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Dept. of Biological Sciences

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Research Theme

Laboratory of Biomolecular Function Group

Research area

  1. Structural and Functional Whole-Cell Study of an Extremely Thermophilic Model Organism.
  2. DNA Repair Systems.
  3. Protein Engineering.

1) A Whole-Cell Study of a Model Organism: It is supposed that the minimum gene set essential for a free-living organism is about 1,500, which comprise of genes that are common to almost all organisms including Homo sapiens. We selected an extreme thermophile, Thermus thermophilus HB8, to understand the mechanisms of all the biological phenomena occurring in it by investigating the components’ molecular function at the atomic level on the basis of their three-dimensional structures. This “Structural and Functional Whole-Cell Study” represents the first step toward the “atomic-resolution biology” of the 21st century (http://www.thermus.org).

2) DNA Repair Systems: Among the proteins from T. thermophilus HB8, we are particularly interested in the DNA repair systems, which are known to interact with DNA replication and transcription systems and are common to many organisms including Homo sapiens. About forty DNA repair enzymes from T. thermophilus HB8 have been studied by biophysical and biochemical methods.

3) Protein Engineering: The reaction mechanisms have been studied by biophysical methods. New enzymes were created by changing the substrate specificity and thermostability.

Members

Seiki KURAMITSU (Professor) kuramitu@bio.sci.osaka-u.ac.jp
Ryoji MASUI (Associate Professor) rmasui@bio.sci.osaka-u.ac.jp
Noriko NAKAGAWA (Assistant Professor) naka5@bio.sci.osaka-u.ac.jp

Contact

TEL:06-6850-5433 FAX:06-6850-5442
e-mail: kuramitu@bio.sci.osaka-u.ac.jp
Home Page: http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/kuramitu/

Laboratory of Structural Biology Group

Research area

  1. Functional mechanisms of proteins/complexes based on their three-dimensional structures.
    1. Structures and enzymatic reaction mechanisms of heme oxygenase and ferredoxin-dependent bilin reductases.
    2. Structure and assembly of tobacco necrosis virus.
    3. Structures and reaction mechanisms of the proteins involved in iron-sulfur cluster biosynthesis.
  2. Biogenesis of the iron-sulfur clusters and maturation of iron-sulfur proteins: genetic and structural biological studies of ISC and SUF machineries.
  3. Molecular mechanisms of energy conversion systems and biosynthetic pathways of pigments in photosynthetic green sulfur bacteria and heliobacteria.

Each protein/complex plays the specific role in the living systems. Focusing on several biologically important systems, we study the three-dimensional structure, function, and biosynthesis of the proteins/complexes using X-ray crystallography, spectroscopy, biochemistry, and molecular genetics.

Members

Keiichi FUKUYAMA (Professor) fukuyama@bio.sci.osaka-u.ac.jp
Yasuhiro TAKAHASHI (Associate Professor) ytaka@bio.sci.osaka-u.ac.jp
Hirozo OHOKA (Associate Professor) ohoka@bio.sci.osaka-u.ac.jp

Home Page

http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/fukuyama/

Laboratory of Molecular Genetics

Research Interests

  1. Molecular mechanisms of initiation of eukaryotic DNA replication.
  2. Molecular mechanism of recovery from replication-fork arrest.
  3. Molecular mechanism of chromosome cohesion.

Genetic information should be correctly inherited from cell to cell, generation to generation. DNA replication is tightly regulated to duplicate the genome exactly once in a cell cycle. In addition, when replication fork is stalled by shortage of nucleotides or at the damaged sites, various reactions such as checkpoint regulation, DNA repair and recombination are essential to maintain and recover replication fork. Our laboratory aims to elucidate these genetic mechanisms at a molecular level.

Members


Hisao MASUKATA (Professor), Takuro NAKAGAWA (Assistant Professor), Tatsuro TAKAHASHI (Assistant Professor)

Contact

Tel. 06-6850-5432 Fax. 06-6850-5440
e-mail:masukata@bio.sci.osaka-u.ac.jp
Home Page:http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/masukata/

Laboratory of Synaptic Plasticity

Research Areas

  1. Long-term synaptic plasticity
    Brain memory is formed and stored in a neuronal network. The network is modified by experience. This modification is realized through the changes in synaptic transmission efficiency in the short term and through the formation/elimination of synapses in the long term. Although the short-term events have recently been well analyzed, the long-term events remain nearly unapproached. We, using cultured brain slices which can be maintained stably for weeks-months, are challenging the mechanism of the experience-induced long-term synaptic modification.
  2. Activity-dependent neuronal survival
    Activity-dependent neuronal survival Neurons are ensured to survive when active. What mechanisms underlie the activity-dependent survival? Neurotrophic substances supplied from target tissues are believed to be responsible. But will they be all?
  3. Glial cell physiology
    In brain, neurons are outnumbered by glial cells. Classical textbooks tell that glial cells are dull housekeepers. But recent findings suggest that those cells play more crucial roles for the brain’s higher-order activity.


Cultured rat brain slice (left), maintaining its original neural circuit (right ; red color indicated activated state)

Members

Akihiko OGURA (Professor), Keiko TOMINAGA-YOSHINO (Associate Professor)

Contact

Tel. 06-6850-5426 Fax. 06-6850-5441
e-mail:oguraa@bio.sci.osaka-u.ac.jp
Home Page:http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/ogura/index.html

Laboratory of Plant Development

The formation of a plant body relies on coordinated division, differentiation and expansion of cells. In order to understand the underlying mechanisms, we study both inter-cellular communication and cellular events. So far we have discovered key enzymes for biosynthesis of cytokinins, which constitute a class of plant hormones, and receptors of cytokinins. In the figure, the left plant is a wild-type Arabidopsis and the right one is an Arabidopsis that lacks genes for cytokinin receptors. We are also searching for novel inter-cellular signaling molecules, and identified several molecules that regulate plant development. We also work on cytoskeletons, which play important roles in the oriented cell expansion and cell division, and also on biosynthesis of cellulose.

Members

Tatsuo KAKIMOTO (Professor) kakimoto@bio.sci.osaka-u.ac.jp
Shinobu TAKADA (Assistant Professor)

Tel/Fax

Tel / Fax. 06-6850-5421

Laboratory of Nuclear Function

Research area

Elucidation of molecular mechanisms for cell proliferation

  1. Cell cycle control of chromosomal DNA replication.
  2. Monitor system of cell cycle progression.
  3. System analysis of DNA replication.

Faithful replication of genetic information and transmission of the replicated information to daughter cells are essential for self-replicating cells. In eukaryotes, genetic information is stored in a nucleus as chromosomes, complexes of nucleic acids and proteins. However, little is known about higher-order structure of chromosome, and molecular details of machineries involved in chromosomal replication and transmission. Such supra-molecular machineries play central role in cell proliferation. Defect in replication and/or transmission process should result in the arrest of cell proliferation, leading to senescence or apoptosis of cells. The generation of abnormal chromosome in replicating cells would result in the formation of tumors. Our research goal is to understand a self-replicating system through systems biological analysis of a cell-tree extract of Xenopus eggs. Eventually, we would like to understand the basic principles underlining the regulation of cell proliferation.

