The Graduate School of Life Science : Biosystems ScienceCourse

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The Graduate School of Life Science : Biosystems ScienceCourse Higher Order Cellular Functions
Functional Genome Science
Environmental Life Science
Animal Behavior and System Control
Reproductive and Developmental Sciences

Membrane proteins including receptors, the cytoskeleton, and intracellular vesicle transport play a pivotal role in maintaining cell morphology, polarity, adhesion, and differentiation under the control of a complex signal transduction network. In order to understand higher order cellular functions, we have to know functions of signaling proteins and how these proteins are regulated in a whole cell system. We tackle these problems using plants, model organisms, and animal models, from the viewpoint of molecular genetics, cell biology, physiology and biochemistry.

Laboratory of Molecular Interaction WebSite


Biomembranes are essential for multiple cellular activities including cell shape, cell
polarity, vesicle transport, and organelle functions. Because biomembranes consist of lipid bilayers which are composed of various lipid molecules in an asymmetrical manner between bilayers; lipids are believed to play an important role for membrane
functions. However, there is still so much which remains to be learned, because lipids are elusive small molecules. The aim of our laboratory is to elucidate the roles of lipid dynamics in various cellular functions by using yeast as a model organism.

Kazuma Tanaka (Professor) Takuma Kishimoto
(Assistant Professor)
Tetsuo Mioka
(Assistant Professor)
Keywords lipid asymmetry, cell polarity, vesicle transport, molecular cellular biology, molecular genetics, yeast

Laboratory of Plant Morphology and Gene Function WebSite

Plants Cultured cells Bioinformatics

Plants are commonly considered as inanimate and “still life” objects, however, we are simply limited in our abilities to directly sense their movement in our temporal sense. Upon close evaluation with time-lapsed photography, it becomes evident that plants are very animated and their dynamic movement and development is revealed. The plant hormone “Auxin” has a central functional role in plant morphogenesis. The main focus of this laboratory pertains to the study of “Early-Auxin Inducible Genes” and to investigate the functional roles of auxin in the synthesis of new organs (Organogenesis). We primarily utilize Arabidopsis as a functional model system for both forward and reverse genetics. In addition, we also use both potato and carrot as additional models.

Masaaki K. Watahiki (Associate Professor)
Keywords Auxin, feedback regulation, gene expression, molecular biology, plant physiology, genetics, plants, Arabidopsis, carrot, potato

Laboratory of Plant Evolutional and Developmental Biology WebSite

Plants Cultured cells Bioinformatics

Plants possess multiple attractive features and potential that we, as humans, simply lack. For example, plants are readily capable to regenerate an entire organism from a single cell by using only light, water and micronutrients. In addition, stem cells for most plant species possess capabilities for indefinite cell proliferation. Plants are capable of surviving exposure to dynamic seasonal conditions from summer to winter. While plants are actively photosynthesizing, plants will never die from “cancer-like” effects even in continuous exposure to sunlight. Over the course of millions of years, plants have evolved many unique and beneficial characteristics which have the potential to bring great value for human beings and our mother earth. One of our primary goals is to unveil these powerful attributes of plants or plant cells and to learn their underlying mechanisms. As a result, these findings may enable us to develop novel plants which are capable of enhanced growth and productivity even under harsh environmental conditions.

Tomomichi Fujita (Professor) Teh Ooikock
(Assistant Professor)
Keywords Molecular & cell biology, Eco-Evo-Devo, Bryophytes, cell proliferation and differentiation, environmental response, phytohormone, cell polarity, asymmetric cell division, cell cycle regulation, cell-cell communication, perception and mind in plant life, space utilization science

Laboratory of Gut Physiology WebSite

Animals Microorganisms Cultured cells

Our research focuses on the mutually beneficial symbiotic relationships between gut microbes and host species. In particular, we are interested in the immune response, inflammatory reaction, and energy/lipid metabolism in response to changes in the gut microflora. In terms of applied science, we investigate whether pre/probiotics prevent and/or treat some diseases including allergies, obesity, and metabolic syndrome. Furthermore, we are also interested in studying the gut physiology of hibernating mammals.

