VictorJuiz/thesis huggingface dataset:
Characterization of Altered MicroRNA Expression in Cervical Cancer

Cervical cancer is the third most common cancer among women worldwide, and the fourth leading cause of cancer mortality. Despite significant declines in the incidence and mortality rates of cervical cancer in Canada, it remains the 4th most common cancer in women aged 20-29 years. In order to gain novel insights into cervical cancer tumourigenesis and clinical outcome, we investigated and characterized the alterations in microRNA (miRNA) expression in this disease. Firstly, we performed global miRNA expression profiling of cervical cancer cell lines (n=3), and patient specimens (n=79). From this analysis, we identified miR-196b to be significantly down-regulated in cervical cancer, and characterized its role in regulating the HOXB7~VEGF axis. The global miRNA expression data also led to the development of a candidate 9-miRNA signature that was prognostic for disease-free survival in patients with cervical cancer, although we were unable to validate this signature in an independent cohort. This report describes important considerations concerning the development and validation of microRNA signatures for cervical cancer. Our investigations also led us to a comparison of three methods for measuring miRNA abundance: the TaqMan Low Density Array, the NanoString nCounter assay, and single-well quantitative real-time PCR. Our findings demonstrated limited concordance between the TLDA and NanoString platforms, although each platform correlated well with PCR, which is considered the gold standard for nucleic acid quantification. Furthermore, we examined biases created by amplification protocols for microarray studies. Our analysis demonstrated that performing a correction using the LTR-method (linear transformation of replicates) could help mitigate, but not completely eliminate such biases. Overall, this report presents insights into the role of miRNAs in cervical cancer, as well as an evaluation of technical considerations concerning miRNA and mRNA expression profiling studies.

Keywords: microRNA
miR-196b
HOXB7
VEGF
cervical cancer
miRNA
TLDA
NanoString
Advisor: Liu, Fei-Fei
Investigation into the Role of Antioxidants in Tumorigenesis

The role of antioxidants in cancer has been controversial for a long time. Although the public’s belief is that antioxidants prevent and/or inhibit cancer, there is increasing evidence to suggest the opposite: that cancer cells require antioxidants to survive. We wanted to interrogate the role of antioxidants in cancer by investigating both upstream regulators and downstream effectors of antioxidant signaling. We have identified protein tyrosine phosphatase non-receptor type 12 (PTPN12) as a novel regulator of antioxidant signaling in cancer. PTPN12 reduces reactive oxygen species (ROS) levels by promoting activity of the forkhead box O (FOXO) family of antioxidant transcription factors. We have also elucidated the impact of glutathione (GSH), the most abundant antioxidant in the cell, on tumorigenesis. We have found that GSH is required for cancer initiation, yet dispensable once transformation has occurred due to compensation provided by the thioredoxin (TXN) antioxidant pathway. Together, these studies expand our knowledge of the role of antioxidants in cancer and provide numerous avenues of research for the future.

Keywords: antioxidant
cancer
Advisor: Mak, Tak W.
Molecular Mechanisms of Hematopoietic Stem Cell Development: The Role of Retinoic Acid Signaling

Molecular Mechanisms of Hematopoietic Stem Cell Development- The Role of Retinoic Acid Signaling Bhaskar Chanda For the Doctor of Philosophy Medical Biophysics University of Toronto 2013 Abstract During mouse embryonic development, the formation of blood or hematopoiesis occurs in multiple phases. The first phase or primitive hematopoiesis generates a restricted subset of blood cell lineages but is devoid of lymphoid and hematopoietic stem cell (HSC) potential. The next phase of hematopoiesis, also known as definitive hematopoiesis, is characterized by its ability to generate multilineage hematopoietic progenitors and HSCs from a specialized population of endothelial cells known as hemogenic endothelium (HE). Such endothelial to hematopoietic transitions (EHT) have been recently observed at a clonal level, however, molecular mechanisms that underlie EHT leading to the specification of HSCs have remained poorly understood. Here we show that retinoic acid (RA) signaling plays a pivotal role in embryonic hematopoiesis and HSC development. RA signaling inhibits primitive hematopoiesis, and promotes definitive hematopoiesis. This inductive effect of RA signaling extends to the specification of HSCs. Activation of the RA signaling pathway ex vivo in AGM-derived HE dramatically enhanced the repopulating potential, whereas its conditional inhibition in vivo abrogated HSC development. These repressive and inductive effects of RA signaling were mediated primarily via retinoic acid receptor (RAR)- &alpha;. We further analyzed the mechanistic basis of RA signaling with a combined use of cellular, molecular and biochemical assays, and show that &beta;-catenin dependent Wnt signaling is the downstream mediator of RA signaling. Collectively, this thesis provides new insight into molecular mechanisms that control embryonic hematopoiesis and identify the RA pathway as a key regulator of definitive hematopoiesis and HSC specification.

