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Genome Network Analysis in thermo-tolerant evolution of Escherichia coli

Research Project

Project/Area Number 20370092
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Evolutionary biology
Research InstitutionOsaka University

Principal Investigator

YOMO Tetsuya  Osaka University, 大学院・情報科学研究科, 教授 (00222399)

Co-Investigator(Kenkyū-buntansha) KISHIMOTO Toshihiko  東邦大学, 理学部, 准教授 (90339200)
Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥20,670,000 (Direct Cost: ¥15,900,000、Indirect Cost: ¥4,770,000)
Fiscal Year 2010: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2009: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2008: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Keywordsトランスクリプトーム解析 / プロテオーム解析 / 耐熱化機構 / 大腸菌 / 諭
Research Abstract

For elucidation of the mechanism of evolution, we have developed thermo-tolerant E. coli and analyzed mutation of genome DNA, gene expression (transcriptome), and protein expression and thermo-stability (proteome) of several strains of E. coli through thermo-tolerant evolution process. Whole-genome sequence analysis revealed the transition from positive to neutral in mutation fixation, accompanied with a considerable escalation of spontaneous substitution rate in the late fitness recovery phase. Moreover, transcriptome analysis revealed transition from increase to convergence in fluctuation of gene expression, and proteome analysis revealed that no remarkable change in thermo-stability of expressed proteins.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (97 results)

All 2011 2010 2009 2008

All Journal Article (25 results) (of which Peer Reviewed: 22 results) Presentation (67 results) Book (3 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Cooperative adaptation to establishment of a synthetic bacterial mutua lism.2011

    • Author(s)
      Kazufumi Hosoda, Shingo Suzuki, Yoshinori Yamauchi, Yasunori Shi roguchi, Akiko Kashiwagi, Naoaki Ono, Kotaro Mori, Tetsuya Yomo.
    • Journal Title

      PLoS ONE

      Volume: Vol.6 No.2

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transition frpositive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.2010

    • Author(s)
      Toshihiko Kishimoto, Leo Iijima, Makoto Tatsumi, Naoaki Ono, Ayana Oyake, Tomomi Hashimoto, Moe Matsuo, Masato Okubo, Shingo Suzuki, Kotaro Mori, Akiko Kashiwagi, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo
    • Journal Title

      PLoS Genetics. 6巻10

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.2010

    • Author(s)
      Takaaki Horinouchi, Kuniyasu Tamaoka, Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu
    • Journal Title

      BMC Genomics. 11巻579

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Refined method for the genomic integration of complex synthetic circuits.2010

    • Author(s)
      Bei-Wen Ying, Yoichiro Ito, Yostihiro Shimizu, Tetsuya Yomo.
    • Journal Title

      J Biosci Bioeng.

      Volume: Vol.110 No.5

    • NAID

      110007988801

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.2010

    • Author(s)
      Toshihiko Kishimoto, Leo Iijima, Makoto Tatsumi, Naoaki Ono, Ayana Oyake, Tomomi Hashimoto, Moe Matsuo, Masato Okubo, Shingo Suzuki, Kotaro Mori, Akiko Kashiwagi, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo.
    • Journal Title

      PLoS Genetics

      Volume: Vol.6 No.10

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.2010

    • Author(s)
      Takaaki Horinouchi, Kuniyasu Tamaoka, Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu.
    • Journal Title

      BMC Genomics

      Volume: Vol.11 No.579

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolvability and single-genotype fluctuation in phenotypic properties : a simule heteropolymer model.2010

    • Author(s)
      Chen T, Vernazobres D, Yomo T, Bornberg-Bauer E, Chan HS.
    • Journal Title

      Biophysical Journal

      Volume: Vol.98 No.11 Pages: 2487-2496

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Qbeta replicase2010

    • Author(s)
      Urabe, H., Ichihashi, N., Matsuura, T., Hosoda, K., Kazuta, Y., Kita, H., Yomo, T.
    • Journal Title

      Biochemistry (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions2010

    • Author(s)
      Sunami, T., Hosoda, K., Suzuki, H., Matsuura, T., Yomo, T.
    • Journal Title

      Langmuir (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantifying epistatic interactions among the components constituting the protein translation system.2009

