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Zentrum für Biosystemanalyse

Overview
Works: 23 works in 23 publications in 1 language and 63 library holdings
Roles: Contributor
Publication Timeline
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Most widely held works by Zentrum für Biosystemanalyse
Transcriptome dynamics to unravel PC12 cell fate decisions by Barbara Offermann( )

1 edition published in 2017 in English and held by 16 WorldCat member libraries worldwide

Abstract: The PC12 cell line is a well-established cell model system for analysing cell fate decisionmaking processes. When stimulated with the growth factor EGF the cells proliferate increasingly, when stimulated with the nerve growth factor NGF the cells differentiate into sympathetic-like neurons. Both processes are regulated via the ERK/MAPK pathway. In this context, signal duration of activated ERK seems to be the key mechanism for the emergence of the distinct cell fates. Whereas NGF stimulation results in sustained ERK activation and neuronal differentiation of the cell line, EGF stimulation activates ERK transiently and results in enhanced cell proliferation. How the temporal dynamics of ERK signalling are encoded and translated in order to specify cell fates has not been fully understood yet. <br>This thesis is the first comparison of the EGF and NGF induced transcriptome of PC12 cells on a time scale of 24 hours with high sample density. It was shown that the EGF and NGF stimulus activate a very similar set of genes, which initiates and modulates the cell fate decision. These genes' expression dynamics, however, were different depending on the stimulus used: EGF stimulation induced a short impulse-like gene expression pattern, whereas NGF stimulation resulted in a long-sustained response. In line with previous studies it was demonstrated, that immediate early genes such as Egr1, Fos and Junb show an increased stability in the case of NGF stimulation. It was shown, that this is most likely due to a delayed negative transcriptional feedback via Fosl1, Atf3, Maff, Klf2 und Zfp36l2. Moreover it was demonstrated, that both cell fates, proliferation as well as differentiation, are not solely dependent on the ERK/MAPK pathway. Within the first hour after stimulation with EGF cross-talk between the MAPK and PI3K pathways seems necessary in order to induce enhanced cell proliferation. After stimulation with NGF a more complex and sequential activation of different pathways was identified. In this context the activation of the Il6 pathway and the uPA/uPAR complex seems to be of special importance. The activation of these two pathways was exclusively seen after NGF-stimulation, which encourages further research to gain a deeper understanding of their function in the process of neuronal differentiation. Additionally, Dusp6 was identified as a potentially important modulator of the PC12 cell fate. In summary, this thesis analyses and compares the EGF and NGF induced transcriptome of PC12 cells from a systems biology perspective. Most importantly, it was shown, that the activation of a similar set of genes may result in distinctly different cellular behaviour depending on the genes' expression dynamics
Hepatocyte ploidy is a diversity factor for liver homeostasis by Clemens Kreutz( )

1 edition published in 2017 in English and held by 3 WorldCat member libraries worldwide

Abstract: Polyploidy, the existence of cells containing more than one pair of chromosomes, is a well-known feature of mammalian hepatocytes. Polyploid hepatocytes are found either as cells with a single polyploid nucleus or as multinucleated cells with diploid or even polyploid nuclei. In this study, we evaluate the degree of polyploidy in the murine liver by accounting both DNA content and number of nuclei per cell. We demonstrate that mouse hepatocytes with diploid nuclei have distinct metabolic characteristics compared to cells with polyploid nuclei. In addition to strong differential gene expression, comprising metabolic as well as signaling compounds, we found a strongly decreased insulin binding of nuclear polyploid cells. Our observations were associated with nuclear ploidy but not with total ploidy within a cell. We therefore suggest ploidy of the nuclei as an new diversity factor of hepatocytes and hypothesize that hepatocytes with polyploid nuclei may have distinct biological functions than mono-nuclear ones. This diversity is independent from the well-known heterogeneity related to the cells' position along the porto-central liver-axis
Modulating Nucleation by Kosmotropes and Chaotropes : Testing the Waters by Ashit Rao( )

1 edition published in 2017 in English and held by 3 WorldCat member libraries worldwide

