Division of Integrated Life Science
In this division, education and research are focused on the elucidation of basic mechanisms regulating the chromosome transmission, 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.
Department of Gene Mechanisms
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, maintenance and repair, etc.) in unicellular and multicellular organisms.
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Laboratory of Chromosome Transmission
Member
- NAKASEKO, YukinobuAssociate Professor
Research outline
Chromosomes transmit genetic information and play an essential role in maintaining not only individuals but also their species. All organisms have chromosomes, and the fundamental mechanism for their function is considered to be common in many aspects. To elucidate the functions of chromosomes at the molecular level, we analyze molecular organization of chromosomes, in addition to a set of genes involved in chromosome function、using fission yeast Schizosaccharomyces pombe as a model system.
Main themes
- Isolation of growth-deficient mutants
- Analysis of genetic interaction of growth-deficient mutants
- Analysis of chromosome function based on artificial modification
Keywords
- Chromosome
- Genetic interaction
- Mutant
- Fission yeast
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Laboratory of Gene Biodynamics
Member
- SHIRAISHI, HideakiAssociate Professor
Research outline
Microalgae living in water have evolved in a variety of ways that are hidden from the human eye, and some of them possess traits that are useful to humankind. We will study the genetics, proliferation, and morphogenesis of microalgae with such useful traits, and through these studies, build a foundation for the effective utilization of microalgae.
Main themes
- Molecular genetics of the filamentous cyanobacterium Arthrospira platensis (Spirulina).
- Analysis of the heredity, growth, and morphogenesis of the filamentous cyanobacterium A. platensis
- Study of the motility mechanism of filamentous cyanobacteria.
Keywords
- microorganism
- microalgae
- cyanobacteria
- blue-green algae
- cell motility
- molecular genetics
- spirulina
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Laboratory of Cell Cycle Regulation
Member
- AOKI, KazuhiroProfessor
- HONDA, NaokiSpecially Assigned Professor
- GOTO, YuheiAssociate Professor
Research outline
A cell is a vessel stuffed with proteins, nucleic acids, lipids, and small compounds. Within the cell, an immense number of physicochemical reactions are constantly taking place. Cells maintain homeostasis at various levels, from the cellular to the organismic, by perceiving external substances, processing this information within intricate intracellular networks, and manifesting adaptive phenotypes. Our research focuses on elucidating the mechanisms underlying the cellular information processing (encoding) and cell fate decision making (decoding). In addition to the development of quantitative measurement and perturbation techniques, we aspire to address the fundamental question of “what is life?” through approaches such as reconstructing a cell on a computer.
Main themes
- Visualization and manipulation of molecules involved in cell cycle progression
- Understanding and manipulation of biological functions that emerge in cell populations
- Elucidation of intracellular mechanical properties and their physiological significance
- Implementation of whole cell modeling
- Development and application of novel biosensors and optogenetic tools
Keywords
- Imaging
- Optogenetics
- Simulation
- Signal transduction
- Information processing
- Collective cell migration
- Cell mechanics
Department of Cell and Developmental Biology
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.
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Laboratory of Cell Recognition and Pattern Formation
Member
- UEMURA, TadashiProfessor
- USUI, TadaoSenior Lecturer
- HATTORI, YukakoAssistant Professor
Research outline
We are trying to unravel underlying mechanisms of adaptations to nutrient balances using Drosophila species. We are also taking interspecies approaches to understand contributions of symbiotic microorganisms to animal growth and reproductive manipulation (“male killing”). By using Drosophila somatosensory neurons, we are dissecting operating principles of neuronal circuits that evoke selective behavioral outputs in response to nociceptive stimuli. We are also interested in how genomic information and cells cooperatively build up the entire body of an organism, and trying to understand common principles of epithelial morphogenesis beyond hierarchies of genome, cells and tissues. To conduct these studies, we make full use of molecular, optogenetic, and physiological approaches, imaging, single-cell analysis and multi-omics.
Main themes
- Nutri-developmental biology: deciphering regulatory systems of host animals and symbiotic microorganisms that govern nutritional adaptability to ensure animal growth, reproduction, and aging
- Neuroscience: operating principles of neuronal circuits that evoke selective behavioral outputs in response to nociceptive stimuli
- Morphogenesis: common principles of epithelial morphogenesis beyond hierarchies of genome, cells and tissues
- Reproductive parasites: a comprehensive study of “male killing” caused by insect symbionts
Keywords
- animal growth
- aging
- nutrients
- microbes
- neuronal circuits
- morphogenesis
- reproductive parasites
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Laboratory of Signal Transduction
Member
- KUSAKABE, MoriouSenior Lecturer
- MIYATA, YoshihikoAssistant Professor
Research outline
We are interested in identifying and elucidating molecular mechanisms and biological functions of signal transduction pathways that regulate cell fate decision during cell proliferation, cell differentiation and developmental processes. Our current research focus is primarily on protein phosphorylation-dependent intracellular signal transduction pathways, which are strictly regulated by various protein kinases. Our main experimental systems are mammalian cultured cell lines and African clawed frog (Xenopus laevis) early embryos.
Main themes
- Regulatory mechanisms of protein kinase signal transduction in cell fate decision
- Molecular mechanisms of signal transduction in cellular processes
- Molecular mechanisms of signal transduction in developmental processes
Keywords
- Signal transduction
- Protein kinase
- Xenopus laevis
Department of Plant Gene and Totipotency
The department pursues the basic research and application of molecular and cellular principles related to plant growth and development. We take approaches by cell biology, chemical biology, molecular and cellular biology, molecular genetics, and genomics.