Members

Haruhiko TAKISAWA (Professor) takisawa@bio.sci.osaka-u.ac.jp
Yumiko KUBOTA (Associate Professor) ykubota@bio.sci.osaka-u.ac.jp
Masato KANEMAKI (Assistant Professor) mkanemaki@bio.sci.osaka-u.ac.jp

Home Page

http://www.bio.sci.osaka-u.ac.jp/%7Etakisawa/english/research_e.html

Laboratory of Developmental Biology

Project: Mechanisms of animal embryogenesis

We all have developed from fertilized eggs of 100 µm in diameter. Have you thought about how it can be possible? Our laboratory is working on mechanisms how eggs develop into a well organized adult body using micromanipulative and molecular approaches.
In animal development, embryonic cells not only proliferate, but also generate various types of cells such as epidermis, muscle, neuron, and blood cells. All of these cells are originally derived from a fertilized egg. What kinds of mechanisms are involved in these processes in which some cells are fated to become muscle and other cells to become neuron? Namely, cellular and molecular mechanisms of cell fate determination during embryogenesis are the theme of our laboratory.
We use embryos of ascidian (sea squirt, Halocynthia roretzi) as experimental materials. Ascidian has been regarded as a primitive chordate that evolved to basic vertebrates. Fertilized eggs develop into tadpole larvae within 35 hours of development (Figure). Its embryogenesis has been intensively described in details so that we can predict which cells of the early embryo give rise to which cells of the tadpole larva (Figure, bottom).
Ascidian embryos provide us the unique possibility of understanding various mechanisms of fate determination in every cell type, because the tadpole consists of a small number of cells, and of a few types of tissue. Understanding fate determination mechanisms using this simple model organism with the basic body plan of Chordates would contribute to our knowledge in Developmental Biology.

Members

Hiroki NISHIDA (Professor), Gaku KUMANO (Assistant Professor), Atsuo NISHINO (Assistant Professor)

Contact

Tel. 06-6850-5472
e-mail:hnishida@bio.sci.osaka-u.ac.jp
Home Page:http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/nishida/index.html

Laboratory of Evolutionary Biology

Research Areas

  1. Biology of dicyemid mesozoans.
  2. Developmental mechanisms of neural crest cells.

We study dicyemid mesozoans which may occupy a phylogenetic position between unicellular protozoans and truly multicellular metazoans. The accompanying picture shows an individual stained with DAPI. These slender animals, measuring about 1 mm in total length, inhabit the kidney of cephalopod mollusks. The dicyemid body consists of only 20 to 40 cells and represents the smallest number of cells in the animal kingdom. We pursue a synthetic biology of dicyemids, which includes systematics, phylogeny, development, ultrastructure, coevolution with cephalopod hosts.

Another research area is the study of developmental mechanisms of neural crest cells of which migration and differentiation are attributable to characterization of the vertebrate body plan. We study how these cells migrate and how these cells differentiate into a variety of cells such as pigment cells, ganglion cells, and locally chondrocytes. The mouse is used as a model system under the viewpoint of molecular developmental biology and the lamprey, the most primitive living vertebrate, is used under the viewpoint of evolutionary developmental biology.

Members

Kazuhiko TSUNEKI (Professor), FURUYA (Associate Professor),
Kazuo ITO (Associate Professor)

Contact

Tel. 06-6850-5804 Fax. 06-6850-6769
e-mail:tsuneki@bio.sci.osaka-u.ac.jp

Laboratory of Signal Transduction

We, all of the animal species, utilize sensory signals to communicate and/or to survive. Our laboratory is specifically interested in the mechanism of sensory signal transduction, especially the mechanism of photoreception.

Light is the sensory signal in vision, and is detected by sensory cells, photoreceptors. Vertebrate photoreceptors hyperpolarize in response to light, and this electrical signal is processed and then transmitted to the brain to evoke our visual sensation. There are two types of photoreceptors in vertebrates, rods and cones. Rods are very sensitive to light and mediate twilight vision. Cones are much less sensitive and mediate daylight vision. In addition to the difference in the light-sensitivity, there are other differences in the response characteristics between rods and cones. Because rods and cones are the detectors of light signals, our way of vision is determined by the characteristics of these photoreceptors: twilight vision by rods and daylight vision by cones. We want to understand at the molecular level the mechanisms that characterize rod and cone photoresponses. Phototransduction in vertebrates is one of the best understood systems in the study of signal transduction, and therefore, our study will certainly contribute generally.

Members

Satoru KAWAMURA (Professor), Shuji TACHIBANAKI (Associate Professor), Yasutaka WADA (Assistant Professor)

Contact

TEL:06-6879-4610
e-mail: kawamura@fbs.osaka-u.ac.jp
Home Page: http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/kawamura/

Laboratory of Plant Cell Biology

When you see a wide spectrum of morphology and function in living things, you may ask about the physiological significance of (Why questions) as well as the underlying mechanisms of (How questions) such phenomena. Both questions strongly motivate you to get deeper insight into life. We are investigating plant life, using multidisciplinary approaches, according to the interests of individual lab members.

  1. Plants respond to environmental fluctuations very sensitively and very tactfully. We are dissecting such aspects of plants mainly at the cellular level, including cytoplasmic motility, organelle movement and positioning, and bending of stems and petioles.
  2. Higher plant cells organize the mitotic apparatus lacking centrosome. We are elucidating its molecular mechanisms, especially focusing on the mode of microtubule organization. Furthermore, molecular basis of the cellulose synthesis, an essential process for cell division and elongation growth, is also under investigation.
  3. Plants form their bodies by consecutively adding the respective parts, namely, root, stem, and leaf. These processes are always accompanied by characteristic pattern formation. We are asking the history and mechanism of pattern formation by developing new methods to observe cellular events in vivo.


Over-expression of plant-specific kinesin TBK5 in tobacco cultured cells induced formation of a centrosome-like structure.

Members

Shingo Takagi (Assistant Professor) shingot@bio.sci.osaka-u.ac.jp
Tetsuhiro Asada (Associate Professor) tasada@bio.sci.osaka-u.ac.jp

Contact


Tel / Fax: +81-(0)6-6850-5818 (Takagi), -6776 (Asada)
Home Page:http://www.bio.sci.osaka-u.ac.jp/dbs01/re-paper-temp.php?id=1

Laboratory of Membrane Biology

Research Subjects

Molecular mechanisms of intracellular ion homeostasis and ion transport across the biological membranes

  1. Molecular mechanisms of the Na+/H+ antiporters from bacteria and yeasts.
  2. Regulatory mechanisms of mammalian intracellular and organella pH.
  3. Intracellular traffic of membrane vesicles and pH regulation.
  4. Intracellular pH regulation and apoptosis.

