Data files

The file contains simulated data of the electron transport chain model (EcoliETC1) for varying parameter values, i.e. a local sensitivity analysis.

This data file shows results from the different chemostat experiments.Gene expression rates are presented.

Mutants with defects in glucose transport systems were analyzed in a bioreactor and the transcription of certain uptake systems analyzed. Transcription profiles between batch and chemostat conditions were compared

by-product formation rates and glucose uptake rates of mutants with linear electron transport chain at different aerobiosis levels

The ArcA phosphorylation state was determined for mutants with linear respiratory chain at defined aerobiosis levels.

Gene expression levels in mutants with linear ETC were determined by RealTime RT-PCR

This document shows the ArcA phosphorylation levels at different aerobiosis units, measured using Phos-tag gels, western immunoblotting. Exposed films were quantitated using ImageJ and the results shown here.

The data that was published in Alexeeva et al. [1-3] and Alexeeva [4] is an important prerequisite for SUMO. It is used for the development of the models and for the comparison with the SUMO data. By means of the program EasyNPlot [5] the data in the important plots of [1-3] and of the plot of the ArcA activity in [4] was digitalized. The result can be found in the attached files.

[1] Svetlana Alexeeva, Bart de Kort, Gary Sawers, Klaas J. Hellingwerf, and M. Joost Teixeira de Mattos. Effects of ...

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under aerobic batch conditions with glucose as substrate.

Transcription of glucose uptake transport systems in a mutant background under anaerobic batch conditions.

Transcription of glucose uptake transport systems in a mutant background under aerobic batch conditions.

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under anaerobic batch conditions with glucose as substrate.

Transcriptional profiles of steady-state chemostat cultures were measured at a range of oxygen levels using microarrays. Oxygen levels were defined by the aerobiosis scale of Alexeeva et al. (2002).

The abscissa of the plots shows the percentage of aerobiosis that is a physiological measure for oxygen availability (http://www.ncbi.nlm.nih.gov/pubmed/11844770).

1. Grey Boxes: Enzymes & Reactions blue lines/symbols: flux in mmol per gramm dry cell weight an hour red lines/symbols: mRNA levels

2. White Boxes: Intracellular and extracellular metabolites blue lines/symbols: concentration of the metabolites (extracellular: mM, intracellular: AU)

3. Yellow Boxes: Aggregated Quantities as yield, ...

This .csv file contains the filtered datset of the aerobic to anaerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).

This .csv file contains the filtered datset of the anaerobic to aerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an aerobic to anaerobic transition.

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an anaerobic to aerobic transition.

This .csv file contains the entire transcriptional dataset of the aerobic to anaerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

This .csv file contains the entire transcriptional dataset of the anaerobic to aerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

This .pdf file shows a graphical representation of the physiological measurements from the Sheffield Infors chemostat which were made during acetate calibration and also when sampling for the steady-state transcriptional profiles.

This .csv file contains growth parameters measured from chemostat runs of the Sheffield Infors chemostats. The runs were carried out for acetate calibration purposes and for sampling for the steady-state transcriptional profiles.

Columns: Date O2_input (% total) Aerobiosis level (%AAU) OD600 Redox (mV) pO2 (μM) DCW (g/L) Viable cell counts (CFU/ml) RespRate (mmol/h/gDCW) RespRate STDEV [Acetate] (mM) Qacet (mmoles/h/gDCW)

A .pdf files showing graphs of FNR activity at varying aerobiosis levels

Top graph shows no acetate re-calibration Bottom graph shows data with acetate re-calibration

This .csv file shows FNR activity at different aerobiosis levels

Columns a_old Desired aerobiosis level (Aerobiosis units or %AAU) Bgal_activity Average FNR reporter activity (Miller units) Bgal_STDEV STDEV of FNR reporter activities (Miller units) rDOT(μM) Dissolved oxygen tension (μM) DCW DCW (g/L) [acetate] Extracellular acetate concentration (mM) Qacetate Acetate flux (mmoles/h/gDCW) a_new Actual aerobiosis level in sampled chemostat

his document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.

Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried out in Infors-Bioreactors at 0, 20, 50, 80, 100 and 120% aerobiosis. All data ...

This is the csv version of the file: 091016 quinones complete data magdeburg

This document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.

Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried ...