Graduate School of Life and Environmental Sciences

Doctoral Program in Life Sciences and Bioengineering

Fostering students to become leading researchers in today’s bioscience and biotechnology fields
Life Sciences and Bioengineering


The aim of the Life Sciences and Bioengineering Program is to conduct pioneering education and research in the areas of biological functions and their application and development. In recent years, the main focus of bioscience and biotechnology has been the molecular biology of genes. However, we will need to deepen further our understanding of the static and dynamic behavior of cells more precisely with the biochemical and molecular levels and develop methods to utilize these functions. Moreover, we need to develop materials related to our way of life that utilize the characteristics of biological resources. In these circumstances, with the aim of fostering students to become leading researchers in today’s bioscience and biotechnology fields, our interdisciplinary curriculum that includes biology, chemistry and engineering is structured by combining the fundamental academic discipline of the “Biochemistry of Cell Functions” and the applicable academic discipline of the “Engineering Science of Biological Functions”.

Message from the Chair



生物機能科学専攻長 田中俊之

Degree Granted

Academic YearDoctor of Philosophy in Agricultural ScienceDoctor of Philosophy in BiotechnologyDoctor of PhilosophyTotal

Fields of research

Biochemistry of Cell Functions Field

To develop useful natural or synthetic bioactive compounds, the following research projects are going on.

  1. Identification of molecular targets of the bioactive compounds in mammalian and plant cells and their action mechanisms.
  2. Antioxidative responses to photooxidative stresses.
  3. Biosynthesis of aroma compounds
  4. Semiochemicals mediating interactions among insects, plants and animals

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Complex information regarding extracellular stimuli such as hormones and stress, is converted and summarized when transmitted from the cell membrane to the inside of the nucleus and is important in cell regulation. The gene expression response mechanism plays an important role in the maintenance of homeostasis in a living organism, and its breakdown leads failure of vital functions. This laboratory identifies acceptor signal functions, epigenetic chemical modification regulation of DNAs and transcription factors, and the catalytic function of modification enzymes, as well as analyzes the genome responsive region. Our mission is to clarify the molecular mechanism of life span and aging using nematode genetics and to understand the mechanisms involved in adult diseases, such as hypertension, pregnancy-associated hypertension and diabetes, by preparing and analyzing the genetically-engineered mice.

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In addition to searching for novel life phenomena and various latent faculties in microorganisms, we are carrying out basic research to identify the structure and function of proteins and enzymes that are involved in such phenomena at the molecular level. Methods to cultivate microorganisms with new functions are developed based on acquired fundamental knowledge through the basic research, and applied research is carried out for the biotechnological application of such microorganisms and the production of useful substances. Furthermore, we have been pioneering new fields in bio-molecular engineering, medicine, environment, and foods based on genomic information.
Themes (examples)

  1. Screening of new metabolism, and functional analysis of physiological functions.
  2. Metabolic engineering, and the discovery, analysis, design, and restructuring of useful enzymes and genes.
  3. Functional analysis of enzymes involved in cleavage and synthesis of a C-N bond and their molecular evolution.
  4. Development of novel functions in the super biocatalyst of microorganisms and enzymes.
  5. Functional analysis of the nucleic acid related enzymes and its application in DNA/RNA engineering.

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Our laboratory carries out three-dimensional structural analysis of proteins involved in signal transduction and transcription regulation to elucidate their molecular mechanisms at the atomic level. Moreover, we aim to create artificial functional proteins based on the gained structural and functional informations.

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Our laboratory is involved in the research fields of gametogenesis and fertilization. We are particularly interested in two processes: the recognition and fusion between male and female gametes, and the RNA metabolism in germ cell during differentiation. We also plan to develop our research findings to applied research in the medical and environmental fields.

Current research projects:

  1. Transcriptional and translational regulation of genes during gametogenesis
  2. Functional roles of proteins involved in fertilization, egg activation, and early embryonic development
  3. Authentication mechanism of mammalian sperm in the female reproductive tract
  4. Development of reproductive and developmental technologies for future life

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Mitosis is a cellular process in which duplicated DNA is eqully segregated into daughter cells. A failure of mitosis may lead to several diseases including cancer. In our laboratory, we are studying for the chromosome dynamics and the underlying molecular mechanism during mitosis using Xenopus egg system and culture cells. We also analyze the regulation of chromosome structure and functions by the nucleolus.

  1. Analysis for dynamics of mitotic chromosomes.
  2. Analysis for function of condensin complex.
  3. Analysis for novel function of the nucleolus.

