Graduate Theses & Dissertations

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Cytokinin biosynthesis, signaling and translocation during the formation of tumors in the Ustilago maydis-Zea mays pathosystem
Cytokinins (CKs) are hormones that promote cell division. During the formation of tumors in the Ustilago maydis-Zea mays pathosystem, the levels of CKs are elevated. Although CK levels are increased, the origins of these CKs have not been determined and it is unclear as to whether they promote the formation of tumors. To determine this, we measured the CK levels, identified CK biosynthetic genes as well as CK signaling genes and measured the transcript levels during pathogenesis. By correlating the transcript levels to the CK levels, our results suggest that increased biosynthesis and signaling of CKs occur in both organisms. The increase in CK biosynthesis by the pathosystem could lead to an increase in CK signaling via CK translocation and promote tumor formation. Taken together, these suggest that CK biosynthesis, signaling and translocation play a significant role during the formation of tumors in the Ustilago maydis-Zea mays pathosystem. Author Keywords: Biosynthesis, Cytokinins, Signaling, Translocation, Ustilago maydis, Zea mays
Cytokinins in nematodes
To investigate cytokinins (CKs) in nematodes, CK profiles of a free-living Caenorhabditis elegans and a plant parasitic Heterodera glycines (soybean cyst nematode, SCN) were determined at the egg and larval stages. SCN had higher total CK level than C. elegans; however, CKs in SCN were mostly inactive precursors, whereas C. elegans had more bioactive forms. This is the first study to show that methylthiols are present in nematodes and may affect plant infection. In infectious SCN larvae, methylthiol levels were much higher than in eggs or C. elegans larvae. Furthermore, The CK profiles of SCN-susceptible and resistant Glycine max cultivars at three developmental stages revealed that, regardless of the resistance level, SCN infection caused an increase in root CKs. One resistant cultivar, Pion 93Y05, showed significantly high levels of bioactive N6-isopentenyladenine (iP) in the non-infected roots which indicated a potential role of CKs in soybean resistance to SCN. Author Keywords: Cytokinins, HPLC-MS/MS, Nematode, SCN resistance, Soybean
Daphnia pulicaria responses to temperature and nutrients stress
Warming climates have had various consequences on terrestrial and aquatic food webs that are expected to persist. There is evidence suggesting that certain organisms are better equipped to handle changing climates compared to others. Therefore, the purpose of my thesis was to study the adaptability of Daphnia under temperature stress and nutrient limitation. First, to examine the effects of dietary phosphorus limitation and temperature on daphniid life-history and population growth, a series of experiments were conducted in the laboratory. In general, I found that Daphnia body growth rates and life-history traits to food carbon to phosphorus (C:P) ratios change with temperature. Next, I identified a protocol to limit the genomic DNA (gDNA) from ribonucleic acid (RNA) extractions. I found that using a modified phenol-chloroform extraction protocol was the most effective way to remove gDNA from extracted Daphnia RNA samples. Overall, results from this study show that temperature and food quality interactions are more complicated than previously thought. Furthermore, the RNA extraction protocol developed will be useful in future studies examining gene expression responses in Daphnia. Author Keywords: ecological stoichiometry, gene expression, life-history, nutrient limitation, RNA puritiy, temperature
De novo transcriptome assembly, functional annotation, and SNP discovery in North American flying squirrels (genus Glaucomys)
Introgressive hybridization between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) has been observed in some areas of Canada and the USA. However, existing molecular markers lack the resolution to discriminate late-generation introgressants and describe the extent to which hybridization influences the Glaucomys gene pool. I report the first North American flying squirrel (genus Glaucomys) functionally annotated de novo transcriptome assembly with a set of 146,621 high-quality, annotated putative species-diagnostic SNP markers. RNA-sequences were obtained from two northern flying squirrels and two southern flying squirrels sampled from Ontario, Canada. I reconstructed 702,228 Glaucomys transcripts using 193,323,120 sequence read-pairs, and captured sequence homologies, protein domains, and gene function classifications. These genomic resources can be used to increase the resolution of molecular techniques used to examine the dynamics of the Glaucomys hybrid zone. Author Keywords: annotation, de novo transcriptome, flying squirrels, high-throughput sequencing, hybridization, single nucleotide polymorphisms
Deep learning for removal of non-resonant background in CARS hyperspectroscopy
