Laboratories

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.

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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.

  • 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
  • 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
  • Laboratory of Cell Cycle Regulation

    Member

    • AOKI, KazuhiroProfessor
    • NAKAOKA, HidenoriAssistant 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.

  • Laboratory of Cell Recognition and Pattern Formation

    Member

    • UEMURA, TadashiProfessor
    • USUI, TadaoSenior Lecturer
    • HATTORI, YukakoAssistant Professor
    • HARUMOTO, ToshiyukiProgram-Specific Assistant 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
  • 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.

  • Laboratory of Plant Molecular Biology

    Member

    • KOHCHI, TakayukiProfessor
    • YASUI, YukikoAssociate Professor
    • YOSHITAKE, YosihiroAssistant 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
  • Laboratory of Molecular and Cellular Biology of Totipotency

    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.

  • Laboratory of Biosignals and Response

    Member

    • NAGAO, MasayaProfessor
    • KAMBE, TaihoAssociate Professor
    • NISHINO, KatsutoshiAssistant Professor
    • NISHITO, YukinaProgram-Specific Assistant 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
  • Laboratory of Applied Molecular Microbiology

    Member

    • YAMANO, TakashiAssociate Professor
    • TSUJI, YoshinoriAssistant 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
  • 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 and study of regulatory mechanisms of development in response to environmental signals.

  • 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
  • Laboratory of Ecosystems and Coevolution

    Member

    • TOJU, HirokazuProfessor

    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
  • 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.

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

  • 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

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.

  • 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.

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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.

  • Laboratory of Single-Molecule Cell Biology

    Member

    • WATANABE, NaokiProfessor
    • YAMASHIRO, SawakoSenior Lecturer
    • 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.

  • Laboratory of Molecular and Cellular Biology

    Member

    • SAKAMAKI, KazuhiroProfessor

    Research outline

    Apoptosis, or programmed cell death, plays an important role in many biological processes, including embryogenesis, maintenance of tissue homeostasis, and elimination of improper cells such as unfunctional or harmful cells in both animals and plants. Our main research project is to understand the molecular and cellular mechanisms of apoptotic cell death in vitro and in vivo, using cultured cells, medaka, Xenopus, and mouse as model systems. We also investigate to develop new methods and techniques for imaging and simulating of such a vital phenomenon. In conjunction with these studies, we have been challenging to pursue the biological significance of cell death.

    Main themes

    • Elucidation of the biological significance of apoptotic cell death by molecular evolutionary analyses
    • Elucidation of the cell death signal transduction mechanism by visualization with biosensors and computer simulation
    • Elucidation of the physiological role and pathological pathogenic mechanism of cell death in living organisms using model animals

    Keywords

    • cell death
    • apoptosis
    • bioinformatics
    • optogenetics
  • 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
  • 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.

    • Laboratory of Molecular Neurobiology

      Member

      • KIMURA, IkuoProfessor
      • OHUE, RyujiAssistant Professor
      • IKEDA, TakakoAssistant Professor
      • WATANABE, KeitaProgram-Specific Assistant Professor
      • TAKADA, HiromiProfessor

      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
    • Laboratory of Genetics

      Member

      • IGAKI, TatsushiProfessor
      • KANDA, HiroshiAssociate Professor
      • ENOMOTO, MasatoAssistant Professor
      • TANIGUCHI, KiichiroProgram-Specific Senior Lecturer
      • NAGATA, RinaProgram-Specific Assistant 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

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

    • Laboratory of Functional Biology

      Member

      • KAKIZUKA, AkiraProfessor
      • IMAMURA, HiromiAssociate Professor
      • KOIKE, MasaakiAssistant Professor

      Research outline

      In our laboratory, using animal models of human diseases, such as neurodegenerations, cancers, and obesity-related diseases, and using metabolite imaging techniques, we aim to elucidate molecular bases of such diseases and develop new therapeutic agents or strategies to cure or prevent them.

      Main themes

      In our laboratory, the following three human diseases are taken up as the research of the higher order control system in the organism, and how the organism control system is broken in these diseases is studied.

      1. Researches aiming to understand the molecular mechanisms that disrupt the survival and maintenance of function of nerve cells in neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, as well as to prevent or cure the neurodegenerative diseases
      2. Researches aiming to clarify the mechanism of cell death that breaks down in cancer cells, and to establish a new treatment strategy that causes cell death specifically in cancer cells by repairing the breakdown.
      3. Researches aiming to clarify the regulation mechanism of energy and lipid metabolism in vivo which is collapsed by obesity and diabetes from the viewpoint of the action of the nuclear receptor.

      Keywords

      • drug development
      • neurodegenerative diseases
      • cancers
      • obesity and diabetes
      • energy metabolism
      • VCP
      • ATP

    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.

    • 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
    • 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

    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 are built 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.

    • Laboratory of Bioimaging and Cell Signaling

      Member

      • MATSUDA, MichiyukiProfessor
      • YUKINAGA, HirokoAssistant Professor

      Research outline

      We challenge to elucidate intra- and inter-cellular signal transduction of normal and pathological tissues by using biosensors based on fluorescent proteins, state-of-the-art microscopy, and techniques of cell biology, biochemistry, and molecular biology. We use mouse, organoids derived from mice and humans, as well as various tissue culture cells to study the following three research areas: Anti-cancer drug resistance in pancreatic cancer, regulation of glia activity, and quiescence of neural stem cells. We are in charge of a fluorescence microscopy facility, where multi-photon microscopes, confocal microscopes, and bioimaging software such as MetaMorph, Imaris, and Volocity, are available.

      Main themes

      • Intra- and inter-cellular signal transduction in live cells and mice.
      • Live imaging of pancreatic cancer.
      • Live imaging of glia.
      • Proteostatic regulation of neural stem cells.
      • Lysosomal regulation of quiescence.

      Keywords

      • fluorescent protein
      • multiphoton microscopy
      • signal transduction
      • neural stem cells
      • lysosomes
      • quiescence regulation
    • Laboratory of Theoretical Biology

      Member

      • HONDA, NaokiSpecially Assigned Professor

      Research outline

      To understand the mechanisms behind dynamic and complex biological phenomena, we are combining mathematical modeling and machine learning for decoding the governing rules or equations that govern biological system.

      Main themes

      • Inference of axon wiring rules from neural connectome data
      • Reconstruction of spatial transcriptome from one-cell RNA-seq data
      • Identification of governing equations from multicellular live imaging data
      • Data-driven modeling for early detection of neurodegenerative diseases
      • Deciphering behavioral strategies and mental fluctuations from behavioral data
      • Mathematical modeling of immune system/stem cell homeostasis/morphodynamics

      Keywords

      • Data-driven biology
      • Data Science
      • Differential Equations
      • Stochastic Processes
      • Bayesian statistics
      • Deep Learning
    • 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.

    • 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
    • Laboratory of Genome Stress Response

      Member

      • YASUHARA, TakaakiProfessor
      • MU, AnfengAssistant Professor

      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
    • 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
    • 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.

    • 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
    • Laboratory of Cell Division and Differentiation

      Member

      • TOYOSHIMA, FumikoProfessor
      • VANDENBON, AlexisAssociate Professor
      • ISHIBASHI, RikiAssistant Professor
      • KOBAYASHI, YoshihikoAssistant 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
    • 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

    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.

    • 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