VictorJuiz/thesis huggingface dataset:
Evolution and functional specializations in nocturnal environments: insights from visual pigments in Chiroptera

Sensory systems act as a direct interface between organisms and their environment, constituting an ideal model to investigate how diverse evolutionary pressures shaped sensory adaptation. At the molecular level, vision is initiated through activation of visual pigments, light-sensitive complexes expressed in photoreceptor cells in the retina that have been shown to evolve in response to changes in ecology and light environment. In this thesis, I employ molecular evolutionary analyses and experimental characterization of visual pigments to study the molecular basis of visual system specializations in bats, one of the most striking and ecologically diverse mammalian radiations. In Chapter 2, I review recent work on the ecological and evolutionary pressures mediating sensory adaptation in vertebrates, including remarkable specializations of bats. In Chapter 3, I use comparative sequence analysis to test whether ecological factors known to influence bat visual ecology mediate shifts in evolutionary pressure in cone opsin genes, Lws and Sws1. I find significant evidence that long-term shifts in selection constraint in cone opsins occur in response to ecological factors underlying reliance on visual information and exposure to varying light environments. In Chapters 4 and 5, I focus my study on the evolution of the dim-light visual pigment rhodopsin (Rh1) in response to echolocation, a remarkable sensory adaptation of bats. In Chapter 4, I experimentally characterize rhodopsin of several bat species and find that changes in kinetic properties that influence dim-light visual performance are associated with differing echolocation abilities. In Chapter 5, I reconstruct and experimentally resurrect the ancestral rhodopsin pigment of Chiroptera and Scrotifera. I find that changes in rhodopsin kinetics occurred during the evolution of bats are likely associated with the origins of echolocation. This thesis combines in vitro and in silico approaches to investigate visual pigment evolution in Chiroptera. More broadly, this thesis also discusses the role of diverse ecological pressures in shaping visual gene evolution, the molecular underpinnings of visual pigment function and adaptation to light-limited environments as well as the complex interactions between sensory specializations.

Keywords: Evolution of bat vision
Evolution of opsin function
Likelihood codon-based models
Molecular evolution
Sensory systems
Visual ecology
Advisor: Chang, Belinda SW
The Biological Basis of Clinical Heterogeneity in Childhood Arthritis

Childhood arthritis, or juvenile idiopathic arthritis (JIA), encompasses a heterogeneous set of inflammatory diseases with chronic joint inflammation. To effectively treat patients, we require a disease classification that describes homogeneous patient groups. This thesis establishes foundations for a data-driven, clinically and biologically based disease classification for JIA using a systems-based approach. This approach comprises established machine learning methods such as dimensionality reduction, which summarizes numerous features as summary indicators, and cluster analysis, which groups together patients with similar characteristics. We applied this approach, using probabilistic principal component analysis and Gaussian mixture models, to heterogeneous clinical, protein expression, and gene expression data, identifying indicators in each data type that distinguished patients from each other as well as clinically and biologically homogeneous and meaningful patient groups. Patient groups derived from clinical and protein expression data predicted disease course, highlighting the importance of combining clinical phenotypes with biological parameters. We further modified and tested this approach using non-negative matrix factorization adapted into a nested framework and applied it to clinical data sets describing affected joints and entheses, identifying indicators and patient groups describing localized groupings of co-involved joints and entheses. Our findings demonstrate the importance of exploring multiple facets of disease in a data-driven manner and point at the power and utility of comprehensively defining JIA.

Keywords: disease classification
juvenile idiopathic arthritis
machine learning
Advisor: Yeung, Rae SM
Parent Concern About Children's Reading

This dissertation used mixed methods to explore the phenomenon of parent concern about children’s reading. In Study 1, an existing database was used to consider the value of parent concern as a predictor of, and screening measure for, word-level reading difficulties. Parents of grade 2 children (N = 294) responded to the question “Have you ever been concerned about this child’s ability to learn to read?” and their children completed a timed test of word-level reading skills and a test of sentence memory. A subgroup of children (n = 91) received additional reading-related tests, including tests of phonological awareness, rapid naming, language, memory, and verbal IQ. In the overall sample, 23% of parents responded affirmatively to the parent concern question. Parent concern was a significant predictor of reading skill, and, for some outcomes, added value beyond the other reading-related predictors. It identified children with word-level reading difficulties with acceptable specificity but not always with adequate sensitivity. When parents appeared inaccurate, this corresponded with variation in children’s reading-related skills, as well as their time of birth relative to the school year. Study 2 elaborated on these results by asking a new group of 70 parents the same question. Eleven of 17 concerned parents who met study criteria were interviewed and their children received a battery of reading and reading-related tests. Similar to the results of Study 1, parent concern was reliably accompanied by reading and/or reading-related difficulties. Factors that appeared to influence parent concern included feedback from others, comparisons parents made (between the child and others, their own development, and standards), and children’s emotions and behaviours. Parents doubted their concern and were uncertain about what constituted normal reading development. However, they reported many signs of reading difficulty, including poor word reading, reading fluency, comprehension, spelling, and writing, as well as difficulties with work completion, lack of interest in reading independently or reading challenging material, and negative emotions related to reading. The results from both studies are discussed and practical implications are provided. Overall, this dissertation provides support for the value of parent concern in identifying children with reading difficulties.

