Graduate Theses & Dissertations

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Evaluating Environmental DNA (eDNA) Detection of Invasive Water Soldier (Stratiotes Aloides)
In 2008, the first North American water soldier (Stratiotes aloides) population was discovered in the Trent River, Ontario. Water soldier is an invasive aquatic plant with sharp, serrated leaves that has the potential to spread rapidly through dispersed vegetative fragments. Although it is too late to prevent water soldier establishment in the Trent River, its local distribution remains limited. In this study, environmental DNA (eDNA) was explored as a potential tool for early detection of water soldier. Species-specific markers were designed from chloroplast DNA regions matK and rbcL, and a qPCR assay with rbcL primers yielded the most sensitive detection of water soldier eDNA. Positive detections were obtained from six of 40 sampling locations, of which five were collected in Seymour Lake, an area with large patches of water soldier. As water soldier plants were known to be present at these sites, high eDNA concentrations were expected. The sixth positive detection from Trent Lock 5 (50 km downstream of Lake Seymour) was unexpected as it was obtained at a site with no water soldier sightings. This is one of the first studies to demonstrate the effectiveness of eDNA detection from aquatic plants. Author Keywords: aquatic plant, eDNA, environmental DNA, invasive species, Stratiotes aloides, water soldier
Evaluation of silver nanoparticles (AgNPs) and anti-GD2-AgNP antibody-drug conjugates as novel neuroblastoma therapies
Neuroblastoma (NB) has one of the highest mortality rates in pediatric oncology due to relapsed and refractory disease. Current aggressive multi-modal treatments are inhibited by dose-limiting toxicities and are associated with late-effects and secondary malignancies, emphasizing the necessity for novel therapeutics. Uniquely, most NB cells highly express disialoganglioside (GD2) a cell surface glycolipid that can provide a target for tumour-specific delivery. This study demonstrates a comprehensive evaluation of silver nanoparticles (AgNPs) and the first preliminary evaluation of anti-GD2-AgNP antibody-drug conjugates (ADCs) against NB in vitro. This present study validates the potential for AgNPs as an anti-cancer agent against NB as AgNPs demonstrated preferential toxicity towards NB cells through metabolic inhibition and indicative morphological alterations, while a less tumorigenic cell line demonstrated resistance to AgNP treatment. Therefore, this work identified an AgNP cell-type-dependent cytotoxicity effect. Low conjugation efficiency of the anti-GD2 monoclonal antibody, 14.G2a, to NHS-activated AgNPs failed to exert greater toxicity than the AgNPs alone. Collectively, this thesis provides novel information regarding the anti-cancer effects of AgNPs against NB with recommendations for anti-GD2-AgNP ADCs. Author Keywords: ADC, Chemotherapy, GD2, Neuroblastoma, Silver nanoparticles
Evaulating the American Woodcock Singing-Ground Survey Protocol in Ontario using Acoustic Monitoring Devices
The breeding phenology of American Woodcocks (Scolopax minor) was evaluated in Ontario, Canada to determine if changes in dates of courtship activity have introduced negative bias into the American Woodcock Singing-ground Survey (SGS). Long-term woodcock phenology and climate data for Ontario were analysed using linear regression to determine if woodcock breeding phenology has changed between 1968 and 2014. There was no significant trend in woodcock arrival date, but arrival date was correlated with mean high temperature in March. In 2011-2013, programmable audio-recording devices (song meters) were deployed at known woodcock singing-grounds to determine if peaks in courtship activity coincided with survey dates used by the SGS. Spectrogram interpretation of recordings and data analyses using mixed-effects models indicated the SGS survey dates were still appropriate, except during the exceptionally early spring in 2012 when courtship displays were waning in one region during the survey window. The methods for interpretation of song meter recordings were validated by conducting point counts adjacent to song meters deployed at singing-grounds, and at randomly selected locations in woodcock habitat. Recommendations for the SGS protocol are included. Author Keywords: detectability, phenology, Scolopax minor, Singing-ground Survey, song meter
Evidence for hybrid breakdown in the cattail (Typha) hybrid swarm in southern Ontario
Heterosis, expressed as phenotypic superiority over parental species, typically peaks in first generation hybrids (F1s), while later generations (F2 +) exhibit lower fitness. The decrease in hybrid fitness is called hybrid breakdown. The overall incidence of hybrid breakdown in invasive hybrid zones remains poorly understood. The Laurentian Great Lakes (LGL) region contains a hybrid zone comprised of: native Typha latifolia, Typha angustifolia, and hybrid Typha × glauca. F1 T. × glauca display heterosis and are invasive, while later generation hybrids are relatively rare. To investigate possible hybrid breakdown, I compared seed germination and plant growth of backcrossed and advanced-generation (F2) hybrids to F1s and T. latifolia. I found evidence for hybrid breakdown in F2s and backcrossed hybrids, expressed as reduced growth and germination rates. Expression of hybrid breakdown in F2s and backcrosses may explain their relative rarity in the LGL hybrid zone. Author Keywords: Advanced-generation hybrids, Backcrossed hybrids, Hybridization, introgression, Invasive species, plant competition
