Graduate School of Science and Technology, Degree Programs in Life and Earth Sciences
Degree Program in Life and Agricultural Sciences
Overview
The rich foundation of human survival has been supported by sustainable food production and technological innovation. Behind this lies our predecessors’ efforts toward a healthy global environment, ecosystem, and social infrastructure. By learning about their experiences, organized as disciplines, and by generating new innovations based on this knowledge, we will aim for consolidation and sustainable development of the foundation of our survival. A mission of our doctoral degree program in Life and Agricultural Sciences is to foster researchers and educators who are committed to learning about the diverse biological functions of animals, plants, and microorganisms around us and the molecular roles of chemical compounds related to those organisms (basic science). These researchers and educators will actively utilize the knowledge obtained (biotechnology) to solve emerging challenges in the fields of food, health, and the environment, and also contribute to global social development.
Message from the Chair
Since ancient times, human beings have used the power of living organisms around us to produce and process food and life-related materials. With the advent of life sciences, it became possible to achieve a molecular-level understanding of these biological phenomena in cells and living organisms. This, in turn, enabled us to artificially modify and utilize specific enzymes, genes, and bioactive substances to efficiently control or imitate biological functions (emergence of biotechnology). This trend has continued to accelerate as genomic information about a wide variety of organisms has accumulated. Today, it is even possible to freely edit the genomes of diverse organisms. On the other hand, the rapid progress in science and technology has created new issues that are beyond the scope of existing academic disciplines. To respond to the ever-changing needs of society, we must foster students capable of solving problems through original research based on broad insight and interdisciplinary training, as well as providing opportunities for society members to engage in continuing education.
Under these circumstances, our degree program aims to foster internationally active researchers (in industry, government, or academia) and university faculties through world-class education and research aimed at elucidating the biological functions and bioactive substances of animals (animal life science), plants (chemical life science), and microorganisms (applied microbiology), as well as their utilization and development (bioengineering). One predecessor of this program is the doctoral program in Life Sciences and Bioengineering in the Graduate School of Life and Environmental Sciences, which was established in 2001. In addition, with the cooperation of research institutes (National Research and Development Agency) in Tsukuba, we also provide education in a Cooperative Graduate School System, in which internationally active researchers are invited as professors or associate professors of the University. We are looking forward to your participation in this degree program, which aims to foster talented students who can cope not only with issues in the field of life and agricultural sciences, but also with various problems beyond their specialized field.
Chair Takeo USUI
Degree Awarded and Academic Competences
Doctor of Philosophy in Life and Agricultural Sciences
The degree is awarded to those who are committed to learning about the diverse biological functions of animals, plants, and microorganisms around us and the molecular roles of chemical compounds related to those organisms. They will actively utilize the knowledge obtained to solve emerging challenges in the fields of food, health, and the environment, and also contribute to global social development.
Academic Competences
Our Curriculum is systematically designed to enable students to gain the following specific competences:
- Ability to execute research
- Expertise and ethics
- Ability to publish research results
- Adaptability to various research tasks
Fields of research
Chemical Life Science Field
To develop useful natural or synthetic bioactive compounds, the following research projects are going on.
- Identification of molecular targets of the bioactive compounds in mammalian and plant cells and their action mechanisms.
- Antioxidative responses to photooxidative stresses.
- Biosynthesis of aroma compounds
- Semiochemicals mediating interactions among insects, plants and animals
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.
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.
Animal Life Science Field
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.
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:
- Transcriptional and translational regulation of genes during gametogenesis
- Functional roles of proteins involved in fertilization, egg activation, and early embryonic development
- Authentication mechanism of mammalian sperm in the female reproductive tract
- Development of reproductive and developmental technologies for future life
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.
- Analysis for dynamics of mitotic chromosomes.
- Analysis for function of condensin complex.
- Analysis for novel function of the nucleolus.
In Animal Bioresource Engineering, research is mainly carried out in the following four areas
- Somatic cell nuclear transfer Research on the genome reprogramming mechanism is conducted using nuclear transfer technology.
- 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.
- 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.
- Establishment of new stem cell lines New stem cells which are essential for human clinical application are being established using various animal species
Our laboratory is focusing on the molecular and cellular mechanisms of nervous system development and maintenance. To understand the role of each components such as genes, proteins, and the structure of synapses, we are analyzing both in-vitro and in vivo functions of those components using culture cells and a model organism C. elegance. Especially, by developing novel analyzing methods and visualizing technologies, the dynamics of those components and spatiotemporal changes are observed in cells and animals, responding to environmental changes. Those methods are also applied to build screening systems for drug candidates for neurodegenerative or psychiatric diseases, to understand neuronal regulation animal behaviors involved in habitat selection or defense against pathogens. Followings are featured research topics currently performed:
- Molecular analysis of components regulating neuronal circuit formation and maintenance
- Development of disease-model animals and screening systems isolating drug candidates
- Development of novel visualization technologies for the in-vivo neuronal functions.
