Graduate School of BIOSTUDIES Kyoto University
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Graduate School of BIOSTUDIES
Kyoto University Contact

Graduate School of Biostudies Kyoto Univ. 【Inquiries concerning entrance examinationand "Global Frontier in Life Science”】
Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501

Student Affairs Section

Phone 075-753-9222
FAX
075-753-9229
Email kyomu@adm.lif.kyoto-u.ac.jp【Other Inquiries】

General Affairs Section

Phone 075-753-9221 FAX 075-753-9247
Email soumu@adm.lif.kyoto-u.ac.jp

https://www.lif.kyoto-u.ac.jp/e/2022

Graduate School of BIOSTUDIES,
Kyoto University

Expand your horizons!
In 1999, the Graduate School of Biostudies (GSB)

As scientists, we sometimes encounter phenomena

was established as Japan's first independentthat we have never seen before or that we cannot

graduate school by a group of faculty members who

explain with our previous knowledge. We need toshare a common language of molecular biology anddetermine whether an observation is due to our own

whose research transcends the traditional

operational error, can be explained by known

framework of science, medicine, agriculture, andprinciples, or is a "seed" that will lead to a newpharmacology. The GSB is organized into two

discovery. By finding and nurturing these "seeds," wemultidisciplinary divisions: the Division of Integrated

will be able to design new research projects. In turn,Life Science and the Division of Systemic Life

preliminary experiments may inform our conjectures

Science. In order to broaden the research scope andabout the principle behind them, leading to a formal

educational area, the Radiation Biology Center andhypothesis, and if we can prove the hypothesis

the Research Center for Dynamic Living Systems

through experiments, we can submit it as a paper. In

were added to the two Divisions in 2018. Further

order for a paper to be accepted by the scientificinitiatives in the GSB include the Advanced Life

community, it needs to be recognized as "good" by

Science Promotion Project for young faculty

several world-leading researchers. With this in mind,

members, and industry-university joint laboratories in

it is important to build an international network.

both divisions.

Faculty members of the GSB have organized

To develop creative individuals who can discover andinternational conferences on world-standard model

solve problems on their own, the GSB emphasizesorganisms established in our school, as well as

the participation of students in "free and originaltechnical workshops on fluorescence imaging andresearch" conducted by faculty members. In theinformation processing using next-generationlaboratories where faculty members are exploring thesequencers. These events have brought a stream offrontiers of life science, students share theirworld-class investigators to our GSB students.

challenges and develop their scientific way of

To encourage students to interact with scientists

thinking, logic, and empirical skills. The fact thatfrom around the world, the GSB provides remotemany research papers have been published withlectures with overseas universities, a program forstudents as the first authors shows that students do

sending students abroad, an international student

not help faculty members with their research but playseminar program in which students invite overseas

a leading role in science under the guidance ofstudents and young researchers to participate, afaculty members. To date, 1,674 master's degree

program to support students from outside Japan,

graduates and 505 doctoral degree recipients haveand a system for transferring credits and promoting

contributed not only to the field of academic

joint research through inter-university agreements.

research but also to the development of society at

We, the faculty and staff of the GSB, will do ourlarge. This has been the joy of all the facultyutmost to support students as they gain scientificmembers who have been involved in research andexperience and establish a firm foundation for theireducation.

future careers.

Dean, FUKUZAWA, HideyaG r a d u a t e

S c h o o l

o f

B I O

S T U D I E S ,MISSIONS of our GRADUATE SCHOOL

1

Provide education for
pursuing the new biostudies
at the world's top level
To meet the demands of the industry,college, research institutes andadministrative organizations, individuals are
educated in the life sciences and master thetechniques for the society needs.

2

Train individuals to apply the new life
sciences for the protection of the global
environment and for human welfare
Integrate the knowledge and technology inthe old fields of science, agriculture,
medicine and pharmacology, and nurtureindividuals who can contribute to thehuman society in the 21st century.

K y o t o

Admissions Policy of the Graduate School of Biostudies
Master’ s Program

Doctoral Program

As an advanced discipline that holds the key to the future of humankind, the life

As an advanced discipline that holds the key to the future of humankind, the life

sciences today are undergoing a major evolutionary change. In response to thissciences today are undergoing a major evolutionary change. In response to thisglobal trend, the Graduate School of Biostudies was founded in 1999 as Japan’ s

global trend, the Graduate

first independent graduate school focused on the life sciences with the

School of Biostudies was founded in 1999 as Japan’ s first independent

objective of building a world-class center for research and developing

graduate school focused on life sciences with the objective of building a

individuals who can lead the life sciences field into the next generation. Ourworld-class center for research and developing individuals who can lead the life

school has engineered a true fusion of cutting-edge areas in several existingsciences field into the next generation. Our school has engineered a true fusion

fields. By harnessing the common language of “cells, molecules, and genes”

of cutting-edge areas in several existing fields. By harnessing thethat together form the fundamental principles of life, we have developed an

3

integrated understanding of diverse life forms and the environments they help

Nurture individuals who canunderstand the various vital
phenomena of the living organisms
as a systemic function, andpursue these systemic functions

shape, and have launched innovative efforts in research and education that willproduce a new set of values for the future and dignity of life.
To meet the diverse expectations of society for advances in the life sciences,which are becoming increasingly sophisticated and complex, our school seeks
students from a broad spectrum of backgrounds who share these ideals of our

Nurture individuals who will be leaders in
the human society to pursue their activities
for the welfare and happiness of humans in
the 21st century, where humans will beliving in harmony with other living beings.

school, who possess basic academic skills and research aptitudes in the life
sciences, and who demonstrate a strong sense of ethics and responsibility intheir academic research. We especially welcome students who possess apioneering spirit to help propel the comprehensive and advanced branches ofthe life sciences, free from preconceptions, while fully appreciating the dignity

OPERATION POLICIES of our GRADUATE SCHOOL

of life. Accordingly, the Graduate School of Biostudies endeavors to cultivate
individuals with the following attributes:
1. Researchers ready to discover, or to shed fresh light on, fundamental
principles of life, who will pioneer new areas of the life sciences;Training of individuals with the mostadvanced knowledge of the life
sciences for the next generation

1

The graduate student studies a higher level oflife sciences beyond the structures of past life
science - related fields at each undergraduatelevel to understand the integrated life sciences.
The goal is to nurture a new type of individualwith creative and innovative abilities to cope withthe various unknown themes to be confronted
by human beings in the next generation.

Training to establish self
for society

2

In the Graduate School of Biostudies,
individuals are trained to make a healthy
and fair judgment based on the academic
background of the staff and their prospects
for the future; and, establish a new system
to evaluate the effects of education frommultiple aspects from the past.

2. Researchers and engineers committed to global environmental conservationand gains in human health, welfare, and well-being, who are ready to makesocial contributions through roles in public and private research institutions;
3. Educators and working professionals with a broad-based understanding of
the varied phenomena of life in general, who are ready to make social
contributions through roles in education, industry, the news media, andgovernment;
4. Researchers, educators, engineers, and working professionals who possess
strong communication skills that enable them to hold discussions withresearchers and others from Japan and around the world in life
science–related fields.

3
503

Activation and flexibility ofstaff in the human relations
Research is pursued by each staff
member independently to develop a newlife science based on active exchange
among the various laboratories in thegraduate school.

4common language of “cells, molecules, and genes” that together form thefundamental principles of life, we have developed an integrated understandingof diverse life forms and the environments they help shape, and have launchedinnovative efforts in research and education that will produce a new set ofvalues for the future and dignity of life.
To meet the diverse expectations of society for advances in the life sciences,which are becoming increasingly sophisticated and complex, our school seeks
students from a broad spectrum of
backgrounds who share these ideals of our school, who possess broad
academic knowledge and advanced expertise gained through their master’ s
education, who possess strong research ability,
and who demonstrate an even stronger sense of ethics and responsibility intheir academic research. We especially welcome students who possess apioneering spirit to help propel thecomprehensive and advanced branches of the life sciences, free frompreconceptions, while fully appreciating the dignity of life. Accordingly, theGraduate School of Biostudies endeavors tocultivate individuals with the following attributes:
1. Researchers ready to discover, or shed fresh light on, fundamental principles
of life, who will produce world-class research results in new areas of the life
sciences;
2. Researchers and advanced engineers committed to global environmental
conservation and gains in human health, welfare, and well-being, who are
ready to assume a leading role in public and private research institutions;
3. Educational leaders and high-level working professionals with a broad-based
understanding of the varied phenomena of life, who are ready to assume aleading role in education, industry, the news media, and government;

Use of current post-doctoral systemand evaluation of academic activities

The entrance exam will comprise achievement tests that include an assessmentof the applicant’ s ability to think logically in English, a skill that is required to

4. Researchers, educational leaders, advanced engineers, and high-level working

Full use should be made of the current system, toprovide the increasing necessary number of
instructors per student, for the intensive training
to become life scientists at an international level,
for true development of a new research field.

read and analyze an article published in an international journal; an assessment

professionals equipped with strong logical explanation and communicationof the applicant’ s general knowledge of molecular biology, cell biology,

skills, who can convey their ideas broadly to others in Japan and around thebiochemistry, and other life science fields; an assessment of the applicant’ sworld and assume a leading role in a variety of fields.

Promotion of gender equality
To promote gender equality, we draw up the action plan.
Also we enhance the research environment and support for child-rearing and caregiving.

Graduate School of BIOSTUDIES, Kyoto University

U n i v e r s i t yfundamental knowledge as required to pursue his or her intended field of study;

The entrance exam will comprise achievement tests that include an assessment

an assessment of the applicant’ s judgement, thinking ability, communicationof the applicant’ s ability to think logically in English, which is required forskills, initiative, and ethical perspective. Admissions decisions will be madeinternational communication; a presentation of the applicant’ s researchbased on the applicant’ s overall performance on these exams.

findings during their master’ s program or elsewhere; and an oral exam toassess the applicant’ s judgement, thinking ability, communication skills,
initiative, and ethical perspective. Admissions decisions will be made based on
the applicant’ s overall performance on these exams.

Graduate School of BIOSTUDIES, Kyoto University04

G r a d u a t e

S c h o o l

o f

B I O

S T U D I E S ,Curriculum Policies of the Graduate School of Biostudies

U n i v e r s i t y

Diploma Policy of the Graduate School of Biostudies

Master’ s Program

Doctoral Program

Master’ s Program

Doctoral Program

The Master’ s Program offers courses that appropriately combine lectures,

The Doctoral Program is comprised of lab-based research guidance and lectures

As an advanced discipline that holds the key to the future of humankind, the life

As an advanced discipline that holds the key to the future of humankind, the life

advanced studies, practical training, lab experiments, and seminars on

designed to cultivate greater breadth of scholarly knowledge and advanced

sciences are currently undergoing a major evolutionary change. The Graduate

sciences are currently undergoing a major evolutionary change. The Graduate

specialized subjects in order to achieve the objectives set forth in the Diploma

expertise in order to achieve the objectives set forth in the Diploma Policy.

School of Biostudies seeks to respond to this global change by building a

School of Biostudies seeks to respond to this global change by building a

Policy. Courses conducted in English are also offered for international students.

