Graduate Theses & Dissertations

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Characterization of a Zn(II)2Cys6 transcription factor in Ustilago maydis and its role in pathogenesis
Ustilago maydis (D.C.) Corda is a biotrophic pathogen that secretes effectors to establish and maintain a relationship with its host, Zea mays. In this pathosystem, the molecular function of effectors is well-studied, but the regulation of effector gene expression remains largely unknown. This study characterized Zfp1, a putative U. maydis Zn(II)2Cys6 transcription factor, as a modulator of effector gene expression. The amino acid sequence of Zfp1 indicated the presence of a GAL4-like zinc binuclear cluster as well as a fungal specific transcription factor domain. Nuclear localization was confirmed by tagging Zfp1 with enhanced green fluorescent protein. Deletion of zfp1 resulted in attenuated hyphal growth, reduced infection frequency, an arrest in pathogenic development, and decreased anthocyanin production. This phenotype can be attributed to the altered transcript levels of genes encoding predicted and confirmed U. maydis effectors in the zfp1 deletion strain during pathogenic growth. Complementation of zfp1 deletion strain with tin2, an effector involved in anthocyanin induction, suggested this effector is downstream of Zfp1 and its expression is influenced by this transcription factor during in planta growth. When wild-type zfp1 was ectopically inserted in the zfp1 deletion strain, pathogenesis and virulence were partially restored. This, coupled with zfp1 over-expression strains having a similar phenotype as the deletion strains, suggested Zfp1 may interact with other proteins for full function. These findings show that Zfp1, in conjunction with one or more binding partners, contributes to U. maydis pathogenesis, virulence, and anthocyanin production through the regulation of effector gene expression. Author Keywords: effector, pathogenesis, transcription factor, Ustilago maydis, Zea mays, zinc finger
Characterization of frog virus 3 and its binding partner LITAF
Iridoviruses are large (120-200nm) double stranded DNA viruses that contain an icosahedral capsid. The iridoviridae family is composed of five genera that infect a wide range of poikilothermic vertebrates (Lymphocystivirus, Ranavirus and Megalocyivirus) and invertebrate hosts (Iridovirus, Chloriridovirus). Frog virus 3 (FV3) is a member of the Ranavirus genus, and is commonly used as a model system to study iridoviruses. I was interested in understanding virus-host interaction in FV3. I studied two viral genes, FV3 97R and FV3 75L. Here I demonstrate that 97R localizes to the endoplasmic reticulum (ER) at 24 hours post-transfection. However, at 35 hours post-transfection 97R localizes to the ER but also begins to form concentrated pockets, continuous with the nuclear membrane This study found that 97R possess a unique phenotype and that its localization to the ER is mediated through its C-terminus transmembrane domain. FV3 75L encodes an 84 amino acids protein. I showed that FV3 75L localizes to the early endosomes, while its cellular binding partner, LITAF, localizes to late endosome/lysosome. Interestingly, when FV3 75L and LITAF are co-transfected into cells, LITAF can alter the subcellular localization of FV3 75L to late endosome/lysosomes. A physical interaction between LITAF and FV3 75L was demonstrated through a pull-down assay and that a highly conserved domain found in both proteins may mediate the interaction. LITAF has been proposed to function in protein degradation, but there is still uncertainty on LITAF's specific role. I was interested in further characterizing LITAF and its implications in protein degradation and a neurodegenerative disorder. At least 9 mutations of LITAF are associated with Charcot-Marie-Tooth disease type 1C (CMT1C), which belongs to the group of most common heritable neuromuscular disorders, affecting approximately one in 2500 people. We show that LITAF mutants G112S and W116G mislocalize from the late endosome/lysosome to the mitochondria while the T49M and P135T mutants show partial mislocalization with a portion of the protein present in the late endosome/lysosome and a portion of the protein localized to the mitochondria. Since LITAF is believed to play a role in protein degradation, it is possible that the specific characteristics of CMT1C may occur though impaired degradation of Schwann cell membrane proteins, such as PMP22. I was able to show that when WT LITAF is present, there is a decrease in the PMP22 intracellular levels, which suggest that LITAF plays an important role in protein degradation, and also in other types of CMT. Insight into how mutations in LITAF cause CMT1C may not only help better understand cellular pathways, but also further elucidate the role LITAF's viral homolog FV3 75L during viral infection. Author Keywords: 75L, Charcot-Marie-Tooth, CMTC1, ER, FV3, LITAF
Characterizing the demographic history and prion protein gene variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)
Assessments of the adaptive potential of natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. The range of stressors species face in a human-dominated landscape, often have contrasting effects. White-tailed deer (Odocoileus virginianus, deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability, caused by climate change. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. High throughput sequencing was used to assess neutral genomic variation and variation in the gene responsible for the protein that misfolds into prions when deer contract CWD, known as the PRNP gene. Neutral variation revealed a high number of rare alleles and no population structure, consistent with an expanding population of deer. Functional genetic variation revealed that the frequencies of variants associated to CWD susceptibility and disease progression were evenly distributed across the landscape and the frequencies were consistent with deer populations not infected with CWD. These findings suggest that an observable shift in PRNP allele frequencies likely coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and genetic variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits. Author Keywords: Canadian wildlife, population genetics, prion, PRNP, RADseq, ungulate
