Life Sciences Commons^™

Towards Understanding And Improving Speech Processing, Sonia Yasmin

Electronic Thesis and Dissertation Repository

This dissertation explores mechanisms for understanding and improving speech processing. First, I used EEG to investigate the acoustic and semantic processing of continuous naturalistic speech masked by multi-talker babble. I found that different features of the same speech signal are reflected in different aspects of the neural tracking response, which are themselves differentially affected by noise. These findings point to a complex relationship between speech intelligibility and neural speech encoding.

Next, I systematically reviewed the current advancements in speech enhancement technologies. I find that speech enhancement algorithms are limited in their generalizability to speech-noise (i.e., babble). I demonstrate that, for …

Ecological Drivers Of Songbird Stopover Behaviour During Autumn Migration In Eastern New Brunswick, Andrew T. Beauchamp

Electronic Thesis and Dissertation Repository

As songbirds migrate, they must periodically stop to rebuild the energy needed for flight. Individual traits, local habitat characteristics, and the surrounding landscape can affect stopover refuelling and movement, yet the relative importance of endogenous and exogenous factors and the interrelation between refuelling and movement is less well understood owing to the challenge of measuring these aspects concurrently in free-living songbirds. I applied physiological profiling and habitat assessment together with radio telemetry and radar technologies to evaluate key ecological drivers of stopover performance in songbirds. In my first research chapter, I evaluated how refuelling and diel activity differed among five …

Understanding Mechanisms Underlying Changes In Parental Care Behaviour In Response To Perceived Paternity In Sunfish, Emma Churchman

Electronic Thesis and Dissertation Repository

Parental care is essential for the survival of many young animals but presents significant costs to the caring parent. To mitigate these costs, parental care systems have evolved to optimize survival and fitness. According to parental investment theory, care allocation is influenced by the offspring’s value, which is often linked to their relatedness to the parent. In this thesis, I explore how hormones and gene expression influence parental care, focusing on bluegill sunfish (Lepomis macrochirus) and the hybrids they produce with pumpkinseed sunfish (Lepomis gibbosus). By manipulating direct and indirect paternity cues – swapping eggs between …

The Roles Of Fabp3 In Endothelial Dysfunction And The Transcriptomic Insights Into Cardiovascular Disease, Chi Hien Nguyen

Electronic Thesis and Dissertation Repository

Heart-type fatty acid binding protein (FABP3) is an effective biomarker for cardiac injuries. However, it has also been tested as a biomarker in patients with peripheral artery diseases; these conditions are complications of atherosclerosis, which is driven by endothelial dysfunction. As FABP3 release is not exclusive to the heart but appears to characterize cardiovascular events, whether FABP3 influences endothelial function is not known. Additionally, the transcriptomic profiles of endothelial cells during cardiovascular stresses remain under-investigated. This thesis investigates the multifaceted role of FABP3 and the transcriptomic alterations in endothelial cells under different cardiovascular stressors, offering novel insights into endothelial dysfunction …

Determining The Effects Of Mistranslating Transfer Rna Variants On Drosophila Melanogaster, Joshua R. Isaacson

Electronic Thesis and Dissertation Repository

Transfer RNAs (tRNAs) play a central role in translation as adaptor molecules between mRNA and protein. Variant tRNAs can cause the misincorporation of an amino acid into a growing polypeptide. Mistranslating tRNA variants are surprisingly common in humans but the effects of mistranslating tRNA variants on eukaryotic biology are poorly understood. My thesis aimed to create a model of tRNA-induced mistranslation using the fruit fly Drosophila melanogaster and characterize the effects of mistranslating tRNA variants on eukaryotic biology.

I first integrated a gene encoding a serine tRNA variant that induced proline-to-serine (P>S) mistranslation into the fly genome. Proteins isolated …

Identification And Characterization Of Isoflavone Reductase Family Members In Soybean, Negin Azizkhani

Electronic Thesis and Dissertation Repository

Soybean’s yield is threatened by Phytophthora sojae, a pathogen responsible for stem and root rot disease. Glyceollins, unique antimicrobial agents specific to soybeans in partially preventing P. sojae infection, are derived from the isoflavonoid branch of the general phenylpropanoid pathway. One pivotal enzyme exclusively involved in glyceollin synthesis in soybean is the isoflavone reductase (GmIFR), which catalyzes the 2'-hydroxydaidzein conversion to 2'-hydroxy-2,3-dihydrodaidzein as a precursor for glyceollin biosynthesis. To comprehensively identify all members of the GmIFR gene family within the soybean genome, keyword and blast protein searches were conducted, identifying 98 putative GmIFRs. Among these candidates, …

Characterizing Hypoxia, Neutrophil Persistence And Revascularization In The Murine Db/Db Model Of Type Ii Diabetic Impaired Skin Healing, Michael R. Grynyshyn

Electronic Thesis and Dissertation Repository

Impaired skin healing represents a significant clinical burden. In the diabetic, inflammatory aberrations, hypoxia and insufficient angiogenesis all result in negative wound healing outcomes - repeated infections, poor perfusion and ultimately amputation. Previous research has reported comparable levels of neutrophils in closed wounds up to 4-12 weeks old. Our study interest was in investigating the dynamics of hypoxia resolution, neutrophil persistence and angiogenic response in the db/db model. Contrary to our hypothesis, we observed significantly higher hypoxic load in the wild types at days 3 and 7. Additionally, we observed significantly elevated neutrophil numbers at day 7 db/db wound bed …

Development Of An In Vitro Model Of Mitochondrial Dna Copy Number Depletion Via Stable Inducible Expression Of D1135a Mutant Dna Polymerase Gamma, Amanda L. Morin

