Innerhalb der Arthropodensystematik sind die phylogenetischen Beziehungen der höheren Crustaceataxa seit langem von besonderen Interesse. Ziel dieser Arbeit ist die Rekonstruktion der phylogenetischen Verwandtschaftsverhältnisse mit Hilfe molekularer Datensätze für die Phyllopoda, die zusammen mit den Anostraca die Branchiopoda bilden und der Astacoidea (Astacida), einer Teilgruppe der Flusskrebse. Folgende molekulare Marker kamen zum Einsatz: 1) Für die Phyllopoda: Die 3. Domäne der mitochondrial codierten 12S rRNA, unter Berücksichtigung von Sekundärtrukturinformationen, das nukleare Gen EF-1 alpha und die Positionen von Introns im Gen EF-1 alpha. 2) Für die Astacoidea: Die 3. Domäne der 12S rRNA und das mitochondrial codierte Gen cox1. Durch die Wahl der molekularen Marker, die mit unterschiedlichen computerkladistischen Methoden ausgewertet wurden, konnten für die meisten Fragen eine eindeutige und im Fall der Astacoidea überraschende phylogenetische Aussage getroffen werden. Die gewonnenen Hypothesen werden ausführlich im Licht morphologischer Hypothesen diskutiert. / The phylogenetic relationships of the higher arthropod taxa are still of special interest. Especially the interrelationships of the different Crustacea taxa have long been debated. The focus of this investigation is to make a contribution to the phylogenies of two Crustacea taxa using molecular markers: The Phyllopoda which belong together with the Anostraca to the branchiopods, and of the Astacoidea, one of the two higher crayfish taxa (Astacida). The following molecular markers were used: 1) Phyllopoda: the 3rd domain of the mitochondrial encoded 12S rRNA taking into account informations of the secondary structure, the nuclear encoded proteingene EF-1 alpha and the positions of introns found in the coding region of EF-1 alpha. 2) Astacoidea: the 3rd domain of the 12S rRNA and the mitochondrial encoded proteingene cox1. The choice of the mentioned markers in combination with different computercladistical methods allowed to give a satisfying, and in the case of the Astacoidea a more surprising answer to most addressed phylogenetic questions. The gained hypotheses are then discussed in detail in the light of morphological features and hypotheses.

Die Familie der Physciaceen (lichenisierte Ascomyceten) und deren kompatible Photobionten wurden mit Hilfe von nrITS-Sequenzierungen untersucht. Es wurde Frisch- oder Herbarmaterial bearbeitet, das weltweit gesammelt worden war und 23 der 27 Physciaceengattngen repräsentierte. Die Sequenzdaten erlaubten eine differenzierte taxonomische Bearbeitung beider Biontengruppen. Basale Linien der Physciaceenphylogenie waren eng korreliert mit der Verteilung mehrerer phänotypischer Merkmale. Es konnte gezeigt werden, daß die Caliciaceen, eine andere Flechtenfamilie, die Schwestergruppe zu einer der vier Hauptlinien der Physciaceen bilden. Alle Proben der Physciaceen waren mit Algen aus der Gattung Trebouxia assoziiert. Ein Datensatz von über 300 Trebouxia nrITS-Sequenzen wurde zusammengestellt, der eine zuvor ungekannte Diversität innerhalb der Gattung Trebouxia repräsentiert. Die Taxonomie dieser Gattung wurde revidiert und ein System zur Abgrenzung und Zuordnung von nrITS-Varianten vorgeschlagen, das eine Strukturierung der gefundenen Diversität erlaubt. Viele der untersuchten Physciaceenarten erschienen hoch selektiv in Bezug auf ihre kompatiblen Photobionten. Im Gegensatz dazu konnte bei keinem der Photobionten eine Beschränkung auf nur eine Mycobiontenlinie gezeigt werden. Die Beschränkung vieler Mycobionten auf einen bestimmten Photobionten wurde als eine ökologische Abhängigkeit des Mycobionten von seinem kompatiblen Photobionten interpretiert. Daher wurde untersucht, ob Artbildungsereignisse in Trebouxia, Artbildungsereignisse in den assoziierten Physciaceen auslösen können. In einem Vergleich der Trebouxia- mit der Physciaceenphylogenie konnten jedoch keine korrelierten Verzweigungsmuster festgestellt werden. Hauptlinien der Trebouxien waren allerdings mit Umweltparametern, wie z.B. Substrat-pH und Makroklima korreliert. Die Evolution der Physciaceen war von diesen Faktoren offensichtlich deutlich weniger abhängig.Die nrSSU-Gene der Physciaceen enthielten mehr Introns als die aller anderen bekannter Organismengruppen. Der einzigartige Datensatz konnte genutzt werden, um konservierte Regionen innerhalb dieser Introns zu identifizieren. Auf diese konservierten Regionen konnten Primer konstruiert werden, die mit allen Introns einer Insertionsstelle kompatibel waren. Mit Hilfe dieser Primer konnten Introns detektiert werden, die bei der nrSSU-Sequenzierung unerkannt geblieben waren.