Intracellular ionic conditions are strictly regulated. We are interested in cellular pH and Na+ conditions which affect regulation of cell growth, cell differentiation and even apoptotic cell death. The alteration of the ionic conditions causes various diseases and weakens bacteria and yeast for high salinity conditions. The regulation requires various ion transporters which exist in biological membranes like cytoplasmic and organella membranes. We currently focus on Na+/H+ antiporters, which are ubiquitously found in cell membranes of the most organisms, from bacteria to human. Ion transfer within this transporter molecule is not described in detail at the molecular level. We have analyzed amino acid residues and topological arrangement of the residues required for the ion transport in bacteria antiporter with molecular genetical and biochemical methods. We also try to make a crystal of the antiporter and analyze the three dimensional structure, at present. We have also found new types of regulatory proteins of yeast and mammalian antiporters. New antiporters have been discovered by us for various organella membranes of human cell. Understanding of the fine molecular mechanism of the antiporters from bacteria and mammalian cells will give a clue for constructing gene engineered plants and also drugs for human.

Members

Hiroshi KANAZAWA (Professor), Keiji MITSUI (Assistant Professor), Masafumi MATSUSHITA (Assistant Professor)

Contact

Tel. 06-6850-5812
e-mail:kanazawa@bio.sci.osaka-u.ac.jp

Laboratory of Biological Molecular Energy Transduction

Research area

  1. Dynamic Structural Physiology on Motor, Pump and Switch Proteins (T. Arata). We are developing site-directed mutagenesis-based ESR techniques to map intersite distance and mobility on the protein surface. Our interest is now focused on supra-molecular protein complexes during activity such as myosin-actin, kinesin-tubulin and calcium-switch troponin-tropomyosin-actin, and also on calcium pump ATPase and photo-switch rhodopsin in membrane etc.
  2. Non-identical Two-Heads Myosin and Cell Growth/ Differentiation (A. Inoue). Based on the non-identical two-headed structure of myosin, we are analyzing genes from two myosin heavy chains consisting a myosin molecule. We are also identifying a factor at molecular level that has activity to differentiate an immature cell to muscle using skeletal, smooth, and heart muscle or activity to guide nerve etc.

Members

Toshiaki ARATA (Associate Professor) arata@bio.sci.osaka-u.ac.jp
Akio INOUE (Associate Professor) inoue@bio.sci.osaka-u.ac.jp

Contact

Tel. +81-6-6850-5427 Fax. +81-6-6850-5441
Home Page:http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/bioerg/index.html

Laboratory of Molecular Biology and Education

Cells are sensitive to changes in the environment surrounding them and respond by various mechanisms. Control of gene expression is one such mechanism and the control at the transcriptional level is well known. Recently, another mechanism for the control of gene expression has been discovered. Gene expression is controlled at the level of degradation of mRNAs (refer to the right figure). How is mRNA degradation controlled? How is the rate of mRNA degradation controlled? Response to environmental changes involves tactics other than control of gene expression. By moving themselves, cells can escape from unfavorable circumstances such as loss of nutrition. In addition, cells can quickly repair the plasma membranes when damaged by external factors such as force, strong lights, and so on. What mechanisms underlie such abilities of cells? Our research goal is to answer these questions.

Research Projects

  1. Mechanism for amoeboid movement.
  2. Mechanism for membrane repair.
  3. Novel mechanism in control of gene expression.
Multicellular slug of cellular slime mold, Dictyostelium discoideum (above) and multinucleate plasmodium of true slime mold, Physarum polycephalum (bottom). When the rate of mRNA degradation is low, almost mRNA molecules are translated for production of protein (gene expression is ON; upper panel). When the rate of mRNA degradation is high, almost mRNA molecules are degraded without translation (gene expression is OFF; lower panel).

Members

Satoshi OGIHARA (Professor), Tetsuro YONESAKI (Professor)

Contact

Tel. 06-6850-5811 (Ogihara) 06-6850-5813 (Yonesaki) Fax. 06-6850-5817
Home Page:
http://www.bio.sci.osaka-u.ac.jp/~ogihara/index.html
http://www.bio.sci.osaka-u.ac.jp/~yonesaki/index2.htm

Laboratory of Theoretical Biology

Living systems are highly complex where huge number of dynamic elements interact each other. For example, in the developmental process where the networks of genes regulate the spatiotemporal gene expression, nature of the network itself as well as role of each gene could affect the morphogenesis.
To analyze the biological phenomena as complex dynamical systems, physics and mathematics such as statistical mechanics and nonlinear dynamical systems are helpful. Based on these fields, currently our laboratory is building up the following mathematical models and examining them in computers: Transcriptional network evolution of embryonic development, and emergence of multi-cellular dynamics during life cycle of social amoeba. Through the physical and mathematical analyses of the models consistently with molecular genetic data, our missions are to uncover the function of the molecular networks, the logic of the network evolution, and the collective information processing of cells.

Members

Koichi FUJIMOTO (Specially Appointed Associate Professor)

Contact

Tel / Fax: 06-6850-5822
e-mail: fujimoto@bio.sci.osaka-u.ac.jp
Home Page: http://www.bio.sci.osaka-u.ac.jp/~fujimoto/

Laboratory of Neural Circuit Function

Research Projects

Nervous systems of animals have been studied extensively at molecular, cellular and behavioral levels. However, one of the missing pieces of information in neurobiology is an understanding of the nervous system as "a system", not just as a field for many biological reactions. We need to know how these different levels of activities in an animal's nervous system are related to each other to facilitate appropriate responses to ever-changing environmental information.
Our interest is to understand how environmental signals are received, integrated and assessed in the intact neuronal network of the nematode C. elegans, one of the simplest nervous systems. Through integrative studies at molecular, cellular and behavioral levels, we would like to understand how environmental signals activate or inactivate a subset of neurons in the network for appropriate behavior, how the neuronal activations and inactivations are modified by learning, and how these neuronal activities are regulated by gene products.

　

Members

Kotaro KIMURA (Specially Appointed Associate Professor)

Contact

Tel: 06-6850-6706, Fax: 06-6850-6769
e-mail:kokimura@bio.sci.osaka-u.ac.jp
Home Page:http://www.bio.sci.osaka-u.ac.jp/%7ekokimura/e/Top.html

Laboratory of Organic Biochemistry(Department of Chemistry)

Research Interests

  1. Chemical synthesis of oligosaccharides
  2. Chemical synthesis of glycoproteins and glycopeptides
  3. Elucidation of oligosaccharide functions
  4. Elucidation of plant oligosaccharides

The oligosaccharides of protein have been thought to concern with protein conformation, dynamics, protein trafficking and glycoprotein lifetime in blood. We have examined synthesis of homogeneous glycoproteins having human complex type oligosaccharide in order to evaluate oligosaccharide functions. We have synthesized several small glycoproteins (amino acids 40-76 residues), erythropoietin analogue (amino acids 166 residues), and co-stimulate glycoprotein of T-cell (amino acids 120 residues). In order to synthesize these glycoproteins, the polypeptide sequence of target glycoprotein were divided into several segments and these were synthesized by solid phase peptide synthesis. After prepared both glycopeptide-thioester and peptide, these were coupled by repetitive Native Chemical Ligation (NCL). After construction of the glycosylated polypeptide chain, we examined folding experiments and evaluated effect of oligosaccharide during protein folding process. In addition, glycoproteins folded was analyzed its structure by NMR and CD spectra in order to evaluate conformational differences between glycosylated and nonglycosylated proteins. In our laboratory, we would like to elucidate oligosaccharide functions by use of such chemical approach.