Evidence of an Interaction Between Memory Stores for Long-Term Context Fear Memory in the Rat
Memories which typically require the hippocampus (HPC) can become represented in structures outside of the HPC, and therefore resistant to HPC damage, but, the properties of these memories are poorly understood. Some research has suggested that the HPC continually contributes to memories that are resistant to hippocampal damage, and without this support, they are weaker and more susceptible to loss. However, this hypothesis has yet to be tested experimentally. We examined this possibility in rats by assessing decay and extinction of a context fear memory that had become independent of the HPC via repeated learning episodes. We found that HPC-independent context fear memories decay and extinguish faster without continued HPC support, suggesting that the HPC plays a continued role in long-term memory. We also provide new evidence of a persistent interaction between the HPC and other memory systems, which strengthens non-HPC representations so that they withstand HPC damage at longer intervals. Author Keywords: consolidation, context fear, hippocampus, memory, retrograde amnesia
Executive Function as a Predictor of Emotional, Behavioural, and Social Competence Problems in Children with Epilepsy
The study aimed to examine the association between different components of executive function (EF) and emotional, behavioural, and social competence problems (EBSP) in children with epilepsy. Although there is evidence of an association between EBSP and EF in typically developing children, little research has examined this relation in children with epilepsy. The sample comprised of 42 children with epilepsy, aged 6.0 to 18.1 years old. Results showed that EBSP were associated with EF in these children; however, different components of EF were related to different EBSP. Shifting was a significant predictor of emotional, behavioural, and social competence problems in children with epilepsy, whereas inhibition was a significant predictor of behavioural problems. This suggests that children with epilepsy, with different EF profiles may be at-risk for developing different types of problems. These results may aid researchers and clinicians with the development of new techniques to identify and treat children with EBSP. Author Keywords: behavioural problems, emotional problems, epilepsy, executive function, social competence
Executive Function, Emotion Regulation, and Social Problem Solving, in Adolescence and Early Adulthood
Research to date on social problem solving typically focuses on elementary school aged children. However, adolescents and young adults may experience more novel and emotionally complex social conflicts that require different skills to navigate them successfully. Previous research has highlighted executive function (EF) and emotion regulation as possible skills that help with social problem solving. The current study examined the potential relation between EF, emotion regulation, and social problem solving. The sample consisted of 174 participants with a mean age of 19.60 years. Results showed that the shifting component of EF was associated with being able to take different perspectives when coming up with a solution for a social conflict involving a romantic partner. Additionally, emotion regulation was associate with perspective taking in the overall social problem solving process with a romantic partner. These results suggest that both EF and emotion regulation are involved in the ability to take different perspectives during a social conflict in this age range. Author Keywords: Emotion Regulation, Executive Function, Social Problem Solving
Exonic Trinucleotide Microsatellites
Trinucleotide repeats (TNRs) are a class of highly polymorphic microsatellites which occur in neutral and non-neutral loci and may provide utility for individual- and population-identification. Exonic trinucleotide motifs, in particular, offer additional advantages for non-human species that typically utilize dinucleotide microsatellite loci. Specifically, the reduction of technical artifacts, greater separation of alleles and greater specificity of amplification products leading to more efficient multiplexing and cross-taxa utilization. This study aims to identify and characterize polymorphic trinucleotide repeats and conserved primer sequences which are conserved across Cervidae (deer) species and their potential for individual identification in forensic wildlife investigations. Chapter one provides a broad introduction to trinucleotide microsatellites, chapter two deals with data-mining TNRs and chapter three applies the identified TNRs as genetic markers for individual identification. Results demonstrate proof-of-concept that exonic TNRs are capable of giving random match probabilities low enough to be employed in individual identification of evidentiary samples. Author Keywords: DNA typing, Exons, Genetic Markers, Individual Identification, Trinucleotide, Wildlife Forensics
Exploring Characteristics of those Utilizing Different Modalities of Treatment for Substance Use Disorders
