Global regulation of genome expression : Single cell analysis of environmental stress response
Project/Area Number |
17076016
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Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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Allocation Type | Single-year Grants |
Review Section |
Science and Engineering
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Research Institution | Hosei University |
Principal Investigator |
ISHIHAMA Akira Hosei University, 企画・戦略本部, 特任教授 (80019869)
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Co-Investigator(Kenkyū-buntansha) |
MAGARIYAMA Yukio 農業食品産業技術総合研究機構, 食品総合研究所, 上席研究員 (40343818)
YAMAMOTO Kaneyoshi 法政大学, 生命科学部, 准教授 (40351580)
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Project Period (FY) |
2005 – 2009
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Project Status |
Completed (Fiscal Year 2009)
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Budget Amount *help |
¥96,900,000 (Direct Cost: ¥96,900,000)
Fiscal Year 2009: ¥17,800,000 (Direct Cost: ¥17,800,000)
Fiscal Year 2008: ¥19,600,000 (Direct Cost: ¥19,600,000)
Fiscal Year 2007: ¥19,700,000 (Direct Cost: ¥19,700,000)
Fiscal Year 2006: ¥19,900,000 (Direct Cost: ¥19,900,000)
Fiscal Year 2005: ¥19,900,000 (Direct Cost: ¥19,900,000)
|
Keywords | ナノバイオロジー / システム生物学 / ゲノム / 転写制御 / 一細胞観察 / プロモーター / 転写因子 / 大腸菌 / 環境応答 / プロモーター強度 / マイクロマニュピュレーション / ストレス応答 / 単一細胞 / 転写ネットワーク / 細胞個性学 / 転写因子ネットワーク / 細胞制御 / 転写包括制御 / ゲノム転写 / 転写装置 / 一細胞生命科学 |
Research Abstract |
The model bacterium, Escherichia coli, is able to survive under various stressful conditions in nature by forming the bacterial community, in which each cell plays a different physiological role. For search of the role each plays, single-live cell observation systems were developed using newly constructed cell chips, and transcription in individual cells was analyzed. Towards understanding the regulation mechanism of genome transcription, we also performed the systematic analysis of regulatory roles of a to tal of 300 transcription factors from E. coli.
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Report
(6 results)
Research Products
(235 results)
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[Journal Article] Enhancement of the synthesis of RpoE and StpA by polyamines at the level of translation in Escherichia coli under heat shock conditions.2009
Author(s)
Terui, Y., Higashi, K., Tabei, Y., Tomitori, H., Yamamoto, K., Ishihama, A., Igarashi, K., Kashiwagi, K.
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Journal Title
J. Baceriol. 191(17)
Pages: 5348-5357
Related Report
Peer Reviewed
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[Journal Article] Anaerobiosis-Induced novel nucleoid protein of Escherichia coli : Architectural rofe in genome DNA compaction.2009
Author(s)
Teramoto, J., Yamada, K., Kobayashi, N., Kori, A., Yoshimurd, S.H., Takeyasu, K., Ishihama, A.
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Journal Title
Micro-Nano Mechatronics Human Sci. 2009
Pages: 179-182
Related Report
Peer Reviewed
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[Journal Article] Single live-bacterial cell assay of promoter activity and regulation : Escherichia coli gcl promoter.2009
Author(s)
Teramoto, J., Yamanishi, Y., Magdy, E-S.H., Hasegawa, A., Nakajima,M., Shimada, T., Arai, F., Fukuda, T., Ishihama. A.
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Journal Title
Micro-Nano Mechatronics Human Sci. 2009
Pages: 175-178
Related Report
Peer Reviewed
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[Journal Article] Enhancement of the synthesis of RpoE and StpA by polyamines at the level of translation in Escherichia coli under heat shock conditions.2009
Author(s)
Terui, Y., Higashi, K., Tabei, Y., Tomitori, H., Yamamoto, K., Ishihama. A., Igarashi, K., Kashiwagi, K.
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Journal Title
J.Bacteriol. 191
Pages: 5348-5357
Related Report
Peer Reviewed
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[Journal Article] Characterization of CitA-CitB signal transduction activating genes involved in anaerobiccitrate catabolism in Escherichia coli.2009
Author(s)
Yamamoto, K., Matsumoto, F., Minagawa, S., Oshima, T., Fujita, N., Ogasawara, N., Ishihama, A.
