TY - JOUR A1 - Wagner, Toni U. A1 - Fischer, Andreas A1 - Thoma, Eva C. A1 - Schartl, Manfred T1 - CrossQuery : A Web Tool for Easy Associative Querying of Transcriptome Data N2 - Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deepsequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types. KW - CrossQuery Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-76088 ER - TY - JOUR A1 - Kraeussling, Michael A1 - Wagner, Toni Ulrich A1 - Schartl, Manfred T1 - Highly Asynchronous and Asymmetric Cleavage Divisions Accompany Early Transcriptional Activity in Pre-Blastula Medaka Embryos N2 - In the initial phase of development of fish embryos, a prominent and critical event is the midblastula transition (MBT). Before MBT cell cycle is rapid, highly synchronous and zygotic gene transcription is turned off. Only during MBT the cell cycle desynchronizes and transcription is activated. Multiple mechanisms, primarily the nucleocytoplasmic ratio, are supposed to control MBT activation. Unexpectedly, we find in the small teleost fish medaka (Oryzias latipes) that at very early stages, well before midblastula, cell division becomes asynchronous and cell volumes diverge. Furthermore, zygotic transcription is extensively activated already after the 64-cell stage. Thus, at least in medaka, the transition from maternal to zygotic transcription is uncoupled from the midblastula stage and not solely controlled by the nucleocytoplasmic ratio. KW - Fische KW - Embryo Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-68906 ER - TY - THES A1 - Wagner, Toni T1 - Activity and Crosstalk of STAT3 and BMP Signalling Pathways in Pluripotency Control of Mouse and Medaka Stem Cells T1 - Aktivität und Verschaltung von STAT3 und BMP Signalwegen in der Pluripotenzkontrolle von Maus und Medaka Stammzellen N2 - - 77/83 allerdings inaktiv in Kulturen und Embryonen von Medaka. Dieser Unterschied wird durch Daten aus humanen ES-Zellkulturen unterstützt. Letztere sind ebenfalls komplett STAT3 unabhängig. Die BMP-Smad Kaskade wiederum ist in Medaka-Stammzellen aktiv, Antidifferenzierungsgene wie id2, die durch BMP direkt kontrolliert werden, sind dementsprechend exprimiert. Diese Daten stimmen wiederum mit dem Maussystem überein, während humane ES-Zellen diesbezüglich bislang nicht untersucht wurden. Die Interaktion zwischen verschiedenen Signalwegen ist ein bisher noch nicht gut verstandenes Gebiet. Die Integration verschiedener Signale ist aber speziell für Stammzellen, die ihr Differenzierungsschicksal von winzigen Abweichungen in der Signalmixtur abhängig machen, von entscheidender Bedeutung. Im zweiten Teil der hier vorgelegten Arbeit konnte eine Interaktion zwischen dem BMP-Rezeptor 1a und STAT3 nachgewiesen werden. Diese Interaktion ist offenbar Teil eines variablen Komplexes. Zum ersten Mal war es auch möglich, funktionale Konsequenzen für STAT3 nach Stimulierung des BMP-Rezeptors 1a zu dokumentieren. Nach Belegung des BMP-Rezeptors 1a mit dem mutierten BMP2-A34D wird STAT3 trotz Aktivierung durch Phosphorylierung an Tyrosin 705 im Zytoplasma von Maus Stammzellen festgehalten. Zusammengenommen konnte hier gezeigt werden, dass eine Interaktion zwischen den bislang als isoliert betrachteten Signalwegen BMP-Smad und STAT3 besteht. Des Weiteren wurde das Medaka-Stammzellkultursystem benutzt, um zu zeigen, dass STAT3 für die Pluripotenz von Stammzellen nur im Maussystem eine Rolle spielt, wohingegen BMPZielgene wie id2 in bislang allen getesteten ES-Zellkultursystemen aktiv sind. KW - Stammzellen KW - Pluripotency KW - ES-Cells KW - STAT3 KW - BMP KW - Medaka Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-26495 ER - TY - JOUR A1 - Schul, Daniela A1 - Schmitt, Alexandra A1 - Regneri, Janine A1 - Schartl, Manfred A1 - Wagner, Toni Ulrich T1 - Bursted BMP Triggered Receptor Kinase Activity Drives Smad1 Mediated Long-Term Target Gene Oscillation in c2c12 Cells JF - PLoS ONE N2 - Bone Morphogenetic Proteins (BMPs) are important growth factors that regulate many cellular processes. During embryogenesis they act as morphogens and play a critical role during organ development. They influence cell fates via concentration-gradients in the embryos where cells transduce this extracellular information into gene expression profiles and cell fate decisions. How receiving cells decode and quantify BMP2/4 signals is hardly understood. There is little data on the quantitative relationships between signal input, transducing molecules, their states and location, and ultimately their ability to integrate graded systemic inputs and generate qualitative responses. Understanding this signaling network on a quantitative level should be considered a prerequisite for efficient pathway modulation, as the BMP