Members

Yasuhiro KAJIHARA (Professor), Takeshi ISHIMIZU (Assistant Professor)

Contact

Tel: +81-6-6850-5380, Fax: +81-6-6850-5382
e-mail:kajihara@chem.sci.osaka-u.ac.jp
Home Page:http://www.chem.sci.osaka-u.ac.jp/lab/kajihara/index.html

Laboratory of Intracellular Signaling

Cells that constitute multicellular organisms are equipped with a signal transduction system, which enables cells to respond appropriately to the surrounding environment such as stimulation with various hormones and growth factors and physical interaction with other cells. Malfunction of the signaling system leads to various diseases, such as unlimited proliferation of cancerous cells. In our laboratory, we are engaged in two major themes and doing research with latest techniques of molecular biology using primary cultured neurons and genetically engineered mice.

  1. Signal transduction that regulates cell motility and morphology: We are investigating the mechanism of how neurons make a network by extending neurites such as axons and dendrites, and also examining how cells move in response to external stimuli and why cancerous cells have increased motility rate.
  2. Signal transduction that responds to oxidative stress: Recent studies have indicated that reactive oxygen species are not only toxins, which stimulate ageing and cancer formation, but also they are vital for cells. We are investigating how cells respond to this newly emerged key player in signal transduction.

Members

Hiroaki MIKI (Professor), Yosuke FUNATO (Assistant Professor)

Contact

TEL. 06-6879-8631 FAX. 06-6879-8633
e-mail: hmiki@protein.osaka-u.ac.jp
Home Page:http://www.protein.osaka-u.ac.jp/intra_signal/

Laboratory of Epigenetics (Institute for Protein Research)

Research Programs

  1. Regulation of DNA methylation and DNA methyltransferases.
  2. Structure and function of DNA methyltransferases.
  3. Suppression mechanisms of methylated genes.

In vertebrates, genomic DNA is often methylated at the 5th position of cytosine in the sequence of CpG. Different from prokaryote, the DNA methylation in vertebrates functions as a regulatory mechanism for the gene expression. Its contribution to the gene expression is independent of DNA sequences, and thus is called “epigenetic” regulation. The DNA methylation specifically plays roles in tissue-specific gene expression, genomic imprinting, X-chromosome inactivation, replication timing, and carcinogenesis. Our final goal is to elucidate the mechanisms how DNA methylation state and the expression of methylated genes are regulated.

Members

Shoji TAJIMA (Professor), Isao SUETAKE (Associate Professor), Hironobu KIMURA (Assistant Professor)

Contact

Tel. +81-6-6879-8627 Fax. +81-6-6879-8629
e-mail:tajima@protein.osaka-u.ac.jp

Laboratory of Proteins Involved in Homeostatic Integration(Institute for Protein Research)

Research Projects

  1. Molecular mechanism of circadian rhythms.
  2. Autonomic regulation of homeostasis.
  3. Signal transduction in neuronal cells.

In mammals, the master circadian clock is located in the suprachiasmatic nucleus of the hypothalamus. We have been searching for molecules involved in generation of the circadian clock and its synchronization to the environment, and studying their functions in the circadian clock and the homeostatic integration. In addition, we are studying molecular functions of signal transduction molecules such as protein kinases and NO synthases in these neuronal systems.

Members

Nobuaki OKUMURA (Associate Professor)

Contact

Tel. 06-6879-8632 Fax. 06-6879-8633
Home Page: http://www.protein.osaka-u.ac.jp/metabolism/taisha.html

Laboratory of Regulation of Neuronal Development (Institute for Protein Research)

Research Subjects

  1. Molecular mechanisms of neuronal development.
  2. Molecular mechanisms of neuronal death in Alzheimer's disease.
  3. Methodology of gene transfer to postmitotic neurons.

Our basic aim is to give an account, with molecular words, of the lives of vertebrate neurons (nerve cells) - how they come, survive, and die. We pay specific attention to the fact that neurons are postmitotic cells, which completely lose their capability to divide and proliferate. We are studying the function of neuronal mitotic suppressor necdin and its related family members. Information about these proteins may provide a unified view on cell cycle regulation, terminal differentiation, and death of neurons. We are also investigating the pathological function of the Alzheimer amyloid precursor protein (APP) to clarify the molecular mechanism of neuronal death in Alzheimer’s disease. We are developing methods by which cloned genes with unknown functions are efficiently transferred into neurons in culture and those in the brain of experimental animals to elucidate their roles in neuronal differentiation and death.


Translocations of the necdin protein in neurons

Members

Kazuaki YOSHIKAWA (Professor), Tsuyoshi OHKUMO (Assistant Professor), Koichi HASEGAWA (Assistant Professor)

Contact

Tel. 06-6879-8621 Fax. 06-6879-8623
Home Page: http://www.protein.osaka-u.ac.jp/regulation

Laboratory for Molecular Biophysics (Institute for Protein Research)

Research area

  1. Investigation on the conformational change of the H+-ATP synthase β subunit and its role in the rotational catalytic reaction. Structure-function relationship of the c subunit in H+-ATP synthase F0 as studied by high resolution solid-state NMR.
  2. Elucidation of the mechanism of G protein activation by model membrane proteins and peptides of the receptor.
  3. Development of solution and solid-state NMR methodologies for the structure analyses of larger proteins and membrane proteins.

The objective of our investigation is to elucidate the structure-function relationship of the biological macromolecules using nuclear magnetic resonance (NMR) and molecular biological methods. NMR can provide information on the molecular structure at atomic resolution of proteins at work. Taking this advantage, we are trying to understand the biological activities on the basis of molecular structure. Specifically, we are interested in the mechanism of energy conversion and signal transduction (Figure). To challenge these systems, we are also developing new methodologies in solution and solid-state NMR.

Members

Toshimichi FUJIWARA (Professor), Takahisa IKEGAMI (Associate Professor), Yoh MATSUKI (Assistant Professor)

Home Page

http://www.protein.osaka-u.ac.jp/biophys/bussei.html

Laboratory of Regulation of Biological Reactions (Institute for Protein Research)

Research Projects

  1. Molecular mechanism of redox metabolisms in photosynthetic and non-photosynthetic plastids.
  2. Molecular mechanism of chloroplast biogenesis in higher plants.