Substance use disorder (SUD) is a pervasive psychological disorder detrimentally impacting both individuals and society on a psychological, economic, and social level. The best protocol for treating SUD as well as what defines success in treatment is often debated in the research. However, researchers agree that different psychosocial factors can influence outcomes. The literature suggests that mood, dark personality traits (narcissism and psychopathy), social supports, and state of change may be associated with treatment for SUD. The current study explored whether these factors predicted the type of treatment (abstinence-based or harm reduction) individuals with SUD were in. The sample consisted of 37 participants in a 12-step abstinence-based program and 65 in a harm reduction program at a local hospital. Results indicated that those in abstinence-based groups reported significantly fewer symptoms of anxiety and depression, lower levels of narcissism and psychopathy, more social supports, and advanced stage of change in comparison to those attending a harm reduction program. In addition, depression, narcissism, and perceived social support were significant predictors of treatment group membership. These findings suggest that those involved in abstinence-based groups appear to experience overall more wellness than those in harm reduction. Although further research is needed to specify the relations among factors, this study is a step towards understanding the difference between people who utilize one program versus another. Author Keywords: Abstinence, Addiction, Harm Reduction, Personality, Treatment
Exploring reproduction in wild blue lupine (Lupinus perennis) in comparison to L. polyphyllus and L. albus
Wild lupine (Lupinus perennis) restoration efforts seek to increase and connect populations, using seeds, to facilitate the recovery of endangered butterflys in Ontario. This study observed plant growth and phytohormone levels of L. albus, L. polyphyllus, and L. perennis through stages of seed development, each with varying strategies in growth and reproductive investment. L. polyphyllus is similar to L. perennis in morphology, acting as similar comparable with L. albus, a well-studied annual, as an outgroup comparator. Wild lupines showed a lack of sexual reproductive effort as they did not put as much effort into above ground growth, and few in the population reproduces. They also showed cis-zeatin, a weaker cytokinin, throughout development and had higher amounts of abscisic acid at the end of seed maturity, impacting their ability to develop and germinate. These factors contribute to why wild lupines are difficult to restore using seeds, limiting expansion and challenging restoration. Author Keywords: L. albus, L. perennis, L. polyphyllus, plant physiology, seed development, Wild blue lupine
Exploring the Role of Natural Antisense Transcripts in the Stress Response of Ustilago maydis
Fungal pathogens adapt to environmental changes faster than their hosts, due in part to their adaptive mechanisms exhibited in response to stress. Ustilago maydis was used to investigate potential natural antisense transcript (NAT) RNA-mediated mechanisms that enhance fungal adaptation to stress. Of the 349 NATs conserved amongst U. maydis and two related smut fungi, five NATs were identified as having altered transcript levels in response to multiple stress conditions. Subsequently, antisense transcript expression vectors were created for select NATs and transformed into U. maydis haploid cells. When exposed to stress conditions, two antisense expressing mutant strains exhibited alterations in growth. RT-qPCR analysis of mRNA complementary to expressed NATs revealed no significant change in mRNA levels, which suggests NAT expression may influence stress response through dsRNA formation or other RNA mediated mechanisms. These results establish a basis for further investigations into the connection between NATs and the stress response of fungi. Author Keywords: natural antisense transcripts, non-coding RNAs, stress response, Ustilago maydis
Exploring the Scalability of Deep Learning on GPU Clusters
In recent years, we have observed an unprecedented rise in popularity of AI-powered systems. They have become ubiquitous in modern life, being used by countless people every day. Many of these AI systems are powered, entirely or partially, by deep learning models. From language translation to image recognition, deep learning models are being used to build systems with unprecedented accuracy. The primary downside, is the significant time required to train the models. Fortunately, the time needed for training the models is reduced through the use of GPUs rather than CPUs. However, with model complexity ever increasing, training times even with GPUs are on the rise. One possible solution to ever-increasing training times is to use parallelization to enable the distributed training of models on GPU clusters. This thesis investigates how to utilise clusters of GPU-accelerated nodes to achieve the best scalability possible, thus minimising model training times. Author Keywords: Compute Canada, Deep Learning, Distributed Computing, Horovod, Parallel Computing, TensorFlow

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Graduate student theses produced at Trent University. You may also browse theses and dissertations by year, program, or author.

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