Studies

112 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
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Assays: Generation of uniformly 13C-labelled E. coli extract, LC-MS based absolute quantification of extracellular metabolites, LC-MS based absolute quantification of intracellular metabolites

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

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

Assays: Metabolomics external metabolites measurements

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

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

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

Assays: GLC incubation, Steady state

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).
Regulation
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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
(from WP3&6).
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
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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.

Assays: Boolean Network Simulation, Bottom up creation of the network from literature, Yeast Interaction Network Analysis

Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.

Assays: Steady state study of the effect of gene regulation on yields of end-pro..., Time-dependent simulations

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