Kei Sonoyama (Associate Professor)
Keywords gut physiology, mammals, gut microbiota, allergies, metabolic syndrome, hibernation

Biomedical Animal Research Laboratory WebSite

Animals Cultured cells Bioinformatics

Naked mole-rat (NMR, Heterocephalus glaber), a subterranean mammal native to Africa, is the longest-living rodent (around 30 years) and exhibit extraordinary cancer-resistance, although its body mass is similar to that of the house mouse. One of our research goals is to reveal the molecular mechanisms of NMR's longevity and cancer-resistance. Understanding the anti-cancer and longevity mechanisms may lead to advances in human treatments in the future. We are also interested in studying the regulation of unique eusociality observed in NMR.

Kyoko Miura
(Associate Professor)
Yoshimi Kawamura (Assistant Professor)
Keywords naked mole-rat, senescence, aging, cancer, eusociality, molecular biology, next-generation sequencing

Genetic information of living organisms has been accumulated in genome and chromosomes during evolution for more than 3 billion years. A major goal of life science is to understand how the genetic information is transmitted during evolution, and realized as the phenotypes of cells and individuals from the aspect of genome dynamics, and regulation system of genome function using various model organisms. The importance of this approach also increasing in the fields of clinical medicine and application biology. Students are expected to learn regulation mechanisms of genome function, and to specialize in structural dynamics of chromatin, molecular basis of transcriptional regulation, function of non-coding RNAs, molecular mechanism of meiosis and genetic disease, molecular basis of sex determination, sex chromosome evolution, function of oncogenes, and regulation mechanism of cell proliferation.

Laboratory of Cell function and Structure III WebSite


For many years, DNA was known as the key cellular component which captured encoded genetic information and served as the template for active cellular components; beginning with RNA and subsequently functional proteins. However, active RNA molecules and epigenetic modifications have been recently shown to play critical and highly specific regulatory roles for important biological activities. By using plants as our model system, we study the functional mechanisms of non-coding RNAs and epigenetic regulation. We are very interested to understand how the effects of the epigenetic regulation impact the capability of plants to adapt to their environment. A main objective of our studies is to identify novel gene regulation factors. Secondly, we also aim to develop enhanced plants through application of the identified regulation factors.

Atsushi Kato (Professor) Hidetaka Ito
(Assistant Professor)
Keywords environmental adaptation, transposon, plant molecular genetics, epigenetics, plant breeding, environmental stress, evolution

Laboratory of Environmental Molecular Bioscience WebSite

Animals Cultured cells

In multicellular higher animals, various signals are used to stimulate cells towards either a proliferating, differentiating or apoptotic state. The regulatory systems which control the switching of these cellular states can be affected by various environmental stress factors including carcinogens and by reactive oxygen species that are induced by stress factors. Undesirable apoptosis and misregulation of cellular functions, resulting in excessive proliferation, brings different diseases such as cancer and neurodegenerative diseases at various levels within higher animals. We are interested to study the relationship between cellular systems responding to environmental stresses and various diseases. We specifically focus on the protein products of proto-oncogenes.

Sanae Ariga (Professor)    
Keywords cell proliferation/differentiation/transformation/apoptosis, biochemistry,
molecular biology, cell biology, higher animals, proto-oncogenes, oxidative stress, neurodegenerative diseases, signal response

Laboratory of Gene Function and Regulation WebSite

Animals Cultured cells

We are mainly interested in analyzing the functions and control mechanisms of the genes and factors that are involved in the regulation of animal development, differentiation and dedifferentiation. We use multiple model systems such as silkworm, insect culture cells and culture cells of mouse and humans to enable us to address these questions. We place special emphasis on characterizing transcriptional regulation by using molecular biology, molecular genetics, cytogenetics and developmental biology approaches.

Shigeharu Takiya
(Associate Professor)
Ikuya Yoshida
(Assistant Professor)
Keywords silkworm, silk genes, Hox genes, transcriptional regulation, transcription factor,
insects, ecdysis, insect hormone, metamorphosis, culture cells, mammals, X
chromosome, inactivation and reactivation, ES cells, pluripotency, molecular
biology, genetics

Laboratory of Animal Genetics

Animals Cultured cells Bioinformatics

Completion of the genome sequence project and development of next-
generation sequencing technique have dramatically changed a design of
research strategy in biomedical science. However, functions of all genes in the
whole genome are not well understood even now. We elucidate functions of
disease-related genes by use of gene-manipulated rats and mice generated in
our laboratory.