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Laboratory of Plant Molecular Biology
Member
- KOHCHI, TakayukiProfessor
- YASUI, YukikoAssociate Professor
- YOSHITAKE, YoshihiroAssistant Professor
Research outline
Using the liverwort Marchantia polymorpha as a model, we aim to elucidate the molecular mechanisms of environment-dependent regulation of growth and development. In particular, we are focusing on the induction of light-dependent sexual reproduction and investigating the relationship between chromatin modification and gene expression. We are also interested in the evolution of phytohormone signal transduction related to reproduction.
Main themes
- Light perception and signal transduction in plants
- Sex determination and differentiation in a haploid system
- Environmental regulation of chromatin status
- Evolution of plant hormone signaling
Keywords
- Environmental responses of plants
- Plant growth and development
- Plant sexual reproduction and differentiation
- Land plant evolution
- Liverwort Marchantia polymorpha
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Laboratory of Plant Chemical Biology
Member
- NAKANO, TakeshiProfessor
- MIYAKAWA, TakuyaAssociate Professor
- YAMAGAMI, AyumiAssistant Professor
Research outline
Plant growth has been administrated by cooperative regulations between plant cell differentiation/division/elongation and photosynthesis. Based on these scientific aspects, our laboratory is trying to reveal the plant growth mechanisms by ‘chemical biology’ and ‘molecular and cellular biology’.
Main themes
- Growth regulation by plant hormone signaling
- Chloroplast regulation by brassinosteroid
- Chemical functions to regulate plant growth and differentiation
- Plant biomass production regulated by chemicals and genes
- Protein function to regulate plant growth mechanism by structural biology
Keywords
- Plant hormone
- Steroid hormone
- Plant growth
- chloroplast
- chemical biology
- Molecular and cellular biology
- Structural biology
Department of Applied Molecular Biology
Signal response mechanisms have evolved in organisms through adaptations to fluctuations or changes in the natural environment. 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.
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Laboratory of Biosignals and Response
Member
- NAGAO, MasayaProfessor
- KAMBE, TaihoAssociate Professor
Research outline
We isolate and identify compounds that have useful activities for our health from natural resources and examine the mechanism how these compounds work on our body.
Our research also focuses on understanding of the physiological functions of trace minerals such as zinc, iron, and copper through functional analyses of their transporters. In particular, our projects on zinc aim at maintaining and improving our health through applying our research results.Main themes
- Isolation and identification of useful bioactive compounds from natural resources
- Understanding of the physiological functions of trace mineral transporters
- Studies on the roles of trace elements on melanin synthesis
- Food science research aimed at preventing zinc deficiency
Keywords
- Immunoregulation
- Lifestyle-related diseases
- Functional food
- Trace minerals
- Melanin
- Transporter
- Zinc
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Laboratory of Applied Molecular Microbiology
Member
- YAMANO, TakashiAssociate Professor
Research outline
We elucidate the molecular mechanisms of photosynthesis, liquid-liquid phase separation, CO2-concentrating mechanisms, metabolism, proliferation, and reproduction. By incorporating cutting-edge technologies such as molecular genetics, high-resolution imaging, multi-omics analysis, and bioinformatics, we will contribute to solving various problems facing humanity, such as next-generation energy, production of useful materials, food, biomaterials, and environmental bioremediation.
Main themes
- Elucidation and application of the molecular basis of the photosynthetic CO2-concentrating mechanism
- Elucidation and application of molecular mechanisms of emergence, disappearance, and inheritance of photosynthetic organelles with liquid-liquid phase separation
- Elucidation of gene expression regulatory network by environmental sensing including CO2, nitrogen, and light
- Elucidation of protein phosphorylation and other signaling mechanisms involved in cell survival and reproduction
- Development and utilization of genome information and genome resources of the green alga Chlamydomonas reinhardtii
Keywords
- Environmental response of plants
- Photosynthesis
- CO2-concentrating mechanisms
- Liquid-liquid phase separation
- Bioimaging
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Laboratory of Molecular Biology of Bioresponse
Member
- KATAYAMA, TakaneProfessor
- KATOH, ToshihikoAssistant Professor
Research outline
Our research group is focused on elucidating the mechanism underlying the symbiosis and co-evolution between gut microbes and the host. We are addressing the question from the enzymological and ecological viewpoints by examining how gut microbes assimilate host glycans such as human milk oligosaccharides and mucin O-glycans in the gut ecosystem.
Main themes
- Breastmilk-mediated symbiosis between infants and bifidobacteria
- Mucin O-glycan assimilation pathways in gut microbes
- Aromatic amino acid metabolism in gut microbes
- Development of an apical aerobic co-cultivation system
Keywords
- Gut microbe
- Symbiosis
- Carbohydrate metabolism
- Amino acid metabolism
- Enzyme
Department of Responses to Environmental Signals and Stresses
We aim at understanding fundamental systems underlying environmental responses by organisms through structural-functional study of information molecules involved in environmental responses, study of regulatory mechanisms of development in response to environmental signals, and ecosystem-level study of multi-species (multi-genome) systems.