Abstract: Water is a fundamental solvent sustaining life, key to the conformations and equilibria associated with solute species. Emerging studies on nucleation and crystallization phenomena reveal that the dynamics of hydration associated with mineral precursors are critical in determining material formation and growth. With certain small molecules affecting the hydration and conformational stability of co-solutes, this study systematically explores the effects of these chaotropes and kosmotropes as well as certain sugar enantiomers on the early stages of calcium carbonate formation. These small molecules appear to modulate mineral nucleation in a class-dependent manner. The observed effects are finite in comparison to the established, strong interactions between charged polymers and intermediate mineral forms. Thus, perturbations to hydration dynamics of ion clusters by co-solute species can affect nucleation phenomena in a discernable manner
MICA: multiple interval-based curve alignment by Martin Raden( )

1 edition published in 2018 in English and held by 3 WorldCat member libraries worldwide

Abstract: MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments.<br>Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data.<br>The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA
Alterations of Gab2 signalling complexes in imatinib and dasatinib treated chronic myeloid leukaemia cells by Sebastian Halbach( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Background:<br>The Gab2 docking protein acts as an important signal amplifier downstream of various growth factor receptors and Bcr-Abl, the driver of chronic myeloid leukaemia (CML). Despite the success of Bcr-Abl tyrosine kinase inhibitors (TKI) in the therapy of CML, TKI-resistance remains an unsolved problem in the clinic. We have recently shown that Gab2 signalling counteracts the efficacy of four distinct Bcr-Abl inhibitors. In the course of that project, we noticed that two clinically relevant drugs, imatinib and dasatinib, provoke distinct alterations in the electrophoretic mobility of Gab2, its signalling output and protein interactions. As the signalling potential of the docking protein is highly modulated by its phosphorylation status, we set out to obtain more insights into the impact of TKIs on Gab2 phosphorylation.<br>Findings:<br>Using stable isotope labelling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry (MS), we show now that imatinib and dasatinib provoke distinct effects on the phosphorylation status and interactome of Gab2. This study identifies several new phosphorylation sites on Gab2 and confirms many sites previously known from other experimental systems. At equimolar concentrations, dasatinib is more effective in preventing Gab2 tyrosine and serine/threonine phosphorylation than imatinib. It also affects the phosphorylation status of more residues than imatinib. In addition, we also identify novel components of the Gab2 signalling complex, such as casein kinases, stathmins and PIP1 as well as known interaction partners whose association with Gab2 is disrupted by imatinib and/or dasatinib.<br>Conclusions:<br>By using MS-based proteomics, we have identified new and confirmed known phosphorylation sites and interaction partners of Gab2, which may play an important role in the regulation of this docking protein. Given the growing importance of Gab2 in several tumour entities we expect that our results will help to understand the complex regulation of Gab2 and how this docking protein can contribute to malignancy
A red light-controlled synthetic gene expression switch for plant systems by Konrad Müller( )

1 edition published in 2014 in English and held by 2 WorldCat member libraries worldwide

Abstract: On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants. For this purpose, we applied an interdisciplinary synthetic biology approach comprising mammalian and plant cell systems to customize and optimize a split transcription factor based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). Implementation of the system in transient assays in tobacco protoplasts resulted in strong (95-fold) induction in red light (660 nm) and could be instantaneously returned to the OFF state by subsequent illumination with far-red light (740 nm). Capitalizing on this toggle switch-like characteristic, we demonstrate that the system can be kept in the OFF state in the presence of 740 nm-supplemented white light, opening up perspectives for future application of the system in whole plants. Finally we demonstrate the system's applicability in basic research, by the light-controlled tuning of auxin signalling networks in N. tabacum protoplasts, as well as its biotechnological potential for the chemical-inducer free production of therapeutic proteins in the moss P. patens
Aminoacyl-tRNA-charged eukaryotic elongation factor 1A is the bona fide substrate for Legionella pneumophila effector glucosyltransferases by Tina Tzivelekidis( )

1 edition published in 2011 in English and held by 2 WorldCat member libraries worldwide

