VictorJuiz/thesis huggingface dataset:
Gene Duplication and Functional Expansion in the Plant Shikimate Kinase Superfamily

The shikimate pathway links carbohydrate metabolism to the biosynthesis of the aromatic amino acids and an enormous variety of aromatic compounds with essential functions in all kingdoms of life. Aromatic compounds derived from the plant shikimate pathway have substantial biotechnological value and many are essential to the diet of metazoans whose genomes do not encode shikimate pathway enzymes. Despite its importance to the physiology of plants and human health the regulatory mechanisms of the plant shikimate pathway are not well understood. Shikimate kinase (SK) genes encode an intermediate step in the shikimate pathway and were previously implicated in regulation of the plant shikimate pathway. The distribution of SK genes in higher plants was resolved using phylogenetic and biochemical methods. The two SK isoforms of Arabidopsis thaliana, AtSK1 and AtSK2, were functionally characterized. AtSK1 expression is induced by heat stress and the recombinant enzyme was shown to form a homodimer which is important for maintaining the stability and activity of the enzyme at elevated temperatures. The crystal structure of AtSK2, the first reported plant SK structure, identified structural features unique to plant SKs which may perform important regulatory functions. The resolution of bona fide SKs in higher plants led to the discovery of two novel neofunctionalized homologs - Shikimate Kinase-Like 1 (SKL1) and SKL2. These novel genes evolved from SK gene duplicates over 400 million years ago and are found in all major extant angiosperm lineages, suggesting they were important in the development of biological properties required by land plants. The description of albino and variegated skl1 mutants in Arabidopsis thaliana implicate the SKL1 gene product as an important regulator of chloroplast biogenesis. Functional assays were attempted to determine the biochemical function of SKL1 and recombinant constructs of the Arabidopsis thaliana SKL1 protein were crystallized towards structure determination. The results of this thesis further our understanding of the organization and regulation of the plant shikimate pathway. Furthermore, the discovery of SKL1 may yield important insights into chloroplast biogenesis and function. The evolution of the plant SK superfamily highlights the utility of SKs as scaffolds for functional innovation.

Keywords: shikimate kinase
gene duplication
Advisor: Christendat, Dinesh
Plant-pollinator Interactions in a Changing Climate

Climate change is shifting the seasonal timing of many biological events, and the possibility of non-parallel shifts in different taxa has raised concerns about phenological decoupling of interacting species. My thesis investigates interactions between climate, phenology, and pollination, using the plants and pollinators of Rocky Mountain meadows as a study system. Interannual variation in timing of snowmelt since the 1970s has been associated with changes in the assemblages of concurrently flowering species in these meadows, suggesting that plant species differ in their phenological responses to climate. Differences between plants and pollinators in responsiveness to changing climate could, in principle, cause early-flowering plants to flower too early in warm years, before pollinators are active. In fact, I found only transient evidence for pollinator deficits in one early-flowering species (Mertensia fusiformis), even in an early-snowmelt year. However, the assemblage of pollinators visiting M. fusiformis does change predictably over the season, with likely consequences for selection on floral morphology in years when pollen is limiting. Hence, early- and late-flowering populations may evolve in response to phenology of the pollinator community. Differences between plant and pollinator phenologies appear to be due to generally lower temperature thresholds for development in plants, combined with microclimate differences between the soil and the above-ground nests of some pollinators. Phenological decoupling between plants and pollinators seems possible but unlikely to be catastrophic, since many taxa possess adaptations to temporally variable environments. Nevertheless, for many species, adaptation to novel climates will entail evolutionary change, and species interactions can influence evolutionary trajectories. For species affected by increasing late-summer drought, earlier flowering may be advantageous. However, in laboratory experiments, bumble bees avoid rare, unfamiliar flower types, causing simulated plant populations to fail to adapt to changing conditions. Overall, my work emphasizes the importance of the interplay between species interactions and environmental change.