Courses conducted in English are also offered for international students. The

world-class center for research and by training human resources to lead the life

world-class center for research and training human resources to lead the life

The curriculum is specifically designed in accordance with the following

curriculum is specifically designed in accordance with the following principles.

sciences field into the next generation. Our school has engineered a true fusion

sciences field into the next generation. Our school has engineered a true fusion

1. The curriculum is organized and delivered to further develop broad scholarlyof cutting-edge areas in several existing fields and harnessed the commonof cutting-edge areas in several existing fields and harnessed the common

knowledge and advanced, specialized knowledge cultivated throughlanguages of cellular and molecular biology and genetics that together

languages of cellular and molecular biology and genetics that together

education in the Master’ s Program, and to enable students to acquire thearticulate the fundamental principles of life. Furthermore, it has developed anarticulate the fundamental principles of life. Furthermore, it has developed an

basic capabilities required of an independent researcher who can perform

integrated understanding of diverse life forms and the environments they help

integrated understanding of diverse life forms and the environments they help

a foundation of competence for occupations that demand advanced

well in an international setting. Moreover, research guidance is provided

shape, adding the perspective of mathematical science, and has launchedshape, adding the perspective of mathematical science, and has launchedexpertise, based on the basic academic capabilities and specializations

through special seminars and special workshops in individual research labs

innovative efforts in research and education that will define a new set of values

innovative efforts in research and education that will define a new set of values

developed through education in the undergraduate program, as well as toto cultivate advanced competence in research planning and implementation,

for the future and dignity of life.

for the future and dignity of life.

enable the pursuit of cross-disciplinary study unencumbered by existinga capacity to explain research findings theoretically, communication skills,

To meet the diverse expectations of society for advances in the life sciences,

To meet the diverse expectations of society for advances in the life sciences,fields of specialization, which allows students to apply broad visions to put

and firm ethical integrity and a strong sense of responsibility in academic

which are becoming increasingly sophisticated and complex, the Graduate

which are becoming increasingly sophisticated and complex, the Graduate

their own research into perspective and build systems of knowledge.

research. Learning outcomes in each course are evaluated through written

School of Biostudies confers the degree of Master of Biostudies on students

School of Biostudies confers the degree of Doctor of Biostudies on students

Moreover, the curriculum includes practical training, lab experiments,

examinations, report examinations, and the outcomes of workshops, lab

who maintain enrollment for the requisite period, complete curricular courses,

who maintain enrollment for the requisite period, complete curricular courses,

experiments, and practical training.

earn the prescribed number or more of credits in accordance with theearn the prescribed number or more of credits in accordance with the

Curriculum Policy, and pass a review and examination of a master’ s thesis

Curriculum Policy, and pass a review and examination of a doctoral dissertation
prepared after undergoing the required research guidance. A further prerequisite

principles.
1. The curriculum is organized and delivered to cultivate broad scholarly
knowledge spanning all domains of the life sciences, research capability instudents’ field of specialization, and specialized knowledge that will provide

workshops, and tutorials held in individual research labs that are designed tocultivate competence in research implementation, a capacity to explain

2. Special emphasis is placed on students’ proactive pursuit of a research topic
that contributes to an academic or practical area of the life sciences,

prepared after undergoing the required research guidance. A further prerequisite

integrity and a sense of responsibility in academic research. Learning

mediated by research guidance and practical education, and leads to afor degree conferment is the attainment of the following:

for degree conferment is the attainment of the following:outcomes in each course are evaluated through written examinations, reportdoctoral dissertation that contributes to the generation of new knowledge.

1. Broader-based scholarly knowledge; research capability in their field of

1. Broad-based scholarly knowledge and advanced, specialized knowledge to

examinations, and the outcomes of workshops, lab experiments, andThis dissertation is assessed by a panel of three examiners and one or more

specialization; and advanced, specialized knowledge required forresearch findings theoretically, communication skills, and firm ethicalpractical training.
2. Emphasis is placed on students’ proactive pursuit of a research theme thatexpert examiner in accordance with the Diploma Policy.
The curriculum created on the basis of the above policies is presented incontributes academically or practically to the life sciences, mediated bycurriculum maps, and the details of each individual course are clearly stated inresearch guidance and practical education, and leads to a master’ s thesis

the syllabus.

with theoretical value. This thesis is assessed by a panel of three examiners
in accordance with the Diploma Policy.
The curriculum created on the basis of the above policies is presented in

occupations that demand advanced expertise
2. Firm ethical integrity and a sense of responsibility in academic research in
the life sciences field
3. Appropriate capabilities in research implementation in order to set topics and●The Life-Science Experiments and Exercises(20 credits : compulsory)

Requirements forcompleting the Doctoral program●"The Life-Science Special Exercises"(8 credits : compulsory)●Common Compulsory Subject (1 credit)●Common Compulsory Subject (1 credit)●Common Elective Subjects (at least 9 credits)●Common Elective Subjects (at least 1 credit)

For graduation, the student must have enrolled

For graduation, the student must have enrolled forfor at least two years and have completed at

at least three years and have completed at least 10

least 30 credits. It is also required to pass thecredits. It is also required to pass the probation

probation and an examination upon completionand the examination (thesis defense) uponof the Master’ s thesis written under thecompletion of a Doctoral thesis written under thesupervision of faculty.

supervision of faculty.

Graduate School of BIOSTUDIES, Kyoto University

research in the life sciences field
3. Advanced capabilities in research planning and execution in order to set
unique topics and themes based on scholarly knowledge, techniques, andskills in the life sciences field, and to achieve solutions and development

and fields related thereto, and to deepen mutual understanding

Requirement forcompleting the Master’ s program

occupations
2. Firm ethical integrity and a strong sense of responsibility in academic

sciences field, and to achieve solutions and development thereof

promote one’ s research findings to researchers in one’ s own specialization

the syllabus.

engage as independent researchers or lead careers in advanced professional

themes based on scholarly knowledge, techniques, and skills in the life

4. Appropriate skills in theoretical explanation and communication required tocurriculum maps, and the details of each individual course are clearly stated in05

K y o t o

5. A master’ s thesis, presented with theoretical rigor and clarity, withappropriate setting of research goals, planning, and execution ofexperimental work related thereto and discussion in regard to the findings
thereof

thereof through planning and implementation of joint research with otherresearch institutions as necessary
4. Advanced skills in theoretical explanation and communication required topromote one’ s research findings to researchers in one’ s own specializationand fields related thereto, and to deepen mutual understanding
5. Doctoral dissertation that includes research findings demonstrating new
discoveries or concepts that contribute academically or practically to the life
sciences
Candidates considered to have made outstanding progress in their studies andresearch may be eligible for completion of the doctoral program in a reduced
period of enrollment.

Graduate School of BIOSTUDIES, Kyoto University

06

G r a d u a t e

S c h o o l

o f

B I O

S T U D I E S ,K y o t o

U n i v e r s i t y

Composition of Departments

Research Laboratories in the Graduate School of Biostudies
Division of Integrated Life Science

Division of Systemic Life Science

In this division, education and research are focused on the elucidation of basic mechanisms regulating the chromosome transmission,

In this division, education and research are focused on the elucidation of the fundamentals of molecular andsystemic biology, cell biology and immunology. Experimental approaches are taken with viruses,
microorganisms, cultured cells and animals. We pursue education and research to elucidate the molecular
aspects of Systemic Life Science.

chromosome replication, RNA architecture, cell cycle, cellular transport, cell polarity, signal transduction, growth and development,
developmental plasticity, bioconversion, and environmental adaptation. Experimental approaches are taken with microorganisms,
plants, and animals. We pursue education and research to elucidate the molecular aspects of Integrative Life Science.

Dept. of Gene Mechanisms

Chromosome Transmission/Gene Biodynamics/Cell Cycle Regulation

9

Major interest is the molecular mechanism of higher order phenomena (cell proliferation, morphogenesis,
canceration, aging, etc.) and the cellular function (cell cycle, chromosome replication, segregation, maintenanceand repair, etc.) in unicellular and multicellular organisms.

Dept. of Cell and Developmental Biology

Cell Recognition and Pattern Formation/Signal Transduction

Plant Molecular Biology/Molecular and Cellular Biology for Totipotency

11

13

The department pursues the basic research and application of molecular and cellular principles related toplant growth and development. We take approaches by cell biology, chemical biology, molecular and cellularbiology, molecular genetics, and genomics.

Dept. of Applied Molecular Biology

Biosignals and Response/Applied Molecular Microbiology/
Molecular Biology of Bioresponse

Plant Developmental Biology/
Plasma Membrane and Nuclear Signaling

15

Developmental Neurobiology/Biochemical Cell Dynamics/
Multidisciplinary Biology

18

19

Molecular and Cellular Immunology/Ultrastructural Virology

21

We study on mammalian development, differentiation, aging and viral immunity. We utilize molecular biology anddevelopmental engineering as tools of analyses to elucidate mechanisms at molecular, cellular and animal levels.

Dept. of Human-Residential Bifidobacteria (HRB) Research (Industry-Academia Collaboration Course) Symbiotic and Coevolutionary Mechanisms

Attached
Research Centers
07

Radiation System Biology/Mutagenesis/Late Effects Studies/Genome Repair Dynamics/
Chromosome Function and Inheritance/Stress Responsecontrolled biophotonics/Dynamic Genome Systems

We aim at understanding the life as dynamic living systems. We observe the dynamic behavior of molecules and cellswith cutting-edge technologies of microscopy, optogenetics, and mouse genomics. Based on the accumulated
multidimensional data, we will uncover the working principles of life by the approaches of mathematics and informatics.

Graduate School of BIOSTUDIES, Kyoto University

26

Cancer, autoimmune diseases, and life-style related diseases can be caused by genetic abnormalities andaberrant response mechanisms. We aim to reveal dysfunctional biological mechanisms of cell proliferation,
cancer, and immunological, genetic diseases.
Functional Biology

28

Using animal models of human diseases, such as neurodegenerations, cancers, and obesity-relateddiseases, and using metabolite imaging techniques, we aim to elucidate molecular bases of such diseases
and develop new strategies to cure or prevent them.
Science Communication/Chromosome Function and Inheritance29

The Department of Biology Education and Heredity is composed of the Laboratory of Science Communication,
the Laboratory of Bioeducation, and the Laboratory of Chromosome Function and Inheritance. The Laboratoryof Chromosome Function and Inheritance studies the mechanisms of meiosis using cell biological andgenetic approaches. The department as a whole focuses on training internationally-minded scientists,
developing English-based science education and communication at the highest levels.

Dept. of Systems Biology

Bioimaging and Cell Signaling/Theoretical Biology/Brain Development and Regeneration

31

By the use of cutting-edge technologies of microscopy, optogenetics, and chemical biology, we will study the
information that living organism perceive. Based on the accumulated information, mathematical models arebuilt to understand systematically the mechanism of information processing of living organisms. We will
also analyze the molecular mechanisms that regulate quiescence and activation of adult neural stem cells.

Dept. of Genome Biology

Genome Maintenance/Genome Damage Signaling/Cancer Cell Biology/
Chromatin Regulatory Network

34

Genome and epigenome information are maintained by an intricate molecular system acting against exogenousand endogenous perturbations. We aim to study defects in these mechanisms that result in human disorders.
41

Our center is trying to elucidate basic mechanisms behind biological responses to irradiation as well as chromosomal damages,
and thereby pursue fundamental basis for evaluation of radiation exposure risks and for development of innovative cancer radiation
therapy. To achieve the goals, our center promotes collaborations in the intranational and international research communities.
Bioimaging/Multiscale Biomechanics/PhysiologicalResearch Center for Dynamic Living Systems Cutting-edge
Network/Biological Function Manipulating/Spatio-temporally

24

22

The mission of this department is to elucidate the mechanisms underlying symbiosis between
bifidobacteria and their human host, and to understand the molecular basis of the health-promoting effects ofprobiotic Bifidobacterium strains.

Radiation Biology Center

Molecular and Cellular Biology/Immunobiology/
Molecular Cell Biology and Development

Molecular Neurobiology/Genetics

Dept. of Biology Education and Heredity

The development, function, and maintenance of tissues and organs are regulated by a coordinated interplay ofcell-intrinsic programs and intercellular signals. We seek their mechanisms at cellular, organellar andmolecular mechanisms using various model systems, including the brain and immune systems.

Dept. of Molecular and Cellular Biology

23

The objectives of our studies are to clarify the mechanisms that regulate hierarchical structures composing
cells, tissues, organs, at the molecular, cellular, and individual levels, especially about cell growth,differentiation, cell death, cell-cell interactions, and histogenesis.

