VictorJuiz/thesis huggingface dataset:
The Orphan Nuclear Receptor EAR-2 (NR2F6) is a Leukemia Oncogene and Novel Regulator of Hematopoietic Stem Cell Homeostasis and Differentiation

The orphan nuclear receptor EAR-2 (NR2F6) is a gene that I previously found to be expressed at a higher level in clonogenic leukemia single cells than in leukemia cells that can not divide. For this thesis I undertook to perform the first investigations of the roles EAR-2 may play in normal haematopoiesis and in the pathogenesis of acute myelogenous leukaemia. Here, I show that EAR-2 is overexpressed in the bone marrow of patients with MDS, AML and CMML compared to healthy controls and that EAR-2 is a gatekeeper to hematopoietic differentiation. Over-expression of EAR-2 prevents the differentiation of cell lines, while knock down induces their spontaneous differentiation. In vitro, primary bone marrow cells that over-express EAR-2 do not differentiate into granulocytes in suspension culture, but have greatly extended replating capacity in colony assays. In vivo, overexpression of EAR-2 in a chimeric mouse model leads to a condition that resembles myelodysplastic syndrome characterised by hypercellular bone marrow, an increase in blasts, abnormal localization of immature progenitors, morphological dysplasia of the erythroid lineage and a competitive advantage over wild-type cells, that eventually leads to AML in a subset of the mice. Furthermore, animals that are transplanted with grafts of sorted bone marrow develop a rapidly fatal leukemia that is characterized by pancytopenia, enlargement of the spleen, infiltration of blasts into the spleen, liver and peripheral blood. Interestingly, development of leukemia is preceded by expansion of the stem cell compartment. Overexpression of EAR-2 increases the maintenance of KSL primitive bone marrow cells in ex vivo suspension culture, while knockdown of EAR-2 induces rapid differentiation of KSL cells into granulocytes. These data establish that EAR-2 is a novel oncogene that regulates hematopoietic cell differentiation. Furthermore, I show that EAR-2 is also a novel negative regulator of T-cell lymphopoiesis, and demonstrate that down-regulation of EAR-2 is important for the survival, proliferation and differentiation of T-cell progenitors. Overall, this work establishes that expression of EAR-2 is an important determinant of cell fate decisions in the hematopoietic system.

Keywords: leukemia
stem cells
cancer
nuclear receptor
NR2F6
Advisor: Wells, Richard
Changes in the Neural Bases of Emotion Regulation Associated with Clinical Improvement in Children with Anxiety Disorders

Background: The present study was designed to examine prefrontal cortical processes in anxious children that mediate cognitive regulation in response to emotion-eliciting stimuli, and the changes that occur after anxious children participate in a cognitive behavioral therapy treatment program. Methods: Electroencephalographic activity was recorded from clinically anxious children and typically developing children at pre- and post-treatment sessions. Event-related potential components were recorded while children performed a go/no-go task using facial stimuli depicting angry, calm, and happy expressions. Results: At pre-treatment, anxious children had significantly greater posterior P1 and frontal N2 amplitudes than typically developing children, components associated with attention/arousal and cognitive control, respectively. For the anxious group only, there were no differences in neural activation between face (emotion) types or trial (Go vs. No-go) types. Anxious children who did not improve with treatment showed increased cortical activation within the time window of the P1 at pre-treatment relative to comparison and improver children. From pre- to post-treatment, only anxious children who improved with treatment showed increased cortical activation within the time window of the N2. Conclusions: At pre-treatment, anxious children appeared to show increased cortical activation regardless of the emotional content of the stimuli. Anxious children also showed greater medial-frontal activity regardless of task demands and response accuracy. These findings suggest indiscriminate cortical processes that may underlie the hypervigilant regulatory style seen in clinically anxious individuals. Neural activation patterns following treatment suggest that heightened perceptual vigilance, as represented by increased P1 amplitudes for non-improvers, may have prevented these anxious children from learning the treatment strategies, leading to poorer outcomes. Increased cognitive control, as represented by increased N2 amplitudes for improvers, may have enabled these anxious children to implement treatment strategies more effectively, leading to improved treatment outcomes. Hence, P1 activation may serve as a predictor of treatment outcome, while N2 activation may serve as an indicator of treatment-related outcome. These findings point to the cortical processes that maintain maladaptive functioning versus the cortical processes that underlie successful intervention in clinically anxious children.