Keywords: pollination
phenology
climate change
bees
Advisor: Thomson, James
Measuring the Shape and Size of the Foodshed

This thesis explores indicator tools to measure the ecological impacts of changes to the food system. The concept of a ‘foodshed’ provides a framework to explore the relationships between ecological impacts and where food system activities occur. Indicators of resource use and reuse are developed to describe the shape and size of the foodshed. Paper 1 presents a review of six indicator-based tools from the literature. Using a three criteria definition of ecological sustainability in the food system - increased resource efficiency, decreased pollutant loading, and increased output reuse - Paper 1 examines the suitability of these tools for evaluating the impacts of municipal food policy driven-changes in the location of activities, processes within activities and diet composition. Paper 2 describes the shape of a foodshed, and investigates how changes in Toronto’s waste management impacted the reuse of food-related nitrogen. Reuse increased from 1% in 1990 to at least 4.7% in 2001, through backyard composting and the land application of processed sewage. By 2004, in spite of household organics collection, reuse decreased to 2.3%, due to a reduction in land-applied sewage. The analysis suggests that sewage management has a larger impact on the reuse of food nitrogen than household solid waste management. Paper 3 quantifies the size of the foodsheds of Canada and the Greater Toronto Area (GTA), and evaluates the feasibility of self-sufficiency and its impact on the total land area used for production. Nationally, there is sufficient harvested land area to meet 95% of the land area needed for self-sufficiency. Self-sufficiency is only feasible for the GTA by drawing from a foodshed extending 400 kilometres beyond its boundary. Given current yields, total self-sufficiency would occupy more land area than currently used domestically and abroad. Higher yields or a change in diet could decrease the size of the foodshed.

Keywords: food systems
nutrient cycling
land use
foodshed
indicators
ecological sustainability
Advisor: Maclaren, Virginia W.
The Impact of Prophylactic Salpingo-oophorectomy on Health in Women who carry a BRCA1 or BRCA2 Mutation

Prophylactic salpingo-oophorectomy, the preventive removal of the ovaries and fallopian tubes, is recommended to women who carry a BRCA1 or BRCA2 mutation in order to reduce the risk of breast, ovarian and fallopian tube cancer. The short and long term health and quality of life effects of this procedure are not well understood. We examined the actual and perceived reduction in cancer risk associated with this surgery. The impact of prophylactic salpingo-oophorectomy on health-related quality of life, psychological distress, cancer worry, menopausal symptoms, and sexual function during the year following surgery was also evaluated. In our prospective study, prophylactic salpingo-oophorectomy was associated with an 80% reduction in ovarian and fallopian tube cancer risk. The residual risk for primary peritoneal cancer was 0.2% per year or 4.3% at 20 years after salpingo-oophorectomy. Most women accurately perceived their risk of breast cancer. However, the risk for ovarian cancer was overestimated, particularly by women who carry a BRCA2 mutation. Physical and mental health-related quality of life did not decrease in the year following surgery; and psychological distress was similar to levels experienced by the general population. Most women were significantly less worried about cancer after the surgery, however, a subset of women continued to experience significant cancer specific distress after prophylactic salpingo-oophorectomy. Women who underwent prophylactic salpingo-oophorectomy when premenopausal experienced a significant worsening of vasomotor symptoms and a decline in sexual functioning. Hormone replacement therapy mitigated these symptoms, but not to pre-surgical levels. Dyspareunia was somewhat alleviated by hormone replacement therapy, however, the decrease in sexual pleasure was not. Satisfaction with the decision to undergo prophylactic salpingo-oophorectomy was high regardless of these symptoms. These studies will provide women who are considering prophylactic salpingo-oophorectomy with information about the reduction in cancer risk associated with the surgery and the possible effects experienced during the year following surgery.

Keywords: prophylactic salpingo-oophorectomy
BRCA1 and BRCA2
ovarian cancer
fallopian tube cancer
breast cancer
quality of life
Advisor: Narod, Steven
A Study of the Flow of Microgels in Patterned Microchannels

This work describes the results of experimental study of the flow of soft objects (microgels) through microchannels. This work was carried with the intention of building a fundamental biophysical model for the flow of neutrophil cells in microcirculatory system. In Chapter 1 we give a summary of the literature describing the flow of cells and “model cells” in microchannels. Paramount to this we developed methods to modify microchannels fabricated in poly(dimethyl siloxane) (PDMS). Originally, these microchannels could not be used to mimic biological microenvironments because they are hydrophobic and have rectangular cross-sections. We designed a method to create durable protein coatings in PDMS microchannels, as outlined in Chapter 3. Surface modification of the channels was accomplished by a two-step approach which included (i) the site-specific photografting of a layer of poly(acrylamide) (PAAm) to the PDMS surface and (ii) the bioconjugation of PAAm with the desired protein. This method is compatible with different channel geometries and it exhibits excellent longevity under shear stresses up to 1 dyn/cm. The modification was proven to be successful for various proteins of various molecular weights and does not affect protein activity. The microchannels were further modified by modifying the cross-sections in order to replicate cardiovascular flow conditions. In our work, we transformed the rectangular cross-sections into circular corss-sections. Microchannels were modified by polymerizing a liquid silicone oligomer around a gas stream coaxially introduced into the channel, as outlined in Chapter 3. We demonstrated the ability to control the diameter of circular cross-sections of microchannels. The flow behaviour of microgels in microchannels was studied in a series of experiments aimed at studying microgel flow (i) under electrostatic interactions (Chapter 4), (ii) binding of proteins attached to the microgel and the microchannel (Chapter 5) and (iii) under the conditions of varying channel geometry (Chapter 6). This work overall present’s new methods to study the flow of soft objects such as cells, in the confined geometries of microchannels. Using these methods, variables can be independently probed and analyzed.