Dept. of Functional Biology

We aim at understanding fundamental systems underlying environmental responses by organisms throughstructural-functional study of information molecules involved in environmental responses and study ofregulatory mechanisms of development in response to environmental signals.

Dept. of Molecular and Developmental Biology

Dept. of Animal Development and Physiology

Dept. of Signal Transductions

Signal response mechanisms have evolved in organisms through adaptations to fluctuations or changes in the naturalenvironment. These mechanisms are being elucidated using various model organisms at different levels (individual, organ,
tissue, cell, molecule and gene), and directing this knowledge toward applications with benefits to human welfare is a priority.

Dept. of Responses to Environmental Signals and Stresses

Single-Molecule Cell Biology

We will challenge direct viewing of biomolecular dynamics using single-molecule imaging and multi-target
super-resolution microscopy IRIS. By elucidating the molecular basis of morphogenesis and the action ofdrugs, we will pursue principles in biology and seeds for drug development.

We are studying signal transduction mechanisms that control organogenesis and animal growth in response to nutrition
and growth factors. We are also dissecting operating principles of neuronal circuits that evoke behaviors to sensory stimuli.

Dept. of Plant Gene and Totipotency

Dept. of Molecular and System Biology

Dept. of Mammalian Regulatory Network

Cell Regulation and Molecular Network/RNA Viruses/
Cell Division and Differentiation/
Cellular and Molecular Biomechanics

38

Laboratories consisting of this Department study multi-dimensional networks of life signals that contributeto the integrity of higher organisms. Studies also include those utilizing viruses, animal models, andbiomaterials, serving to establish basic principles in life science.
43

Dept. of Advanced Imaging (Industry-Academia Collaboration Course)

Spatiotemporal Optical Control /Optical Neural and Molecular Physiology

40

We will understand the principle of biological functions by measuring and manipulating dynamics of genes andmolecules multidimensionally with cutting-edge imaging, optical control technologies, and optical probes.

Graduate School of BIOSTUDIES, Kyoto University

08

Division of Integrated Life Science ｜ Department of Gene Mechanisms

Laboratory of
Chromosome
Transmission

Division of Integrated Life Science ｜ Department of Gene Mechanisms

Laboratory of
Cell Cycle
Regulation

Assoc. Prof.

NAKASEKO, Yukinobu

Main theme
We are focusing on analyzing the genes
involved in regulation of chromosome
function. Especially, the genes essential for
mitosis have been studied. Fission yeast
Schizosaccharomyces pombe is used as amodel system. This yeast has all basic
features essential for eukaryotic cell
division. Many genes have been identified
which regulate the cell cycle of this yeast.
Also, their functions as well as their primarystructure have been shown to be conserved
among all eukaryotic cells. We are trying tocharacterize these genes and their functions
by genetical approach.

Professor

ISHIKAWA, Fuyuki
Main theme
Stable maintenance of genetic information
is essential for cell viability. Genetic
instability, a condition in which the genome
is not properly maintained, causes
numerous pathologies including cancer
and aging. Transposable elements (TEs)mobilize to other genomic loci andcomprise ~45% of our genome. We areinterested in how TEs destabilize genetic
information and cause various
diseases-associated phenotypes. Agingcan be defined as the accumulation ofdamaged cells caused by various stresses.
Stress is generally considered to be
non-adaptive. However, low-dose stresscan act in an adaptive role by fostering cell
resistance to prospective lethal stresses.
This process is termed acquired tolerance(or hormesis) and its molecular

Elucidation of whole functional network ofthese genes is one of a goal in our research.

Laboratory ofGene Biodynamics

Assoc. Prof.

SHIRAISHI, Hideaki

Main theme
We are interested in the mechanism of growth,development and evolution of photosynthetic
microorganisms and currently focusing on the
study of the edible cyanobacterium Arthrospira(Spirulina) platensis. A. platensis is afilamentous alkalophilic cyanobacterium thathas been traditionally consumed as food bypeople living along the shores of alkaline lakes
in several regions in the world. Because it canbe cultured under alkaline conditions where
growth of other microalgae is suppressed, it
can be produced in mass cultures outdoors as
an almost single algal strain. Because of its
easiness of mass culture, it is commercially
produced in many subtropical areas in the

Lab URL

09

Graduate School of BIOSTUDIES, Kyoto University

http://kuchem.kyoto-u.ac.jp/seika/

mechanisms remain largely unknown. We
are trying to understand how acquired
tolerance is induced molecularly. Arguably,
cancer cells in vivo acquire stressresistance through experiencing
ever-lasting environmental changes. As
such, inhibiting the acquired tolerance incancer cells may lead to fragility of cancers
to various stresses, including iatrogenic
ones.
• Functional roles of acquired tolerance invarious physiological and pathologicalconditions.

Assoc. Prof.

MIYOSHI, Tomoichiro

Assist. Prof.

NAKAOKA, Hidenori• Development of therapeutic strategies
for cancer by elucidating themechanisms of cellular senescence.
• Mechanisms of retrotransposition and its
impact on genomic instability in the
mammalian genome.

world and consumed worldwide as food, foodadditives, and feed for animals and fishes. We
are currently focusing on developing tools formolecular genetic studies of thiscyanobacterium.

Filamentous cyanobacterium Arthrospira platensis
and the aggregated expolysaccharides produced bythem

In general, cells exposed to lethal stress undergo cell death (A). However, cells
preconditioned with mild stress can become resistant to subsequent lethal stresses (B). This
process is called acquired tolerance or hormesis: an adaptive behavior that is crucial forsurvival in an ever-changing environment. In vivo, cancer cells can experience environmental
changes such as hypoxia and iatrogenic stress. This is in contrast to normal cells that live ina stable niche given by the tissue. It is possible that cancer cells are pre-conditioned by theenvironmental changes to prepare for the prospective lethal stress. Therefore, inhibition ofthis acquired tolerance may make cancer cells sensitive to anti-cancer therapeutics.

http://www.fish.lif.kyoto-u.ac.jp/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

10Division of Integrated Life Science ｜ Department of Cell and Developmental Biology

Division of Integrated Life Science ｜ Department of Cell and Developmental Biology

Laboratory of
Cell Recognition and
Pattern Formation

Laboratory of
SignalTransduction

Senior Lecturer

KUSAKABE, Morioh

Main theme
Professor

UEMURA, Tadashi
Senior Lecturer

USUI, Tadao

Main theme

3. Epithelial morphogenesis consistingof complex levels of hierachy

We are interested in:
1. Contributions of nutrients andassociated microbes to animal growth
and aging

4. Reproductive manipulation ( “malekilling” ) caused by insect symbionts

We are interested in identifying andelucidating molecular mechanisms that
regulate cell proliferation, cell differentiationand developmental processes. The current
topics include 1) regulatory mechanisms andfunctions of the MAP kinase cascade
pathways, 2) identification of novel signaltransduction mechanisms, 3) roles of protein
kinases in cell regulation, 4) signalingmechanisms in developmental processes.

Assist. Prof.

MIYATA, Yoshihiko

Microinjection into Xenopus laevis
embryos at the cleavage stage

2. Neuronal circuits that evoke selective
behaviors in response to sensory
stimuli
Program-Specific Senior Lecturer 

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Assist. Prof.

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This study was published in Nucleic Acids Research on September 14, 2021.

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Lab URL

11

Graduate School of BIOSTUDIES, Kyoto University

Lab URL

Telomere proteins Stn1 and Ten1 are involved in tandem-repeat stability in thefission yeast genome 

HATTORI, Yukako

http://www.signal.lif.kyoto-u.ac.jp/ᄝ       

http://www.cellpattern.lif.kyoto-u.ac.jp/

Fission yeast Stn1-Ten1 complex was identified as
telomeric proteins that regulate telomerase reactions
and telomere protection. Using atemperature-sensitive stn1 allele, stn1-1, Io Yamamoto(research associate, Laboratory of Cell Cycle
Regulation) and Prof. Fuyuki Ishikawa havedemonstrated that stn1 dysfunction leads to genomic
instability not only at telomeres, but also at theribosomal RNA coding regions (rDNA). Telomeres andrDNA share the tandemly repetitive nature of DNA.
Together, their results indicate that Stn1-Ten1 is
involved in genomic stability at tandem repeats ingeneral. It is known that tandem repeats comprisefragile sites, where DNA double-strand breaks
frequently happen, leading to abnormal chromosome
formation. Given that Stn1 and Ten1 are highly
conserved among eukaryotes, we propose that
Stn1-Ten1 plays a role in preventing chromosome
anomalies in humans.

(a)

(b)

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(c)signal intensities         

KONDO, Takefumi

Multiciliated cell differentiation in asalt-and-pepper pattern

WT

stn1 (1)stn1 (2)stn1-1 (1)stn1-1 (2)stn1-1 (3)Legends to figure(a) Wild-type fission yeast cells (WT), two independent
strains of stn1∆ cells overexpressing wild-type stn1 (stn1, 1
and 2) and three stn1∆ cells with overexpression of
stn1-1 (stn1-1, 1, 2 and 3) were grown at 25 ° C for one or ten
days. Genomic DNAs were analyzed for rDNA repeats inSouthern blotting experiments. The three stn1-1 expressing
clones showed rDNA repeat instability indicated byheterogenous migration of the signals. (b) Schematic
representation of rDNA repeats at the left and right arms ofchromosome 3. (c) Signal intensities in (a) were quantitatedalong the x-y direction. stn1-1 clones showed dynamicchanges of signal patterns in ten days of culture (compare
red lines at Day 10 and blue lines at Day 1), whereas WT and
stn1 clones did not.

For further information, please refer to the URL below.

https://academic.oup.com/nar/article/49/18/10465/6370253?login=false
https://doi.org/10.1093/nar/gkab767

Graduate School of BIOSTUDIES, Kyoto University

12Division of Integrated Life Science ｜ Department of Plant Gene and Totipotency

Division of Integrated Life Science ｜ Department of Plant Gene and Totipotency

Laboratory of
Molecular and Cellular
Biology for
Totipotency

Laboratory of
Plant Molecular
Biology

Professor

Professor

KOHCHl, Takayuki
Assoc.Prof.

YASUI, Yukiko

Assist. Prof.

NAKANO, Takeshi
Main theme
Research in this laboratory focuses on
the adaptive regulation of growth anddevelopment to environmental
conditions and its evolution by using
model photosynthetic organisms.
Especially with the liverwort Marchantia
polymorpha, which is a basal land plant
ideal for comparative evolutionary

studies and amenable to molecular
genetic manipulation, we aim toelucidate principles and ancestral
molecular mechanisms ofphotomorphogenesis, growth phasetransition, phytohormone signaling,meristem function, sex determination,and sex differentiation in land plants.

YOSHITAKE, Yoshihiro

Graduate School of BIOSTUDIES, Kyoto University

Major research topics are:Plant growth has been administrated bycooperative regulations between plant
cell differentiation/division/elongationand photosynthesis. Based on thesescientific aspects, our laboratory istrying to reveal the plant growthmechanisms by ‘chemical biology’ and‘molecular and cellular biology’ .

(1) Growth regulation by plant hormone
signaling

Assoc.Prof.

http://www.plantmb.lif.kyoto-u.ac.jp//

MIYAKAWA,Takuya(2) Chloroplast regulation byprassinosteroid(3) Chemical functions to regulate plant
growth and differentiation(4) Plant biomass production regulated
by chemicals and genes(5) Evolution and diversity of steroid
hormones

Lab URL

13

Main theme

http://plantchembio.sun.bindcloud.jp/index.html

Assist. Prof.

YAMAGAMI, Ayumi

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

14

Division of Integrated Life Science ｜ Department of Applied Molecular Biology

Division of Integrated Life Science ｜ Department of Applied Molecular Biology

Laboratory of
Biosignals andResponse

Laboratory ofApplied Molecular
Microbiology

Professor

Professor

NAGAO, Masaya
Assoc. Prof.

