The National Institute for Basic Biology
Department of Basic Biology, School of Life Science, SOKENDAI (the Graduate University for Advanced Studies)

CELL BIOLOGY

1. 

   DIVISION OF CELLULAR DYNAMICS

   Name：UEDA, Takashi
   Contact：tueda@nibb.ac.jp
   

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   Research Summary

   Membrane trafficking among single membrane-bounded organelles plays pivotal roles in various cell activities in eukaryotic cells, which are also critical in multiple layers of higher-ordered functions of multicellular organisms. Although the basic framework of membrane trafficking is well conserved among eukaryotic lineages, recent studies have also suggested that each lineage has acquired a unique membrane trafficking system during evolution. Our research focuses on mechanisms of diversification of membrane trafficking. We are especially interested in how membrane trafficking pathways have been diversified during land plant evolution, which should be also associated with neofunctionalization and/or novel acquisition of organelles in plants. For insights into these points, we are currently conducting comparative analyses between Arabidopsis thaliana and the liverwort, Marchantia polymorpha. Systematic analyses of machinery components of membrane trafficking such as RAB GTPases and SNARE proteins are revealing unique evolutionary paths, which angiosperms and bryophytes followed during evolution.

2. 

   DIVISION OF QUANTITATIVE BIOLOGY

   Name：AOKI, Kazuhiro
   Contact：k-aoki@nibb.ac.jp
   

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   Research Summary

   A living cell acts as an input-output (I/O) unit, which senses the environment and its internal states, processes information, and responds appropriately to adapt to changes. Our laboratory is interested in the system of intracellular signaling networks. Especially, we focus on the ERK MAP kinase pathway, which is related to cell proliferation, differentiation, and tumorigenesis in mammalian cells. We aim to quantitatively decipher the mechanisms of how signaling dynamics encode cellular decision-making. For this purpose, we are developing tools to visualize, quantify, and manipulate intracellular signaling with fluorescence imaging and optogenetic techniques.

3. 

   DIVISION OF CHROMATIN REGULATION

   Name：Nakayama, Jun-ichi
   Contact：jnakayam@nibb.ac.jp
   

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   Research Summary

   Multicellular organisms are made up of diverse populations of many different types of cells, each of which contains an identical set of genetic information coded in its DNA. Cell differentiation and the process of development itself depend on the ability of individual cells to maintain the expression of different genes, and for their progeny to do so through multiple cycles of cell division. In recent years, we have begun to understand that the maintenance of specific patterns of gene expression does not rely on the DNA sequence, but rather takes place in a heritable, “epigenetic” manner. DNA methylation, chromatin modifications, and RNA silencing are some of the best known epigenetic phenomena. Our division investigates how modifications to the structure and configuration of chromatin (complexes of nuclear DNA and proteins) contribute to epigenetic gene regulation by studying events at the molecular scale in the model organism, fission yeast, ciliate Tetrahymena, and in cultured mammalian cells.

4. 

   LABORATORY OF STEM CELL BIOLOGY

   Name：TSUBOUCHI, Tomomi
   Contact：ttsubo@nibb.ac.jp
   

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   Research Summary

   DNA is constantly damaged from both endogenous and exogenous sources. One of the most important challenges for all living organisms is to prevent genome instability that can lead to malfunction of a cell. Our group is interested in the strategies through which cells protect themselves from alterations in the genome. To date, much information has been gained from various model organisms and tissue culture cells, and we are beginning to learn that the choice of genome-maintenance strategies taken by a cell depends on the cell type, cell cycle- and developmental stages. In the laboratory of stem cell biology, we are currently focusing our attention on the genome maintenance mechanisms of embryonic stem cells, and their roles during differentiation and reprogramming processes.

DEVELOPMENTAL BIOLOGY

1. 

