maintain the energy supply in different environments and to understand the unique features of energy metabolism in pathogenic organisms. If we could understand the mechanism, it would provide important information for fighting the infectious diseases caused by bacteria and parasites, in addition to basic knowledge on the molecular mechanism of biological adaptation. As a model system, we selected Ascaris suum, which is a parasitic nematode that resides in our small intestine, where the oxygen tension is quite limited. The rather large size of A. suum facilitates biochemical study, and its life cycle has been well characterized. It is closely related to Caenorhabditis elegans, which is a well-known free-living nematode, for which the entire genome sequence has been reported. In addition to parasitic nematodes, we have been studying malaria parasites, trypanosomes, and Cryptosporidium.

Major projects

- Human succinate dehydrogenase and mitochondrial myopathy
- Ascaris suum and Caenorhabditis elegans
- molecular mechanism of adaptation to low oxygen tension
- mitochondrial quinol-fumarate reductase
- C. elegans as a model system of parasitic nematodes and ageing
- Malaria and Trypanosome: characterization of mitochondria as a target for the chemotherapy
- Escherichia coli and Mycobacterium : succinate dehydrogenase complex and regulation of energy supply
- RNA and RNA-binding proteins
- mitochondriral translation system
- ribosome biogenesis of Eukarya and Archaea

General Description

Aim of our department is to contribute to global health and welfare from basic research. Our department, formerly named Biochemistry and Nutrition, was renamed on April 1st, 1996 to Department of Biomedical Chemistry as newly affiliating with Biomedical Science Division of International Health, Graduate School of Medicine, The University of Tokyo. Professor Kita moved from Institute of Medical Science, The University of Tokyo, on March 1st, 1998. Therefore, we are quite new and all of our members are highly motivated to development of new scientific fields.

Research Activities

A. Human mitochondria

1) Succinate–ubiquinone reductase (Complex II)
2) Mitochondrial myopathy

B. Ascaris suum and Caenorhabditis elegans

1) Molecular mechanism of adaptation to low oxygen tension (the regulation of the gene expression of mitochondrial proteins)
2) Mitochondrial quinol–fumarate reductase (structure–function relationship, enzyme evolution)
3) C. elegans as a model system of parasitic nematodes and ageing (expression of foreign genes, gene knockout, oxygen stress)

C. Malaria, Trypanosomes, and Cryptosporidium (Plasmodium falciparum,

Trypanosoma brucei, Trypanosoma cruzi, and Cryptosporidium parvum)
1) Characterization of mitochondria as a target for chemotherapy
2) Molecular biology of mitochondrial DNA
3)Structure-based drug design (SBDD)

D. Protein synthesis

1)Mitochondrial protein synthesis
2)Biogenesis of cytoplasmic ribosomes

Ultimately, we would like to develop anti-parasitic drugs for use in endemic areas. As described in “Current Research,” the parasite metabolic system is an attractive target for chemotherapy because it is different from the host metabolic system and because it is essential for parasite survival. Trypanosome alternative oxidase (TAO) in trypanosome mitochondria and its specific inhibitor, ascofuranone, are excellent examples in this regard. As Dr. Opperdoes pointed out, ascofuranone is the most potent TAO inhibitor known. With its high selectivity and low toxicity, ascofuranone is a potential next-generation anti-trypanosomal agent. Indeed, current studies are examining the molecular mechanism of ascofuranone and ways of improving its efficacy in vivo.
Therefore, we want to contribute to global health and welfare through basic research and by training young scientists to be thoughtful, powerful colleagues.

Course Description

Biochemistry and Nutrition I (2 credits)
Professor Kita and Staff

This course is comprised of lectures, seminars, and experiments to provide basic concepts and newer vistas for understanding nutrition with special reference to biochemistry and physiological chemistry. These include the structure and function of biomolecules, metabolism, its regulation, and underlying mechanism at either molecular, cellular or systemic level, organ biochemistry, or organ/organ interaction, and homeostasis.

Biochemistry and Nutrition II (2 credits) Professor Kita and Staff

In this course nutrition is considered under physiological and pathological conditions. We deal with biological rhythms, growth/aging, fasting/obesity, deficiency, malnutrition/overnutrition, acquired and inborn errors of metabolisms, infectious and chronic diseases, diet therapies, enzyme/coenzyme therapies, and parental nutrition.

Teaching Staff

Kiyoshi KITA: Professor and Chair, since 1998
B.Pharm.Sc., Faculty of Pharmaceutical Sciences, The University of Tokyo, 1974
D.Pharm.Sc., The University of Tokyo, 1980
Visiting Scientist, Illinois University, 1987-1988
Associate Professor, Institute of Medical Sciences, The University of Tokyo, 1991-1998

Yoh-ichi WATANABE: Associate Professor, since 2007
B.Eng., Faculty of Engineering, The University of Tokyo, 1988
M.Eng., Graduate School of Engineering, The University of Tokyo, 1990
Ph.D., The University of Tokyo, 1994
JSPS Research Fellow (The University of Tokyo), 1993-1994
Granted Researcher of JICA (Institute for Medical Research, Malaysia), 1994-1995
Research Associate of Parasitology, Institute of Medical Sciences, The University of Tokyo, 1995-1996
NEDO Postdoctoral Fellow (The University of Tokyo), 1996
Postdoctoral Fellow (Faculty of Medicine, Dalhousie University, Canada), 1996-2000
Research Associate, Graduate School of Medicine, The University of Tokyo, 2000-2001
Lecturer, Graduate School of Medicine, The University of Tokyo, 2001-2007

Kimitoshi SAKAMOTO: Assistant Professor, since 2007
B.Agricul., Faculty of Agriculture, Kyoto University, 1994
M.Agricul., Graduate School of Agriculture, Kyoto University, 1996
Ph.D., Kyoto University, 1999
JSPS Research Fellow, 1998-2000
CREST Research Fellow, 2000-2002
AIST Research Fellow, 2002
NEDO Research Fellow (AIST), 2002-2003
Research Associate, The University of Tokyio, 2003-2007

Tomoo Shiba: Assistant Professor, since 2009
B.Eng., Faculty of Engineering, Osaka University, 1993
M.Eng., Graduate School of Engineering, Osaka University, 1995
Ph.D., Graduate School of Pharmaceutical Sciences., The University of Tokyo, 2000
Research Fellow (The University of Tokyo), 2000-2001
Postdoctoral Fellow (High Energy Accelerator Research Organization), 2001-2005
Research Associate, Graduate School of Arts and Sciences, The University of Tokyo, 2005-2009

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