KAMBE, Taiho

Assist. Prof.

FUKUZAWA, Hideya
Main theme
Bio-prospecting, a research strategy
searching for compounds that possess
beneficial activity for health from natural
sources, is one of the projects in thislaboratory. Especially, compounds thatare useful for treatment oflifestyle-related diseases and cancer are
the main targets of our bio-prospecting.

We are also studying how organisms
perceive environmental signals andtransduce these signals into changes ingene expression, focusing mainly on themolecular and cellular basis of zincmetabolism (such as uptake, storage,
delivery, and maintenance of metal
concentration in cells) in mammal.

NISHINO, Katsutoshi

Main theme
We are focusing on the molecular basisof biological functions of microalgae
contributing to production of food, biofueland industrial materials throughphotosynthesis. Especially, we employ agreen alga, Chlamydomonas reinhardtii, asa model eukaryotic photosynthetic
microorganism using genomic,
proteomic, genetic, molecular andbiochemical techniques.
The current projects are(1) Molecular characterization of the
carbon-concentrating mechanism(CCM) supporting photosynthetic
carbon fixation, biofuel production,and cell proliferation.

Stimulation of lipid accumulation by plant extracts

Lab URL

15

Graduate School of BIOSTUDIES, Kyoto University

http://www.seitaijoho.lif.kyoto-u.ac.jp/(2) Elucidation of regulatory systems
controlling photosynthesis andcarbon/nitrogen metabolisms bysensing environmental factors
including changes of levels in CO2
concentration, light and nutrients.
(3) Development and utilization of
genome information and genome
resources of the green alga
Chlamydomonas reinhardtii.
(4) Molecular control and signaling of
sexual reproduction and oil production
by nutrient starvation.

Assoc. Prof.

YAMANO, Takashi

Assist. Prof.

TSUJI, Yoshinori(5) Identification of factors essential for
intracellular signal transduction
including calcium-dependent
retrograde signal from chloroplast to
nucleus and DYRK family of protein
kinases supporting cell survival.

http://www.molecule.lif.kyoto-u.ac.jp/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

16

Division of Integrated Life Science ｜ Department of Applied Molecular Biology

Division of Integrated Life Science ｜ Department of Responses to Environmental Signals and Stresses

Laboratory of
Molecular Biology ofBioresponse

Laboratory of
Plant Developmental
Biology

Professor

Professor

KATAYAMA, Takane
Assist. Prof.

KATOH, Toshihiko

ARAKI, Takashi
Main theme
We are conducting research focusing on
the symbiosis and co-evolution between
gut microbes and the host. In particular,
we are trying to understand themolecular basis of how gut microbes
proliferate and persist in the host gut by
assimilating milk oligosaccharides andmucin O-glycans produced by the host.

Lab URL

17

Graduate School of BIOSTUDIES, Kyoto University

・Symbiosis between bifidobacteria andinfants mediated through breastmilk
・Carbohydrate assimilation mechanism
in gut microbes
・Aromatic amino acid metabolism in gut
microbes
・Development of an apical aerobic
co-cultivation system

http://www.bunshioutou.lif.kyoto-u.ac.jp/

Main theme
We are interested in molecularmechanisms underlying plant's
responses to environment. Plants have
evolved plastic developmental programswith both genetic and epigenetic basis toadapt their sessile mode of life tochanging environment. Using anangiosperm, Arabidopsis thaliana and aliverwort, Marchantia polymorpha asmodel systems, we have been

investigating (1) regulation of growthphase transition (especially reproductive
transition) in response to environmental
signals, (2) mechanism of day-length
perception by photoreceptors andcircadian clock, (3) long-distancesystemic signaling (e.g. florigen) in thecontrol of development, (4) sexual
reproduction processes (especially,
germline specification andgametogenesis), and (5) origin andevolution of regulatory systems forplastic development.

http://www.plantdevbio.lif.kyoto-u.ac.jp/

Assoc. Prof.

YAMAOKA, Shohei

Assist. Prof.

INOUE, Keisuke

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

18

Division of Integrated Life Science ｜ Department of Responses to Environmental Signals and Stresses

Laboratory of
Plasma Membrane
and Nuclear Signaling

Division of Integrated Life Science ｜ Department of Molecular and Developmental Biology (Cooperation Course)

Assoc. Prof.

Laboratory ofBiochemical
Cell Dynamics

Professor

YOSHIMURA, Shigehiro

SUZUKI, Jun
AFFILIATION：
Institute for Advanced Study

Assist. Prof.

KUMETA, Masahiro

Main theme
Our laboratory studies dynamic properties ofcellular proteins and membrane in cellularenvironments by using a variety oftechniques in biochemistry, cellular biology
and biophysical approaches. We are alsointerested in how those dynamics of cellulararchitectures are related to diseases.
Specific research topics include:(1) Cytoskeletal dynamics in cell motility andmetastasis: intracellular dynamics ofactin cytoskeleton is elucidated by ourlive-cell nano-imaging technique.
(2) Molecular mechanism of signaltransduction: how plasma membraneand membrane -bound proteins
coordinates endocytic process.
Lab URL(3) Virus vs host cell at cell surface: imaging
viral particle at the host plasma
membrane to elucidate the mechanismof viral infection and proliferation.
(4) Proteins in molecular crowding: dynamic
assembly and disassembly of proteinsand nucleic acids in cellularenvironments.
(5) How do cells feel force?: elucidating
molecular
mechanism of
mechano-sensing
and -responses
by combining
variousbiophysicalapproaches

Main theme
In principle, we identify specific genes
regulating the biological phenomenon with ourinterests. The main approaches are as follows:
Expression cloning using cDNA library,functional screening using sgRNA library in a
CRISPR/Cas9 system, biochemical approach incombination with mass spectrometry. By
establishing the robust experimental systems,
we try to reveal the secrets of biologicalphenomenon. Currently, we are interested in the
biological phenomenon called phospholipid
scrambling that regulates blood coagulation,
engulfment of dead cells, cell fusion, cancer
progression, stress response, regulation ofbrain/bone/muscle functions and so on. In spiteof its importance in various biological systems,
much is unknown about how phospholipid

http://www.chrom.lif.kyoto-u.ac.jp/

scrambling is regulated. We are going to
uncover the mechanisms.

Research Topic・Identification of novel scramblases onplasma membranes
・Identification of novel scramblases on
intracellular membranes
・Identification of regulators or subunits inscramblases
・Understanding physiological roles ofscramblases
・Understanding how diseases occur by
scramblase deficiency
・Understanding mechanisms of removal ofunwanted cells
・Developing in vivo screening systems

http://www.callus.lif.kyoto-u.ac.jp

Lab URL

Division of Integrated Life Science ｜ Department of Molecular and Developmental Biology (Cooperation Course)

Laboratory ofDevelopmental
Neurobiology

Professor

TANIGUCHI, Yuichi

Professor

AFFILIATION：
Institute for Advanced StudyKENGAKU, Mineko
AFFILIATION：
Institute for Advanced Study

Main theme
Neurons in the mammalian brain are orderly
arranged in cortices and nuclei for integration
into specific neural circuits. During
development, neurons directionally migratefrom the birthplace to their destination within
the cortex, and then arborize well-patterned
dendrites and axons to contact with their
specific synaptic counterparts. Failures inthese processes lead to neurodevelopmental
and neuropsychiatry diseases. The major goalof our research is to clarity the mechanismsof cortical lamination and functional wiring of
neurons in the brain. We also aim to develop

Lab URL

19

Graduate School of BIOSTUDIES, Kyoto University

Laboratory ofMultidisciplinary
Biology

Main theme
imaging techniques for real-time observationof molecular and cellular dynamics ofneuronal migration and dendrite patterning todiscover novel phenomena and rules inneuronal motility in the developing brain.

http://www.kengaku.icems.kyoto-u.ac.jp

Research Topic

We aim to understand the working principle ofcomplex biological systems (e.g. the cell andgenome) constituted with a wide variety ofmolecules. Based on knowledge of multiple
academic fields including biology, physics,
chemistry, computer science, engineering andinformatics, we challenge development of new
innovative technologies and creation of new life
science fields.

Nucleosome-resolved 3D
genome structure

・Elucidating the working principles of the
genome based on molecular or atomic
structures
・Understanding the constitutional principlesof single cells
・New principles and methods in diseasediagnosis and treatment

Single molecule fluorescence microscope

https://taniguchi.icems.kyoto-u.ac.jp/en

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

20Division of Integrated Life Science ｜ Department of Molecular and Cellular Biology (Cooperation Course)

Laboratory of
Molecular andCellular Immunology

Laboratory of Symbiotic andCoevolutionary Mechanisms

Professor

NODA, Takeshi（Concurrent post）

AFFILIATION：Institute for Life and Medical Sciences

Main theme
Virus infections, such as influenza A epidemic,
Ebola hemorrhagic fever, Middle East
respiratory syndrom, Zika virus infection areimportant diseases and outbreaks of newly
emerging viruses are serious problems formodern society. Higher animals, including
humans, are genetically equipped withmechanisms, collectively known as innate
immunity, to counteract viral infections. During
the course of replication, many viruses
generate double-stranded (ds)RNA, which isvirtually absent in normal cells and likely
serves as a "foreign molecule" in cells. An RNA
helicase, RIG-I, functions as a sensor for viraldsRNA. RIG-I is composed of three domains : a
Caspase recruitment domain (CARD), a

Laboratory of
Ultrastructural
Virology

DExD/H helicase domain, and a C-terminal
domain (CTD)(Figure). CTD senses viral dsRNA
produced in the cytoplasm, leading to a
conformational change. This conformationalchange releases CARD, which signals to
downstream, resulting in the activation ofgenes including those for type I interferon andother cytokines. The purpose of our project is
to clarify the molecular mechanism underlying
the antiviral innate immunity regulated by
RIG-I, and to develop new diagnostic andtherapeutic means for viral infections.

Assist. Prof.

MURAMOTO, Yukiko

Research Theme

Probiotics are defined as “live microorganisms
that, when administered in adequate amounts,
confer a health benefit on the host," andbifidobacteria and lactobacilli are most commonlyused as probiotics in food and medicine globally.
Research suggests that bifidobacteria haveco-evolved with hominids for over 15 million years,
and we have collectively named the species thatare characteristic of the human intestinal tract as“Human-Residential Bifidobacteria (HRB)".
Accumulating evidence shows that HRB plays an
extremely important role in human health.
However, the mechanisms behind the probiotic
effect of bifidobacteria remain unclear, because
probiotics research has historically focused on
the human (host) side (e.g., functional evaluation
through clinical trials) and research from thebacterial side is limited. To address this researchgap, our department will promote research fromthe probiotic side. Specifically, we will elucidate

SAKANAKA, Mikiyasu

the molecular mechanisms underlying symbiosis
and coevolution between HRB and humans.

Research Topics

・Elucidation of the symbiotic and co-evolutionary
mechanisms between bifidobacteria,
gut bacteria, and humans.
・Understanding the molecular basis ofhealth-promoting effects of probiotics anddevelopment of technologies for social
implementation.

Visiting Professor

XIAO, Jin-zhong

Visiting Assoc. Prof.

ODAMAKI, Toshitaka

Distinctive differences in ecological distribution ofbifidobacteria (HRB vs non-HRB).

NODA, Takeshi
Sex-determining genes on the sex chromosomes of a haploid organism-The sex chromosomes of the oldest origin of living organisms

Main theme
Virus infections are accompanied bynumerous ultrastructural changes in viral andcellular components. Our laboratory has been
investigating the replication mechanism of
influenza and Ebola viruses from theultrastructural point of view, by using different
microscopic methods such as electron
microscopy and high-speed atomic force
microscopy. Visualization andcharacterization of the virus life cycle at thenano-mesoscopic level give us uniqueknowledge and novel paradigms, which will
advance our understanding of molecularbasis of the replication mechanism.