Kazuhiro Kitada(Associate Professor)
Keywords Animal models for human diseases, gene manipulation, rat, mouse

All living things are exposed to environmental stresses. Understanding the physiological processes that underlie stress injury and the mechanisms by which living organisms adapt and acclimatize to environmental stress is important to achieve a good understanding of basic concepts in biology. We will study, through lectures, how living organisms sense and respond to environmental changes, which finally lead to reconstitution of the organism. Subjects covered in the course will include: 1) energy conversion systems for photosynthesis and mass production, 2) metabolic regulation controlled by functional RNA species and post-translational processes, such as ubiquitin-mediated protein degradation, and 3) cellular regulation, such as cell division, cell differentiation, and development triggered by chromatin remodeling, gene regulation, and growth regulators.

Laboratory of Cell Structure and Function – (Yamaguchi & Sato Lab) WebSite

Plants Microorganisms Cultured cells Bioinformatics

Plant growth and development are controlled by the concerted actions of many
signaling pathways which are triggered by developmental and metabolic cues.
Nutrients such as sugars and nitrogen compounds play an important role as
signaling molecules that modulate the expression of many plant genes involved in
diverse physiological processes, such as germination, seedling development,
flowering, senescence, and pathogen responses. Our goal aims to clarify
signaling networks which mediate nutrient utilization and plant growth regulation.

Junji Yamaguchi (Professor) Takeo Sato
(Assistant Professor)
Keywords environmental adaptation, molecular biology, plant science, ubiquitin-
proteasome system, metabolic regulation, plant immunity, proteome, biotic and
abiotic stress

Laboratory of Cell Structure and Function – (Chiba Lab) WebSite

Plants Cultured cells Bioinformatics

The control of gene expression is exerted by multiple steps such as transcription, RNA
processing and export, mRNA stability, translation and post-translational events. The recent discovery of biologically active small RNAs has enhanced the impact of post-transcriptional regulation, and in particular, the alterations of mRNA stability on gene regulation. The control of mRNA turnover is thought to be an important component of the rapid response to environmental changes. The goal of our projects is to demonstrate the importance of mRNA turnover control in regulating gene expression in response to several stress conditions in plants.

Yukako Chiba (Associate Professor)
Keywords stress response, regulation of gene expression, mRNA degradation, Arabidopsis,
molecular biology

Laboratory of Cell Structure and Function (Takada Lab) WebSite


The aim of our laboratory is to understand the molecular mechanisms which govern the adaptation of living organisms to diverse environmental conditions. In particular, we are interested in characterizing the adaptive responses of bacteria to low temperature conditions. Our recent studies focus on the following subjects: 1) The relationship between structural and functional characteristics of cold-adapted enzymes from psychrophilic and psychrotrophic bacteria. 2) The regulation mechanisms for the cold-inducible expression of genes encoding the cold-adapted enzymes.

Yasuhiro Takada (Associate Professor)
Keywords extreme environments, adaptation to environment, psychrophilic bacteria, cold-
adapted enzymes, cold-inducible gene expression

Laboratory of Molecular Biology WebSite

Plants Cultured cells

Cystathionine γ-synthase (CGS), the first committed enzyme of methionine biosynthesis in higher plants, is feedback-regulated at the step of its mRNA degradation. During translation of CGS mRNA, a methionine metabolite S-adenosylmethionine directs ribosomes to arrest at a specific site, which then induces CGS mRNA degradation. We are studying molecular mechanism of CGS mRNA degradation coupled with ribosome arrest.

Satoshi Naito (Professor)    
Keywords molecular biology, plant physiology, Arabidopsis, methionine biosynthesis,
mRNA degradation, translation arrest, nascent peptide, in vitro translation

Laboratory of Plant Adaptation Biology WebSite

Plants Microorganisms Bioinformatics

Photosynthesis integrates various biological processes of plant cells. We study the environmental adaption, agricultural applications and the evolution of photosynthesis by using the model photosynthetic organisms including Arabidopsis, green algae and cyanobacteria. One of the goals of our research is to prolong the photosynthetically active duration of crops by engineering plant metabolism.

Ayumi Tanaka (Professor) Ryouichi Tanaka
(Associate Professor)
Hisashi Ito
(Assistant Professor)
Atsushi Takabayashi (Assistant Professor)
Keywords photosynthesis, molecular biology, plant physiology, plants, algae, cyanobacteria, chlorophyll

Functions of the nervous system, including sensory integration, motor control, learning, memory, and motivation, are closely associated with animal behavior at the level of the organism. Analyses of the neuronal and circuit operations underlying these functions are conducted at the level of integration by directly relating them to organism-level behavior. Students are expected to develop a systematic understanding of the leading-edge knowledge and concepts attained by state-of-the-art experimental techniques, including molecular biology, biophysics, neuroendocrinology, and systems physiology, as well as techniques for reconstruction of nervous functions by computer simulation together with its significance in biological research.