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Journal Title
Biosci.Biotechnonl.Biochem. 73
Pages: 346-350
Related Report
Peer Reviewed
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[Journal Article] On-chip cell immobilization and monitoring system using thermosensitive gel controlled by suspended polymeric microbridge.2009
Author(s)
Yamanishi, Y., Teramoto, J., Magariyama, Y., Ishihama, A., Fukuda, T., Arai, F.
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Journal Title
IEEE Transaction NanoBioscience 8
Pages: 312-317
Related Report
Peer Reviewed
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[Journal Article] On-chip temperature control under suspended microbridge for cell immobilizsiion and cutture system.2009
Author(s)
Yamanishi, Y., Teramoto, J., Magariyama, Y., Iahihama, A., Fukuda, T., Arai, F.
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Journal Title
Proc. 13^<th> Internatl. Conf. Miniaturized Systems for Chemist.Life Sci 2009
Related Report
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[Journal Article] Characterization of CitA-CitB signal transduction activating genes involved in anaerobic citrate catabolism in Escherichia coil2009
Author(s)
Yamamoto, K., Matsumoto, E, Minagawa, S., Oshima, T., Fujita, N., Ogasawara, N. and Ishihama, A.
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Journal Title
Biosci. Biotechnol. Biochem 73
Pages: 346-350
Related Report
Peer Reviewed
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[Journal Article] The uncharacterized YdhM is the regulator of the nemA gene, coding for N-ethylmaleimide reductase.2008
Author(s)
Umezawa, Y., Ogasawara, H., Shimada, T., Kori, A., Ishihama, A.
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Journal Title
J. Bacteriol. 190(17)
Pages: 5890-5897
Related Report
Peer Reviewed
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[Journal Article] Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli.2008
Author(s)
Yamamoto, K., Matsumoto, F., Oshima, T., Fujita, N., Ogasawara, N., Ishihama, A.
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Journal Title
Biosci. Biotechnol. Biochem. 72(11)
Pages: 3011-3014
NAID
Related Report
Peer Reviewed
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[Journal Article] Single live-bacterial cell assay of promoter activity and regulation2008
Author(s)
Teramoto, J., Hasegawa, A., Kori, A., Magdy, E-S., Nakajima, M.,,Lin, Y-C., Yamanshi, Y., Arai, F., Fukuda,T. and Ishihama, A
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Journal Title
Micro-Nano Mechatronics and Human Science 2008
Pages: 301-306
Related Report
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[Journal Article] Anaerobic regulation of citrate fermentation by CitAB in Escherichia2008
Author(s)
Yamamoto, K., Matsumoto, F., Oshima, T., Fujita, N., Ogasawara, N. and Ishihama, A
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Journal Title
Biosci. Biotechnoi. Biochem 72
Pages: 3011-3014
Related Report
Peer Reviewed
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[Journal Article] On-chip temperature sensing and control for cell immobilization and culture system2008
Author(s)
Yamanishi, Y., Chow, E., Teramoto, J., Magariyama, Y., Ishihama, A., Fukuda, T. and Arai, F
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Journal Title
Micro-Nano Mechatronics and Human Science 2008
Pages: 295-300
Related Report
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[Journal Article] Genomic SELEX search for target genes under the control of PhoQP-RstBA signal relay cascade.2007
Author(s)
Ogasawara, H., Hasegawa, A., Kanda, E., Miki, T., Yamamoto, K., Ishihama, A.
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Journal Title
J. Bacteriol. 189(13)
Pages: 4791-4799
Related Report
Peer Reviewed
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[Journal Article] Enhancement of the synthesis of RpoN, Cra and H -NS by polyamines at the level of translation Escherichia coli cultured with glucose and glutamate.2007
Author(s)
Terui, Y., Higashi, K., Taniguchi, S., Shigemasa, A., Nishimura, K., Kashiwagi, K., Yamamoto, K., Ishihama, A., Igarashi, K.
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Journal Title
J. Bacteriol 189(6)
Pages: 2359-2368
Related Report
Peer Reviewed
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[Journal Article] folA a new member of the TyrR regulon in Escherichia coli K-12.2007
Author(s)
Yang, J., Ogawa, Y., Camakaris, H., Shimada, T., Ishihama, A., Pittard, A.J.
