Department of Bioscience & Biotechnology


Department of Bioscience and Biotechnology covers a wide range of research fields concerned with function and interaction of biomolecules in the cellular system, genetic breeding and bioprocess engineering, biomaterial design, functional foods and medicines, and so on.

The Department of Bioscience and Biotechnology consists of four educational courses, Molecular Biosciences, Systems Biology, Applied Molecular Microbiology and Biomass Chemistry and Food Science & Biotechnology. The aim of this graduate course is to educate students in Applied Bioscience, especially in basic molecular biology, food science, environmental science, and material science, which covers a wide range of research fields related to function and interaction of biomolecules in the cellular system, genetic breeding and bioprocess engineering, biomaterial design, functional foods and medicines, and so on.
The objectives of each educational courses are as follows:
(*-marked laboratories belong to the Department of Innovative Science & Technology which opens only for Ph.D. candidate students.)


Educational Course 1: Molecular Biosciences

This course is principally concerned with nurturing scholars who have potential to understand structure-function relationships of biomolecules involved in a variety of bioreactions at an atomic level. The education programs offered in this course are designed in close relationship with researches in a wide range of molecular biosciences, including organic chemistry, biochemistry, molecular biology, and cell biology. Graduate students have an opportunity to take lectures in advanced molecular biosciences and, in addition, to join seminars on individual areas in molecular biosciences held separately for each laboratory.

1.Biochemistry

Makoto KIMURA, Ph.D., M.Sc., Professor
Yoshimitsu KAKUTA, Ph.D., M.Sc., Associate Professor
Takashi NAKASHIMA, Ph.D., M.Sc., Assistant Professor

1) Structural biology on biopolymers involved in translation (Protein-protein interaction, Protein-RNA interaction, Ribonucleases, Ribosome, Site-directed mutagenesis)
2) Structure-function relationship of enzymes (Sulfotransferase, Active site, Catalytic mechanism)
3) Structure of biopolymers (Crystallization, X-ray crystallography)
4) Bioengineering of biopolymers (Branching enzymes, Starches)
2.Marine Biochemistry

Miki NAKAO, Ph.D., M.Sc., Professor
Tomonori SOMAMOTO, Ph.D., M.Sc., Associate Professor

1) Molecular evolution of innate and adaptive immune factors in aquatic animals such as bony fish
2) Structure and function of the complement system in fish and some marine invertebrates
3) Molecular and cellular analysis of adaptive immune response in fish against viral infection
4) Development and analysis of reaction mechanism of fish vaccine and immunostimulants for better control of infectious diseases in aquaculture
5) Biochemical identification of molecules responsible for healthy growth of aquacultured vertebrates and invertebrates
3.Marine Resource Chemistry *

Makoto ITO, Ph.D., M.Sc., Professor
Nozomu OKINO, Ph.D., M.Sc., Associate Professor

1) Marine biotechnology and microbiology (Novel enzymes, Inhibitors, Polyunsaturated fatty acids, Labyrinthulea)
2) Glycobiology/technology and lipidbiology/technology (Glycosphingolipids, Sphingolipids, Metabolism, Microdomains, Signal transduction, Post-translational modification)
3) Infection and symbiosis of microbes (Receptor, Fish pathogens, Opportunistic pathogens, Atopic dermatitis)
4.Applied Plant Science

Etsuko NISHIMOTO, Ph.D., M.Sc., Associate Professor

1) Sub-cellular biology of higher plant based on advanced laser spectroscopy
2) Structure, dynamics and function of phyto-proteins
3) Elementary photophysical processes of photosynthesis
5.Plant Nutrition

Ken MATSUOKA, Ph.D., M.Sc., Professor
Takeo YAMAKAWA, Ph.D., M.Sc., Associate Professor
Akiko MARUYAMA-NAKASHITA, Ph.D., M.Sc., Associate Professor
Masamichi KIKUCHI, Ph.D., M.Sc., Research Associate

1) Nutritional control of protein localization and protein degradation in plant cells (Autophagy, endocytosis)
2) Regulation of cellular and organelle dynamics (Cytokinesis, nutritional regulation of cell cycle, exocytosis)
3) Production of useful compounds in crops using transgenic approach (Recombinantprotein production, regulation of protein glycosylation)
4) Symbiotic nitrogen fixation in legumes (nodulation, Rj-gene)
5) Rational fertilizer use (Efficiency, nitrogen loss, pollution, resource recycling)
6) Physiological and biochemical aspects of mineral and nitrogen nutrition (Mineral absorption, nitrogen metabolism, carbon skeleton, abiotic stress, sulfur assimilation and metabolism)
7) Transcriptional regulation responding to nutrient starvation (Sulfur deficiency, regulatory element, transcriptional network)
6.Molecular Gene Technology *