In this work, a deep learning approach proposed by Valensise et al. [3] for extracting Raman resonant spectra from measured broadband CARS spectra was explored to see how effective it is at removing NRB from our experimentally measured “spectral-focusing”-based approach to CARS. A large dataset of realistic simulated CARS spectra was used to train a model capable of performing this spectral retrieval task. The non-resonant background shape used in creating the simulated CARS spectra was altered, to mimic our experimentally measured NRB response. Two models were trained: one using the original approach (Specnet) and one using the updated NRB “Specnet Plus”, and then tested their ability to retrieve the vibrationally resonant spectrum from simulated and measured CARS spectra. An error analysis was performed to compare the model's retrieval performance on two simulated CARS spectra. The modified model's mean squared error value was five and two times lower for the first and second simulated CARS spectra, respectively. Specnet Plus was found to be more effective at extracting the resonant signals. Finally, the NRB extraction abilities of both models are tested on two experimentally measured CARS hyperspectroscopy samples (starch and chitin), with the updated NRB model (Specnet Plus) outperforming the original Specnet model. These results suggest that tailoring the approach to reflect what we observe experimentally will improve our spectral analysis workflow and increase our imaging potential. Author Keywords:
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
Genetic variation is the raw material and basis for evolutionary changes in nature. The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision making. Whole genome analysis can be an asset to conservation biology and the management of species through the generation of more precise and novel metrics. This thesis uses whole genome re-sequencing to characterize the demographic history and quantify genomic metrics relevant to conservation of caribou (Rangifer tarandus) in Québec, Canada. We calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) of recent population declines and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium showed Gaspêsie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based off this metric alone. Inbreeding measures suggested nuanced patterns of inbreeding and correlated to the demographic models. This study suggests that while the Québec populations are all under decline, they harbour enough ancestral genetic variation to replenish any lost diversity, if conservation decisions are made in favour of these populations, specifically supporting NC. Author Keywords:
Denizens of Virtual Worlds
This thesis studies a subset of players of video games called “power-gamers” who play games in a way that mirrors labour as opposed to leisure. Through ethnographic fieldwork and exploration this thesis examines what constitutes “power-gaming” and seeks to unpack the differences between skill, fun, and labour. Chapter One analyzes how ethnographic fieldwork is performed in virtual worlds, and the necessary frameworks inherent to this. Chapter Two explores facets of technical hobbies, masculinity, skill, and how they relate to power-gaming. Chapter Three explores how different cultures globally choose to play-games, and the forms of sociability involved in this play. Chapter Four examines reality in relation to virtual worlds, and how players in virtual worlds explore and unpack their surroundings, which mirrors many scientific practices in the real world. Chapter Five explores narrative structure in games, and their relation to power-gaming practices. Chapter Six concludes with a discussion of power-gamers as a neo-liberal workforce. Author Keywords: game design, neo-liberalism, playbour, power-gamer, sociability, virtual-ethnography
Dennis Lee's Testament
The future-poetry of Dennis Lee published in Testament (2012) is the culmination of four cycles of creativity in his lifetime, each seeking a Real beyond the nihilism of technological modernity. Ultimately, Lee wagers the role of the poet and the future of poetic language on Earth on a non-modern that risks entangling the poet who enters void and embodies its meaninglessness. CHAPTER ONE: To approach this wager, the thesis first identifies the sources in philosophy of a Canadian Romantic modernism embraced by George Grant in collegial exchanges with Dennis Lee during the period of Civil Elegies (1972). Grant elicits a politics out of Nietzsche; Lee extends a poetics out of classical experimental modernism, made intelligible in this thesis by Mallarmé’s “cadence” or “rhythm” of things in nothingness and by Beckett’s word-play at the impasse of naming. CHAPTER TWO: To think beyond the mastery of the world by technique is to encounter a choice between silence as assumed by Grant and nonsense as explored by Lee during the period of Alligator Pie (1974) and The Gods (1979). CHAPTER THREE: The example of Paul Celan and his revisiting of Hölderlin provokes Lee to attend upon cadence at the level of the discrete word, an experiment with the dissolution of language and selfhood anticipated in the period of Riffs (1993) and Nightwatch (1996). Here, the undermusic felt to belong to the life-world (Lebenswelt) impacts as affect, in contrast to Celan’s alienated death-walk. CHAPTER FOUR: In the spirit of “post-internet poetry,” and by means of the spontaneous polyphonic scoring of cadence, Lee transforms the modernist impasse at the void into a further contradiction, the living of which may allow the poet access to a non-modern, but at a cost: the loss of poetry to incomprehension and insignificance, the reduction of the poet to a medium of the void, the dissolving of structure into materialities colliding in chance. Author Keywords: Dennis Lee, George Grant, Nonsense, Paul Celan, Technological Modernity, Void
Desire to be Zine
