Katja Rateitschak

Katja Rateitschak
University of Rostock · Fachgebiet Systems Biology and Bioinformatics Group

PhD

About

52
Publications
3,962
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1,133
Citations
Citations since 2017
0 Research Items
391 Citations
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20172018201920202021202220230204060
20172018201920202021202220230204060

Publications

Publications (52)
Article
Full-text available
Human and canine mammary tumours show partial claudin expression deregulations. Further, claudins have been used for directed therapeutic approaches. However, the development of claudin targeting approaches requires stable claudin expressing cell lines. This study reports the establishment and characterisation of canine mammary tissue derived cell...
Article
The epithelial-mesenchymal transition (EMT) is the crucial step that cancer cells must pass before they can undergo metastasis. The transition requires the activity of complex functional networks that downregulate properties of the epithelial phenotype and upregulate characteristics of the mesenchymal phenotype. The networks frequently include reci...
Article
Human and canine mammary tumours show partial claudin expression deregulations. Further, claudins have been used for directed therapeutic approaches. However, the development of claudin targeting approaches requires stable claudin expressing cell lines. This study reports the establishment and characterisation of canine mammary tissue derived cell...
Article
Despite temporal changes in the quantities of molecules, the functioning of cells also depends on their distribution within cells and in their extracellular environment. The dynamics of molecules are often governed by diffusion in heterogeneous environments consisting of dynamically changing impenetrable barriers (excluded volumes). This provides a...
Article
Full-text available
Background: Recent findings suggest that in pancreatic acinar cells stimulated with bile acid, a pro-apoptotic effect of reactive oxygen species (ROS) dominates their effect on necrosis and spreading of inflammation. The first effect presumably occurs via cytochrome C release from the inner mitochondrial membrane. A pro-necrotic effect - similar t...
Article
The canonical Wnt signalling pathway plays a critical role in development and disease. The key player of the pathway is beta-catenin. Its activity is mainly regulated by the destruction complex consisting of APC, Axin and GSK3. In the nucleus, complex formation of beta-catenin and TCF initiates target gene expression. Our study provides a comprehe...
Article
The canonical Wnt signalling pathway plays a critical role in development and disease. The key player of the pathway is β-catenin. Its activity is mainly regulated by the destruction complex consisting of APC, Axin and GSK3. In the nucleus, the complex formation of β-catenin and TCF initiates target gene expression. Our study provides a comprehensi...
Data
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We present the mathematical model, model parameters, supplementary figures and a list of abbreviations. (PDF)
Article
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The present work exemplifies how parameter identifiability analysis can be used to gain insights into differences in experimental systems and how uncertainty in parameter estimates can be handled. The case study, presented here, investigates interferon-gamma (IFNγ) induced STAT1 signalling in two cell types that play a key role in pancreatic cancer...
Article
Full-text available
To gain insights into the molecular action of erlotinib in pancreatic cancer (PC) cells. Two PC cell lines, BxPC-3 and Capan-1, were treated with various concentrations of erlotinib, the specific mitogen-activated protein kinase kinase (MEK) inhibitor U0126, and protein kinase B (AKT) inhibitor XIV. DNA synthesis was measured by 5-bromo-2'-deoxyuri...
Article
Interferon-γ (IFNγ)-mediated signal transduction via upregulation of signal transducer and activator of transcription (STAT) 1 leads to the expression of the mucin (MUC) 4 gene in pancreatic cancer cells. Upregulation of STAT1 may also implicate STAT1 tyrosine- or serine-phosphorylation. Experimental data indicate that reaction steps involved in IF...
Article
Full-text available
The extent of proteolytic processing of the amyloid precursor protein (APP) into neurotoxic amyloid-β (Aβ) peptides is central to the pathology of Alzheimer's disease (AD). Accordingly, modifiers that increase Aβ production rates are risk factors in the sporadic form of AD. In a novel systems biology approach, we combined quantitative biochemical s...
Article
We investigate simple one-dimensional maps which allow for exact solutions of their related statistical properties. In addition to the originally refined dynamical description a coarsegrained level of description based on certain partitions of the phase space is selected. The deterministic micropscopic dynamics is shifted to a stochastic symbolic d...
Article
Full-text available
In Alzheimer disease (AD), the intracerebral accumulation of amyloid-β (Aβ) peptides is a critical yet poorly understood process. Aβ clearance via the blood-brain barrier is reduced by approximately 30% in AD patients, but the underlying mechanisms remain elusive. ABC transporters have been implicated in the regulation of Aβ levels in the brain. Us...
Conference Paper
Full-text available
Background: Alzheimer's disease (AD) is a neurodegenerative disorder characterized by amyloid plaques in the brain of affected individuals. Our study aims at (i) modeling the interactome of neuronal factors central to the proteolytic processing of amyloid precursor protein (APP) and (ii) evaluating the influence of SORLA/SORL1, an inhibitor of APP...
Article
Originally implicated in the regulation of survival, proliferation and differentiation of haematopoietic cells, the JAK-STAT pathway has also been linked to developmental processes, growth control and maintenance of homeostasis in a variety of other cells and tissues. Although it remains a complex system, its relative simplicity and the availabilit...
Article
The extent of proteolytic processing of the amyloid precursor protein (APP) into neurotoxic amyloid-b (Ab) pep-tides is central to the pathology of Alzheimer's disease (AD). Accordingly, modifiers that increase Ab production rates are risk factors in the sporadic form of AD. In a novel systems biology approach, we combined quantitative biochemical...
Article
is the key player of the canonical Wnt pathway. Its activity is mainly regulated via protein degradation. In the nucleus, its interaction with TCF initiates target gene expression. Although the functional relevance is unclear, it has been shown that antagonists are also capable of nucleo-cytoplasmic shuttling. The focus of our systems biology analy...
