Graduate Theses & Dissertations

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Correlating density of states features with localization strength in disordered interacting systems
Johri and Bhatt found singular behavior near the band edge in the density of states as well as in the inverse participation ratio of the Anderson model. These singularities mark a transition to an energy range dominated by resonant states. We study the interacting case using an ensemble of two-site Anderson-Hubbard systems. We find the ensemble-averaged density of states and generalized inverse participation ratio have more structure than in the non-interacting case because there are more transitions and in particular the transitions depend on the ground state. Nonetheless, there are regions of sharp decline in the generalized inverse participation ratio associated with specific density of state features. Moreover these features move closer to the Fermi level with the addition of interactions making them more experimentally accessible. Unfortunately resonances unique to interacting systems cannot be specifically identified. Author Keywords: Correlated electrons, Disorder, Localization
Corticosterone Promotes Development of Cannibalistic Morphology and Inhibits Tissue Regeneration in Axolotls (Ambystoma mexicanum)
Salamanders are capable of tissue regeneration throughout all life-stages, which requires the dedifferentiation of mature cells to regrow lost tissues. Dedifferentiation is promoted by degradation of the extracellular matrix by matrix metalloproteases, as well as lysosomal degradation of intracellular and cell-surface proteins that mark cells as part of a mature lineage. Salamanders are also capable of developing cannibalistic phenotypes, plastic traits that are elicited by environmental stressors that result in elevated circulating glucocorticoid (e.g., corticosterone) levels that underlie many fundamental adaptive changes in morphology. Interestingly, the direct effect of corticosterone on regeneration and the cannibalistic phenotype have yet to be examined. In the present thesis, axolotls (Ambystoma mexicanum) were exposed to exogenous corticosterone and 50% of the distal tail tissue was removed. The effects of high corticosterone levels on matrix metalloprotease (MMP-2, MMP-9) and lysosomal acid phosphatase (LAP) activity were assessed; these are two classes of enzymes which are markers of extracellular matrix and intracellular remodeling during regeneration, respectively. We found that elevated corticosterone levels inhibited tissue regeneration, by prolonging the dedifferentiation phase as indicated by increased LAP and reduced MMP-2 and MMP-9 activity. Elevated corticosterone levels also promoted the cannibalistic morphology and this effect was strongest among smaller individuals. Author Keywords: amphibian, cannibalistic morphology, corticosterone, dedifferentiation, regeneration, stress
Creation During Abandonment
This thesis addresses the excavation and analysis of the Hingston Group, a small courtyard group just south of the ceremonial core of the Ancient Maya city of Ka’kabish in North-Central Belize. I use settlement and household archaeological theory to understand the functions, occupation history, and status of this residential group. I also rely on entanglement theory, along with the hypothesizes presented by Palka (2003) and McAnany (1995), to create a possible interpretation for the reasons why we see what we do in the Hingston Group during its main period of occupation. The Hingston Group is composed of three structures and two chultuns (underground storage areas). Research teams excavated both chultuns during prior field seasons and found burials from the Postclassic and Late Formative Periods. This information led to the assumption that the occupation of these structures would correspond to one, or both, of these periods. However, we found that this courtyard group was occupied during a period when the rest of the core of Ka’kabish was abandoned. Along with this, excavators found an ephemeral occupation into the Colonial Period; these two new periods of occupation have expanded our understanding of the chronological history of Ka’kabish. Author Keywords: formative to postclassic, household archaeology, Maya, settlement archaeology
Critical Analysis of the Adoption of Maize in Southern Ontario and its Spatial, Demographic, and Ecological Signatures
This thesis centers on analyzing the spatial, temporal, and ecological patterns associated with the introduction of maize horticulture into Southern Ontario - contextualized against social and demographic models of agricultural transition. Two separate analyses are undertaken: a regional analysis of the spread of maize across the Northeast using linear regression of radiocarbon data and a standard Wave of Advance model; and a local analysis of village locational trends in Southern Ontario using a landscape ecological framework, environmental data and known village sites. Through the integration of these two spatial and temporal scales of analysis, this research finds strong support for both migration and local development. A third model of competition and coalescence is presented to describe the patterning in the data. Author Keywords: Demographic Modeling, Environmental Modeling, Geostastical Analysis, Maize, Ontario Archaeology, Spread of Agriculture
Critical Topographies of two films
The following thesis is a work in Critical Topography that choses as its site of study two documentary films. The films being studied are El Sol del Membrillo by Victor Erice and Rivers and Tides by Thomas Riedelsheimer. My approach to critical topography in the thesis is twofold: first, I have traced the topical motifs that have appeared to me as I looked at the two films; second, I have translated the films into writing –with the purpose of creating a sourcebook for my analysis- thus bounding the visual content of the films into the delineated space of the written word. I have sought in my analysis to make visible the numerous conceptual, aesthetic, and philosophical notions that are repeated in each film. These notions include materiality, formal operations, temporality, memory, and failure. All of which are ideas that find expression - despite their significant differences - in both documentary films. Author Keywords: Art, Critical Topography, Film Studies, Land Art, Painting, Time
Cultivating Change
The global food system has been criticized for being environmentally, economically and socially unsustainable. As part of a local food movement, farmers’ markets (FM) are undergoing a revival in response to the escalating food system globalization of the past century. Despite the prevalence of FMs as formalized organizations, there remains a significant range in their operational strategies. Through 41 questionnaires and 17 interviews with market administrators across Ontario, in collaboration with the Haliburton County Farmers’ Market Association, I explored these strategies and analyzed the influence of community characteristics on FM operations. Factors that appear to have a significant impact on FM governance and management are market size and age, willingness to adapt to change, and relationships with external organizations. My findings suggest that democratic vendor engagement and documentation of procedural systems can help optimize market administration. In terms of vendor relationships, primary concerns include regulation of resellers, diplomatic vendor pool design, and creation of a collaborative atmosphere. As well, I conclude that customers are best viewed as socially invested stakeholders with a strong interest in learning about local food production. Author Keywords: farmers’ markets, global food system, local food systems, Ontario farmers’ markets, sustainability
Cytokinin Oxidase/Dehydrogenase (CKX) Gene Family in Soybeans (Glycine max)
Glycine max (soybean) is an economically important plant species that registers a relatively low yield/seed weight compared to other food and oil seed crops due to higher rates of flower and pod abortion. Alleviation of this abortion rate can be achieved by altering the sink strength of the reproductive organs of soybeans. Cytokinin (CK) plays a fundamental role in promoting growth of sink organ (flowers and seeds) by increasing the assimilate demand. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that catalyses the irreversible breakdown of active CKs and hence reduce the cytokinin content. The current thesis uncovers the members of CKX gene family in soybeans and the natural variations among CKX genes within soybean varieties with different yield characteristics. The identification of null variants of OsCKX2 that resulted in large yield increases by Ashikari et al. (2005) provided a rationale for current thesis. The soybean CKX genes along with the ones from Arabidopsis, Rice and Maize were used to construct a phylogenetic tree. Using comparative phylogeny, protein properties and bioinformatic programs, the potential effect of the identified natural variations on soybean yield was predicted. Five genes among the seventeen soybean CKXs identified, showed polymorphisms. One of the natural variations, A159G, in the gene GmCKX16 occurred close to the active site of the protein and was predicted to affect the activity of enzyme leading to higher accumulation of CKs and hence increased seed weight. Use of such natural variations in marker assisted breeding could lead to the development of higher yielding soybean varieties. Author Keywords: CKX, Cytokinins, Seed weight, Seed Yield, SNPs, Soybeans
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:

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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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