Dates : Dec 21 (Fri) to Dec 23 (Sun)
Venue : Pacifico Yokohama
The purpose of this symposium is to discuss the role of women scientists, especially junior scientists, in the field of Biophysics. Women scientists have played and continue to play an important role in the field of Biophysics, and BSJ has regularly held workshops and seminars on this subject during its annual meeting. However, this year, the symposium is open to the general public for the first time, and we want the discussion to be understandable by a large scientific as well as non-scientific audience. The presentations by women scientists actively engaged in biophysical research and education will illustrate the many scientific challenges, interests and opportunities in the field. We hope that the symposium will help attract future generation of women scientists and that their number will keep growing.
In the current of gender equality and equality of opportunity, new support programs for women's scientists have started, which is a result of longtime efforts for gender equality of a number of scientific societies. It is time we should discuss what the aims of the programs are, what the programs are changing, and what is required to promote the gender equality. In this symposium, we will examine the aims and actual problems of the program to discuss the fact and future of the gender equality in academe.
Representative researchers in brain science are going to demonstrate their recent achievements and future goals. They use combination of imaging analysis as well as other methodology. Though neuroscience needs multiple methodologies, they show how biophysical methodology is useful to make a break through in neuroscience.
Akinao Nose
(1Graduate School of Frontier Sciences, 2Graduate School of Science, University of Tokyo)
"Molecular assembly at the nascent synapse imaged in vivo"
Kei Ito (Institute of Molecular and Cellular Biosciences, University of Tokyo)
"Functional neuroanatomy of the Drosophila brain"
Okamura Hitoshi (Graduate School of medicine, Kobe University)
"Imaging of biological clocks: can peripheral cells know the rising of the sun?"
Suguru Kawato1,2
(1Graduate School of Arts and Sciences, University of Tokyo, 2Bioinformatics Project, JST)
"Memory and synaptic plasticity: Sex hormones are modulators of synapses"
Masahiro Sokabe1,2,3
(1Department of Physiology, Nagoya University Graduate School of Medicine,
2ICORP/SORST, Cell Mechanosensing, JST,
3Department of Molecular Physiology, National Institute for Physiological Sciences)
"Analysis of tripartite synapses using membrane potential imaging:
memory enhancement and neuroprotection by neurosteroids"
Manabu Tanifuji (Riken Brain Institute)
"Representation of object images in visual association cortex and object
recognition"
In recent years, biochemical and molecular biological characterizations of intracellular signaling systems have been making marvelous advancements, with regard to who are the players of this game and who can interact with whom in this game. However, the design principles of the intracellular signaling systems, developed during evolution, have virtually remained unknown. To elucidate such a fundamental design or strategy of intracellular signaling, single-molecule imaging technology could make unique and/or great contributions, because it might reveal how each individual signaling molecule moves around in cells and interacts with others, and thus could elucidate elementary molecular processes, including their on and off rates of interactions, in living cells. We believe that we are at the dawn of single-molecule systems biology of intracellular signaling. With this in mind, in this symposium, new methodologies for single-molecule experiments and analysis will be presented, and the initial data for such an understanding will be discussed.
Rinshi S. Kasai (Kyoto University / JST-ICORP)
"Very dynamic equilibrium of GPCR monomers and dimers:
single-molecule tracking studies of formyl-peptide receptor "
Gaudenz Danuser (CIMBio, the Scripps Research Institute,)
"Probing cytoskeleton structural dynamics and function
by single particle tracking methods"
Ken Ritchie （Purdue University, Dept. Physics）
「Single molecule imaging of diffusion in E. Coli membranes」
Takashi Funatsu (Graduate School of Pharmaceutical Sciences, the University of Tokyo)
"Single-molecule imaging and quantification of mRNAs in living cells"
Daniel Choquet （University of Bordeaux, Cellular Physiology of Synapse）
"A new function of glutamate receptor surface diffusion
in regulating synaptic transmission"
Emerging technologies that enable engineering of nano- or cell-scale devices and systems from biological and/or artificially-created molecules have been receiving increasing attention. This symposium focuses on the "molecular computing" that tries to realize non von Neumann-type information processing paradigms by using biological and/or artificially-created molecules as a computing unit, and "molecular communication" that tries to realize non electromagnetic-wave based communication paradigms by using biological and/or artificially-created molecules as an information medium. This symposium tries to identify technologies necessary to create such computing and communication paradigms. This symposium also discusses related research in the field of synthetic biology and nanomachines and to evaluate how existing research may help create new computing and communication paradigms.