Keywords: early identification
literacy
parent concern
reading difficulties
school psychology
screening
Advisor: Willows, Dale M.
Religion and Refugees: The Evolution of Resettlement in the United States and Canada

This dissertation compares the evolution of refugee resettlement policy in the United States and Canada between 1945 and 1980. The contingent responses of both countries to displaced people after the Second World War evolved in the context of subsequent refugee crises during the Cold War, generating institutional configurations that became formalized in major refugee legislation passed in 1976 (Canada) and 1980 (United States). The mobilization and engagement of religious groups with the policy process was a central dynamic over time. In the United States, their interaction with Congress produced a corporatist structure of cooperation that persists to this day; nine voluntary groups implement the entirety of the United States’ annual resettlement program. In Canada, decision-making was centred in the bureaucracy, where a reluctant partnership with religious groups produced privately-funded refugee sponsorship as a complement to government-managed refugee programs.

Keywords: Canada
Cold War
Immigration Policy
Refugee Policy
Refugee Resettlement
United States
Advisor: Hansen, Randall
Age-Related Deficits and Benefits in Task Performance: The Impact of Cognitive Control

Converging evidence has demonstrated age-related reductions in the ability to selectively focus on task-relevant information, while simultaneously ignoring task-irrelevant information (i.e., cognitive control). Although reduced cognitive control in older adults is typically associated with deficits in attention and memory, recent work has shown that this cognitive pattern can be advantageous in certain contexts. This thesis investigates how reduced control in older adults is associated with an age-related pattern of benefits and deficits on memory tasks with different demands and characteristics. Studies 1 and 2 explored whether older adults show better performance than younger adults on an implicit memory task that relies on conceptual knowledge of previous irrelevant information. Studies 3 and 4 explored how age differences in cognitive control influence memory for different types of associations, and the neural correlates of that effect. Studies 1 and 2 showed that when exposed to distractor words in the context of an incidental encoding task, older adults displayed a memory advantage for those words when they became relevant on a conceptually based general knowledge task, relative to younger adults. Study 3 showed that older adults had preserved memory for meaningful associations that are consistent with prior knowledge, but not arbitrary associations. Reduced cognitive control, in the form of controlled retrieval, accounted for that age effect. Finally, using functional magnetic resonance imaging (fMRI), Study 4 demonstrated that older adults engaged control regions to a lesser extent than younger adults during the retrieval of arbitrary associations. Moreover, activation of the default network (DN), a set of regions implicated in prior knowledge and commonly less modulated with age due to reduced control, accounted for older adults’ enhanced memory for meaningful associations. In sum, older adults’ pattern of cognition, characterized by reduced cognitive control, was associated with better performance on implicit memory tasks that depend on conceptual knowledge of previous distractors, and preserved memory for meaningful, but not arbitrary, associations.

Keywords: aging
cognitive control
memory
Advisor: Hasher, Lynn
Grady, Cheryl L.
Voluntary Teacher Professional Learning: To Educate for Democratic Peace in Egypt and in Canada

Education for democratic peacebuilding citizenship includes four essential components: encounters with conflict, practice of dialogue, recognition of diversity and building pedagogical community. Teachers can help one another to interpret, to learn, and to implement these pedagogical practice dimensions, in order to equip their students with democratic agency and values to participate in peacebuilding social change. This comparative case study research examines how two groups of private school teachers—four of mixed faith in a Muslim-majority context (Cairo) and three Muslim teachers in a Christian and secular-majority context (Toronto)—voluntarily embarked on two journeys of non-formal professional learning to improve their teaching for democratic peace. The researcher developed and facilitated a six-session reflective and dialogic professional learning course for democratic peacebuilding, and studied how each group of teachers understood and taught democratic peacebuilding and how they participated in the learning processes of this course. Data included asynchronous discussion transcripts and semi-structured interviews before and after course participation. The teachers in both contexts described using similar dialogic pedagogies to teach for democratic peacebuilding citizenship (including constructive communication, active listening, discussions and debates), while addressing different types of conflicts relevant to each political-cultural context. In Egypt, a relatively authoritarian country, teachers chose to emphasize conflicts pertaining to inclusion and re-humanization of diversity and identity recognition, within and beyond their school communities. In Canada, a relatively democratic country, teachers chose to discuss one conflict issue with which they all particularly identified— Islamophobia—from the viewpoint of Muslim minoritized communities in Canada. Other conflicts they addressed were broad current and historical issues such as Syrian refugees and colonialism. Participating teachers’ dialogic interactions evidently promoted their understandings of and engagement with democratic peacebuilding. In particular, all seven teachers in both groups apparently gained awareness of how they could infuse conflict (resolution) and peacebuilding pedagogies into their entire interactions with students, including their students’ own roles and involvement in the classroom, versus limiting peace education to teaching discrete lessons. This comparative inquiry contributes to understanding the principles of quality teacher education and peacebuilding education practices, relevant both to conflict zones and to democratic, culturally diverse settler societies.