Keywords: Childhood Anxiety
EEG/ERP
Facial Expressions
Cognitive Behaviour Therapy
Advisor: Lewis, Marc D.
Patterns and Processes in Forest Insect Population Dynamics

This dissertation is concerned with effects dispersal and forest structure on forest insect population dynamics, and with identifying generating processes by comparing observed patterns to model predictions. In chapter 2, we investigated effects of changing forest landscape patterns on integro-difference models of host-parasitoid population dynamics. We demonstrated that removing habitat can increase herbivore density when herbivores don't disperse far, and parasitoids disperse further, due to differences in dispersal success between trophic levels. This is a novel potential explanation for why forest fragmentation increases the duration of forest tent caterpillar outbreaks. To better understand spatial model behaviour, we proposed a new local variation of the dispersal success approximation. The approximation successfully predicts effects of habitat loss and fragmentation on realistically complex landscapes, except when outbreak cycle amplitude is very large. Local dispersal success is useful in part because parameters can be estimated from widely available habitat data. In chapter 3, we investigated how well a discretized integro-difference model of mountain pine beetle population dynamics predicted the occurrence of new infestations in British Columbia. We found that a model with a large dispersal kernel, and high emigration from new, low severity infestations yielded the best predictions. However, we do not believe this to be convincing evidence that many beetles disperse from new, low severity infestations. Rather, we argued that differences in habitat quality, detection errors, and Moran effects can all confound dispersal patterns, making it difficult to infer dispersal parameters from observed infestation patterns. Nonetheless, predicting infestation risk is useful, and large kernels improve predictions. In chapter 4, we used generalized linear mixed models to characterize spatial and temporal variation in the propensity of jack pine trees to produce pollen cones, and account for confounding effects on the relationship between pollen cone production and previous defoliation by jack pine budworm. We found effects of stand age, and synchronous variation in pollen cone production among years. Accounting for background patterns in pollen cone production clarified that pollen cone production declines in with previous defoliation, as expected.

Keywords: host-parasitoid population dynamics
spatial-temporal model
forest insect outbreak
habitat fragmentation
dispersal
Dendroctonus ponderosae
landscape ecology
Malacosoma disstria
Choristoneura pinus
Pinus banksiana
integro-difference model
Advisor: Fortin, Marie-Josee
Modulation of Cell Motility by EGF-like Repeats in Dictyostelium discoideum

Dictyostelium discoideum is a social amoebozoan that is used a model system for studying a variety of cell and developmental processes, especially cell motility and chemotaxis. Genome analyses suggest that this model organism possesses a higher percentage of Epidermal Growth Factor (EGF)-like (EGFL) repeats than any other sequenced eukaryote, including humans. EGFL repeats share strong sequence similarity with EGF. In mammals, EGF binds to an EGF receptor (EGFR) to initiate intracellular signalling that regulates a diversity of cellular processes including cell motility and chemotaxis. Some EGFL repeats, like EGF, have also been shown to increase the rate of cell motility by binding to the EGFR and activating EGFR-dependent signalling. Despite their abundance in Dictyostelium, a function for EGFL repeats in this model eukaryote had not previously been studied. This thesis presents a collection of studies that investigated the function of a specific EGFL repeat from the extracellular, cysteine-rich, calmodulin (CaM)-binding protein CyrA. A synthetic peptide (DdEGFL1), equivalent in sequence to the first 18 amino acids of the first EGFL repeat (EGFL1) of CyrA, was shown to increase random cell motility and cAMP-mediated chemotaxis via a novel signalling pathway that did not require either of the two cAMP receptors that are active during early development of Dictyostelium. Several intracellular signalling components were identified and then incorporated into a model detailing the signal transduction regulating EGFL repeat-enhanced cell movement in Dictyostelium. Finally the expression, secretion, and localization of CyrA are presented to couple the findings from studies on DdEGFL1 function with those for the full-length protein. In mammals, a protein that localizes to the extracellular matrix (ECM) and modulates cellular processes by binding to a cell surface receptor and initiating intracellular signalling is termed a ‘matricellular’ protein. The research presented in this thesis suggests that CyrA is the first matricellular protein identified in Dictyostelium.

Keywords: Dictyostelium
Cell motility
Chemotaxis
EGF-like
Matricellular
Extracellular matrix
Peptide
Protein
Advisor: O'Day, Danton H.
Vocabulary Growth in Armenian-English Bilingual Kindergarteners

