Below is a list of thesis abstracts by fourth-year students in the Integrated Science Program:
THESIS PRESENTATIONS – MARCH 28, 2017
HEATHER SUMMERS-MODEL FOR PREDICTING CORAL BLEACHING THREATS
SUPERVISOR: DR. J. STONE (BIOLOGY)
Acropora cervicornis and Acropora palmata are important reef-building corals listed as Critically Endangered by the International Union for Conservation of Nature. With population reductions exceeding 80% in regions of the Caribbean over the past 30 years, there is an urgency to protect Acropora spp. and promote their recovery. Acropora decline is the product of compounding effects from local stressors and global factors linked to climate change including ocean acidification, sea level rise, disease, increased severity of hurricanes, and coral bleaching but in various geographic locations these factors contribute differentially to declines. Eleven sites off the coast of South Eleuthera, Bahamas were selected, five lacking Acropora served as control sites. All sites were evaluated for abundance of predators, herbivores, macroalgal, and live scleractinian corals and sites with Acropora were assessed for coral bleaching intensity as a proxy for health. Water measurements of pH, salinity, temperature, and depth were recorded. Analysis of Variance showed significant interactions between temperature, depth, and pH on coral bleaching with data showing warmer, shallower, more acidic sites having a greater detrimental impact on coral health. Observations were subjected to Principal Component Analysis (PCA) producing clear clusters of site- and species-specific data. Factor loadings contributing to the PCA can be used to identify traits associated with increased or decreased coral bleaching. The variables assessed at each site will provide a more complete understanding of the physical and ecological factors affecting Acropora health, necessary knowledge to devise effective conservation and restoration practices for degraded coral reefs.
ALEX DHALIWAL – GLUCOSE VITRIFIES DEHYDRATED LIPID MEMBRANES
SUPERVISOR: DR. M. RHEINSTADTER (PHYSICS & ASTRONOMY)
The interaction of phospholipid bilayers and monosaccharides constitutes one of the most important and fundamental physical relationships in cellular biology, as both elements are ubiquitous to living cells. The physical effects of sugars in bilayer systems have been studied for decades due to their membrane stabilization properties . Sugars have been observed to decrease phase transition temperature, thicken bilayers, and promote more fluid structures, all of which are in support of the hypothesis that sugars allow bilayers to mimic a hydrated state ; however, an exact molecular mechanism regarding this interaction is unknown . Notably, the influence of sugar concentration on bilayer properties in dehydrated settings has been hotly debated.
We provide data regarding the position and physical effects of glucose within oriented 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) samples using both X-ray diffraction and Molecular Dynamics (MD) simulations . Glucose preferentially localizes to the outer head region of phospholipid bilayers. At reduced concentrations, it results in an increase in water penetration into the bilayer, increasing lateral diffusion. At high concentrations, it functions to vitrify the bilayer structure, allowing it to adopt a disorganized, fluid-like structure while maintaining a reduced range of lipid motions. This supports the evidence regarding the function of sugars as cryoprotective agents, as they promote the retention of fluid-like bilayer properties in environments of reduced hydration in a concentration-dependent manner. These findings corroborate and reinforce previous results regarding sugar-lipid interactions through a unified molecular mechanism.
 Crowe, J. H. Trehalose As a “Chemical Chaperone.” In Molecular Aspects of the Stress Response: Chaperones, Membranes and Networks; Springer New York: New York, NY, 2007; pp. 143–158.
 Crowe, J. H.; Crowe, L. M.; Chapman, D. Preservation of Membranes in Anhydrobiotic Organisms: The Role of Trehalose. Science (80). 1984, 223, 701–704.
 Andersen, H. D.; Wang, C.; Arleth, L.; Peters, G. H.; Westh, P. Reconciliation of Opposing Views on Membrane-Sugar Interactions. Proc. Natl. Acad. Sci. U. S. A.2011, 108, 1874–1878.
 Dhaliwal, A., Rheinstädter, M. Exploring the Molecular Mechanism for the Vitrifying Properties of Glucose in Dehydrated Lipid Bilayers Using X-Ray Diffraction and Molecular Dynamics Simulations. In Preparation
MARTYN SIEK – LOW CONCENTRATION REMOVAL OF MANGANESE USING SINGLE CHAMBER MICROBIAL ELECTROLYSIS CELLS AND VARIOUS APPLIED VOLTAGES
SUPERVISOR: DR. Y. KIM (CIVIL ENG)
With the rapid development of manufacturing industries, the dangers of heavy metal discharge into the environment have become increasingly prevalent in recent decades. These contaminants are often toxic and non-biodegradable.Therefore, it is imperative that efficient and effective heavy metal ion removal methods are implemented. Currently, there exist many methods of heavy metal ion removal, which vary in their degree of effectiveness and economic viability for many metals, but are primarily tailored to large-scale industrial operations. The use of microbial electrolysis cells (MECs) is an emerging technology that employs electrically mediated microbes to economically precipitate low concentrations of heavy metals on a cathode while producing hydrogen. This study aims to explore the capabilities of MECs in terms of their ability to remove manganese at various applied voltages. Four single chamber MECs were fed solution which included phosphorus buffer solution, 5 mg/L manganese, 2 g/L sodium acetate as well as various minerals and vitamins in a 4-day cycle. MECs were supplied with 0.6, 0.9, 1.2 V as well as an uncoupled to serve as a fixed voltage control. Data recovered from this study was able to determine that the 0.6 V application was most efficient at removing manganese from solution across all reactors, averaging a removal efficiency of 40%. Healthy reactors were also able to remove manganese at a 1.2 V application. Future studies should focus on different voltage applications and higher manganese concentrations to expand the capabilities of this emerging technology.