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Laboratory of Plant Developmental Biology
Member
- ARAKI, TakashiProfessor
- YAMAOKA, ShoheiAssociate Professor
- INOUE, KeisukeAssistant Professor
Research outline
We are interested in molecular mechanisms underlying plant’s responses to environment and developmental processes regulated by them. Plants have evolved plastic developmental programs with both genetic and epigenetic basis to adapt their sessile mode of life to changing environment. Using an angiosperm, Arabidopsis thaliana and a liverwort, Marchantia polymorpha as model systems, we have been investigating growth phase transition in response to environmental signals such as day length, sexual reproduction processes from germline specification to gametogenesis, and evolution of regulatory systems. By studying two representative model species from phylogenetically distant clades, we aim to elucidate general principles of environmental response and development in land plants.
Main themes
- regulation of growth phase transition (especially reproductive transition) in response to environmental signals
- mechanism of day-length perception by photoreceptors and circadian clock
- long-distance systemic signaling (e.g. florigen) in the control of development
- sexual reproduction processes (especially, germline specification and gametogenesis)
- origin and evolution of regulatory systems for plastic development
Keywords
- sexual reproduction
- germline
- gametogenesis
- photoreceptor
- florigen
- Arabidopsis
- Marchantia
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Laboratory of Ecosystems and Coevolution
Member
- TOJU, HirokazuProfessor
- FUJITA, HiroakiAssistant Professor
Research outline
Throughout its four-billion-year evolution, life has expanded into diverse environments. In the history of life, symbiosis has brought about innovations, resulting in explosive evolution and species diversification in new environments. We aim to understand how interactions between species have organized ecosystems on the Earth. Combining fieldwork in natural ecosystems with genomics and information science, we will decipher the driving principles of life systems at the population, community, and ecosystem levels from phenomena at the molecular and cellular levels.
Main themes
- Roles of microbiomes in environmental adaptations of plants
- Coevolutionary history of land plants and mycorrhizal/endophytic symbionts
- Effects of aquatic/gut microbiomes on fish’s physiology and ecology
- Coevolution of invertebrates and their symbionts/parasites
- Multistability and temporal dynamics of ecosystems
Keywords
- Coevolution
- Biodiversity
- Ecosystem functions
- Microbiome dynamics
- Multistability
- Dysbiosis
- Hierarchy of life
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Laboratory of Plasma Membrane and Nuclear Signaling
Member
- YOSHIMURA, ShigehiroAssociate Professor
- KUMETA, MasahiroAssistant Professor
Research outline
We are interested in how non-structured proteins interact, assemble and function in the intracellular milieu. By elucidating the phase behavior of non-structured proteins, we understand how intracellular membrane-less organelles assemble, dissolute, and function upon various stimuli. We especially focus on how the cell cycle, cell signaling, intracellular transport, and innate immune system are regulated by phase behaviors of non-structured proteins. We tackle these questions through biochemistry, biophysics, informatics, and various imaging techniques.
Main themes
- How liquid-liquid phase separation regulates structural and functional dynamics of intracellular membrane-less organelles.
- How post-translational modifications regulate liquid-liquid phase separation.
- How the innate immune system uses intracellular membrane-less organelles.
Keywords
- Liquid-liquid phase separation
- intracellular membrane-less organelle
- intrinsically disordered protein
- innate immune system
- anti-retrovirus
Department of Molecular and Developmental Biology
The development, function, and maintenance of tissues and organs are regulated by a coordinated interplay of cell-intrinsic programs and intercellular signals. We seek their mechanisms at cellular, organellar and molecular mechanisms using various model systems, including the brain and immune systems.
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Laboratory of Developmental Neurobiology
Member
- KENGAKU, MinekoProfessor
Research outline
Neurons in the mammalian brain are orderly arranged and form specific neural circuits. We study the mechanism of brain development with special focus on directional migration of newborn neurons, arborization and connection of well-patterned axons and dendrites, and activity-dependent circuit remodeling during postnatal development. We use multidisciplinary approach including cell biology, mouse genetics, imaging, biophysics and bioengineering.
Main themes
- Dynamic cell motility control in the developing mouse brain
- Activity-dependent circuit remodeling during postnatal development
- Mechanobiology research on brain development using bioengineering and live-cell imaging
Keywords
- brain development
- neuron
- cell migration
- mechanobiology
- live imaging
- organelle transport
- cytoskeleton
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Laboratory of Biochemical Cell Dynamics
Member
- SUZUKI, JunProfessor
Research outline
Our lab aims to understand the principles of “removing unnecessary cells in tissues and replacing them with new ones” and “removing unnecessary compartments in cells and replacing them with new ones” while considering the process of removal and renewal that takes place daily in the body as Renovation. We also challenge the control of removal, since inadequate removal leads to diseases such as cancer, tissue dysfunction, and neurodegenerative diseases. In particular, we are conducting an unbiased screening approach to understand the regulatory mechanism of lipid dynamics in cell membranes, which is important to regulate removal.
Main themes
- Molecular Mechanisms of Cellular Renovation
- Molecular Mechanisms of Tissue Renovation
- Dysfunction in Renovation and Diseases
- Lipid dynamics of plasma membrane and cellular organelles
- Developing unbiased screening system
Keywords
- Renovation
- Cell
- Tissue
- Disease
- Neuron
- Lipid
- Screening
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Laboratory of Multidisciplinary Biology
Member
- TANIGUCHI, YuichiProfessor
Research outline
We aim to understand the working principle of complex biological systems (e.g. the cell and genome) constituted with a wide variety of molecules. Based on knowledge of multiple academic fields including biology, physics, chemistry, computer science, engineering and informatics, we challenge development of new innovative technologies and creation of new life science fields.