   DIVISION OF EMBRYOLOGY

   Name：FUJIMORI, Toshihiko
   Contact：E-mail: fujimori@nibb.ac.jp
   

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   Research Summary

   The aim of our research is to understand the events underlying early mammalian development during the period from the pre-implantation to establishment of the body axes. An understanding of early events during embryogenesis in mammals, as compared to other animals, has been relatively delayed. This is mainly due to the difficulties in approaching the developing embryos in the uterus of the mother. The other characteristic of mammalian embryos is their highly regulative potential. The pattern of cell division and allocation of cells within an embryo during the early stages vary between embryos. The timing of the earliest specification events that control the future body axes is still under discussion. Functional proteins or other cellular components have not been found that localize asymmetrically in the fertilized egg. We want to provide basic and fundamental information about the specification of embryonic axes, behaviors of cells and the regulation of body shape in early mammalian development.

EVOLUTIONARY BIOLOGY AND BIODIVERSITY

1. 

   DIVISION OF EVOLUTIONARY BIOLOGY

   Name：HASEBE, Mitsuyasu
   Contact：E-mail: mhasebe@nibb.ac.jp
   

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   Research Summary

   We aim to discover key genetic changes that resulted in the evolution of influential novel traits in land plants. For this purpose, we select new key-stone model organisms, sequence the genomes, establish genome editing techniques, and investigate mechanistic novelty at both cellular and organismal levels. We focus on the following questions: (1) Evolution of body plan in land plants (2) Evolution of carnivorous plants and plant movement (3) Molecular mechanisms of reprogramming from differentiated cells to stem cells Please visit our web page for more details. http://www.nibb.ac.jp/evodevo/research_00_EN.html Students who are interested in entering our graduate school for a 5 year PhD course are welcome to apply to the internship program.

2. 

   LABORATORY OF EVOLUTIONARY GENOMICS

   Name：SHIGENOBU, Shuji
   Contact：E-mail : shige@nibb.ac.jp
   

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   Research Summary

   The term "symbiogenomics” (= symbiosis + genomics) was coined to describe the use of “omic” approaches for defining symbiosis in molecular terms, aiming to understand the network of biological interactions at molecular and genetic levels. We pioneered the symbiogenomics of host-microbe interface in symbioses observed in insects. We mainly study the symbiosis between the pea aphid and the bacterial symbiont Buchnera as a model. Aphid species bear intracellular symbiotic bacteria in the cytoplasm of bacteriocytes, specialized cells for harboring the bacteria. The mutualism is so obligate that neither can reproduce independently. We take advantage of state-of-the-art genomics, such as next-generation sequencing technologies, which has allowed us to find key molecules for symbioses including a transcription factor expressed preferentially in the bacteryocyes and a novel secretion peptide. References: Shigenobu, S., and Wilson, A.C.C. (2011). Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont. Cell. Mol. Life Sci. 68, 1297–1309.

3. 

   LABORATORY OF BIORESOURCES

   Name：NARUSE, Kiyoshi
   Contact：naruse@nibb.ac.jp
   

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   Research Summary

   Medaka is a small egg-laying fresh water fish found in brooks and rice paddies in Eastern Asia. This species has a long history as an experimental animal, especially in Japan, and many inbred lines and mutants have been established so far. Using these various medaka resources, we are currently studying the evolution of the sex determination system, the molecular/neural bases of social behaviors and pigment cell development. In addition to these activities, our laboratory is managing medaka resource center as the National BioResource Project medaka supported by AMED, Japan. We can provide several medaka resources and the genome editing platform for establishing KO medaka to medaka community.

ENVIRONMENTAL BIOLOGY

1. 

   DIVISION OF ENVIRONMENTAL PHOTOBIOLOGY

   Name：MINAGAWA, Jun
   Contact：E-mail: minagawa@nibb.ac.jp
   

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   Research Summary

   Plants and algae have a large capacity of acclimating themselves to changing environments. We are interested in these acclimation processes, in particular, how efficiently yet safely they harness sunlight for photosynthesis under the changing light environment. Using a model green alga, we are studying the molecular mechanisms underlying the photoacclimation of the photosynthetic machinery. We are also applying the knowledge obtained in studies of a model green alga to various phytoplankton including diatoms in subarctic oceans, prasinophytes in subtropical oceans, and Symbiodinium in corals in tropical oceans, to explore how these environmentally important photosynthetic organisms thrive in their ecological niche.