CHARLOTTE TOUSAW – THE IMPACT OF VARYING NUTRIENT PULSE REGIMES ON ALGAE POPULATION GROWTH
SUPERVISOR: DR. J. KOLASA (BIOLOGY)
In a self-sustaining designer ecosystem, a key factor to consider is the optimization of nutrient transfers between different trophic levels. In particular, the energy transfer from terrestrial primary producers to aquatic primary producers is an important step in this process. This project aims to determine the impacts of different nutrient pulse regimes, or different methods for nutrient renewal, on the growth of algal populations. Algal populations were subjected to one of three nutrient renewal regimes: constant nutrient replacement (control), alternating low-high nutrients, and constant followed by alternating low-high nutrients to determine the rate of growth in response to nutrient replacements. Nutrients were replaced every other day for 29 days, and the chlorophyll content of each sample was measured daily for the duration of the experiment to monitor algal population growth. Preliminary results show variations between the treatments and further analysis will be performed to determine the statistical significance of these differences. Results of this study will help to determine the rate and amount of nutrients to be added to the primary aquatic production tank of the designer ecosystem to improve the overall efficiency of the system.
MINDY CHAPMAN – EFFECTS OF STEROIDAL HORMONES FROM BIRTH CONTROL ON LIPID MEMBRANES.
SUPERVISOR: DR. M. RHEINSTADTER (PHYSICS & ASTRONOMY)
All commercially available pharmaceutical products must undergo rigorous testing to determine their safety and efficacy, however, how these drugs interact with our bodies on a cellular level is often unknown. Hormonal oral contraceptives are commonly used by women to prevent pregnancy and treat symptoms, such as acne. While the drug mechanism that causes the desired effect – prevention of ovulation – is well understood, little is known about how the synthetic steroidal hormones interact with human cells. The understanding of these non-specific interactions could provide insight into the underlying causes of documented side effects and the interactions of oral contraceptives with the human body.
Molecular Dynamics (MD) simulations were used to examine the behaviour of lipid membrane systems when introduced to norethindrone and 3thynyl 3stradiol, two hormones used in oral contraceptives. Simulations containing 10mol% norethindrone, 10mol% ethynyl estradiol, and a10mol% mix, with a 90mol% 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane were run for 200ns. From this, we visualized the location of the hormone molecules in the system, their effect on the membrane, and obtained electron density profiles of the system. This was compared to analysis of X-ray diffraction data of analogous experimental systems to observe whether MD corroborates the experimental results. Our understanding of the interactions between oral contraceptives and human tissue will be improved, and potentially identify the underlying causes of their side effects.
MICHAEL WANG – A LANDAU-BRAZOVSKII MODEL OF DIBLOCK COPOLYMER PHASE STABILITY
SUPERVISOR: DR. AN-CHANG SHI (PHYSICS)
A block copolymer is a single molecular chain made from two or more covalently bound polymers of different chemical character. The simplest type of system is the diblock copolymer, with two different polymer segments. In a melt, diblock copolymers exhibit well-understood macromolecular self-assembly into lamellar, cylindrical, or spherical phases depending on both relative chain size and intermolecular interactions. This self-assembly has useful synthetic applications as it affects material properties. The spherical phases are the focus of this project, as not only can conventional “hard sphere” phases – sc, bcc, fcc, etc. – be formed, but because the polymer spheres are malleable aggregates the Frank-Kasper “soft sphere” phases also arise – notably A15 and sigma phases. The sigma phase is particularly complex, with 30 distinct sphere positions in a tetragonal unit cell. It is also typically a brittle and undesirable product. An established Landau-Brazovskii free energy functional was used to compare the stability of the dominant phases for diblock copolymers: lamellar, cylindrical, bcc, fcc, gyroid, A15, and sigma. This involved developing novel functions to describe both the A15 and sigma phases, which have not been studied in this manner before. The free energy functional was applied to each phase description with varied linear and quadratic terms to determine under what conditions a given phase is stable. This showed which terms were important to stabilize the soft phases rather than the hard phases.
ANGELICO OBILLE – DEVELOPING BIOTINYLATED CELLULOSIC SURFACES USING THIOL-ENE CLICK CHEMISTRY ON ALKENE-FUNCTIONALIZED PAPER
SUPERVISOR: DR. JOSE MORAN-MIRABAL (CHEM BIO)
Paper-based scaffolds are inexpensive, biocompatible, and environmentally-friendly platforms for analytical testing purposes. The applications for a novel method of modifying cellulose in the form of paper have been developed and explored. The key step in this method is to functionalize surfaces of the cellulosic material with alkene functionality using a novel synthetic method. The alkene-functionalized surface can then be subject to thiol-ene click reactions to apply various properties on the material depending on the specific thiol that is clicked. For example, hydrophobicity can be achieved by clicking octadecanethiol and hydrophilicity can be achieved by clicking mercaptohexanol. This concept is extended to bioapplications with thiolated biotin being grafted onto the material. Biotinylated scaffolds have numerous applications, given the specific and strong interactions between biotin and biotin-binding proteins, such as avidin and streptavidin. These biotin-binding proteins have four non-cooperative biotin-binding sites, and thus grafting thiolated biotin onto paper allows for the material to be used as a scaffold to bind to other biotinylated biomolecules. This reveals the potential for using cellulosic materials for biomolecule detection and screening assays. The main methods of verification used for this covalent cellulose modification technique include: contact angle measurements, Fourier transform infrared spectroscopy, and fluorescence microscopy. Optimal conditions for this method of modification have been determined. Furthermore, patterning approaches have been explored to develop paper-based analytical devices. Overall, the thiol-ene click reaction on alkene-functionalized paper ultimately contributes to the engineering goal of creating greener alternatives for current technologies.