The plant organelles, collectively referred to as plastids, play a diverse set of physiological functions including photosynthesis, and soluble and membrane-bound proteins, localized in certain subplastidal compartments, are involved in the organelle functions. We have been studying the function and biogenesis of plastid proteins with techniques of biochemistry, genetics, and cell biology, using higher plants and cyanobacteria. Current projects are the following: i) Reducing equivalents are utilized by combination of ferredoxin and ferredoxin-dependent enzymes, enabling plants to assimilate inorganic raw materials. The electron transfer and catalytic mechanisms of these enzymes are studied. ii) Cytosolically synthesized polypeptides are transported into chloroplasts and converted to functional mature proteins. The mechanisms of protein translocation across membranes and iron-sulfur cluster assembly and involvements of molecular chaperones are studied. iii) Malaria cells contain an organelle called apicoplast, in which redox metabolisms for parasite vitality take place. We are studying maralia Fd and its redox enzymes to explore how redox cascade is operative in apicoplasts.

Members

Toshiharu HASE (Professor), Masato NAKAI (Associate Professor), Yoko KIMATA-ARIGA (Assistant Professor)

Home Page

http://www.protein.osaka-u.ac.jp/enzymology/indexE.html

Laboratory of Protein Synthesis and Expression (Institute for Protein Research)

Research area

  1. Structure and function of extracellular ligands and their receptors implicated in cell adhesion and neural guidance/morphogenesis.
  2. Establishment of high-capacity recombinant protein production system using mammalian cells for structural analysis of extracellular proteins.
  3. Development of innovative methods for visualization of biological macromolecules using election microscopy.

Cellular response to the extracellular environment depends on the "sensing" the extracellular cues by use of the receptor-ligand system. Binding of ligands to the extracellular domain of the receptors transduce signals into cells that initiates various cellular events, ultimately changing the cell fate. Our study focuses on questions such as how receptors recognize their specific ligands, how this recognition leads to structural change in the receptor complex, and how the information cross the plasma membrane without transporting chemical entity. Using structural, as well as chemical approach, we would tackle on this difficult problem to obtain insights into the mechanism of transmembrane signaling.


Close-up structure of ligand binding pocket in integrin α II β3.
Two drug molecules against coronary artery thrombosis (yellow stick models) dock
similarly to the receptor at the interface between α (magenta) and β (cyan) subunits.

Members

Junichi TAKAGI (Professor), Kenji IWASAKI (Associate Professor), Terukazu NOGI (Assistant Professor)

Contact

Tel. 06-6879-8607 Fax. 06-6879-8609
e-mail: takagi@protein.osaka-u.ac.jp
Home Page:http://www.protein.osaka-u.ac.jp/rcsfp/synthesis/

Laboratory of Protein Organic Chemistry (Institute for Protein Research)

Research Programs

  1. Establishment of a methodology for synthesis of protein
  2. Chemical synthesis of a membrane proteinmembrane
  3. Chemical synthesis of a modified histone
  4. Analysis for structure and function of a single transmembrane receptor

We have been working on establishing a methodology for synthesis of protein. Development of auxiliaries for peptide ligation and designing a building block are main components for this study. Also, we have been trying to establish a way to isolate a protein that is insoluble or a highly adhesive to a solid support for RH-HPLC. Based on these experiments, we have been focusing on a chemical synthesis of membrane proteins. We are also interested in a function of a receptor involved in the signal transduction system and histone. In order to contribute for the structural chemistry and biology on the receptor, we synthesize a peptide of a transmembrane-juxtamembrane sequence with stable isotope labels for a solid state NMR experiment. Also, using a combination of biological and chemical methods, we started working on a preparation of a single transmembrane receptor in a full length. For histones, in order to understand correlation between the function and the modification, we are synthesizing the histone in a full length.

Schematic representation of receptor tyrosine kinase. The red circle indicates the region where we are interested in.

Members

Saburo AIMOTO (Professor), Toru KAWAKAMI (Associate Professor), Takeshi SATO (Assistant Professor), Toshiaki HARA (Assistant Professor)

Contact

Tel. 06-6879-8601 Fax. 06-6879-8603
e-mail:aimoto@protein.osaka-u.ac.jp
Home Page:http://www.protein.osaka-u.ac.jp/organic/

Laboratory of Protein Folding (Institute for Protein Research)

Current Research Programs

  1. Observation of folding processes and clarification of the mechanism of protein folding.
  2. Analysis of structural stability and dynamics of protein molecules.
  3. Analysis of structural stability and the mechanism of formation of amyloid fibrils.

Protein folding is a process in which an extended polypeptide chain acquires a unique folded conformation with biological activity. However, the exact molecular mechanism remains unknown. Clarifying the mechanism of protein folding is essential to improve our understanding of the structure and function of proteins. It is also important to design engineered proteins with improved functions.

Moreover, protein folding plays important roles in many biological phenomena. For an example, the deposition of amyloid fibrils has been suggested to play a central role in over 20 degenerative disorders including Alzheimer's and prion diseases. Because the amyloid fibril deposition is often caused by misfolding of an originally functional protein, these diseases are called "folding disease". In order to establish therapeutic treatments, clarifying the molecular mechanism of folding diseases is essential.

We are studying the conformational stability of proteins, molecular basis of folding reaction, and structures and formation of amyloid fibrils. These studies are performed using various observation methods, including spectroscopies (NMR, CD, IR), physicochemical methods (calorimetry, ultracentrifugation), and fluorescence microscopy, as well as gene manipulations for recombinant proteins by using the E.coli and yeast expression systems.


Fig. An image of amyloid fibrils of amyloid-β peptide obtained using total internal reflection fluorescence microscopy.

Members

Yuji GOTO (Professor)ygoto@protein.osaka-u.ac.jp
Kazumasa SAKURAI (Assistant Professor)sakurai@protein.osaka-u.ac.jp

Home Page

Contact

Tel: 06-6879-8614 , Fax: 06-6879-8616

http://www.protein.osaka-u.ac.jp/physical/yoeki.html

Laboratory of Extracellular Matrix Biochemistry (Institute for Protein Research)

Research area

  1. Structure and function of extracellular matrix proteins and their receptors.
  2. Mechanisms of cell-extracellular matrix interactions.
  3. Development of artificial extracellular matrices for tissue engineering and regeneration medicine.

Our long-term goal is to understand the molecular mechanisms defining morphogenetic interactions of cells with their surrounding microenvironment, i.e., extracellular matrices. We are particularly interested in the roles of the basement membrane in histogenesis and organogenesis, with an emphasis on the molecular interactions of basement membrane proteins with their cognitive receptors on the cell surface, as well as the resulting signaling events that regulate proliferation, differentiation, apoptosis, and motility of cells.

