Data files

Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.

For each modeled 3D structure of LHD (see Part 1: 3D structure modeling for LDH enzymes) was computed electrostatic potential by using the UHBD program. The files are in GRD format (binary) and can be visualized with the graphical programs as CHIMERA or VMD.

The output includes the similarity matrix of LDH enzymes based on comparison of the electrostatic potentials at allosteric and catalytic binding sites, separately. The similarity indices were generated by the PIPSA program (http://projects.villa-bosch.de/mcmsoft/pipsa/3.0/).

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.

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model .

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α.

Assessment of kinetic parameters of LDH to include in a catabolic model.

An extended model description of the TryS model

The file contains the initial rate measurements of TbTryS obtained under different substrate and product initial concentrations.

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.

S. pneumoniae RNA-Seq Barcodes: HPUra 1: CAGATC HPUra 2: ACTTGA Kanamycin: AGTCAA

S. pneumoniae RNA-Seq Barcodes: Control 1: CAGATC Control 2: ACTTGA

E. coli RNA-Seq Barcodes: Trimethoprim 1: CCGTCC Trimethoprim 2: GTAGAG

E. coli RNA-Seq Barcodes: Control 1: AGTTCC Control 2: ATGTCA

E. coli DNA-Seq Barcodes: control 1: GTGGCC control 2: GTTTCG Trimethoprim 1: CACTCA Trimethoprim 2: CAGGCG

S. pneumoniae kanamycin DNA PE2

S. pneumoniae kanamycin DNA PE1

S. pneumoniae HPUra 2 DNA PE2

S. pneumoniae HPUra 2 DNA PE1