MIRIAM KRZYZEWSKA – INVESTIGATING THE COGNITIVE, BEHAVIOURAL, AND NEUROPATHOLOGICAL EFFECTS OF A COMPLEX DIETARY SUPPLEMENT ON A MURINE MODEL OF ALZHEIMER’S DISEASE (3X-TG AD MICE)
SUPERVISOR: DR. S. BECKER (PNB)
Alzheimer disease (AD) is the utmost prevalent age-dependent neurodegenerative disorder, representing a serious health problem in the industrialized world. AD is a progressive neurodegenerative illness resulting in deterioration of cognitive abilities ranging from short term memory to language abilities, and the development of psychiatric manifestations such as anxiety, and depression. AD is characterized by several pathological hallmarks, including extracellular Aβ-plaques, and intraneuronal neurofibrillary tau tangles. A complex dietary supplement (CDS) developed by Dr. Rollo et al. at McMaster has been found to successfully extend the lifespan, and delay the onset of cognitive decline in both wildtype mice, and a murine model of accelerated aging. To build on these results, a study is being conducted to determine if the CDS provides similar benefits in AD when administered to a triple-transgenic mouse model of AD (3xTg-AD), in comparison to B6129SF2/J wildtype controls. The study will evaluate the behavioural effects, and assess the neuropathology at 11.5 months of age by quantifying Aβ-plaques by ELISA. Of particular interest in this study, the spontaneous alternation behaviour (SAB) test will be administered, and is intended to measure visuospatial working memory and navigational strategies. It is predicted that treated AD mice will score better on the SAB test, and will display a lower Aβ count than control AD mice, but both more than the wildtype. The aim of the present study is to thoroughly characterize the age-related changes in 3xTg-AD mice in comparison to controls, and to assess the effects of a CDS on both groups.
KYRA SIMONE – QUANTIFYING EVAPOTRANSPIRATION EDGE EFFECTS IN PEATLAND SYSTEMS: IMPLICATIONS FOR AT-RISK REPTILES
SUPERVISOR: DR. J.M.WADDINGTON (GEOG/EARTH SCI)
The immense biodiversity of near-northern Ontario peatlands is both mighty and delicate. Here, mosses of the genus Sphagnum provide critical habitat for at-risk Blanding’s turtles and eastern Massasauga rattlesnakes. However, impending highway expansion and increased urbanization within the Georgian Bay region will soon result in the destruction of a large Massasauga hibernaculum.
Peat-forming Sphagna grow in rock depressions and are vulnerable to desiccation, especially along margins where advecting air adds kinetic and thermal energy. Post-development, restoration must consider the role of enhanced marginal evapotranspiration in moss moisture levels, which are directly tied to thermal conditions required by at-risk reptiles.
This study takes an integrative hydrological, ecological, and climatological approach to examining peatland ecosystems as at-risk reptile habitat, and conceptualizes the spatial extent of the marginal region most affected by hot, dry air from adjacent rock barrens. Evaporation and precipitation rates, water table position, moss temperature moisture, and atmospheric parameters were measured at a peatland in the municipality of Carling during summer 2016. These measurements were considered in association with data from other Nobel projects by McMaster Ecohydrology Group, including vegetation and tree distribution, canopy closure, peat depth profiles, and aerial imagery.
Findings will be used to parameterize the Peatland Hydrological Impacts model to examine how evapotranspiration affects the “life zone” of rattlesnake habitat. This augmented understanding of edge effects on evapotranspiration will clarify several ecohydrological considerations vital in the effective restoration of peatlands disturbed by development.
TIMOTHY FERNANDES – WINTER MIGRATION AND HABITAT SELECTION IN LARGEMOUTH BASS (MICROPTERUS SALMOIDES)
SUPERVISOR: DR. S. DUDLEY (BIOLOGY)
No abstract avaialble.
DEEP INAMDAR – PREDICTING THE CONSEQUENCES OF CHANGES IN PREDATORY FUNCTIONAL DIVERSITY
SUPERVISOR: DR. B. BOLKER (MATH/STATS/BIO)
Predator functional diversity is the variation in a specified functional criterion among ecosystem predator species. Over the past three decades, changes in predator functional diversity have been widely observed in nature. Ecologists are interested in the associated implications and research in the field has led to a basic framework for predicting the consequences of changes in predator functional diversity. Under this framework, a mechanistic understanding of observed trends has yet to be established. This study introduces a novel framework where predators were modeled using a Holling type II functional response, which is a function of attack rate and handling time. Prey size dependent risk was incorporated in the model by defining the attack rate and handling time by functions of size. Prey growth and individual variation in growth were simulated by a linear advection term and diffusion term, respectively. The consumption rate of the system was established by summing over the consumption rates for each predator at each size class. The study used the fully developed model to investigate the aggregate effects of multiple independently acting predators. Simulations were run with a factorial combination of the parameters within the attack rate and handling time size-dependent functions. The advection and diffusion terms were held constant at values that represented reasonable growth dynamics. Predator functional diversity was quantified by calculating functional dispersion from the aforementioned parameters. The data correlated functional dispersion with all the summary values. Overall, the findings suggest that predator functional diversity has a large impact on predator prey systems.
