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Development of microfluidic platforms for functional evaluation of artificial gene networks

Planned Research

Project AreaSynthetic biology for the comprehension of biomolecular networks
Project/Area Number 23119006
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionThe University of Tokyo

Principal Investigator

Rondelez Yannick  東京大学, 生産技術研究所, 准教授 (10548770)

Co-Investigator(Renkei-kenkyūsha) FUJII TERUO  東京大学, 生産技術研究所, 教授 (30251474)
KANEDA SHOHEI  東京大学, 生産技術研究所, 助教 (10542467)
Project Period (FY) 2011-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥77,090,000 (Direct Cost: ¥59,300,000、Indirect Cost: ¥17,790,000)
Fiscal Year 2015: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000)
Fiscal Year 2014: ¥14,430,000 (Direct Cost: ¥11,100,000、Indirect Cost: ¥3,330,000)
Fiscal Year 2013: ¥14,560,000 (Direct Cost: ¥11,200,000、Indirect Cost: ¥3,360,000)
Fiscal Year 2012: ¥16,900,000 (Direct Cost: ¥13,000,000、Indirect Cost: ¥3,900,000)
Fiscal Year 2011: ¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Keywordsマイクロ・ナノデバイス / マイクロ液滴 / マイクロ流体デバイス / 合成生物学 / In vitro反応ネットワーク / DNA toolbox / in vitro反応ネットワーク / in vitro 反応ネットワーク / 遺伝子
Outline of Final Research Achievements

To establish fundamental experimental technologies to support development of the research area of synthetic biology, we developed microfluidic platform can be used for evaluation for functions of artificial gene networks and artificial metabolic pathways. In particular, (1) microchamber-based microfluidic platforms, (2) microdroplet-based microfluidic platform and (3) microfluidic platforms for other groups in this research area. In the development of (2) microdroplet-based microfluidic platform, a microfluidic device can search conditions of concentrations of target molecules in reaction networks in a high-throughput manner (screen ten-thousands conditions of concentrations at once) could be successfully realized.

Report

(6 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (41 results)

All 2016 2015 2014 2013 2012 Other

All Journal Article (17 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 17 results) Presentation (19 results) (of which Invited: 13 results) Book (2 results) Remarks (1 results) Patent(Industrial Property Rights) (2 results) (of which Overseas: 2 results)

  • [Journal Article] Nano systems and devices for applications in biology and nanotechnology2016

    • Author(s)
      Perret, G., P. Ginet, M. C. Tarhan, A. Baccouche, T. Lacornerie, M. Kumemura, L. Jalabert et al.
    • Journal Title

      Solid-State Electronics

      Volume: 115 Pages: 66-73

    • DOI

      10.1016/j.sse.2015.08.019

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Synthesis of Programmable Reaction-Diffusion Fronts Using DNA Catalyzers2015

    • Author(s)
      A. S. Zadorin, Y. Rondelez, J.-C. Galas, A. Estevez-Torres
    • Journal Title

      PRL

      Volume: 114 Issue: 6 Pages: 068301-068301

    • DOI

      10.1103/physrevlett.114.068301

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Pursuit-and-evasion Reaction-diffusion Waves In Micro-reactors with Tailored Geometry2015

    • Author(s)
      A. Zambrano, A. Zadorin, Y. Rondelez, A. Estévez-Torres, J.-C. Galas
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 119.17 Issue: 17 Pages: 5349-5355

    • DOI

      10.1021/jp509474w

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Automated Design of Programmable Enzyme-Driven DNA Circuits2014

    • Author(s)
      1. H. van Roekel, L. Meijer; S. Masroor, G. Zandra, A. Estevez-Torres, Y. Rondelez, A. Zagaris, M. Peletier, P. Hilbers, T. de Greef
    • Journal Title

      ACS Synthetic Biology

      Volume: 1 Issue: 6 Pages: 735-745

    • DOI

      10.1021/sb500300d

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic DNA reaction network: a walkthrough2014

    • Author(s)
      A. Baccouche, K. Montagne, A. Padirac, Y. Rondelez
    • Journal Title

      Methods

      Volume: 67 Issue: 2 Pages: 234-279

    • DOI

      10.1016/j.ymeth.2014.01.015

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computer Assisted Design for Scaling Up Systems based on DNA Reaction Networks2014

    • Author(s)
      N. Aubert, T. Fujii, M. Hagiya,
    • Journal Title

      J. R. Soc. Interface

      Volume: 11 Issue: 93 Pages: 2131167-2131167

    • DOI

      10.1098/rsif.2013.1167

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-throughput and Long-term Observation of Compartmentalized Bioc hemical Oscillators2013

    • Author(s)
      Hasatani, K., Loecmach, M., Estevez-Torres, A., Fujii, T., Rondelez, Y.
    • Journal Title