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Journal Title
J. Bacteriol. 189(16)
Pages: 6080-6084
NAID
Related Report
Peer Reviewed
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[Journal Article] Multi-scale genetics towards understandig the regulatory roles of all 300 transcription factors from a single organism Escherichia coli2007
Author(s)
Ishihama, A., Ogasawara, H., Teramoto, J., Shimada, T., Hasegawa, A., Umezawa, Y., Yabuki, K., Ishida, Y., Inaba, T., Kori, A., Yamada, K., Kitai, Y., Kobayashi, N., Kato, D. and Yamamoto, K
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Journal Title
Micro-Nano Mechatronics and Human Science 2007
Pages: 35-37
Related Report
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[Journal Article] Genomic SELEX search for target genes under the control of PhoQP-RstBA signal relay cascade2007
Author(s)
Ogasawara, H., Hasegawa, A., Kanda, E., Miki, T., Yamamoto, K. and Ishihama, A.
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Journal Title
J. Bacteriol. 189
Pages: 4791-4799
Related Report
Peer Reviewed
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[Journal Article] Preparation and preliminary X-ray diffraction analysis of crystals of bacterial flagellar sigma factor o^<28> in complex with the o^<28>-bindingregion of its anti-sigma factor FlgM2007
Author(s)
Okuda, K., Ichihara, H., Takahashi, H., Fujita, N., Ishihama, A. and Hakoshima, T.
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Journal Title
Acta Crystallogr F63
Pages: 196-199
Related Report
Peer Reviewed
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[Journal Article] A novel two-component signaling system that activates transcription of an enerohemorrhagic Escherichia coli effector involved in remodeiing of host actin2007
Author(s)
Reading, C.R., Torres, A.G., Kendall, M.M., Huges, D.T., Yamamoto, K. and Sperandio, V.
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Journal Title
J. Bacteriol. 189
Pages: 2468-2476
Related Report
Peer Reviewed
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[Journal Article] Enhancement of the synthesis of RpoN, Cra and H-NS bypolyamines at the level of translation Escherichia coli cultured with glucose and glutamate2007
Author(s)
Terui, Y., Higashi, K., Taniguchi, S., Shigemasa, A., Nishimura, K., Kashiwagi, K., Yamamoto, K., Ishihama, A. and Igarashi,
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Journal Title
J. Bactereiol. 189
Pages: 2359-2368
Related Report
Peer Reviewed
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[Journal Article] folA a new member of the TyrR regulon in Escherichia coli K-122007
Author(s)
Yang, J., Ogawa, Y., Camakaris, H., Shimada, T., (shihama, A. and Pittard, A.J.:
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Journal Title
J. Bacteriol. 189
Pages: 6080-8084
Related Report
Peer Reviewed
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[Journal Article] Enhancement of the synthesis of RpoN, Cra and H-NS by polyamines at the level of translation Escherichia coli cultured with glucose and glutamate.2007
Author(s)
Terui, Y., Higashi, K., Taniguchi, S., Shigemasa, A., Nishimura, K., Kashiwagi, K., Yamamoto, K., Ishihama, A., Igarashi, K.
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Journal Title
J. Bacteriol. 189
Pages: 2359-2368
Related Report
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[Journal Article] Genomic SELEX search for target genes under the control of PhoQP-RstBA signal relay cascade.2007
Author(s)
Ogasawara, H., Hasegawa, A., Kanda, E., Miki, T., Yamamoto, K, Ishihama.A.
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Journal Title
J. Bacteriol. 189(In press)
Related Report
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[Journal Article] Anaerobic regulation of citrate metabolism by CitAB two-component signal transduction in Escherichia coli.2007
Author(s)
Yamamoto, K., Matsumoto, F., Oshima, T., Fujita, N., Ogasawara, N., Ishihama, A
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Journal Title
J. Biolechnol. 130(In press)
Related Report
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[Journal Article] Enhancement of +1 frameshift by polyamines during translation of polypeptide release factor 2 in Escherichia coli.2006
Author(s)
Higashi, K., Kashiwagi, K., Taniguchi, S., Terui, Y., Yamamoto, K., Ishihama, A., Igarashi, K.
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Journal Title
J. Biol. Chem. 281
Pages: 9527-9537
Related Report
Peer Reviewed
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[Journal Article] The dynamic state of DNA topology is essential for genome condensation in bacteria.2006
Author(s)
Ohniwa, R.L., Morikawa, K., Kim, J., Ohta, T., Ishihama, A., Wada, C., Takeyasu, K.
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Journal Title
EMBO J. 25
Pages: 5591-5602
Related Report
Peer Reviewed
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[Journal Article] Enhancement of+1 frameshift by polyamines during translation of polypeptide release factor 2 in Escherichia coli.2006
Author(s)
Higashi, K., Kashiwagi, K., Taniguchi, S., Terui, Y., Yamamoto, K., Ishihama, A., Igarashi, K.