JAMES ST PIERRE – ANTIBIOTIC-INDUCED MICROBIOTA ALTERATION DIFFERENTIALLY AFFECTS GUT PERMEABILITY IN TWO STRAINS OF MICE
SUPERVISOR: DR. J. FOSTER (PSYCHIATRY AND BEHAVIOURAL NEUROSCIENCE)
The gut-brain axis is being increasingly recognized in the fields of neuroscience and psychiatry for its role in mental health and neurological diseases. A new idea in the field suggests that poor intestinal wall function, or a “leaky gut”, increases communication between the gut bacteria (gut microbiota) and the brain. This study examined the impact of host genetics on antibiotic-induced changes in gut permeability and microbiome composition, an interaction that has not yet been examined in the literature. Microbiome analysis was done on stool samples from a previous graduate project investigating the impact of three different antibiotic treatments and a control treatment on gut permeability and behaviour in two different strains of mice. Quantitative polymerase change reaction (qPCR) analysis was done on samples to determine the total amount of bacterial 16S rRNA gene DNA present. qPCR data was combined with bacterial community relative abundance data (found through prior high-throughput sequencing of the 16S rRNA variable region 3) to recover absolute taxa abundances. Absolute abundances were then analyzed through principal coordinate analysis. The association of strain differences, antibiotic treatment, and gut permeability with microbiome composition was assessed with the adonis test. Antibiotic-induced changes in microbiome composition affected gut permeability differentially in BALB/c and C57BL/6 mice. This suggests that the effect of antibiotic-induced perturbation of gut bacterial communities on gut permeability depends on the genetically-related initial bacterial composition. As treatments altering microbiota composition are explored, the impact of host genetics on gut bacterial communities must be taken into account.
THESIS PRESENTATIONS – MARCH 29, 2017
KYLEE INNES – COMPARISON OF SUBSTRATE UTILIZATION IN YOUNG BOYS AND GIRLS DURING MODERATE INTENSITY EXERCISE
SUPERVISOR: DR. B. TIMMONS (PEDIATRICS)
Studies demonstrate differences between men and women in substrate utilization during prolonged exercise. However, due to limited literature comparing substrate utilization between boys and girls at various stages of pubertal development, it is not known at what point of development these differences appear. The purpose of this study was to compare substrate utilization in healthy, active girls (10.1±0.9years old, n=9) and boys (9.1±1.2 years old, n=7) during prolonged submaximal exercise. The study involved two visits. During the first visit, participants completed an aerobic fitness test (VO2maxtest) on a cycle ergometer. At the second visit, participants underwent two 30-min bouts of cycling at 60% VO2max. At the end of each 30-min bout, gas exchange measurements (VO2, VCO2, and respiratory exchange ratio (RER)) were recorded and used to calculate rate of fat and carbohydrate oxidation, and their relative contribution to total energy expenditure. A mixed two-way ANOVA was used to compare boys and girls, over time. Average fat oxidation at 30 min was 5.49±2.45 and 10.27±4.16 mg/kgFFM/min for girls and boys, respectively (p<0.001). At 60 min, fat oxidation was 8.07±3.13 and 10.70±3.52 mg/kgFFM/min for girls and boys, respectively (p<0.005). Tukey HSD post hoc analysis revealed a significant difference in fat oxidation over time in girls (p<0.005) but no significant difference over time in boys (p=0.92). Differences in biological age may contribute to the observed results. These findings shed light on possible differences in substrate utilization that arise in the early pubertal stages of development.
ELIZABETH SANGSTER – DEVELOPMENT OF THE CONTROL OF BREATHING IN HIGHLAND DEER MICE (PEROMYSCUS MANICULATUS)
SUPERVISOR: DR. G. SCOTT (BIOLOGY)
The unremitting hypoxia encountered at high altitude challenges native mammals to maintain metabolism and thermoregulation, despite constrained oxygen supply. Many highland taxa exhibit physiological specializations for overcoming this challenge, including enhanced pulmonary O2 uptake and diffusion. These specializations have primarily been investigated on adult highland taxa, with little insight into whether these differences are present from birth. Here, we examined whether highland deer mice would exhibit deeper tidal volumes and reduced hypoxia sensitivity at ages 7, 14, 21, and 30 days post birth compared to lowland mice, as is observed with adult highland mice. The hypoxic ventilatory response and arterial O2 saturation were assessed, with mice exposed to step-wise decreases in inspired O2 fraction. Preliminary results suggest that the deeper tidal volumes characteristic of adult highland deer mice appear to be fixed from 7 days post birth. 7 day old mice appeared to exhibit limited responsiveness to hypoxia challenge, while mice age 14, 21, and 30 days increase their breathing with a blunting of the response with increasing age. When challenged with hypoxia, highlanders breathe at a lower frequency compared to lowlanders, and maintain deep tidal volumes. Higher arterial O2 saturation was also observed in highlanders compared to lowlanders, which may be the result of deeper tidal volumes, in addition to high hemoglobin affinities. This research not only provides valuable insight into the relationships and interactions between developmental plasticity and genotypic adaptation in deer mice, but also provides us with a deeper understanding of the development of highland taxa.
LORYN BYRES – LSR2 AND THE REGULATION OF ANTIBIOTIC PRODUCTION INSTREPTOMYCES VENEZUELAE
SUPERVISOR: DR. M. ELLIOT (BIOLOGY)
Streptomyces are a genus of Gram-positive actinobacteria that produce many secondary metabolites, including most naturally synthesized antibiotics. Lsr2 is a nucleoid-associated protein, well conserved throughout actinobacteria. It functions as a dimer and is involved in the transcriptional repression of a variety of genes, including those involved in antibiotic production in Streptomyces. Streptomyces also possess a second, duplicated, copy of lsr2, lsrL. LsrL may form both homodimers, and heterodimers with Lsr2, and these associations may alter the proteins’ function. A mutant construct of lsr2, R82A, exists. It is expected that R82A may act as a dominant negative effector, where it dimerizes with wildtype Lsr2 in Streptomyces, inhibiting its ability to bind DNA and act as a repressor, and allowing for active transcription of silent metabolic clusters. Our objective is to increase our understanding of the roles of Lsr2 and LsrL in gene regulation in Streptomyces, and to determine the efficacy of R82A as a dominant negative effector.