Members

Kiyotoshi SEKIGUCHI (Professor), Masashi YAMADA (Assistant Professor), Sugiko FUTAKI (Assistant Professor)

Home Page

http://www.protein.osaka-u.ac.jp/chemistry/

Laboratory of Supramolecular Crystallography (Institute for Protein Research)

Research area

  1. Operating a synchrotron beamline for biological macromolecular assemblies.
  2. Developing a new crystallographic techniques for structure determination of biological macromolecular assemblies.
  3. Structural studies of biological macromolecules and biological macromolecular assemblies.
  4. Structural proteomics on proteins working in brain and nervous system.

Macromolecule assemblies, consisting of proteins, nucleic acids, and other substances, play key roles in all living system. Our laboratory works on structure determination of biological macromolecular assemblies using X-ray diffraction technique. Development of tools for X-ray crystallography of biological macromolecular assemblies, including the synchrotron radiation beamline at SPring-8, is also one of our main works. We are also working on structural proteomics project as one of the core groups of the Japanese National Project on Protein Structural and Functional Analyses. The main aim of our project is to elucidate the structure and function of the proteins that play key roles in brain and nervous system.

Members

Atsushi NAKAGAWA (Professor), Mamoru SUZUKI (Associate Professor), Eiki YAMASHITA (Assistant Professor)

Contact

e-mail:atsushi@protein.osaka-u.ac.jp
Home Page:http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/index.html

Laboratory of Protein Profiling and Functional Proteomics(Institute for Protein Research)

Research Programs

  1. Development of chemical/analytical methods and softwares for analyses of protein primary structures.
  2. Hardware development for high-sensitivity MS.
  3. MS analysis of post-translational modifications.
  4. Development of a chemical derivatization method for high sensitive detection of sugar chains of glycoproteins.
  5. Development of chemical and separation methods for proteomic analysis.
  6. Study on fragmentation of peptides and carbohydrates in MS.

Mass spectrometry (MS) is a well accepted technique for the analyses of chemical structures of biological compounds. We have been working to develop methods for determining primary structures and post-translational modifications of proteins by using MS. In conjunction with accumulating protein and gene sequence databases, we are using state-of-the-art MS for large-scale protein identification which is indispensable for proteomics research. We also apply the above developed methods to the structural analysis of micro quantities of peptides, proteins, and their related substances.

PE : phosphatidylethanolamine

Members

Toshifumi TAKAO (Professor)

e-mail

tak@protein.osaka-u.ac.jp

Laboratory of Genome-Chromosome Functions (Institute for Protein Research)

Research Subjects

  1. Molecular mechanism of homologous recombination.
  2. Molecular mechanism of recognition of homologous chromosomes during meiosis.
  3. Selection of DNA repairs pathways.

Information on chromosomes in human is transmitted precisely from cells to cells and from parents to children. An exchange of DNAs, referred to as “recombination” maintains genome homeostasis by stabilizing information in genome. On the other hand, recombination produces diversity in genome, which might be a driving force for evolution. Dysfunction of the recombination leads to instability of genome, which is often associated with onset of cancers and of miscarriages. Our laboratory is trying to understand recombination at a molecular level.


Localization of two proteins Rad51 (green) and Dmc1 (Red) on meiotic chromosomes

Members

Akira SHINOHARA (Professor), Miki SHINOHARA (Assistant Professor),
Saori MORI (Assistant Professor), Takehiko USUI (Assistant Professor)

Contact

Tel / Fax. 06-6879-8624, 8626
e-mail:ashino@protein.osaka-u.ac.jp
Home Page:http://www.protein.osaka-u.ac.jp/genome/index-english.html

Laboratory of Protein Informatics (Institute for Protein Research)

Research Theme

  1. Construction and management of the database for protein threedimensional structures as the PDBj (Protein Data Bank Japan), a member of the wwPDB (world-wide PDB).
  2. Bioinformatics studies focused on protein structures and proteinprotein interactions.
  3. Development of new algorithms and softwares for large scale simulation calculations by parallel computers to examine free energy landscapes of biomolecular systems for structure and energetic analysis and prediction.

Our laboratory manages the protein structure database as PDBj, and develops several tools and derived databases for advanced usages. The research aim of our laboratory is to elucidate the relationships between structures and functions of biological macromolecules, and mutual interactions (proteomics) by structural bioinformatics and molecular simulations, covering the quantum mechanical and molecular mechanical analyses.

Fig. 1: Top Page of the PDBj
(http://www.pdbj.org)

Fig.2 : Network among the structual motifs of ligand binding sites in proteins (Kinjo & Nakamura (2009) Structure)

Members

Haruki NAKAMURA (Professor), Akira R. KINJO (Associate Professor),
Yu TAKANO (Assistant Professor), Takashi KOSADA (Technical Assistant)

Contact

Tel. 06-6879-4311, 8634 Fax. 06-6879-8636
e-mail:harukin@protein.osaka-u.ac.jp
Home Page:
http://www.protein.osaka-u.ac.jp/rcsfp/pi/
http://www.pdbj.org/

Laboratory of Protein Crystallography (Institute for Protein Research)

Research Projects

  1. Structural studies of photosynthetic energy-transducing membrane protein complex and related redox enzymes
  2. Crystal structure analyses of dynein motor
  3. High resolution structural analysis of rat liver vault

Three-dimensional protein structure brings us a deeper insight into the biological function. X-ray crystallography is the best method to determine atomic coordinates of protein molecules. The main aim of our group is the X-ray structure determination of the biological macromolecular assemblies including membrane protein complexes, in order to elucidate the molecular mechanism of the highly organized biological processes at atomic level.

Crystal Structure of the cytochrome b6f complex

 

Members

Genji KURISU (Professor), Hideaki TANAKA (Assistant Professor)

Contact

Tel: 06-6879-8604, Fax: 06-6879-8606
e-mail:gkurisu@protein.osaka-u.ac.jp

Home Page:
http://www.protein.osaka-u.ac.jp/crystallography/

Laboratory of Theoretical andComputational Biomolecular Science (Institute for Protein Research)

Research Projects

It has been shown that the behaviors of bio molecules, which are related to biology functions, can be treated as problems in physics or chemistry. However, its principle has not been solved yet. This is because that we still have difficulty for describing the free energy of the system including biological molecules and solvent molecules. Recently, our research group theoretically found out a dominant physicochemical factor for a protein folding. In order to describe the free energy of the system, we focused on the water molecules around a protein and the behavior of them is treated with liquid state theories. Furthermore, we can build up a more realistic system based on statistical mechanics.
Now we aim to clarify static and the dynamic behavior of the biological molecule including the protein based on the factor, and we are devoting our energies to the development of the method for predicting the native structure of proteins especially. So far, we are developing a software with a wide use by making a combination with a molecular simulation methods or bioinformatics. It aims at the applications of the drug design and pathology, etc.