Chemical characterization of dissolved organic matter in relation with hydrography in the Arctic Ocean
In this thesis, water mass distribution of dissolved organic matter (DOM) characteristics (i.e. molecular weight, fluorescent components, thiols and humic substances concentration) was observed in the Arctic Ocean. For the first time, DOM molecular weight (MW) in Beaufort Sea was assessed using asymmetrical flow field-flow fractionation, as well as the first monitoring of thiols and humic substances (HS) using cathodic stripping voltammetry (CSV) in the Arctic Ocean. Based on fluorescence property, DOM characterization was carried out using parallel factor analysis – excitation-emission matrices. Pacific winter waters in the Canada Basin showed higher MW DOM associated with higher fluorescence intensity. High HS was associated with the Arctic outflow waters in top 300 m of the Canadian Arctic Archipelago. Interestingly, maximum thiol concentration was associated with the subsurface chlorophyll-a maximum at most sites, but not universal along the study area. Comparable distributions of CSV-based HS and humic-like fluorescent components suggest similar sources/ processes in the Arctic Ocean. The findings in this thesis suggested DOM characteristics could be used as fingerprints in tracing water masses in the Arctic Ocean. Author Keywords: Asymmetrical flow field-flow fractionation, Cathodic stripping voltammetry, DOM, Metal-binding ligands, Molecular weight, PARAFAC-EEMs
Chew the Fat
Fatty acid analysis was performed on archaeological bone from various fauna from sites in the Canadian arctic to better understand the preservation of fatty acids and their potential applications to palaeoecological and palaeodietary studies. These data were complemented by analyses of modern bone and soft tissue samples from livestock and harp seals (Pagophilus groenlandicus). Results of modern analyses revealed that in terrestrial species, bone has inherently lower concentrations of most fatty acids relative to other soft tissues (adipose, marrow, and muscle). These analyses suggest that the distribution of fatty acids in bone is unique compared to other tissues, and the types and abundances of fatty acids in bone may be linked to dietary sources of lipids. Of the archaeological samples analyzed, terrestrial species (caribou [Rangifer tarandus]) generally exhibited higher concentrations of saturated fatty acids compared to marine species (ringed seals [Pusa hispida] and polar bears [Ursus maritimus]), whereas marine species had higher concentrations of monounsaturated fatty acids compared to terrestrial species. Results of analyses on both modern and archaeological samples provided insight into the degradation of fatty acids in bone, and the rapid loss of polyunsaturated fatty acids in particular. Because the abundances of fatty acids are likely altered in the burial environment, it is recommended that future analyses incorporate compound specific isotope analysis to focus on applications of fatty acids that are typically in the highest abundance and arguably have undergone the least amount of change, including palmitic (C16:0) and stearic acid (C18:0) Author Keywords: Archaeological Science, Bone Lipids, Fatty Acid Analysis, GC-MS, Lipid Preservation, Palaeoecology
Childhood Precursors of Adult Trait Incompleteness
Previous research has suggested that childhood sensory sensitivity may predict adult obsessive compulsive (OC) behaviours. To date, however, research has not addressed how the separate dimensions – harm avoidance and incompleteness - may influence this relationship or why it exists. The current study used a retrospective design to test a) if sensory sensitivity in childhood predicts trait incompleteness in adulthood, as well as b) if emotion regulation variables mediate this relationship. Questionnaires pertaining to OC dimensions and childhood anxieties were completed independently by 172 undergraduate participants and their primary childhood caregiver. Results showed a linear relationship between sensory sensitivity in childhood and incompleteness in adults. Emotion regulation variables failed to mediate this relationship, although a trend for mediation was present. Additionally, exploratory analysis found perfectionism in childhood to be a predictor of trait incompleteness but not harm avoidance, whereas physical anxieties predicted harm avoidance and not incompleteness. Results are discussed in the context of clinical and theoretical implications. Author Keywords: Distress Tolerance, Harm Avoidance, Incompleteness, Obsessive Compulsive Disorder, Sensory Sensitivity, Symmetry
Childhood diet and feeding practices at Apollonia
This study analyses deciduous dental pathology and stable carbon and nitrogen isotopes to investigate the relationship between dietary composition, feeding practices, and oral health in a subadult skeletal sample from the Greek colonial site of Apollonia Pontica, Bulgaria (5th to 3rd century BC). Stable isotope analysis of 74 bone collagen samples indicates that weaning began between the ages of 6 months and 1 year, and was complete by the age of 4. The stable isotope data are consistent with a diet of primarily terrestrial C3 resources. The deciduous dentitions of 85 individuals aged between 8.5 months and 10.5 years were examined for evidence of a number of pathological conditions. The presence of dental caries, calculus, occlusal tooth wear and an abscess indicate that foods introduced early in life affected the oral health of these individuals. Overall, the deciduous dental data correlate well with the stable isotope data and ancient textual sources regarding infant and childhood dietary composition and feeding practices. Author Keywords: breastfeeding, deciduous dentition, dental pathology, stable carbon and nitrogen isotopes, weaning
Civic Agriculture