pathway is a prime target for therapeutic invention. Hence, we quantified the spatial distribution of the main signal transducer of the BMP2/4 pathway in response to different types and levels of stimuli in c2c12 cells. We found that the subcellular localization of Smad1 is independent of ligand concentration. In contrast, Smad1 phosphorylation levels relate proportionally to BMP2 ligand concentrations and they are entirely located in the nucleus. Interestingly, we found that BMP2 stimulates target gene expression in non-linear, wave-like forms. Amplitudes showed a clear concentration-dependency, for sustained and transient stimulation. We found that even burst-stimulation triggers gene-expression wave-like modulations that are detectable for at least 30 h. Finally, we show here that target gene expression oscillations depend on receptor kinase activity, as the kinase drives further expression pulses without receptor reactivation and the target gene expression breaks off after inhibitor treatment in c2c12 cells. KW - gene expression KW - BMP signaling KW - SMAD signaling KW - genetic oscillators KW - cell fusion KW - DNA-binding proteins KW - luciferase KW - kinase inhibitors Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130131 VL - 8 IS - 4 ER - TY - JOUR A1 - Wagner, Toni U. A1 - Fischer, Andreas A1 - Thoma, Eva C. A1 - Schartl, Manfred T1 - CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data JF - PLoS ONE N2 - Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types. KW - Microarray data KW - Sprouting angiogenesis KW - Cell-line KW - Biology Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134787 VL - 6 IS - 12 ER - TY - JOUR A1 - Schartl, Manfred A1 - Kneitz, Susanne A1 - Wilde, Brigitta A1 - Wagner, Toni A1 - Henkel, Christiaan V. A1 - Spaink, Hermann P. A1 - Meierjohann, Svenja T1 - Conserved expression signatures between medaka and human pigment cell tumors N2 - Aberrations in gene expression are a hallmark of cancer cells. Differential tumor-specific transcript levels of single genes or whole sets of genes may be critical for the neoplastic phenotype and important for therapeutic considerations or useful as biomarkers. As an approach to filter out such relevant expression differences from the plethora of changes noted in global expression profiling studies, we searched for changes of gene expression levels that are conserved. Transcriptomes from massive parallel sequencing of different types of melanoma from medaka were generated and compared to microarray datasets from zebrafish and human melanoma. This revealed molecular conservation at various levels between fish models and human tumors providing a useful strategy for identifying expression signatures strongly associated with disease phenotypes and uncovering new melanoma molecules. KW - Biologie Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-75848 ER - TY - JOUR A1 - Thoma, Eva C. A1 - Wischmeyer, Erhard A1 - Offen, Nils A1 - Maurus, Katja A1 - Sirén, Anna-Leena A1 - Schartl, Manfred A1 - Wagner, Toni U. T1 - Ectopic expression of Neurogenin 2 alone is sufficient to induce differentiation of embryonic stem cells into mature neurons N2 - Recent studies show that combinations of defined key developmental transcription factors (TFs) can reprogram somatic cells to pluripotency or induce cell conversion of one somatic cell type to another. However, it is not clear if single genes can define a cells identity and if the cell fate defining potential of TFs is also operative in pluripotent stem cells in vitro. Here, we show that ectopic expression of the neural TF Neurogenin2 (Ngn2) is sufficient to induce rapid and efficient differentiation of embryonic stem cells (ESCs) into mature glutamatergic neurons. Ngn2-induced neuronal differentiation did not require any additional external or internal factors and occurred even under pluripotency-promoting conditions. Differentiated cells displayed neuron-specific morphology, protein expression, and functional features, most importantly the generation of action potentials and contacts with hippocampal neurons. Gene expression analyses revealed that Ngn2-induced in vitro differentiation partially resembled neurogenesis in vivo, as it included specific activation of Ngn2 target genes and interaction partners. These findings demonstrate that a single gene is sufficient to determine cell fate decisions of uncommitted stem cells thus giving insights into the role of key developmental genes during lineage commitment. Furthermore, we present a promising tool to improve directed differentiation strategies for applications in both stem cell research and regenerative medicine. KW - Physiologie Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-75862 ER -