500 Naturwissenschaften und Mathematik
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Alveolar echinococcosis, which is caused by the metacestode stage of the small fox tapeworm Echinococcus multilocularis, is a severe zoonotic disease with limited treatment options. For a better understanding of cestode biology the genome of E. multilocularis, together with other cestode genomes, was sequenced previously. While a few studies were undertaken to explore the E. multilocularis transcriptome, a comprehensive exploration of global transcription profiles throughout life cycle stages is lacking. This work represents the so far most comprehensive analysis of the E. multilocularis transcriptome. Using RNA-Seq information from different life cycle stages and experimental conditions in three biological replicates, transcriptional differences were qualitatively and quantitatively explored. The analyzed datasets are based on samples of metacestodes cultivated under aerobic and anaerobic conditions as well as metacestodes obtained directly from infected jirds. Other samples are stem cell cultures at three different time points of development as well as non-activated and activated protoscoleces, the larval stage that can develop into adult worms. In addition, two datasets of metacestodes under experimental conditions suitable for the detection of genes that are expressed in stem cells, the so-called germinative cells, and one dataset from a siRNA experiment were analyzed. Analysis of these datasets led to expression profiles for all annotated genes, including genes that are expressed in the tegument of metacestodes and play a role in host-parasite interactions and modulation of the host's immune response. Gene expression profiles provide also further information about genes that might be responsible for the infiltrative growth of the parasite in the liver.
Furthermore, germinative cell-specific genes were identified. Germinative cells are the only proliferating cells in E. multilocularis and therefore of utmost importance for the development and growth of the parasite. Using a combination of germinative cell depletion and enrichment methods, genes with specific expression in germinative cells were identified. As expected, many of these genes are involved in translation, cell cycle regulation or DNA replication and repair. Also identified were transcription factors, many of which are involved in cell fate commitment. As an example, the gene encoding the telomerase reverse transcriptase (TERT) was studied further. Expression of E. multilocularis tert in germinative cells was confirmed experimentally. Cell culture experiments indicate that TERT is required for proliferation and development of the parasite, which makes TERT a potentially interesting drug target for chemotherapy of alveolar echinococcosis.
Germinative cell specific genes in E. multilocularis also include genes of densoviral origin. More than 20 individual densovirus loci with information for non-structural and structural densovirus proteins were identified in the E. multilocularis genome. Densoviral elements were also detected in many other cestode genomes. Genomic integration of these elements suggests that densovirus-based vectors might be suitable tools for genetic manipulation of tapeworms. Interestingly, only three of more than 20 densovirus loci in the E. multilocularis genome are expressed. Since the canonical piRNA pathway is lacking in cestodes, this raises the question about potential silencing mechanisms. Exploration of RNA-Seq information indicated natural antisense transcripts as a potential gene regulation mechanism in E. multilocularis. Preliminary experiments further suggest DNA-methylation, which was previously shown to occur in platyhelminthes, as an interesting avenue to explore in future.
The transcriptome datasets also contain information about genes that are expressed in differentiated cells, for example the serotonin transporter gene that is expressed in nerve cells. Cell culture experiments indicate that serotonin and serotonin transport play an important role in E. multilocularis proliferation, development and survival.
Overall, this work provides a comprehensive transcription data atlas throughout the E. multilocularis life cycle. Identification of germinative cell-specific genes and genes important for host-parasite interactions will greatly facilitate future research. A global overview of gene expression profiles will also aide in the detection of suitable drug targets and the development of new chemotherapeutics against alveolar echinococcosis.
Bevor ein zellbasiertes GTMP erstmalig beim Menschen angewendet werden kann, müssen verschiedene notwendige nicht-klinische Studien durchgeführt werden. Wichtig ist hier u.a. die Untersuchung der Biodistribution im Tiermodel. Diese umfasst die Verteilung, das Engraftment, die Persistenz, die Eliminierung und gegebenenfalls die Expansion der humanen Zellen in verschiedenen Organen, meistens im Mausmodel. Deshalb wurde eine qPCR-basierte Analysenmethode entwickelt, mit der humane genomische DNA innerhalb von muriner genomischer DNA bestimmt werden kann, und entsprechend den regulatorischen Richtlinien der European Medicines Agency und des International Council for Harmonisation validiert. Anschließend wurde diese Methode innerhalb einer präklinischen worst-case Szenario Biodistributionsstudie angewendet. Das Ziel dieser Studie war die Untersuchung des Biodistributionsprofils von genetisch modifizierten Blood Outgrowth Endothelial Cells von Hämophilie A Patienten 24 Stunden und sieben Tage nach intravenöser Applikation einer Dosis von 2x106 Zellen. Die Isolation, genetische Modifikation und die Expansion der Zellen sollte entsprechend den Richtlinien der Guten Herstellungspraxis durchgeführt werden. Hierbei ist die Auswahl und Anwendung geeigneter und essentieller Rohstoffe wichtig. Gleichermaßen ist die Durchführung einer definierten Qualitätskontrollstrategie notwendig und die Patientenzellen sollten nur innerhalb von nicht-klinischen Studien eingesetzt werden, wenn alle Akzeptanzkriterien erfüllt wurden. Die Validierung der qPCR-Methode zeigte eine hohe Genauigkeit, Präzision und Linearität innerhalb des Konzentrationsintervalls von 1:1x103 bis 1:1x106 humanen zu murinen Genomen. Bei Anwendung dieser Methode für die Biodistributionsstudie konnten nach 24 Stunden humane Genome in vier der acht untersuchten Mausorgane bestimmt werden. Nach sieben Tagen konnten in keinem der acht Organe humane Genome nachgewiesen werden...
The goal of this doctoral thesis is to identify appropriate methods for the estimation of connectivity and for measuring synchrony between spike trains from in vitro neuronal networks. Special focus is set on the parameter optimization, the suitability for massively parallel spike trains, and the consideration of the characteristics of real
recordings. Two new methods were developed in the course of the optimization which outperformed other methods from the literature. The first method “Total spiking probability edges” (TSPE) estimates the effective connectivity of two spike trains, based on the
cross-correlation and a subsequent analysis of the cross-correlogram. In addition to the estimation of the synaptic weight, a distinction between excitatory and inhibitory connections is possible. Compared to other methods, simulated neuronal networks could be estimated with higher accuracy, while being suitable for the analysis of massively parallel spike trains. The second method “Spike-contrast” measures the synchrony of parallel spike trains
with the advantage of automatically optimizing its time scale to the data. In contrast to other methods, which also adapt to the characteristics of the data, Spike-contrast is more robust to erroneous spike trains and significantly faster for large amounts of parallel spike trains. Moreover, a synchrony curve as a function of the time scale is generated by Spike-contrast. This optimization curve is a novel feature for the analysis of parallel spike trains.