Main themes
- Elucidating the working principles of the genome
- Understanding the constitutional principles of cellular systems
- New principles and methods in disease diagnosis and treatment
Keywords
- Genome/Epi-genome
- Single cell omics
- Genome sequencing
- Bioinformatic analyses
- Molecular dynamics simulation
- Microscopy developments
- Physical/Mathematical modeling
Department of Molecular and Cellular Biology
We are studying aging, host responses to viral infections, and immune regulation at the molecular, cellular, and individual levels using molecular/genetic/cell biological and morphological/structural approaches.
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Laboratory of Ultrastructural Virology
Member
- NODA, TakeshiProfessor
- SUGITA, YukihikoAssociate Professor
- NAKANO, MasahiroAssistant Professor
- MURAMOTO, YukikoAssistant Professor
Research outline
Our laboratory studies highly pathogenic human viruses such as influenza virus, Ebola virus, and SARS-CoV-2. Our goal is to understand the mechanisms of virus replication and pathogenesis at the molecular, cellular, organ, and individual levels. To this end, we use state-of-the-art techniques such as cryo-electron microscopy and human respiratory organoid models.
Main themes
- Mechanism of influenza virus replication
- Structural analysis of Ebola virus
- Studies on replication and pathogenesis of SARS-CoV-2
- Structural analysis on virus neutralization by antibodies
Keywords
- Influenza virus
- Ebola virus
- SARS-CoV-2
- Cryo-electron microscopy/3D electron microscopy
- High-speed atomic force microscopy
- Respiratory organoids
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Laboratory of Aging and Infection Control
Member
- KAGE-NAKADAI, ErikoProfessor
- TANIMOTO, YoshihikoAssistant Professor
Research outline
Based on the mechanisms of aging and infection, we hope to construct control methods through food and indigenous microorganisms. Using C. elegans and mice as model organisms, we aim to elucidate the mechanisms of interaction between the commensal microbiota and host aging, infection, and inflammation, as well as to understand phenomena such as mitochondrial quality control and epigenetics, which are closely related to aging, and develop methods to extend healthy life span.
Main themes
- Methods to control aging and elucidation of its mechanisms
- Imaging technology focusing on mitochondria and epigenetics
- Anti-infective effects and improvement of host resistance against bacterial infection
- Host inflammation suppression by intestinal bacteria
- Interaction between host and skin and gut microbiota
Keywords
- Aging
- Inflammation
- Epigenetics
- Mitochondria
- Microbiota
- Food
- C. elegans
Department of Human-Residential Bifidobacteria (HRB) Research (Industry-Academia Collaboration Course)
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 of probiotic Bifidobacterium strains.
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Laboratory of Symbiotic and Coevolutionary Mechanisms
Member
- SAKANAKA, MikiyasuProgram-Specific Associate Professor
- ODAMAKI, ToshitakaVisiting Professor
Research outline
Research suggests that bifidobacteria have co-evolved with hominids for over 15 million years. Our research group has focused on the species that are characteristic of the human intestinal tract as “Human-Residential Bifidobacteria (HRB)” to elucidate the mechanisms underlying symbiosis between HRB and their human host.
Main themes
- Elucidation of the symbiotic and co-evolutionary mechanisms between bifidobacteria, gut bacteria, and humans.
- Understanding the molecular basis of health-promoting effects of probiotics and development of technologies for social implementation.
Keywords
- Bifidobacteria
- Symbiosis
- Co-evolution
Division of Systemic Life Science
In this division, education and research are focused on the elucidation of the fundamentals of molecular and systemic 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.
Department of Molecular and System 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 of drugs, we will pursue principles in biology and seeds for drug development.
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Laboratory of Single-Molecule Cell Biology
Member
- WATANABE, NaokiProfessor
- YAMASHIRO, SawakoAssociate Professor
- MIYAMOTO, AkitoshiAssistant Professor
Research outline
In the cell, molecules often change their behavior by chemical and mechanical stimuli in seconds. By observing individual single-molecules mediating signal- and mechano-transductions, our laboratory is committed to solve the complex system of life. We are also extending the application of our original multiplexed, high-density labeling super-resolution microscopy IRIS to elucidation of remodeling processes of body structures including the brain and nerve system. High resolution imaging is also applied to real-time monitoring of the action of target-based anti-cancer drugs.
Main themes
- Single-molecule imaging of mechanotransduction and its underlying signaling
- Elucidation of tissue remodeling process by multiplexed super-resolution microscopy IRIS
- Imaging-based elucidation of the mechanism of action of drugs for drug discovery
Keywords
- molecular mechanosensing
- retrograde actin flow and cytoplasmic convection
- actin turnover
- formin homology proteins
- allosteric effects of target-based drugs
- multiplexed super-resolution microscopy
Department of Animal Development and Physiology
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.
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Laboratory of Immunobiology
Member
- TAKAHARA, KazuhikoAssociate Professor
Research outline
We focus on functions of innate pathogen recognition receptors (PRRs) expressed on immune cells, the mechanism of eliminating pathogens and the negative action of pathogens to suppress host immunity to establish infection. In particular, we attempt to identify immunosuppressive factors of pathogens and develop substances that suppress excessive inflammatory responses such as sepsis as well as cytokine storm. In addition, by examining the cooperation between PRRs and hormone receptors, we would clarify the unprecedented outcome of the innate immune reactions. On the other hand, we are also interested in development and function of γδT cells, the first T cells in the body.
Main themes
- Functional analyses of PRRs on dendritic cells and macrophages, and subsequent responses.
- Identification of immunosuppressive factors of pathogens and their applications for excess immune responses, e.g., sepsis.