Keywords: Hematopoietic Stem Cells
Retinoic Acid Signaling
Wnt Signaling
Raldh2
Advisor: Gordon, Keller
Mechanisms of Memory Deficits in Mouse Models of Alzheimer's Disease

Alzheimer’s disease (AD), a neurodegenerative disorder initially characterized by mild memory impairments, progresses to global cognitive deficits and eventually death. AD pathological hallmarks are plaques and tangles. Acute and chronic effects of familial Alzheimer’s disease (FAD) genes were examined in WT and transgenic mice respectively. We used viral vectors to acutely express FAD genes encoding the Swedish, Indiana, and Swedish and Indiana double mutation, of amyloid precursor protein (APP) in the hippocampal CA1 region (which exhibits early AD pathology) in mice. Acute expression of FAD genes produced deficits in the formation but not retreival of spatial memory. We next examined spine density as changes are thought to affect synaptic plasticity. Acute expression of FAD genes did not affect the structure (dendritic length, intersections and nodes), but decreased spine density in infected CA1 neurons. Amyloid beta (Aβ) binds to excitatory synapses, particularly to GluA2-AMPA receptors (AMPAR) leading to endocytosis. Therefore,, acute CA1 expression of FAD genes produced spatial memory formation deficits mediated by impairments in dendritic spine plasticity and transmission via AMPAR endocytosis. Additionally, infusing GluA2-3Y, a peptide that prevents Aβ induced AMPAR endocytosis in acute and chronic (TgCRND8) AD mouse models expressing double mutated APP genes, was similarly able to rescue the spatial memory and spine density deficits. Since the transcription factor CREB is critical for normal memory formation across species, we investigated its role in TgCRND8 mice. We observed additional deficits in the dorsal hippocampus of TgCRND8 mice, including 1) biochemistry (CREB activation), 2) neuronal structure, and 3) neuronal network activity. Moreover, locally and acutely increasing CREB function in the CA1 region of TgCRND8 mice was sufficient to restore function in each domain independent of plaque load or aggregated Aβ levels. Together, these studies indicate that targeting GluA2 or CREB may be useful therapeutic strategies in treating AD.

Keywords: Alzheimer's disease
Memory
Advisor: Josselyn, Sheena
Moleculary Systematics and Biogeography of the Galaxidae

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

Keywords: Galaxiidae
Systematics
Biogeography
Molecular clock
Vicariance
Dispersal
Advisor: Baker, Allan
Identification and Characterization of Genes in the Lafora Disease Pathway

Lafora disease (LD) is an adolescent-onset autosomal recessive progressive myoclonus epilepsy. The main clinical symptoms of the disease are worsening seizures, neurodegeneration and usually death within ten years. No therapeutics or interventions exist for this devastating disease. Mutations in two genes, EPM2A (laforin) and EPM2B (malin) are causative of more than 90 percent of LD. The pathognomonic sign of LD is the presence of abnormal glycogen which precipitates and accumulates into starch-like masses called Lafora bodies (LB). There are two main hypotheses of LB formation. Glycogen is synthesized through the combined activities of glycogen synthase (GS) and branching enzyme (BE). One hypothesis is that LB form due to an overactivation of GS, causing a misbalance between synthesis and branching. Here, malin and laforin regulate levels of GS and other protein(s) involved in glycogen synthesis and when missing, result in their overaccumulation and thus overactivation of synthesis in relation to branching. The second hypothesis is based on evidence of increased phosphorylation of glycogen in LB. In this hypothesis, glycogen becomes abnormal because of the hyperphosphorylation, causing it to precipitate. Laforin is a glycogen phosphatase, and removes phosphate from glycogen. When missing, as in LD, glycogen becomes hyperphosphorylated and forms LB. A role for malin is less clear in this hypothesis. In this thesis, I identify and characterize a third gene, PRDM8, causing an early onset form of LD in a large consanguineous family. I show that it both interacts with laforin and malin and results in their relocation to the nucleus. I also characterize a laforin-interacting protein, Epm2aip1, finding an important role for this previously uncharacterized protein in glycogen metabolism. Epm2aip1-/- mice exhibit hepatic insulin resistance, decreased hepatic glycogen synthesis, increased liver fat, and resistance against obesity in adulthood. Epm2aip1 associates with glycogen synthase (GS), and its absence impairs the allosteric activation of GS by glucose-6-phosphate. Finally, I find that genetically removing PTG, an activator of GS, from mice with Lafora disease results in near-complete disappearance of LB, and resolution of the neurodegeneration and myoclonic epilepsy. This work has revealed a gateway to the treatment of this devastating and fatal disease.

