Data files

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).

Untargeted and targeted metabolic analysis on T. b. brucei 427 grown under oxidative stress with methylene blue has been carried out. This work has been completed with 11 bio-reps and found significant metabolic changes as you can see in the IDEOM file attached. 'Comparison' tab in the data spread sheet shows heat maps and fold change analysis regarding different metabolite levels (T: T brucei, TMB: T. brucei exposed to methylene blue, numbers: time points, 0, 5, 60 & 120min). If you double ...

Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells under high pH stress (pH8.7)

Intracellular concentrations of 50 metabolites measured by LC-MS using isotope ratio based mass spectrometry technique

Concentrations of 22 extracellular metabolites (major medium components) from T. b. brucei 427

Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells exposed to methylene blue

In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a ...

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, ...

Table describing the catabolite repression of β-xylosidase by different carbon sources(glucose, sorbitol, fructose, maltose, glycerol. mannitol) in various mutants of CcpA cofactors (HprK, crh)

Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an ...

List of protein identified proteins in SPINE experiment.

mRNAs with decreased abundance in all replicates with an average fold change of at least 1.5

GEO format data

Phosphorylation site of the HPr protein detected ba mass spectromety

Describes the assumptions made, how to integrate the new reactions to the rest of the glycolysis model, the parameters needed and the preliminary parameter values collected from the litterature.

call ConvertStdModel2SBTtest('Conti_Ferm_Std', 'CD_Transcriptomic.csv', 'glucose.csv', 'OD.csv',0)

transcriptome, glucose, biomass data inside

acetic acid pulse 100mM acetic acid step 50mM, 70mM

• automated integration of transcriptomic and reactome data to differential equations
• structure of the paths is maintained
• continuous fermentation model in standard format for data integration, two component model (cell and fermenter)

call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example

where model_map is the desired mapping of species, reaction_compounds_final.csv is the entire network, extracellular.txt is a manual ...

acetic acid addition

step experiment: 50mM, 70mM, 100mM, 120mM

pulse 200mM

pulse acetic acid: 70mM (2x), 80mM, shift to 4.5, pulse acetic acid: 70mM

acetic acid addition 70mM

Basic Graph statistics

RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners

_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes

betw: betweeness of nodes clos: closeness of nodes neigh: neighbours node_degree: number of edges per node path: shortest paths ...