    • Author(s)
      Matsuura, T., Kazuta, Y., Aita, T., Adachi, J., Yomo, T.
    • Journal Title

      Molecular Systems Biology 5巻297

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] How selection affects phenotypic fluctuation.2009

    • Author(s)
      Ito, Y., Toyota, H., Kaneko, K., Yomo, T.
    • Journal Title

      Molecular Systems Biology 5巻264

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Population Analysis of Structural Properties of Giant Liposomes by Flow Cytometry.2009

    • Author(s)
      Nishimura, K., Hosoi, T., Sunami, T., Toyota, T., Fujinami, M., Oguma, K., Matsuura, T., Suzuki, H., Yomo, T.
    • Journal Title

      Langmuir

      Pages: 10439-10443

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantifying epistatic interactions among the components constituting the protein translation system.2009

    • Author(s)
      Matsuura, T., Kazuta, Y., Aita, T., Adachi, J., Yomo, T.
    • Journal Title

      Mol. Syst. Biol., 5

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Noisy cell growth rate leads to fluctuating protein concentration in bacteria2009

    • Author(s)
      Tsuru, S., Ichinose, J., Kashiwagi, A., Ying, B-W., Kaneko, K., Yomo, T.
    • Journal Title

      Physical Biology 6(3)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system.2009

    • Author(s)
      Ou, J., Furusawa, C., Yomo, T., Shimizu, H.
    • Journal Title

      BioSystems 97(3)

      Pages: 160-164

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] How selection affects phenotypic fluctuation.2009

    • Author(s)
      Ito, Y., Toyota, H., Kaneko, K., Yomo, T.
    • Journal Title

      Mol. Syst. Biol., 5

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum2009

    • Author(s)
      Kihara, K., Mori, K., Suzuki, S., Ono, N., Furusawa, C., Yomo, T.
    • Journal Title

      BioSystems 96(2)

      Pages: 141-164

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Takeshi Sunami, Tomoaki Matsuura, Hiroaki Suzuki, Tetsuya Yomo
    • Journal Title

      Cell-Free Protein Production Methods and Protocols (Methods in Molecular Biology Vol.607)(Humana Press)

      Pages: 243-256

    • Related Report
      2009 Annual Research Report
  • [Journal Article]2009

    • Author(s)
      Takeshi Sunami, Hiroshi Kita, Kazufumi Hosoda, Tomoaki Matsuura, Hiroaki Suzuki, Tetsuya Yomo
    • Journal Title

      Methods in Enzymology Volume 464(Academic Press, New York)

      Pages: 19-29

    • Related Report
      2009 Annual Research Report
  • [Journal Article]2009

    • Author(s)
      Hayashi, Y., Aita, T., Yomo, T.
    • Journal Title

      Contemporarv Trends in Bacteriophaee Research(Nova Science Publishers Inc., New York)

      Pages: 179-190

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Evolution of carrying capacity in evolution experiments focusing on asingle locus on the Escherichia coli chromosome.2009

    • Author(s)
      Mori, K., Kashiwagi, A., Urabe, I., Yomo, T.
    • Journal Title

      BioSystems 95 (2)

      Pages: 114-119

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Construction of Escherichia coli gene expression level perturbationcollection.2009

    • Author(s)
      Kashiwagi, A., Sakurai, T., Tsuru, S., Ying, B-W., Mori, K., Yomo, T.
    • Journal Title

      Metab. Eng. 11

      Pages: 56-63

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Model-based analysis of non-specific binding for background correctionof high-density oligonucleotide microarrays.2009

    • Author(s)
      Furusawa, C, Ono, N., Suzuki, S., Agata, T., Shimizu, H., Yomo, T.
    • Journal Title

      Bioinformatics 25

      Pages: 36-41

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive analysis of the effects of Escherichia coli ORFs on protein translation reaction. : .2008

    • Author(s)
      Kazuta, Y., Adachi, J., Matsuura, T., Ono, N., Mori, H., andYomo, T.
    • Journal Title

      Mol. Cell. Proteomics 7 (8)

      Pages: 1530-1540

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.2008

    • Author(s)
      Ono, N., Suzuki, S., Furusawa, C, Agata, T., Kashiwagi, A., Shimizu, H., Yomo, T.
    • Journal Title