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In Animal Bioresource Engineering, research is mainly carried out in the following four areas

  1. Somatic cell nuclear transfer Research on the genome reprogramming mechanism is conducted using nuclear transfer technology.
  2. Micro-insemination By injecting spermatids directly into ovum, reproduction techniques which are not possible in normal breeding have been developed, such as taking abnormal sperm to create offspring.
  3. Cryopreservation of gametes and embryos In addition to the development of stable cryopreservation techniques for sperms, ova, and embryos, we are studying techniques for preservation (storage) and thawing which can be easily carried out by anyone.
  4. Establishment of new stem cell lines New stem cells which are essential for human clinical application are being established using various animal species

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Sessile nature of plants has driven evolution of plant-specific systems to monitor fluctuating environment and modulate their mode of growth. Regulation of reversible chromatin modifications is one of the mechanisms for rapid response to environmental changes through alteration in gene expression. Our laboratory aims (1) to clarify genomic and epigenomic mechanisms of environmental stress responses (mainly drought and salinity) in plants by molecular and genomics approaches, and (2) to modify function of the genome towards establishment of stress-tolerant crops by newly developed genome engineering techniques including targeted insertion of engineered endogenous transposons in rice.

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Engineering for Application of Biological Functions Field

This laboratory carries out production technology R&D for foods, medicine, and useful materials in the industry, using energy saving and environmentally friendly methocls.

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Microbes have thrived on Earth since long before multicellular organism appeared. These microbes have evolved during the long history of Earth and have also greatly contributed in developing the current eco-systems. The strategies that the microbes use to survive are fascinating and keep on attracting our curiosity. In our laboratory, we are interested in understanding the diversity and fundamental of life through the amazing life of microbes.

1. ERATO Nomura Microbial Community Control Project
Our research activities aim to create a deeper understanding of microorganisms. To clarify community adaptation to the environment and microbial interactions with other environmental organisms, we will develop novel technologies to image and analyze microbial communities from the individual to the community level. We will clarify the role of heterogeneity and cell-cell interactions within these communities.

Project Website

2. Cell-cell interaction
While bacteria are known as unicellular organisms, they exert various functions by interacting with each other. Our laboratory analyzes cell-cell communication via signal compounds (quorum sensing) and interactions via membrane vesicles to understand their biological roles. We also expect to establish new biotechnologies based on our new understandings.

3. Biofilm
Many bacteria live in actual environment forming biofilm, which are cell aggregates covered with extracellular matrix. Dental plaques, microbial mats, aggregates (flocks) in water, and activated sludge used in effluent treatment are also closely related with biofilms. In our laboratory, we have developed an original microscopy system to analyze biofilms. It is expected that the research achievements will lead to improvement of water treatment technology using activated sludge or prevention and therapy of infection caused by pathogenic bacterium in the future.

4. Bioconversion
Bioconversion is to convert an inexpensive substance to a valuable one by using metabolic functions. Our laboratories study the production of biosurfactants, which are expected to be utilized for cosmetics and drugs.

Targeting microorganisms, photosynthetic cells, plant cells, insect cells, animal cells, and their related symbiotic systems, we are studying Cell Cultivation Engineering (Biochemical engineering) as related to the expansion of elicited biological functions, the development of potential biological functions, and their application, such as development of useful substance production system, environment assessment method, environmental purification system, detoxification system, and new microbial detachment.

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Studies are carried out in the interdisciplinary fields of macromolecular chemistry and biochemistry. Specifically, the roles three mutually interactive forces – Coulomb’s force, hydrogen bonding, and hydrophobic interaction – within and between molecules play in the morphology of macromolecular chains and the formation of macromolecular complexes are experimentally and scientifically clarified using synthetic macro-molecules with simple chemical structures (chain polymers, nanogel fine particles, etc). Based on this basic research, the mechanisms of molecular recognition, transportation, material transformation, and energy transduction which occur in a biological system are considered from the standpoint of macromolecular chemistry. In addition, concept establishment and its verification are sought for the application to biosensor, membrane separation technologies, etc.

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In our laboratory, we study filamentous fungi, some types of microbes. Filamentous fungi are multi-cellular, eucaryotic organisms, the same as humans, animals and plants, and are characterized by differentiation in form and diverse metabolisms. We concentrate on the unique metabolisms of filamentous fungi in order to clarify such mechanisms, taking full advantage of molecular biology, -omics (genomics, etc.), enzymes, and filamentous fungi genetics and genetic recombination technology. Insights gained from the study can be useful in growth control technology of pathogenic filamentous fungi of animals and plants, and the cultivation of filamentous fungi used in the brewing and fermentation industry of Koji mold, etc.

