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BACKGROUND Eukaryotic cells have evolved various response mechanisms to counteract the deleterious consequences of oxidative stress. Among these processes, metabolic alterations seem to play an important role. RESULTS We recently discovered that yeast cells with reduced activity of the key glycolytic enzyme triosephosphate isomerase exhibit an increased(More)
Mitochondrial morphology is regulated in many cultured eukaryotic cells by fusion and fission of mitochondria. A tightly controlled balance between fission and fusion events is required to ensure normal mitochondrial and cellular functions. During ageing, mitochondria are undergoing significant changes on the functional and morphological level. The effect(More)
Cells must be able to process multiple information in parallel and, moreover, they must also be able to combine this information in order to trigger the appropriate response. This is achieved by wiring signalling pathways such that they can interact with each other, a phenomenon often called crosstalk. In this study, we employ mathematical modelling(More)
The mathematical modeling and description of complex biological processes has become more and more important over the last years. Systems biology aims at the computational simulation of complex systems, up to whole cell simulations. An essential part focuses on solving a large number of parameterized differential equations. However, measuring those(More)
The understanding and modelling of biological systems relies on the availability of numerical values for physical and chemical properties of biological macro molecules. Kinetic parameters, rate constants, specificities and half-lifes are examples of those properties. This data is mostly published in free text form in scientific journals, which is(More)
Classification into multiple classes when the measured variables are outnumbered is a major methodological challenge in -omics studies. Two algorithms that overcome the dimensionality problem are presented: the forest classification tree (FCT) and the forest support vector machines (FSVM). In FCT, a set of variables is randomly chosen and a classification(More)
Developing accurate kinetic models depends on the availability of kinetic parameters, which can usually only be found in published articles. The extremely large number of publications makes it advantageous to develop tools for automated recognition and extraction of entities related to enzyme kinetics from text. The idea of this project is to provide a tool(More)
In an "aging society," health span extension is most important. As in 2010, talks in this series of meetings in Rostock-Warnemünde demonstrated that aging is an apparently very complex process, where computational work is most useful for gaining insights and to find interventions that counter aging and prevent or counteract aging-related diseases. The(More)
the effect of methylglyoxal (MG) metabolism on growth and lifespan in P. anserina [1]. Methylglyoxal (2-oxopropanal) is generated enzymatically by three types of enzymes (methylglyoxal synthase, cytochrome P450 isozyme and amine oxidase) and non-enzymatically as a side product of glycolysis from dihydroxyacetone phosphate and glyceraldehyde-3-phosphat. MG(More)
Recently, an enzyme (Cre recombinase) has been developed by directed evolution that successfully removes the HIV genome from the nuclear DNA of infected cells. To explore this idea further, we hypothesized that a replication deficient virus (called "police virus"), added externally, can deliver such a recombinase which excises the integrated HIV DNA from(More)