Abstract: Legionella pneumophila, which is the causative organism of Legionnaireś disease, translocates numerous effector proteins into the host cell cytosol by a type IV secretion system during infection. Among the most potent effector proteins of Legionella are glucosyltransferases (lgt's), which selectively modify eukaryotic elongation factor (eEF) 1A at Ser-53 in the GTP binding domain. Glucosylation results in inhibition of protein synthesis. Here we show that in vitro glucosylation of yeast and mouse eEF1A by Lgt3 in the presence of the factors Phe-tRNAPhe and GTP was enhanced 150 and 590-fold, respectively. The glucosylation of eEF1A catalyzed by Lgt1 and 2 was increased about 70-fold. By comparison of uncharged tRNA with two distinct aminoacyl-tRNAs (His-tRNAHis and Phe-tRNAPhe) we could show that aminoacylation is crucial for Lgt-catalyzed glucosylation. Aminoacyl-tRNA had no effect on the enzymatic properties of lgt's and did not enhance the glucosylation rate of eEF1A truncation mutants, consisting of the GTPase domain only or of a 5 kDa peptide covering Ser-53 of eEF1A. Furthermore, binding of aminoacyl-tRNA to eEF1A was not altered by glucosylation. Taken together, our data suggest that the ternary complex, consisting of eEF1A, aminoacyl-tRNA and GTP, is the bona fide substrate for lgt's
Metabolic response to XD14 treatment in human breast cancer cell line MCF-7 by Daqiang Pan( )

1 edition published in 2016 in English and held by 2 WorldCat member libraries worldwide

Robust optimal design of experiments for model discrimination using an interactive software tool by Johannes Stegmaier( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Mathematical modeling of biochemical processes significantly contributes to a better understanding of biological functionality and underlying dynamic mechanisms. To support time consuming and costly lab experiments, kinetic reaction equations can be formulated as a set of ordinary differential equations, which in turn allows to simulate and compare hypothetical models in silico. To identify new experimental designs that are able to discriminate between investigated models, the approach used in this work solves a semi-infinite constrained nonlinear optimization problem using derivative based numerical algorithms. The method takes into account parameter variabilities such that new experimental designs are robust against parameter changes while maintaining the optimal potential to discriminate between hypothetical models. In this contribution we present a newly developed software tool that offers a convenient graphical user interface for model discrimination. We demonstrate the beneficial operation of the discrimination approach and the usefulness of the software tool by analyzing a realistic benchmark experiment from literature. New robust optimal designs that allow to discriminate between the investigated model hypotheses of the benchmark experiment are successfully calculated and yield promising results. The involved robustification approach provides maximally discriminating experiments for the worst parameter configurations, which can be used to estimate the meaningfulness of upcoming experiments. A major benefit of the graphical user interface is the ability to interactively investigate the model behavior and the clear arrangement of numerous variables. In addition to a brief theoretical overview of the discrimination method and the functionality of the software tool, the importance of robustness of experimental designs against parameter variability is demonstrated on a biochemical benchmark problem. The software is licensed under the GNU General Public License and freely available at http://sourceforge.net/projects/mdtgui/
Exometabolom analysis of breast cancer cell lines: metabolic signature by Lucas Willmann( )

1 edition published in 2015 in English and held by 2 WorldCat member libraries worldwide

Abstract: Cancer cells show characteristic effects on cellular turnover and DNA/RNA modifications leading to elevated levels of excreted modified nucleosides. We investigated the molecular signature of different subtypes of breast cancer cell lines and the breast epithelial cell line MCF-10A. Prepurification of cell culture supernatants was performed by cis-diol specific affinity chromatography using boronate-derivatized polyacrylamide gel. Samples were analyzed by application of reversed phase chromatography coupled to a triple quadrupole mass spectrometer. Collectively, we determined 23 compounds from RNA metabolism, two from purine metabolism, five from polyamine/methionine cycle, one from histidine metabolism and two from nicotinate and nicotinamide metabolism. We observed major differences of metabolite excretion pattern between the breast cancer cell lines and MCF-10A, just as well as between the different breast cancer cell lines themselves. Differences in metabolite excretion resulting from cancerous metabolism can be integrated into altered processes on the cellular level. Modified nucleosides have great potential as biomarkers in due consideration of the heterogeneity of breast cancer that is reflected by the different molecular subtypes of breast cancer. Our data suggests that the metabolic signature of breast cancer cell lines might be a more subtype-specific tool to predict breast cancer, rather than a universal approach
Kif3a Guides Microtubular Dynamics, Migration and Lumen Formation of MDCK Cells by Christopher Böhlke( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: The microtubular motor Kinesin-2 and its subunit Kif3a are essential for the formation of primary cilia, an organelle implicated in a wide spectrum of developmental abnormalities. Outside cilia, Kinesin-2 mediated transport has been implicated in vesicle and N-cadherin transport, but it is unknown if and how extraciliary Kif3a affects basic cellular functions such as migration or the formation of multicellular structures. Here we show that tetracycline inducible depletion of Kif3a in MDCK cells slows epithelial cell migration. Microtubules at the leading edge of Kif3a depleted cells failed to grow perpendicularly into the leading edge and microtubular dynamics were dampened in Kif3a depleted cells. Loss of Kif3a retarded lateral membrane specification and completely prevented the formation of three-dimensional spheres in collagen. These data uncover that Kif3a regulates the microtubular cytoskeleton in the cell periphery and imply that extra-ciliary Kif3a has an unexpected function in morphogenesis
Protocol: an improved and universal protocol for whole-mount immunolocalization in plants by Taras Pasternak( )