This thesis explores access to feminist zine culture and community, specifically if, and how, access has been altered in the age of digital technologies and increased access to digital spaces. Results from a questionnaire completed by 8 young feminist zine-makers and readers of marginalized genders indicated that though the modern boundaries of what a zine is has been expanded to include e-zines, there remains a preference toward print zines in zine-making and reading practices. Results also revealed that while there is a preference toward accessing feminist zine culture and community in-person in theory, participants were more likely to access feminist zine culture and community online in reality. This project found that digital technologies and the Internet have affected feminist zine culture in multiple ways, ranging from the Internet creating a new access points to community, to the Internet making it easier to find, purchase, and distribute zines. Author Keywords: Digital Media, Feminism, Feminist Zine Culture, Feminist Zines, Materiality, Print Media
Detecting anti-estrogens and anti-androgens in surface waters impacted by municipal wastewater discharges and agricultural runoff
This study focused on detecting 22 target anti-estrogenic and anti-androgenic compounds in surface waters influenced by both discharges of municipal wastewater and agricultural runoff in Canada and Argentina. Polar organic chemical integrative samplers (POCIS) were used to monitor the target compounds in surface waters. The removals of the target compounds in a municipal wastewater treatment plant (WWTP) in Canada were also evaluated. In both Canada and Argentina pesticides with potential anti-estrogenic and anti-androgenic activities were detected in the surface waters. The highest concentrations were found in Argentina (up to 1010 ng L-1) in areas impacted by heavy agricultural practices. Cyproterone acetate and bicalutamide were the only two anti-cancer drugs detected only at the Canadian study site, the Speed River, ON. In the Guelph WWTP, that discharges into the Speed River, these target compounds were not all efficiently removed (>70%) during treatment. Overall, this study provides insight to possible anti-estrogenic and anti-androgenic compounds that may be contributing to endocrine disrupting activities in surface waters. Author Keywords: Anti-androgens, Anti-estrogens, Cancer Therapy Drugs, Current use pesticides, Pharmaceuticals and Personal Care Products, Polar Organic Chemical Integrative Samplers
Detection of four at-risk freshwater pearly mussel species (Bivalvia
Environmental DNA (eDNA) detection uses species-specific markers to screen DNA from bulk samples, such as water, to infer species presence. This study involved the development and testing of species-specific markers for four freshwater pearly mussels (Unionidae). The markers were applied to water samples from intensively sampled mussel monitoring sites to compare species detections from eDNA with established sampling method detections. Target species were detected using eDNA at all sites where they had previously been detected by quadrat sampling. This paired design demonstrated that eDNA detection was at least as sensitive as quadrat sampling and that high species specificity can be achieved even when designing against many sympatric unionids. Detection failures can impede species conservation efforts and occupancy estimates; eDNA sampling could improve our knowledge of species distributions and site occupancy through increased sampling sensitivity and coverage. Author Keywords: conservation genetics, cytochrome oxidase subunit I (COI), environmental DNA (eDNA), quantitative PCR (qPCR), species at risk (SAR)
Determinants of Deviance
Background: Researchers have provided evidence that attachment may be independently linked to early adversity and criminal behaviour. In this study, I examined the combined associations among these variables in a student and community sample. Method: The first study consisted of undergraduate students (n = 590) who completed surveys to assess early adversity (Felitti, et al., 1988), attachment (Scharfe, 2016), and criminal behaviours. Participants were grouped based on their reports of adverse experiences and engagement in criminal behaviour. The second study was a replication of the first using a community sample (n = 294). Results: My hypotheses were partially supported, and my findings were consistent across Study 1 and Study 2. As I expected, there was a significant main effect for adversity when examining the mean scores of the attachment representations for attachment to mothers (Study 1 F (16, 1763.402) = 3.61, p < .001; Study 2 (F (16, 849.942) = 2.377, p = .002) and attachment to fathers (Study 1 F (16, 1763.402) = 4. 349, p < .001; Study 2 (F (16, 840.776) = 3.067 p < .001)). From examining the means, I concluded that participants who reported greater adversity reported higher insecure-avoidant and lower secure attachment to mothers and fathers. There were no significant main effects for criminal behaviour or significant interaction effects. Impact: To date, no study has explored all three variables explicitly. My findings are able to highlight the critical importance of secure attachment relationships and add further comprehension to exploring factors associated to criminal behaviour. Author Keywords: Attachment, Criminal Behaviour, Early Adversity

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Format: 2024/03/04