Daisuke Kiga
(Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology)
" Molecular Computing and Molecular Communication:
Synthetic approach using biomolecules"
Masami Hagiya (Department of Computer Science, the University of Tokyo)
"Molecular Computing --- past 10 years and future 10 years"
Akira Suyama (Department of Life Sciences, the University of Tokyo)
"Applications of molecular computing"
Andrew Turberfield (Dept. of Physics, Oxford Univ.)
「DNA nanotechnology」
Masahiko Hara1, 2
(1Department of Electronic Chemistry, Tokyo Institute of Technology, 2RIKEN Frontier Research System)
"From Spatio-Temporal Functions to Unconventional Computation"
Tsuneo Urisu (Division of Biomolecular Sensing, Institute for Molecular Science)
"Development of Ionchannel Biosensor and Applications"
Satoshi Hiyama1，Yuki Moritani1，Tatsuya Suda1, 2
(1Research Laboratories, NTT DoCoMo, Inc., 2Information and Computer Science,
University of California, Irvine)
"Molecular Communication Using Vesicles and Molecular Motors"
Recent achievements in structural biology have successfully provided numerous "static images" of folded proteins. Although these have provided significant insight into the aspects of protein molecules, conformational transitions associated to biological reactions are still difficult to understand only from such a "static view" of protein molecules. Development of techniques to reveal the "dynamical aspects" of a protein molecule is inevitably required for the future success in structural biology. In this symposium, we invite several young investigators who are actively developing such techniques to discuss the future prospect in this research field.
Daizo Hamada
(Department of Developmental Infectious Diseases, Research Institute,
Osaka Medical Center for Maternal and Child Health)
"Overview: Dynamical aspects of a protein molecule involved in various reactions"
Ryo Kitahara (RIKEN, SPring-8)
"Observation of meta-stable states of proteins by variable pressure NMR"
Kenji Sugase (Suntory Institute for Bioorganic Research)
"Metastable structure detected by relaxation dispersion NMR spectroscopy"
Hidekazu Hiroaki (Division of Structural Biology, Kobe University Graduate School of Medicine)
"Detection of structure transition of proteins by NMR H/D-exchange experiments"
Masaru Kawakami (School of Materials Science, JAIST)
" Mechanical responses and conformational dynamics of a single protein molecule
studied by AFM"
Tomoshi Kameda (CBRC, AIST)
"Visualization of structural transition by computer simulation"
Satoshi Ohnishi (RIKEN, GSC)
"Extracting structural information from unfolded polypeptides:
Challenge to the random-coil dogma"
As the number of the proteins and nucleic acids whose three-dimensional (3D) structure were already determined has been increased very rapidly, the next important step to clarify the mechanism of several phenomena in life is to understand the biomolecular interactions based on their 3D structures.. Especially the molecular recognition realized in the proteins and nucleic acids is the key for understand the mechanism. Most traditional researches indicate that the molecular recognition involves the thermodynamic process including huge number of freedom with solvent molecules. In this symposium, the strategy, recent topics and problems for the thermodynamic understanding of the biomolecular interactions based on the 3D structures, and the database for the basis of these researches will be discussed.
