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Axel Kowald

Publications and source records attributed to Axel Kowald.

14 recordsLinked to original sources
PubMed2006

A tree-based decision rule for identifying profile groups of cases without predefined classes: application in diffuse large B-cell lymphomas.

In this paper, we examined the utility of a forward growing classification tree as a supplement to cluster analysis for deriving a decision rule for the identification of profile groups when the cases do not belong to predefined classes. The technique was applied for the identification of low and high proliferation profile groups of diffuse large B-cell lymphomas according to the immunohistochemical expression levels of proliferation proteins. In a forward growing classification tree method, the size of the tree is controlled by the improvement (threshold value) in the apparent misclassification rate after each split. The classes used in the tree were defined using k-means clustering. The decision rule consisted of the splitting points of the split variables used. The methodology was applied to the histology data from 79 cases of diffuse large B-cell lymphomas. Ten classes of individual cases were derived from k-means clustering. Then, a classification tree with a threshold of 2% was used to derive the decision rule. Branches at the left side of the tree consisted of individuals with a low proliferation profile and branches at the right side of the tree consisted of cases with a high proliferation profile. The classification tree, as a supplement method, not only identified but also provided decision rules for identifying profile groups. Finally, it also allowed for exploration of the data structure.

Algorithms↗
PubMed2006

A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast.

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 techniques to analyse dynamic mechanisms and measures of crosstalk. We present a dynamic mathematical model that compiles current knowledge about the wiring of the pheromone pathway and the filamentous growth pathway in yeast. We consider the main dynamic features and the interconnections between the two pathways in order to study dynamic crosstalk between these two pathways in haploid cells. We introduce two new measures of dynamic crosstalk, the intrinsic specificity and the extrinsic specificity. These two measures incorporate the combined signal of several stimuli being present simultaneously and seem to be more stable than previous measures. When both pathways are responsive and stimulated, the model predicts that (a) the filamentous growth pathway amplifies the response of the pheromone pathway, and (b) the pheromone pathway inhibits the response of filamentous growth pathway in terms of mitogen activated protein kinase activity and transcriptional activity, respectively. Among several mechanisms we identified leakage of activated Ste11 as the most influential source of crosstalk. Moreover, we propose new experiments and predict their outcomes in order to test hypotheses about the mechanisms of crosstalk between the two pathways. Studying signals that are transmitted in parallel gives us new insights about how pathways and signals interact in a dynamical way, e.g., whether they amplify, inhibit, delay or accelerate each other.

Monte Carlo Method↗
PubMed2006

New analytical tools for studying autoimmune diseases.

Protein microarrays with immobilised proteins on their surface are new analytical tools to overcome the current limits with respect to sample volume and throughput. They have a great potential as well with respect to multiplexing of complex samples, as a research tool and in diagnostics. Based on recent advances in this technology, new applications for protein microarrays in studying autoimmune diseases were described. Required tools for bioinformatical analysis of protein microarrays concerning normalisation, clustering and classification methods are discussed. The huge potential of this technology as well as future requirements such as protein microarray based diagnostics are presented.

Animals↗
PubMed2005

Estimation of the mtDNA mutation rate in aging mice by proteome analysis and mathematical modeling.

The accumulation of mitochondria containing mutated genomes was proposed to be an important factor involved in aging. Although the level of mutated mtDNA has shown to increase over time, it is currently not possible to directly measure the mtDNA mutation rate within living cells. The combination of mathematical modeling and controlled experiments is an alternative approach to obtain an estimate for the mutation rate in a well-defined system. In order to judge the relevance of mitochondrial mutations for the aging process, we used a mouse model to study age-related alterations of the mitochondrial proteins. Based on these experimental data we constructed a mathematical model of the mitochondrial population dynamics to estimate mtDNA mutation rates. Mitochondria were isolated from mouse brain and liver at six different ages (newborn to 24-months). A large-gel 2D-electrophoresis-based proteomics approach was used to analyze the mitochondrial proteins. The expression of two respiratory chain complex I subunits and one complex IV subunit decreased significantly with age. One subunit of complex III and one subunit of complex V increased in expression during aging. Together, these data indicate that complex I and IV deficiency in aged tissues might be accompanied by feedback regulation of other protein complexes in the respiratory chain. When we fitted our experimental data to the mathematical model, mtDNA mutation rate was estimated to be 2.7x10(-8) per mtDNA per day for brain and 3.2x10(-9) per mtDNA per day for liver. According to our model and in agreement with the mitochondrial theory of aging, mtDNA mutations could cause the detrimental changes seen in mitochondrial populations during the normal lifespan of mice, while at the same time ensure that the mitochondrial population remains functional during the developmental and reproductive period of mice.