      Bioinformatics 24(10)

      Pages: 1278-1285

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] 高温適応進化における大腸菌の発現パターンの再編2010

    • Author(s)
      北原和樹, 岸本利彦, 小野直亮, 古澤力, 鈴木真吾, インベイウェン, 四方哲也
    • Organizer
      BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会)
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-09
    • Related Report
      2010 Annual Research Report
  • [Presentation] Genome-wide mutation and transcriptional reorganization in the thermal adaptive Escherichia coli from laboratory evolution2010

    • Author(s)
      Bei-Wen Ying, Kazuki Kitahara, Leo Ijima, Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Tetsuya Yomo
    • Organizer
      BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会合同大会)
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-07
    • Related Report
      2010 Final Research Report
  • [Presentation] Construction of high temperature genetic engineering system for thermo-tolerant E. coli2010

    • Author(s)
      Toshihiko Kishimoto, Saeko Shimada, Ayana Oyake, Tomomi Hashimoto, Tetsuya Yomo
    • Organizer
      BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会合同大会)
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-07
    • Related Report
      2010 Final Research Report
  • [Presentation] 複数系列の大腸菌の高温適応進化過程におけるゲノム変異解析2010

    • Author(s)
      飯島玲生, 小宅綾菜, 橋本智美, 金子冬郎, 鈴木真吾, 岸本利彦, 應〓文, 四方哲也
    • Organizer
      BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会)
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] Construction of high temnerature genetic engineering system for thermo-tolerant E.coli.2010

    • Author(s)
      Toshihiko Kishimoto, Saeko Shimada, Ayana Oyake, Tomoni Hashimoto, Tetsuya Yomo.
    • Organizer
      BMB2010(第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会)
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] 複雑システムとしての生物の進化2010

    • Author(s)
      四方哲也
    • Organizer
      理研ASI細胞システムコロキウムシリーズI「理論生物学」鈴木梅太郎記念ホール
    • Place of Presentation
      理化学研究所和光キャンパス
    • Year and Date
      2010-12-03
    • Related Report
      2010 Final Research Report
  • [Presentation] 複雑システムとしての生物の進化2010

    • Author(s)
      四方哲也
    • Organizer
      理研ASI細胞システムコロキウムシリーズI「理論生物学」
    • Place of Presentation
      鈴木梅太郎記念ホール(理化学研究所和光キャンパス)(招待発表)
    • Year and Date
      2010-12-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] 細胞の個性と環境応答2010

    • Author(s)
      四方哲也
    • Organizer
      JSME26(第26回日本微生物生態学大会)
    • Place of Presentation
      筑波大学
    • Year and Date
      2010-11-26
    • Related Report
      2010 Final Research Report
  • [Presentation] 細胞の個性と環境応答2010

    • Author(s)
      四方哲也
    • Organizer
      JSME26(第26回日本微生物生態学大会)
    • Place of Presentation
      筑波大学(招待発表)
    • Year and Date
      2010-11-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] 大腸菌の耐熱進化における細胞内状態の最適化-細胞内DNA、RNA、タンパク質の適応変化2010

    • Author(s)
      應〓文、北原和樹、飯島玲生、小野直亮、鈴木真吾、古澤力、岸本利彦、四方哲也
    • Organizer
      「細胞を創る」研究会3.0
    • Place of Presentation
      東京大学生産技術研究所
    • Year and Date
      2010-11-12
    • Related Report
      2010 Annual Research Report
  • [Presentation] 長期実験室内進化からみた大腸菌の変異と発現の変遷2010

    • Author(s)
      應〓文、北原和樹、飯島玲生、小野直亮、古澤力、鈴木真吾、岸本利彦、四方哲也
    • Organizer
      第12回日本進化学会大会
    • Place of Presentation
      東京工業大学大岡山キャンパス
    • Year and Date
      2010-08-03
    • Related Report
      2010 Final Research Report
  • [Presentation] 長期実験室内進化からみた大腸菌の変異と発現の変遷2010

    • Author(s)
      應〓文、北原和樹、飯島玲生、小野直亮、古澤力、鈴木真吾、岸本利彦、四方哲也
    • Organizer
      第12回日本進化学会大会
    • Place of Presentation
      東京工業大学 大岡山キャンパス
    • Year and Date
      2010-08-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] 高温適応進化における大腸菌の発現プロフィールのスナップショット2010