      Chemical Communication

      Volume: 49 Issue: 73 Pages: 8090-8092

    • DOI

      10.1039/c3cc44323j

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spatial waves in synthetic biochemical networks2013

    • Author(s)
      A. Padirac, T. Fujii, A. Estévez-Torres, Y. Rondelez
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 135 Issue: 39 Pages: 14586-14592

    • DOI

      10.1021/ja403584p

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Scaling down DNA circuits with competitive neural networks2013

    • Author(s)
      A Genot, T. Fujii & Y. Rondelez
    • Journal Title

      J. R. Soc. Interface

      Volume: 10 Issue: 85 Pages: 20130212-20130212

    • DOI

      10.1098/rsif.2013.0212

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In vitro regulatory models for systems biology2013

    • Author(s)
      A. Genot, T. Fujii & Y. Rondelez
    • Journal Title

      Journal of Biotechnology Advances

      Volume: 31 Issue: 6 Pages: 789-796

    • DOI

      10.1016/j.biotechadv.2013.04.008

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Predator-prey molecular ecosystems2013

    • Author(s)
      T. Fujii & Y. Rondelez
    • Journal Title

      ACSnano

      Volume: 7 Issue: 1 Pages: 27-34

    • DOI

      10.1021/nn3043572

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolution of Cheating DNA-based Agents Playing the Game of Rock-Paper-Scissors2013

    • Author(s)
      N. Aubert, Q. H. Dinh, M. Hagiya, T. Fujii, H. Iba, N. Bredeche, Y. Rondelez
    • Journal Title

      Advances in Artificial Life

      Volume: 12 Pages: 1143-1150

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nucleic acids for the rational design of reaction circuits2012

    • Author(s)
      A. Padirac, T. Fujii & Y. Rondelez
    • Journal Title

      Curr. Op. Biotech.

      Volume: 24 Issue: 4 Pages: 1-6

    • DOI

      10.1016/j.copbio.2012.11.011

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bottom-up construction of in vitro switchable memories.2012

    • Author(s)
      A. Padirac, T. Fujii & Y. Rondelez
    • Journal Title

      PNAS

      Volume: 109 Issue: 47

    • DOI

      10.1073/pnas.1212069109

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computing with Competition in Biochemical Networks2012

    • Author(s)
      Genot, A., Fujii, T., and Rondelez, Y.
    • Journal Title

      Physical Review Letters

      Volume: 109 Issue: 20 Pages: 208102-208102

    • DOI

      10.1103/physrevlett.109.208102

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Competition for Catalytic Resources Alters Biological Network Dynamics2012

    • Author(s)
      Yannick Rondelez
    • Journal Title

      PHYSICAL REVIEW LETTERS

      Volume: 108 Issue: 1 Pages: 18102-18102

    • DOI

      10.1103/physrevlett.108.018102

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quencher-free multiplexed monitoring of DNA reaction circuits2012

    • Author(s)
      A. Padirac, T. Fujii & Y. Rondelez
    • Journal Title

      Nucleic Acids Research

      Volume: 40 Issue: 15 Pages: e118-e118

    • DOI

      10.1093/nar/gks621

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] DNA-encoded programs : In vitro models of biological networks2016

    • Author(s)
      rondelez
    • Organizer
      aSSB-Evry'16 Thematic Research School
    • Place of Presentation
      Evry France
    • Year and Date
      2016-03-25
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] High throughput approach to synthetic molecular circuits2015

    • Author(s)
      rondelez
    • Organizer
      「細胞を創る」研究会8.0
    • Place of Presentation
      大阪大学吹田キャンパス 銀杏会館,大阪
    • Year and Date
      2015-11-12
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Degradation Controlled Nonlinearities in DNA Networks2015

    • Author(s)
      K. Montagne, G. Gines , Y. Rondelez.
    • Organizer
      DNA21
    • Place of Presentation
      Boston USA
    • Year and Date
      2015-08-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] Microscopic Agents Programmed by DNA Circuits2015

    • Author(s)
      G. Gines, A. Zadorin, T. Fujii, Y. Rondelez
    • Organizer
      DNA21
    • Place of Presentation
      Boston USA
    • Year and Date
      2015-08-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] DNA Circuitry2015

    • Author(s)
      rondelez
    • Organizer
      Systems Chemistry 2015
    • Place of Presentation
      Rolduc Netherlands
    • Year and Date
      2015-05-19
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Yannick Rondelez2014

    • Author(s)
      6. Gordon Research Conference on Oscillations & Dynamic Instabilities
    • Organizer
      Rational building of molecular programs with DNA
    • Place of Presentation
      Girona, Spain
    • Year and Date
      2014-08-13 – 2014-08-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Parameter landscapes for dynamical reaction networks programs2014