Laboratory of System Neurobiology WebSite


When animals receive sensory stimuli from environment, they perform appropriate behaviors via sensory perception and motor planning that is mediated by their central nervous system. By using a combination of behavioral analyses, electrophysiology, optical imaging and mathematical approaches, we study the neural basis underlying wind-elicited behavior in the cricket model system. The ultimate goal of our research is to generate a complete understanding of whole neural circuits and information processing from sensory inputs to motor output in specific behaviors.

Hiroto Ogawa (Professor)
Keywords insects,brain,nervous system,neuron,neurophysiology,imaging

Laboratory of Behavior and Neurobiology - (Mizunami Lab) MizunamiWebSite


We study the functional organizations of insect “microbrains” to clarify common
principles and diversities of brain mechanisms among insects and mammals. By studying their molecular, neural, and systems mechanisms, our research has demonstrated that crickets and cockroaches possess excellent learning capabilities.

Makoto Mizunami (Professor)    
Keywords brain, learning, olfaction, crickets, cockroaches, fruit flies, Drosophila

Laboratory of Behavior and Neurobiology - (Soma Lab) WebSite


Our research incorporates both mechanistic and functional approaches to address the question why living things show such a great diversity in behaviors and their underlying cognitive functions. We focus primarily on functional aspects and we investigate the behavioral ecology of passerine birds (mainly Estrildid finches) with particular interest in social communication; including courtships and parent-offspring interactions,
reproduction, development and life history.

Masayo Soma (Associate Professor)
Keywords songbird, social behavior, development, learning, courtship, cognition, ethology, behavioral ecology

Laboratory of Behavioral and Neural Biology – (Matsushima Lab) WebSite


Animals optimize their behavior by precisely estimating benefits, costs and time. By using domestic chicks and songbirds as models, my laboratory focuses on two main questions: (1) How do animals perform evaluation of risks associated with food resources. (2) How does social competition over food resources influence decision making. By using an integrated approach of cognitive neuroscience and behavioral ecology, we aim to increase our understanding of the evolution of animal behaviors.

Toshiya Matsushima (Professor)
Keywords behavioral ecology, cognitive neuroscience, neuroeconomics, decision making, basal ganglia

Laboratory of Molecular Neuroethology Laboratory WebSite


Animal behavior is influenced by both environmental and genetic factors. However, much remains to be learned regarding how and when the environmental and genetic
factors act and how developing behavior itself affects the molecular basis in the neuronal substitute. The primary focus of our laboratory is to elucidate these questions by using songbirds as an animal model for vocal learning and to identify its critical period.

Kazuhiro Wada (Associate Professor)
Keywords animal behavior, gene expression, learning and memory, individual difference, songbird, communication, epigenetics

Laboratory of Neurocybernetics WebSite

Animals Bioinformatics

The aim of our research is to elucidate the neuronal mechanism of real time adaptability in animal behavior. In order to better understand the mechanisms of real time adaptation, we have focused our research on elucidating the functions of the central nervous systems by which animals alter their behaviors in order to respond to the demands of a changing environment. Since insects possess rather simple and identical nervous systems, they provide us with an ideal model system to effectively investigate the neuronal mechanisms of adaptive behavior.

Hitoshi Aonuma
(Associate Professor)
Hiroshi Nishino
(Assistant Professor)
Keywords neuroethology, mobiligence, neurogenetics, modelling, simulation, robotics

Laboratory of Neurobiology (Tanaka Lab) WebSite


Our goal is to reveal how neuronal circuits work as a system to process sensory inputs, and how this processing is modulated by a specific environment or by the mental state or the condition of the body. The answers to these questions would reveal how an animal displays adaptive behavior in response to a given situation that changes every moment, or even develops intelligent behavior to cope with a difficult situation. To study these problems in our laboratory, we are utilizing two invertebrate animals, the fly and the cephalopod.

