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Biomedical subjects

Uros Petrovic

Publications and source records attributed to Uros Petrovic.

7 recordsLinked to original sources
PubMed2006

Role of oxidative stress in the extremely salt-tolerant yeast Hortaea werneckii.

Eukaryotic halotolerant microorganisms are important as model organisms to understand the general mechanisms of resistance to environmental salinity. The ability of the extremely halotolerant black yeast Hortaea werneckii to combat oxidative stress was addressed, using hydrogen peroxide to generate the reactive oxygen species. Increasing environmental salinity was found to have no effect on its high ability to degrade hydrogen peroxide but resulted in a decrease in viability in response to externally added hydrogen peroxide, suggesting that the latter property determines the upper limit of the salt tolerance of H. werneckii. A refinement of the model of adaptation of H. werneckii to high-salinity environments is proposed.

Adaptation, Physiological↗
PubMed2005

Ammodytoxin, a secretory phospholipase A2, inhibits G2 cell-cycle arrest in the yeast Saccharomyces cerevisiae.

Ammodytoxin (Atx), an sPLA2 (secretory phospholipase A2), binds to g and e isoforms of porcine 14-3-3 proteins in vitro. 14-3-3 proteins are evolutionarily conserved eukaryotic regulatory proteins involved in a variety of biological processes, including cell-cycle regulation. We have now shown that Atx binds to yeast 14-3-3 proteins with an affinity similar to that for the mammalian isoforms. Thus yeast Saccharomyces cerevisiae can be used as a model eukaryotic cell, which lacks endogenous phospholipases A2, to assess the in vivo relevance of this interaction. Atx was expressed in yeast cells and shown to be biologically active inside the cells. It inhibited G2 cell-cycle arrest in yeast, which is regulated by 14-3-3 proteins. Interference with the cell cycle indicates a possible mechanism by which sPLA2s are able to cause the opposing effects, proliferation and apoptosis, in mammalian cells.

14-3-3 Proteins↗
PubMed2005

TA-clustering: cluster analysis of gene expression profiles through Temporal Abstractions.

This paper describes a new technique for clustering short time series of gene expression data. The technique is a generalization of the template-based clustering and is based on a qualitative representation of profiles which are labelled using trend Temporal Abstractions (TAs); clusters are then dynamically identified on the basis of this qualitative representation. Clustering is performed in an efficient way at three different levels of aggregation of qualitative labels, each level corresponding to a distinct degree of qualitative representation. The developed TA-clustering algorithm provides an innovative way to cluster gene profiles. We show the developed method to be robust, efficient and to perform better than the standard hierarchical agglomerative clustering approach when dealing with temporal dislocations of time series. Results of the TA-clustering algorithm can be visualized as a three-level hierarchical tree of qualitative representations and as such easy to interpret. We demonstrate the utility of the proposed algorithm on a set of two simulated data sets and on a study of gene expression data from S. cerevisiae.

Algorithms↗
PubMed2004

Ammodytoxin, a neurotoxic secreted phospholipase A(2), can act in the cytosol of the nerve cell.

Recent identification of intracellular proteins that bind ammodytoxin (calmodulin, 14-3-3 proteins, and R25) suggests that this snake venom presynaptically active phospholipase A(2) acts intracellularly. As these ammodytoxin acceptors are cytosolic and mitochondrial proteins, the toxin should be able to enter the cytosol of a target cell and remain stable there to interact with them. Using laser scanning confocal microscopy we show here that Alexa-labelled ammodytoxin entered the cytoplasm of the rat hippocampal neuron and subsequently also its nucleus. The transport of proteins into the nucleus proceeds via the cytosol of a cell, therefore, ammodytoxin passed the cytosol of the neuron on its way to the nucleus. Although it is not yet clear how ammodytoxin is translocated into the cytosol of the neuron, our results demonstrate that its stability in the cytosol is not in question, providing the evidence that the toxin can act in this cellular compartment.

Animals↗
PubMed2004

Microarray data mining with visual programming.

UNLABELLED: Visual programming offers an intuitive means of combining known analysis and visualization methods into powerful applications. The system presented here enables users who are not programmers to manage microarray and genomic data flow and to customize their analyses by combining common data analysis tools to fit their needs. AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog.

Chromosome Mapping↗
PubMed2002

Cellular responses to environmental salinity in the halophilic black yeast Hortaea werneckii.

The development of crop plants with increased salt tolerance necessitates the study of naturally salt-tolerant eukaryotic species. We studied the bio-synthesis of glycerol as a compatible solute in the halophilic eukaryotic microorganism, black yeast Hortaea werneckii. A restriction fragment-differential display technique was used to investigate the transcriptome of the organism. Eight differentially expressed genes were identified in response to growth at different salinities. Although the putative functions of their products, P-type ATPase, ubiquinone reductase, aconitase, RNA helicase, Asn-tRNA ligase, isoamyl alcohol oxidase, and phosphatidylinositol-3-kinase, are not intimately related within the cellular machinery, the results presented here are sufficient to propose a model which describes how H. werneckii adapts to extremely high salinities. Some of these mechanisms of adaptation to raised environmental salinity are similar to those in other salt-sensitive species, e.g. glycerol accumulation, there also appear to be novel mechanisms present such as the use of different energy production mechanisms and post-transcriptional regulation of gene expression. Our results have also provided new data on two genes from two other fungal species, the Neurospora crassa B1D1.130 gene and the Aspergillus ustus amdS-A gene.

Adaptation, Physiological↗