    • Author(s)
      北原和樹、岸本利彦、小野直亮、古澤力、鈴木真吾、應〓文、四方哲也
    • Organizer
      第12回日本進化学会大会
    • Place of Presentation
      東京工業大学 大岡山キャンパス
    • Year and Date
      2010-08-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] 複数系列の大腸菌の高温適応進化過程におけるゲノム変異解析2010

    • Author(s)
      飯島玲生、小宅綾菜、橋本智美、金子冬朗、鈴木真吾、岸本利彦、應〓文、四方哲也
    • Organizer
      第12回日本進化学会大会
    • Place of Presentation
      東京工業大学 大岡山キャンパス
    • Year and Date
      2010-08-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] 大腸菌の耐熱進化時に見られる相互作用の解析2010

    • Author(s)
      小宅綾菜、岸本利彦、四方哲也
    • Organizer
      第12回日本進化学会大会
    • Place of Presentation
      東京工業大学 大岡山キャンパス
    • Year and Date
      2010-08-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] 大腸菌高温適応時にみられる細胞挙動の解析2010

    • Author(s)
      橋本智美、小宅綾菜、岸本利彦、四方哲也
    • Organizer
      第12回日本進化学会大会
    • Place of Presentation
      東京工業大学 大岡山キャンパス
    • Year and Date
      2010-08-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] Synthetic Toggle Switch for Selective Gene Expression in Bacteria.2010

    • Author(s)
      Yuki Matsumoto, Yoichiro Ito, Bei-Wen Ying, Tetsuya Yomo.
    • Organizer
      ibio2010
    • Place of Presentation
      Dalian Municipal Party Committee Hotel, China
    • Year and Date
      2010-07-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] Biological Noise Induced Gene Production in Bacteria-a Universal Principle in the Adaptive Response to Starvation.2010

    • Author(s)
      Bei-Wen Ying, Saburo Tsuru, Yuki Matsumoto, Yoshihiro Shimizu, Yoichiro Ito, Tetsuya Yomo.
    • Organizer
      ibio2010
    • Place of Presentation
      Dalian Municipal Party Committee Hotel, China
    • Year and Date
      2010-07-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] Biological Noise Induced Gene Production in Bacteria-a Universal Principle in the Adaptive Response to Starvation2010

    • Author(s)
      Bei-Wen Ying, Saburo Tsuru, Yuki Matsumoto, Yoshihiro Shimizu, Yoichiro Ito, Tetsuya Yomo
    • Organizer
      ibio2010, Dalian Municipal Party Committee Hotel
    • Place of Presentation
      China
    • Year and Date
      2010-07-25
    • Related Report
      2010 Final Research Report
  • [Presentation] Constructive approach to proto-cellular life.2010

    • Author(s)
      四方哲也
    • Organizer
      UK-Japan Workshop on Synthetic Biology
    • Place of Presentation
      British Embassy, Tokyo
    • Year and Date
      2010-01-21
    • Related Report
      2010 Final Research Report
  • [Presentation] Constructive approach to proto-cellular life2010

    • Author(s)
      Yomo, T.
    • Organizer
      UK-Janan Workshop on Synthetic Biology
    • Place of Presentation
      British Embassy, Tokyo
    • Related Report
      2009 Annual Research Report
  • [Presentation] Laboratory evolution of thermal adaptive Escherichia coli2010

    • Author(s)
      Iijima, L., Ying, BW., Ono, N., Suzuki, S., Kishimoto, T., Tatsumi, M., Mori, K., Furusawa, C., Yomo, T.
    • Organizer
      定量生物学の会第2回年会
    • Place of Presentation
      大阪大学コンベンションセンター、銀杏会館
    • Related Report
      2009 Annual Research Report
  • [Presentation] 大腸菌高温適応進化過程における細胞間相互作用の増殖速度への影響2009

    • Author(s)
      小宅綾菜、橋本智美、青柳美穂、岸本利彦、四方哲也
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2009-12-12
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] Genome-wide analysis of thermal adaptive Escherichia coli from laboratory evolution.2009