Satoru KUHARA, Ph.D., M.Sc., Professor
Kosuke TASHIRO, Ph.D., M.Sc., Associate Professor
Shigeru MUTA, Ph.D., M.Sc., Assistant Professor

1) The cellular gene regulation system using experimental and computational strategy
2) Identification of gene regulatory network
3) Gene regulation in cellular differentiation
4) Microbial Genome, Development of systems for environmental microorganism
7.Protein Chemistry & Engineering

Yoshizumi ISHINO, Ph.D., M.Sc., Professor
Takeshi YAMAGAMI, Ph.D., M.Sc., Assistant Professor

1) Structural and functional studies on nucleic acid-related enzymes
2) Molecular mechanisms of DNA replication and recombinatinal repair
3) Development of useful enzymes for genetic engineering techniques
4) Microbiology of extremophiles
8.Pesticide Chemistry

Akinori HIRASHIMA, Ph.D., M.Sc., Associate Professor
Naotaka YAMADA, Ph.D., M.Sc., Assistant Professor

1) Study on growth-behaviour control in Insect (Octopamine receptor, Tyramine receptor, Homology modeling)
2) Molecular modeling of sex-pheromone regulators (Syntheses, Structure-activity relationship, Octopamine receptor)
3) Elucidation of stress reaction and genome drug design of anti-stressors (Stress, Tribolium freemani, Bombyx mori)
4) Inhibition of tyramine β-hydroxylase (Molecular design, Pharmacophore model)
5) Regulators of plant growth and development (Syntheses, Structure-activity relationship)
6) Inhibitors of carotenoid biosynthesis (Syntheses, Structure-activity relationship)
9.Plant Molecular Biosciences

Takahiro NAKAMURA, Ph.D., M.Sc., Associate Professor

1) Genetic coordination in nucleus, chloroplast, and mitochondria
2) Organellar gene expression
3) Cytoplasmic male sterility and the restorer of fertility
4) Engineering of custom RNA & DNA binding proteins

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Educational Course 2: Systems Biology

Systems biology is a multi-disciplinary study field aiming to understand organism’s form and functions as integrated and interacting networks of genes, proteins, and metabolites. This course consists of seven laboratories conducting researches in top-down systematic analysis of complex interactions, integrated bioprocess development, functional genomics, and gene/cell engineering of plants and animals. This course provides practical training for students having different scientific backgrounds but sharing intense interests in theoretical and experimental researches on basics and applications of bioresources using bioinformatics, omics, and genetic/cellular technologies. Our goal is to prepare graduate students for high impact careers in researches at academics and bio-industries.

1.Applied Biological Regulation Technology *

Masahiro OKAMOTO, Ph.D., M.Sc., Professor
Taizo HANAI, Ph.D., M.Sc., Associate Professor
Hiroyuki HAMADA, Ph.D., M.Sc., Assistant Professor

1) Development of a system for the inference of larger scale genetic networks
2) Development of biochemical engineering analyzing tool-kit
3) Nonlinear numerical optimization technique based on evolutional computing (genetic algorithm, genetic programming)
4) Bioinspired design of adaptive routing of packets and traffic congestion control
5) Improvement of biofuel production by metabolic engineering
6) Construction of artificial gene network by synthetic biology
7) Mathematical modeling of cell cycle arrest and apoptosis
8) Mathematical modeling of synchronization of heart beating rhythms
2.Cellular Regulation Technology *

Sanetaka SHIRAHATA, Ph.D., M.Sc., Professor
Yoshinori KATAKURA, Ph.D., M.Sc., Associate Professor
Kiichiro TERUYA, Ph.D., M.Sc., Assistant Professor

1) Development of functional waters and foods for prevention and improvement of oxygen-stress-related diseases
2) Analysis of molecular basis for aging and its application to development of anti-aging foods
3) Efficient preparation of human monoclonal antibodies by using in vitro immunization and gene technology
3.Silkworm Genetics

Yutaka BANNO, Ph.D., M.Sc., Associate Professor
Kohji YAMAMOTO, Ph.D., M.Sc., Assistant Professor

1) Lepidopteran stress-responding enzyme such as superoxide dismutase
2) Development of genetic resources studies in silkworm
3) Collection, evaluation and preservation of silkworm genetic resources
4) Genetic analysis of mutants in silkworm
4.Plant Genetics

Toshihiko KUMAMARU, Ph.D., M.Sc., Associate Professor

1) Collection, evaluation and preservation of rice genetic resources
2) Mutagenesis and mutation spectrum in rice
3) Genetic analysis of induced mutants in rice: Starch, protein and lipid stored in grain
4) Genome analysis of the useful genes in rice
5.Metabolic Architecture Design *