Keywords: conflict
cultural diversity
democratic citizenship education
dialogue
peacebuilding
teacher professional learning
Advisor: Bickmore, Kathy
Chancery Officials and the Business of Communal Administration in Republican Florence. Ventura and Niccolò Monachi, Chancellors of Florence (1340-48/1348-75)

This dissertation studies the chancery of the Florentine Republic by examining the administrative offices that constituted the institution and some of the notary-administrators who held principal positions within it. The scholarship on Florentine government often presupposes the existence of some kind of permanent bureaucratic workforce that provided stability for the city’s system of amateur, short-term political office. My dissertation instead suggests that the susceptibility to change in Florentine government extended also to its administrative organization. It can be found at the level of institutional dynamics, but it was also experienced by chancery officials themselves who continually had to negotiate the forces of instability in the performance of their duties, ultimately affecting their attitudes towards their work. The first half of this dissertation considers the institutional dynamics of impermanence within the chancery through an examination and description of the three main offices of the institution during the republican period: the notary of the priors, the notary of legislation, and the chancellor. The main contention of this section is that within the institution of the chancery there was an apparent tension between the semi-permanent, rationalizing force of a very few administrative agents and the impermanent destabilizing force of hundreds of administrative agents who cycled through the chancery. The second half of the dissertation then turns to look in detail at the lives and careers of two long-serving chancellors, Ventura Monachi (chancellor, 1340-1348) and his son Niccolò Monachi (chancellor, 1348-1375). In his lyric poetry, Ventura negotiates the incessant forces of unpredictability as both a notary-administrator and chancellor, while Niccolò’s book of ricordanze demonstrates how even a notary-administrator who operated as a semi-permanent official was vulnerable to the shifting political sands of the Florentine commune. This study contributes a new set of insights and perspectives to our understanding of the institution of the Florentine chancery through an examination of the relationship between socio-political dynamics and institutional form; the formation of an administrative habitus as evidenced by the exchange of symbolic capital in municipal poetry and communal art; and, the everyday functionality of an institution structurally based on a persistent tension between stability and instability.

Keywords: bureaucracy
civic art
Florence
municipal poetry
republicanism
ricordanze
Advisor: Robins, William
Compatible pollen responses in Arabidopsis thaliana: Investigations into stigma-expressed genes

The Brassicaceae “dry” stigmas lack surface secretions, meaning there is strict control of compatible pollen responses. This consists of processes which facilitate pollen water uptake and germination, and cell wall modifications for pollen tube growth through the stigma towards the ovules. This basal compatible pollen response pathway is triggered by a Brassicaceae family-specific recognition system that leads to an exocyst complex-mediated regulated secretion of factors from the stigmatic papillae towards the compatible pollen grain. Physiological requirements for compatible pollen germination on the stigma, such as polarized secretion, are well-studied; however, the signalling components upstream of these processes during the compatible pollen response are unknown. The work presented in this thesis demonstrates use of a reverse-genetics approach to identify candidate genes that may be involved in the compatible pollen response pathway. Candidate genes were chosen based on stigma-specific expression patterns using available transcriptome datasets. The pseudokinase BRASSIKIN1 (BKN1) and its closely-related paralogue, BKN2, were identified as candidate signalling proteins. An E6-like protein (E6L1) was also identified as a protein that may be involved in early pollen reception. Mutant analyses for each of these genes in Arabidopsis thaliana uncovered a role for each during early compatible pollen responses. BKN1 and BKN2 appear to function redundantly, where double amiRNA lines showed reduced pollen adhesion, pollen hydration and seed set, while knockout lines for E6L1 displayed comparatively mild fertility defects. The evidence presented in this thesis supports that the BKNs and E6L1 are involved in early compatible pollen responses in the stigma, and the reverse-genetics approach presented here represents a useful tool for identifying candidate genes involved in compatible pollen responses in the stigma.