This thesis is focused on extracting meaningful statistics for the characterization and classification of biological, medical, and financial data and contains four chapters. The first chapter contains theoretical background on scaling and wavelets, which supports the work in chapters two and three. In the second chapter, we outline a methodology for representing sequences of DNA nucleotides as numeric matrices in order to analytically investigate important structural characteristics of DNA. This methodology involves assigning unit vectors to nucleotides, placing the vectors into columns of a matrix, and accumulating across the rows of this matrix. Transcribing the DNA in this way allows us to compute the 2-D wavelet transformation and assess regularity characteristics of the sequence via the slope of the wavelet spectra. In addition to computing a global slope measure for a sequence, we can apply our methodology for overlapping sections of nucleotides to obtain an evolutionary slope. In the third chapter, we describe various ways wavelet-based scaling may be used for cancer diagnostics. There were nearly half of a million new cases of ovarian, breast, and lung cancer in the United States last year. Breast and lung cancer have highest prevalence, while ovarian cancer has the lowest survival rate of the three. Early detection is critical for all of these diseases, but substantial obstacles to early detection exist in each case. In this work, we use wavelet-based scaling on metabolic data and radiography images in order to produce meaningful features to be used in classifying cases and controls. Computer-aided detection (CAD) algorithms for detecting lung and breast cancer often focus on select features in an image and make a priori assumptions about the nature of a nodule or a mass. In contrast, our approach to analyzing breast and lung images captures information contained in the background tissue of images as well as information about specific features and makes no such a priori assumptions. In the fourth chapter, we investigate the value of social media data in building commercial default and activity credit models. We use random forest modeling, which has been shown in many instances to achieve better predictive accuracy than logistic regression in modeling credit data. This result is of interest, as some entities are beginning to build credit scores based on this type of publicly available online data alone. Our work has shown that the addition of social media data does not provide any improvement in model accuracy over the bureau only models. However, the social media data on its own does have some limited predictive power.

Ophiostoma novo-ulmi is the causal agent of Dutch elm disease (DED) which has had a severe impact on the urban landscape in Canada. This research program focused on developing molecular genetic strategies to control this pathogenic fungus. The first strategy involved the development of RNA interference (RNAi) for the down-regulation of genes involved in pathogenicity. An efficient RNAi cassette was developed to suppress the expression of the endopolygalacturonase (epg1) locus which encodes a cell-wall degrading enzyme. This epg1-RNAi cassette significantly reduced the amount of polygalacturonase activity in the fungus and resulted in almost complete degradation of epg1 mRNA. The need for a native promoter to selectively down-regulate specific gene loci was addressed by developing a carbon-catabolite regulated promoter (alcA) to drive the expression of the epg1-RNAi cassette. The expression of an alcA-driven epg1-RNAi cassette resulted in the down-regulation of epg expression under glucose starvation but normal levels of expression in high glucose. The expression could therefore be controlled by culture conditions. The second strategy explored the potential of using dsRNA viruses to vector disruptive RNAi cassettes. An isolate of O. novo-ulmi strain 93-1224 collected in the city of Winnipeg, was infected by two dsRNA mitoviruses which upon sequence characterization were named OnuMV1c and OnuMV7. To assess the transmissibility of this dsRNA virus the infected isolate 93-1224 was paired with three naive isolates of the related fungi O. ulmi and O. himal-ulmi. Through the use of nuclear and mitochondrial markers it was determined that the virus OnuMV1c may not rely on mitochondrial fusion for transmission but may have a cytoplasmic transmission route. This investigation of gene expression and manipulation has provided tools to help understand gene regulation in O. novo-ulmi. It has also added to our knowledge of mitoviruses, their transmission and potential use as a biological control. By enhancing our understanding of transmissible hypovirulence this work contributes to efforts to develop a new approach to target DED as well as a potential model for the control of other fungal diseases. / Graduate / 0307 / 0306 / 0369 / jscarneiro@hotmail.com

No / Heterozygous germline defects in a gene encoding a type II receptor for bone morphogenetic proteins (BMPR-II) underlie the majority of inherited cases of the vascular disorder known as pulmonary arterial hypertension (PAH). However, the precise molecular consequences of PAH causing mutations on the function of the receptor complex remain unclear. We employed novel enzymatic and fluorescence activity based techniques to assess the impact of PAH mutations on pre-mRNA splicing, nonsense-mediated decay (NMD) and receptor complex interactions. We demonstrate that nonsense and frameshift mutations trigger NMD, providing further evidence that haplo-insufficiency is a major molecular consequence of disease-related BMPR2 mutations. We identified heterogeneous functional defects in BMPR-II activity, including impaired type I receptor phosphorylation, receptor interactions and altered receptor complex stoichiometry leading to perturbation of downstream signalling pathways. Importantly, these studies demonstrate that the intracellular domain of BMPR-II is both necessary and sufficient for receptor complex interaction. Finally and to address the potential for resolution of stoichiometric balance, we investigated an agent that promotes translational readthrough of a BMPR2 nonsense reporter construct without interfering with the NMD pathway. We propose that stoichiometric imbalance, due to either haplo-insufficiency or loss of optimal receptor-receptor interactions impairs BMPR-II mediated signalling in PAH. Taken together, these studies have identified an important target for early therapeutic intervention in familial PAH.