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General Information info

Manuscript title Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.
PubMed ID 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 Downloadarticle Zampar_2013.pdf
Project name not specified

Experiment Description info

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

Experimental Details info

Temperature (0C) 30.0
pH 5.0
Carbon source glucose,
Culture mode batch
Process condition aerobic
Dilution rate (h-1)
Working volume (L) 2.0
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 procedure:

Extraction technique: not used

Sample analyzing method: HPLC-UV/RI

Methods description - Notes

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.

[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.

Data file
Downloadmetabolites KIMODATAID61_v0.xlsx
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Submission and curation info

Entered by Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Interests: mathematical modeling, accessible data, use of data

Created 2013-06-11 18:31:52 UTC

Updated 2014-06-12 22:53:50 UTC

Version 0

Status (reviewed) 2013-12-06 17:17:38 UTC

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