As a first step towards elucidating the functional role of the Lsr2 proteins, the physical interactions between Lsr2, LsrL, and R82A were probed in vivo, using bacterial two-hybrid analyses. The two genes were reciprocally cloned into the two-hybrid vectors, and the intraspecific and interspecific protein interactions were tested in a pair-wise manner. Overexpression conditions were then identified, to allow for purification of the proteins for future investigations. Lsr2 may be an effective target to increase antibiotic production in Streptomyces, making it important to fully understand the role of both genes in the cell.
MEENA AL SAIGH – THE ROLE OF NRF2 IN PERIODONTAL DISEASE
SUPERVISOR: DR. M. GLOGAUER
Periodontal disease is an oral condition that affects over two thirds of the world’s population. It clinically manifests itself in several forms, but one of the more severe forms is the inflammatory disorder known as periodontitis. Periodontitis is characterized by the build-up of bacteria on the teeth and surrounding gum tissues, and can result in progressive tissue destruction, loosening of the teeth, and eventual tooth loss. Due to the asymptomatic nature of periodontitis, it is important to find new therapeutic strategies to combat this difficult to treat disease.
Preliminary data has shown that patients with periodontitis have reduced levels of antioxidants due to the down-regulation of the transcription factor NrF2 in neutrophils. Antioxidants are essential to controlling reactive oxygen species (ROS), which are produced by several immune cells, including neutrophils. Having an imbalance of ROS and antioxidants results in oxidative stress, which can potentially lead to tissue destruction. Therefore, the purpose of this study is to investigate the role NrF2 and its therapeutic potential to regulate antioxidant levels.
This study was carried out at the University of Toronto under the supervision of Dr. Michael Glogauer. The study was conducted in vitro using neutrophil cells that were isolated from murine bone marrow. The neutrophils were treated with pathogenic and commensal strains of bacteria, and the level of nucleic and cytoplasmic NrF2 protein was observed using Western Blot analysis. Our results suggest that pathogenic and commensal bacteria differentially activate NrF2, whereby pathogenic bacteria suppressed NrF2 activation while commensals promoted NrF2 activation. With this information, we can better understand how pathogens regulate NrF2 and identify what causes the down-regulation of NrF2 in periodontitis patients. We hypothesize that using NrF2 activators may be a potential therapeutic strategy to treat patients with periodontitis.
MAX LAUCH – WAVE PROPERTIES FOR ELASTIC-LIQUID INTERFACES
SUPERVISOR: DR. K. DALNOKI-VERESS (PHYSICS & ASTRONOMY)
No abstract available.
TRISTAN GOODWILL – MODIFICATIONS TO THE HIGGS PROPAGATOR IN EXTRA DIMENSIONS
SUPERVISOR: DR. C. BURGESS (PHYSICS & ASTRONOMY)
The Standard Model of particle physics is a remarkably accurate description of the elementary particles and interactions that make up the universe. Despite its success, the model does not allow physicists to calculate the effects of gravity. Historical efforts to design a new quantum theory to describe gravitational effects, along with the already understood electroweak and strong interactions, led to the development of string theory in the later half of the 20th century. The success of string theory as an extra-dimensional theory of quantum gravity leads to questions about the non-gravitational manifestations of the extra dimensions. We explored how an extra-dimensional spin-0 particle could affect the observed properties of the Higgs boson, the recently confirmed particle responsible for giving mass to other particles. These effects could influence the experimental results gathered at the LHC and other particle accelerators, and may provide evidence for extra dimensions. In particular, the new particle would shift the mass of the Higgs boson and allow some produced Higgs particles to decay into undetectable states, decreasing the number of observed Higgs bosons. We then compare the effects of this shifted mass and Higgs loss to LHC data and determine whether this form of extra dimensional interaction has already been ruled out by measurements of the Higgs boson lifetime.
SUPRIYA SINGH – THE INFLUENCE OF LAND USE ON DISSOLVED ORGANIC CARBON IN A COMPLEX GREAT LAKES WATERSHED
SUPERVISOR: DR. S. CAREY (GEOG/EARTH SCI)
Freshwater ecosystems such as wetlands are sensitive to global climate change as they display the implications of anthropogenic activities and are one of the most active carbon reservoirs on Earth. Carbon is transferred from terrestrial to aquatic environments such as wetlands through dissolved organic matter (DOM). The portion of this carbon that is stored in wetlands often flows downstream in the form of dissolved organic carbon (DOC). Understanding the quantity and quality of DOC is crucial as elevated DOC concentrations have negative implications on photosynthesis-dependent aquatic organisms and enhances metal solubility. Complex watersheds that contain varying land use types may have different sources inputting DOC into freshwater ecosystems with relatively varying concentrations. As such, the objective of this research is to quantify and characterize DOC concentration and quality in a complex Great Lakes watershed, specifically in the Spencer Creek watershed, Hamilton, ON. Flow regimes and other geochemical parameters will be linked to DOC characterization through weekly measurements of stream flow and water chemistry made at 16-subcatchments throughout an entire year. Fluorescence spectroscopy methods will be used to fingerprint unique DOC signatures that will be accordingly related to land use types for each of the subcatchments. This research will contribute to the overall understanding of how different land use types influence DOC concentrations, and may lead to strategies for how to reduce DOC in freshwater systems. Specifically in Hamilton Harbour, the results of this study will inform future remediation actions taken by the city.