Hiroyuki WARIISHI, Ph.D., M.Sc., Professor

1) Systems Biology of Lignin Biodegradation
2) Omic Studies on Basidiomycetes
3) Metabolic Architecture Design for the higher production of target metabolites
4) Applied Enzymology and Microbiology
6.Bio-Process Design *

Fumihide SHIRAISHI, Ph.D., M.Sc., Professor

1) Development of an efficient method for analysis of large-scale metabolic reaction systems
2) Dynamic sensitivity analysis of large-scale metabolic reaction systems
3) Development of photocatalytic processes for purification of air and water
7.Metabolic Regulation Research *

Shigeki FURUYA, Ph.D., M.Sc., Professor

1) Functional genomic analysis of animal models for human serine deficiency (knockout mouse, metabolic disease model, brain dysfunction, neuron-glia interaction)
2) Molecular basis for metabolite-gene regulatory networks in animal nervous tissues (amino acids, brain, transcriptomics, proteomics, metabolomics)
3) Molecular mechanisms underlying recognition of amino acids deficiency (metabolic homeostasis, cell function, signal transduction)

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Educational Course 3: Applied Molecular Microbiology & Biomass Chemistry

In this course, broad subjects in fundamental and applied aspects of microorganisms in the environmental, food and medical microbiology and biotechnology are covered. In addition, the better understand in a basic concept of bio-production processes and thereby to design advanced bio-based materials from molecular levels to superstructures in the bottom-up architecture are trained.

1.Soil Microbiology

Kenji SAKAI, Ph.D., M.Sc., Professor
Yukihiro TASHIRO, Ph.D., M.Sc., Assistant Professor

1) Ecology and utilization of thermotolerant / thermophilic microorganisms (Lactic acid fermentation, Open system, Biodegradation, Plant growth promoting bacteria)
2) Analysis and breeding of microbial consortium (Microbial community structure, Uncultured microorganism, Metagenome, FISH)
3) Systematic microbial transformation of biomass waster (Biorefinery, Composting, Wastewater treatment, Nitrogen removal, Liquid fertilizer)
2.Applied Microbiology

Kaoru TAKEGAWA, Ph.D., M.Sc., Professor
Sadazo YOSHINO, Ph.D., M.Sc., Associate Professor
Yujiro HIGUCHI, Assistant Professor

1) Yeast cell biology and biotechnology (Fission yeast, Foreign gene expression, Vesicle trafficking, Vacuolar protein sorting)
2) Genetics and breeding in saccharolytic Clostridium and Bacillus (Degradation, Gene cloning, Acetone/butanol fermentation)
3) Genetics and breeding in fungi (Aspergillus, Trichodema, Glycosylation)
4) Glycoscience and glycotechnology (Glycosphingolipids, Lipid raft, Glycosyltransferase, Transglycosylation of glycosidases)
3.Microbial Technology *

Kenji SONOMOTO, Ph.D., M.Sc., Professor
Jiro NAKAYAMA, Ph.D., M.Sc., Associate Professor
Takeshi ZENDO, Ph.D., M.Sc., Assistant Professor

1) Diversified microbial utilization of renewable resources (Biodegradable plastic materials, Biodiesel fuel, Medically functional foods and food materials)
2) Bioprocess development and control of anaerobic fermentation (Lactic acid fermentation, Acetone-butanol-ethanol fermentation)
3) Biochemistry, genetics and fermentation of bacteriocins of lactic acid bacteria
4) Peptide engineering of lantibiotics containing unusual amino acids
5) Characterization of microbial diversity in fermented foods and human intestine by molecular approaches (Nukadoko, Correlation between microflora and allergy)
6) Characterization of chemical signals controlling microbial behavior (Bacterial pheromone)
4.Biomacromolecular Materials *

Daisuke TATSUMI, Ph.D., M.Sc., Associate Professor

1) Creation of Novel Fibrous Materials from Natural Polymer Solutions (liquid crystal, fiber, film, gel)
2) Functionalization of Biomacromolecular Materials (Cellulose, Chitin etc.)
3) Structure and Rheological Properties of Fiber Networks (floc, viscoelasticity, power law)
5.Microbial Genetics

Katsumi DOI, Ph.D., M.Sc., Senior Assistant Professor

1) Surver, development and preservation on microbial genetic resources
2) Bacteriophages and plasmids of industrial bacteria (contamination and control, functional analysis, recombinant DNA, vectors and lytic enzymes)
3) Screening of useful enzymes from extremophiles
4) Structural and functional analyses of extremozymes
5) Biotechnological application of extremophiles and extremozymes
6) Genetics and breeding in industrial microorganisms (gene manipulation, gene cloning and analysis, gene expression and regulation)
6.Biomaterial Design *

