Studies112 Studies visible to you, out of a total of 242
Flux will be measured using the metabolomics platforms based on absolute quantification method (isotope ratio based MS technique) by LC-MS, using heavy-isotope labelled precursors of the metabolites of interest. For example, 15N labelled cysteine, glycine and glutamate will be used to determine rates of synthesis of glutathione. 15N-labelled methionine to measure S-adenosyl methionine (and its decarboxylated form, as well as methionine cycle intermediates). 15N labelled arginine is used as precursor
Person responsible: Dong-Hyun Kim
The steady state anaerobic culture (D = 0.1 h-1) was pertrubed by sudden increase of the extracellular glucose up to 1 g/L and both extra- and intracellular transient metabolite concentrations were measured
Person responsible: Maksim Zakhartsev
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during glucose pulse, Dynamics of intracellular metabolites during glucose pulse, Dynamics of macromolecules during glucose pulse, MOSES: dynamic model of glucose pulse
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
This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.
Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus
Assays: FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
Our current gene-expression model (Haanstra et al. 2008 PMID: 19008351) will be parameterized for the different genes of interest.
The framework of this gene expression model has been used to include mRNA half life data into the model of glycolysis
For the enzymes of redox metabolism we will use newly measured rates of transcription, RNA precursor degradation, mRNA degradation, concentrations of mature mRNAs and proteins, enzyme turnover, Vmax values and metabolic fluxes (WP3&5).
Assays: No Assays
We are in the process of construct an ODE model of the trypanothione pathway. As input we will use
newly determined and existing kinetic data and measured metabolite concentrations at the boundaries
Recently the glycolysis model was extended with the pentose phosphate pathway. This pathway will yield the NAPDH that maintains trypanothione in a reduced state.
For some complex enzymes (i.e trypanothione synthase) we are intensively discussing the kinetic data obtained on the
Assays: No Assays
To model the ENA1 transcriptional regulation a model has to be established. First this will be just a graphical representation, it shall then be extended to a boolean model and shall at one point be converted to a kinetic model.
Person responsible: Falko Krause
Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.
Person responsible: Sara Jabbari