    • Author(s)
      インベイウェン、北原和樹、飯島玲王、小野直亮、鈴木真吾、岸本利彦、古澤力、四方哲也
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2009-12-10
    • Related Report
      2010 Final Research Report
  • [Presentation] Phenotypic fluctuation induced biological adaptation.2009

    • Author(s)
      Bei -Wen Ying, Yoichiro Ito, Yoshihiro Shimizu, Yuki Matsumoto, Junya Ichinose, Saburo Tsuru, Tetsuya Yomo
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島文理大学
    • Year and Date
      2009-10-30
    • Related Report
      2010 Final Research Report
  • [Presentation] Phenotypic fluctuation induced biological adaptation2009

    • Author(s)
      Bei-Wen Ying, Yoichiro Ito, Yoshihiro Shimizu, Yuki Matsumoto, Junya Ichinose, Saburo Tsuru, Tetsuya Yomo
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島文理大学, 2009年10月30日-11月1日
    • Year and Date
      2009-10-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] Adaptive response to environmental changes utilizing the bistability of the lactose operon2009

    • Author(s)
      Yoshihiro Shimizu, Bei-Wen Ying, Junya Ichinose, Yoichiro Ito, Tetsuya Yomo
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島文理大学, 2009年10月30日-11月1日
    • Year and Date
      2009-10-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] 大腸菌ゲノムの高温適応進化2009

    • Author(s)
      四方哲也
    • Organizer
      「細胞を創る」研究会2.0
    • Place of Presentation
      東京大学鉄門記念講堂
    • Year and Date
      2009-10-03
    • Related Report
      2010 Final Research Report
  • [Presentation] Phenotypic fluctuation in experimental evolution.2009

    • Author(s)
      四方哲也
    • Organizer
      International Symposium on Complex System Biology
    • Place of Presentation
      The University of Tokyo, Japan
    • Year and Date
      2009-09-30
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] How Darwinian selection affects phenotypic fluctuation.2009

    • Author(s)
      四方哲也
    • Organizer
      13th Evolutionary Biology Meeting at Marseilles
    • Place of Presentation
      Marseilles, France
    • Year and Date
      2009-09-25
    • Related Report
      2010 Final Research Report
  • [Presentation] 遺伝子発現揺らぎを用いた適応応答2009

    • Author(s)
      四方哲也
    • Organizer
      日本遺伝学会第81回大会
    • Place of Presentation
      信州大学
    • Year and Date
      2009-09-17
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] 実験室内進化させた高温適応大腸菌のゲノムワイド解析2009

    • Author(s)
      應〓文、北原和樹、飯島玲生、小野直亮、鈴木真吾、岸本利彦、古澤力、四方哲也
    • Organizer
      第11回日本進化学会大会
    • Place of Presentation
      北海道大学
    • Year and Date
      2009-09-04
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] Constructive approach to proto-cellular life.2009

    • Author(s)
      四方哲也
    • Organizer
      Workshop OQOL'09 : Open Questions on the Origins of Life 2009
    • Place of Presentation
      San Sebastian, Spain
    • Year and Date
      2009-05-21
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] Construction of Escherichia coli gene expression level perturbation collection2009

    • Author(s)
      Akiko Kashiwagi, Takahiro Sakurai, Saburo Tsuru, Bei-Wen Ying, Kotaro Mori, Tetsuya Yomo
    • Organizer
      APBioChEC'09 (Asia Pacific Biochemical Engineering Conference 2009)
    • Place of Presentation
      Kobe International Conference Center, Japan
    • Related Report
      2009 Annual Research Report
  • [Presentation] A model-based analysis method for detection of single-base substitution using resequencing microarrays2009

    • Author(s)
      Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Hiroshi Shimizu, Tetsuya Yomo
    • Organizer
      APBioChEC'09 (Asia Pacific Biochemical Engineering Conference 2009)
    • Place of Presentation
      Kobe International Conference Center, Japan
    • Related Report
      2009 Annual Research Report
  • [Presentation] Adaptive phenotypic change in a synthetic ecosystem composed of two strains of Escherichia coli.2009