Aging↗
PubMed2005

Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.

One of the most important antioxidant enzymes is superoxide dismutase (SOD), which catalyses the dismutation of superoxide radicals to hydrogen peroxide. The enzyme plays an important role in diseases like trisomy 21 and also in theories of the mechanisms of aging. But instead of being beneficial, intensified oxidative stress is associated with the increased expression of SOD and also studies on bacteria and transgenic animals show that high levels of SOD actually lead to increased lipid peroxidation and hypersensitivity to oxidative stress. Using mathematical models we investigate the question how overexpression of SOD can lead to increased oxidative stress, although it is an antioxidant enzyme. We consider the following possibilities that have been proposed in the literature: (i) Reaction of H(2)O(2) with CuZnSOD leading to hydroxyl radical formation. (ii) Superoxide radicals might reduce membrane damage by acting as radical chain breaker. (iii) While detoxifying superoxide radicals SOD cycles between a reduced and oxidized state. At low superoxide levels the intermediates might interact with other redox partners and increase the superoxide reductase (SOR) activity of SOD. This short-circuiting of the SOD cycle could lead to an increased hydrogen peroxide production. We find that only one of the proposed mechanisms is under certain circumstances able to explain the increased oxidative stress caused by SOD. But furthermore we identified an additional mechanism that is of more general nature and might be a common basis for the experimental findings. We call it the alternative pathway mechanism.

Humans↗
PubMed2005

Profiling of alopecia areata autoantigens based on protein microarray technology.

Protein biochips have a great potential in future parallel processing of complex samples as a research tool and in diagnostics. For the generation of protein biochips, highly automated technologies have been developed for cDNA expression library production, high throughput protein expression, large scale analysis of proteins, and protein microarray generation. Using this technology, we present here a strategy to identify potential autoantigens involved in the pathogenesis of alopecia areata, an often chronic disease leading to the rapid loss of scalp hair. Only little is known about the putative autoantigen(s) involved in this process. By combining protein microarray technology with the use of large cDNA expression libraries, we profiled the autoantibody repertoire of sera from alopecia areata patients against a human protein array consisting of 37,200 redundant, recombinant human proteins. The data sets obtained from incubations with patient sera were compared with control sera from clinically healthy persons and to background incubations with anti-human IgG antibodies. From these results, a smaller protein subset was generated and subjected to qualitative and quantitative validation on highly sensitive protein microarrays to identify novel alopecia areata-associated autoantigens. Eight autoantigens were identified by protein chip technology and were successfully confirmed by Western blot analysis. These autoantigens were arrayed on protein microarrays to generate a disease-associated protein chip. To confirm the specificity of the results obtained, sera from patients with psoriasis or hand and foot eczema as well as skin allergy were additionally examined on the disease-associated protein chip. By using alopecia areata as a model for an autoimmune disease, our investigations show that the protein microarray technology has potential for the identification and evaluation of autoantigens as well as in diagnosis such as to differentiate alopecia areata from other skin diseases.

Adult↗
PubMed2005

Morpho-dynamic changes of mitochondria during ageing of human endothelial cells.

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 of ageing on fusion and fission of mitochondria and consequences of altered fission and fusion activity are still unknown although theoretical models on ageing consider the significance of these processes. Human umbilical vein endothelial cells (HUVECs) have been established as a cell culture model to follow mitochondrial activity and dysfunction during the ageing process. Mitochondria of old and postmitotic HUVECs showed distinct alterations in overall morphology and fine structure, and furthermore, loss of mitochondrial membrane potential. In parallel, a decrease of intact mitochondrial DNA (mtDNA) was observed. Fission and fusion activity of mitochondria were quantified in living cells. Mitochondria of old HUVECs showed a significant and equal decrease of both fusion and fission activity indicating that these processes are sensitive to ageing and could contribute to the accumulation of damaged mitochondria during ageing.

Cells, Cultured↗
PubMed2005

Directionality theory: a computational study of an entropic principle in evolutionary processes.

Analytical studies of evolutionary processes based on the demographic parameter entropy-a measure of the uncertainty in the age of the mother of a randomly chosen newborn-show that evolutionary changes in entropy are contingent on environmental constraints and can be characterized in terms of three tenets: (i) a unidirectional increase in entropy for populations subject to bounded growth constraints; (ii) a unidirectional decrease in entropy for large populations subject to unbounded growth constraints; (iii) random, non-directional change in entropy for small populations subject to unbounded growth constraints. This article aims to assess the robustness of these analytical tenets by computer simulation. The results of the computational study are shown to be consistent with the analytical predictions. Computational analysis, together with complementary empirical studies of evolutionary changes in entropy underscore the universality of the entropic principle as a model of the evolutionary process.

