DataEntryID 61
    General information
      Manuscript title: Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/23549479
      Journal: Molecular Systems Biology
      Year: 2013
      Authors: Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni  and Matthias Heinemann
      Affiliations: ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
      Keywords: diauxic shift, metabolome, S. cerevisiae, extracelullar
      Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbndFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--7d0701e6f2de25c722da805360a4a45d70d9fb0a/Zampar_2013.pdf
      Project name: not specified

    Experiment description
      Organism: Saccharomyces cerevisiae
      Strain: FY4
      Data type: time-series data of metabolites
      Data units: (mM) and (gDW/L)
      Execution date: not specified

    Experimental details
      Temperature (°C): 30.0
      pH: 5.0
      Carbon source: glucose
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): —
      Working volume: 2.0 L
      Biomass concentration (g/L): correlation of OD with biomass: 0.486 gDW/L OD
      Medium composition: minimal defined medium with 5 g/L glucose
      General protocol information: Sampling Method: 1 ml samples and centrifuged for 4 min at 4000, r.p.m at 4 ºC; Quenching: —; Extraction list: not used; Analysis list: HPLC-UV/RI;
      Methods description: Biomass concentrations were monitored by measuring optical density (OD) at 600nm with a spectrophotometer (model Novaspec II, Pharmacia Biotech, USA). The correlation of OD with biomass dry weight (0.486 gDW/l OD) had previously been determined from a batch culture grown on 10 g/l glucose minimal medium. To determine the extracellular concentrations of glucose, ethanol, acetate, pyruvate, succinate and glycerol, 1 ml samples were taken and centrifuged for 4 min at 4000 r.p.m. at 4ºC. The supernatant was analyzed with an HPLC system (Agilent HP1100) as described by [1], equipped with a polymer column (Aminex HPX-87H from BioRad, Switzerland). As eluent 5mM H2SO4 was used and the column was heated to 60ºC. The compounds were detected and quantified with a refractive index (RI) detector and an UV/Vis-detector (DAD). For absolute quantification, calibration curves with external standards for the corresponding pure substance obtained from Sigma (Switzerland) were used.

----------References------------
[1] Heer D, Sauer U (2008). Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain. Microb Biotechnol 1: 497–506. http://doi.org/bmdjnc 
      Data file: http://kimosys.org/repository/61/download?parameter=1147; 
      Alternative formats: no files uploaded

    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2013-06-11 18:31:52 UTC
      Updated: 2020-04-24 16:10:32 UTC
      Version: 0
      Status: (reviewed) 2013-12-06 17:17:38 UTC
      Views: 251
      Downloads: 64