Data files

amino acid auxotrophy for streptococcus pyogenes in CDM-IMIKRO (not CDM-LAB) as function of final growth yield (OD600 at stationary phase) in 96well plates (200 ul culture)

S. pyogenes was grown in C-limited cultures at pH 6.5 and 7.5 and at a growth rate of 0.05 The glnA mutant strain shows decreased growth in low glutamine and excess glutamate conditions and no growth at all in low glutamine and low glutamate conditions. Preliminary results of glucose-limited chemostat cultures indicate a reversion of the pH dependency of the shift from homolactic to more mixed acid fermentation: wild type - lactate/formate ratio at pH 6.5 = 11.8, at pH 7.5 = 2.8 glnA mutant - ...

In order to construct an in vivo-like buffer for S. pyogenes, the intracellular concentrations of Fe, K, Mg, Mn Na, P and S elements were determined via ICP-AES (inductively coupled plasma atomic emissionspectroscopy) method at the Institute of Land Use, University of Rostock. The samples for the analysis were obtained from a steady state culture grown on CDM-LAB with glucose.

Data sheet from the Neves et al JBC, 2002 publication. Used as a test data set for data upload.

Measurements on Km, Vmax and allosteric activation or inhibition of the main L-lactate dehydrogenase

overview of sysmo-LAB2

qATP values were calculated based on fermentation product formation and expected used biochemical pathways. These were averaged and used for calculation of the ATP required for maintenance and for growth. These data were subsequently used to calculate the qATP at the maximal growth rate by extrapolation

E. faecalis was gucose-pulsed after resuspension in 100 mM MES buffer at pH 6.5 Intra- and extracellular metabolites concentrations were followed in time

. L. lactis (NZ9000), E. faecalis (V538) and S. pyogenes (M49) wild type strain and their ldh- mutants were grown in batch cultures at 37°C in anaerobic 96 wells plates in either TH-broth supplemented with 0.5% (w/v) yeast (THY) or a chemically defined medium for LAB (pH 7.4) (CDM-LAB (10)). Both media were buffered with either 100 mM MES buffer or 100 mM MOPS buffer for growth at pH 6.5 and 7.5 respectively.

S. pyogenes was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

E. faecalis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

L. lactis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05, 0.15 and 0.40

In this experiment we glucose-pulsed an L. lactiss cultures re-suspended in 100 mM MES buffer at pH 6.5. Samples were taken in time to study intra- and extracellular metabolites. These data are used to construct a kinetic model of the catabolism of E. L. lactis

Glucose pulsed S pyogenes with 5 mM glucose in 100 mM MES buffer at pH 6.5 and followed intracellular metabolites in time

Glucose pulsed L. lactis with 20 mM glucose in 100 mM MES buffer at pH 6.5 and followed intracellular metabolites in time

L. lactis was grown in LAB medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.

MIAPE based Gel Electrophoresis Data Entry Worksheet

This files contains the parameter values, life-times, half-lives and errors associated with modeling the decay of the transcriptome, based on 3 models described in Deneke et al. "Complex degradation processes lead to non-exponential decay patters and age-dependent decay rates of messenger RNA". PLoS One. 2013;8(2):e55442

The file contains the normalized relative read counts (RPM) of 2 mRNA decay experiments. Columns in blue correspond to experiment 1, columns in violet correspond to experiment 2. The time points are in column headers. The last 3 columns contain parameters and half lives calculated from an exponantial fit of all data points. Normalization was done in 2 steps :first by calculating RPM i.e. reads per million of aligned reads to unique ORFs, second by normalizing this to the total amount of mRNA ...