2. 

   DIVISION OF PLANT ENVIRONMENTAL RESPONSES

   Name：MORITA, Miyo T.
   Contact：E-mail: mimorita@nibb.ac.jp
   

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   Research Summary

   Plant organs are capable of sensing various vectorial stimuli, such as light, gravity, touch, and humidity. Plants then reorient their growth direction so as to be in a suitable position to survive and acclimate to their environment. These type of responses of plant organs to directional stimuli are referred to as tropisms. We are conducting research with the greatest focus on the molecular mechanism of gravitropism using Arabidopsis thaliana. In gravity sensing cells, plastids accumulating starch at a high-density (amyloplasts) relocate toward the direction of gravity. Amyloplast relocation serves as a physical signal trigger for biochemical signal transduction, which in turn leads to the regulation of polar auxin transport necessary for change in the direction that a given plant is growing. We are currently investigating how the gravity sensing cell detect the position of amyloplast and how the positional signal is linked to the regulation of polar auxin transport. Gravitropism also affects overall architecture of plants by controlling the growth angles of lateral roots and branches. We also investigate the mechanism underlying the plant architecture controlled by gravity.

THEORETICAL BIOLOGY

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   LABORATORY OF GENOME INFORMATICS

   Name：UCHIYAMA, Ikuo
   Contact：E-mail: uchiyama@nibb.ac.jp
   

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   Research Summary

   The accumulation of biological data has recently been accelerated by various high-throughput “omics” technologies such as genomics, transcriptomics, proteomics, and so on. The field of genome informatics is aimed at utilizing this data, or finding some principles behind the data, for understanding complex living systems by integrating the data with current biological knowledge using various computational techniques. In this laboratory we focus on developing computational methods and tools for comparative genome analysis, which is a useful approach for finding functional or evolutionary clues to interpreting the genomic information of various species. The current focus of our research is on the comparative analysis of microbial genomes, the number of which has been increasing rapidly. Extracting useful information from such a growing number of genomes is a major challenge in genomics research. Interestingly, many of the completed genomic sequences are closely related to each other. We are now trying to develop methods and tools to conduct comparative analyses not only of distantly related genomes but also of closely related genomes, since we can extract different types of information about biological functions and evolutionary processes from comparisons of genomes at different evolutionary distances.

IMAGING SCIENCE

1. 

   LABORATORY FOR SPATIOTEMPORAL REGULATIONS

   Name：NONAKA, Shigenori
   Contact：E-mail: snonaka@nibb.ac.jp
   

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   Research Summary

   In spite of superficially bilateral symmetry, our bodies are highly asymmetric along the left-right (L-R) axis, for example in the placement of internal organs. Our main aim is to clarify the mechanism by which mammalian embryos generate and establish the L-R asymmetry. Also, we are working for the application of light-sheet microscopy, which enables deep and long-term imaging of living specimens, such as gastrulating mouse embryos.

2. 

   LABORATORY OF BIOTHERMOLOGY

   Name：KAMEI, Yasuhiro
   Contact：E-mail : ykamei@nibb.ac.jp
   

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   Research Summary

   Our group is developing gene-expression manipulation methods using ‘light’. Studies of cell fates, cell-cell interaction, and analysis of non-cell autonomous phenomena require an experimental system with fine control of gene expression. To achieve timing-controlled gene expression at the single-cell level we have developed a microscope, IR laser evoked gene operator (IR-LEGO), using the heat shock stress response system (Ref.). This system can be applied to many species, such as C. elegans, zebrafish, medaka and Arabidopsis. Currently we are mainly studying single cell gene knock-out systems using the cre-loxP recombination system applied to medaka mutants. Ref.: Kamei Y., Suzuki M., Watanabe K., et al. (2009) Infrared laser-mediated gene induction in targeted single cells in vivo. Nature Methods 6, 79-81.