- Cross talk between PRRs and hormone receptors.
- Functional analyses of pathogen recognition receptors in disease models.
- Development and function of γδT cells.
Keywords
- Dendritic cells
- Macrophages
- Lectin
- Polysaccharides
- Immune suppression
- Sepsis
- γδT cells
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Laboratory of Molecular Cell Biology and Development
Member
- KITAJIMA, TomoyaVisiting Professor
- TAKASATO, MinoruVisiting Associate Professor
- OBATA, FumiakiVisiting Associate Professor
- KONAGAYA, YumiVisiting Associate Professor
- KONDO, TakefumiVisiting Associate Professor
Research outline
Kitajima lab
Meiosis in oocytes is prone to chromosome segregation errors and thus frequently produces aneuploid eggs. The aneuploidy of eggs is a leading cause of pregnancy loss and congenital diseases such as Down syndrome. Using mouse oocytes as a model, combined with live imaging techniques, micromanipulation, and genetic approaches, we aim to understand the molecular mechanism of meiotic chromosome segregation and the causes of chromosome segregation errors in oocytes.
Takasato Lab
What is the goal of regenerative medicine research using human pluripotent stem cells? We believe that one of the ultimate goals is the complete creation of any organ in vitro. To approach this goal, our laboratory aims to construct 3D organs at a higher level by the directed differentiation of human ES/iPS cells towards organoids. We also aim to contribute to pure developmental biology by elucidating the developmental mechanisms of meso- and endodermal organs.
Obata lab
Diet influences organismal healthspan by altering nutritional balance and gut microbiota, yet the molecular mechanisms are not fully understood. Our laboratory studies the functions of each nutrient and gut bacterial species that are dynamically altered in response to various dietary conditions. We aim to elucidate evolutionarily conserved “dietological” mechanisms that govern organismal homeostasis and healthspan by utilising Drosophila’s short lifecycle and genetics. We also study the molecular basis of feeding (blood feeding) or developmental origins of health and diseases (DOHaD) hypothesis.
Konagaya lab
Tissue homeostasis relies on constant tissue renewal, notably within the rapidly regenerating intestinal epithelium. Precise control of cell proliferation during differentiation is critical for maintaining tissue homeostasis, as its disruptions lead to atrophy or cancer. Our research focuses on elucidating how cell proliferation and differentiation are orchestrated in the intestinal epithelium. In particular, we aim to uncover the molecular mechanisms underlying the cell fate decision of intestinal epithelial stem cells by live imaging of mouse intestinal organoids, multiplexed tissue imaging, and quantitative analyses.
Kondo lab
Embryonic development is a dynamic and beautiful phenomenon that proceeds with remarkable precision. Our goal is to elucidate the principles that ensure the accuracy of the entire developmental process. We view development as an information network system consisting of multiple hierarchies of “genome”-“cell”-“tissue”, and study the feedback mechanisms between the layers by quantitatively measuring and analyzing the dynamics at each layer using techniques such as single cell genomics, imaging and large-scale data analysis.
Main themes
Kitajima lab
- Molecular mechanisms of meiotic chromosome segregation in mouse oocytes
- Live imaging of chromosome dynamics in oocytes
- Aging-associated deterioration of chromosome segregation in oocytes
Takasato lab
- Study to elucidate the mechanism of pluripotent stem cell fate determination
- Study to elucidate the connection between tissues and the division of roles between them
- Study to elucidate the mechanism of self-organization
- Study to elucidate vascularization and maturation of organs
Obata lab
- Elucidation of functions of each nutrient and gut bacterial species
- Elucidation of the mechanism by which early life environment alters homeostasis
- Elucidation of the amino acid regulation of healthspan
- Molecular basis of thermotolerance
- Molecular basis of feeding/blood feeding
Konagaya lab
- Investigation of the coordinated control of cell proliferation and differentiation in mouse intestinal epithelium
- Analysis of the role of mechanical sensing in stem cell maintenance in mouse intestinal epithelium
- Development of fluorescent reporters using machine learning algorithms for protein structure prediction
Kondo lab
- Elucidation of the rules governing how cells process the gene expression information to drive morphogenesis.
- Understanding the mechanism by which tissue morphological changes control gene expression and cell differentiation.
- Comprehensive analysis of cell differentiation dynamics in entire embryonic development.
- Development and application of single-cell and spatial genomics analysis techniques.
Keywords
- Oocyte（Kitajima lab）
- Chromosome segregation（Kitajima lab）
- Live imaging（Kitajima lab）
- Aging（Kitajima lab）
- Developmental Biology（Takasato lab）
- Regenerative Medicine（Takasato lab）
- Pluripotent Stem Cell（Takasato lab）
- Directed Differentiation（Takasato lab）
- Organoid（Takasato lab）
- Urinary Tract System（Takasato lab）
- Nutrient（Obata lab）
- Gut microbiota（Obata lab）
- Healthspan（Obata lab）
- Developmental environment（Obata lab）
- Feeding behaviour（Obata lab）
- Thermotolerance（Obata lab）
- Amino acid（Obata lab）
- Quantitative biology（Konagaya lab）
- Live-cell imaging（Konagaya lab）
- Intestinal organoids（Konagaya lab）
- Cell cycle（Konagaya lab）
- Cell signaling（Konagaya lab）
- Machine learning（Konagaya lab）
- Embryogenesis（Kondo lab）
- Single-cell genomics（Kondo lab）
- Epithelial morphogenesis（Kondo lab）
- Cell fate control（Kondo lab）
- Cell differentiation（Kondo lab）
- Genetics（Kondo lab）
- Imaging（Kondo lab）
Department of Signal Transductions
Cancer, autoimmune diseases, and life-style related diseases can be caused by genetic abnormalities and aberrant response mechanisms. We aim to reveal dysfunctional biological mechanisms of cell proliferation, cancer, and immunological, genetic diseases.