Shun-ichi Kidokoro, Maiko Uozaki, Aya Yamamoto
(Department of Bioengineering, Nagaoka University of Technology)
"Recent progress of calorimetry for evaluating biomolecular interactions"
Akinori Sarai (Department of Bioscience and Bioinformatics, Kyushu Institute of Technology)
"Thermodynamic databases and analyses on biomolecular interactions"
Ryota Kuroki (Quantum Beam Science Directorate, Japan Atomic Energy Agency)
"Characteristics of the hydrating water molecules on the surface of protein
observed by X-ray and neutron diffraction"
Minoru Saito (Graduate School of Science and Technology, Hirosaki University)
"Computational analysis and prediction of thermodynamic properties of molecular
interactions"
Hidetaka Torigoe (Faculty of Science, Tokyo University of Science)
"Thermodynamic properties of the intermolecular interactions involving nucleic
acids"
Masayuki Oda1, Nobutoshi Ito2, Takeshi Tsumuraya3, Ikuo Fujii3
（1Graduate School of Agriculture, Kyoto Prefectural University, 2School of Biomedical Science,
Tokyo Medical and Dental University, 3Graduate School of Science, Osaka Prefecture University）
"Antigen recognition and hydrolytic mechanism of catalytic antibody"
Protein dynamics are intimately connected to the structure-function relationship in many biological systems. For understanding biological phenomena in terms of physical chemistry, determination of static structures of biological molecules is a starting point rather than the end. Some of the functionally-important processes in protein motions involve relatively small alterations in overall structure. Vibrational spectroscopy is a powerful tool to investigate subtle structural changes and dynamics of biological molecules at a chemical-bond resolution. In this symposium, the speakers will show forefronts of vibrational spectroscopies, such as FT-IR spectroscopy with ATR technique, time-resolved resonance Raman spectroscopy, and nonlinear Raman techniques for interface-specific observation and vibrational imaging. It will be discussed how the spectroscopy can contribute to the progress in biophysics.
Yuji Furutani，Hideki Kandori
(Department of Materials Science and Engineering, Nagoya Inst. of Tech.)
"FT-IR Study of Protein-Protein Interaction -Rhodopsin as a Model System-"
Masayo Iwaki，Peter R. Rich (Department of Biology, University College London)
"ATR-FTIR: Probing Enzymatic Reactions under Physiological Conditions"
Tahei Tahara (Molecular Spectroscopy Laboratory, RIKEN)
"Development of Novel Nonlinear Spectroscopy and Its Application to Soft
Interfaces"
Yasuhisa Mizutani (Department of Chemistry, Graduate School of Science, Osaka University)
"Protein Dynamics Probed by Time-resolved Resonance Raman Spectroscopy"
Takashi Ogura (Grad. Sch. Life Sci., Univ. Hyogo)
"Probing a Single Molecular Vibration in Mitochondria during Turnover"
Hideaki Kano，Hiro-o Hamaguchi
(Department of Chemistry, School of Science, The University of Tokyo)
"Vibrational Imaging of a Living Cell by Nonlinear Raman Spectroscopy"
Recent genome analysis shows that no less than one third of the transcription products are not translated into proteins (nc RNA) and are directly involved in the important cellular processes. The study of ncRNA, processing, structure, and function, is very important for the future biology. In this symposium, the recent progress in this field will be discussed.
Isao Tanaka (Faculty of Advanced Life Science, Hokkaido University)
"Molecular basis of tRNA acetylation for maintaining the decoding fidelity "
Osamu Nureki (Graduate School of Bioscience and Biotechnology, Tokyo Institute of technology)
"Structural basis for dynamic mechanism of non-coding RNA maturation"
Makoto Kimura
(Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture
Kyushu University)
"Structural biology on the pre-tRNA processing ribozyme, ribonuclease P"
Toshio Uchiumi (Faculty of Science, Niigata University)
"Functional Structure of rRNA involved in Translation Process"
Masaru Tanokura
Graduate School of Agricultural and Life Sciences Applied Biological Chemistry, University of Tokyo)
"Crystal structure and dsRNA cleavage activity of the RNase III domain of Dicer"
In many countries, the early phase of structural proteomics is ending and structural biology is entering a new era, where structural data seem to accumulate at an ever faster pace. In this symposium we will discuss bioinformatics tools needed to produce, handle, classify and organize this huge flow of structural data. We will also discuss new prediction and analysis tools that are motivated by this growing amount of structural data.