This thesis re-imagines the social sustainability of civic agriculture. This entails critically examining the idea of sustainability and exposing why a tendency to undertheorize its social dimension is problematic for how we think about sustainability, and consequently for how we do sustainability. What is demonstrated is that we can overcome this tendency by adopting Stephen McKenzie's understanding of social sustainability as a positive condition and/or process within a community. Once brought into contact with the concept of civic agriculture as presented by Thomas A. Lyson, and expanded upon by others, this broadened understanding of social sustainability reveals that we can think of civic agriculture as both a means to, and an expression of, social sustainability. Specifically, this thesis argues that it is civic agriculture's community problem-solving dimension which animates civic agriculture in such a way that it creates the sort of condition and/or enables the sort of process which reflect aspects associated with a substantive and/or procedural understanding of social sustainability. This re-imagining of the social sustainability of civic agriculture provides ways to defend civic agriculture from its critics and is exemplified by drawing from a personal encounter with civic agriculture. In the end, it is proposed that in light of this research there are now good reasons to re-examine civic agriculture and to critically re-imagine what qualifies who as a civic agriculturalist so that the contextual nature of the social sustainability of civic agriculture can be better respected. Author Keywords: civic agriculture, community problem solving, local food systems, social sustainability, Stephen McKenzie, Thomas A. Lyson
Civil Aviation and Scheduled Air Services in Colonial Botswana, 1935-1966
This thesis provides an in-depth and chronological study of the development of civil aviation in the Bechuanaland Protectorate (today’s Botswana), and the role played by the British Government in the development of this form of transport. The thesis argues that Her Majesty’s Government’s neglect and very little interest in its protectorate’s civil aviation represented a form of underdevelopment. The study also reveals the constant contradiction between the neglect of the imperial government and the constant lobbying on the part of colonial administration in the Protectorate for the establishment of an air service. To the colonial administrators, civil aviation represented a symbol of modernity and progress as well as more practical advantages such as mobility. The thesis finally concludes that the Bechuanaland Protectorate’s first airline was established due to growing nationalism both locally and on the continent, at large. The British Government facilitated the establishment of the airline as an attempt to appear benevolent to the protectorate on the eve of independence. Author Keywords:
Class Struggle and Solidarity in Neo-Liberal Times
The lengthy and raucous 1986 Gainers meatpacking plant strike in Edmonton, Alberta was one of the most important events in recent Alberta labour history. In the midst of the economic crisis of the 1980s and the rise of neo-liberal ideas, the strike marked a backlash by both the labour movement and ordinary citizens against attacks on workers and unions. Characterized by widely covered picket line violence, repressive police and court actions, and government unresponsiveness, the strike generated massive solidarity within and beyond the labour movement. This solidarity originated in a rejection of the neo-liberal new reality of Alberta typified by high unemployment, anti-union laws and practices, and lack of government welfare support, and it generated a provincial change the law campaign, national boycott, and rising class consciousness. The working class mobilization during the Gainers strike was a watershed for the Alberta labour movement. Author Keywords: Alberta Federation of Labour, Gainers strike, neo-liberalism, solidarity, working class
Class Struggle, The Communist Party, and the Popular Front in Canada, 1935-1939
This thesis is an attempt to provide a critical history of the Communist Party of Canada (CPC) during the Popular Front era, roughly November 1935 to September 1939. This study contains a detailed examination of the various stages of the Popular Front in Canada (the united front, the height of the Popular Front, and the Democratic front), with special attention paid to the CPC’s activities in: the youth movement, the labour movement, the unemployed movement, the peace movement, and the anti-fascist movement. From this I conclude that the implementation of the Popular Front, the transformation of the CPC from a revolutionary party to a bourgeois party, was not a smooth process, but instead was punctuated and resisted by elements within the CPC in what can be considered a process of class struggle internal to the CPC itself. Author Keywords: Canada, communism, Great Depression, labour, Popular Front, socialism
Cloud Versus Bare Metal
A comparison of two high performance computing clusters running on AWS and Sharcnet was done to determine which scenarios yield the best performance. Algorithm complexity ranged from O (n) to O (n3). Data sizes ranged from 195 KB to 2 GB. The Sharcnet hardware consisted of Intel E5-2683 and Intel E7-4850 processors with memory sizes ranging from 256 GB to 3072 GB. On AWS, C4.8xlarge instances were used, which run on Intel Xeon E5-2666 processors with 60 GB per instance. AWS was able to launch jobs immediately regardless of job size. The only limiting factors on AWS were algorithm complexity and memory usage, suggesting a memory bottleneck. Sharcnet had the best performance but could be hampered by the job scheduler. In conclusion, Sharcnet is best used when the algorithm is complex and has high memory usage. AWS is best used when immediate processing is required. Author Keywords: AWS, cloud, HPC, parallelism, Sharcnet

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Graduate student theses produced at Trent University. You may also browse theses and dissertations by year, program, or author.

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