VictorJuiz/thesis huggingface dataset:
Epigenomic Studies of Twins and Brain Diseases

It has been generally accepted that complex diseases are caused by genetic and environmental factors; however, both genetic and epidemiological research programs are facing significant difficulties in explaining the etiopathogenesis of complex diseases. It has been suggested lately that inclusion of putative epigenetic disease mechanisms may enable one to bypass the limitations of the traditional research strategy and allow the integration of genetic and environmental risk factors into a new theoretical framework. In this thesis, we analyzed normal human twins to demonstrate that monozygotic twins exhibit numerous epigenetic differences, not all of which were caused by environmental factors. We also showed that dizygotic twins were epigenetically even more divergent than monozygotic twins, which suggests that heritability may not be an exclusive function of DNA, but may also extend to epigenetic factors. In order to address the role of epigenetic factors in diseases, we performed large-scale epigenomic studies of singletons and twins who were discordant for major depressive disorder and Alzheimer's disease. We investigated DNA modification patterns across multiple tissue types and applied a series of innovative analytical techniques to explore the various aspects of DNA modification differences between normal and diseased individuals. In the major depressive disorder study, we investigated the confounding effects of disease heterogeneity and the age-dependent changes in variation of DNA modification. We uncovered several unknown epigenetic facets, such as long-range epigenetic effects, epigenetic outliers, and changes in the epigenomic networks. In the Alzheimer's disease study, we found evidence for loss of epigenetic uniqueness in the aging brain, which progresses faster in patients with dementia. This work adds to the notion that epigenomic studies can transform our understanding regarding the origin of complex diseases.

Keywords: Epigenetics
Major Depressive Disorder
Alzheimer's Disease
Monozygotic Twins
DNA modification
Complex Diseases
Advisor: Petronis, Arturas
For the Love of Metaphysics: From the Revolution in Thinking towards the Renewal of Thinking

One of Kant’s most original insights is the notion that we can construct a philosophical argument—a transcendental argument—whose central premise makes a first-personal appeal to our moral sentiments. Kant characterizes the epistemic force that accrues to the concepts and ideas that are justified by this form of philosophical argument as “moral belief” or “moral certainty,” and he calls the propositions that are demonstrated by such arguments “postulates of practical reason.” My dissertation has two interrelated aims. First, to exhibit the most significant repercussions of this basic Kantian insight for philosophical methodology, for our conceptions of human freedom and moral agency, and for the possibility of religious belief. Second, to show that Franz Rosenzweig’s theism is supported by what we may regard as a transcendental argument that reveals the conditions of possibility for understanding ourselves as beings endowed with ethical value. Because the repercussions of Kant’s discovery of a “moral proof” came into focus in the two decades after the publication of the first Critique, my dissertation starts by interpreting the philosophical significance of the early reception of Kant’s Critical philosophy. I argue that two of Kant’s earliest critics, Salomon Maimon and F. H. Jacobi, compelled the post-Kantian idealists to broaden the scope of Kant’s “moral proof” and transform his original insight into the idea that philosophy as a whole should be established on a practical foundation. My dissertation then examines how J.G. Fichte and F.W.J. Schelling appropriated Kant’s idea of a “moral proof” and transformed the idea into the more radical view that reason, as a whole, is practical. The final part of my dissertation brings the discussion about the nature of transcendental arguments to bear on topics in the philosophy of religion. I show how the metaphysical and theological framework that Schelling develops in his 1809 Philosophical Investigations into the Essence of Human Freedom and in his 1811–1815 Ages of the World fragments grounds his conception of freedom and moral agency, and I argue that Schelling’s theology is the main source of inspiration for that developed by Rosenzweig in the Star of Redemption.

