Synthetic Biology Lab

English

Paper

花井 准教授

2019年

  • Hiroshi Honjo, Kenshiro Iwasaki, Yuki Soma, Keigo Tsuruno, Hiroyuki Hamada, Taizo Hanai: Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production., Metabolic Engineering, accepted.
  • Yasutaka Hirokawa, Takeshi Kubo, Yuki Soma, Fumiko Saruta and Taizo Hanai: Enhancement of acetyl-CoA flux for photosynthetic chemical production by pyruvate dehydrogenase complex overexpression in Synechococcus elongatus PCC 7942., Metabolic Engineering, accepted.
  • Naruhiko Sawa, Tsuneyuki Tatsuke, Atsushi Ogawa, Yasutaka Hirokawa, Takashi Osanai, Taizo Hanai: Modification of carbon metabolism in Synechococcus elongatus PCC 7942 by cyanophage-derived sigma factors for bioproduction improvement, Journal of Bioscience and Bioengineering, 127, 256-264 (2019).

2018年

  • Yasutaka Hirokawa, Yu Kanesaki, Sayuri Arai, Kayoko Hayashihara, Akio Murakami, Kazunori Shimizu, Hiroyuki Honda, Hirofumi Yoshikawa, Taizo Hanai: Mutations responsible for alcohol tolerance in the mutant of Synechococcus elongatus PCC 7942 (SY1043) obtained by single-cell screening system., Journal of Bioscience and Bioengineering, 125, 572-577 (2018).

2017年

  • Yasutaka Hirokawa, Shingo Matsuo, Hiroyuki Hamada, Fumio Matsuda, Taizo Hanai: Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution, Microbial Cell Factories, 16, 212-224 (2017).
  • Sayuri Arai, Kayoko Hayashihara, Yuki Kanamoto, Kazunori Shimizu, Yasutaka Hirokawa, Taizo Hanai, Akio Murakami, Hiroyuki Honda: Alcohol-tolerant mutants of cyanobacterium Synechococcus elongatus PCC 7942 obtained by single-cell mutant screening system, Biotechnology and Bioengineering, 114, 1771-1778 (2017).
  • Yasutaka Hirokawa, Ryota Goto, Yoshitaka Umetani, Taizo Hanai: Construction of a novel D-lactate producing pathway from dihydroxyacetone phosphate of the Calvin cycle in cyanobacterium, Synechococcus elongates PCC 7942, Journal of Bioscience and Bioengineering, 124, 54-61 (2017).
  • Yuki Soma, Yuri Fujiwara, Takuya Nakagawa, Keigo Tsuruno, Taizo Hanai: Reconstruction of a metabolic regulatory network in Escherichia coli for purposeful switching from cell growth mode to production mode in direct GABA fermentation from glucose, Metabolic Engineering, 43, 54-63 (2017).
  • Yuki Soma, Taiki Yamaji, Fumio Matsuda, Taizo Hanai: Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli, Journal of Bioscience and Bioengineering, 123, 625-633 (2017).
  • Yasutaka Hirokawa, Yuki Maki, Taizo Hanai: Improvement of 1,3-propanediol production using an engineered cyanobacterium, Synechococcus elongatus by optimization of the gene expression level of a synthetic metabolic pathway and production conditions, Metabolic Engineering, 39, 192-199 (2017).
  • Yasutaka Hirokawa, Yudai Dempo, Eiichiro Fukusaki, Taizo Hanai: Metabolic engineering for isopropanol production by an engineered cyanobacterium, Synechococcus elongatus PCC 7942, under photosynthetic conditions, Journal of Bioscience and Bioengineering, 123, 39-45 (2017).

2016年

  • Yasutaka Hirokawa, Yuki Maki, Tsuneyuki Tatsuke, Taizo Hanai: Cyanobacterial production of 1,3-propanediol directly from carbon dioxide using a synthetic metabolic pathway, Metabolic Engineering, 34, 97-103 (2016).
  • Sayuri Arai, Mina Okochi, Kazunori Shimizu, Taizo Hanai, Hiroyuki Honda: A single cell culture system using lectin-conjugated magnetite nanoparticles and magnetic force to screen mutant cyanobacteria., Biotechnology and Bioengineering, 113, 112-119(2016).