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In our laboratory, we carry out research in food biotechnology, using techniques in biochemistry, applied microbiology, molecular biology, etc. Our goal is to identify problems regarding foods which contain primary products such as plants, animals, and microorganisms as raw materials.

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Filamentous fungi are able to produce many kinds of bio-active chemicals and enzymes, for which they are essential for our society. However, the most part of the ability is remained to be studied. In the natural habitats, they are interacting with the other creatures such as microorganisms, plants, and animals, under which conditions the ability of filamentous fungi may be specifically activated. The goal of our group is to understand if interaction with the others affects the physiology of filamentous fungi. In addition, novel bio-active chemicals and enzymes are sought under the combined culture conditions, and the molecular mechanisms underlying the regulation are investigated.

  1. Activating fungal secondary metabolism by biological interactions
  2. Elucidating molecular mechanisms underlying the fungal interaction
  3. Investigating fungal physiology and ecology in complex environments

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Insects are very interesting creatures, demonstrating a high level of interaction between organisms, such as various endosymbiotic phenomena, parasitism, reproductive manipulation, morphology manipulation, and sociality. Research from many different approaches on the phenomena is carried out, from evolutionary diversity to ecological interaction and from physiological functions to its molecular mechanisms. Regarding the unique, interesting phenomena of the organisms, the diversity and commonality of organisms, as well as their macrobiology and microbiology, are surveyed in an integrated manner through the thorough clarification from many approaches at the molecular level to the evolutionary level.

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Our laboratory aims to develop methods for exploring microbial and genetic resources widely distributed in the environments, which could contribute to creating new bioprocesses for biochemical and bioenergy production, and environmental pollution control.

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Research and development on molecular- and cellular-based sensing technology for evaluation of food quality to scientifically support creation of value-added food products in food industry.

  1. Screening and utilization of biomolecules for sensing food quality.
  2. Analyses on structure-function relationship of advanced glycation end products

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Biochemistry of Cell Functions Field

Biochemistry of Bioactive Molecules
ProfessorHiroshi MATSUMOTO
ProfessorTakeo USUI
Associate ProfessorYukari SUNOHARA
Assistant ProfessorOsamu NEGISHI
Assistant ProfessorShigeru MATSUYAMA
Assistant ProfessorTakuya YAMAGUCHI
Genomic Biology
ProfessorAkiyoshi FUKAMIZU
ProfessorKeiji TANIMOTO
Assistant ProfessorJunji ISHIDA
Assistant ProfessorKoichiro KAKO
Assistant ProfessorHiroaki DAITOKU
Assistant ProfessorJundai KIM
Assistant ProfessorHitomi MATSUZAKI
Molecular Microbial Bioengineering
ProfessorMichihiko KOBAYASHI
Associate ProfessorYoshiteru HASHIMOTO
Assistant ProfessorTakuto KUMANO
Structural Biochemistry
ProfessorToshiyuki TANAKA
Assistant ProfessorYoko NAGUMO
Molecular and Developmental Biology
ProfessorTadashi BABA
Associate ProfessorShin-ichi KASHIWABARA
Assistant ProfessorYoshinori KANEMORI
Biology for Gene Regulation
Associate ProfessorKeiji KIMURA
Animal Bioresource Engineering
ProfessorAtsuo OGURA
Associate ProfessorKimiko INOUE
Plant Environmental Genomics
ProfessorYoshiki HABU

Engineering for Application of Biological Functions Field

Bioreaction Engineering
ProfessorSosaku ICHIKAWA
Associate ProfessorHidehiko HIRAKAWA
Assistant ProfessorKaori YOKOTANI
Applied Microbiology
ProfessorNobuhiko NOMURA
Cell Cultivation Engineering
ProfessorHideki AOYAGI
Biomimetic Chemistry
Assistant ProfessorAkihiko SHIMADA
Assistant ProfessorKazuyoshi OGAWA
Ecological Molecular Microbiology
ProfessorNaoki TAKAYA
ProfessorAkira NAKAMURA
Assistant ProfessorNorio TAKESHITA
Assistant ProfessorYutaka YAWATA
Functional Foods and Food Chemistry
Associate ProfessorShigeki YOSHIDA
Bioprocess Engineering
Associate ProfessorNakao NOMURA
Fungal Interaction and Molecular Biology
Associate ProfessorDaisuke HAGIWARA
Assistant ProfessorSyunichi URAYAMA
Molecular and Cellular Chronobiology
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Evolutionary Biology of Symbiosis
ProfessorTakema FUKATSU
Molecular Neurobiology
Associate ProfessorMotomichi DOI
Applied Bioengineering of Microbial Ecosystems
ProfessorNobutada KIMURA
Food Molecular Engineering
Associate ProfessorToshiro KOBORI