Applied Microbiology Field
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)
- Screening of new metabolism, and functional analysis of physiological functions.
- Metabolic engineering, and the discovery, analysis, design, and restructuring of useful enzymes and genes.
- Functional analysis of enzymes involved in cleavage and synthesis of a C-N bond and their molecular evolution.
- Development of novel functions in the super biocatalyst of microorganisms and enzymes.
- Functional analysis of the nucleic acid related enzymes and its application in DNA/RNA engineering.
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.
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.
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.
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.
- Activating fungal secondary metabolism by biological interactions
- Elucidating molecular mechanisms underlying the fungal interaction
- Investigating fungal physiology and ecology in complex environments
- Culturing the uncultured fastidious microorganisms in the environment and exploring their novel biological functions
- Omics-driven discovery of novel microbial and genetic resources
- Ecophysiology and diversity of uncultured microorganisms in the environments (gut, plants, deep subsurface, etc.)
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.
Biochemical Engineering 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.
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.
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.
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.
- Screening and utilization of biomolecules for sensing food quality.
- Analyses on structure-function relationship of advanced glycation end products
Faculty
Chemical Life Science Field
| Biochemistry of Bioactive Molecules | Prof | Takeo USUI |
| Prof | Hideyuki SHIGEMORI | |
| Assoc Prof | Yukari SUNOHARA | |
| Assoc Prof | Jun FURUKAWA | |
| Assoc Prof | Kosumi YAMADA | |
| Asst Prof | Shigeru MATSUYAMA | |
| Asst Prof | Yoko NAGUMO | |
| Structural Biochemistry | Prof | Toshiyuki TANAKA |
| Functional Foods and Food Chemistry | Assoc Prof | Shigeki YOSHIDA |
Animal Life Science Field
| Genomic Biology | Prof | Akiyoshi FUKAMIZU |
| Prof | Keiji TANIMOTO | |
| Asst Prof | Junji ISHIDA | |
| Asst Prof | Koichiro KAKO | |
| Asst Prof | Hiroaki DAITOKU | |
| Asst Prof | Hitomi MATSUZAKI | |
| Molecular and Developmental Biology | Assoc Prof | Shin-ichi KASHIWABARA |
| Asst Prof | Yoshinori KANEMORI | |
| Biology for Gene Regulation | Prof | Keiji KIMURA |
| Animal Bioresource Engineering | Prof | Atsuo OGURA |
| Assoc Prof | Kimiko INOUE | |
| Molecular Neurobiology | Prof | Motomichi DOI |
Applied Microbiology Field
| Molecular Microbial Bioengineering | Prof | Michihiko KOBAYASHI |
| Assoc Prof | Yoshiteru HASHIMOTO | |
| Asst Prof | Takuto KUMANO | |
| Applied Microbiology | Prof | Nobuhiko NOMURA |
| Assoc Prof | Andrew S. UTADA | |
| Assoc Prof | Masanori TOYOFUKU | |
| Ecological Molecular Microbiology | Prof | Naoki TAKAYA |
| Prof | Toshiaki NAKAJIMA | |
| Prof | Akira NAKAMURA | |
| Assoc Prof | Bei-Wen YING | |
| Assoc Prof | Norio TAKESHITA | |
| Assoc Prof | Yutaka YAWATA | |
| Asst Prof | Yuki DOI | |
| Asst Prof | Syunsuke MASUO | |
| Fungal Interaction and Molecular Biology | Assoc Prof | Daisuke HAGIWARA |
| Asst Prof | Syunichi URAYAMA | |
| Applied Bioengineering of Microbial Ecosystems | Prof | Hideyuki TAMAKI |
| Evolutionary Biology of Symbiosis | Prof | Takema FUKATSU |
Biochemical Engineering Field
| Bioreaction Engineering | Prof | Sosaku ICHIKAWA |
| Assoc Prof | Hidehiko HIRAKAWA | |
| Cell Cultivation Engineering | Prof | Hideki AOYAGI |
| Asst Prof | Masato TAKAHASHI | |
| Biomimetic Chemistry | Asst Prof | Kazuyoshi OGAWA |
| Bioprocess Engineering | Assoc Prof | Nakao NOMURA |
| Food Molecular Engineering | Assoc Prof | Toshiro KOBORI |