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E-GEOD-27046 - Characterization of lactic acid and acetic acid mutants in batch fermentation

Status
Released on 1 March 2012, last updated on 15 March 2012
Organism
Clostridium thermocellum DSM 1313
Samples (24)
Array (1)
Protocols (7)
Description
Four C. thermocellum DSM-1313 derived strains were assessed using metabolite and DNA microarray tools in order to better understand carbon and electron flow within this organism. C. thermocellum is able to ferment cellulose into its fermentation end products L-lactate, acetate, formate, hydrogen gas, and ethanol, with the latter being the desired end product to be used as biorenewable fuel. In addition to the parent strain (genotype: hpt spo0A), strains with either or both of the genes encoding lactate dehydrogenase (ldh) and phosphate acetyltransferase (pta) deleted were studied. The strains used are a parent strain (M1726: genotype: hpt spo0A), and strains with either the gene encoding lactate dehydrogenase (M1629: hpt spo0A ldh) or phosphate acetyltransferase (M1630: hpt spo0A pta) deleted, or with both genes deleted (M1725: hpt spo0A ldh pta). Controlled batch fermentations using cellobiose as sole carbon source were grown for each strain, and samples in mid-exponential phase and at the time of carbon depletion were examined by DNA microarray. Four strains were grown each as three independent biological replicates (fresh batch of media was made before each run). Per fermentation, two samples were taken for DNA microarray analysis as was determined by the optical density: mid-exponential was defined as O.D. 0.4 (measured by Dasgip probe); point of carbon depletion was defined by both the maximum O.D. reached and observation that no base was added to the fermentation to control pH. In total, 4 strains x 3 fermentation x 2 time points per fermentor = 24 arrays. Parent strain was used as reference strain.
Experiment type
transcription profiling by array 
Contacts
Courtney M Johnson, Douwe van der Veen, Lee R Lynd, Steven D Brown
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-27046.idf.txt
Sample and data relationshipE-GEOD-27046.sdrf.txt
Raw data (1)E-GEOD-27046.raw.1.zip
Processed data (1)E-GEOD-27046.processed.1.zip
Array designA-GEOD-13117.adf.txt
Links