    • Author(s)
      Hosoda, K., Shiroguchi, Y., Yamauchi, Y., Mori, K., Suzuki, S., Kashiwagi, A., Yomo, T.
    • Organizer
      International Symposium on Complex System Biology
    • Place of Presentation
      The University of Tokyo, Japan
    • Related Report
      2009 Annual Research Report
  • [Presentation] Analysis of adaptive gene expression to nutrient depletion out of native regulatory mechanisms.2009

    • Author(s)
      Tsuru, S., Ying, B.W., Mori, K., Ushioda, J., Kashiwagi, A., Yomo, T.
    • Organizer
      International Symposium on Complex System Biology
    • Place of Presentation
      The University of Tokyo, Japan
    • Related Report
      2009 Annual Research Report
  • [Presentation] Genome-wide mutation analysis of the thermostable bacteria from experimental evolution.2009

    • Author(s)
      Iijima, L., Ying, BW, Ono, N., Suzuki, S., Mori, K., Tatsumi, M., Kishimoto, T., Furusawa, C., Yomo,
    • Organizer
      International Symposium on Complex System Biology
    • Place of Presentation
      The University of Tokyo, Japan
    • Related Report
      2009 Annual Research Report
  • [Presentation] How Darwinian selection affects phenotypic fluctuation2009

    • Author(s)
      Yomo, T.
    • Organizer
      13th Evolutionary Biology Meeting at Marseilles
    • Place of Presentation
      Marseilles, FRANCE
    • Related Report
      2009 Annual Research Report
  • [Presentation] Transcriptome analysis of thermal adaptive Escherichia coli2009

    • Author(s)
      Kitahara, K., Ying, B-W., Ono, N., Suzuki, S., Kishimoto, T., Furusawa, C., Yomo, T.
    • Organizer
      The 8th International Workshop on Advanced Genomics
    • Place of Presentation
      National Center of Sciences, Tokyo
    • Related Report
      2009 Annual Research Report
  • [Presentation] Genome-wide analysis of thermal adaptive Escherichia coli from laboratory evolution2009

    • Author(s)
      インベイウェン、北原和樹、飯島玲王、小野直亮、鈴木真吾、岸本利彦、吉澤力、四方哲也
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2009 Annual Research Report
  • [Presentation] 大腸菌の実験室内での高温適応進化2009

    • Author(s)
      飯島玲生、インベイウェン、鈴木真吾、岸本利彦、小野直亮、吉澤力、四方哲也
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2009 Annual Research Report
  • [Presentation] 耐熱進化させた大腸菌のトランスクリプトーム解析2009

    • Author(s)
      北原和樹、インベイウェン、小野直亮、鈴木真吾、岸本利彦、古澤力、四方哲也
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2009 Annual Research Report
  • [Presentation] 大腸菌ゲノムの高温適応進化2009

    • Author(s)
      四方哲也
    • Organizer
      「細胞を創る」研究会2.0
    • Place of Presentation
      東京大学 鉄門記念講堂
    • Related Report
      2009 Annual Research Report
  • [Presentation] Laboratory evolution of thermal adaptive Escherichia coli2009

    • Author(s)
      Iijima, L., Ying, BW., Ono, N., Suzuki, S., Kishimoto, T., Tatsumi, M., Mori, K., Furusawa, C., Yomo, T.
    • Organizer
      「細胞を創る」研究会2.0
    • Place of Presentation
      東京大学 鉄門記念講堂
    • Related Report
      2009 Annual Research Report
  • [Presentation] 大腸菌と溶菌性RNAバクテリオファージQβの実験室内共培養系における個体群動態とRNAバクテリオファージ集団のゲノム塩基配列変化2009

    • Author(s)
      柏木明子、四方哲也
    • Organizer
      第11回日本進化学会大会
    • Place of Presentation
      北海道大学
    • Related Report
      2009 Annual Research Report
  • [Presentation] 耐熱性を進化させた大腸菌のゲノム変異の解析2009

    • Author(s)
      飯島玲生、應〓文、小野直亮、鈴木真吾、森光太郎、辰巳誠、岸本利彦、古澤力、四方哲也
    • Organizer
      第11回日本進化学会大会
    • Place of Presentation
      北海道大学
    • Related Report
      2009 Annual Research Report
  • [Presentation] Fitness-induced attractor selection upon a genetic switch2008

