Dataset Information

VanEunen2012 - Yeast Glycolysis (glucose upshift)

ABSTRACT: This is corresponding to the model of yeast glycolysis "glucose upshift" condition described in the paper "Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics" by van Eunen et al published in Plos Comput Biol, 2012.

SUBMITTER: Shodhan Rao

PROVIDER: MODEL1403250001 | BioModels | 2014-09-15

REPOSITORIES: BioModels

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Publications

Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics.

van Eunen Karen K Kiewiet José A L JA Westerhoff Hans V HV Bakker Barbara M BM

PLoS computational biology 20120426 4

A decade ago, a team of biochemists including two of us, modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract. Moreover, when the same model was later applied to different experimental steady-state conditions, it often exhibited unrestrained metabolite accumulation.Here we resolve this issue by showing that the results of such ab initio modeling ...[more]

PMID: 22570597

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Project description:Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours. Groups of assays that are related as part of a time series. FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition Keywords: time_series_design

Dataset Information

VanEunen2012 - Yeast Glycolysis (glucose upshift)

Publications

Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics.

Similar Datasets

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