Keywords: Lafora disease
Glycogen
Epilepsy
Advisor: Scherer, Stephen
Minassian, Berge
Making Imperial Futures: Concepts of Empire in the Anglo-Spanish Sphere, 1762-71

My dissertation, Making Imperial Futures: Concepts of Empire in the Anglo-Spanish Sphere, 1763-71, engages the grand narrative of exploration at the point at which that very concept was reaching the point of exhaustion and argues that the rough completion of European cartographical knowledge of the world had a profound impact on the evolution of the imperial experience. I examine the evolving concept of empire within a context of cross-imperial knowledge and rivalry, Enlightenment ideals and the changing ways in which Europeans related to the concept of a progressive future. Furthermore, I challenge the historiographically dominant notion that the British and Spanish experiences of empire are best categorized and isolated as distinct historical subjects. The first section shows that British successes in the Seven Years’ War energised the British imperial imagination, generating a broad-based debate on how best to exploit the situation and opening up the opportunity to put more than one approach into action when Britain and Spain went to war in 1762. But the Peace of Paris brought discord, and a perceived need for the government to discipline the imperial imagination and to establish an approved pathway for the future of empire in the Atlantic world. The second part looks at how the Spanish government applied state power in direct pursuit of the pan-Atlantic imperial project. In particular, it re-examines the expulsion of the Jesuits from the Spanish empire in 1767 and makes the argument that the expulsion was a response to the perceived Jesuit threat to pan-Atlantic imperial norms. My third section suggests that the experimental burst of modern, state-centric imperialism that began in the wake of the Seven Years’ War suffered a reversal during the Falklands Crisis of 1770-1, during the general historical moment in which Europeans finished constructing their shared cartographical conception of the world. Although the growth of state power and impetus was temporarily reversed to some extent in the 1770s, this period helps prefigure the more extensive shift from empires primarily based on exploration and tenuous consolidation to empires that depended on dense, active exploitation to lend validity to their ontological claims.

Keywords: Imperialism
Spain
Great Britain
Latin America
18th century
Exploration
Advisor: Mills, Kenneth
Mori, Jennifer
Comrades and Citizens: Great War Veterans in Toronto, 1915-1919

This is a history of returned soldiers of the Great War in Toronto covering the period from when they began returning home in 1915 through to the end of demobilization in late 1919. Based largely in newspaper research, the focus is the discourse of returned men, as they were frequently called, and the role they played in Toronto and in Canada more broadly. The dissertation examines veterans' attitudes, the opinions they expressed, the goals they collectively pursued, the actions they took and their significance as actors and symbols in the public sphere. The study shows that during and immediately after the war returned soldiers played a prominent role in public debate over conscription and wartime politics, the status of non-British immigrants in Canada, the Red Scare and re-establishment policy. In exploring these topics the study elaborates on the identities veterans collectively adopted and constructed for themselves as comrades and citizens. Class, definitions of masculinity, British-Canadian ethno-nationality and experience as soldiers all affected formulations of veteran citizenship and comradeship. Returned soldiers' representations of their citizenship resonated powerfully in Canadian society. The experiences and symbolism of returned soldiers generated interest in civilian society that granted them easy access to the public sphere and encouraged pro-war politicians to use returnees to promote the war effort. Veterans took advantage of their access to the press and public stages to broadcast their own views and claim that their service gave them special rights to intervene in public affairs. Comradeship was vitally important to returned soldiers and set them apart from civilians, but it was neither a simple nor stable category. Veterans' debates and the history of veterans' associations testify to the fact that collective service in the war did not erase civilian identities and create a stable platform for united collective activism after the war. Furthermore, comradeship sometimes existed uneasily with the rights and responsibilities of citizenship. Parliamentary methods were fundamental to veterans' activism, but their politics were also performative, often pursued and proclaimed at street level, and a minority of veterans threatened and engaged in violence they claimed was justified.

