Die hier vorliegende Arbeit zeigt die molekulare Evolution des Melatoninrezeptor 1 B-Gens (MTNR1B) und des Fat Mass and Obesity Associated-Gens (FTO). Für beide Gene wurden in genomweiten Assoziationsstudien (GWAS) Varianten entdeckt, welche zu der Entwicklung einer Adipositas bzw. deren Folgeerkrankungen beitragen können. So wurde für Einzelbasenaustausche (SNPs) im MTNR1B (rs10830963, rs4753426) eine Verschlechterung der Nüchternglukose sowie der Insulinausschüttung gezeigt. Zudem wurde für die Allelfrequenz des rs4753426 C-Allels ein Zusammenhang mit der täglichen Sonnenscheindauer beschrieben. Im FTO wurde eine (tagging) Variante im ersten Intron identifiziert (rs9939609), welche einen erhöhten Körpermasseindex (BMI) zu vermitteln scheint und robust repliziert werden konnte. Zusätzlich konnte in den Sorben, einer in der Lausitz ansässigen Volksgruppe, eine Variante im dritten Intron (rs17818902) beschrieben werden, die ein zusätzliches, stärkeres Assoziationssignal mit einem erhöhten BMI zeigte. Dies führte zu der Fragestellung, ob MTNR1B und FTO einer Konservierung unterlegen sind. Zudem interessierten populationsspezifische Unterschiede, um die Untersuchungen in den Kontext der Hypothese des sparsamen Genotyps stellen zu können. Demnach haben Individuen mit einer genetischen Veranlagung, die ihnen eine effizientere Energiespeicherung ermöglicht, zu Zeiten von Nahrungsmangel einen Fitness-Vorteil gegenüber Nicht-Trägern. Die Konservierung zwischen den Spezies wurde mit Phylogenetic Analysis by Maximum Likelihood (PAML) betrachtet, eine Analyse die auf dem Verhältnis von nichtsynonymen zu synonymen Basenaustauschen innerhalb einer kodierenden Sequenz beruht. Die Selektion innerhalb bzw. zwischen menschlichen Populationen wurde anhand verschiedener populationsgenetischer Variablen näher beleuchtet. Sowohl für MTNR1B als auch für FTO konnte gezeigt werden, dass sie über die betrachteten Spezies im Durchschnitt stark oder sehr stark konserviert sind, was die physiologische Relevanz dieser Gene untermauert. Für MTNR1B zeigte sich zudem, dass es auf dem Ast zum Menschen nicht konserviert, sondern positiv selektioniert ist. Dies kann als Anzeichen für durch die Umwelt bedingte Einflüsse gedeutet werden. Essentielle Residuen des Rezeptors sind jedoch auch hier hochgradig konserviert. Die populationsgenetischen Variablen implizieren bei beiden Genen eine nicht-neutrale Selektion. Während sich beim MTNR1B insbesondere populationsspezifische Unterschiede anhand des Fixierungsindex Fst zeigten, konnten für FTO marginal signifikante Korrelationen zwischen der Konservierung der Haplotypen und der Stärke der Assoziation mit BMI in den Sorben gezeigt werden. Für beide Gene kann die Hypothese des sparsamen Genotyps nicht prinzipiell ausgeschlossen werden, allerdings sind weitere Untersuchungen diesbezüglich von Nöten.

Accessibility of high-throughput genotyping technology makes possible genome-wide association studies for common complex diseases. When dealing with common diseases, it is necessary to search and analyze multiple independent causes resulted from interactions of multiple genes scattered over the entire genome. The optimization formulations for searching disease-associated risk/resistant factors and predicting disease susceptibility for given case-control study have been introduced. Several discrete methods for disease association search exploiting greedy strategy and topological properties of case-control studies have been developed. New disease susceptibility prediction methods based on the developed search methods have been validated on datasets from case-control studies for several common diseases. Our experiments compare favorably the proposed algorithms with the existing association search and susceptibility prediction methods.