JULIANNA STANGROOM – ANCIENT DISEASE DETECTION WITH THE LAWRENCE LIVERMORE MASSIVE MICROBIAL ARRAY
SUPERVISOR: DR. H. POINAR (ANTHROPOLOGY)
Determining the presence of infectious diseases in archaeological remains is primarily conducted by identification of gross morphological skeletal changes. This approach, however, tends to be inexact and limited to few diseases. Ancient DNA (aDNA) provides a greater degree of specificity and breadth for pathogen detection. Unfortunately, large-scale aDNA studies remain uncommon due to the expense of sequencing and the uncertainties introduced by PCR-based methods. Microarrays present a potential alternative that is both affordable and accurate. However, only one study has been conducted to determine the ability of microarrays to detect pathogen aDNA from teeth.
The Lawrence Livermore Massive Microbial Detection Array (LLMDA) has a high degree of sensitivity and is the most comprehensive array to date. The objective of this project was to determine if the LLMDA could detect pathogenic aDNA in multiple samples, its threshold limitations, the affordability of those limitations, and its ability to detect co-infection.
12 individual tooth samples from the mid to late-Medieval period (11h- 15thcentury) provided by Sydvestjyske and Moesgaard museums. DNA was extracted, purified, amplified, and then sent to Lawrence Livermore for detection.
The DNA concentration of 7 samples was below the LLMDAs detection limit. 4 samples contained DNA from environmental bacteria. A single sample contained DNA from multiple bacteria implicated in periodontal disease.
The LLMDA is capable of detecting pathogenic aDNA from multiple sources in teeth. Its detection limit has been confirmed to be 250 ng of DNA. To achieve this concentration is not much more affordable than sequencing methods, however may be revisited as alternative methods of amplification are considered.
JAIME KNOCH – DO IMMUNE CELLS PREVENT METABOLISM OF L-KYNURENINE INTO NEUROTOXIC METABOLITES IN AN IN VITRO N2A CELL MODEL?
SUPERVISOR: DR. P. FORSYTHE (MEDICINE)
Depression is the leading cause of disability worldwide and suicide is the tenth leading cause of death. The kynurenine pathway is an essential metabolic pathway of tryptophan that has many neuroactive metabolites and has been implicated in major depressive disorder and suicide. In particular, the pathway has a neurotoxic “arm” and a neuroprotective “arm”, and environmental conditions such as inflammation and stress have been shown to upregulate the neurotoxic side of the pathway. In this study we grow neuronal cells and add the precursor of the kynurenine pathway, L-kynurernine to the culture with quinolinic acid, a neurotoxic agent, which should shunt the pathway towards the neurotoxic arm. We then introduce mast cells – which are thought to be neuroprotective – to see if they will help to restore the pathway to its equilibrium state. We use an MTT assay to assess cell viability and survival after these treatments. Through this research, we hope to elucidate some of the neuroimmunological effects of mast cells on the kynurenine pathway, and gain a better understanding of its dysregulation in major depressive disorder.
STEPHANIE BLACK – EFFECTS OF MEMBRANE PHYSICAL PROPERTIES ON DIACYLGLYCEROL KINASE EPSILON (DGKƐ) ACTIVITY
SUPERVISOR: DR. R.M. EPAND (BIOCHEM & BIOMED SC)
Diacylglycerol kinases (DGK) are a key family of enzymes whose members catalyze the conversion of diacylglycerol (DAG) into phosphatidic acid (PA) through the addition of a phosphoryl group from adenosine triphosphate (ATP). Both DAG and PA are critical signalling molecules, and DGK effectively serves as a switch by terminating the signalling of one lipid molecule for another. There are ten known mammalian isoforms of DGK, and the epsilon isoform is the only isoform known to be permanently membrane-bound, among other unique properties. Defects or deletions of DGKɛ within mammalian cells influence the progression of several disease states, including epilepsy, cancer, heart, and renal diseases. With our research group having recently developed a protocol to obtain purified DGKɛ, it is now possible to study the interaction of DGKɛ with model membranes. This project aims to investigate how the biophysical environment of the cell membrane influences the function of DGKɛ. Large unilamellar vesicles (LUVs) are employed as model membranes, and their lipid compositions are varied to address how membrane curvature, anionic lipids, and cholesterol each impact the activity of DGKɛ. Our results showed that intrinsic curvature significantly influences DGKɛ activity, as opposed to anionic lipids which did not show significance. Further, it was found that cholesterol displays an inhibitory effect on DGKɛ. It is therefore important to thoroughly characterize how membrane physical properties modulate the function DGKɛ, in hopes of laying the foundation for further studies on the disease states associated with the physiological role of the enzyme.
LUCIA KRIVANKOVA-SMAL – UNDERSTANDING LARGE-SCALE CRUSTAL STRUCTURE AT THE CANADIAN NUCLEAR LABS RADIOACTIVE CONTAINMENT FACILITY
SUPERVISOR: DR. A. DICKIN (GEOG/EARTH SCI)
The Grenville Province results from a ca. 1 Ga continental collision, which caused a large thrust sheet to be exhumed from the deep crust and then to be transported horizontally, giving rise to a ramp flat thrust architecture. Subsequently the crust underwent folding and erosion, leaving a complex pattern of tectonic ‘outliers’ and ‘windows’. When the underlying crust (parautochthon) peaks through the overlying crust (allochthon), the structure is a tectonic window. A piece of crust entrained to the bottom of the allochthon is considered a duplex. The parautochthon, allochthon, and duplex have different ages, which can be mapped by Neodymium (Nd) isotopes. This project involves detailed Nd age mapping of a tectonic window in the Chalk River area from surface and borehole samples to reconstruct the 3-dimensional structure tectonic history. Nd isotope analysis was conducted on over 20 rock samples, and crustal formation ages were mapped and analyzed in ArcGIS. The analysis discovered locations where the parautochthon and duplex are both seen at the surface due to the vertical displacement of the Mattawa Fault, which cuts through the window. The local 3-dimensional structure was reconstructed, giving clues on how the duplex behaves on a larger scale, and ultimately supporting a ramp flat thrust regional architecture.