1 edition published in 2015 in English and held by 2 WorldCat member libraries worldwide

Abstract: Rapid advances in microscopy have boosted research on cell biology. However sample preparation enabling excellent reproducible tissue preservation and cell labeling for in depth microscopic analysis of inner cell layers, tissues and organs still represents a major challenge for immunolocalization studies. Here we describe a protocol for whole-mount immunolocalization of proteins which is applicable to a wide range of plant species. The protocol is improved and robust for optimal sample fixation, tissue clearing and multi-protein staining procedures and can be used in combination with simultaneous detection of specific sequences of nucleic acids. In addition, cell wall and nucleus labelling can be implemented in the protocol, thereby allowing a detailed analysis of morphology and gene expression patterns with single-cell resolution. Besides enabling accurate, high resolution and reproducible protein detection in expression and localization studies, the procedure takes a single working day to complete without the need for robotic equipment.<br><br>Keywords<br><br>Immunolocalization - Tissue multi-protein expression - Whole-mount - 3D reconstruction - Protein-protein interaction
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems by Sita Johanna Saunders( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein-binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap
Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development by Hauke Busch( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems
Microtubule associated protein 1b (MAP1B) is a marker of the microtubular cytoskeleton in podocytes but is not essential for the function of the kidney filtration barrier in mice by Markus Gödel( )

1 edition published in 2015 in English and held by 2 WorldCat member libraries worldwide

Abstract: Podocytes are essential for the function of the kidney glomerular filter. A highly differentiated cytoskeleton is requisite for their integrity. Although much knowledge has been gained on the organization of cortical actin networks in podocyte's foot processes, less is known about the molecular organization of the microtubular cytoskeleton in primary processes and the cell body. To gain an insight into the organization of the microtubular cytoskeleton of the podocyte, we systematically analyzed the expression of microtubule associated proteins (Maps), a family of microtubules interacting proteins with known functions as regulator, scaffold and guidance proteins. We identified microtubule associated protein 1b (MAP1B) to be specifically enriched in podocytes in human and rodent kidney. Using immunogold labeling in electron microscopy, we were able to demonstrate an enrichment of MAP1B in primary processes. A similar association of MAP1B with the microtubule cytoskeleton was detected in cultured podocytes. Subcellular distribution of MAP1B HC and LC1 was analyzed using a double fluorescent reporter MAP1B fusion protein. Subsequently we analyzed mice constitutively depleted of MAP1B. Interestingly, MAP1B KO was not associated with any functional or structural alterations pointing towards a redundancy of MAP proteins in podocytes.<br>In summary, we established MAP1B as a specific marker protein of the podocyte microtubular cytoskeleton
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains by Patrick R Wright( )

1 edition published in 2014 in English and held by 2 WorldCat member libraries worldwide

Abstract: CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict tar- gets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de
Automated system for the cell-free protein microarray synthesis and the label-free molecule-protein interaction analysis by Jürgen Burger( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Driving the model to its limit : profile likelihood based model reduction by Tim Maiwald( )

1 edition published in 2016 in English and held by 2 WorldCat member libraries worldwide

The infinitely many genes model for the distributed genome of bacteria by Franz Baumdicker( )

1 edition published in 2012 in English and held by 2 WorldCat member libraries worldwide

Abstract: The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 1011 and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality
Lessons learned from quantitative dynamical modeling in systems biology by Andreas Raue( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here
 
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Alternative Names
Albert-Ludwigs-Universität Freiburg Rektorat Zentrum für Biosystemanalyse

Center for Biological Systems Analysis

University of Freiburg Center for Biological Systems Analysis

ZBSA

Languages
English (20)