2015年

  • Keigo Tsuruno, Hiroshi Honjo, Taizo Hanai: Enhancement of 3-hydroxypropionic acid production from glycerol by using a metabolic toggle switch., Microbial Cell Factories, 14, 155-169(2015).
  • Yuki Soma, Taizo Hanai: Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production., Metabolic Engineering, 30, 7-15(2015).
  • Hiroshi Honjo, Keigo Tsuruno, Tsuneyuki Tatsuke, Masaki Sato, Taizo Hanai: Dual synthetic pathway for 3-hydroxypropionic acid production in engineered Escherichia coli., Journal of Bioscience and Bioengineering, 120, 199-204 (2015).
  • Yasutaka Hirokawa, Iwane Suzuki, Taizo Hanai: Optimization of isopropanol production by engineered cyanobacteria with a synthetic metabolic pathway, Journal of Bioscience and Bioengineering, 119, 585-590 (2015).

2014年

  • Yuki Soma, Keigo Tsuruno, Atsushi Yokota, Taizo Hanai: Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch, Metabolic Engineering, 23, 175-184(2014).
  • Sayuri Arai, Mina Okochi, Taizo Hanai, Hiroyuki Honda: Micro-compartmentalized cultivation of cyanobacteria for mutant screening using glass slides with highly water-repellent mark, Biotechnology Reports, 4, 151-155(2014).

2013年

  • Tamami Kusakabe, Tsuneyuki Tatsuke, Keigo Tsuruno, Yasutaka Hirokawa, Shota Atsumi, James C. Liao, Taizo Hanai: Engineering synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light, Metabolic Engineering, 20, 101-108 (2013).

2012年

  • Yuki Soma, Kentaro Inokuma, Tsutomu Tanaka, Chiaki Ogino, Akihiko Kondo, Masahiro Okamoto, Taizo Hanai: Direct isopropanol production from cellobiose by engineered Escherichia coli using a synthetic pathway and a cell surface display system, Journal of Bioscience and Bioengineering, 114, 80-85 (2012).

2011年

  • Yuki Kuriya, Shigemitsu Tanaka, Genta Kobayashi, Taizo Hanai and Masahiro Okamoto: Development of an Analytical Pipeline for Optimizing Substrate Feeding and Eliminating Metabolic Bottlenecks, Chem-Bio Informatics, 11, 1-23 (2011).

2010年

  • Ieong Wong, Shota Atsumi, Wei-Chih Huang, Tung-Yun Wu, Taizo Hanai, Miu-Ling Lam, Ping Tang, Jian Yang, James C. Liao and Chih-Ming Ho: An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study, Lab Chip, 10, 2710-2719 (2010).
  • Kentaro Inokuma, Masahiro Okamoto, Taizo Hanai: Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping, Journal of Bioscience and Bioengineering, 110, 696-701 (2010).

2009年

  • Hiroyuki Hamada, Yoshihiko Tashima, Yu Kisaka, Kazunari Iwamoto, Taizo Hanai, Yukihiro Eguchi, Masahiro Okamoto: Sophisticated Framework between Cell Cycle Arrest and Apoptosis Induction Based on p53 Dynamics, PLoS ONE, 4, e4795(2009).

2008年

  • Shota Atsumi, Taizo Hanai, James C. Liao: Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels, Nature, 451, 7174, 86-89(2008).
  • Shota Atsumi, Anthony F. Cann, Michael R. Connor, Claire R. Shen, Kevin M. Smith, Mark P. Brynildsen, Katherine J.Y. Chou, Taizo Hanai, James C. Liao: Metabolic engineering of Escherichia coli for 1-butanol production, Metabolic Engineering, 10, 6, 305-311(2008).
  • Hideaki Shinto, Yukihiro Tashiro, Genta Kobayashi, Tatsuya Sekiguchi, Taizo Hanai, Yuki Kuriya, Masahiro Okamoto, Kenji Sonomoto: Kinetic study of substrate dependency for higher butanol production in acetone-butanol-ethanol fermentation, Process Biochemistry, in press.
  • Yoshihiko Tashima, Hiroyuki Hamada, Masahiro Okamoto, Taizo Hanai: Prediction of Key Factor for Control of G1/S Phase in Mammalian Cell Cycle by using System Analysis, Journal of Bioscience and Bioengineering, accepted.
  • Chinatsu Arima, Kazumi Hakamada, Masahiro Okamoto, and Taizo Hanai: Modified Fuzzy Gap statistic for estimating the preferable number of clusters in fuzzy k-means clustering, Journal of Bioscience and Bioengineering, 105, 3, 273-281 (2008).