Vocabulary plays an important role in language and literacy development. However, little is known about vocabulary development in young children who need to learn an official or majority language, in addition to a minority language spoken at home. This dissertation concerned English (majority) and Armenian (minority) vocabulary development in young bilingual children. First, a parallel bilingual vocabulary test was developed, which included picture identification and picture naming tasks to assess listening (receptive) and speaking (expressive) vocabularies in the two languages. Then, the vocabulary test was used to compare bilingual vocabulary growth and examine individual differences in vocabulary performance. Twenty Junior and twenty-two Senior Kindergarten bilingual children were tested twice on the vocabulary tasks over a six-month interval. Information was also obtained on environmental (parental education, Armenian/English language exposure) and child characteristics (nonverbal cognitive abilities, phonological short-term memory) related to vocabulary development, as potential predictors of individual vocabulary performances. Children showed growth over time in all four vocabulary tasks. However, less growth was observed in Armenian expressive than in Armenian receptive, English receptive, and English expressive vocabulary. Children had high exposure to Armenian at home; however, consistent with their exposure to English through peers, most were proficient in English vocabulary. The findings suggest a preference to use English and the influential role of English language exposure on higher proficiency in English vocabulary. These findings imply a potential risk for Armenian language maintenance, which warrants future studies. English language exposure and phonological short-term memory were both unique predictors of English vocabulary, whereas Armenian language exposure was the only unique predictor of Armenian vocabulary. Therefore, providing additional minority language exposure might be the best way to enhance and maintain minority vocabulary and language. This dissertation had three novel contributions. It provided a sound and replicable method to develop a bilingual vocabulary test in other minority languages. The vocabulary test made it possible to compare performance across minority and majority languages directly and confidently for the first time. Finally, the relative values of four different characteristics were examined in predicting individual differences in minority and majority vocabulary performances.

Keywords: bilingual
vocabulary
Advisor: Johnson, Carla J.
The Politics of Microfinance: A Comparative Study of Jamaica, Guyana and Haiti

The microfinance revolution of the 1980s acclaimed micro-credit as a tool that would improve the lives of economically active people trapped in poverty. The 2006 Nobel prize awarded to Mohammed Yunus and Grameen Bank confirmed for the industry’s advocates that microfinance was a panacea, and billions of dollars have been channeled to financial services for the poor. However, a series of high-profile scandals in 2010 shook development agencies’ faith in micro lending, and support has waned in light of evidence that microfinance alone cannot change structural inequalities and end poverty. I show that politics operate throughout the industry, reproducing inequalities within the process of micro lending. In my political ethnographic study of 460 people in three countries, I find that race and class politics is entrenched in all three countries, yet there are different outcomes related to attitudes of microfinance managers. In Jamaica and Guyana, micro lenders demonstrate that historically rooted racial and class biases go beyond gender to determine the allocation of micro loan resources. Ingrained biases interfere with the allocation of loans to the urban poor because discriminatory practices reinforce pre-existing social divisions. The Haiti case is hopeful: lenders, particularly the caisses populaires (credit unions), are made up of socially conscious people who recognize the country’s exclusionary politics. Managers and staff have class origins similar to the clients they serve and view micro loans as a tool to contest class and race-based oppressions. Haiti’s case suggests that collective systems such as those found in the caisses populaires and informal banks are effective because they relate to people’s history; and managers influenced by the masses, organize financial programs that are responsive to their clients and remain free from elite capture. This bottom-up approach in microfinance determines a greater level of social transformation for the urban poor.

Keywords: politics
microfinance
gender
cooperatives
race
Caribbean
informal banks
poverty
clientelism
inequality
Advisor: Teichman, Judith A.
Identifying Mechanisms by which Escherichia coli O157:H7 Subverts Interferon-gamma Mediated Signal Transducer and Activator of Transcription-1 Activation

Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is a foodborne pathogen that causes significant morbidity and mortality in developing and industrialized nations. EHEC infection of host epithelial cells is capable of inhibiting the interferon gamma (IFNγ) pro-inflammatory pathway through the inhibition of Stat-1 phosphorylation, which is important for host defense against microbial pathogens. The aim of this thesis was to determine the bacterial factors involved in the inhibition of Stat-1 tyrosine phosphorylation. Human HEp-2 and Caco-2 epithelial cells were challenged directly with either EHEC or bacterial culture supernatants, stimulated with IFNγ, and then protein extracts were analyzed by immunoblotting. The data showed that IFNγ-mediated Stat-1 tyrosine phosphorylation was inhibited by EHEC secreted proteins. Using 2D-Difference Gel Electrophoresis, EHEC Shiga toxins were identified as candidate inhibitory factors. EHEC Shiga toxin mutants were then generated, complemented in trans, and mutant culture supernatant was supplemented with purified Stx to confirm their ability to subvert IFNγ-mediated cell activation. I conclude that E. coli-derived Shiga toxins represent a novel mechanism by which EHEC evades the host immune system.

