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Self-affine tiles and fractals are known as examples in analysis and topology, as models of quasicrystals and biological growth, as unit intervals of generalized number systems, and as attractors of dynamical systems. The author has implemented a software which can find new examples and handle big databases of self-affine fractals. This thesis establishes the algebraic foundation of the algorithms of the IFStile package. Lifting and projection of algebraic and rational iterated function systems and many properties of the resulting attractors are discussed.
Objektive Eingruppierung sequenzierter Tollwutisolate mithilfe des Affinity Propagation Clusterings.
(2018)
Das International Committee on Taxonomy of Viruses (ICTV) reguliert die Nomenklatur von Viren sowie die Entstehung neuer Taxa (dazu gehören: Ordnung, Familie, Unterfamilie, Gattung und Art/Spezies). Dank dieser Anstrengungen ist die Einteilung für verschiedenste Viren in diese Kategorien klar und transparent nachvollziehbar. In den vergangenen Jahrzehnten sind insgesamt mehr als 21.000 Datensätze der Spezies „rabies lyssavirus“ (RABV) sequenziert worden. Eine weiterführende Unterteilung der sequenzierten Virusisolate dieser Spezies ist bislang jedoch nicht einheitlich vorgeschlagen. Die große Anzahl an sequenzierten Isolaten führte auf Basis von phylogenetischen Bäumen zu uneindeutigen Ergebnissen bei der Einteilung in Cluster. Inhalt meiner Dissertation ist daher ein Vorschlag, diese Problematik mit der Anwendung einer partitionierenden Clusteringmethode zu lösen. Dazu habe ich erstmals die Methodik des affinity propagation clustering (AP) für solche Fragestellungen eingesetzt. Als Datensatz wurden alle verfügbaren sequenzierten Vollgenomisolate der Spezies RABV analysiert. Die Analysen des Datensatzes ergaben vier Hauptcluster, die sich geographisch separieren ließen und entsprechend als „Arctic“, „Cosmopolitain“, „Asian“ und „New World“ bezeichnet wurden. Weiterführende Analysen erlaubten auch eine weitere Aufteilung dieser Hauptcluster in 12-13 Untercluster. Zusätzlich konnte ich einen Workflow generieren, der die Möglichkeit bietet, die mittels AP definierten Cluster mit den Ergebnissen der phylogenetischen Auswertungen zu kombinieren. Somit lassen sich sowohl Verwandtschaftsverhältnisse erkennen als auch eine objektive Clustereinteilung vornehmen. Dies könnte auch ein möglicher Analyseweg für weitere Virusspezies oder andere vergleichende Sequenzanalysen sein.
As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. In my dissertation, I address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or—if not—where the exon gains and losses are plausible given the species tree. The multi-species gene finding problem is formulated as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach.
I tested the novel approach on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that the new method is well-suited for annotation of a large number of genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C++ as part of the gene finder AUGUSTUS.
Tuberculosis (TB) has tremendous public health relevance. It most frequently affects the lung and is characterized by the development of unique tissue lesions, termed granulomas. These lesions encompass various immune populations, with macrophages being most extensively investigated. Myeloid derived suppressor cells (MDSCs) have been recently identified in TB patients, both in the circulation and at the site of infection, however their interactions with Mycobacterium tuberculosis (Mtb) and their impact on granulomas remain undefined. We generated human monocytic MDSCs and observed that their suppressive capacities are retained upon Mtb infection. We employed an in vitro granuloma model, which mimics human TB lesions to some extent, with the aim of analyzing the roles of MDSCs within granulomas. MDSCs altered the structure of and affected bacterial containment within granuloma-like structures. These effects were partly controlled through highly abundant secreted IL-10. Compared to macrophages, MDSCs activated primarily the NF-κB and MAPK pathways and the latter largely contributed to the release of IL-10 and replication of bacteria within in vitro generated granulomas. Moreover, MDSCs upregulated PD-L1 and suppressed proliferation of lymphocytes, albeit with negligible effects on Mtb replication. Further comprehensive characterization of MDSCs in TB will contribute to a better understanding of disease pathogenesis and facilitate the design of novel immune-based interventions for this deadly infection.