Studies

112 Studies visible to you, out of a total of 243

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

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

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

A set of isogenic mutant strains was constructed which lack NADH Dehydrogenase I as well as two terminal oxidases, resulting in strains with linear respiratory chain. The different strains hence differ in the terminal oxidase and express either cytochrome bo, cytochrome bdI or cytochrome bdII.
The different strains were cultivated in glucose-limited chemostats with defined low levels of oxygen supply. Biomass and by-product formation, gene expression and the phosphorylation state of the important
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Assays: Determination of by-product formation and glucose uptake of mutants with..., Deternination of ArcA phosphroylation level in mutants with linear ETC a..., Gene expression analysis of mutants with linear electron transport chain...

Cells are starved. Potassium and subsequently glucose are added to the medium. Proton and potassium fluxes across the plasma membrane are recorded before and after these events for WT and mutants lacking specific transporter proteins.

Person responsible: Simon Borger

Assays: No Assays

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...

Effect of benzoate treatment (high concentrations) on ATP levels and Pdr12 expression after pretreatment of cells with low concentrations of benzoic acid.

Person responsible: Martin Valachovic

Assays: No Assays

To see changes in ATP levels in cells with induced ABC transporters. Cells with Pdr12 pump by 10 mM benzoic acid are used.

Person responsible: Martin Valachovic

Assays: ATP measurement under 10mM benzoic acid stress

ATP levels of cells stressed with higher concentrations of benzoic acid (30 mM and 50 mM).

Person responsible: Martin Valachovic

Assays: ATP measurement under 30mM benzoic acid stress, ATP measurement under 50mM benzoic acid stress

Conversion from KEGG Reactome Information to SBTOOLBOX2 format.

Person responsible: Sebastian Curth

Assays: Example for model derivation from KEGG, Integration of data into the model

During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of single cells. Due to this new insight the number of single cell studies rises continuously (for recent reviews see (1,2,3)). However, many of the single cell techniques applied do not allow monitoring the development and behavior of one specific single cell in time (e.g. flow cytometry or standard
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Assays: Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae usin...

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