Keywords: escherichia coli
stat1
gamma interferon
subversion
Advisor: Sherman, Philip M.
Modulators of Hedgehog Signaling in Neoplasia

The Hedgehog (Hh) signaling pathway plays a critical role in modulating various developmental processes that requires fine tuning of the Hh signal, such that dysregulation can lead to cellular events involved in cancer. To elucidate the factors responsible for aberrant Hh activation and subsequent tumorigenesis, I investigated three distinct modulators of Hh signaling: (1) p53 tumour suppressor (2) primary cilia (3) PTHLH. During chondrocyte development, abnormal Hh signalling can result in benign cartilage tumours, called Enchondroma. As precursor lesions, enchondroma may progress to malignant neoplasia, collectively known as chondrosarcoma. Although the molecular events involved in this progression are poorly understood, inactivation of the p53 tumour suppressor has been identified in approximately one-third of chondrosarcoma. Using an enchondroma mouse model, I showed that p53 deficiency can cause chondrosarcoma to develop. The combined inhibitory effects of Hh and p53 pathways on the pro-apoptotic factor, IGFBP-3, suppressed apoptosis and was demonstrated to play a critical role in the progression to chondrosarcoma. The primary cilium is an organelle that serves as a signaling centre for the Hh pathway to allow for greater control of the signal output. Loss of primary cilia results in abnormal Hh signaling that is associated with cancer and various developmental defects. I observed a depletion of primary cilia in both human Chondrosarcoma and Enchondroma tumours compared to normal cartilage. Analysis of cilia-deficient mice revealed that defective ciliogenesis alone could lead to the formation of benign cartilage tumours. Furthermore, loss of primary cilia potentiated the effect of Hh signaling activation, revealing a novel role in cartilage tumorigenesis. Parathyroid-like hormone (PTHLH) is an essential inhibitor of the Hh pathway during chondrocyte development, however its function as a regulator of Hh in other tissue types are largely unknown. Through activation of PKA, PTHLH suppresses the activation of Gli transcription factors; downstream effectors of the Hh pathway. Using irradiated Ptch+/- mice that exhibit a high incidence of skin and brain tumours, I demonstrated that treatment with PTHLH agonist, PTH (1-34), results in inhibition of the Hh pathway, increased survival and a reduction in tumour incidence and size. Thus, PTH (1-34) may have therapeutic potential for Hhrelated cancers, especially given its known clinical safety in treating osteoporosis.

Keywords: Hedgehog
Chondrosarcoma
Advisor: Alman, Benjamin
Targeted Drug Delivery to Breast Cancer using Polymeric Nanoparticle Micelles

Broad distribution and activity limit the utility of anti-cancer compounds by causing unacceptable systemic toxicity and narrow therapeutic indices. To improve tumour accumulation, drug-loaded macromolecular assemblies have been designed to replace conventional surfactant-based formulations. Their nanoscale size enhances tumour accumulation via hyperpermeable vasculature and reduced lymphatic drainage. Incorporating targeting ligands introduces cell specificity through receptor-specific binding and uptake, enabling drugs to reach intracellular targets. In this work, the targeting properties of polymer nanoparticle micelles of poly(2-methyl-2-carboxytrimethylene carbonate-co-D,L-lactide)-graft-poly(ethylene glycol)-furan (poly(TMCC-co-LA)-g-PEG) were verified using in vitro and in vivo models of breast cancer. To select a relevant mouse model, the vascular and lymphovascular properties of two tumour xenograft models were compared. Greater accumulation of a model nanocarrier was observed in orthotopic mammary fat pad (MFP) tumours than size matched ectopic subcutaneous tumours, suggesting that the organ environment influenced the underlying pathophysiology. Immunostaining revealed greater vascular thickness, density and size, and thinner basement membranes in MFP tumours, likely contributing to greater blood perfusion and vascular permeability. Based on these observations, MFP tumour-bearing mice were used to characterize the pharmacokinetics and biodistribution of a taxol drug, docetaxel, encapsulated in poly(TMCC-co-LA)-g-PEG nanoparticles. The nanoparticle formulation demonstrated longer docetaxel circulation in plasma compared to the conventional surfactant-based formulation. As a result, greater docetaxel retention was uniquely measured in tumour tissue, extending exposure of tumour cells to the active compound and suggesting potential for increased anti-cancer efficacy. Furthermore, active targeting of antibody-modified nanoparticles to live cells was shown to be selective and receptor-specific. Binding isotherms were used to quantify the impact of antibody density on binding strength. The equilibrium binding constant increased linearly with the average number of antibodies per particle, which is consistent with a single antibody-antigen interaction per particle. This mechanistic understanding enables binding behaviour to be adjusted in a predictive manner and guides rational nanoparticle design. These studies validate poly(TMCC-co-LA)-g-PEG nanoparticles as a platform for targeted delivery to cancer on both a tissue and cellular level, forming a compelling justification for further pre-clinical evaluation of this system for safety and efficacy in vivo.

Keywords: Drug delivery
Cancer
Chemotherapy
Anti-cancer therapy
Polymeric nanoparticles
Nanoparticle micelles
Pharmacokinetics
Biodistribution
Live cell binding
Tumour xenograft models
Tumour pathophysiology
Orthotopic tumour model
Nanoparticle targeting
Passive targeting
Active targeting
Formulations
Antibody targeting
Breast cancer
Advisor: Shoichet, Molly