Studies

112 Studies visible to you, out of a total of 230

Predictions made using the core model for combinatorial perturbations to the model simulating combined effects from OE, KO mutants, perturbations and time series concentrations.

Person responsible: Niels Zondervan

Assays: Combinatorial mutant, perturbation and time series predictions

Contains copy number per locus tag at different times of Growth between 0.25h and 96 hours.
M. pneumoniae was grown in Batch, cells attached to the bottom of the flask (single cell layer), non stirred, non aerated.

Person responsible: Niels Zondervan

Assays: No Assays

Personalized liver function tests: A Multiscale Computational Model Predicts Individual Human Liver Function From Single-Cell Metabolism

Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches. We report a multiscale mathematical model of the Human liver comprising the scales from single hepatocytes, over representation of ultra-structure and micro-circulation
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Assays: Galactose Modelling

Computational modeling of human caffeine clearance by the liver.

More information available from
https://github.com/matthiaskoenig/caffeine

Assays: No Assays

Internal metabolites concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations
External metabolite concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations
Mutant (OE, KO, perturbation) metabolite measurements

Person responsible: Niels Zondervan

Assays: Metabolomics external metabolites measurements

Growth-factor deprived mCFU-E cells (5x106 cells per condition) and BaF3-EpoR cells (1x107 cells per condition) were stimulated with different Epo doses and absolute concentrations were determined for pEpoR (B), pAKT (C), ppERK (D). The scale for pS6 (E) was estimated in arbitrary units. GTP-Ras (F) and ppERK were determined upon stimulation with indicated, color-coded Epo doses. pEpoR was analyzed by immunoprecipitation followed by immunoblotting, GTP-Ras was analyzed after pulldown using a
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Assays: Mathematical models of the Epo-induced AKT, ERK and S6 activation., Source data for Figure 2: Experimental time-resolved quantitative immuno...

No description specified

Assays: Metabolic pathway curation

Genotype: Wildtype (M145E)
Medium: Phosphate-limited (F134)

Assays: Online/offline measurements, metabolomics, proteomics, transcriptomics

No description specified

Person responsible: Ron Henkel

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

No description specified

Assays: Whole genome sequencing (Illumina)

Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources

Assays: Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry)

Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.

Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, NimbleGen Transcriptomics Templates, RT-PCR Excel Template

Transcriptional response to a sudden increase in extracellular ligand (hormone), for the six network designs of (A). The transcriptional response is taken to equal the ratio ReNrL/Retotal, i.e., the fraction of REs attaching ligand-bound NR. The ligand concentration was increased from 0 to 0.005 nM and maintained constant at the latter level. The observation that design 6 is higher than all other designs at long times is robust for parameter changes up to a factor of 3.

Assays: Model nuclear receptor (NR) signaling

Lactic acid bacteria generally use homolactic fermentation for generation of ATP. Here we studied the role of Arginine and Glutamine metabolism on the general physiology of the lactic acid bacteria Streptococcus pyogenes.
A deletion mutant of glnA (glutamine synthetase) has been constructed in the S. pyogenes M49 591 background. 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.
An arcA
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Assays: Characterization of flux distribution of S. pyogenes M9 wild type and th...

Pyruvate kinase (PYK, EC 2.7.1.40) is a key step in glycolysis converting phosphoenolpyruvate into pyruvate. The activity of PYK is activator-dependent, with the allosteric activation mostly being due to fructose-1,6-bisphosphate (FBP).

Person responsible: Stefan Henrich

Assays: literature values for allosteric regulation of pyruvate kinase

Pyruvate formate-lyase (PFL) is an important enzyme in the metabolic pathway of lactic acid bacteria (LAB) and is held responsible for the regulation of the shift between homolactic acid to mixed acid fermentation. PFL catalysis the reversible reaction of acetyl-CoA and formate into pyruvate and CoA. A glycyl radical, who is regenerated within the reaction, is involved; therefore, PFL works only under strictly anaerobic conditions. For its activation, the C-terminal domain has to bind to the
...

Person responsible: Stefan Henrich

Assays: Pyruvate formate-lyase (PFL): literature review, structure analysis and ...

The reconstruction of the metabolic networks is done by sequence comparison with already annotated genomes of L. lactis, L. plantarum, B. subtilis and E. coli

Person responsible: Not available

Assays: Genome-Scale Model Enterococcus faecalis V583, Genome-scale model of Streptococcus pyogenes

The two lactic acid bacteria L. lactis and S. pyogenes were studied with respect to the concentration of intracellular metabolites involved in glycolysis in time upon a glucose pulse. Models that describe this behavior are also constructed

Assays: Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Model of L. lactis glycolysis, Regulation of the activity of lactate dehydrogenases from four lactic ac...

Lactic acid bacteria generally use homolactic fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three lactic acid bacteria Lactococcus lactis, Enterococcus faecalis and Streptococcus pyogenes. Surprisingly deletion of the ldh genes hardly affected the growth rate in chemically defined medium, however growth rate was affected in rich medium. Furthermore, deletion of ldh affected the ability for utilization of various
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Assays: BIOLOG substrate utilization assay, Maximal specific growth rates of the three lactic acid bacteria and thei..., Physiological characterization of Lactic acid bacteria grown in C-limite...

we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll
...

Assays: Flux Balance Analysis of multi-compartment metabolic model of growing Ar...

For all experiments, primary CFU-E cells were starved and stimulated with 5 U/ml Epo. At the indicated time points, samples were subjected to quantitative immunoblotting. Experimental data (black circles) with estimated standard errors and trajectories of the best fit (solid lines) are represented. Mass spectrometry data represent replicates of four independent experiments.

Assays: Model for JAK2/STAT5 signaling, Source data for Figure 3A: Experimental quantitative immunoblotting data.

This study includes the experimental data for model validation and the model predictions of that data set.

Assays: GLC incubation, Steady state

This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.

Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLCtr, GLYtr, HK, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, TPI, Trophozoite Isolation and Lysate Preparation

Since over 40 enzymes will be investigated for their mRNA abundance, processing, and degradation kinetics, the less tedious and more accurate Next Generation Sequencing of the entire mRNA repertoire of the cell is employed. To optimise the proportion of useful sequence, while including RNA fragments that are products of of degradation, rRNA is depleted using the eukaryotic Ribominus kit (Ambion). Two biological replicates are treated with Sinefungin and Actinomycin D to inhibit RNA processing and
...

Person responsible: Christine Clayton

Assays: Modelling the gene expression cascade with length-dependent processes, mRNA decay assay, pre-mRNA processing rate

For cells to accurately read out the genomic content, high fidelity during transcription is required. This is mainly established by the accuracy of the active centre of RNA polymerase (RNAP). Based on in vitro experiments with Escherichia coli RNAP it was also suggested that proofreading of transcription via RNA hydrolysis by RNAP may contribute to overall fidelity and processivity. RNAP’s intrinsic cleavage activity is stimulated by the highly conserved Gre factors suggesting that Gre factors
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Assays: RNA-Seq

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