Keywords: transcendental arguments
freedom
reason
Advisor: Franks, Paul
Oxidative Stress Mechanisms in Alcohol Developmental Toxicity

Consumption of alcohol (ethanol, EtOH) during pregnancy can result in a spectrum of anomalies termed the Fetal Alcohol Spectrum Disorders (FASD), characterized by structural and behavioural deficits, while in utero exposure to methanol (MeOH), a structurally similar alcohol, enhances structural malformations in rodents. The mechanisms underlying these toxicities are unclear, however reactive oxygen species (ROS) have been implicated. I hypothesize that prenatal exposure to EtOH or MeOH enhance the formation of ROS, which oxidatively damage fetal cellular macromolecules (DNA, protein, lipids) and/or alter fetal redox-sensitive signal transduction, causing structural birth defects and postnatal neurodevelopmental deficits. If so, then altering the balance of pathways of ROS formation and detoxification, and repair of oxidatively damaged DNA, should determine teratological risk. This hypothesis was tested using the free radical spin trapping agent phenylbutylnitrone (PBN), and pharmacological and genetic modulations of the ROS-forming enzyme NADPH oxidase (NOX), the antioxidative enzyme catalase and the DNA repair enzyme oxoguanine glycosylase 1 (OGG1). Embryonic EtOH exposure oxidatively damaged embryonic DNA and enhanced structural malformations, which were: (1) blocked by the free radical spin trapping agent PBN; (2) decreased in transgenic mice expressing human catalase (hCat); (3) exacerbated in acatalasemic (aCat) mice; and, (4) exacerbated in OGG1 knockout mice in a genotype-dependent fashion. Fetal EtOH exposure enhanced fetal brain DNA oxidation and postnatal behavioural deficits in CD-1 mice, and in OGG1 knockout mice in a gene dose-dependent fashion; both effects were blocked by PBN. Interestingly, untreated OGG1 knockout mice exhibited a learning deficit compared to wild-type littermates, constituting the first report of a phenotype for these mice. Embryonic MeOH exposure enhanced embryopathies, embryonic protein oxidation and upregulated mRNA and protein expression of embryonic ROS-initiating NOXs in CD-1 embryos, providing the first evidence of NOX involvement in MeOH embryotoxicity. Embryopathies were respectively decreased and increased in hCat and aCat embryos. These results suggest that ROS are involved in the teratological mechanism of EtOH and MeOH, and that embryonic catalase, NOX, and DNA damage and repair are determinants of risk.

Keywords: oxidative stress
fetal alcohol spectrum disorder
teratogenesis
embryology
methanol
ethanol
Advisor: Wells, Peter G.
Relationships Between Operating Conditions, Carbon Deposition, and Performance in Solid Oxide Fuel Cells

This research examines the effect of solid oxide fuel cell (SOFC) operating conditions on carbon deposition in nickel/yttria-stabilized-zirconia (Ni/YSZ) anodes and the effect of carbon deposition on impedance spectra of polarized SOFCs. Although Ni/YSZ anodes are susceptible to degradation from carbon deposition, Ni/YSZ is still a competitive material set compared to coke-resistant alternatives due to its relative cost and elemental abundance. Thus, it is important to more clearly define coking thresholds with respect to temperature (T), molar steam:carbon ratio (SC), fuel utilization (Uf ), current density (i), and mole fraction of ethane in the fuel (fC2H6). The quantification of gasified carbon (QGC) method was developed for in-situ measurement of carbon deposition on operating SOFCs. Deposited carbon is gasified with H2O, and carbon mass is measured by quantification of evolved CO. It was shown that deposited carbon can be gasified after 100 hours residence time. The accuracy of the QGC method was validated using a thermogravimetric analyzer. Carbon deposition thresholds were measured on button cells with 10 hour carbon deposition periods using CH4 reformate gas mixtures. The constituent concentrations of CH4 reformate gas mixtures were developed mathematically for different SC and Uf. Homogeneous decomposition of C2H6 convolutes carbon mass measurements and limited the study of fC2H6. The coking threshold at open circuit in the SC domain (Uf = 0) was measured to be approximately 1.04 and 1.18 for 600 and 700°C, respectively. The coking threshold at open circuit in the Uf domain (SC = 0.03) was measured to be approximately 36% and 32% for 600 and 700°C, respectively. Coking thresholds agree well with thermodynamic equilibrium calculations when the properties of solid phase carbon are modified appropriately. This observation was further supported by experiments with varying current density. Using measured coking thresholds, the Gibbs free energy of carbon on Ni/YSZ cermets at 600°C was calculated to be 6.91±0.08 kJ-mol-1. Coking on a polarized SOFC was found to be minimally detectable by impedance spectroscopy. The results from this work can be readily applied to SOFC system design, numerical simulations of SOFC anodes, and design of anodes with material gradients.