Keywords: microgels
microchannels
shear stress
electrostatic interactions
receptor-ligand binding
protein patterning
model cell
Advisor: Wheeler, Aaron
Kumacheva, Eugenia
Evolution of Urban Built Space: Markets and Decisions

To understand the factors that influence the spatio-temporal distribution of built space, and thus population in an urban area, play an extremely important role in our greater understanding of urban travel behaviour. Existing location of activity centres, especially home and work, strongly influences the short-term individual-level decisions such as mode of transportation, and long-term household-level decisions such as change in job and residential location. Conditions in the built space market also affect households’ and firms’ location and relocation decisions, and hence influence the general travel patterns in an urban area. This research addresses two very important, but at the same time, not very widely investigated dimensions that play a key role in the evolution of built space and population distribution: Markets and Decisions. A disequilibrium based microsimulation modelling framework is developed for the built space markets. This framework is then used to operationalize the Greater Toronto and Hamilton Area’s owner-occupied housing market within Integrated Land Use Transportation and Environment (ILUTE) modelling system. Simulation results captured heterogeneity in the transaction prices, due to type of dwellings and different market conditions, in a very disaggregate fashion. On the decisions side, this research first developed a generic multidimensional modelling framework that captures the behaviour of builders in terms of the supply of new built space. The where, when, how much, and what type of supply decisions were incorporated within a single framework. This modelling framework was then applied to estimate a model for the supply of new office space in the Greater Toronto Area (GTA). Estimation results indicated a risk taker behaviour on the builders’ part, while market conditions and supply of resources (labour, construction cost etc.) were also found to be important factors in decision making. In addition to that, this research also developed a comprehensive hedonic analysis for the asking rent of office space in the Greater Toronto Area. The effects of accessibility, quality, location, and market conditions on rent were explored. Data indicated a high degree of spatial heterogeneity and clustering effects. Spatial analysis techniques were incorporated within the hedonic framework to capture these effects. Estimation results indicated that access to transport infrastructure, distance from CBD, and vacancy rate were significant in explaining the variation in the rent.

Keywords: Integrated Urban Evolution Modelling, Microsimulation, Dynamics, Markets, Disequilibrium, Multidimensional Decisions Modelling
Advisor: Miller, Eric
Why does Speech Understanding in Noise Decline with Age? The Contribuition of Age-related Differences in Auditory Priming, Stream Segregation, and Listening in Fluctuating Maskers

Competing speech seems to pose a greater challenge to spoken language comprehension than does competing noise, especially for older adults. The difficulties of older adults may be due to declines in auditory and cognitive processing. However, evidence suggests that the use of top-down information processing to overcome this interference may be preserved in aging. This research investigated the effect of speech- and noise masking on language comprehension, as well as age-related differences in the use of top-down processing to overcome masking. Topic I examined whether younger and older adults gain the same release from masking given a partial preview of a target sentence in quiet (auditory prime) prior to hearing the full sentence in noise, and investigated the auditory factors contributing to the advantage provided by the primes. Results showed that despite age-related declines in overall performance, younger and older listeners benefited similarly from priming. This benefit was not attributable to cues about the target talker’s voice or fluctuations in the amplitude envelope of the target sentences. Topics II and III examined the effect of speech- and noise masking on the time-course of stream segregation. The analyses revealed that stream segregation takes time to build up when a speech target is masked by other speech, but not when it is masked by noise. Subsequent analyses showed that in younger adults, the delay in segregation under speech masking was primarily due to the vocal similarities between the talkers, with interference from the semantic content of the masker playing a secondary role in impeding performance. The results also showed that older listeners were less efficient than younger listeners in segregating speech from speech-like maskers. Furthermore, older listeners benefited less than younger listeners when the amplitude envelope modulations of maskers were limited. Overall, the findings indicate that some of the language comprehension difficulties experienced by older listeners in noisy environments may be due to age-related declines in stream segregation and a decreased ability to benefit from fluctuations in the amplitude envelopes of maskers. However, benefit from priming may help offset some of these age-related declines in auditory scene analysis.