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Journal Title
J. Biol. Chem. 281
Pages: 9527-9537
Related Report
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[Journal Article] The dynamic state of DNA topology is essential for genome condensation in bacteria.2006
Author(s)
Ohniwa, R.L., Mirikawa, K., Kim, J., Ohta, T., Ishihama, A., Wada, C., Takeyasu, K.
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Journal Title
EMBO J. 25
Pages: 5591-5602
Related Report
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[Journal Article] Multi-scale genetics towards understanding the hierarchy of transcription factor network in genome regulation.2006
Author(s)
Ishihama, A., Ogasawara, H., Shimada, T., Teramoto, J., Hasegawa, A., Umezawa, Y., Yabuki, K., Ishida, Y., Inaba, T., Matsui, M., Kori, A., Yamada, K., Hirao, K., Yamamoto, K.
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Journal Title
Micro-Nano Mechatronics Human Sci. 2006(In press)
Related Report
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[Journal Article] Enhancement of +1 frameshift by polyamines during translation of polypeptide release factor 2 in Escherichia coli2006
Author(s)
Higashi, K., Kashiwagi, K., Taniguchi, S., Terui, Y., Yamamoto, K., Ishihama, A., Igarashi, K.
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Journal Title
Related Report
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[Journal Article] Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli.2005
Author(s)
Yamamoto, K., Hirano, K., Ohshima, T., Aiba, H., Utsumi, R., Ishihama, A.
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Journal Title
J. Biol. Chem. 280(2)
Pages: 1448-1456
Related Report
Peer Reviewed
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[Journal Article] Cross-talks in signal transduction network among all two-component systems in Escherichia coli2005
Author(s)
Yamamoto, Y., Hirano, K., Ohshima, T., Aiba, H., Utsumi, R., Ishihama, A.
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Journal Title
J.Biol.Chem. 280(2)
Pages: 1448-1456
Related Report
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[Journal Article] Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli2005
Author(s)
Ogasawara, H., Teramoto, J., Hirao, K.Yamamoto, K., Ishihama, A., Utsumi, R.
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Journal Title
Related Report
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[Journal Article] Studies of Schizosaccharomyces pombe TFIIE indicate conformational and functional changes in RNA polymerase II at transcription initiation2005
Author(s)
Hayashi, K., Watanabe, T., Tanaka, A., Furumoto, T., Sato-Tsuchiya, C., Kimura, M., Yokoi, M., Ishihama, A., Hanaoka, F., Ohkuma, Y.
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Journal Title
Genes Cells 10(1)
Pages: 207-224
Related Report
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[Journal Article] The fission yeast protein, Ker1p, is an ortholog of RNA polymerase I subunit A14 in Saccharomyces cerevisiae, and is required for stable association of Rrm3 and RPA21 in Pol I2005
Author(s)
Imazawa, Y., Hisatake, K., Mitsuzawa, H., Matsumoto, M., Tsukui, T., Nakagawa, K., Nakadai, T., Shimada, M., Ishihama, A., Nori, Y.
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Journal Title
J.Biol.Chem. 280(12)
Pages: 11467-11474
Related Report
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[Journal Article] Asymmetric swimming pattern of Vibrio alginolyticus cells with single polar flagella2005
Author(s)
Magariyama, Y., Ichiba, M., Nakata, K., Baba, K., Ohtani, T., Kudo, S., Goto, T.
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Journal Title
Biophys.J. 88(5)
Pages: 3648-3658
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[Presentation] Growth phase-dependent regulation of csgD, the master regulator of biofilm formation : Interplay between multiple transcription factors.2009
Author(s)
Ishihama. A., Ogasawara, H., Shimada, T., Teramoto, J., Kori, A., Yamada, K., Yamamoto, K.
Organizer
3^<rd> Internatl. Conf. Environ. Indust. Appl. Microbiol.(BioMicroWorld2009)
Place of Presentation
Lisbon(Portugal)
Related Report
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[Presentation] Control of biofilm formation by Escherichia coli : Interplay between multiple transcription factors.2009
Author(s)
Ogasawara, H., Kori, A., Yamada, K., Yamamoto, K., Ishihama, A.
Organizer
20^<th> Internatl.Symp.Micro-NanoMechatronics Human Sci., Symp. "Systems Cell Engineering by Multi-scale Manipulation"
Place of Presentation
Nagoya, Univ.(Japan)
Related Report
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[Presentation] Single live-bacterial cell assay of promoter activity and regulation : Escherichia coli gcl promoter.2009
Author(s)
Teramoto, J., Yamanishi, Y., Magdy, E-S.H., Hasegawa, A., Nakajima, M., Arai, F., Fukuda, T., Ishihama, A.