Recent advances in next generation sequencing have provided unprecedented opportunities for high-throughput genomic research, inexpensively producing millions of genomic sequences in a single run. Analysis of massive volumes of data results in a more accurate picture of the genome complexity and requires adequate bioinformatics support. We explore computational challenges of applying next generation sequencing to particular applications, focusing on the problem of reconstructing viral quasispecies spectrum from pyrosequencing shotgun reads and problem of inferring informative single nucleotide polymorphisms (SNPs), statistically covering genetic variation of a genome region in genome-wide association studies. The genomic diversity of viral quasispecies is a subject of a great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software cannot be used to simultaneously assemble and estimate the abundance of multiple closely related (but non-identical) quasispecies sequences. Here, we introduce a new Viral Spectrum Assembler (ViSpA) for inferring quasispecies spectrum and compare it with the state-of-the-art ShoRAH tool on both synthetic and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. While ShoRAH has an advanced error correction algorithm, ViSpA is better at quasispecies assembling, producing more accurate reconstruction of a viral population. We also foresee ViSpA application to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations. Due to the large data volume in genome-wide association studies, it is desirable to find a small subset of SNPs (tags) that covers the genetic variation of the entire set. We explore the trade-off between the number of tags used per non-tagged SNP and possible overfitting and propose an efficient 2LR-Tagging heuristic.

The inherent genetic similarity between oat (<i>Avena sativa</i> L.) and wild oat (<i>Avena fatua</i> L.) precludes selective herbicide use to control wild oat. Consequently, large reductions in oat yield and quality due to wild oat consistently constrain oat production in western Canada. Traditionally, delayed seeding followed by tillage prior to planting was used to control wild oat, but new studies have shown that this practice also results in substantial reductions to oat yield and quality. Thus, new methods are needed to ameliorate the adverse effects of wild oat competition on oat. Planting more competitive varieties with earlier emergence and larger seeds may minimize losses associated with wild oat competition. Therefore, the objectives of this research were i) to determine the influence of wild oat emerging at different times and varying densities on oat yield and quality and ii) to determine the relative importance of seed size and genotype in affecting wild oat oat competition. High densities of early emerging wild oat greatly reduced oat yield and increased wild oat contamination. Observed oat yield losses were as great as 70% and resulted in a 15% wild oat contamination level. Wild oat that emerged before oat also had higher biomass and reproductive output than wild oat that emerged after oat. Furthermore, early emerging wild oat reduced percentage plump oat kernels and increased percentage thin kernels. Oat plants established from large caryopses produced 18% more biomass and 15% more panicles m^-2 than plants established from small caryopses. In addition, wild oat produced 31% less biomass and fewer panicles m^-2 when grown with oat plants established from large caryopses. CDC Boyer appeared to be the most competitive of the varieties examined, having significantly higher biomass and panicle production both in the presence and absence of wild oat competition. Conclusions that emerge from this research are i) emergence time is critical to wild oat oat competition, ii) it is essential for oat producers to control early emerging wild oat and ensure crop emergence precedes wild oat emergence, iii) planting large seed of competitive cultivars may improve the competitive response of oat to wild oat.

The purpose of this project is to better understand the influences underlying gender differences in the brain using Four Core Genotype mice. Four Core Genotype mice are transgenic mice in which the SRY gene has been translocated from the Y chromosome to another location. This enables separation of the genetic sex and gonadal sex. For example, there are female mice based on sexual organs but their chromosomes are XY(UY- in mice). This allows us to determine whether sexual differentiation in the brain is due to genes or hormones. In this project, I looked at a sexually dimorphic area of the brain, the Bed Nucleus of the Stria Terminalis (BNST), which is twice as large in males than in females. I hypothesize that both chromosomes and gonadal hormones play a part in sexually differentiating the brain including the BNST and thus I predict that the size of the BNST will be the same in XX males (UUSRY) and XY females (UY-). I measured the BNST from five XX female (UU) and five XY male(UY-SRY) four core genotype mouse brains and confirmed that the BNST is larger in males than in females, as it is in normal mice (p= .057). I processed and measured the size of the BNST in ten brains of XX males and XY females to see if the size of the BNST matches the chromosomes or the gonads. The results had a trend in the data that suggested chromosomes play more of an effect on sexual differentiation of the BNST. The overall goal of this project is to contribute to research examining the causes of gender identity in humans by relating this work to other works in the field.