Lab URL

21

The department of Human-Residential Bifidobacteria (HRB) Research was established in October 2020 as
an industry-academia research collaboration between Morinaga Milk Co. Ltd., and the Graduate School of
Biostudies, Kyoto University. The mission of this department is to elucidate the mechanisms underlying
symbiosis between bifidobacteria and their human host, and to understand the molecular basis of thehealth-promoting effects of probiotic Bifidobacterium strains.

Project-Specific
Assoc. Prof.

Graduate School of BIOSTUDIES, Kyoto University

https://www.facebook.com/NodaLab/

This study was published in Current Biology on 3rd November, 2021.

Scanning electron micrograph of Ebola
viruses budding from cell surface.

A research group led by Professor Takayuki Kohchi, in
collaboration with other research groups in Japan andoverseas, has identified a sex-determining gene in a
haploid system. Sex chromosomes and sex determinants
have been studied in diploid organisms (e.g., mammals inwhich XY is male and XX is female), but sex-determining
genes on sex chromosomes in haploid organisms, whose
genetic behavior is fundamentally different, have been
unknown. In this study, they identified feminization genes(feminizers) based on experiments analyzing genefunction on the sex chromosomes of females of theliverwort Marchantia polymorpha, which spend most of
their life cycles in the haploid form. It was an unexpecteddiscovery that the gene, along with a homologous geneon the male sex chromosome, had a function of inducing
sexual reproduction. The identified gene is older than any
other sex-determining genes known so far.

TOPICSNAKANO, Masahiro

Department Overview

Professor
AFFILIATION：
Institute for Life and Medical Sciences

Assist. Prof.

Division of Integrated Life Science ｜ Department of Human-Residential Bifidobacteria (HRB) Research (Industry-Academia Collaboration Course)

Identification of the sex-determining factor in the liverwort
Marchantia polymorpha reveals unique evolution of sex
chromosomes in a haploid system.

Iwasaki, M., et al. Curr. Biol. 31:5522-5532.e7. (2021)
DOI：https://doi.org/10.1016/j.cub.2021.10.023

Graduate School of BIOSTUDIES, Kyoto University

22Division of Systemic Life Science ｜ Department of Molecular and System Biology

Division of Systemic Life Science ｜ Department of Animal Development and Physiology

Laboratory ofSingle-Molecule
Cell Biology

Assoc. Prof.

SAKAMAKl, Kazuhiro

Laboratory of
Molecular andCellular Biology

Main theme
Professor

WATANABE, Naoki
Senior Lecturer

YAMASHIRO, Sawako

Assist. Prof.

MIYAMOTO, Akitoshi

Main theme
Our laboratory aims at bridging the gap
between molecular activities and cell
physiology by visualizing signaltransduction and cell structure
remodeling processes with live-cell
fluorescence single-molecule (eSIMS)
microscopy. We also invented
super-resolution microscopy called IRIS,
which achieves ultra-high density (=high-fidelity) labeling and unlimited

multiplexed staining in a single
specimen. By real-time andhigh-resolution monitoring of cellstructures and adhesion/signaling
molecules, our laboratory unveils real
spatiotemporal dynamics of molecularmechanotransduction,
pathophysiological cell signaling, bodystructure remodeling and actions oftarget-based drugs at unprecedented
resolution.

Apoptosis, or programmed cell death, plays animportant role in many biological processes,
including embryogenesis, maintenance oftissue homeostasis, and elimination of
improper cells such as unfunctional or harmful
cells in both animals and plants. Our main
research project is to understand themolecular and cellular mechanisms ofapoptotic cell death in vitro and in vivo, using
cultured cells, medaka and mouse as model
systems. We also investigate to develop new
methods and techniques for imaging andsimulating of such a vital phenomenon. In
conjunction with these studies, we have beenchallenging to pursue the biologicalsignificance of cell death.

http://www.MCB.lif.kyoto-u.ac.jp//

Lab URL

Assoc. Prof.

TAKAHARA, Kazuhiko

Main theme
Our interest is the induction and control of
immunity. We focus on dendritic cells (DC),which are a primary antigen-presenting cell in
the immune system. We are especiallyinterested in functions of lectin molecules
expressed on DC and its relative, macrophage,that recognize polysaccharides on pathogenic
agents. The study includes analyses ofinteraction between polysaccharides andLab URL

23

Graduate School of BIOSTUDIES, Kyoto University

http://www.pharm2.med.kyoto-u.ac.jp/

Mouse lectins expressedon DCs/macrophages

Laboratory of
Immunobiology

lectins, and subsequent cellular and systemic
responses in co-operation with TLR signaling. In
this study, we found that certain
lectin-polysaccharide interaction induced
immune suppressive environment, amelioratingexcessive and lethal inflammation. By thesestudies, we would like to develop new methods
to control immune system.

http://zoo.zool.kyoto-u.ac.jp/imm/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

24Division of Systemic Life Science ｜ Department of Animal Development and Physiology (Collaboration Course)

Division of Systemic Life Science ｜ Department of Signal Transductions

GBS’ s Collaboration Course in the RIKEN KOBE BDR

Laboratory of
Molecular Cell Biology
and Development
Visiting Professor

KITAJIMA, Tomoya

Laboratory of
Molecular
Neurobiology
Main theme
Meiosis in oocytes is prone to chromosome
segregation errors and thus frequently
produces aneuploid eggs. The aneuploidy ofeggs is a leading cause of pregnancy loss andcongenital diseases such as Down syndrome.
We aim to understand the causes ofchromosome segregation errors in oocytes.
We will reveal molecular mechanisms of how
unique features of oocytes and age -related
effects predispose to chromosome
segregation errors. The mechanisms in
oocytes will be compared with those in eggs
and zygotes, by which we will understanddifferentiation of intracellular mechanisms
Lab URL

Visiting Assoc. Prof.

TAKASATO, Minoru

In our previous study, we developed a protocol
generating self -organizing kidney organoids
from human iPS cells. While these kidneyorganoids comprise all anticipated renal
tissues, they are still far from the real humankidney in terms of their size, tissue complexity,
maturity and functionality. We study to achieve
the ultimate goal of generating a functional
and transplantable three -dimensional kidney.
We appreciate knowledge from basic
developmental biology that is essential forsuch regenerative studies; therefore, we are

Visiting Assoc. Prof.

WANG, Dan Ohtan

Visiting Assoc. Prof.

OBATA, Fumiaki“RNA” and “Brain” are the two keywords of ourresearch. Using dynamic synapses and theirassociation with intellectual ability, memory,and susceptibility to neurological disorders as
the conceptual framework, we are studying anovel RNA neuroepigenetic mechanism in thecentral nervous system regarding to synapse
function. The outcome of this quest will allow
us to understand the regulatory mechanismsof gene networks for experience -based
behavioral changes and diseases, over ourlifespan. Our research is embraced by current

25

Nutrition and gut microbiota are vital players
for organismal homeostasis and therefore
influence our healthspan. Diet contributes tometabolic and physiological homeostasis byaltering nutritional balance and gut microbiota,
however our understanding of the molecularmechanism is far from complete. Ourlaboratory studies the functions of eachnutrient and gut bacterial species using amodel organism Drosophila melanogaster. We
also aim to elucidate mechanistically how
early -life diet alters life -long health. Our goal is

Graduate School of BIOSTUDIES, Kyoto University

Prometaphase belt ofchromosomes

also highly interested in studies of humanembryology. Particularly, we are focusing on
uncovering the developmental mechanisms of
the human mesoderm and kidney.

Our research aims at understanding themolecular mechanism of homeostasis
maintaining, especially focuses on
dietary/nutritional function, endocrine
metabolism, and cancer. Based on thisresearch, we aim to provide valuable
insight into the development of functional
foods, supplements, and medicinal drugs.

1. Dietary signaling via nutrient-sensing
receptors and metabolic syndrome

Assoc. Prof.

KATOH, Hironori

2. Non-genomic effects via sex steroid
hormone receptors and neurologicaldisorders
3. Metabolic regulation and signaltransduction in cancer cells
Assist. Prof.

OHUE, Ryuji

A kidney organoid
generated from humanpluripotent stem cells

revolution in quantitative and omics
technology, fluorescence imaging, and genetic
animal model systems.

Building andmaintaining neuronal
networks and cognitive
functions requiremRNA localization andregulated protein
synthesis.

https://www.bdr.riken.jp/en/research/labs/wang-do/index.html

Main theme

Lab URL

Main theme

https://www.bdr.riken.jp/jp/research/labs/takasato-m/index.html

Main theme

Lab URL

Professor

KIMURA, Ikuo

http://chromosegr.riken.jp/index_en.html

Main theme

Lab URL

through development. By understanding how
aging affects chromosome segregation in
oocytes, we will provide insights into how
events at cell, tissue and organ levels areinterconnected at different life stages.

to reveal evolutionally -conserved “dietological"
mechanisms that govern organismal ageing
and lifespan.

https://www.bdr.riken.jp/en/research/labs/obata-f/index.html

Drosophila intestineand gut microbiota

http://www.biosystem.lif.kyoto-u.ac.jp/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

26

Division of Systemic Life Science ｜ Department of Signal Transductions

Division of Systemic Life Science ｜ Department of Functional Biology

Laboratory of
Functional
Biology

Laboratory of
Genetics

Professor

Professor

IGAKI, Tatsushi
Assoc. Prof.

KANDA, Hiroshi

KAKIZUKA, Akira
Main theme

Research subjects

Main theme

Our research focuses on the molecular basisof cell-cell communication that governs
tissue growth, homeostasis, and cancer. We
take advantage of the powerful genetics ofDrosophila.

1. Mechanism of cell competition

Using animal models of human diseases,
such as neurodegenerations, cancers,
and obesity-related diseases, and using
metabolite imaging techniques, we aim toelucidate molecular bases of suchdiseases and develop new strategies tocure or prevent them.
One of the main features of life science
research in the coming years will be thatthe results obtained from fundamental
research should ideally be directly
connected to the good of society. From
this standpoint, in addition to handling

2. Genetic basis of tissue growth regulation
3. Molecular basis of tumor progression andmetastasis
4. Mechanism of aging

Assist. Prof.

ENOMOTO, Masato

topics with high scientific significance,
we aim to contribute to the developmentof treatments for neurodegenerative
diseases, cancers, and obesity-relateddiseases from our research results.
We hold the same view on scientificeducation, and through training
individuals to communicate their ideas
logically yet effectively, as well as bynurturing their creativity, in addition tostrengthening their practical researchskills, we aim to cultivate opinion leaders
standing at the core of life science
research in the 21st century.

Assoc. Prof.

IMAMURA, Hiromi

Assist. Prof.

KOIKE, Masaaki

Left: Polarity-deficient cells (green; losers) are eliminated from epithelium by wild-type cells (magenta;
winners) through cell competition.
Right:Malignant tumor cells (magenta) are invading and metastasizing from the eye disc to the brain(blue) in Drosophila larva.

Lab URL

27

Graduate School of BIOSTUDIES, Kyoto University

http://www.lif.kyoto-u.ac.jp/labs/genetics/

http://www.funcbiol.lif.kyoto-u.ac.jp/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

28

Division of Systemic Life Science ｜ Department of Biology Education and Heredity

Laboratory of
ScienceCommunication

Specially Assigned Professor

HEJNA, James Alan

Division of Systemic Life Science ｜ Department of Biology Education and Heredity

Assoc. Prof.

Assoc. Prof.

