Epigenetic landscape defined by artificial genetic circuit

• Project/Area Number: 23680031
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: KIGA Daisuke 東京工業大学, 総合理工学研究科(研究院), 准教授 (30376587)
• Project Period (FY): 2011-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥27,040,000 (Direct Cost: ¥20,800,000、Indirect Cost: ¥6,240,000); Fiscal Year 2013: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000); Fiscal Year 2012: ¥10,400,000 (Direct Cost: ¥8,000,000、Indirect Cost: ¥2,400,000); Fiscal Year 2011: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
• Keywords: 人工遺伝子回路 / 合成生物学 / エピジェネティック・ランドスケープ / 数理モデル / 分化

Outline of Final Research Achievements

Cell diversification in multi-cellular organism can be described by a trajectory on a programed landscape which is defied by molecular networks inside and between cells. Especially in such networks between cells, allocations of cells are an important parameter of the program. Here, artificial genetic circuits constructed in this study are used for pursuing mechanisms in cell diversification process.

Research Products

• [Journal Article] Effects of downstream genes on synthetic genetic circuits (2014)
  • Author(s): Takefumi Moriya, Masayuki Yamamura, Daisuke Kiga
  • Journal Title: BMC Systems Biology Volume: 8(suppl 4) Issue: S4 Pages: 1-10
  • DOI: 10.1186/1752-0509-8-s4-s4
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] General applicability of synthetic gene-overexpression for cell-type ratio control via reprogramming (2013)
  • Author(s): K. Ishimatsu
  • Journal Title: ACS Synthetic Biology Volume: - Issue: 9 Pages: 638-644
  • DOI: 10.1021/sb400102w
  • Peer Reviewed / Open Access
• [Journal Article] Synthetic Biology and Dual Use (2013)
  • Author(s): Daisuke Kiga
  • Journal Title: Journal of Disaster Research Volume: 8 Pages: 698-704
  • Peer Reviewed
• [Journal Article] 細胞内における人工遺伝子回路の構築 (2013)
  • Author(s): 関根亮二、木賀大介
  • Journal Title: 生物工学会誌 Volume: 91 Pages: 327-333
  • NAID: 110009616008
  • Open Access
• [Journal Article] Cultivation of Synthetic Biology with the iGEM Competition (2013)
  • Author(s): Thiprampai Thamamongood
  • Journal Title: Journal of Advanced Computational Intelligence and Intelligent Informatics Volume: 17.2 Pages: 161-166
  • Peer Reviewed
• [Journal Article] Design strategy for an initial state-independent diversity generator (2012)
  • Author(s): Ryoji Sekine
  • Journal Title: Chem-Bio Informatics Journal Volume: 12 Pages: 39-49
  • Peer Reviewed
• [Journal Article] T unability of the ratio of cell states after the synthetic diversification by the diversity generator (2012)
  • Author(s): 関根 亮二, 山村 雅幸, 萩谷 昌巳, 木賀 大介
  • Journal Title: Communicative and Integrative Biology Volume: 5巻 Issue: 4 Pages: 393-394
  • DOI: 10.4161/cib.20310
  • Peer Reviewed
• [Journal Article] Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling (2011)
  • Author(s): Sekine, R., Yamamura, M., Ayukawa, S., Ishimatsu, K., Akama, S., Takinoue, M., Hagiya, M., Kiga, D.
  • Journal Title: Proc.Natl.Acad.Sci.U.S.A. Volume: 108 Issue: 44 Pages: 17969-17973
  • DOI: 10.1073/pnas.1105901108
  • Peer Reviewed
• [Presentation] シンポジウム 「細胞を創る研究と社会との関わり」について、今、一度振り返る (2013)
  • Author(s): 加藤和人 木賀大介
  • Organizer: 細胞を創る研究会 6.0
  • Place of Presentation: 鶴岡メタボロームキャンパス レクチャーホール・山形県鶴岡市
  • Year and Date: 2013-11-14 – 2013-11-15
• [Presentation] Implementation of artificial genetic circuits based on deformation of a nullcline (2013)
  • Author(s): Daisuke Kiga
  • Organizer: The first annual winter q-bio meeting
  • Place of Presentation: Honolulu, USA
• [Presentation] Conferring multipotency to the bistable system by overexpression of genes (2012)
  • Author(s): Daisuke Kiga
  • Organizer: Joint Conference on Informatics in Biology, Medicine and Pharmacology
  • Place of Presentation: Tokyo、Japan
• [Presentation] ヌルクラインの変形に基づく人工遺伝子回路の実装 (2012)
  • Author(s): 木賀大介
  • Organizer: 第35回分子生物学会シンポジウム 複雑な生命システムへの理論的・構成的アプローチ
  • Place of Presentation: 福岡、日本
• [Presentation] 数理モデルと定量結果とに基づいた人工遺伝子回路の改善サイクル (2012)
  • Author(s): 木賀大介
  • Organizer: 定量生物学の会 第五回年会
  • Place of Presentation: 東京、日本
  • Invited
• [Presentation] 遺伝子大量発現によって双安定システムに多能性を与える (2012)
  • Author(s): 石松愛
  • Organizer: 第64回日本生物工学会大会 神戸国際会議場
  • Place of Presentation: 神戸、日本
• [Presentation] Synthetic Biology (2012)
  • Author(s): Daisuke Kiga
  • Organizer: Japanse-French Frontier Science Symposium (日仏先端科学シンポジウム)
  • Place of Presentation: Nice, France
  • Invited
• [Presentation] Waddingtonの地形の概念を人工遺伝子回路でデザインする (2011)
  • Author(s): 木賀大介
  • Organizer: 第84回日本生化学会 シンポジウム「ゲノムデザインの最前線」内
  • Place of Presentation: 京都国際会館, Kyoto, Japan
• [Presentation] Tunable synthetic phenotypic diversification on Waddington’s landscape through autonomous signaling (2011)
  • Author(s): 木賀大介
  • Organizer: 第４９回日本生物物理学会年会 シンポジウム「生命システムの情報処理」内
  • Place of Presentation: Hyogo, Japan
• [Presentation] A repeat of the synthetic diversification by periodical dilution
  • Author(s): Ryoji Sekine
  • Organizer: COLD SPRING HARBOR ASIA CONFERENCES on Synthetic Biology
  • Place of Presentation: Suzhou, China