JESSE PROVOST – RECTILINEAR LINE VORTEX STABILITY: COMPARING THE BIOT-SAVART LAW AND THE LOCAL INDUCTION APPROXIMATION
SUPERVISOR: DR. B. PROTAS (MATH&STATS)
In vortex dynamics, the Biot-Savart law describes the velocity induced in a fluid by a vortex. One area of vortex dynamics studies the motion induced on a vortex by the vortex itself. One would assume that you could use the Biot-Savart law to describe how a vortex moves. However, this is not common practice, as the local induction approximation that significantly reduces the computation and complexity of the problem of describing vortex motion. Another rigorously studied area of vortex dynamics is vortex stability. The problem of vortex stability can be stated as a question: If a vortex is agitated (perturbed) in some way, will the vortex remain intact, or will the vortex disperse? This question is widely answered using the local induction approximation. This purpose of this study is to determine if the stability results differ when using the Biot-Savart law or the local induction approximation.
To do a comparison analysis we study the simplest three-dimensional vortex: the rectilinear line vortex. The rectilinear line vortex can be thought of as an infinitely long line of vorticity. To compare the two methods, we apply tools from linear stability theory and shape calculus to determine the stability results from both methods. If the results differ, then it shows that there are some inconsistencies when using the local induction approximation. This means that stability results from the literature may also be different when using the Biot-Savart law, which is interesting considering these results are widely used in aerodynamics.
BIANCA BANTOTO – POLYSUBSTANCE USE AND SUICIDALITY AMONG METHADONE MAINTENANCE PATIENTS: A MULTI-CENTRE INVESTIGATION
SUPERVISOR: DR. Z. SAMAAN (PSYCHIATRY AND BEHAVIOURAL NEUROSCIENCE)
Suicidal behaviour is a devastating and critical issue among individuals using illicit opioids, yet little research has been conducted on risk factors within this vulnerable population. Given the rising enrollment in methadone maintenance treatment (MMT) programs, the most widely used treatment for opioid use disorder, investigation into suicidal behaviour in this particular group is imperative. The primary objective of this study is to investigate the relationship between polysubstance use and suicidality among MMT patients. This cross-sectional multi-centre study recruited patients (n=681) receiving methadone for opioid use disorder from methadone clinics across Southern Ontario between May 2013 and March 2016. Demographic information, clinical history, psychiatric assessment, methadone dose, and treatment duration were collected using structured interviews. Study objectives were addressed using a descriptive statistical summary and a multivariable logistic regression model generated in STATA 13. By recognizing polysubstance use as a risk factor for suicidal behaviour in this population, suicide risk may be better assessed, and as such, appropriate action may be taken in preventing suicide among MMT patients.
EVA CLARK-LEPARD – PERCEPTIONS OF SELF-EFFICACY AND ATTITUDES ABOUT SEXUALITY AMONG UNDERGRADUATE STUDENTS IN HUMAN SEXUALITY COURSES
SUPERVISOR: DR. A. KHAN (PNB)
Researchers have been interested in learning about sexual attitudes and people’s ability to manage their sexual health for decades. However, extensive research on student attitudes conducted in the 1980s and 1990s cannot accurately be applied to current undergraduate students, as cultural and societal views are continuously shifting. Beyond this, the advent of the Internet has provided a medium to easily access a large variety of information about sexuality. In terms of the acquisition of these attitudes and behaviours, students’ experience of sexual health education are inconsistent across North America, making human sexuality courses at the university level vital to this learning process.
The aim of this project is to investigate changes in student attitudes and sexual self-efficacy, which is defined as an individual’s belief in their ability to perform a particular behaviour in a sexual situation, after taking an undergraduate human sexuality course. A novel questionnaire exploring STIs, contraception, masturbation, reproductive anatomy, reproductive physiology, consent, unwanted pregnancy, sexual orientation, and paraphilias was used. This questionnaire was delivered at the beginning and the end of term in biology-based and psychology-based courses. It is hypothesized that student sexual self-efficacy will increase and students will gain a greater acceptance of the diversity of sexual behaviour.
This investigation will provide insight into the efficacy of undergraduate courses as sex education and highlight how aspects of human sexuality understood by students, allowing professors to reflect on their pedagogical practices. As well, it can be used to improve university wide programming with regard to sexual health.
DEVON CRAWFORD – THE MECHANISMS OF SERIAL ORDER PROCESSING
SUPERVISOR: DR. E. SERVICE (LINGUISTICS AND LANGUAGES)
An extensive body of literature indicates functional similarities between verbal and visuo-spatial domains of short-term memory (STM) with respect to serial order processing (i.e., the mind’s ability to remember sequential information), highlighting the possibility of a domain-general ordering mechanism. Moreover, a growing body of work has elucidated strong relations between serial order STM capacity and word-learning ability (see Baddeley, Gathercole & Papagno, 1998, for a review), suggesting that a similar domain-general ordering mechanism may be at play within the language acquisition system. The present project aimed to directly address these two related themes by first studying a) whether serial order processing is domain-general and then b) whether serial order STM underlies vocabulary learning. In a series of experiments, we provide direct evidence that common ordering mechanisms are employed by the verbal and visuo-spatial STM domains.
BIRAN FALK-DOTAN – ARE WE SMARTER AFTER EXERCISE?