Keywords: solid oxide fuel cell
coking, carbon deposition
Advisor: Kesler, Olivera
Structural and Functional Characterization of the Essential AAA+ ATPases Rvb1 and Rvb2 of S. cerevisiae

Rvb1 and Rvb2 are essential proteins of the AAA+ superfamily of ATPases associated with a diversity of cellular activities. The Rvbs are components of several chromatin remodeling complexes and the R2TP complex, which is involved in the assembly of small nucleolar ribonucleoprotein complex, RNA polymerase II, Telomerase complex, and Phosphatidyl inositol 3' kinase-related kinases. As such, the Rvbs play an integral role in regulating gene expression, cell signaling, cell growth, and the DNA damage response. Their involvement in these processes is conserved from yeast to human and aberrations in Rvb regulation have been linked to a variety of carcinomas. Because Rvbs are essential in a host of cell processes, defining their molecular and biological functions will aid in future research and application. This work provides a structural, functional, and behavioral characterization of Rvb1 and Rvb2 of S .cerevisiae. Rvb1 and Rvb2 together were demonstrated to form a heterohexameric ring complex. Electron microscopy analysis of the endogenous Rvb1/Rvb2 complex showed similar hexameric rings as those observed for the recombinant Rvb1/Rvb2 complex suggesting that this complex is physiologically relevant. The Rvb1/Rvb2 complex exhibited synergistically enhanced ATP-hydrolysis and DNA unwinding activities in comparison to either subunit alone. The Walker B motif involved in ATP-hydrolysis was found to be essential in both subunits for cell viability and for ATPase activity. Synthetic genetic analysis of RVB1 and RVB2 genes with non-essential genes in S. cerevisiae revealed that both RVBs share a high percentage of genetic iii interactions, indicating that they are both involved in the same cellular pathways. In addition, Rvb1 and Rvb2 are highly co-localized in the nucleus during normal cell growth and under various stress conditions suggesting that their function in the cell resides predominantly in the nucleus and may involve the Rvb1/Rvb2 complex. This work will lend general knowledge towards furthering our understanding of these important proteins and provide a foundation for studies of the human Rvbs in cancer therapies.

Keywords: ATPases
DNA
Advisor: Houry, Walid
Lives Worthy of Life and Remembrance: Memorialization of the National Socialist Aktion T4 Euthanasia Programme

It is estimated that over 70,000 German and Austrian victims deemed mentally and physically disabled by the Nazis lost their lives in the National Socialist euthanasia programmed entitled Aktion T4. These murders prove to be the first instance of mass gassings of a selection of society deemed unwanted, and provided the intellectual and technological framework that was employed in the Extermination Camps. And yet a void in memorialization exists for the topic. Deficient memorialization of such a historically important event in German and Austrian society raises questions as to why this Nazi programme was not memorialized to the same degree as other historical events and victim groups of the Holocaust. The scarce number of representations of the victims in the forms of literature, art, monuments and memorials is indicative of a reluctance or selective remembering of the topic in WWII memorialization practices. The void in memorialization of Aktion T4 is founded in three important and influential factors. Firstly, the negative stigmas associated with mental and physical disabilities, both in confronting the topic, but also presenting it on public display. Secondly, the legal issues in that only a very few number of doctors, caregivers, or commanders of the killing centres were prosecuted and sentenced for their crimes, but rather continued to practice without any repercussions. Finally, the addressing of the topic of German suffering and the representation of German people as victims, and not solely as the perpetrators of WWII. This complex dichotomy of presenting German people as both victims and perpetrators within the same action results in a political nervousness and general avoidance. The topic of Aktion T4 memorialization is pertinent as it speaks not only to the history of the mentally and physically disabled victims, but also to the treatment of people with disabilities today. The memorialization of Aktion T4 and the representation of its victims is an important topic which has been long delegated to the margins of Holocaust memory work. These first victims represent a selected eradication of a group of society deemed unworthy of life, and unworthy of belonging to the German population.