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Laboratory of Molecular Neurobiology
Member
- KIMURA, IkuoProfessor
- IKEDA, TakakoAssistant Professor
- TAKADA, HiromiAssistant Professor
- WATANABE, KeitaProgram-Specific Assistant Professor
Research outline
Our research aims at understanding the molecular mechanism of homeostasis maintaining, especially focuses on dietary/nutritional function and endocrine metabolism. Based on this research, we aim to provide valuable insight into the development of functional foods, supplements, and medicinal drugs.
Main themes
- Dietary signaling via nutrient-sensing receptors and metabolic syndrome
- Non-genomic effects via sex steroid hormone receptors and neurological disorders
Keywords
- Food & Nutrition
- Endocrinology & Metabolism
- G protein-coupled receptor
- Fatty acids
- Sex steroid hormone
- Obesity
- Gut microbes
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Laboratory of Genetics
Member
- IGAKI, TatsushiProfessor
- KANDA, HiroshiAssociate Professor
- ENOMOTO, MasatoAssistant Professor
- TANIGUCHI, KiichiroProgram-Specific Senior Lecturer
- NAGATA, RinaAssistant Professor
Research outline
Our research focuses on the molecular basis of cell-cell communications, particularly cell competition, cellular cooperation, and organ-organ interaction, that regulate tissue homeostasis, cancer, and aging. We take advantage of the powerful genetics of Drosophila.
Main themes
- Mechanism of cell competition
- Molecular basis of tumor progression and metastasis
- Genetic basis of tissue growth and homeostasis
- Mechanism of aging
Keywords
- cell competition
- cell-cell cooperation
- tumor progression
- aging
- inter-organ communication
- imaging
- Drosophila
Department of Functional Biology
Cell–cell adhesion is essential for the establishment of multicellular organisms. We purse the systemic regulation mechanisms of cell–cell adhesion and signal transduction. We aim to elucidate the mechanisms of tissue formation and the pathogenesis of various diseases caused by disruption of cell–cell adhesion. We also aim to establish the basis for drug discovery and development, and to establish new therapeutic strategies.
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Laboratory of Functional Biology
Member
- ODA, YukakoProfessor
- OGAWA, KeigoProgram-Specific Assistant Professor
Research outline
Our research aims to elucidate the regulation mechanisms of cell–cell adhesion in multicellular organisms. We will focus on physiologically active peptides that induce cell–cell adhesion to understand the construction, maintenance, and repair mechanisms of multicellular organisms. We will also work on the control of various diseases caused by disruption of cell–cell adhesion, such as inflammation, cancer, and aging, and on the development of drug discovery.
Main themes
- Induction and regulation of epithelial cell-cell adhesion
- Understanding of epithelial-immune interactions
- Control of invasive and metastatic cancers
- Elucidation of stress response in epithelial cells
- Understanding of individual aging starting from intestinal barrier function
Keywords
- epithelial cell
- cell–cell adhesion
- physiologically active peptide
- disease
Department of Biology Education and Heredity
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 Laboratory of Chromosome Function and Inheritance studies the mechanisms of meiosis using cell biological and genetic approaches. The department as a whole focuses on training internationally-minded scientists, developing English-based science education and communication at the highest levels.
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Laboratory of Science Communication
Member
- GUY, Adam TsudaAssociate Professor
- HEJNA, James AlanSpecially Assigned Professor
Research outline
Our laboratory engages in the development and implementation of new approaches to the internationalization of science education and communication. We are dedicated to training the next generation of scientists to communicate their knowledge and expertise not only to the international scientific community but locally to the citizens who ultimately support basic research.
Main themes
- Increasing the exposure of Japanese students to foreign peers. We are forging new partnerships with foreign universities to foster joint distance-learning courses, with active student participation in English.
- Establishing partnerships with foreign universities to encourage short-term reciprocal exchanges of graduate students for collaborative research.
- Expanding the opportunities for students to present their research in English to a broad audience.
Keywords
- Science communication
- English education
- Joint distance learning
- International student exchange
- Collaborative research
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Laboratory of Chromosome Function and Inheritance
Member
- CARLTON, PeterAssociate Professor
Research outline
Infertility is a very common problem in modern society, while the basic mechanisms ensuring meiosis, the specialized cell division that generates sperm and oocytes, are not understood well. By using diverse techniques (cutting-edge imaging technology, genetics, AI-based prediction analysis, genomic sequence analysis), we aim to uncover the molecular mechanisms executing complex cellular processes in meiosis. Our focus includes control of chromosome dynamics, DNA double strand breaks, homologous recombination, and cell cycle control during meiotic prophase. By understanding these basic mechanisms of meiosis, we aim to contribute to the understanding of infertility problems caused by defective oocyte or sperm production.