Keywords: Arabidopsis thaliana
Brassicaceae
pollen-pistil interactions
pseudokinases
receptor kinases
signalling
Advisor: Goring, Daphne R
Amyloid Beta Accumulation in Mouse Brain in Response to Vitamin D Receptor Ligands, Cholesterol and Age

Alzheimer’s disease (AD) is a neurodegenerative disease characterized by the accumulation of amyloid beta (Aβ) plaques. Aging, vitamin D deficiency and high cholesterol are AD risk factors. Activation of the vitamin D receptor (VDR) increases P-gp expression for Aβ efflux and lowers peripheral cholesterol. However, the effect on neprilysin for Aβ degradation and β-secretase protein (BACE-1) for Aβ synthesis is not entirely defined. We described in vitro strategies for identifying selective VDR analogs for activation of brain P-gp but not intestinal calcium channel, TRPV6. Upon improving the GAL4-hVDR luciferase reporter assay by adding ketoconazole to inhibit the bioactivation and degradation enzymes, we showed that the Teijin analogs induce brain P-gp but remain hypercalcemic. We then demonstrated, with various hypercholesterolemic mouse models: C57BL/6 mice fed high fat/high cholesterol (WD) or vitamin D deficient diets or Ldlr-/- mice; that plasma and liver cholesterol but not brain cholesterol levels were elevated with WD and decreased with 1,25(OH)2D3 or dietary vitamin D3. 1,25(OH)2D3 and atorvastatin co-administered to C57BL/6 mice lowered brain Aβ40 significantly, without affecting brain cholesterol. 1,25(OH)2D3 treatment increased P-gp expression in the young (8-weeks) and middle-aged (4-8 months) but not old (10-months) C57BL/6 mice and decreased the Aβ42/Aβ40 ratio for the middle-aged and old mice. Significant, negative correlations were observed for P-gp protein and mRNA expressions of neprilysin and Cyp46a1, the brain cholesterol metabolic enzyme whereas a significant, positive correlation was observed for Bace-1 protein vs. brain Aβ levels. Overall, brain cholesterol did not change nor correlate with brain Aβ although plasma cholesterol and brain Aβ levels were positively correlated. It is concluded that high peripheral cholesterol and age-related changes in P-gp, neprilysin, and Cyp46a1 are risk factors for brain Aβ accumulation. Effects in brain cholesterol may be revealed in future experiments with longer duration of WD and 1,25(OH)2D3 and atorvastatin treatment.

Keywords: Age
Amyloid beta
Cholesterol
Reporter assay
Vitamin D Receptor
Vitamin D Receptor Ligand
Advisor: Pang, K. Sandy
Mechanisms Structuring Dragonfly Communities across Canopy and Forest Cover Gradients

Forest regrowth, which is occurring across North America, may have large impacts on the structure of larval dragonfly assemblages. My thesis examined how habitat selection, movement behaviour, and species-sorting shape aquatic larval dragonfly assemblages in response to landscape heterogeneity, including forest cover in the landscape and canopy cover over ponds. The mechanisms structuring aquatic communities across environmental gradients are often difficult to distinguish, so I used multiple approaches to assess the contributions of different mechanisms to these observed patterns. Firstly, I tested the role of adult habitat selection versus larval species-sorting in structuring larval dragonfly assemblages across a canopy gradient using artificial aquatic habitats (i.e. mesocosms) placed across gradients of artificial shading and of natural canopy cover. Adult dragonflies preferentially visited aquatic mesocosms situated under open canopy. I tested for species-sorting effects by placing larvae in mesocosms across a natural canopy cover gradient, but found no evidence of differential mortality or growth. Secondly, I examined the effects of forest cover in the terrestrial landscape on adult dragonfly movement. Adults showed preferences for open field environments rather than closed forest environments, moving marginally more often in fields, more often towards fields, and flying longer in fields. However, adults’ direction of movement also depended on what environments they were released in, and their flight times were species-specific. Lastly, I investigated how forest cover in the landscape and pond canopy cover affected the distribution of larval dragonflies, as well as their reassembly in ponds following a drying event. Both local (pond canopy cover, permanence, and area) and landscape (pond connectivity based on distance and amount of forest cover between ponds) heterogeneity affected species diversity and recovery following a drying event. My thesis work provides new insights into how aquatic communities are structured by forest and canopy cover, and how they might respond to forest regrowth.

Keywords: Aquatic-terrestrial linkages
Behaviour
Canopy cover
Community assembly
Forest cover
Odonata
Advisor: McCauley, Shannon J