Keywords: memorialization
Holocaust
German Studies
euthanasia
Aktion T4
Disability Studies
WWII
monuments
memorials
German suffering
Advisor: Soldovieri, Stefan
The Incidence, Co-occurrence, and Predictors of Dysphagia, Dysarthria, and Aphasia after Acute Ischemic Stroke

Background- Dysphagia, dysarthria and aphasia are frequent sequelae of stroke. We sought to identify their frequency, co-occurrence, and predictors of them after acute ischemic stroke. Methods- First, we used the Registry of the Canadian Stroke Network’s (RCSN) database (2003–2008) from one stroke centre to identify a random sample of 250 patients with acute ischemic stroke confirmed by magnetic resonance imaging (MRI). We conducted a medical chart review to derive frequency estimates for the presence of dysphagia, dysarthria and aphasia and identified clinical predictors of them from the RCSN database. Second, we conducted a systematic review to identify neuroanatomical predictors of dysphagia after acute ischemic stroke. We searched 14 databases, 17 journals, three conference proceedings and the grey literature using the Cochrance Stroke Group search strategy. We pooled individual level data for the dysphagia outcome, calculating relative risks according to neuroanatomical lesion sites. Finally, from the medical chart review, we evaluated MRI scans for patients with acute lesions within 14 days of stroke onset, deriving clinical and neuroanatomical predictors of the three impairments, using logistic regression. Results – First, incidence estimates for dysphagia, dysarthria, and aphasia were 44% (95% CI, 38-51), 42% (95% CI, 35-48) and 30% (95% CI, 25-37), respectively. The highest clinical predictors were non-alert level of consciousness for dysphagia (OR 2.6, CI 1.03-6.5), symptoms of weakness for dysarthria (OR 5.3, CI 2.4-12.0), and right-sided symptoms for aphasia (OR 7.1, CI 3.1-16.6). Second, for our systematic review, we reviewed 964 abstracts, accepting 84 for full review. Seventeen met our inclusion criteria, providing individual results for 656 patients. Predictors of dysphagia included pontine (RR 3.7, 95% CI 1.5-7.7), medial medullary (RR 6.9, 95% CI 3.4-10.9) and lateral medullary (RR 9.6, 95% CI 5.9-12.8) lesions. Finally, 160 patients met our eligibility criteria for MRI analysis. Strongest predictors included medullary lesions (OR 6.2, 95% CI 1.5 – 25.8) for dysphagia, pontine lesions (OR 7.8, 95% CI 2.7 – 22.9) for dysarthria, and insular lesions (OR 34.4, 95% CI 4.2 – 283.4) for aphasia. Conclusions- We computed the frequency of dysphagia, dysarthria, and aphasia, identifying clinical and whole brain neuroanatomical predictors of their presence.

Keywords: stroke
MRI
dysphagia
dysarthria
aphasia
Advisor: Martino, Rosemary
PDGF-A Signalling Regulates Radially Oriented Movements of Mesoderm Cells During Gastrulation in Xenopus

The molecular regulation and cellular basis of morphogenesis during Xenopus gastrulation has been a topic of extensive study. In particular, the convergent extension movements that occur in the chordamesoderm are well understood, however less is known about the morphogenesis of other mesoderm regions. Since most of the morphogenetic movements occurring during gastrulation appear to be region autonomous, it is necessary to understand these region specific movements and their contribution to the gastrulation process in order to understand gastrulation as a system. The organization of cells in a region can be indicative of the cell movements that are occurring in that region. Using scanning electron microscopy, I have analyzed the organization of cells in the prechordal mesoderm (PCM) of the gastrula, which is the sub-region of anterior mesoderm that gives rise to the muscles of the ii head. I found that during the middle of gastrulation, PCM cells were oriented with their long axes perpendicular to the overlying blastocoel roof (BCR) and that the orientation of these cells is BCR dependent. By the end of gastrulation, I found that the PCM had thinned from a multi-layered tissue to single layer of cells in contact with the BCR, suggesting radial interaction of the PCM. Furthermore, cells in corresponding regions on the lateral and ventral sides of the embryo were found to be oriented similarly, suggesting that radially directed movements could be common throughout the anterior mesoderm. Three isoforms of the Platelet Derived Growth Factor A (PDGF-A) are expressed in the BCR and its cognate receptor, PDGFRα, is expressed in the PCM. I have shown that two isoforms of the PDGF-A isoforms (lf-PDGF-A and int-PDGF-A) remain associated with the surface of secreting cells and thus signal over a short range, while a third (sf-PDGF-A) is diffusible and can signal over long distances. My work has shown that radial intercalation of the PCM is instructively regulated by a concentration gradient of sf-PDGF-A, which forms in the mesoderm over a distance of approximately 200 μm by the diffusion of molecules through intercellular gaps. My work describes for the first time, the molecular regulation of radial intercalation.