Main themes
- Understanding mechanisms of chromosome dynamics during meiosis
- Cell cycle regulation, DNA double strand break formation/repair/recombination regulations, Genome structure analysis
- Analysis of chromosome structures using high/super-resolution microscopy or live imaging
- AI-based protein structure/function analysis
- Genetics and molecular biology with genome-editing technology in the model organism C. elegans
Keywords
- Meiosis
- High/super resolution microscopy and live imaging
- Chromosome dynamics
- Genomic sequence analysis
- AI-based protein structure/function analysis
- Cell cycle, DNA double strand break, recombination regulation
- Genetics
Department of Systems Biology
We aim to understand living systems from cellular to animal individual levels focusing on developmental and regulatory mechanisms with cutting-edge research tools, such as molecular genetics, molecular visualization sensors, optogenetics, live imaging and mathematical modeling.
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Laboratory of Brain Development and Regeneration
Member
- IMAYOSHI, ItaruProfessor
- GUY, Adam TsudaAssociate Professor
- SAKAMOTO, MasayukiAssociate Professor
- SUZUKI, YusukeAssistant Professor
Research outline
Our laboratory aims at understanding the mechanisms of development and regeneration processes in the mammalian brain, and their functional outcomes on neural circuits, higher brain functions, and animal behaviors. We are focusing on the regulatory mechanism of cell growth, differentiation, and quiescence of neural stem cells. We are also 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 themes
- Neural development and regeneration
- Neural stem cell regulations
- Neurogenesis in the postnatal and adult brains
- Optical manipulations of cellular gene expressions
- Optics development for imaging and manipulations
Keywords
- Neural development
- Neural stem cells
- Neurogenesis
- Hippocampus
- Optogenetics
- Individuality
- Transcription factor
Department of Genome Biology
Genome and epigenome information are maintained by an intricate molecular system acting against exogenous and endogenous perturbations. We aim to study defects in these mechanisms that result in human disorders.
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Laboratory of Genome Maintenance
Member
- MATSUMOTO, TomohiroProfessor
- FURUYA, KanjiSenior Lecturer
Research outline
Attachment of the spindles to the kinetochores is one of the most important processes for equal segregation of chromosomes. The kinetochore, a key player of this process, can be found only at a fix position per chromosome. We are interested in the positioning of the kinetochore and study the underlying mechanisms. The spindle checkpoint delays the onset of anaphase until the spindles are attached properly to the kinetochores. We study molecular events in mitosis that are necessary to satisfy this checkpoint.
Main themes
- Chromosome segregation
- Kinetochore
- Spindle checkpoint
Keywords
- Kinetochore/centromere
- Chromosome
- Spindle checkpoint
- Fission yeast
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Laboratory of Genome Stress Response
Member
- YASUHARA, TakaakiProfessor
- MU, AnfengAssistant Professor
- IGARASHI, TaichiProfessor
Research outline
Cells have sophisticated mechanisms to respond to cellular stresses from external stressors, thereby maintaining homeostasis. Our laboratory aims to elucidate the molecular mechanisms of cellular stress responses, especially the ones caused by genotoxic stresses, and the fundamental mechanisms underlying many types of diseases caused by inefficient stress responses. We hope to contribute to solving various problems in this age of long-life expectancy, such as cancer and infertility in reproductive medicine.
Main themes
- The molecular mechanisms of cellular stress response
- Genomic instability induced by abnormal transcription-associated DNA repair pathways
- The stress responses mediated by phase separation of RNA-binding proteins
- Disease-related genome abnormalities caused by aging
- The fundamental mechanism of diseases, such as cancer and chromosomal anomaly
Keywords
- Cellular stress response
- DNA damage repair
- Genomic instability
- Transcription
- Phase separation
- Cancer
- Aging/Senescence
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Laboratory of Cancer cell Biology
Member
- HARADA, HiroshiProfessor
- NAM, Jin-MinAssociate Professor
- KOBAYASHI, MinoruProgram-Specific Assistant Professor
Research outline
Tumor microenvironment is highly heterogeneous and dynamic. Hypoxic, acidic, and nutrients-depleted microenvironments exist in solid tumors and induce malignant phenotype and chemo/radioresistance of cancer cells. We aim to elucidate molecular mechanisms responsible for cellular adaptive responses to the tumor-specific microenvironment and malignant progression of cancer cells in order to understand the nature of cancers and lead to the development of novel strategies for cancer therapy.
Main themes
- Cellular adaptive responses to tumor microenvironment, e.g. hypoxia
- Molecular mechanisms underlying malignant progression and chemo/radioresistance of cancer cells
- Molecular mechanisms underlying the onset of hypoxia-associated diseases
Keywords
- cancer
- tumor microenvironment
- hypoxia
- HIF-1
- molecular mechanism
- malignant progression
- therapy resistance
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Laboratory of Chromatin Regulatory Network
Member
- IKURA, TsuyoshiAssociate Professor
Research outline
Recent advances in computational technologies such as mathematical modeling and machine learning for constitutive analysis of biological functions, in addition to conventional element-reduction approaches such as genetics and molecular biology, have enabled us to understand biological systems in a more integrated manner. In our Lab, we aim to analyze the diversity of aging and cancer signals induced by various external stresses such as genome damage stress, oncogenic stress or nutrient starvation, focusing on chromatin dynamics, using bioimaging analysis, single cell analysis, and machine learning, and to uncover universal rules behind such diversity, thereby constructing a novel biological concept for stress responses.
Main themes
- Chromatin dynamics in DNA damage response
- Epigenome analysis in cellular senescence
- The role of chromatin regulation in energy metabolism
Keywords
- chromatin
- ageing signal
- diversity in cellular responses
Department of Mammalian Regulatory Network
Laboratories consisting of this Department study multi-dimensional networks of life signals that contribute to the integrity of higher organisms. Studies also include those utilizing viruses, animal models, and biomaterials, serving to establish basic principles in life science.