Biological Evolution↗
PubMed2005

Non-parametric classification of protein secondary structures.

Proteins were classified into their families using a classification tree method which is based on the coefficient of variations of physico-chemical and geometrical properties of the secondary structures of proteins. The tree method uses as splitting criterion the increase in purity when a node is split into two subnodes and the size of the tree is controlled by a threshold level for the improvement of the apparent misclassification rate (AMR) of the tree after each splitting step. The classification tree method seems effective in reproducing similar structural groupings as the method of dynamic programming. For comparison, we also used another two methods: neural networks and support vector machines. We could show that the presented classification tree method performs better in classifying proteins into their families. The presented algorithm might be suitable for a rapid preliminary classification of proteins into their corresponding families.

Algorithms↗
PubMed2005

On the relevance of mitochondrial fusions for the accumulation of mitochondrial deletion mutants: a modelling study.

The molecular mechanisms underlying the aging process are still unclear, but the clonal accumulation of mitochondrial deletion mutants is one of the prime candidates. An important question for the mitochondrial theory of aging is to discover how defective organelles might be selected at the expense of wild-type mitochondria. We propose that mitochondrial fission and fusion events are of critical importance for resolving this apparent contradiction. We show that the occurrence of fusions removes the problems associated with the idea that smaller DNA molecules accumulate because they replicate in a shorter time--the survival of the tiny (SOT) hypothesis. Furthermore, stochastic simulations of mitochondrial replication, mutation and degradation show that two important experimental findings, namely the overall low mosaic pattern of oxidative phosphorylation (OXPHOS) impaired cells in old organisms and the distribution of deletion sizes, can be reproduced and explained by this hypothesis. Finally, we make predictions that can be tested experimentally to further verify our explanation for the age-related accumulation of mitochondrial deletion mutants.

Aging↗
PubMed2004

Finding kinetic parameters using text mining.

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 parameters is an expensive task, and finding them in the literature is very laborious. We developed a text mining system that supports researchers in their search for experimentally obtained parameters for kinetic models. Our system classifies full text documents regarding the question whether or not they contain appropriate data using a support vector machine. We evaluated our approach on a manually tagged corpus of 800 documents and found that it outperforms keyword searches in abstracts by a factor of five in terms of precision.

Computational Biology↗
PubMed2004

Alternative pathways might mediate toxicity of high concentrations of superoxide dismutase.

One of the most important antioxidant enzymes is superoxide dismutase (SOD), which catalyzes the dismutation of superoxide radicals to peroxide. The gene for CuZnSOD lies in humans on chromosome 21, and its activity is increased in patients with Down syndrome. However, instead of being beneficial, increased lipid peroxidation is associated with this increased expression, and also studies on bacteria and transgenic animals show that high levels of SOD actually lead to increased lipid peroxidation and hypersensitivity to oxidative stress. Using mathematical models, we investigated the question of how overexpression of SOD can lead to increased oxidative stress, although it is an antioxidant enzyme. We considered several possibilities that have been proposed in the literature, such as CuZnSOD-catalyzed hydroxyl radical formation, superoxide-mediated inhibition of membrane peroxidation, and short-circuiting of the Cu(I)ZnSOD/Cu(II)ZnSOD redox cycle. We found that one of the proposed mechanisms under certain circumstances is able to explain the increased oxidative stress caused by SOD. Furthermore, we identified an additional mechanism that agrees well with experimental observations. We call it the "alternative pathway" mechanism, because it depends on superoxide radicals having alternative pathways besides their reaction with SOD. The alternative pathway mechanism is a very general explanation for SOD-associated oxidative stress, because it does not depend on the specific type of SOD, nor on the redox status of the cell. We therefore think that it might be the common mechanism for the detrimental effects seen in cells and organisms with increased levels of the different forms of superoxide dismutase.

Antioxidants↗
PubMed2002

Lifespan does not measure ageing.

The Gompertz equation, which describes the increase of mortality over time, is often used to measure the rate of the ageing process. However, a recent article argued that it is incorrect to use the function for this purpose and that its use should therefore be discouraged (Driver 2001). I believe that this conclusion is based on misunderstandings and that the Gompertz function (if used appropriately) is actually well suited to measure the ageing rate. Here I will solve the 'paradox' posed by the author and argue that it is actually lifespan that is inadequate to measure ageing and not the Gompertz function.

Aging↗