CARLTON, Peter

GUY, Adam Tsuda

Main theme
Our laboratory engages in the development
and implementation of new approaches to theinternationalization of science education andcommunication, based on principles of active
learning. The particular challenges we are
addressing often involve overcoming thedifferences in culture and pedagogicaltraditions between Japanese and Western
societies. Our efforts are chiefly in the
educational arena, aimed at training the next
generation of scientists to communicate theirknowledge and expertise not only to theinternational scientific community but locallyto the citizens who ultimately support basic
research. Our activities entail the following:

1. Increasing the exposure of Japanese
students to foreign peers. We are forging
new partnerships with foreign universities
to foster joint courses, using live Internet
connections, with active student
participation in English.
2. Establishing partnerships with foreign
universities to encourage short-term
reciprocal exchanges of graduate
students for collaborative research.
3. Expanding the opportunities for students
to present their research in English to abroad audience.

Main theme
To create haploid gamete cells (sperm or egg
cells) from diploid precursors in meiosis,
homologous chromosomes must pair, recombine,and then separate from each other, reducing the
genome by half.
Recombination between homologous
chromosomes is initiated in meiotic prophaseby programmed DNA double-strand breaks;
these breaks are then repaired throughhomologous recombination, giving rise to
genetic crossovers that link homologous
chromosomes until they divide.
Using the model organism Caenorhabditis elegans,
we are working to determine the molecularmechanisms of recombination initiation and repair
in the context of chromosome dynamics,

combining molecular genetics, biochemistry andcytology with high-resolution microscopy andquantitative image analysis. Since errors duringmeiosis are common in humans and can lead toinfertility and developmental defects,
understanding these mechanisms is important
for achieving improvements in humanreproductive health.
Our current research focuses on the following areas:- Understanding mechanisms of chromosome
dynamics and regulation during meiosis- Phosphoregulation of the synaptonemal complex- Analysis of chromosome structures using
super-resolution microscopy

Lab URL

Discovery of a mechanism that maintains flexible photosynthetic activity bychanging the localization of chloroplast protein
Most microalgae overcome the difficulty of acquiring
CO2 in aquatic environments by inducing a
CO2-concentrating mechanism (CCM). LC-inducible
protein B (LCIB), structurally characterized ascarbonic anhydrase, is essential for the CCM
operation and changes its localization in thechloroplast stroma. Although the physiologicalimportance of LCIB localization changes has beenshown, the factors necessary for the localization
changes remain uncertain. A research group led by
Takashi Yamano, Chihana Toyokawa, and Hideya
Fukuzawa examined showed a series of evidence tosupport that the reversible localization changes of
LCIB was switched at an external CO2 concentration

boundary of ~7 µM without any requirement for light,
photosynthetic electron flow, and de novo protein
synthesis other than LCIC. Because LCIB is one of the
key factors for driving the CCM and homologs of LCIB
are highly conserved in algal species harboring a
CCM, elucidating part of the mechanism of LCIB
localization change will provide essential insights for
CCM research, especially for the introduction of CCM

Graduate School of BIOSTUDIES, Kyoto University

into terrestrial plants to improve crop productivity andreduce CO2 emissions.
The findings were published in the following article.
Takashi Yamano, Chihana Toyokawa, Daisuke
Shimamura, Toshiki Matsuoka, Hideya Fukuzawa.
CO₂-dependent migration and relocation of LCIB, apyrenoid-peripheral protein in Chlamydomonas
reinhardtii. Plant Physiology, 188(2), 1081–1094(2022)

https://doi.org/10.1093/plphys/kiab528

Tumor progression by a cell-cell interaction between cellswith distinct oncogenic mutations
This study was published in Developmental Cell on Aug 9, 2021
Cancer tissue often comprises multiple tumor cellswith distinct oncogenic mutations. The researchgroup of Professor Tatsushi Igaki and Assistantprofessor Masato Enomoto found that two distinct
benign tumors with Ras or Src activation mutuallytransform into malignant tumors via cell-cellinteraction when they are emerged adjacent to eachother in Drosophila epithelia. Mechanistically, Ras
and Src cells upregulate the ligand Delta and its
receptor Notch respectively, and the Delta-Notch
interaction occurs at the boundary between thesecells. Activated Notch signaling in Src cells
downregulates cell adhesion and cell death, leading
to malignant transformation. Simultaneously, Notch
signaling in Src cells induces IL-6, which activates

JAK-STAT signaling in neighboring Ras cells totransform them into malignant tumors. Thesefindings provide a mechanistic explanation for how
heterogeneity of tumor cells drives cancer
progression.

TOPICSTOPICS

http://www.carltonlab.org

29

Laboratory of
Chromosome Function
and InheritanceFor further information, please refer to the URL below.

URL: http://doi.org/10.1016/j.devcel.2021.07.002

Graduate School of BIOSTUDIES, Kyoto University

30Division of Systemic Life Science ｜ Department of Systems Biology

Division of Systemic Life Science ｜ Department of Systems Biology

Laboratory of
Bioimaging andCell Signaling

Professor

MATSUDA, Michiyuki（Concurrent post）
Main theme

Professor

MATSUDA, Michiyuki
Assoc. Prof.

KOBAYASHI, Taeko

Assist. Prof.

YUKINAGA, Hiroko

Laboratory ofTheoretical
Biology

Main theme

Research objects

・Development of fluorescent andluminescent biosensors to visualize
signal transduction in living cells.
・Intercellular/intracellular signaling inliving cells and living mice.
・Live imaging of pancreatic cancer.
・Live imaging of glia.
・Analyses of proteostasis andlysosomal regulation to maintainneural stem cells in the adult brain.

https://sites.google.com/view/theoretical-biology/

Specially Assigned Professor

HONDA, Naoki

Lab URL

Live coverage of the battle between NK cells and cancer cells.
The research group led by Professor Michiyuki
Matsuda of the Graduate School of Life Sciences
visualized the process of cancer cell elimination by
natural killer (NK) cells, one of innate immune cells, on
the lung capillaries of living mice using multiphoton
microscopy and ultra-sensitive bioluminescence
technique. They found that cancer cells that reachedthe lungs were attacked by NK cells approximately
once every two hours, and although they were initiallyeliminated at about one-half the rate, they acquired
resistance after 24 hours. They also showed that the
blood coagulation system contributes to thisacquisition of resistance.

remained unknown how they are actually eliminated.
By using fluorescent biosensors and multiphoton
microscopy, a microscope that can observe deep into
living tissues, we can analyze in detail how immune
cells fight against cancer cells. Based on theobservation, we hope to propose a new paradigm toprevent cancer cell proliferation and metastasis."

TOPICS

Our research has been focused on thevisualization of activities of various
kinases and G proteins in living cells
using biosensors based on the principleof the Förster resonance energy transfer(FRET). Our most recent study created
FRET-based optogenetic tools whichenables molecular activity control atsingle-cell resolution. These sensors andoptogenetic tools will lead us to ‘talk’with live cells under microscope tofacilitate deeper understandings of thebiological systems. Multiphoton
microscopy of various tissues andorgans of mice expressing our biosensor
will reveal relationship between signaltransduction and cellular behavior inphysiological and pathologicalconditions.

Our laboratory aims to elucidate theoretical
logic of dynamic living systems. By
developing and simulating mathematicalmodels, we are trying to understandmechanisms underlying phenomena in abottom-up manner. We are also utilizing
machine learning to extract hidden rules ofdynamic, complicated phenomena fromexperimental quantitative data in a top-downmanner. By means of these theoretical
approaches, we are studying neuronal wiringin the brain, emotional neural dynamics,
noise-resistant embryonic development,
mechano-chemical mechanism of collective

cell migration, cytoskeleton-based cellularmorphogenesis, identification of intracellular
information processing and animal
behavioral strategy.

Cancer cells gain resistance to NK cells in 24 hours
NK cell inthe blood

Comments from researchers:
It is well known that immune cells play an importantrole in suppressing cancer cell metastasis, but it

NK cell on
the blood vessel
cancer cell

platelet

4 hrs

The marker of cancer cell

NK cell

capillary

24 hrsPlatelets work to dislodge the marker

alveolus

The findings were published in “eLife “.
For further information, please refer to the URL below.

https://www.fret.lif.kyoto-u.ac.jp/rab/ichise_2022e.html
https://doi.org/10.7554/eLife.76269
Lab URL

31

Graduate School of BIOSTUDIES, Kyoto University

http://www.fret.lif.kyoto-u.ac.jp/mi.htm

Graduate School of BIOSTUDIES, Kyoto University

32

Division of Systemic Life Science ｜ Department of Systems Biology

Division of Systemic Life Science ｜ Department of Genome Biology

Laboratory of
GenomeMaintenanceLaboratory ofBrain Development
and Regeneration

Professor

Professor

MATSUMOTO, Tomohiro

IMAYOSHI, Itaru

Assoc. Prof. (Concurrent post)

GUY, Adam Tsuda

Senior Lecturer

YAMADA, Mayumi

Main theme
Our laboratory aims at understanding
the mechanisms of development andregeneration processes in the
mammalian brain, and their functional
outcomes on neural circuits, higher brain
functions, and animal behaviors. We arefocusing on the regulatory mechanismof cell growth, differentiation, andquiescence of neural stem cells. We arealso focusing on the functional

contribution of newly-generated neurons
to neural circuits and animal behaviors.
Our laboratory is also developing novel
optogenetic tools that can manipulate
gene expression of cells by light.

Main theme
The spindle checkpoint, our major
research subject, is a surveillancemechanism to regulate cellular
apparatus for compliance with this rule.
It is a unique negative feedback thatconverts/amplifies a physical signal
sensed by kinetochores (attachment of
the spindle and/or tension) andregulates the timing of the sister
chromatid separation. Mad2, a signal

carrier of this feedback, plays a vital rolein the spindle checkpoint. It is
specifically localized at unattachedkinetochores that are the origin of thecheckpoint signal. Mad2 targets CDC20
and inhibits its activity to promote sister
chromatid separation. We study Mad2, acentral player of the spindle checkpoint,
to reveal mechanisms, which regulate
the activity of Mad2.

Senior Lecturer

FURUYA, Kanji

Assist. Prof.

SUZUKI, Yusuke

Lab URL

33

Graduate School of BIOSTUDIES, Kyoto University

http://brainnetworks.jimdofree.com

http://www.rbc.kyoto-u.ac.jp/radiation_system/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

34

Division of Systemic Life Science ｜ Department of Genome Biology

Division of Systemic Life Science ｜ Department of Genome Biology

Laboratory of
Genome Damage
Signaling

Laboratory ofCancer Cell Biology

Professor

Professor

TAKATA, Minoru

HARADA, Hiroshi
Main theme
DNA damage response (DDR) is thefundamental mechanism that stabilizes
our genome. Genome stability underlies
all biological processes. We try to
identify molecules involved in genome

stability/ replication stress/DDR bymethods such as screening mutations inhuman patients, and further analyze
their function using genome engineeringin various cell lines, iPS cells, and modelorganisms.

Main theme
Cells maintain their function andmorphology by exploiting a suitable
adaptive response system to diverse andcomplex tissue microenvironments.
Several lines of evidence have suggested
that hypoxic, acidic and nutrients-depleted
microenvironments exist in solid tumors
and induce malignant phenotypes andchemo/radioresistance of cancer cells(Figure 1). We aim to elucidate molecularmechanisms responsible for cellular

adaptive responses to the tumor-specificmicroenvironments and malignant
progression of cancer cells (Figure 2).

Assoc. Prof.

NAM, Jin-Min· Cellular adaptive responses to tumor
microenvironments, e.g. hypoxia· Molecular mechanisms underlying
malignant progression and chemo/
radioresistance of cancer cells· Regulatory mechanisms ofcarbohydrate metabolic pathway

Figure 1: Hypoxic tumor cells (green) distant from blood vessels (blue)
are resistant to radiation-induced DNA damage (red).

Figure 2: HIF-1-mediated gene networks responsible for both adaptive
responses to hypoxia and malignant progression of cancer cells.