SUPERVISOR: DR. J. HEISZ (KINESIOLOGY)
Besides its well-established physical health benefits, aerobic exercise can improve performance in several different cognitive measures. In particular, exercise acutely improves executive functioning – activities involving quick self-regulation such as error correction and response inhibition. Although exercise intensity affects heart rate and cortical hemodynamics, few studies compare the cognitive effects of different intensities of exercise; most previous research has compared a physical exercise condition to a rest condition. Further, no previous studies have examined an effect of exercise on fluid intelligence (IQ), a more general construct representing reasoning and problem-solving ability. Fluid IQ tasks activate similar brain regions as executive functioning tasks and fluid IQ ability correlates positively with executive functioning ability, suggesting that these functions may share an underlying mechanism. We investigated whether exercise of different intensities can confer different effects on executive functioning and fluid IQ performance. We compared executive functioning (Stroop task) performance and fluid IQ (Raven’s Advanced Progressive Matrices; RAPM) after low- and high-intensity exercise in a within-subject design. Participants also completed questionnaires to measure physical activity history and mood. Participants’ prefrontal hemodynamics were recorded using functional near-infrared spectroscopy. We found no change in Stroop or RAPM performance between the two sessions, suggesting that low- and high-intensity exercise have the same effect on executive functioning and fluid IQ. Further, physical activity history and mood did not predict cognitive task performance. Previous literature suggests that exercise leads to cognitive improvements relative to rest, but this study suggests that increasing exercise intensity does not lead to greater cognitive improvements.
DAKOTA BINKLEY – DARK FIELD TRANSMISSION ELECTRON MICROSCOPY INVESTIGATION OF BONE ULTRASTRUCTURE
SUPERVISOR: DR. K. GRANDFIELD (MATERIAL SC & ENG)
Bone is a unique hierarchical material that is mostly comprised of collagen and mineral. The ultrastructure of bone is still debated, as the most widely accepted model  has been challenged with advanced transmission electron microscopy (TEM) images , . The traditional model suggests that collagen fibers lay parallel to one another with 40 nm spacing between them, a location termed the gap zone. Most believe that mineral is present within the gap zone and that it can extend past it, creating an overlap zone . Recent bight field (BF) TEM images suggest that mineral surrounds collagen fibrils in stacks , . This alternative model can be extended to suggest that the gap zone is not filled with mineral and is hypothesized to consist of amorphous calcium phosphate (ACP). This study aims to use dark field (DF) TEM imaging to determine the location of crystalline materials in the gap zone.
A longitudinal sectioned femoral diaphysis of mature bovine bone was ion milled until electron transparent and subsequently imaged using a Philips CM-12 TEM microscope at 120 kV. Both BF and DF images were obtained, with DF images highlighting crystals parallel to the collagen fibers (aperture placement on the 002 reflection).
Results suggest some gap zones lack mineral that lies on the 002 plane. DF imaging can only show crystalline mineral and thus we cannot conclude if ACP is necessarily in the gap zone. Therefore, images obtained during the study suggest that all gap zones are not mineralized. Further investigation of the gap zone using advanced spectroscopy and TEM imaging is required to determine the exact composition of the gap zone.
 W. J. Landis, K. J. Hodgens, J. Arena, M. J. Song, and B. F. McEwen, “Structural relations between collagen and mineral in bone as determined by high voltage electron microscopic tomography,” Microsc. Res. Tech., vol. 33, no. 2, pp. 192–202, Feb. 1996.
 E. A. McNally, H. P. Schwarcz, G. A. Botton, and A. L. Arsenault, “A model for the ultrastructure of bone based on electron microscopy of ion-milled sections,” PLoS One, vol. 7, no. 1, pp. 1–12, 2012.
 H. P. Schwarcz, E. A. McNally, and G. A. Botton, “Dark-field transmission electron microscopy of cortical bone reveals details of extrafibrillar crystals,” J. Struct. Biol., vol. 188, no. 3, pp. 240–248, 2014.
 B. Alexander, T. L. Daulton, G. M. Genin, J. Lipner, J. D. Pasteris, B. Wopenka, and S. Thomopoulos, “The nanometre-scale physiology of bone: steric modelling and scanning transmission electron microscopy of collagen-mineral structure.,” J. R. Soc. Interface, vol. 9, no. 73, pp. 1774–86, Aug. 2012.
THESIS PRESENTATIONS – April 4, 2017
JACQUELINE WATT – ELECTROCARDIOGRAPH OUTCOMES AND THEIR ASSOCIATIONS WITH RECOVERY TIME IN AN INCIDENT HEMODIALYSIS COHORT
SUPERVISOR: DR. MICHAEL WALSH AND DR. RULAN PAREKH (CLINICAL EPIDEMIOLOGY)
Sudden cardiac death is common in end stage renal disease patients receiving hemodialysis treatment. This has been linked to the incidence of cardiac arrhythmias during, and shortly after, the treatment period. Sudden cardiac death is a common occurrence for end stage renal disease patients receiving hemodialysis treatment and has been shown to be linked to the incidence of arrhythmias during and shortly after receiving treatment. Arrhythmias can be monitored using electrocardiograph metrics, such as the QT interval. A prolonged QT interval correlates to an increased risk of arrhythmia. While physiological measurements provide evidence supporting the increased risk of arrhythmias in hemodialysis patients, the predictive significance of patient reported data, such as recovery time after dialysis, is limited.
Patients’ quality of life is largely impacted by treatment with dialysis. Dialysis treatment has a large impact on patients’ health-related quality of life. It has been found that this impact can be used to predict mortality. Patient reported recovery time is a simple and effective assessment tool, found to be easily interpretable, stable over time, and sensitive to change. However, this is limited by the fact that the recovery process is not well understood. Previous studies have looked only the association between recovery time and other qualitative data, such as health-related quality of life questionnaires. This study examines the association between recovery time and electrocardiograph metrics and their potential to determine increased risk for the development of arrhythmias.