Data
Cost function for different fixed relative concentrations of STAT1Dn for IFNγ = 100 ng/ml. To estimate an upper boundary for the relative concentration of nuclear STAT1Dn, we fixed the scaling factor WBSTAT1Dn at different increasing values and re-optimized the other parameter values. The respective values of the cost function are summarized in the...
Data
Mathematical model describing the reactions of the network in Figure 3. The reaction network was translated into a system of ordinary differential equations (ODE), which describes temporal changes of the network components as a function of interactions and transport processes. The ODE model is shown in the upper part of Additional file 1. The abbre...
Data
Estimation of parameter values. a While global parameters are independent of the IFNγ concentration, local parameters depend on it. a.u. = arbitrary units. The parameters of the mathematical model include reaction constants and delay times. The parameter values were estimated by global optimization from the protein and mRNA time series. We have use...
Article
Full-text available
Interferon-gamma (IFNγ) is a multifunctional cytokine with antifibrotic and antiproliferative efficiency. We previously found that pancreatic stellate cells (PSC), the main effector cells in cancer-associated fibrosis, are targets of IFNγ action in the pancreas. Applying a combined experimental and computational approach, we have demonstrated a piv...
Article
Transient dynamics of signal transduction pathways play an important role in many biological processes, including cell differentiation, apoptosis, metabolism and DNA damage response. Recent examples of quantitative methods to characterize transient signals include transient metabolic control coefficients and finite time Lyapunov exponents. In our w...
Article
Full-text available
Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to unde...
Article
Signal transducer and activator of transcription (STAT) 1 is essentially involved in the mediation of antifibrotic interferon-gamma (IFN gamma) effects in pancreatic stellate cells (PSC). Here, we have further analysed the activation of the STAT1 pathway in a PSC line by combining quantitative data generation with mathematical modelling. At saturat...
Conference Paper
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Article
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 stabl...
Article
We introduce a symbol sequence generator producing sequences with long-range correlations. We analytically derive the scaling behaviour of block entropies. A similar scaling behaviour was suggested for natural information carrying symbol sequences, e.g. texts.
Article
Full-text available
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 (glyco...
Article
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 ma...
Article
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-...
Article
Full-text available
Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG—‘COmparative Regulatory Genomics’—database. The data were computed based on statistic...
Article
Full-text available
In recent work a deterministic and time-reversible boundary thermostat called thermostating by deterministic scattering was introduced for the periodic Lorentz gas [Phys. Rev. Lett. 84, 4268 (2000)]. Here we assess the nonlinear properties of this dynamical system by numerically calculating its Lyapunov exponents. Based on a revised method for comp...
Article
Full-text available
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...
Article
We present a novel approach for constructing nonequilibrium steady states. It is based on a deterministic and time-reversible mechanism for dissipating energy from a subsystem into a thermal reservoir. The key idea is to thermalize a moving particle by appropriately modeling its microscopic collision rules with a boundary mimicking a thermal reserv...
Article
Full-text available
We apply the Nose-Hoover thermostat and three variations of it, which control different combinations of velocity moments, to the periodic Lorentz gas. Switching on an external electric field leads to nonequilibrium steady states for the four models with a constant average kinetic energy of the moving particle. We study the probability density, the...
Article
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We present a novel mechanism for thermalizing a system of particles in equilibrium and nonequilibrium situations, based on specifically modeling energy transfer at the boundaries via a microscopic collision process. We apply our method to the periodic Lorentz gas, where a point particle moves diffusively through an ensemble of hard disks arranged o...
Article
Full-text available
We present a mechanism for thermalizing a moving particle by microscopic deterministic scattering. As an example, we consider the periodic Lorentz gas. We modify the collision rules by including energy transfer between particle and scatterer such that the scatterer mimics a thermal reservoir with arbitrarily many degrees of freedom. The complete sy...
Article
The entropy analysis of symbol sequences created by symbolic dynamics reveals temporal correlations present in the stationary dynamics. We investigate how noise, introduced in different ways, affects temporal correlations found in the logistic map at the period doubling accumulation point. The deterministic system under consideration yields a highl...
Article
Full-text available
This paper aims to make further contributions to the exploration of the symbolic dynamics generated by the logistic map at Feigenbaum accumulation point. In particular we are interested in the grammar of these sequences; completing earlier studies we study here arbitrary partitions also. Our main aim is the investigation of the special grammars whi...
Article
Symbol sequences play a prominent role in the context of symbolic dynamics. Important features of a dynamical system are reflected by related statistics of subsequences. A dynamical behavior giving rise to a self-similar attractor and universal scaling relations, expressed by critical exponents, will lead to self-similar statistics of subsequences....
Article
Full-text available
The collective behavior of overdamped nonlinear noise-driven oscillators coupled via mean field is investigated numerically. When a coupling constant is increased, a transition in the dynamics of the mean field is observed. This transition scales with the number of oscillators and disappears when this number tends to infinity. Analytical arguments...

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Projects (2)
Project
Study the relation between entropy and information, the physical basis of information, the origin of information