English

In the Roman World, at least 80% and up to 95% of the population lived and

worked in a rural environment, driving the agronomic economy of the empire. During the Late Roman Empire (AD 300-600), there were a number of widespread political, social, and economic changes faced by the people who made up the empire. Through all these changes, the empire maintained its tax collection and households maintained agricultural

production. I will be examining settlement in the rural region of Isauria (Rough Cilicia) to understand the Late Roman agricultural production in a rural environment. This thesis focuses on the decision making that all economic levels of households would face when producing goods within this Late Roman Economy. Using an economic theory of the peasant economy, I develop a framework through which to view the agronomic

production of the Late Roman Period which I use to understand the household as an agent.

Author Keywords: Ancient Economy, Isauria, Late Roman, Peasant Economy, Roman Economy

Maintaining functional connectivity among wildlife populations is important to ensure genetic diversity and evolutionary potential of declining populations, particularly when managing species at risk. The Boreal Designatable Unit (DU) of woodland caribou (Rangifer tarandus caribou) in Ontario, Manitoba, and Saskatchewan has declined in southern portions of the range because of increased human activities and has been identified as 'threatened' by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). In this dissertation, I used ten microsatellite DNA markers primarily from winter-collected fecal samples to delineate genetic structure of boreal caribou in declining portions of the range and increase understanding of the potential influence of the non-threatened Eastern Migratory DU of woodland caribou on genetic differentiation. Eastern migratory caribou are characterized by large home ranges compared to boreal caribou and migrate seasonally into portions of the Boreal DU range. A regional- and local-scale analysis using the spatial Bayesian clustering algorithm in program TESS delineated four regional clusters and 11 local clusters, with the majority of local clusters occurring along the southern periphery of the range. One of those clusters in Ontario corresponded spatially with the seasonal overlap of boreal and eastern migratory caribou and was characterized by substantial admixture, suggesting that the two DUs could be interbreeding. Next, I decoupled the impacts of historical and contemporary processes on genetic structure and found that historical processes were an important factor contributing to genetic differentiation, which may be a result of historical patterns of isolation by distance or different ancestry. Moreover, I found evidence of introgression from a currently unsampled population in northern Ontario, presumably barren-ground caribou (R. t. groenlandicus). Finally, because our analysis suggested recent processes were also responsible for genetic structure, I used a landscape genetics analysis to identify factors affecting contemporary genetic structure. Water bodies, anthropogenic disturbance, and mobility differences between the two DUs were important factors describing caribou genetic differentiation. This study provides insights on where conservation and management of caribou herds should be prioritized in threatened portions of the boreal caribou range and may have implications for future delineation of evolutionarily significant units.

Author Keywords: boreal forest, genetic structure, landscape genetics, microsatellite DNA, Rangifer tarandus, woodland caribou

Strategies to reduce youth crime have been extensively researched and custody is not found to be effective. In the past, custody was a frequently used sentence, and while under the YOA the number of youth in custody was four times higher than that of adults in Canada. The use of custody sentences in Ontario has decreased in recent years, however; it remains above the Canadian average. Currently, alternatives to custody are also being implemented. This study aimed to gather lived experiences of those with firsthand experience in the youth justice system (offenders and staff). These individuals have working knowledge of effective practices for reducing recidivism. Eighteen semi-structured interviews were conducted. Interviews were coded and analysed using Interpretive Phenomenological Analysis. A number of themes emerged, including various views on the benefits of custody, the importance of relationships, challenges of the job and the need for increased focus on prevention.

Author Keywords: Interpretive Phenomenology, Rehabilitation, Treatment, Youth Justice

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

The endangered North Atlantic right whale (Eubalaena glacialis) has been internationally protected from whaling since 1935 but recovery has been slow compared to the southern right whale (Eubalaena australis) due to anthropogenic mortalities and poor reproduction. Prey availability, genetic variability, and alleles of genes associated with reproductive dysfunction have been hypothesized to contribute to low calf production. The North Atlantic Right Whale DNA Bank and Database contains 1168 samples from 603 individuals. I added 115 new genetic profiles to the database which now contains profiles for 81% of individuals alive since 1980. Paternity assignments using these profiles resulted in 62% of sampled calves being assigned a father and only 38% of candidate males being assigned a paternity. This may suggest false exclusion due to genotyping errors or the existence of an unknown group of males. The use of the DNA database allowed for the identification of 10 deceased individuals which has implications for identifying cause of death and reducing mortalities. However, genetic identification is dependent on the time of post-mortem sample collection which influences DNA quantity and quality. An assessment for variations in methylenetetrahydrofolate reductase, a candidate gene associated with reproductive dysfunction, revealed six females heterozygous for a synonymous A/T variant in exon four which may influence reproductive success through changes in enzyme production, conformation or activity.