Lab URL

35

Graduate School of BIOSTUDIES, Kyoto University

http://house.rbc.kyoto-u.ac.jp/late-effect

http://www.rbc.kyoto-u.ac.jp/cancer_biology/

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

36

Division of Systemic Life Science ｜ Department of Genome Biology

Laboratory of
Chromatin
Regulatory Network

Division of Systemic Life Science ｜ Department of Mammalian Regulatory Network (Cooperation Course)

Assoc. Prof.

Professor

IKURA, Tsuyoshi

SUGITA, Masahiko

Laboratory of
Cell Regulation and
Molecular Network

AFFILIATION：
Institute for Life and Medical Sciences

Main theme

Main research topics

Main theme

The purpose of our research is to clarify therole of chromatin dynamics, which is required
for the DNA metabolisms such astranscription, DNA replication, and DNA repair.
In particular, we focus on the molecularmechanisms by which histone modifiercomplexes regulate the histone eviction as
chromatin remodeling machinery upon DNA
damage induced by ionizing radiation. Our goal
is to understand how histone eviction
activates DNA damage signaling pathways
and functions as an anti-cancer signaling.

· Memory of genomic damage

Full attention of this laboratory has been
directed to previously unappreciated aspectsof the acquired immunity that we call “lipid
immunity” . Unlike conventional MHC
molecules that present protein-derived
peptide antigens, molecules of the humangroup 1 CD1 family (CD1a, CD1b, CD1c)
mediate presentation of “lipid” antigens to
specific T lymphocytes. In addition, we haverecently identified a novel lineage ofantigen-presenting molecules, termed LP1,
capable of mediating presentation of“lipopeptide” antigens. By taking cellbiological, immunological and lipid chemical
approaches, this laboratory wishes toestablish a molecular and cellular basis for

TOPICSLab URL· Cellular robustness in genomic stressresponse· Solution of energy metabolism
mechanism in specific cancer cell

http://house.rbc.kyoto-u.ac.jp/mutagenesis2/index1

Lab URLTOMONAGA, Keizo

Laboratory of
RNA Viruses

AFFILIATION：
Institute for Life and Medical Sciences

Main theme

Figure caption
The identification of RNF168 has led to the new conceptthat two distinct converging sub-pathways exist in the
upstream FA pathway to regulate SLX4.

MORITA, Daisuke

MIZUTANI, Tatsuaki

Professorof RNF168. Published in Cell Reports Oct 26th, 2021 issue.

Assist. Prof.

Assist. Prof.

https://www2.infront.kyoto-u.ac.jp/SugitaLab/

Identification of a missing piece to prevent an important hereditary
blood disorder and leukemia
Fanconi anemia (FA) is a devastating childhood disorderand the most common form of Inherited Bone Marrow
Failure Syndrome. It is important to understand how thegenetic defects in FA patients cause bone marrow failure,leukemia, and solid tumors. Professor Minoru Takata,
Program-specific lecturer Dr. Yoko Katsuki, Research fellow
Dr. Masako Abe and others (Graduate School of Biostudies,
Kyoto University) identified the RNF168 enzyme as a
critical component for the proper function of SLX4/FANCP
protein. SLX4 is crucial for resolving the spontaneously
occurring DNA damage by accumulating at the DNA
damage site during the normal blood formation process.
SLX4 has a protein domain called UBZ to bind a chain of asmall protein called “ubiquitin” which serves as a marker of
DNA damage. However, it has been enigmatic how
ubiquitin chain is generated at the DNA damage site. Now
their work showed RNF168 enzyme accumulated at the
DNA damage site, thereby creating a ubiquitin chain. Their
next plan is to identify the protein modified by the actions

lipid immunity and determine how CD1 andLP1 have been evolved to function criticallyin host defense. An important extension ofthis research is a challenge for developing a
new type of lipid-based vaccines against
cancer and microbial infection.

The researches carried out in our laboratory
are focused on several RNA viruses,
including bornavirus, and hepatitis C virus.
All our projects aim to understand thefundamental mechanisms of the replicationand pathogenesis of these viruses. We areinvestigating the replication and persistentmechanism of the bornavirus in the cell
nucleus. The understanding the biologicalsignificance of the endogenous element ofbornaviruses in mammalian genomes is oneof the main focuses of bornavirus
researches. We also aim to develop a novel
RNA virus vector using bornavirus, which
can express stably functional small RNAs.

The understanding of the molecularmechanism of tumorigenesis caused byhepatitis viruses is also the main purpose of
our laboratory.

Assoc. Prof.

HIJIKATA, Makoto

Assoc. Prof.

MAKINO, Akiko

Assist. Prof.

MATSUGO, Hiromichi

https://doi.org/10.1016/j.celrep.2021.109879

https://t.rnavirus.virus.kyoto-u.ac.jp/

37

Graduate School of BIOSTUDIES, Kyoto University

Lab URL

Graduate School of BIOSTUDIES, Kyoto University

38

Division of Systemic Life Science ｜ Department of Mammalian Regulatory Network (Cooperation Course)

Laboratory of
Cell Division and
Differentiation

Division of Systemic Life Science ｜ Department of Advanced Imaging (Industry-Academia Collaboration Course)

Laboratory of Spatiotemporal
Optical Control /Laboratory of Optical Neuraland Molecular Physiology

Professor

TOYOSHIMA, Fumiko
AFFILIATION：
Institute for Life and Medical Sciences

Assoc.Prof.

VANDENBON, Alexis

Assist. Prof.

ISHIBASHI, Riki

Main theme[Toyoshima Group] This group aims to clarify themechanism of organ remodeling during life stages.
In particular, we focus on organ remodelling during
pregnancy, obesity, and aging from the perspectivesof tissue stem cell dynamics, multicellular /multiorgan network, and mechanobiology. We also
aim to apply the mechanism of physiological organ
remodeling to regenerative and anti-aging medicine.

to regenerative medicine
4. CriMGET system: Gene targeting technology

Main theme

5. Bioinformatics methodology for the analysis oflarge biological datasets

This department was launched in
January 2020 as an
academic-industrial cooperation
with Hamamatsu Photonics. In
this department, scientists at
Graduate School of biostudies
and research groups at
Hamamatsu Photonics will
maximize their respective
expertise to develop
next-generation technologies for
microscope. By integrating theknowledge and experience of
academia and companies, we aim[Vandenbon Group] This group is developing
bioinformatics methodology for the analysis of large
biological datasets, including single-cell and spatialtranscriptomics data.

Research subjects
1. Maternal organ remodeling during pregnancy
and maternal-fetal interphaseto achieve innovative opticaltechnology development throughindustry-academia collaboration
and apply it to the elucidation oflife phenomena. In thisdepartment, two laboratories( “Laboratory of Spatiotemporal
Optical Control” and “Laboratory
of Optical Neural and Molecular
Physiology” ) were founded andthey will develop cutting-edge
imaging, optical control
technologies, and probes.
By measuring and manipulating

dynamics of genes and molecules
multidimensionally, they will
understand the principle ofbiological functions.

2. Organ remodeling during obesity and aging
3. Application of physiological organ remodeling
Lab URL

Laboratory of
Cellular and Molecular
Biomechanics

Main theme

https://www2.infront.kyoto-u.ac.jp/Toyoshima-HP/index-En.html

Two-photon fluorescence microscopy has
become a powerful tool for deep imaging of
biological tissues. However, many biologicalphenomena in which intercellular interaction
and communication networks play a crucial role
are invisible because of insufficient imaging
performance of commercial two-photon
fluorescence microscopes. We aim to make theinvisible visible by creating novel opticaltechniques. Our current research focuses on thefollowing subjects;

Professor

ADACHI, Taiji
AFFILIATION：
Institute for Life and Medical Sciences

Main theme
Assist. Prof.

KAMEO, Yoshitaka

Our group aims to clarify the mechanisms by whichcells sense mechanical stimuli and regulate theiractivities in stem cell differentiation, tissue/organ
morphogenesis, and functional adaptation. To better
understand how these dynamical processes aremechano-regulated through complex hierarchicalstructure-function relationships, we are bridging
spatial and temporal scales ranging frommicroscopic (molecular and cellular level)
phenomena to macroscopic (tissue level) behaviors.
Based on multiscale biomechanics integrating
biomechanics and mechanobiology researches, we
combine modeling and simulation with experiments
to elucidate mechano-biochemical couplings in living
system dynamics.
1. Biomechanics and mechanobiology studies of stem
cell differentiation, morphogenesis, and remodeling
Lab URL

39

Graduate School of BIOSTUDIES, Kyoto University

in tissue development and growth.

1. Development of femtosecond lasers forultra-deep imaging and their applications
2. Development of wide-field deep imaging
techniques using spatiotemporal control oflaser pulses and their applications

Laboratory of Spatiotemporal
Optical Control
Program-Specific Professor

ISOBE, Keisuke

3. Development of 4-dimensional optical control
techniques using multiphoton patterned
illumination their applications

2. Understanding the mechanisms of tissue
development and growth emerging frommulticellular dynamics.
3. Clarifying the mechanisms of tissue functional
adaptation in a mechanical environment byremodeling.
4. Elucidation of mechano-biochemical couplingmechanisms in mechanosensory cells.
5. Understanding mechanical behaviors of DNA in cell
nucleus and the impacts on gene transcription.
R: Osteoclast

Mouse femur

B: Osteoblast

Mechanosensor proteins

AFM-TIRF system

1 mm

Adaptation by bone remodeling
Cerebellar
foliation

Proliferation

Mechanosensing mechanisms
Nucleus

DNA melting

Supercoiling

Migration

Main theme
Probing functional neural circuits at highspatial-temporal resolution is crucial tounderstand how neuronal populations work
together to achieve higher brain functions
such as learning and memory. We aim tounderstand these circuit mechanisms with
cutting-edge multiphoton imaging and opticalcontrol technology. Our current research
focuses on the following subjects;

1. Dendritic voltage integration of synaptic
potentials.
2. Circuit mechanisms underlying odor-induced
behaviors.

Laboratory of Optical Neural andMolecular Physiology
Program-Specific Assoc. Prof.

SAKAMOTO, Masayuki

3. Development of fluorescent probes formonitoring neural activity.
In vivo two-photon
imaging fromhead-fixed mouseduring learning

White matter

Simulation of brain morphogenesis

Mechanical behaviors of nuclear acids

https://www2.infront.kyoto-u.ac.jp/bf05/index-e.html

Graduate School of BIOSTUDIES, Kyoto University40Radiation Biology Center (RBC)
Radiation Biology Center, Kyoto University

Departments
Dept. of Mutagenesis

Dept. of Radiation System Biology

How does the cell maintain its integrity in response tovarious stress such as radiation or UV? What kind ofstrategy is employed? To solve these questions and to
elucidate mechanisms of cancer or lifestyle-relateddisorders, we focus on chromatin that is thecharacteristic of eukaryote's genome using proteomics
analysis of chromatin regulator protein complexes,
bioimaging, and mathematical and statistic approaches.

We are pursuing mechanistic understanding of genetic
and epigenetic inheritance by analyzing regulation ofcentromere structure, various cell cycle check points,
and stress responses.
[Staff]

MATSUMOTO, Tomohiro (Prof.)
FURUYA, Kanji (Senior Lecturer)[Staff]IKURA, Tsuyoshi (Assoc. Prof.)

Dept. of Late Effects Studies
We are studying (1) cellular and molecular mechanisms in
response to endogenous DNA damage and replicationstress, and (2) disorders caused by the defects in thesemechanisms such as Fanconi anemia and hereditarybreast and ovarian cancer. We employ technologies in vitro
recapitulation of pathologies with iPS cell lines derived frompatients, genome editing, and analysis of human materials.
[Staff]Message from Director of the Center

Hiroshi Harada

The research in the RBC is in large

basic research on biological effects of radiation. As a Joint Usage

part strongly linked with users of

Research Center, the RBC has been fulfilling its responsibilities as a

Joint Usage Research Center, but

hub for scientists in radiation biology and its related research fields.

at the same time, each member ofto commence novel and deeper research activities from this blessed

We are conducting studies on intracellular andextracellular factors that affect cancer radiation
sensitivity/resistance, such as genetics deficiencies
and tissue microenvironments. Our research focus isranging from molecular, cellular, and tissue levels toexperimental mice and further to cancer patients.