    • Author(s)
      Yomo, T.
    • Organizer
      2008 CSHL Meeting on Engineering Principles in Biological Systems
    • Place of Presentation
      Cold Spring Harbor, NY
    • Year and Date
      2008-12-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] 耐熱性を進化させた大腸菌のゲノム変異の解析2008

    • Author(s)
      飯島玲生、小野直亮、鈴木真吾、岸本利彦、辰巳誠、森光太郎、インベイウェン、古澤力、四方哲也
    • Organizer
      第81回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2008-12-10
    • Related Report
      2010 Final Research Report
  • [Presentation] Adaptive response of fluctuating gene network2008

    • Author(s)
      Yomo, T.
    • Organizer
      3rd Int. Conference on Bio-Inspired Models of Network, Information, and Computing Systems
    • Place of Presentation
      Awaji Yumebutai International Conference Center
    • Year and Date
      2008-11-25
    • Related Report
      2008 Annual Research Report
  • [Presentation] Quantitative expression analysis using oligonucleotide microarrays basedon a physico-chemical model.2008

    • Author(s)
      Ono, N., Suzuki, S., Furusawa, C, Shimizu, H., Yomo, T.
    • Organizer
      3rd International Conference on Bio-Inspired Models of Network, Information, and Computing Systems (BIONETICS 2008)
    • Place of Presentation
      Awaji Yumebutai International Conference Center, Hyogo
    • Year and Date
      2008-11-25
    • Related Report
      2008 Annual Research Report
  • [Presentation] Cellular fluctuation in protein concentration and its role on adaptive response2008

    • Author(s)
      Yomo, T., Tsuru, S., Ichinose, J., Kaneko, K., Ying, B.W.
    • Organizer
      The 9th International Conference on Systems Biology.
    • Place of Presentation
      Goteborg, Sweden
    • Year and Date
      2008-08-25
    • Related Report
      2010 Final Research Report
  • [Presentation] 大腸菌を使った耐熱化実験進化系の中で出現した相互作用を中心とした現象の解析2008

    • Author(s)
      岸本利彦、四方哲也
    • Organizer
      第10回日本進化学会大会
    • Place of Presentation
      東京大学駒場キャンパス
    • Year and Date
      2008-08-23
    • Related Report
      2010 Final Research Report 2008 Annual Research Report
  • [Presentation] Cellular fluctuation in protein concentration and its role on adaptiveresponse2008

    • Author(s)
      Yomo, T., Tsuru, S., Ichinose, J., Kaneko, K., Ying, B-W.
    • Organizer
      The 9th International Conference on Systems Biology (ICSB 2008)
    • Place of Presentation
      Goteborg, Sweden
    • Year and Date
      2008-08-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] Efficient method for integration of complex genetic design into genome2008

    • Author(s)
      Ying, B. W., Ito, Y., Yomo, T.
    • Organizer
      The Fourth International Meeting on Synthetic Biology
    • Place of Presentation
      Hong Kong University ofScience and Technology
    • Related Report
      2008 Annual Research Report
  • [Presentation] Cellular fluctuation in protein concentration and its role on adaptiveresponse.2008

    • Author(s)
      Yomo, T., Tsuru, S., Ichinose, J., Kaneko, K., Ying, B-W.
    • Organizer
      The 9th International Conference on Systems Biology (ICSB 2008)
    • Place of Presentation
      Goteborg, Sweden
    • Related Report
      2008 Annual Research Report
  • [Presentation] Adaptive gene expression to nutrient depletion out of native regulatorymechanisms.2008

    • Author(s)
      Tsuru, S., Ying, B. W., Ushioda, J., Kashiwagi, A., Yomo, T.
    • Organizer
      The 9th International Conference on Systems Biology (ICSB 2008)
    • Place of Presentation
      Goteborg, Sweden
    • Related Report
      2008 Annual Research Report
  • [Presentation] 大腸菌を用いた人工共生系における適応的細胞状態変化2008

    • Author(s)
      細田一史, 森光太郎, 柏木明子, 山内義教, 城口泰典, 四方哲也
    • Organizer
      「細胞を創る」研究会1.0
    • Place of Presentation
      大阪大学銀杏会館
    • Related Report
      2008 Annual Research Report
  • [Presentation] 栄養枯渇に対する本来の制御系を用いない適応的な遺伝子発現2008

