Investigations

A key insight, emerging from discussions and data between the projects PIs, was the importance of switching rates in bistable systems. While the existence of multiple steady states in bistable systems can be described by universal models (that do not differ between different systems), switching rates from one stable state to another depend on the molecular details of the system under consideration.

Aim. Constructing a predictive, dynamic model of the redox metabolism of trypanosomes. Aided by this model we will quantify the impact of gene-expression and metabolic regulation on redox metabolism. The model will be constructed in an iterative cycle of experimentation – modelling – analysis – experimentation, such that it can be extended and refined based on new experimental insights.

The objective of this project is an integrated understanding the metabolic, proteomic and genetic network that controls the transition from growth to glucose starvation. This transition is a fundamental ecophysiological response that serves as a scientific model for environmental signal integration and is pivotal for industrial fermentations of Bacillus that occur predominantly under nutrient starvation.

Keywords: Glucose starvation, Transcriptomics, Proteomics, Metabolomics,Bacillus subtilis,

Clostridia are very ancient bacteria which evolved before the earth had an oxygen atmosphere. To them the air we breathe is a poison. To survive they produce a spore resting stage, resistant to physical and chemical agents.

Some species cause devastating diseases, such as the superbug Clostridium difficile. On the other hand, most are totally harmless, and make a wide range of chemicals useful to man. The best example is Clostridium acetobutylicum which makes butanol. Butanol is an alcohol, which ...

Investigation of how the ENA1 gene is transcriptionally regulated.

Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments the microorganism(s) will come back to another steady state. This investigation deals with these stationary responses of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype ...

Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments there are very quick responses. This investigation deals with this dynamical behaviour (transitions) of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype and mutants experiments ...

The Sulfolobus systems biology (‘‘SulfoSYS’’)-project represented the first (hyper-)thermophilic Systems Biology project, funded within the European trans-national research initiative ‘‘Systems Biology of Microorganisms’’. Within the SulfoSYS-project, focus lies on studying the effect of temperature variation on the central carbohydrate metabolism (CCM) of S. solfataricus that is characterized by the branched Entner–Doudoroff (ED)-like pathway for sugar (glucose, galactose) degradation and the ...

Experimental approaches to evaluate cellular response to Potassium limitation. For this purpose, a series of isogenic strains derived from BY4741 and lacking one (TRK1 or TRK2) or both TRK genes encoding specific potassium uptake systems was constructed using the homologous recombination and Cre-lox system.

Challenge: Comparative analyses, as demonstrated by comparative genomics and bioinformatics, are extremely powerful for (i) transfer of information from (experimentally) well-studied organisms to the other organisms, and (ii) when coupled to functional and phenotypic information, insight in the relative importance of components to the observed differences and simalities. The central principle of this proposal is that important aspects of the functional differences between organisms derive not ...

Investigation of dynamics of the central metabolism (glycolysis, PPP, anaplerotic reactions, purines) of yeast Saccharomyces cerevisiae in anaerobic conditions

Steady state metabolic fluxes and metabolite concentrations of yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

Bacillus subtilis was subjected to various stress conditions like high temperature(57°C), low temperature(16°C), high osmalarity(1.2M NaCl). The above mentioned stress conditions are again split into two different types as 'continuous stress condition' and 'sudden shock'. All the conditions were then done in biological triplicates. Transcriptome for these samples was then analysed with Nimblegen Tiling array.

Cellular parameters of strains lacking both TRK1 and TRK2 genes.

Investigation of the role of 14-3-3 proteins in the S. cerevisiae cation homeostasis

Experimental approaches to study the mechanism and ions involved in potassium uptake after long term potassium starvation.

Properties of cells lacking the NHA1 gene.

This investigation examines the effect of benzoic acid, a food preservative, on the ATP levels of yeast cells.

Handling and manipulation of S. pneumoniae using molecular, cell biological and genetic tools.

The aim of this project is to develop a detailed kinetic model of the CcpA-dependent regulatory network, the key regulon of flux regulation in B. subtilis. Thereby involved are more than 300 genes e.g. catabolism, overflow metabolism, the TCA cycle and amino acid anabolism which are regulated via carbon catabolite regulation (CCR)

High salinity chemostat cultivation, multiomics sampling (proteome, transcriptome, metabolome, fluxome) and modelling of carbon core metabolism of Bacillus subtilis 168.