Canada is the fourth largest producer of farmed salmon in the world, with Atlantic salmon being the major species cultivated. Paradoxically British Columbia (BC), which borders the Pacific Ocean, is the major producer province where Atlantic salmon was introduced in the mid-80’s. Escaped salmon may constitute a threat to natural populations of Pacific salmon as they compete for the same resources such as food and spawning territory. A potential solution to the aquaculture industry would be to further develop the aquaculture of native species in the region. The work presented here used semi-natural spawning channels to evaluate the effects of breeding strategies and early-rearing environments on the immune performance of Chinook salmon. Breeding strategy was tested analyzing artificial hatchery practices versus semi-natural propagation in spawning channels. Early-rearing environmental assessment contrasted indoor plastic hatchery tanks with outdoor gravelled-bottom spawning channels. A disease challenge involving over 1400 fish showed interaction effects between breeding strategy and rearing environment. Fish artificially mated presented a disease susceptibility influenced by the rearing environment. The contrary occurred in the offspring of self-breeding brood stock in the spawning channels, as no differences were observed in their susceptibility to the disease regardless of rearing environment. Monitoring of anti-Vibrio anguillarum antibodies during the disease challenge and a follow up of the survivors in sea net pens further confirmed the interaction between breeding strategy and rearing environment. Gene expression in pre- and post-infected artificially propagated fish showed differential gene expression when analyzed with a 695-gene cDNA microarray for Chinook salmon. Genotyping of major histocompatibility (MH) class II β1 alleles showed a tendency of a higher heterozygosity in survivors as expected, as well as a general tendency of a higher heterozygosity in semi-naturally propagated fish. The latter is likely a direct consequence of MH-linked mate choice, which was recently described in Chinook salmon (Neff et al., 2008). To further characterize the mating system of Chinook salmon in the spawning channels, brood stock were genotyped at 12 microsatellite loci. Females and males were found to mate randomly with regards to genetic pairwise relatedness, but they tended to mate with fish of similar condition as revealed by their pairwise differences in Fulton’s condition factor. This work demonstrated that genotype-by-environment interactions can modify the disease resistance of Chinook salmon. More importantly, these effects were seen after just one round of semi-natural spawning of domesticated hatchery fish, suggesting that further studies on spawning channels may highlight other hidden benefits. Therefore, breeding strategy and early-rearing environment should be considered when propagating cultured stocks. The use of more natural propagation methods such as spawning channels could improve the immune performance of Chinook salmon and help to expand the aquaculture of this native species in BC.

The inherent genetic similarity between oat (<i>Avena sativa</i> L.) and wild oat (<i>Avena fatua</i> L.) precludes selective herbicide use to control wild oat. Consequently, large reductions in oat yield and quality due to wild oat consistently constrain oat production in western Canada. Traditionally, delayed seeding followed by tillage prior to planting was used to control wild oat, but new studies have shown that this practice also results in substantial reductions to oat yield and quality. Thus, new methods are needed to ameliorate the adverse effects of wild oat competition on oat. Planting more competitive varieties with earlier emergence and larger seeds may minimize losses associated with wild oat competition. Therefore, the objectives of this research were i) to determine the influence of wild oat emerging at different times and varying densities on oat yield and quality and ii) to determine the relative importance of seed size and genotype in affecting wild oat oat competition. High densities of early emerging wild oat greatly reduced oat yield and increased wild oat contamination. Observed oat yield losses were as great as 70% and resulted in a 15% wild oat contamination level. Wild oat that emerged before oat also had higher biomass and reproductive output than wild oat that emerged after oat. Furthermore, early emerging wild oat reduced percentage plump oat kernels and increased percentage thin kernels. Oat plants established from large caryopses produced 18% more biomass and 15% more panicles m^-2 than plants established from small caryopses. In addition, wild oat produced 31% less biomass and fewer panicles m^-2 when grown with oat plants established from large caryopses. CDC Boyer appeared to be the most competitive of the varieties examined, having significantly higher biomass and panicle production both in the presence and absence of wild oat competition. Conclusions that emerge from this research are i) emergence time is critical to wild oat oat competition, ii) it is essential for oat producers to control early emerging wild oat and ensure crop emergence precedes wild oat emergence, iii) planting large seed of competitive cultivars may improve the competitive response of oat to wild oat.