Keywords: First World War, 1914-1918
Veterans
Canada
Toronto
history
citizenship
British
masculinity
home front
public sphere
reconstruction
re-establishment
Advisor: Radforth, Ian
Beyond Free and Equal: Subalternity and the Limits of Liberal-democracy

This project seeks to critically examine the hegemony and imperialism of liberal-democratic modernity, and the possibilities for forms of politics that are rooted in subaltern difference. I argue that one of the great challenges in resisting the hegemony of liberal-democracy is that it offers a broad family of both conservative and progressive/critical languages that can be adopted and used by elite and subordinate groups alike. The availability of critical or dissenting languages that are internal to liberal-democracy often entices subordinate groups to make use of them, but this only furthers the subalternization of other distinct normative or practical traditions. I aim to articulate an alternative form of politics that remains rooted in subaltern difference, and is not simply based on an internal or immanent critique of liberal-democracy. This is a type of ethico-politics that seeks to actualize subaltern goods and traditions in its very practice or way of life, and to build its forms of resistance and transformation upon this practice. This dissertation (a) explores some of the key features of this kind of subaltern ethico-politics; (b) examines the ways in which contemporary modes of postcolonial and political thought, especially those with critical or emancipatory intent, often serve to contain and/or efface this form of subaltern praxis; and (c) addresses some of the broader questions and challenges this praxis poses for resistance to imperialism and coalition-building among diverse social movements today.

Keywords: Imperialism
Postcolonialism
Subaltern
Political Theory
Liberalism
Democracy
Advisor: Tully, James
Carens, Joseph
What Violently Elects Us: Filiation, Ethics, and War in the Contemporary British Novel

This dissertation examines the trope of filiation in novels by three contemporary British writers: John Banville, Ian McEwan, and Kazuo Ishiguro. The trope of filiation and the related theme of inheritance has long been central to the concerns of the British novel, but it took on a new significance in the twentieth century, as the novel responded both thematically and formally to the aftermath of the two world wars. This study demonstrates the ways in which Banville, McEwan, and Ishiguro each situate their work in relation to this legacy, by means of an analogy between the inheritance structures figured within their novels and the inheritance performed by their engagement with the genre itself. This study relies on an instructive analogy to similar treatments of the larger problem of cultural filiation by the theorists Emmanuel Levinas and Jacques Derrida. Levinas exposes in his work the ethical and political problems of modernist temporality by critiquing modernity’s rejection of filiation, a rejection modeled also in the lost children, and barren and celibate men and women of modernist novels. Derrida meanwhile provides a way forward with his representation and performance of inheritance as a critical and transformative act, which is characterised on one hand by an ethical injunction, and on the other, by a filtering or a differentiation which changes the tradition even as it reaffirms it.

Keywords: Ethics
Filiation
McEwan, Ian
Ishiguro, Kazuo
Banville, John
Contemporary British Fiction
Advisor: Hutcheon, Linda
Matus, Jill
Biochemical Characterization of Escherichia coli PgaB, an Enzyme Essential for Biofilm Formation

The formation of bacterial biofilms requires an extracellular matrix to facilitate adherence of bacteria to the surface they colonize. Carbohydrate polymers, known as exopolysaccharides, form a key component of most biofilm matrices. A wide variety of medically-important biofilm forming bacterial strains, including S. epidermidis, S. aureus, E. coli, B. pertussis, and Y. pestis generate the same β-1,6-N-acetyl glucosamine (PNAG) homopolymer as a key biofilm matrix exopolysaccharide. In E. coli, as well as in the other bacterial strains, the PNAG undergoes partial enzymatic de-N-acetylation, which is essential for surface attachment and subsequent biofilm formation. In vivo studies implied that the enzyme responsible for carrying out de-N-acetylation in E. coli is PgaB, an enzyme with sequence homologues in many Gram negative species capable of forming biofilms. In this work, the first biochemical characterization of PgaB is presented. We confirmed the activity of PgaB on β-1,6-GlcNAc oligosaccharides. The activity of PgaB is specific for the β-1,6 linkage and no de-N-acetylation of β-1,4-GlcNAc oligosaccharides was detected. Enzyme activity is dependent on the degree of substrate polymerization, as the second order rate constant for pentasaccharide substrate was determined to be four times higher than that of the tetrasaccharide substrate. Oligosaccharide sequencing studies indicate that there may be a pattern in the de-N-acetylation of substrates by PgaB. The central residue is modified in mono-de-N-acetylated pentasaccharide substrate, while di-de-N-acetylated hexasaccharide substrate shows modification mainly at the third and fifth residues from the non-reducing terminus of the substrate. Activity studies revealed that PgaB is activated by Ni2+ as well as by Fe2+, which is uncommon for deacetylase enzymes. Metal coordination to active site residues His184 and His189 was confirmed by mutagenesis studies, which also indicated that the metal likely plays a catalytic role. The results of these metal dependence studies support the observed binding of nickel and iron to the active site in PgaB crystal structures. The characterization studies presented in this thesis allow us to gain a better understanding of the de-N-acetylation aspect of the PNAG biosynthetic process and will serve as a basis for enzyme inhibitor design.

Keywords: PNAG
deacetylase
biofilm
polysaccharide intercellular adhesin
Advisor: Nitz, Mark