濱田 助教

2019年

  • Tatsuya Sekiguchi, Hiroyuki Hamada, Masahiro Okamoto, Inference of General Mass Action-based State Equations for Oscillatory Biochemical Reaction Systems Using k-step Genetic Programming, Applied Mathematics, 10, 627-645, 2019.08.

2018年

  • Ryoichi Sakiyama, Hiroyuki Hamada, Brandon Blau, Nora Freyer, Katrin Zeilinger, Frank Schubert, Toshio Miki, Evaluation of the mass transfer rate using computer simulation in a three-dimensional interwoven hollow fiber-type bioartificial liver, Biotechnology Letters, https://doi.org/10.1007/s10529-018-2609-1, pp.1-12, 2018.09.

2017年

  • Yasutaka Hirokawa, Shingo Matsuo, Hiroyuki Hamada, Fumio Matsuda, Taizo Hanai, Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution, Microbial Cell Factories, https://doi.org/10.1186/s12934-017-0824-4, 16(1), 212, pp.1-12, 2017.11.

2016年

  • Yohei Motomura, Hiroyuki Hamada, Masahiro Okamoto, An Effective Numerical Calculation Method for Multi Time-Scale Mathematical Models in Systems Biology, Applied Mathematics, DOI:10.4236/am.2016.717178, 7, 2241-2268, 2016.
  • 濱田 浩幸, JSAO Grant-MERA受賞報告:心筋拍動能が安定な血液透析治療システム実現のための数理的解析基盤の構築, 人工臓器, 45, 33-34, 2016.

2015年

  • Kazunari Iwamoto, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto, Stochasticity of Intranuclear Biochemical Reaction Processes Controls the Final Decision of Cell Fate Associated with DNA Damage, PLOS ONE, DOI:10.1371/journal.pone.0101333, 9, e101333, 2014.

2013年

  • Hiroyuki Hamada, Fumimasa Nomura, Tomoyuki Kaneko, Kenji Yasuda, and Masahiro Okamoto, Exploring the implicit interlayer regulatory mechanism between cells and tissue: Stochastic mathematical analyses of the spontaneous ordering in beating synchronization, Biosystems, DOI:10.1016/j.biosystems.2013.02.007, 111, 208-215, 2013.

2011年

  • Kazunari Iwamoto, Hiroyuki Hamada and Masahiro Okamoto, Mechanism of cell cycle disruption by multiple p53 pulses, Genome Informatics, 25, 12-24, 2011.
  • Kazunari Iwamoto, Hiroyuki Hamada, Yukihiro Eguchi and Masahiro Okamoto, Mathematical modeling of cell cycle regulation in response to DNA damage: exploring mechanisms of cell-fate determination, Biosystems, 103, 384-391, 2011.
  • Koji Ishii, Hiroyuki Hamada, Masahiro Okamoto, Mathematical modeling for spatiotemporal development of leaf primordium, The proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems, 2, 813-818, 2009.
  • Koji Ishii, Hiroyuki Hamada, Masahiro Okamoto, Mathematical modeling for morphogenesis of leaf with employing cell automata and reaction-diffusion equation, The proceedings of the Fourteenth International Symposium on Artificial Life and Robotics, 14, 456-459, 2009.

2008年

  • Kazunari Iwamoto, Yoshihiko Tashima, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto, Blind spot of G1/S checkpoint: G1/S checkpoint is invaded by DNA-damage after R-point, The proceedings of the International Symposium on Computational Biology and Bioinformatics, 3, 241-246, 2008.
  • Hiroyuki Hamada, Tomokazu Karino, Shinji Namoto, Akihiro C Yamashita, Makoto Ishizaki, Masahiro Okamoto, Development of Computer-Aided Diagnostic System for Peritoneal Dialysis: NAVI Light(TM), The proceedings of International Federation for Medical and Biological Engineering, 25, 1818-1821, 2009.
  • Kazunari Iwamoto, Yoshihiko Tashima, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto, Mathematical modeling and Sensitivity analysis of G1/S phase in the cell cycle including the DNA damage signal transduction pathway, Biosystems, 94, 109-117, 2008.
  • Abdullah Al Mamun, Hiroyuki Hamada, Tomokazu Karino, Shinji Namoto, Akihiro C. Yamashita, Makoto Ishizaki, Masahiro Okamoto, Clinical Application of Computer-Aided Diagnostic System for Harmonious Introduction of Complementary Dialysis Therapy, The Open Biomedical Engineering Journal, 2, 10-16 , 2008.