Biomedical subjects

Katja Rateitschak

Publications and source records attributed to Katja Rateitschak.

5 recordsLinked to original sources

PubMed2006

Intracellular delay limits cyclic changes in gene expression.

Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kappaB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding and mRNA production. This description of natural variability for delays introduces a transition from a stable steady state to limit cycle oscillations and then a second transition back to a stable steady state which has not been observed in previously published models. We demonstrate our approach for two models. The first model describes Hes1 autorepression with equations for Hes1 mRNA production and Hes1 protein translation. The second model describes Hes1 repression by the protein complex Gro/TLE1/Hes1, where Gro/TLE1 is activated by Hes1 phosphorylation. Finally, we discuss our analytical and numerical results in relation to experimental data.

Algorithms↗

PubMed2006

Wnt signal pathways and neural stem cell differentiation.

Self-renewal, migration and differentiation of neural progenitor cells are controlled by a variety of pleiotropic signal molecules. Members of the morphogen family of Wnt molecules play a crucial role for developmental and repair mechanisms in the embryonic and adult nervous system. A strategy of disclosure of the role of different canonical (glycogen synthase kinase-3beta/beta-catenin-dependent) and noncanonical (Ca2+- and JNK-dependent) signal pathways for progenitor cell expansion and differentiations is illustrated at the example of the rat striatal progenitor cell line ST14A that is immortalized by stable retroviral transfection with a temperature-sensitive mutant of the SV40 large T antigen. A shift from permissive 33 degrees C to nonpermissive 39 degrees C leads to proliferation stop and start of differentiation into glial and neuronal cells. Investigation of expression of Wnts, Wnt receptors and Wnt-dependent signal pathway assay point to a stage-dependent involvement of canonical and noncanonical signaling in proliferation and differentiation of ST14A cells, whereby a mutual suppression of pathway activities is likely. Canonical Wnt molecules are not detected in proliferating and differentiating ST14A cells except Wnt2. The noncanonical Wnt molecules Wnt4, Wnt5a and Wnt11 are expressed in proliferating cells and increase during differentiation, whereas cellular beta-catenin decreases in the early phase and is restored in the late phase of differentiation. Accumulation of beta-catenin at the membrane in undifferentiated proliferating cells and its nuclear localization in nondividing undifferentiated cells under differentiation conditions argues for a distinct spatially regulated role of the molecule in the proliferation and early differentiation phase. Ca2+-dependent and JNK-dependent noncanonical Wnt signaling is not detected during differentiation of ST14A cells. Complete exploration of the role of Wnt pathways, for differentiation of the neural progenitor cells ST14A will require Wnt overexpression and exposure of ST14A cells to exogenous Wnts either with purified Wnts or by co-cultures with Wnt producers.

Animals↗

PubMed2004

Annotating significant pairs of transcription factor binding sites in regulatory DNA.

In the presented work we search for transcription factor binding sites (BS) by including additional information about typical BS patterns. The new proposed score combines the ordinary profile score based on TRANSFAC-matrices together with a score based on pairs of BS. The latter score positively weights pairs of BS that tend to occur together in many regulatory DNA-sequences, in contrast to a random background model. The empirical BS pair frequencies result from our evaluation of a large dataset of orthologous genes.

Animals↗

PubMed2003

SIR-dependent repression of non-telomeric genes in Saccharomyces cerevisiae?

The proteins Sir2, Sir3 and Sir4 repress transcription of the silent mating-type loci HML and HMR and of reporter genes inserted at telomeres. Previous microarray analyses suggested that additional non-telomeric genes exist which are repressed by the Sir proteins. In this study, we tested the expression of 12 such genes by Northern analysis and RT-PCR. However, we were unable to verify their SIR-dependent regulation, which suggests that SIR-mediated repression may be restricted to the known repressed regions.

Blotting, Northern↗

PubMed2002

Annotating regulatory DNA based on man-mouse genomic comparison.

Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such conserved elements from upstream regions of orthologous gene pairs from man and mouse. We focus on orthologous genes in order to maximize our chances to find functionally similar regulatory elements. The identification of conserved elements is effected using the Waterman-Eggert local suboptimal alignment algorithm. We have modified an implementation of this algorithm such that it integrates the determination of statistical significance for the local suboptimal alignments. This has the effect of outputting a dynamically determined number of suboptimal alignments that are deemed statistically significant. Comparison with experimentally determined annotation shows a striking enrichement of regulatory sites among the conserved regions. Furthermore, the conserved regions tend to cover the promotor region described in the EPD database.

Algorithms↗