Data files

Excel sheet contains:

• flux distribution solution from best iteration cluster
• quality of the fit (experimental MIDs vs. simulated MIDs)
• Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

• flux distribution solution from best iteration cluster
• quality of the fit (experimental MIDs vs. simulated MIDs)
• Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

• flux distribution solution from best iteration cluster
• quality of the fit (experimental MIDs vs. simulated MIDs)
• Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the ...

batch fermatation - The transition from growing to non-growing Bacillus subtilis cells

batch fermatation - The transition from growing to non-growing Bacillus subtilis cells

B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Here you'll find cell sizes for every sample.

B. subtilis was grown in minimal media in a chemostat at growth rate µ=0.1, with 1.2M NaCl and glycine betaine. Relative quantification for the proteome was done using metabolic labeling.

B. subtilis was grown in minimal media in a chemostat at growth rate µ=0.1, with 1.2M NaCl, without glycine betaine. Relative quantification for the proteome was done using metabolic labeling.

B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Here you'll find cell titers for every sample.

Array hybridisation was done at Roche Nimblegen Inc. It cannot be displayed over here.

SysMo2: Intra- and extracellular metabolome data of the chemostat experiments: nitrogen limitation, nitrogen limitation+ NaCl, nitrogen limitation + glucose

Data sheet generated in Greifswald to measure the response of sigB activity in response to different media composition.

Strain BSA115 is grown until appr. OD 0.25 then expression of sigB is induced by the addition of IPTG. The extend of stress response is measured by the expression of lacZ via beta-Gal assay. The experiment lasts for appr. 400 min.

The stressosome is composed of three proteins that assemble in the form of an icosahedron. Icosahedra can be modelled in different ways with different abstraction levels regarding the original stressosome structure. The pdf-figure introduces geometric modelling of the stressosome using origami and particle dynamics simulations.

The pdf-file shows simulations of a hypothetical model of sigma factor competition. It simulates the dynamics that we can expect from the experiments and prepares for the analysis of the experimental data. Analysis of sigma factor competition is based on a Lineweaver-Burk representation of RNApolymerase and competing sigma factors.

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 ...

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

Phosphorylation site of the HPr protein detected ba mass spectromety

The figure contains information necessary to understand the mathematical model of experiments in BSA115. In these experiments sigB response is artificially initiated by the addition of IPTG while sigB is downstream of a Pspac promoter. The figure shows a flow-chart diagram that combines three hypotheses to explain experiments. It contains the ODEs and the fit of the respective models to the data.