Nobuaki Tanaka
(Associate professor)
Keywords Drosophila melanogaster, Cephalopod, Pygmy squid, sensory processing, neurophysiology, neuroanatomy, genetics, behavioral studies

An important general goal of life science research is to elucidate the factors regulating the formation of germ cells and how a new individual is generated after fertilization. This knowledge can be applied directly to various reproductive manipulations with direct consequences for our life, such as in vitro fertilization, contraception, and production of useful crops. Reproductive and developmental biology have two aspects: pure science, which pursues the mechanisms guaranteeing the continuity and diversity of life; and applied science, which develops technology to artificially control reproduction and development. Social interests in this academic field, as represented by cloned animals and regenerative medicine, are now very high.
In this field, we are studying the general mechanisms of the formation and maturation of germ cells and regulation of cell division and differentiation in development.

Laboratory of Reproductive and Developmental Biology - (Yamashita Lab) WebSite

Animals Cultured cells

The life cycle of many multicellular organisms begins with the union (fertilization) of germ cells (the eggs and the spermatozoa). For sexually reproductive organisms, these processes are indispensable to enable the maintenance of a species beyond the limited life span of individuals. In addition, the recombination of genes during gametogenesis, and the blending of genes by fertilization, gives rise to diversity at organismal level. Consequently, germ cells are responsible for both the continuity and the diversity of life. By using medaka and zebrafish as experimental animal model systems, our research efforts focus on understanding the underlying molecular and cellular mechanisms of oocyte maturation and spermatogenesis.

Masakane Yamashita (Professor)    
Keywords oocyte maturation, spermatogenesis, meiosis, translational control, cell culture, cell growth, cell differentiation

Laboratory of Reproductive and Developmental Biology - (Ogiwara Lab) WebSite

Animals Cultured cells

The supply of germ cells (oocytes) to produce the next generation is the most important function of the ovary. We are studying the unsolved issues associated with ovarian functions. We are analyzing to elucidate the mechanism of oogenesis, ovulation, and tissue repair after ovulation using mouse, medaka, and zebrafish.

Katsueki Ogiwara
(Associate Professor)
Keywords follicle selection, ovulation, tissue repair

Laboratory of Reproductive and Developmental Biology - (Katsu Lab) WebSite

Animals Cultured cells Bioinformatics

Steroid hormones regulate physiological responses in vertebrates by binding to the nuclear receptors (NR), a ligand-activated transcription factor. We study the evolution of vertebrate NRs and investigate how steroid hormones act in many vertebrates. We also analyze the temperature-dependent sex-determination/ differentiation of reptiles, and the effects of endocrine disrupting chemicals; including the evaluations of pharmaceuticals on animals.

Yoshinao Katsu (Professor)
Keywords endocrinology, steroid hormone, nuclear receptor, endocrine disruptor, sex

Laboratory of Reproductive and Developmental Biology - (Kuroiwa & Mizushima Lab) WebSite

Animals Cultured cells Bioinformatics

How is sex determined in animals? We are interested to study sex determination in both birds and mammals. We perform functional analysis of genes that are involved in sex determination of domestic birds such as chicken, quail and emu by using transgenic, genome editing or biotechnological methods. We also aim to identify a novel sex determination gene and to reveal a process of Y-loss in the genus Tokudaia which lacks a Y chromosome.

Asato Kuroiwa (Professor) Hidenari Mizushima
(Assistant Professor)
Keywords sex determination, gene, Y chromosome, bird, mammal, reproductive developmental biology, molecular biology

Laboratory of Reproductive and Developmental Biology - (Kimura Lab) WebSite

Animals Cultured cells

Precise temporal and spatial regulation of gene expression is extremely important for cell differentiation and function. The main focus of our laboratory is to investigate the regulatory mechanism and function of genes and noncoding RNAs in the mammalian ovary, testis, and placenta. We also focus on elucidating the molecular mechanism in spermatogenesis and placental differentiation.

Atsushi P. Kimura (Associate Professor)
Keywords molecular biology, gene expression, epigenetics, long noncoding RNA, genome, ovary, spermatogenesis, placenta, protease

Laboratory of Reproductive and Developmental Biology - (Kotani Lab)


A multicellular organism begins with a single cell, the fertilized egg, and subsequently undergoes differentiation and morphogenesis to become an embryo. All cellular functions and patterning decisions that occur prior to the activation of the zygotic genome depend on maternal factors deposited in the egg during oogenesis, which become active after fertilization. By using zebrafish and mouse as model systems, we investigate the deposition of maternal factors in oocytes that promote developmental processes. Our aim is to identify novel mechanisms of oogenesis and developmental processes by isolating and analyzing maternal factors.

Tomoya Kotani (Associate Professor)
Keywords vertebrate, oocyte, egg, early development, maternal factor, cell biology, molecular biology, molecular genetic

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