Keywords: Developmental Biology
Xenopus
Gastrualtion
Cell Migration
Radial Intercalation
Advisor: Winklbauer, Rudolf
Mitochondrial-localized Phosphatidylethanolamine in Mitochondrial Dynamics and Autophagy

Phosphatidylethanolamine (PE) constitutes a significant proportion of total phospholipids in biological membranes. A major route of PE biosynthesis occurs via the decarboxylation of phosphatidylserine (PS) by the inner-mitochondrial-membrane (IMM)-localized PS decarboxylase (PSD). The only other known phospholipids that are synthesized in mitochondria are the mitochondrial-enriched phosphatidylglycerol (PG) and cardiolipin (CL); the synthesis of other biological lipids occurs mostly in the endoplasmic reticulum (ER). Hence, the mitochondrial-localization of PSD led me to speculate that PE within the mitochondrial membrane might have important functions. In this thesis, I describe my findings that mitochondrial-localized PE plays an important role in mitochondrial membrane remodelling and autophagy, a conserved quality control mechanism. Mitochondrial PE promotes mitochondrial membrane fusion by enhancing the biogenesis of the short isoform of mitochondrial genome maintenance 1 (s-Mgm1), a key mitochondrial fusion protein. The biophysical properties of PE on the mitochondrial membrane also promote fusion likely by increasing the rate of lipid mixing during fusion. In addition, mitochondrial PE is important for oxidative phosphorylation and the maintenance of mitochondrial ATP levels, crucial mitochondrial homeostatic functions. I also demonstrate that a reduction in mitochondrial PE impairs autophagy likely by impeding autophagosome formation, expansion and/or fusion with the vacuole in yeast. My results provide additional insight into the functional importance of mitochondrial PE and highlight the specific lipid composition of the mitochondrial membrane as a key player in mitochondrial membrane fusion and autophagy.

Keywords: Mitochondria
phosphatidylethanolamine
lipids
mitochondrial fusion
mitochondrial dynamics
autophagy
phosphatidylserine decarboxylase
Advisor: McQuibban, G. Angus
For us, by us: political geographies of race, sexuality and health in the work of ethno-specific AIDS service organizations in global-multicultural Toronto

This dissertation traces the role of racialization in the production of spaces of sexual health organizing and social service provision. Drawing on insights from geographies of sexualities and the literatures on critical race theory, it examines how spaces of care that emerged from local responses to HIV/AIDS in 1980s Toronto (e.g., AIDS service organizations or ASOs) became sites for the normalization of whiteness and the exclusion of people of colour. It also documents the ways that activists of colour disidentify with mainstream ASOs by naming the exclusions – and deadly effects – engendered by white normalization and by adopting “for us, by us” approaches to sexual health that symbolically and literally made specific spaces for people of colour. Central to these acts of disidentification, I argue, are geographical discourses and practices, which include place-making tactics that mark certain spaces as “ethno-specific” and the identification and targeting of particular sites (e.g., event-spaces, clubs, neighbourhoods) for sexual health outreach to communities of colour. This dissertation is based on case studies of three ethno-specific ASOs in Toronto: the Black Coalition for AIDS Prevention, the Asian Community AIDS Services, and the Alliance for South Asian AIDS Prevention. Interviews with current and former workers (board members, volunteers and paid staff) form the main archive – along with supplementary archival and media analysis and participant observations – for the analysis that follows. A consideration of the geographies of e-ASOs’ work highlights the political salience of race for sexual and health politics, and provides a forum for bringing geographies of sexualities into conversation with queer of colour analysis. It thus contributes to the theoretical and political project of anti-racist geographies of sexualities not only by naming the exclusions that people of colour face in sexual political spaces, but also by focusing on their tactics of survival, resilience and resistance.

Keywords: AIDS
social services
race
geography
queer
sexual health
Advisor: Leslie, Deborah
Farish, Matthew