Tetsuo KONDO, Ph.D., M.Sc., Professor
Shingo YOKOTA, Ph.D., M.Sc., Assistant Professor

1) A hierarchical organizing design for 3-D nano/micro architecture of bio-based materials
2) Safe and comfortable nano-materials from microbial cellulose fibers
3) Nano-dispersion and dissolution of biomass into water using aqueous counter collision
4) Functionalization of nano-building blocks from bio-based materials
5) Encouraging protoplasts and cells to produce materials by environmental stress
6) Manipulation of movements for microorganisms and cells
7) Surface modification of bio-based nano-materials

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Educational Course 4: Food Science & Biotechnology

This course offers advanced educational programs on study of food function at the molecular, cellular, and model animal levels, dynamic analysis and reaction control of functional factors, analysis and development of novel food processing, manufacturing and sterilization systems, development of measurement technology for processing and quality by biological devices, and molecular and biological technologies ensuring and improving the safety, wholesomeness and soundness of food.

1.Nutrition Chemistry

Masao SATO, Ph.D., M.Sc., Associate Professor
Bungo SHIROUCHI, Ph.D., M.Sc., Assistant Professor

1) Effects of exogenous and endogenous oxycholesterols on lipid metabolism
2) Effects of food ingredients on development of obesity
3) Analysis of relation between serum fatty acid composition and diseases
4) Identification of responsible genes for hypercholesterolemia of disease model animals
5) Effects of food ingredients on lipid metabolism to prevent arteriosclerosis
6) Effects of food ingredients on lymphatic lipid transport
7) Research and development of rapid and sensitive micro-assay for determination of rice lipids
2.Food Chemistry *

Koji YAMADA, Ph.D., M.Sc., Professor
Hirofumi TACHIBANA, Ph.D., M.Sc., Professor
Michiko NONAKA, Ph.D., M.Sc., Research Associate

1) Physiologically functional factors in foods (Proteins, Lipids, Fibers, Antioxidants)
2) Functional assessment of food ingredients (Biochemical tests, Animal cell culture, Animal tests)
3) Prevention of food allergy (Allergen degradation, Control of Ig production, Control of chemical mediator production)
4) Prevention of carcinogenesis
5) Identification and application of the molecular targets of functional food factors
6) Characterization and application of green tea polyphenols signaling pathway
3.Food Analysis *

Toshiro MATSUI, Ph.D., M.Sc., Professor
Mitsuru TANAKA, Ph.D., M.Sc., Assistant Professor

1) Development of functional foods (Hypertension, Diabetes, Lifestyle-related diseases) and elucidation of their physiological mechanism(s)
2) Absorption of bioactive compounds and their mechanism
3) Sorption of volatiles into plastic film (Diffusion, Permeation, Solubility, SP value, Polymer)
4.Food Process Engineering

Mitsuya SHIMODA, Ph.D., M.Sc., Professor
Noriyuki IGURA, Ph.D., M.Sc., Associate Professor
Seiji NOMA, Ph.D., M.Sc., Assistant Professor

1) Novel technologies for the inactivation of microorganisms and enzymes
2) Chemical analysis and sensory evaluation of food flavor
3) Instrumental analysis and sensory evaluation of food texture
4) Novel technologies for the mono-disperse emulsification
5) Modification of functional properties of proteins by food processing technology
5.Food Hygienic Chemistry

Takahisa MIYAMOTO, Ph.D., M.Sc., Professor
Ken-ichi HONJOH, Ph.D., M.Sc., Associate Professor

1) Development of simple and rapid detection methods for food-borne pathogens (E. coli O157, B. cereus, Salmonella, Listeria monocytogenes, Norovirus, enrichment and selective media, DNA probe, SNP, PCR, quantitative RT-PCR, SPR, Fluorogenic assay, Flow cytometry)
2) Studies on mechanism for stress response and recovery from damage of bacteria (Salmonella, Heat, Oxidative stress, Freezing)
3) Microbial control of food and fresh produce, meat, and seafood by chemicals and naturally occurring substances (Slightly acidic hypochlorous water, Chlorine dioxide, Micro bubble, Catechin, Detergents)
4) Study on inhibition of attachment and biofilm formation of food-borne pathogens by chemicals and naturally occurring substances (natural colors, sugar esters, milk peptides)
5) Studies on mechanism and inhibition of contamination of fresh produce by food-borne pathogens from cultivation environment (Salmonella, Listeria monocytogenes, tomato, lettuce)
6) Studies on cold injury and frost hardiness in plants (Frost hardiness, Gene manipulation, Transgenic plant, Chlorella)
7) Genetical improvement of freeze-tolerance of yeast (Saccharomyces cerevisiae, Freeze-tolerance, Gene manipulation)

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