Organizer
3^<rd> Internatl.Conf.Environ.Indust.Appl.Microbiol.(BioMicroWorld2009)
Place of Presentation
Lisbon(Portugal)
Related Report
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[Presentation] Single live-cell cell assay of promoter activity and regulation.2009
Author(s)
Teramoto, J., Yamanishi, Y., Magdy, E-S.H., Hasegawa, A., Shohata, E., Kori, A., Nakajima, M., Arai, F., Fukuda, T., Ishihama, A.
Organizer
20^<th> Internatl.Symp.Micro-NanoMechatronics Human Sci., Symp. "Systems Cell Engineering by Multi-scale Manipulation"
Place of Presentation
Nagoya Univ.(Japan)
Related Report
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[Presentation] A single cell immobilization and culture system under suspenced polymeric microbridge with compartments.2009
Author(s)
Yamanishi, Y., Teramoto, J., Magariyama, Y., Ishihama, A., Fukuda, T., Arai, F.
Organizer
20^<th> Internatl.Symp.Micro-NanoMechatronics Human Sci., Symp. "Systems Cell Engineering by Multi-scale Manipulation"
Place of Presentation
Nagoya Univ.(Japan)
Related Report
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[Presentation] On-chip temperature control under suspended microbridge for cell immobilization and culture system.A2009
Author(s)
Yamanishi, Y., Teramoto, J., Magariyama, Y., Ishihama, A., Fukuda, T., Arai, F.
Organizer
3^<th> Internatl.Conf.Miniaturized Systems for Chemist.Life Sci.(mTAS)
Place of Presentation
Jeju(Korea)
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[Presentation] Multi-factor promoters and multi-factor networks.2008
Author(s)
Ishihama, A., Ogasawara, H., Shimada, T., Teramoto, J., Hasegawa, A., Umezawa, Y., Kori, A., Yamada, K. and Yamamoto, K.
Organizer
20^<th> RNA Polymerase Workshop
Place of Presentation
York, UK
Related Report
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[Presentation] Single live-cell assay of promoter activity and regulation.2008
Author(s)
Teramoto, J., Hasegawa, A., Shohata, E., Kori, A., Magdy, E-S. H. Nakajima, M., Lin, Y-C., Yamanishi, Y., Magariyama, Y, Arai,F., Fukuda, T. and Ishihama, A.
Organizer
Micro-Nano Mechatronics Human Sci. Symp.
Place of Presentation
Nagoya, Japan
Related Report
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[Presentation] On-chip temperature sensing and control for cell immobilization and culture system2008
Author(s)
Yamaristj Y, Chow, E, Teramdo, J., Magariyarta, Y., Ishisma, A, Ftiatia, T and Arai, F
Organizer
Micro-Nano Mechatronics Human Sci. Symp.
Place of Presentation
Napova, Japan
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[Presentation] Multi-factor promoters and multi-factor networks2008
Author(s)
Ishihama, A., Ogasawara, H., Shimada, T., Teramoto, J., Hasegawa, A., Umezawa, Y., Yabuki, K., Ishida, Y., Inaba, T., Kori, A., Yamada, K. and Yamamoto, K
Organizer
20th RNA Polymerase Workshop
Place of Presentation
York, UK
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[Presentation] Multi-Scale Genetics of Transcription Network: Understanding the Regulatory Roles of All 300 Transcription Factors from a Single Organism Escherichia coli2007
Author(s)
A. Ishihama, H. Ogasaawra, J. Teramoto, T. Shimada, A. Hasegawa, Y. Umezawa, K. Yabuki, Y. Ishida, T. Inaba, A. Kori, K. Yamada, Y. Kitai, N. Kobayashi, D. Katoand K. Yamamoto
Organizer
2007 Micro-Nano Mechatronics and Human Science Symp
Place of Presentation
Nagoya, Japan
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[Book] The Nucleoid:an Overview.(A. Beak, R .Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T.Nystree, J. M. Slauch, C. L. Squires, and D. Ussery, eds., In:EcoSal-Escherichia coliand Salmonella:cellular and molecular biology., Chapter 2.6)2009
Author(s)
Ishihama, A.
Publisher
ASM Press
URL
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[Book] Methods in Enzymology, Vol. 4222007
Author(s)
Okada, A., Gotoh, Y., Watanabe, T., Furuta, E., Yamamto, K. and Utsumi, R.
Publisher
Elsevier
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