Es gibt wenige Erkenntnisse über den Zusammenhang zwischen Lamivudin induzierten Resistenzmutationen und Hepatitis B Genotypen. Die vorliegende Studie untersucht das Verhältnis zwischen diesen Mutationen und den Hepatitis B Genotypen A-D. Die Datenbank der US-amerikanischen Kongressbibliothek (Pubmed) wurde nach den Begriffen „HBV OR hepatitis B”, „YMDD”, „genotype”, und „lamivudine” durchsucht. Alle in dieser Suche gefundenen Arbeiten, die bis Juni 2009 veröffentlicht worden waren, wurden in die Studie eingeschlossen. Die Ergebnisse der Literaturanalyse wurden mit den Hepatitis B-Genomdaten zweier Referenzlabore in Tübingen und Melbourne verglichen. Insgesamt konnten 29 Arbeiten aus der Datenbankrecherche in die Literaturanalyse eingeschlossen werden. Diese Studien enthielten Daten zu insgesamt 827 Patienten, deren Hepatitis B Genotyp bekannt war und die eine Lamivudinresistenzmutation aufwiesen. In statistischen Untersuchungen konnte nachgewiesen werden, dass die rtM204V-Mutation die dominierende Mutation bei Infektionen mit Genotyp A ist. Dieses Ergebnis konnte durch die Analyse der Genomdaten der Referenzlabore bestätigt werden. Ferner konnte gezeigt werden, dass bei den Genotypen A, B, und D die rtL180M-Mutation hochsignifikant mit der rtM204V-Mutation verknüpft ist. Die Dissertationsschrift enthält neben dem Artikel „Mutation pattern of lamivudine resistance in relation to hepatitis B genotypes: hepatitis B genotypes differ in their lamivudine resistance associated mutation pattern“ (Damerow, H, Yuen L et al.; J Med Virol. 2010 Nov; 82(11):1850-8) eine Einführung in die Rationale der Studie, eine Zusammenfassung der Ergebnisse sowie ein Fazit.

In the current study, behavioral responses of several species of calanoid copepods to mimics of oceanographic structure were observed and evaluated in the context of foraging and aggregation. Zooplankton distributions in oceanic habitats are often attributed to physical forcing; however, physical factors only act to drive ecological patterns at large scales (m to km). At fine to intermediate scales (cm to m) zooplankton behavior is believed to govern observed distributions, but the mechanisms and ecological significance of these behaviors are not well understood. In a water column, biological activity is often concentrated into one or a few regions, called thin layers, on the order of a meter thick, and zooplankton, such as copepods, must be able to reliably locate and exploit these patches for survival. Thin layers commonly are associated with oceanic structure such as flow gradients, fluid density jumps, or chemical composition gradients. Utilization of mechanosensory or chemosensory cues associated with thin layers may increase foraging success, thus translating into a significant ecological advantage. A laboratory apparatus was developed to create isolated and combined thin layer properties. Copepods then were exposed to laboratory mimics of thin layers. All of the tested species of copepods exhibited behavioral responses associated with area-restricted search behavior to one of the physical gradients (flow velocity or fluid density), but not both. Similar responses were observed for chemical exudate layer experiments and included increased proportional residence times, swimming speeds, and turn frequency. Food layers induced feeding responses from all tested species (increased proportional residence time, decreased swimming speed). Responses to various combinations of gradients were not fully synergistic, but suggested that some copepods employ a cue hierarchy to locate food-rich areas. Velocity or density gradients acted as initial cues for narrowing search regions, while chemical exudates induced responses that strengthened or removed the initial reactions. A simple foraging model was used to illustrate how such behavioral changes can lead to observed aggregations at larger temporal and spatial scales. Consequently, these results suggest that individual responses to oceanographic structure may have far reaching influence on population dynamics, succession, and biodiversity in coastal and pelagic ecosystems.

Cells switch phenotypes or behaviors to adapt to various environmental stimuli. Often there are multiple alternative phenotypes, hence a cell chooses one phenotype among them, a process which we term a ``decision switch'. At the cellular level, decision switches are governed by gene regulation, hence they are intrinsically stochastic. Here we investigate two aspects of decision switches: how copy number of genetic components facilitates multiple phenotypes and how temporal dynamics of gene regulation with stochastic fluctuations affect switching a cell fate. First, we demonstrate that gene expression can be sensitive to changes in the copy number of genes and promoters, and alternative phenotypes may arise due to bistability within gene regulatory networks. Our analysis in phage-lambda-infected E. coli cells exhibit drastic change in gene expression by changing the copy number of viral genes, suggesting phages can determine their fates collectively via sharing gene products. Second, we examine decision switches mediated by temporal dynamics of gene regulation. We consider a case when temporal gene expression triggers a corresponding cell fate, and apply it to the lysis-lysogeny decision switch by phage lambda. Our analysis recapitulates the systematic bias between lysis and lysogeny by the viral gene copy number. We also present a quantitative measure of cell fate predictability based on temporal gene expression. Analyses using our framework suggest that the future fate of a cell can be highly correlated with temporal gene expression, and predicted if the current gene expression is known.