Author Keywords: Eubalaena glacialis, Forensic Identification, Genetic Profiling, North Atlantic Right Whale, Paternity, Reproductive Dysfunction

The amitochondrial protozoan, Giardia intestinalis, encodes four members of the cytochrome b5 (CYTB5) family of heme proteins of unknown function. While homology models can predict the likely fold of these proteins, supporting experimental evidence is lacking. The small size of the cytochromes (~16 kDa) makes them attractive targets for structural analysis by Electron Paramagnetic Resonance spectroscopy (EPR) and Nuclear Magnetic Resonance spectroscopy (NMR). EPR measurements are particularly useful in defining the geometry of the coordination environment of the heme iron; such measurements indicated that the planar imidazole rings of the invariant histidine axial ligands are nearly perpendicular to each other, rather than in the coplanar orientation observed within mammalian CYTB5s. This may be due to geometrical constraints imposed by a one-residue shorter spacing between the ligand pair in the Giardia cytochromes b5 (gCYTB5s). Following optimization of sample and instrument conditions for NMR experiments, a comparison of the 1D 1H-NMR spectra of gCYTB5 isotype I to those of three of its heme-pocket mutants (Tyr51→Phe, Tyr61→F, and Cys84→Ala) were used to tentatively assign the heme methyl and vinyl protons. Mutant Tyr61→F had the greatest effect on the wild-type spectrum due to maximum through-space contacts with the heme macrocycle and its proximity to the His63 axial ligand. These experiments are a prelude to further NMR experiments that can lead to solving the complete structures of these proteins.

Author Keywords: cytochrome b5, heme b, mutant protein, paramagnetic iron, resonant spectroscopy, sequence homology

Following Baudrillard's conceptual and stylistic shift of the mid-70s, this thesis argues that said shift is accounted for by understanding the ontological quandary Baudrillard found himself in after developing a theoretical agonism impossible to divorce from the practice of writing. By tracing the conceptual metamorphoses of key terms including semiotic ambivalence, symbolic exchange and theoretical writing itself as a total agonistic process, this thesis demonstrates that theory is not reducible to epistemic production but is rather the contentious site of challenge and aesthetic (dis)appearance. Each chapter examines a conceptual tension revealing insoluble, conflicting social forms. These forms reveal the reversibility Baudrillard finds at work in all social phenomena. These culminate in a chapter that tackles Baudrillard's writing itself as a social form that endeavours to embody the agonistic theoretical concept as a process rather than remaining a representation, or commentary on, ambivalent social conflict.

Author Keywords: agonist, ambivalence, Baudrillard, reversibility, style, writing

This dissertation offers the dibaajimowin (personal story) of my beading project, which I undertook to understand the enactment of Anishinaabe women's knowledge in graduate research. Framed through the concept of a collective self, which is embedded within the Anishinaabe traditions of storytelling and beading, and drawing further from the aesthetics, processes, and teachings of these traditions so that I proceed in a good way, I am able to tell a story that is wholly Anishinaabe. Through the symbolic literacy present within the pieces of beadwork entitled:"Turtle Woman," "Turtle Woman Meets Grandmother Moon," "Turtle Woman Marries a Beaver," and "Turtle Woman Slays the Big Fish," which I present in the second half of this story, I explore the relationship among Anishinaabe women's knowledges, self, identity, power relations, allyship, sovereignty and good governance in graduate research. I conclude that if graduate research is framed as an extension of an Anishinaabe space, an ethics of responsibility emerges, setting the stage for graduate research that is rooted in responsibility, contributing to efforts of Anishinaabe sovereignty and community wellness. Overall through my conclusion, as well as the process that I employ, I make contributions in the areas of Indigenous thought, Indigenous methodologies, Indigenous governance, feminism, critical theory, pedagogy, and ally theory.

Author Keywords: Anishinaabe, beadwork, Indigenous knowledge, Indigenous methodology, Indigenous women, sovereignty

This study investigates the use of dental calculus for paleodietary studies using stable isotope analysis of a skeletal sample from the Greek colonial site of Apollonia Pontica, Bulgaria (5th to 3rd century BC). A sample of 27 individuals was used to examine the δ13C and δ15N values of paired dental calculus and bone samples, and the dental calculus was analyzed as separate organic and inorganic components. No significant correlation was found between the δ13C values of either the bone collagen and organic dental calculus samples, or the bone apatite and inorganic dental calculus samples. A significant correlation was found between the δ15N values of the bone collagen and organic dental calculus samples; however, the reason for this correlation is unclear. A greater range of variation in the δ13C and δ15N values was found in the organic dental calculus samples compared to the respective bone collagen samples. These results suggest that dental calculus is not an appropriate proxy to bone for paleodietary studies using stable isotope analysis and that any dietary signal is clouded by other data. The oral microbiome is considerably diverse and is the most probable explanation for the great range of stable isotope values obtained from dental calculus. A significant, strong correlation was found between the C/N ratios and δ15N values of the organic dental calculus samples, suggesting that the lowest C/N ratios and δ15N values depict deposits with the least bacterial alteration.

Author Keywords: carbon, dental calculus, nitrogen, paleodietary studies, Social Sciences, stable isotopes

This thesis presents a technique to produce signatures from topologies generated by the Growing Neural Gas algorithm. The generated signatures have the following characteristics: The signature's memory footprint is smaller than the "real object" and it represents a point in the n x m multidimensional space. Signatures can be compared based on Euclidean distance and distances between signatures provide measurements of differences between models. Signatures can be associated with a concept and then be used as a learning step for a classification algorithm. The signatures are normalized and vectorized to be used in a multidimensional space clustering. Although the technique is generic in essence, it was tested by classifying alphabet and numerical handwritten characters and 2D figures obtaining a good accuracy and precision. It can be used for many other purposes related to shapes and abstract typologies classification and associative memory. Future work could incorporate other classifiers.

Author Keywords: Associative memory, Character recognition, Machine learning, Neural gas, Topological signatures, Unsupervised learning