Studies

We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods.

The Lactate dehydrogenases (LDH) are key metabolic enzymes in lactic acid bacteria (LAB). The LDH ( E.C. 1.1.1.27) catalyzes the reaction of pyruvate and NADH into lactate and NAD+.We have carried out an experimental and computational study of the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 3 LDHs from 3 LABs studied at pH 6 and pH 7.

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 ...

The output of the initial model of redox metabolism will be compared to experimental flux and metabolite data. Deviations between model and experiment will be prioritized together with WP2. We will apply Metabolic Control Analysis (Fell 1992 PMID: 1530563) to diagnose which enzymes control the deviating metabolite concentrations and/or rates. When the agreement between model and experiment is sufficient we will first link it to the existing model of trypanosome glycolysis and repeat the same ...

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 ...

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 ...

These templates can be used for a selection of metabolomics data types. There is a MASTER template for general use and adaptation as well as several more specific templates for particular types of experiment (e.g. HPLC), or specific assay types (e.g glucose pulse)

Multi experimental approach to define the gene expression remodelling under potassium starvation conditions.

How does the Volume, internal pH, membrane potential and intracellular cation content change in a time dependent scale during potassium limitation.

How do the fluxes of rubidium (potassium) change during potassium starvation.

What is the proteome of starved cells. Main characteristics?

Are there one or several stationary states for physiological parameters dependent on external KCl? For which range of external potassium the cell is able to maintain a constant pH, potassium content, membrane potential and volume?

How does the current mediated by Trk1,2 depend on external and internal ion concentrations? How is the membrane potential shifted by the concentrations of various ions, especially ammonium?

Does the general proteome of yeast cells change in a strain lacking Trk1,2 transporter? Under which conditions?

Studies on the effect of deletion of genes encoding 14-3-3 proteins on the transcriptional response of yeast cells to potassium starvation.

Studies on genetic interactions between genes encoding 14-3-3 proteins and genes encoding transporters to elucidate which transporter(s) are regulated by 14-3-3 proteins.

Bioinformatic studies to elucidate the role of 14-3-3 proteins in cation homeostasis.

How does the flux of potassium, hydrogen change during potassium uptake? Which ions are involved in maintaining the required charge balance?

How does the transport of potassium and hydrogen ions effect the concentrations in the near surrounding of the cell.

How does the current mediated by Trk1,2 depend on external and internal ion concentrations? How is the membrane potential shifted by the concentrations of various ions, especially ammonium?

At external potassium concentrations in the range of 10uM to 1mM Trk is major cellular uptake system for potassium. This system responds to the activiy of the proton pump. Transmembrane fluxes of protons and potassium cations are analysed in a signal-response relationship.

This study aims to establish the optimum conditions and assay methods for measuring ATP levels

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

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