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Biomedical subjects

N Speer

Publications and source records attributed to N Speer.

3 recordsLinked to original sources

JCell--a Java-based framework for inferring regulatory networks from time series data.

MOTIVATION: JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. AVAILABILITY: The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

Algorithms↗

Gene expression patterns of epithelial cells modulated by pathogenicity factors of Yersinia enterocolitica.

Epithelial cells express genes whose products signal the presence of pathogenic microorganisms to the immune system. Pathogenicity factors of enteric bacteria modulate host cell gene expression. Using microarray technology we have profiled epithelial cell gene expression upon interaction with Yersinia enterocolitica. Yersinia enterocolitica wild-type and isogenic mutant strains were used to identify host genes modulated by invasin protein (Inv), which is involved in enteroinvasion, and Yersinia outer protein P (YopP) which inhibits innate immune responses. Among 22 283 probesets (14,239 unique genes), we found 193 probesets (165 genes) to be regulated by Yersinia infection. The majority of these genes were induced by Inv, whose recognition leads to expression of NF-kappa B-regulated factors such as cytokines and adhesion molecules. Yersinia virulence plasmid (pYV)-encoded factors counter regulated Inv-induced gene expression. Thus, YopP repressed Inv-induced NF-kappa B regulated genes at 2 h post infection whereas other pYV-encoded factors repressed host cell genes at 4 and 8 h post infection. Chromosomally encoded factors of Yersinia, other than Inv, induced expression of genes known to be induced by TGF-beta receptor signalling. These genes were also repressed by pYV-encoded factors. Only a few host genes were exclusively induced by pYV-encoded factors. We hypothesize that some of these genes may contribute to pYV-mediated silencing of host cells. In conclusion, the data demonstrates that epithelial cells express a limited number of genes upon interaction with enteric Yersinia. Both Inv and YopP appear to modulate gene expression in order to subvert epithelial cell functions involved in innate immunity.

Adhesins, Bacterial↗

[Cloning and analysis of a new neurogene in the mouse].

The previously described gene sip1 belongs to transcription factors of the zinc finger family. It has been ascertained recently that this gene is involved in TGF signaling cascade. Mutations in human gene sip1 cause Hirschprung syndrome. The expression of gene sip1 during embryonic mouse development was studied by in situ hybridization and immunostaining. Starting at E12.5, sip1 transcripts are present in a number of tissues: in the cortical plate, ventricular zone of the basal ganglion, thalamus, pons and midbrain, in specific nuclei of the brain stem and in the dorsal part of the spinal cord. In the developing cerebral cortex, sip1 expression is region-specific. In the brain of adult mice, sip1 expression is mostly detected in hippocampus, dentate gyrus, and white matter of the neocortex. Sip1 protein expression in the cerebral cortex is mostly confined to glutamatergic neurons.

Animals↗