A picture of protein folding. Proteins spontaneously fold into the native structure

Members

Yuichi HARANO (Specially Appointed Associate Professor)

Contact

Tel: 06-6879-4327, Fax: 06-6879-4327
e-mail:yharano@protein.osaka-u.ac.jp

Home Page:
http://www.bio.sci.osaka-u.ac.jp/dbs01/re-paper-temp.php?id=76

Laboratory of Signal Networks for Life Maintenance (Institute for Protein Research)

Research Projects

  1. Analysis of signal networks of telomeres during the cell-cycle.
  2. Analysis of molecular bases for Tel2-PIKK network.

Organisms promptly and appropriately respond to various environmental changes for their survival. In order to respond to various forms of stress, cells have developed signal transduction cascades for each stress. We will clarify the molecular bases for networks of proteins or cellular signals, focusing on the key proteins that are commonly involved in several distinct signal transductions. Our current interests are crosstalk of signal transductions for chromosome maintenance and those for nutrient recognition. Our study will contribute to understanding the mechanisms of chromosome disease, cancer or diabetes.

Mitosis of fission yeast. Telomere-binding protein Taz1 is visualized by mCherry (red).
Alfa-tubulin and a nuclear membrane protein are visualized by GFP(green).

Members

Junko KANOH (Specially Appointed Associate Professor)

Contact

Tel: 06-6879-4328, Fax: 06-6879-4329
e-mail:jkanoh@protein.osaka-u.ac.jp

Home Page:
http://www.protein.osaka-u.ac.jp/network/e/index.html

Laboratory of Membrane Protein Chemistry(Institute for Protein Research)

Research Projects

Intracellular membrane fusion is a fundamental and conserved biological reaction which is vital for vesicle trafficking between cellular compartments, organelle morphology, hormone secretion, and neurotransmission. Fusion is regulated by specific proteins and lipids: SNAREs, SNARE chaperones, Rab GTPases, and phopsphoinositides. However, it is unclear how they act together to drive membrane fusion. We have been studying this vital membrane fusion machinery in eukaryotic cells and recently developed reconstituting proteoliposomal fusion with purified components. Our current projects attempt to dissect the ternary synergy of two SNARE chaperone systems and phosphoinositides which is essential for physiological fusion through catalyzing the SNARE complex assembly and remodeling the assembled SNARE complexes. In our future directions, we will further explore the molecular machinery of not only membrane fusion but membrane fission/budding and deformation, by this powerful system of reconstituting proteoliposomes with defined components.

Figure: Yeast vacuoles as a model for intracellular membrane fusion. Yeast vacuoles (lysosomes in mammals) change their organelle morphology through membrane fusion (from C to A) and fission(from A to C) processes to respond the extracellular environments and/or cell cycles.

Members

Joji MIMA (Tenure-track Associate Professor)

Contact

Tel: 06-6879-4326, Fax: 06-6879-4329
e-mail:Joji.Mima@protein.osaka-u.ac.jp

Home Page:
http://www.bio.sci.osaka-u.ac.jp/dbs01/re-paper-temp.php?id=77

Laboratory of Oncogene Reserach (Research Institute for Microbial Diseases)

Research Projects

  1. Studies on the roles of proto-oncogene products in the development of multicellular animals.
  2. Studies on the roles of tyrosine kinases in the neural development.
  3. Studies on the roles of Src family kinases in the metastasis and/or invasion of cancer.

The primary focus of this department is to understand the functions and regulatory mechanisms of proto-oncogene products, which play crucial roles in the cell signaling pathways involved in the development and differentiation of animal cells. Understanding the critical functions of these proto-oncogenes would provide insights into the molecular basis of normal cell development as well as oncogenesis, which can be considered as an aberrant form of differentiation. Presently, we are focusing on the proto-oncogenes encoding protein tyrosine kinases, particularly the Src family of tyrosine kinases (SFK). SFK is known to be involved in regulating cell-cell and cell-substrate adhesion and cell migration. Malignant cancer cells often have elevated SFK activity, suggesting the potential role of SFK in the progression of cancer metastasis. To elucidate the principal functions of SFK and to search for new molecules that can be targeted by drugs to block SFK-mediated cancer progression, we are currently engaged in the above projects.


Potential roles of Src and its regulator Csk
in the regulation of metastasis and invasion of cancers.
In various human cancers, it is known that the kinase activity of Src is elevated.
The activation of Src leads to disruption of cell-cell interaction,
enhancements of substrate adhesion and cell mobility,
and increased secretions of MMPs and cytokines.
As a consequence of these events,
the metastatic and invasive actions of cancer cells are greatly promoted.

Members

Masato OKADA (Professor), Shigeyuki NADA (Associate Professor),
Chitose ONEYAMA (Assistant Professor)

Contact

Tel. 06-6879-8297
e-mail:okadam@biken.osaka-u.ac.jp

Laboratory of Structural Molecular Biology (Institute of Scientific and Industrial Research)

Current Research Programs

  1. Reaction mechanism of copper amine oxidase and catalytic role of the topa quinone cofactor.
  2. Molecular mechanism of the biogenesis of novel built-in type quinone cofactor.
  3. Structural and functional analysis of bacterial two-component system (TCS) aiming at novel drug development.
  4. Development of the new method of pin-point gene and drug delivery system using bionanocapsules derived from hepatitis B virus surface antigen.
  5. Structural biology of multi enzyme complex.

Outlines

The research of this laboratory is focused on the biochemical and molecular biological studies on various enzymes. Their activesite structures and catalytic mechanisms are being investigated by site-directed mutagenesis, various spectroscopies, and X-ray crystallography. Previous conspicuous findings are the copper iondependent, post-translational modification mechanism for the biogenesis of the topa quinone cofactor in copper amine oxidase and the very unique structure of quinohemoprotein amine dehydrogenase (QHNDH) containing a novel built-in type quinone cofactor and internal thioether multi crosslink structures. Furthermore, we determine domains of the TCS proteins and elucidate mechanisms of signal sensing and transcriptional regulation. In addition, we have developed hollow bionanoparticles displaying various bio-recognition molecules, which are expected to be an ideal vector for the tissue- and cell typespecific gene and drug delivery system

X-ray crystal structure of QHNDH and chemical structure of CTQ

Members

Katsuyuki TANIZAWA (Professor) tanizawa@sanken.osaka-u.ac.jp
Toshihide OKAJIMA (Associate Professor) tokajima@sanken.osaka-u.ac.jp
Takashi MATSUZAKI (Assistant Professor) tmatsuza@sanken.osaka-u.ac.jp
Tadashi NAKAI (Assistant Professor) nakaix@sanken.osaka-u.ac.jp

Contact

Tel: 06-6879-8460-8462, Fax: 06-6879-8460
Home Page:http://www.sanken.osaka-u.ac.jp/labs/smb/

Laboratory of Genome Informatics (Research Institute for Microbial Diseases, Genome Information Research Center)

Subject of Research

  1. Development of Genetic Information Analysis System.
  2. Genome Informatics.
  3. Molecular Evolution.

We are developing various software tools that make advanced use of computers and computer network for genome information analysis. We have developed new software with an algorithm that allows the analysis of large scale data such as finding a conserved sequence among the genome sequences already determined. Using these softwares, we analyze genome sequences from various points of view such as gene regulation, gene duplication, molecular evolution and so on. We have also participated in the bacterial genome project with other laboratories at our university.