Hideaki Sugawara (Center for Information Biology and DDBJ, National Institute of Genetics)
"Information flow, sharing and diffusion in a structural proteomics project composed
of diverse players"
Daron M. Standley 1, 2, Haruki Nakamura 1, 2
(Institute for Protein Research, Osaka University and JST-BIRD)
"Structural and functional analysis tools at PDBj"
Yutaka Kuroda (Dept of Biotechnology and Life Sciences, TUAT)
"Prediction of protein domains"
Kei Yura1, 2, 3, Kim Oanh 4, Nobuhiro Go3
(1Quantum Bioinf., JAEA, 2CREST JST, 3Bio-Unit, JAEA, 4Nara Women's Univ.)
"Prediction of biomacromolecule interfaces based on knowledge derived from
protein 3D structures and molecular evolution"
Hiroyuki Toh （Medical Institute of Bioregulation, Kyushu University)
"Prediction of protein-protein interaction"
Mitiko Go1, 2, Kei Yura3, 4, Masafumi Shionyu2
(1Ochanomizu Univ., 2, Dept. of BioScience, Nagahama Inst. of Bio-Science and Technology,
3Quantum Bioinf., JAEA, 4 Bio-Unit, JAEA)
"Alternative Splicing and Its Influence on Protein Conformation"
F1-ATPase is one of the most studied and best understood motor proteins thanks to the availability of molecular structures at atomic resolution by X-ray crystallographic and NMR studies, and innovative progress in nano-biological techniques such as single molecule experiments. The symposium focuses on molecular mechanism of the molecular motor function of F1-ATPase. Through discussion on the mechanism by researchers using various approaches such as single molecule and structural biology experiments, and molecular simulations, the symposium aims at clarifying what has been revealed to date and what has to be elucidated in the future to obtain thorough understanding of the molecular motor mechanism.
Hiroaki Yagi (IPR, Osaka University)
"The analysis of subunit conformational change on ligand binding in F1-ATPase by
NMR"
Mitsunori Ikeguchi (IGSAS, Yokohama City University)
"Conformational changes in F1-ATPase: Molecular dynamics simulation study"
Tomoko Masaike (Department of Physics, Gakushuin University)
"Conformational changes of the catalytic subunit in single F1-ATPase molecules
revealed by TIRF microscopy with polarization modulation"
Nobuyasu Koga，Shoji Takada
(Graduate School of Science, Kyoto University, Faculty of Science, Kobe University, and JST CREST)
"Rotary mechanisms of F1-ATPase revealed by molecular simulations"
Hiroyuki Noji (ISIR, Osaka University)
"Single-molecule studies on F1-ATPase correlating with structural study and
molecular simulation"
Shigehiko Hayashi (Graduate School of Science, Kyoto University)
"Mechanism of chemical-mechanical energy conversion of F1-ATPase molecular
motor studied by hybrid molecular simulations"
This symposium will reflect current research in the field of Biophysics, Cell Biology and Molecular Biology, and emphasize novel approaches in imaging and manipulation techniques for the dissection of biological function of cells and proteins. Speakers will describe state-of-the-art and emerging technologies used in their research field to explore the recent progress, ranging from advanced optical microscopy to MEMS techniques. Topics with these powerful tools and combination of technical tours de force will give researchers, especially young postdoctoral fellows and graduate students, great insight into biological system comprised of molecular and cellular processes, and therefore give the coming generation a new direction. It is hoped that the symposium will encourage both international and domestic cooperation in the field and stimulate young investigators.
Kaoru Kato (Advance Industrial Science and Technology)
"Live cell imaging without staining"
Tomomi Nemoto (National Institute for Physiological Sciences)
"Two-photon microscopy for functional imaging of neural and secretory cells"
Masayoshi Nakasako (Department of Physics, Keio University)
"Utilization of X-ray free electron laser in biophysics"
Takayuki Nishizaka (Department of Physics, Gakushuin University)
"Tracking of motor proteins at the single molecular level revealed
by advanced light microscopes"
Takahiro Hohsaka
(Department of Chemical Materials Science o Medical Polymers,
Japan Advanced Institute of Science and Technology)
"Pin-point fluorescence labeling of proteins through extension of the genetic"
Manuel Thery (Inst. Life Sci. Res. Technol., Commissariat a l’Energie Atomique Grenoble)
「Manipulating the geometry of cell micro-environment
to study the physical law of intra-cellular organization」
Cells are separated from their environments by plasma membranes. Membrane proteins are not only required to mediate transmembrane movements of ions, metabolites and drugs, but also responsible for signal transductions, oxidative protein folding and so on. In this symposium, we would like to focus on the mechanism of energy/signal transductions in the membrane proteins. Recently, the atomic structures of the enzymes are solved by X-ray crystallography, and it is possible to analyze the precise reaction mechanism. At this session, six young researchers will discuss in detail the molecular mechanism of the important membrane proteins based on their own approach.
