Systems Biology

Japanese

Microbial Interaction

Daisuke Watanabe

Assoc.Prof. Watanabe
How do microorganisms behave and interact to build complex ecosystems? We study yeasts and other unicellular organisms familiar to humans at the molecular, metabolic, cellular, and ecological levels to deepen understanding of diversity in the microscopic world. Our achievement will also contribute to modern biotechnology in food and health science

Topics

  1. Microbial ecology in food fermentation
  2. Enforcement/enlargement of the endoplasmic reticulum
  3. TOR (Target of Rapamycin) signaling pathway
Various interactions in microbial ecosystem.
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Environmental Microbiology

Shosuke Yoshida

Prof. YOSHIDA Shosuke
We aim to elucidate the mysteries of microorganisms with unique functions, their enzymes and metabolism, and evolution. We hope to use the strategies that life has created as guideposts for the development of technologies that contribute to the sustainable development goals (SDGs).

Topics

  1. Elucidation of a bacterial PET metabolism
  2. Fermentation of plastics
  3. Visualizing microbiology
PET degradation by I. sakaiensis (A, B) A scanning electron microscopic (SEM) image of I. sakaiensis cells grown on PET film. (C)The degraded PET film surface after washing out the adherent cells. (D) SEM image of the PET film surface treated with purified PETase proteins. Prominent pitting developed on the film surface.
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Structural Life Science

Tomoya Tsukazaki

Prof. Tsukazaki
In the cells, various proteins are involved in a variety of fundamental biological phenomena. To unveil such mechanisms coupled with dynamic interactions and structural changes of biomolecules, including proteins, we conduct basic research through structural biological analyses in combination with other newly developed methods.

Topics

  1. Transportation across cell membranes and protein biogenesis.
  2. Molecular function and dynamics of proteins
  3. X-ray crystallography and cryo-electron microscopy
  4. PiXie (pulse-chase and in vivo photo-cross-linking experiment)
fig
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Gene Regulation Research

Yasumasa Bessho

Prof. Bessho
Using mice and zebrafish as model systems, we will clarify the principles of development and growth. We use not only experimental biology but also information science and nanotechnology in a concerted effort to tackle the mysteries of life.

Topics

  1. Research for somitogenesis in vertebrates as a model system for the biological clock
Transcription factor Hes7, serving as a molecular clock, is specifically expressed in the primordium of somite.
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Systems Neurobiology and Medicine

Naoyuki Inagaki

Prof. Inagaki
We will clarify the mechanism of neural circuit formation and cell migration. The start is not difficult. First, you will acquire the basics of biochemistry and molecular biology, and then you can learn various techniques according to your interests and projects. You will also acquire knowledge and background in basic medicine through daily research and will learn to handle rats, mice, and cultured cells.

Topics

  1. Axon/dendrite formation and neuronal polarization
  2. Mechanical forces for axon guidance and cell migration
  3. Actin waves: a new mechanism for cellular protein transport
  4. Research in medicine: brain diseases and cancer metastasis
Shootin1a (red) is a key molecule involved in axon formation and axon guidance.
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Bioengineering

Ko Kato

Prof. KATO ko
With the aim of contributing to society through biotechnology, we are developing fundamental technologies for the efficient production of biopharmaceuticals and other useful substances in plants.

Topics

  1. Isolation and improvement of elements involved in high expression of transgene
  2. Elucidation of the mechanisms of phenotypic control and adaptive evolution by gene expressions
  3. Elucidation of the environmental adaptation mechanism of plants through gene expression
Plant biotechnology
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Neural Regeneration and Brain Repair

Taito Matsuda

Assoc.Prof. Matsuda
In addition to the direct programming method to convert non-neuronal cells into neurons, human brain organoids, humanized mouse models, and single-cell multi-omics analysis will be utilized to achieve neural regeneration and brain repair under disease conditions.

Topics

  1. Reprogramming Human Somatic Cells into Neurons
  2. Application to Neurological Disease Treatment
  3. Development and Application of Novel Cell Reprogramming Technologies
Conversion to Neurons in the Brain : After a stroke, expressing the transcription factor NeuroD1 in microglia located in the damaged area induces their conversion into neurons.
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Data-driven Biology

Yuichi Sakumura

Prof. Sakumura
We aim to derive the laws between biological functions and molecules through mathematical analysis of experimental data. We also design relational equations that represent biological functions according to the obtained laws and physical conditions. I enjoy this kind of “design within constraints,” and at NAIST, you can study different fields. It can be a little difficult and tiring, but our motto is to enjoy it to the fullest.

Topics

  1. Systems biology on cell morphogenesis and migration
  2. Systems biology on tissue formation
  3. Application of machine learning and control theory to biological data
Examples of system consisting of membrane potential and molecules, and system consisting of neurite length, mechanical force, and molecules. Signal transduction between various quantities are derived from experimental data. System can be reconstructed by integrating these signal transductions.
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