Members

Teruo YASUNAGA (Professor), Shota NAKAMURA (Assistant Professor),
Naohisa GOTO (Assistant Professor)

Contact

Tel. 06-6879-8365
e-mail:yasunaga@gen-info.osaka-u.ac.jp
Home Page:http://www.gen-info.osaka-u.ac.jp

Laboratory of Biohistory (JT Biohistory Research Hall [BRH])

Research themes

  1. Insect's feeding preference and speciation: Molecular mechanism of the host plant selection of swallowtail butterflies.
  2. Vertebrate body patterning: How does the well-patterned morphology is generated in terms of ontogeny and phylogeny?
  3. Development of cellular arrangement: Developmental mechanism of the scale cell arrangement in the butterfly and moth wings.
  4. Phylogeny and evolution: (i) molecular phylogeny and evolution of arthropods; (ii) co-evolution and co-speciation between figs and fig wasps.
  5. Evolution of developmental programs and cell structure/function: Experimental study using the Drosophila and spider models.
  6. Molecular bases of organismal diversity: Relationships between diversity of animal-specific gene families and the Cambrian explosion.
  7. Science communication and production: Presenting and sharing biological research among many people.

BRH performs studies on the evolution and development of organisms, and the study of how to spread science throughout society. The above-mentioned themes are carried out in seven research groups. The staff and other BRH members including Dr. Keiko Nakamura (Director General) and researchers work together in supervising graduate students.

Members

Zhi-Hui SU (Guest Professor) su.zhihui@brh.co.jp
Chikara HASHIMOTO (Guest Professor) hashimoto@brh.co.jp
Hiroki ODA (Guest Associate Professor) hoda@brh.co.jp

Contact

Tel: 072-681-9750, Fax: 072-681-9743

Home Page:http://brh.co.jp

 

Laboratory of Cell Structures and Functions(Kansai Advanced Research Center)

Research area

Our laboratory studies functional organization of the cell nucleus (chromosomes, nuclear envelope, etc.) using mammalian culture cells and fission yeast. Toward this end, we have developed a computer-controlled microscope system that is capable of recording fluorescently-stained proteins in living human cells In fission yeast S. pombe, we have found that telomeres and centromeres greatly change their nuclear positions upon entering meiosis (ref. 1, 2). We are now trying to understand the molecular mechanisms for such nuclear reorganization during meiosis. In human cells, we are trying to understand how nuclei are organized to achieve their functions. (ref. 3, 4).

References

  1. Chikashige et al. Telomere-led premeiotic chromosome movement in fission yeast. Science, 264:270-273 (1994).
  2. Chikashige et al. (2006). Meiotic proteins Bqt1 and Bqt2 tether telomeres to form the bouquet arrangement of chromosomes. Cell 125, 59-69.
  3. Haraguchi et al. Live fluorescence imaging reveals early recruitment of emerin, LBR, RanBP2, and Nup153 to reforming functional nuclear envelopes. J. Cell Sci., 113: 779-794 (2000).
  4. Haraguchi et al. (2001).BAF is required for emerin assembly into the reforming nuclear envelope. J. Cell Sci. 114, 4575-4585.

Members

Yasushi HIRAOKA (Guest Professor), Tokuko HARAGUCHI (Guest Professor), Yuji CHIKASHIGE (Guest Associate Professor)

Address

Kansai Advanced Research Center 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492

Contact

Tel. 81-78-969-2240 Fax. 81-78-969-2249
e-mail:
yasushi@nict.go.jp
tokuko@nict.go.jp
chika@nict.go.jp
Home Page:http://www-karc.nict.go.jp/w131103/CellMagic/index.html

Laboratory of Biomolecular Informatics (RIKEN, Harima)

Research Subjects

  1. Metal-Containing Enzymes Catalyzing Biological Oxidation-Reduction Reactions; Dioxygenase, Monooxygenases, Nitric Oxide Reductases, etc.
  2. Metal-Containing Sensor Proteins Sensing Gas Molecules; Two-Component Systems, etc.
  3. Development of New Techniques Examining Protein Structures and Functions

Metal ions are present in biological system in the form of metal-binding proteins and enzymes, and are involved in physiologically important actions such as biological redox reactions, cellular signal transductions and so on. Our research focuses on understanding the functions of such metalloproteins and metalloenzymes at molecular and atomic levels on the basis of their molecular structures, which are determined by the SPring-8 RIKEN beam line.

Members

Yoshitsugu SHIRO (Professor)

Contact

TEL. 0791-58-2817 FAX. 0791-58-2818
e-mail:yshiro@riken.jp
Home Page:http://www.riken.jp/biometal/

Laboratory of Biomolecular Informatics
(Center for Developmental Biology (CDB), RIKEN)

Research Theme

  1. System-based understanding of circadian and segmentation clocks (Ueda)
  2. Technical developments in system-based understanding of biological phenomena (Ueda)
  3. Functional genomic analysis of the nematode, C. elegans (Sugimoto)
  4. Analysis of dynamic processes involved in the developmental process (Sugimoto)

Ueda Our laboratory uses a variety of complex and dynamic biological systems, such as the mammalian circadian and segmentation clocks, in the hope of fully comprehending the components and networks that make up these types of system (a process known as system identification). Our research also involves predicting and examining the dynamic traits of these systems based on quantitative measurements of the reaction rate and dose dependency of the system components (system analysis). A third aspect of this area of study includes regulating the arbitrary conditions by perturbations to system components (system control). Finally, we are also attempting to prove the principles of operation of biological systems through the construction of an artificial system that, while possessing the same operating characteristics, uses different molecules as its components (system design). Sugimoto Cooperation between groups of genes encoded within an organism's genome is essential to the development of multicellular organisms. Our laboratory aims to examine these developmental programs at the genetic level, and to that end we are employing the nematode, Caenorhabditis elegans as a model organism in the hope of advancing this particular field of research. Together with developing a system for carrying out systematic analysis of gene function, we are also employing a molecular genetic and cell biology analytical approach in an attempt to reveal more about dynamic phenomena involved in development such as cell division and morphogenesis.

Members

Hiroki R. UEDA (Guest Professor), Asako SUGIMOTO (Guest Professor)

Contact

TEL. 0791-58-2817 FAX. 0791-58-2818
e-mail:
uedah-tky@umin.ac.jp
sugimoto@cdb.riken.jp
Home Page:http://www.cdb.riken.jp/en/index.html

 

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