Kenji Inaba (Medical Institute of Bioregulation, Kyushu Univ.)
" How are protein disulfide bonds formed in the cell?"
Takeshi Murata (Kyoto Univ., ERATO, RIKEN)
" How do V-ATPases transport ions?"
Yuji Sugita (RIKEN, CREST)
" How flexible is the structure of Ca2+-pump in membrane? "
Hideki Kandori (Nagoya Institute of Technology)
" How do molecular pumps work?"
Yuki Sudo (Nagoya Univ.)
" How do membrane proteins activate the cognate transducer protein?"
Satoshi Murakami (ISIR., Osaka Univ.)
" How do multi-drug efflux transporters recognize and transport substrates?"
It is expected that an essential understanding of the nature of protein may lead to a genuine understanding of the genome that creates proteins, and also may result in a genuine understanding of cells (physiological phenomenon characterized by properties of proteins) that are operated by proteins as functioning components. Nevertheless, only close inspections of each protein whose function has been highly optimized for the role can hardly provide insight into the nature (the basic ideas behind the designs) of the bio-nano-machine. In this symposium, protein nature will be reconsidered by examining the massive amount of knowledge for functions and structures of various proteins obtained through post-genomic research, and the possibility of unifying comprehension from genome to cells through rediscovery of proteins will be discussed.
Nobuhiro Hayashi (Institute for Comprehensive Medical Science, Fujita Health University)
"A Novel Picture of Life Revealed by Reconsideration of Nature of Protein"
Tetsuya Yomo
(Graduate School of Information Science and Technology, Graduate School of Frontier Bioscience,
Osaka University, ERATO/JST)
"Experimental Rugged Fitness Landscape in Protein Sequence Space"
Yoshifumi Nishimura (Graduate School of Supramolecular Biology, Yokohama City University)
"NMR dynamics and intrinsically disordered state of transcription-related proteins"
Kengo Kinoshita (Institute of Medical Science, Tokyo University)
"Database Analyses of Sequence-Structure-Function Relationship of Proteins"
Kazushige Kawabata (Department of Biological Sciences, Faculty of Science, Hokkaido University)
"Dynamical Effect on Cooperative Phenomena of Cell Systems"
Shigeki Mitaku (Department of Applied Physics, School of Engineering, Nagoya University)
"Amino Acid Sequence Analyses in terms of Physical Properties for Bird-eye View
of Total Proteomes"
The directed motions found in organelles and cells are generated by variety of protein motors. Among these, myosins, kinesins, and dyneins are well known as linear motors moving on protein filaments. Ribosomes are also thought to move linearly along mRNA while translating the mRNA into a protein. At the cellular level, translocational motility of Mycoplasma is driven by gliding proteins. Although there is an apparent similarity in linear movement, molecular mechanisms of the movement may vary from motor to motor, which may reflect functional diversity. In this symposium, we extract a common mechanism underlying their unidirectional movement by characterizing and comparing in detail the molecular mechanism(s) for the motion in each motor. (109 words)
Shiori Toba (Biological ICT group, NICT)
"Introduction of various biological motors and diversity of motion and functions
produced by dynein"
Michio Tomishige (Dept. Applied Physics, Univ. of Tokyo)
"ATP-driven structural changes of walking molecular motor protein kinesin"
Sotaro Uemura (Grad. School of Pharmaceutical Sciences, Univ. of Tokyo)
"The role of ribosome as a molecular motor in protein synthesis system"
Makoto Miyata (Dept. of Biology, Grad. School of Science, Osaka City Univ.)
"Mycoplasma gliding -a novel biomotility mechanism-"
Katsuyuki Shiroguchi (Dept. of Physics, Waseda Univ.)
