Genome Network Analysis in thermo-tolerant evolution of Escherichia coli

• Project/Area Number: 20370092
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Evolutionary biology
• Research Institution: Osaka 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: ¥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.

Research Products

• [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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Qbeta replicase (2010)
  • Author(s): Urabe, H., Ichihashi, N., Matsuura, T., Hosoda, K., Kazuta, Y., Kita, H., Yomo, T.
  • Journal Title: Biochemistry (in press)
  • Peer Reviewed
• [Journal Article] Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions (2010)
  • Author(s): Sunami, T., Hosoda, K., Suzuki, H., Matsuura, T., Yomo, T.
  • Journal Title: Langmuir (in press)
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Noisy cell growth rate leads to fluctuating protein concentration in bacteria (2009)
  • Author(s): Tsuru, S., Ichinose, J., Kashiwagi, A., Ying, B-W., Kaneko, K., Yomo, T.
  • Journal Title: Physical Biology 6(3)
  • 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
  • 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
  • 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 discoideum (2009)
  • Author(s): Kihara, K., Mori, K., Suzuki, S., Ono, N., Furusawa, C., Yomo, T.
  • Journal Title: BioSystems 96(2) Pages: 141-164
  • 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
• [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
• [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
• [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
  • 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
  • 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
  • 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
  • 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
  • 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
• [Presentation] Genome-wide mutation and transcriptional reorganization in the thermal adaptive Escherichia coli from laboratory evolution (2010)
  • 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
• [Presentation] Construction of high temperature genetic engineering system for thermo-tolerant E. coli (2010)
  • 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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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, Dalian Municipal Party Committee Hotel
  • Place of Presentation: China
  • Year and Date: 2010-07-25
• [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
• [Presentation] Constructive approach to proto-cellular life (2010)
  • Author(s): Yomo, T.
  • Organizer: UK-Janan Workshop on Synthetic Biology
  • Place of Presentation: British Embassy, Tokyo
• [Presentation] Laboratory evolution of thermal adaptive Escherichia coli (2010)
  • 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
• [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
• [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
• [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
• [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, 2009年10月30日-11月1日
  • Year and Date: 2009-10-30
• [Presentation] Adaptive response to environmental changes utilizing the bistability of the lactose operon (2009)
  • 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
• [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
• [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
• [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
• [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
• [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
• [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
• [Presentation] Construction of Escherichia coli gene expression level perturbation collection (2009)
  • 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
• [Presentation] A model-based analysis method for detection of single-base substitution using resequencing microarrays (2009)
  • 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
• [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
• [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
• [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
• [Presentation] How Darwinian selection affects phenotypic fluctuation (2009)
  • Author(s): Yomo, T.
  • Organizer: 13th Evolutionary Biology Meeting at Marseilles
  • Place of Presentation: Marseilles, FRANCE
• [Presentation] Transcriptome analysis of thermal adaptive Escherichia coli (2009)
  • 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
• [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、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
• [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
• [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
• [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
• [Presentation] Laboratory evolution of thermal adaptive Escherichia coli (2009)
  • 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
• [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
• [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
• [Presentation] Fitness-induced attractor selection upon a genetic switch (2008)
  • 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
• [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
• [Presentation] Adaptive response of fluctuating gene network (2008)
  • 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
• [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
• [Presentation] Cellular fluctuation in protein concentration and its role on adaptive response (2008)
  • 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
• [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
• [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
  • Year and Date: 2008-08-23
• [Presentation] Efficient method for integration of complex genetic design into genome (2008)
  • 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
• [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
• [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
• [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
• [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
• [Presentation] Simple approach for construction of genome-integrated artificial genetic circuit (2008)
  • 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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [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