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Fluxomic approaches for Yeast metabolism

Research Project

Project/Area Number 24510268
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Genome biology
Research InstitutionKeio University

Principal Investigator

MURRAY Douglas  慶應義塾大学, 政策・メディア研究科(藤沢), 特任准教授 (50458965)

Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2013: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords国際研究者交流 / ドイツ:オーストリア:英 国 / 計算および実験結果の交換 / ドイツ:オーストリア:英国 / 国際的研究者交流 / Germany / Austria / UK / 計算上の結果と実験結果の交換 / ドイツ / オーストリア / 計測データや実験結果の交換
Outline of Final Research Achievements

Eukaryotic metabolism is a complex and highly dynamic process that can have a huge impact on the physiology of the organism. While we understand much about the major systems in metabolism a holistic view of how metabolic events impact metabolism remain elusive. In this project we developed experimental protocols, bioinformatic pipelines and computational tools to assist our understanding of how cellular respiration and bioenergetics influence metabolism. In particular, we concentrated on the the calculation and estimation of pathway fluxes. We applied these methods to precisely controlled continuous cultures of bakers' yeast to reveal nucleotide biosynthesis, large-scale mobilisation of lipids and carbon dioxide assimilation occurs during high respiration states. Currently, we are validating and integrating these data and plan to publish our findings in the public domain soon.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (12 results)

All 2014 2013 2012

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 2 results,  Acknowledgement Compliant: 3 results) Presentation (5 results) (of which Invited: 3 results) Book (1 results)

  • [Journal Article] Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program2014

    • Author(s)
      Cornelia Amariei, Rainer Machne, Viktor Stolc, Tomoyoshi Soga, Masaru Tomita and Douglas B. Murray
    • Journal Title

      Microbial Cell

      Volume: 1 Issue: 9 Pages: 279-288

    • DOI

      10.15698/mic2014.09.166

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Quantifying periodicity in omics data2014

    • Author(s)
      Cornelia Amariei, Masaru Tomita and Douglas B. Murray
    • Journal Title

      Frontiers Cell Develepmantal Biology

      Volume: 2 Pages: 1-9

    • DOI

      10.3389/fcell.2014.00040

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Temporal Partitioning of the Yeast Cellular Network2014

    • Author(s)
      Douglas B. Murray, Cornelia Amariei, Kalesh Sasidharan, Rainer Machné, Miguel A. Aon, David Lloyd
    • Journal Title

      Springer Series in Biophysics

      Volume: 16 Pages: 323-349

    • DOI

      10.1007/978-3-642-38505-6_12

    • ISBN
      9783642385049, 9783642385056
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The dynamics of cellular energetics during continuous yeast culture.2013

    • Author(s)
      Amariei C, Machne R, Sasidharan K, Gottstein W, Tomita M, Soga T, Lloyd D, Murray DB.
    • Journal Title

      Conf Proc IEEE Eng Med Biol Soc.

      Volume: 2013 Pages: 2708-2711

    • DOI

      10.1109/embc.2013.6610099

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] A yeast metabolite extraction protocol optimised for time-series analyses.2012

    • Author(s)
      Sasidharan K, Soga T, Tomita M, Murray DB.
    • Journal Title

      PLoS One

      Volume: 7 Issue: 8 Pages: e44283-e44283

    • DOI

      10.1371/journal.pone.0044283

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Rapid DNA, RNA and protein extraction protocols optimized for slow continuously growing yeast cultures.2012

    • Author(s)
      Sasidharan K, Amariei C, Tomita M, Murray DB.
    • Journal Title

      Yeast

      Volume: 29 Issue: 8 Pages: 311-322

    • DOI

      10.1002/yea.2911

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] Energetic feedback on chromatin state defines a system-wide reset point2014

    • Author(s)
      Douglas B. Murray
    • Organizer
      Understanding Microbial Communities; Function, Structure and Dynamics
    • Place of Presentation
      Isaac Newton Institute for Mathematical Science, Cambridge University (UK)
    • Year and Date
      2014-11-05
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Yeast Respiratory Oscillation: Fluxomic Approaches2014

    • Author(s)
      Douglas B. Murray
    • Organizer
      Stoichiometric modelling (SM) of microbial metabolism
    • Place of Presentation
      Isaac Newton Institute for Mathematical Science, Cambridge University (UK)
    • Year and Date
      2014-11-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Optimal metabolic dynamics resolved by cyclic FBA2014

    • Author(s)
      Sabrina Hoffmann, Willi Gottstein, Rainer Machne, Ralf Steuer, Douglas Murray
    • Organizer
      Stoichiometric modelling (SM) of microbial metabolism
    • Place of Presentation
      Isaac Newton Institute for Mathematical Science, Cambridge University (UK)
    • Year and Date
      2014-11-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Fluxomic approaches in Yeast2014

    • Author(s)
      Douglas B. Murray
    • Organizer
      Metabolomics 2014
    • Place of Presentation
      Tsuruoka (Yamagata, Japan)
    • Year and Date
      2014-06-23 – 2014-06-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] The dynamics of cellular energetics during continuous yeast culture.2013

    • Author(s)
      Douglas Murray
    • Organizer
      Engineering in Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE
    • Place of Presentation
      Osaka, Japan
    • Related Report
      2013 Research-status Report
  • [Book] Systems Biology of Metabolic and Signalling Networks2013

    • Author(s)
      Temporal Partitioning of the Yeast Cellular Network.
    • Total Pages
      375
    • Publisher
      Douglas B. Murray, Cornelia Amariei, Kalesh Sasidharan, Rainer Machne´, Miguel A. Aon, and David Lloyd
    • Related Report
      2013 Research-status Report

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Published: 2013-05-31   Modified: 2021-04-07  

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