"A mechanism of myosin V walking, and to understand biological motors"
Protein-ligand interactions play crucial roles in various biological events. Elucidation of the molecular mechanisms for the protein-ligand interactions requires in-depth understanding of not only the protein structural changes associated with the ligand binding, but also the resultant changes in the biochemical function. This leads to a succinct description of the interactions at the atomic level. This symposium aims to disseminate novel methodologies for depicting the protein-ligand interactions and to share the research strategies and concept by focusing on the structural and physicochemical characterization of the interactions so as to unravel features of ligand recognition mechanisms in general.
Toshio Hakoshima (Structural Biology Laboratory, Nara Institute of Science and Technology)
"Structural basis for peptide recognition by ERM proteins: Specificity and
interference between two binding sites"
Hiroaki Kato (Graduate School of Pharmaceutical Science, Kyoto University)
" Luciferin―Luciferase interaction and control of firefly's luminescent color"
Masao Ikeda-Saito
(Institute of Multidisciplinary Research for Advanced Materials, Tohoku University)
"Heme Catabolism Realized by the Heme-Heme Oxygenase Interaction"
Koichiro Ishimori (Faculty of Science, Hokkaido University)
"Structural and Functional Characterization of Sensor Proteins Regulated
by Heme Binding"
Takeshi Nishino (Nippon Medical School)
" Role of Various Amino Acid Residues in Binding of Substrates or
Inhibitors of Xanthine Oxidoreductase"
Biological systems are hierarchic and work via coupling between different spatio-temporal scales. Simulation study can, in general, connect between a model resolution scale and some larger/longer scales. The peta-flops super-computer will be available in a few years, which would stimulate multi-scale simulations of biological systems. Currently, broad-range simulations, from atomic to individual scales, are performed largely independently. Here, we design inter-discipline talks of four researchers in different resolutions hoping their cross-talks.
Akinori Kidera (International Grad. School of Arts and Sci., Yokohama City University)
" Petascale Biomolecular Simulations "
Chigusa Kobayashi (Inst. Mol. Sci.)
" Molecular simulation of protein translocation by translocon"
Taiji Adachi (Dept Mech Eng & Sci., Kyoto Univ., Riken)
" Multiscale Modeling and Simulation of Actin Cytoskeleton Dynamics "
Shuichi Onami (Genome Sci. Center, Riken)
" Simulations of cellular dynamics based on the dynamics of biomolecular complexes "
Gravity affects growth and morphogenesis in plants, and also influences the size of muscles and the bony labyrinth. Micro-organisms response to gravity and changes the direction of swimming. It is believed that these organisms and tissues sense and response to the gravity or to changes in the gravity vector. Gravi-induced responses might be divided into three temporal phases; sensing the gravity vector, signal transduction and following morphological and/or metabolic changes. Recent progresses in this research field have revealed biophysical basis of sensing and response to the gravity field.
Hitoshi Tatsumi，Masatsugu Toyota，Takuya Furuichi，Masahiro Sokabe
(Nagoya University Graduate School of Medicine)
"Gravity induced Ca ion concentration increases during a parabolic flight
in Arabidopsis seedlings."
Yoshihiro Mogami，Yoshihiro Mogami
(Graduate School of Humanities and Sciences, Ochanomizu University)
"Responses of Paramecium to gravity"
Miyo T. Morita，Moritaka Nakamura，Masao Tasaka
(Graduate School of Biological Sciences, Nara Institute of Science and Technology)
"Molecular genetic analysis of Arabidopsis shoot gravitropism"
Takeshi Nikawa,, Reiko Nakao, Harumi Furochi, Katsuya Hirasaka
(Department of Nutritional Physiology, Institute for health biosciences,
The University of Tokushima Graduate School)
" Molecular mechanism underlying sensing of unloading in skeletal muscle cells"
Kouichi Soga, Kazuyuki Wakabayashi, Takayuki Hoson
(Department of Biology and Geosciences, Graduate School of Science, Osaka City University)
"Signal perception in gravity resistance of plants"」
Noriaki Ihsioka1， Keiji Fukui2
(1JAXA ISAS, 2JSF)
"A New Age of Space Biology"
日本生物物理学会第45回年会実行委員会