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Laboratory of RNA Viruses
Member
- TOMONAGA, KeizoProfessor
- MAKINO, AkikoAssociate Professor
- MATSUGO, HiromichiAssistant Professor
Research outline
We perform virological studies on human pathogenic RNA viruses. Research on evolutionary analysis of endogenous RNA viruses and development of a novel viral vector for gene and cellular therapy are also conducted.
Main themes
- Elucidation of the mechanism of replication and pathogeneses of bornaviruses
- Analysis on virus-host co-evolution using endogenous bornaviruses
- Development of a novel RNA viral vectors for gene and cellular therapy
- Understanding the replication and pathogenesis of SARS-CoV-2
Keywords
- Virus
- Infection
- Evolution
- Viral vector
- Gene and cellular therapy
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Laboratory of Cell Division and Differentiation
Member
- TOYOSHIMA, FumikoProfessor
- VANDENBON, AlexisAssociate Professor
Research outline
This group aims to clarify the mechanism of organ remodeling during life stages. In particular, we focus on pregnancy-, obesity-, and aging-associated organ remodeling from the perspectives of tissue stem cell dynamics, multicellular/multiorgan network, and mechanobiology. We aim to apply the physiological organ remodeling to regenerative and anti-aging medicine. We also study basic research on maternal-fetal medicine. Development of gene-targeting technology and gene therapy methodology support the projects.
Main themes
- Physiological organ remodeling during the life course
- Relevance of maternal organ remodeling in embryonic development
- Application of physiological organ remodeling to regenerative and anti-aging medicine
- Gene targeting technology and Gene therapy
- Bioinformatics methodology for the analysis of large biological datasets
Keywords
- physiological organ remodeling
- pregnancy, aging, obesity
- anti-aging
- regenerative medicine
- maternal-fetal medicine
- gene targeting technology
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Laboratory of Cellular and Molecular Biomechanics
Member
- ADACHI, TaijiProfessor
- MAKI, KoichiroAssistant Professor
Research outline
The Laboratory of Cellular and Molecular Biomechanics aims to clarify the self-organized regulatory mechanisms of diverse biological phenomena through interdisciplinary approaches encompassing mechanics, life science, and medical science. Our research topics cover developmental processes (cell differentiation, morphogenesis, and growth) as well as tissue/organ remodeling and regeneration which underlie functional adaptation to the environment. A major focus of our research is to understand how well-organized dynamics of living systems emerges from complex molecular and cellular interactions. To this end, we are integrating biomechanics and mechanobiology approaches to highlight the roles of “adaptation to mechanical environment” and “hierarchy of structure and function” in the living organisms using mathematical modeling, simulation and experiments.
Main themes
- Functional adaptation mechanisms of bone to mechanical environment
- Continuum mechanics-based modeling for multi-layered brain formation
- Mechano-biochemical coupling mechanisms in osteocytic mechanotransduction
- In silico and in vitro modeling of multicelluar tissue morphogenesis
- DNA transcription mechanisms regulated by nano-scale chromatin dynamics
Keywords
- Bone remodeling
- Tissue morphogenesis
- Cellular mechanosensing
- Molecular dynamics
- Biomechanics
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Laboratory of Mechanosensory Physiology
Member
- NONOMURA, KeikoProfessor
Research outline
Welcome to Laboratory of Mechanosensory Physiology!
We are studying physiological roles of mechanosensation mediated by PIEZO mechanically activated channel (awarded Nobel prize 2021) in tissues/cells including sensory neurons, brain tissue and lymphatic vessels.
Main themes
- Elucidating physiological roles of PIEZO expressing mechanosensory neurons innervating lung and/or other organs. We have been specifically investigating their contribution to breathing pattern of newborns, as starting breathing immediately after birth is critical for survival of mammalian newborns and its underlying mechanism is still mostly elusive.
- Studying the contribution of PIEZO mediated mechanisensation in the brain, focusing on both developmental process and brain function.
- Studying the mechanism in which PIEZO1 mediated mechanosensation contributes to venous/lymphatic valve formation, utilizing KO or reporter mouse lines and cultured endothelial cells.
Keywords
- Mechanically activated channel PIEZO
- Mechanobiology
- Neuroscience
- Sensory neuron
- Brain development
- Organ function
- Lymphatic vessel/Lymph node
Department of Advanced Imaging(Industry-Academia Collaboration Course)
We will understand the principle of biological functions by measuring and manipulating dynamics of genes and molecules multidimensionally with cutting-edge imaging, optical control technologies, and optical probes.
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Laboratory of Spatiotemporal Optical Control
Member
- ISOBE, KeisukeProgram-Specific Professor
Research outline
To make invisible biological phenomena that could not be visualized before due to lack of performance in terms of field of view, depth, and spatio-temporal resolution visible, we will develop lasers optimized for observation of biological tissues and novel laser imaging techniques. We also develop optical manipulation techniques to precisely control the spatio-temporal distribution of laser light in tissues in order to control biological phenomena with light.
Main themes
- Development of femtosecond lasers for ultra-deep imaging and their applications
- Development of wide-field deep imaging techniques using spatiotemporal control of laser pulses and their applications
- Development of 4-dimensional optical control techniques using multiphoton patterned illumination and their applications
Keywords
- femtosecond lasers
- multiphoton microscopy
- four-dimensional optical control
- deep imaging
- ultra-wide-field microscopy
- optogenetics