    • Author(s)
      津留三良, 森光太郎, Bei-WenYing, 潮田純弥, 柏木明子, 四方哲也
    • Organizer
      「細胞を創る」研究会1.0
    • Place of Presentation
      大阪大学銀杏会館
    • Related Report
      2008 Annual Research Report
  • [Presentation] Simple approach for construction of genome-integrated artificial genetic circuit2008

    • Author(s)
      Bei-Wen Ying, Yoichiro Ito, Tetsuya Yomo
    • Organizer
      「細胞を創る」研究会1.0
    • Place of Presentation
      大阪大学銀杏会館
    • Related Report
      2008 Annual Research Report
  • [Presentation] 二重安定性における適応応答2008

    • Author(s)
      清水義博, インベイウェン, 伊藤洋一郎, 一ノ瀬純也, 四方哲也
    • Organizer
      「細胞を創る」研究会1.0
    • Place of Presentation
      大阪大学銀杏会館
    • Related Report
      2008 Annual Research Report
  • [Presentation] リシーケンスマイクロアレイを用いた大腸菌の全ゲノム変異解析2008

    • Author(s)
      小野直亮, 鈴木真吾, 古潭力, 情水浩, 四方哲也
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2008 Annual Research Report
  • [Presentation] 同じ制御下の異なる遺伝子の環境変化に対する発現応答2008

    • Author(s)
      三田弘道, Ying Bei-Wen, 伊藤洋一郎, 四方哲也
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2008 Annual Research Report
  • [Presentation] lacオペロンの二重安定性における環境応答2008

    • Author(s)
      清水義博, インベイウェン, 伊藤洋一郎, 一ノ瀬純也, 四方哲也
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2008 Annual Research Report
  • [Presentation] 生物のゆらぎは進化によっても創られる2008

    • Author(s)
      伊藤洋一郎, 豊田一志, 金子邦彦, 四方哲也
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2008 Annual Research Report
  • [Presentation] 耐熱性を進化させた大腸菌のゲノム変異の解析2008

    • Author(s)
      飯島玲生, 小野直亮, 鈴木真吾, 岸本利彦, 辰巳誠, 森光太郎, インベイウェン, 古滓力, 四方哲也
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会・合同大会
    • Place of Presentation
      神戸国際会議場
    • Related Report
      2008 Annual Research Report
  • [Presentation] 耐熱進化させた大腸菌のトランスクリプトーム解析2008

    • Author(s)
      北原和樹, インベイウェン, 小野直亮, 鈴木真吾, 岸本利彦, 古滓力, 四方哲也
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会・合同大会
    • Place of Presentation
      神戸国際会議場
    • Related Report
      2008 Annual Research Report
  • [Book] 現代生物科学入門9 合成生物学2010

    • Author(s)
      柳川弘志・土居信英・板谷光泰・菅原正・四方哲也
    • Publisher
      岩波書店
    • Related Report
      2010 Annual Research Report
  • [Book] 高等研報告書 : ダイナミックスからみた生命的システムの進化と意義2008

    • Author(s)
      四方哲也(分担)
    • Publisher
      財団法人国際高等研究所発行
    • Related Report
      2008 Annual Research Report
  • [Book] 「生る」(生命誌 年刊号vol. 53-56)中村桂子編2008

    • Author(s)
      四方哲也(分担)
    • Publisher
      JT生命誌研究館
    • Related Report
      2008 Annual Research Report
  • [Patent(Industrial Property Rights)] タンパク質の可逆的デュアルラベリング法2010

    • Inventor(s)
      柳田勇人、松浦友亮、四方哲也
    • Industrial Property Number
      2010-000705
    • Filing Date
      2010-01-05
    • Related Report
      2009 Annual Research Report
  • [Patent(Industrial Property Rights)] エマルジョンを用いたRNAの選択的増幅法2009

    • Inventor(s)
      四方哲也、松浦友亮、市橋伯一、占部博也
    • Industrial Property Number
      2009-168285
    • Filing Date
      2009-07-16
    • Related Report
      2009 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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