    • Author(s)
      Y. Rondelez
    • Organizer
      5. DNATEC 2014
    • Place of Presentation
      Dresden, Germany
    • Year and Date
      2014-05-05 – 2014-05-09
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Rational design of temporal and spatiotemporal emergence2013

    • Author(s)
      Y. Rondelez
    • Organizer
      Advances in Molecular Programming and Computing
    • Place of Presentation
      Copenhaguen
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Rational encoding of reaction- and reaction-diffusion networks using DNA2013

    • Author(s)
      Y. Rondelez
    • Organizer
      6. Solvay Workshop on Patterns and Hydrodynamic Instabilities in Reactive Systems
    • Place of Presentation
      Bruxelles
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Molecular programming with the DNA toolbox2013

    • Author(s)
      Y. Rondelez
    • Organizer
      DNA19 Conference
    • Place of Presentation
      USA Arizona
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] DNA molecular programming goes spatial2013

    • Author(s)
      A. Padirac, J-C. Galas, A. Zadorin, A. Kalley, Y. Rondelez, A. Estévez-Torres
    • Organizer
      DNA19 Conference
    • Place of Presentation
      USA Arizona
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Evolution of Cheating DNA-Based Agents Playing the Game of Rock–Paper–Scissors2013

    • Author(s)
      N. Aubert, H. D. Quang, M. Hagiya, H. Iba, T. Fujii, Y. Rondelez
    • Organizer
      European Conference on Artificial Life
    • Place of Presentation
      Taormine (Italy)
    • Related Report
      2013 Annual Research Report
  • [Presentation] In vitro models of gene regulatory networks2012

    • Author(s)
      Y. Rondelez
    • Organizer
      10. International Workshop on Quantitative Biology
    • Place of Presentation
      Tokyo
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] An in-vitro toolbox to model gene regulatory networks2012

    • Author(s)
      A. Genot, T. Fujii, Y. Rondelez, ,
    • Organizer
      International Biotechnology Symposium
    • Place of Presentation
      Deagu Korea
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Emerging temporal patterns from DNA networks2012

    • Author(s)
      Y. Rondelez
    • Organizer
      Fnano
    • Place of Presentation
      Snowbird USA
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Programming matter(s): from Turing to Kirby and back to E.Coli2012

    • Author(s)
      A. Genot, J. Bath, T. Fujii, Y. Rondelez, A. Turberfield
    • Organizer
      Fnano
    • Place of Presentation
      snowbird USA
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Spatially-resolved DNA ecosystem2012

    • Author(s)
      A. Padirac, A. Estevez-Torres, T. Fujii, Y. Rondelez
    • Organizer
      MicroTAS
    • Place of Presentation
      Okinawa Japan
    • Related Report
      2012 Annual Research Report
  • [Presentation] Predator-Prey DNA oscillators2012

    • Author(s)
      T. Fujii & Y. Rondelez
    • Organizer
      DNA18
    • Place of Presentation
      Aarhus Denmark
    • Related Report
      2012 Annual Research Report
  • [Presentation] Enforcing delays in DNA computing systems2012

    • Author(s)
      14. N. Aubert, Y. Rondelez, T. Fujii & M. Hagiya
    • Organizer
      DNA18
    • Place of Presentation
      Aarhus Denmark
    • Related Report
      2012 Annual Research Report
  • [Book] Evolutionary Computation in Gene Regulatory Network Research2015

    • Author(s)
      Dinh, Q. H., Aubert, N., Noman, N., Iba, H., & Rondelez
    • Total Pages
      269
    • Publisher
      wiley
    • Related Report
      2015 Annual Research Report
  • [Book] Multiscale Analysis and Nonlinear Dynamics: From Molecules to the Brain2013

    • Author(s)
      T. Plasson & Y. Rondelez
    • Total Pages
      305
    • Publisher
      Wiley
    • Related Report
      2013 Annual Research Report
  • [Remarks] Me

    • Related Report
      2013 Annual Research Report
  • [Patent(Industrial Property Rights)] Method of eliminating background in isothermal amplification2016

    • Inventor(s)
      Rondelez Montagne Gines Fujii
    • Industrial Property Rights Holder
      Rondelez Montagne Gines Fujii
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016-02-16
    • Related Report
      2015 Annual Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] MOLECULAR COMPUTING COMPONENT AND METHOD OF MOLECULAR COMPUTING2016

    • Inventor(s)
      Rondelez Gines Fujii
    • Industrial Property Rights Holder
      Rondelez Gines Fujii
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016-02-16
    • Related Report
      2015 Annual Research Report
    • Overseas

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Published: 2011-08-01   Modified: 2019-07-29  

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