Keywords: informational masking
aging
speech perception
hearing
language comprehension
Advisor: Schneider, Bruce A.
Pichora-Fuller, Margaret Kathleen
Bose-Einstein Condensate Wavefunction Reconstruction Through Collisions with Optical Potentials

A new technique for the interferometric measurement of an atomic wavefunction is introduced theoretically, which is able to extract phase and amplitude information in a single measurement. I focus on the application of this technique to the single-particle wavefunction of a Bose condensed cloud of rubidium atoms. The technique differs from existing techniques mainly in its simplicity, as it requires only a single laser beam to be added to a typical Bose-Einstein condensation apparatus. A second novel aspect is the consideration of condensate collisions with an optical potential in the low-intensity limit where the potential barrier may be viewed as a phase mask. The technique is then demonstrated experimentally. A related effect, the transient enhancement of momentum during a collision, first predicted by JG Muga et al., has also been demonstrated. Finally, significant redesign and construction of an apparatus to produce condensates of 87Rb is documented. The main result of this work is the production of pure condensates of up to 150k atoms which can be repeated every 45s. A calibration technique is devised and demonstrated, whereby copies of the condensate are made, and the copies are used to reduce the centre-of-mass momentum uncertainty of the interacting cloud by a factor of five.

Keywords: Bose-Einstein Condensate
wavefunction
Advisor: Steinberg, Aephraim
Passivity Methods for the Stabilization of Closed Sets in Nonlinear Control Systems

In this thesis we study the stabilization of closed sets for passive nonlinear control systems, developing necessary and sufficient conditions under which a passivity-based feedback stabilizes a given goal set. The development of this result takes us to a journey through the so-called reduction problem: given two nested invariant sets G1 subset of G2, and assuming that G1 enjoys certain stability properties relative to G2, under what conditions does G1 enjoy the same stability properties with respect to the whole state space? We develop reduction principles for stability, asymptotic stability, and attractivity which are applicable to arbitrary closed sets. When applied to the passivity-based set stabilization problem, the reduction theory suggests a new definition of detectability which is geometrically appealing and captures precisely the property that the control system must possess in order for the stabilization problem to be solvable. The reduction theory and set stabilization results developed in this thesis are used to solve a distributed coordination problem for a group of unicycles, whereby the vehicles are required to converge to a circular formation of desired radius, with a specific ordering and spacing on the circle.

Keywords: Nonlinear Control Systems
Set Stabilization
Passive Systems
Advisor: Maggiore, Manfredi
Secondary School Students’ Misconceptions in Algebra

This study investigated secondary school students’ errors and misconceptions in algebra with a view to expose the nature and origin of those errors and to make suggestions for classroom teaching. The study used a mixed method research design. An algebra test which was pilot-tested for its validity and reliability was given to a sample of grade 11 students in an urban secondary school in Ontario. The test contained questions from four main areas of algebra: variables, algebraic expressions, equations, and word problems. A rubric containing the observed errors was prepared for each conceptual area. Two weeks after the test, six students were interviewed to identify their misconceptions and their reasoning. In the interview process, students were asked to explain their thinking while they were doing the same problems again. Some prompting questions were asked to facilitate this process and to clarify more about students’ claims. The results indicated a number of error categories under each area. Some errors emanated from misconceptions. Under variables, the main reason for misconceptions was the lack of understanding of the basic concept of the variable in different contexts. The abstract structure of algebraic expressions posed many problems to students such as understanding or manipulating them according to accepted rules, procedures, or algorithms. Inadequate understanding of the uses of the equal sign and its properties when it is used in an equation was a major problem that hindered solving equations correctly. The main difficulty in word problems was translating them from natural language to algebraic language. Students used guessing or trial and error methods extensively in solving word problems. Some other difficulties for students which are non-algebraic in nature were also found in this study. Some of these features were: unstable conceptual models, haphazard reasoning, lack of arithmetic skills, lack or non-use of metacognitive skills, and test anxiety. Having the correct conceptual (why), procedural (how), declarative (what), and conditional knowledge (when) based on the stage of the problem solving process will allow students to avoid many errors and misconceptions. Conducting individual interviews in classroom situations is important not only to identify errors and misconceptions but also to recognize individual differences.

Keywords: Secondary mathematics
Curriculum and instruction
Measurement
Misconceptions
Algebra
Problem Solving
Advisor: McDougall, Douglas Emerson