TAKATA, Minoru (Prof.)
MU, Anfeng (Program-Specific Assist. Prof.)[Staff]Overview

The Radiation Biology Center (RBC) was founded in 1976 to promote

The center was integrated with Graduate School of Biostudies in 2018

Dept. of Genome Repair Dynamics

Dept. of Chromosome Function and InheritanceDept. of Stress Response

Using the model organism Caenorhabditis elegans, we
are working to determine the molecular mechanisms ofrecombination initiation and repair in the context ofchromosome dynamics. Understanding thesemechanisms is important for achieving improvements
in human reproductive health problems such asinfertility and developmental defects.

RBC pursues science with theirown research direction.

position as a part of "Biostudies" looking into the vast areas of life
sciences.

[Staff]

HARADA, Hiroshi (Prof.)
NAM, Jin-Min (Assoc. Prof.)
KOBAYASHI, Minoru (Program-Specific Assist. Prof.)

We will elucidate what kind of molecular reactions
cells would display upon low dose irradiation in termsof stress response. Our main research targets are
regulatory mechanisms of chromatin dynamics,
translational regulation on ribosomes, acquired
resistance mechanisms to low dose irradiation.
[Staff]CARLTON, Peter (Assoc. Prof.)

ISHIKAWA, Fuyuki (Prof.)
MIYOSHI, Tomoichiro (Assoc. Prof.)
NAKAOKA, Hidenori (Assist. Prof.)

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Research Center for Dynamic Living Systems
Research Center for Dynamic Living Systems

Laboratories
Multiscale Biomechanics Team
Cutting-edge Bioimaging Team

(Adachi Lab)

(Matsuda Lab)

Roles of force in hierarchical living systems frommolecular/cellular levels to tissue/organ levels will beclarified by multiscale biomechanics approach throughintegration of in-vitro and in-silico experiments.

By using fluorescence biosensors, we will visualize
molecular activity and cellular function in the tissue
culture cells and the living mice, and thereby decipher
the principle of intercellular communication.
[Staff]Message from Director of the Center

Matsuda Michiyuki

Recent advent of biology largely depends on the reductionist’ s
approach that has been deciphering the function of molecules ofinterest. New functions of molecules are still being discovered, leading
to the discovery of new biological phenomena. Meanwhile, it will be alsoquite important to integrate the huge knowledge accumulated so far
and to deduce common principles of biological phenomena. Theoreticalbiology, mathematical biology, or systems biology are the school ofsuch research area, but their advancement depends on technologicalbreak-through of imaging and omics that fuels these theoreticalresearch field with the ground-truth data and tools for validation. With
this background, a MEXT-supported project named ‘a research andeducation platform for innovative research on dynamic living systems’
were launched by Graduate Schools of Medicine, Biostudies, andInformatics, and by Virus Research Institute and Institute for Frontier
Medical Sciences. Here, to further promote this interdisciplinary
approach, Research Center for Dynamic Living Systems has launched in
2018. Setting the cutting-edge microscopy as the core of technology, we
attempt to understand the biological systems by the collaboration oftheoretical researchers and experimental biologists.

MATSUDA, Michiyuki (Prof.)
KOBAYASHI, Taeko (Assoc. Prof.)

Overview• Course meeting of developmental biology, cellbiology and systems biology: Monthly seminars are
given by foreign or domestic top runners and byyoung researchers. Annual retreat will provide thegraduate students with the opportunity to talk anddiscuss on their data.
• MACS education program: In collaboration withdepartment of mathematics, graduate school ofscience, a series of lectures will be provided under
the title of “Fusion of imaging technology andmathematics” .
• Introduction to mathematics, statics, andcomputational biology: For the graduate students
who belongs to the wet laboratories, the basics ofmathematics and statistics and the use ofmathematical software will be lectured.
• Kyoto University Live Imaging Center: Cutting-edge
microscopes including multiphoton microscopes areavailable for researchers both in and out of Kyoto
University. Technicians maintain the microscopes ingood condition and help researchers for the operation.

Physiological Network Team
(Uemura Lab)
By taking multi-omics and genetic/optogenetic
approaches, we will unravel operating principles ofphysiological mechanisms that control animal
life-history traits and neuronal circuits that evoke
selective behaviors, in response to nutrient balances or
sensory stimuli.
[Staff]

UEMURA, Tadashi (Prof.)

Spatio-temporally controlled
biophotonics Team
(Isobe Lab)
By combining spatio-temporal pattern control of
excitation light pulses with optogenetic technique,we will visualize and manipulate multiceller interactions
within highly scattering tissue.
[Staff]

ISOBE, Keisuke (Program-Specific Prof.)
SAKAMOTO, Masayuki (Program-Specific Assoc. Prof.)[Staff]

ADACHI, Taiji (Prof.)
KAMEO, Yoshitaka (Assist. Prof.)

Biological Function Manipulating Team
(Imayoshi Lab)We will develop genetic and virus vector methods forexpressing fluorescent proteins and functional
molecules in specific cell types of the model organisms,
especially mice. We will also develop novel opticalmethods to manipulate cellular and biological functions.
By integrating these cutting-edge technologies, we will
unveil the regulatory mechanisms underlying brain
development, plasticity, and regeneration.
[Staff]

IMAYOSHI, Itaru (Prof.)

Dynamic Genome Systems Team
(Taniguchi Lab)We aim at revealing the general principle of how the
genome dynamically controls expressions of a huge
number of genes to reproduce complex biological
functions. Towards this goal, we utilize genome-wide or
exhaustive measurements based on high-throughput
imaging and next-generation sequencing coupled withlarge-scale computational analyses.
[Staff]TANIGUCHI, Yuichi (Prof.)

A transgenic mouse expression FRET biosensor (right).
Blue light illumination to cultured cells expressing thelight-induced gene expression system.

43

Graduate School of BIOSTUDIES, Kyoto University

Physical model and simulation of collective cell
migration.

Graduate School of BIOSTUDIES, Kyoto University

44

North Campus

Campus MAP

Total Revenue in Fiscal 2021

Graduate School of Agriculture
Graduate School of Biostudies● Gene Biodynamics

Category
Operational grants
MEXT Research Grants
Other Research Grants
Donations for Research
Funded Research
Collaborative Research
Others
Total

Total (yen)Total Revenue

219,330,205
409,804,560
14,810,958
50,486,000● Applied Molecular Microbiology● Molecular Biology of Bioresponse● Plant Developmental Biology● Symbiotic and Coevolutionary Mechanisms● Developmental Neurobiology

Collaborative
Research● Biochemical Cell Dynamics

Operational grants

9.51%

Faculty of Agriculture Main Bldg

● Multidisciplinary Biology

14.42%

604,564,370
144,538,335● Biosignals and Response

Institute for Integrated
Cell-Material Sciences (iCeMS)

5.07%

77,066,000● Plant Molecular Biology

Main Campus

Others● Molecular and Cellular Biology of Totipotency

Faculty of Medicine Bldg G
South Campus Research Bldg

Hyakumanben(Graduate School of Biostudies)● Chromosome Transmission

1,520,600,428● Cell Cycle Regulation

Imadegawa St.

Hyakumanben● Cell Recognition and Pattern Formation

Kyodai Nogakubu-mae● Plasma Membrane and Nuclear Signaling● Molecular Neurobiology

St.

Funded Research● Immunobiology

MEXT
Research Grants● Science Communication● Graduate School of Biostudies

shioji39.76%● Molecular and Cellular Biology

26.95%

Research Bldg. No.16

Higa(Office)● Signal Transduction

Science Frontier
Laboratory

Clock Tower● Functional Biology● Chromosome Function

Higashiyama higashi ichijo

and Inheritance

3.32%

Faculty of
Medicine Bldg A

Donations for Research● Single-Molecule Cell

Other Research Grants

k

ira

sh

u
Ky

Biology

Higashi-Ichijo St.
St. Kyodai Seimon-mae

Main Gate
Graduate School of Agriculture
Graduate School of Biostudies

Medicine Campus

Graduate School of
Pharmaceutical
Sciences Main Bldg.

Faculty of Medicine Bldg F

Higashioji St.

0.97%

a
aw

● Genetics

Professors Emeriti As of April 1, 2022

● Bioimaging and Cell Signaling● Theoretical Biology● Research Center for Dynamic Living Systems

Graduate School of Biostudies,
Radiation Biology Center

South Campus Research Bldg (Bldg. G)
Science Frontier Laboratory● Genome Maintenance● Genome Damage Signaling

SASAKI, Ryuzo
TAKEICHI, Masatoshi
OHYAMA, Kanji
KUMAGAI, Hidehiko
YANAGIDA, Mitsuhiro
IZUI, Katsura
NAKANISHI, Shigetada
YAMAMOTO, Kenji
KOZUTSUMI, Yasunori
TAKEYASU, Kunio
INOUE, Tan
INABA, KayoYONEHARA, Shin
SATO, Fumihiko
NISHIDA, Eisuke
NEGISHl, Manabu
HEJNA, James Alan
CHISAKA, Osamu

47

Laboratory
Biosignals and Response
Cell Recognition and Pattern Formation
Plant Molecular Biology
Applied Molecular Microbiology
Chromosome Transmission
Plant Physiology
Neuroscience
Applied Molecular Microbiology
Membrane Biochemistry and Biophysics
Plasma Membrane and Nuclear Signaling
Gene Biodynamics
Immunobiology
Molecular and Cellular Biology
Molecular and Cellular Biology of Totipotency
Signal Transduction
Molecular Neurobiology
Science Communication
Bioeducation

Graduate School of BIOSTUDIES, Kyoto University

from

to

April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
April 1, 1999
August 1, 2001
April 1, 1999
April 1, 1999
April 1, 1999
November 1, 2010
April 1, 1999

March 31, 2001
March 31, 2002
March 31, 2003
March 31, 2004
March 31, 2005
March 31, 2005
March 31, 2005
March 31, 2010
March 31, 2012
April 30, 2014
March 31, 2015
March 31, 2016
March 31, 2018
March 31, 2018
March 31, 2018
March 31, 2019
March 31, 2020
March 31, 2022

Pharmaceutical
ScienceCampus● Cancer Cell Biology● Chromatin Regulatory Network

KonoedoriKonoe St.

Marikoji St.

Name

Enrollment period

Institute for Life andMedical Sciences Bldg. No.2

Univ.
Hospital
East
Campus Kyodai● Brain Development and Regeneration● Cell Regulation and Molecular Network

Faculty of Medicine Bldg F● Cell Division and Differentiation● Spatiotemporal Optical Control

Hospital-mae● Optical Neural and Molecular Physiology

Institute for Life andMedical Sciences Bldg. No.3

● RNA Viruses● Ultrastructural Virology

Kasuga St.

Institute for Life andMedical Sciences Bldg. No.1

● Cellular and Molecular Biomechanics

AccessKeihan Limited Exp. 47min

Demachiyanagi Station

Osaka Umeda Station

Hankyu Limited Exp. 41min

Kyoto Kawaramachi
StationOsaka Station

JR Special Rapid Service 29min

Osaka International
Airport (Itami)

Airport Limousine Bus 60min

Kansai International
Airport

JR Airport Express “Haruka” 75min

Kyobashi Station

Graduate School of Biostudies,
Radiation Biology Center

Kyoto
Station

20min Walk
Shijo Kawaramachi
StationKyoto city subway
For Kokusaikaikan
10min
In front of a Kyoto station

Kyoto city bus(201, 31) 20min

Imadegawa Karasuma
Imadegawa
StationKyoto city bus(201) 15min

YoshidaCampus

Kyoto city bus(206) 30min

Graduate School of BIOSTUDIES, Kyoto University

48