Electronic Thesis and Dissertation Repository

Mitochondria are responsible for several crucial cellular processes and contain their own DNA (mtDNA) that exists in several copies. Variation of mtDNA copy number (mtDNA-CN) alters energy metabolism and can modify the epigenome and transcriptome. We hypothesized that inducible expression of polymerase-deficient D1135A dominant-negative DNA polymerase gamma (DN-POLG) would result in mtDNA-CN depletion. Here, an in vitro model expressing D1135A POLG was created using the Flp-InTM T-RExTM-293 stable inducible expression system. Stable integration was confirmed with PCR amplification and Sanger sequencing of post-integration genomic sequences. D1135A POLG expression was confirmed with Western blot of the FLAG-tag antibody. Induction of D1135A …

Frontoparietal Circuitry Underlying Saccade Control In The Common Marmoset, Janahan Selvanayagam

Electronic Thesis and Dissertation Repository

Our visual world is full of far more stimuli than can be processed simultaneously. Yet we are able to efficiently extract behaviourally relevant information from a scene, primarily by performing rapid saccadic eye movements. These processes are under the control the frontoparietal network, two critical nodes of which are: the lateral intraparietal area (LIP) and the frontal eye fields (FEF). Extensive research in the macaque has causally implicated these areas in visual attention and oculomotor control. However, the organization of the activity of single neurons in these areas across cortical layers remains poorly understood as these regions are deep within …

Outclimbing Cognitive Decline: Age, Western Diet, Resistance Exercise, And The Brain., Leila Dzinic

Electronic Thesis and Dissertation Repository

Increased age and obesity diminish motivation, perseverance, and spatial memory function. Aerobic exercise interventions have successfully rescued some of these processes. However, in older and heavier populations aerobic exercise is not as sustainable due to high risk of injury. Resistance exercise consists of physical activity where maximum oxygen consumption is not increased and has been proposed as a safe and effective intervention for this population. Here, we used touchscreen-based cognitive testing to elucidate the influence of resistance exercise on motivation and spatial memory in aged, diet-induced obese mice, using a water restriction procedure I develop in Chapter 2. Mice underwent …

Soybean Arogenate Dehydratases (Gmadts): Involvement In The Cytosolic Isoflavonoid Metabolon Or Trans-Organelle Continuity?, Emily J. Clayton, Nishat S. Islam, Kelsey Pannunzio, Kuflom Kuflu, Ramtin Sirjani, Susanne E. Kohalmi, Sangeeta Dhaubhadel

Biology Publications

Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs …

Artificial Intelligence, Big Data, And Regulation Of Immunity: Challenges And Opportunities, Bhagirath Singh, Anthony M Jevnikar, Eric Desjardins

Microbiology & Immunology Publications

The immune system is regulated by a complex set of genetic, molecular, and cellular interactions. Rapid advances in the study of immunity and its network of interactions have been boosted by a spectrum of "omics" technologies that have generated huge amounts of data that have reached the status of big data (BD). With recent developments in artificial intelligence (AI), theoretical and clinical breakthroughs could emerge. Analyses of large data sets with AI tools will allow the formulation of new testable hypotheses open new research avenues and provide innovative strategies for regulating immunity and treating immunological diseases. This includes diagnosis and …

No Influence Of Steady-State Postural Changes On Cerebrovascular Compliance In Humans, Alicia M. Kells, M Erin Moir, Geoff B. Coombs, Andrew W. D'Souza, Stephen A. Klassen, Baraa K. Al-Khazraji, Kevin Shoemaker

Kinesiology Publications

The aim of this study was to determine the effect of posture changes on vascular compliance in intracranial (brain) vs. extracranial vascular beds (forearm). Eighteen young adults (nine females) performed a supine-to-seated-to-standing protocol involving five minutes of rest in each position. Continuous blood pressure, middle cerebral artery (MCA) blood velocity, and brachial artery blood velocity were recorded at each posture. Three to five consecutive steady-state cardiac cycles at each posture were analyzed by a four-element lumped parameter modified Windkessel model to calculate vascular compliance. Mean arterial pressure (MAP) increased from supine to seated (76[9] vs 81[12] mmHg; P=0.006) and from …

Developing Regulated Crispr Systems To Control Bacterial Microbiomes, Gregory M. Pellegrino

Electronic Thesis and Dissertation Repository

Changes to the human microbiome’s composition and metabolome are associated with numerous diseases and alterations to xenobiotic metabolism. As such, targeting the human microbiome is an increasingly popular option for therapeutic interventions. However, traditional therapies that target the microbiome such as antibiotics lack specificity, which can affect the beneficial species of the microbiome and cause adverse health outcomes such as the rise of antimicrobial-resistant bacteria. Therefore, the research and development of specific, targeted antimicrobial therapies is crucial to effectively treating microbiome dysbioses.
CRISPR and CRISPRi provide easily modifiable, RNA-guided mechanisms mediated by the Cas9 or dCas9 enzymes to induce sequence-specific …

Adaptation Reshapes The Distribution Of Fitness Effects, Diego Tenoch Morales Lopez

Electronic Thesis and Dissertation Repository

The process of adaptation has been of interest since the XIX century, when Darwin first proposed the idea of natural selection. Since then, there has been a myriad of theoretical and empirical works that have expanded the field. From the many evolutionary insights these works have produced, a foundational idea is that spontaneous mutations in the genome of organisms can produce changes to their reproductive success that might confer an advantage for the mutant organisms with respect to their peers. Therefore, mutations drive adaptive evolution by virtue of their heritable effects on fitness. Empirical measures of the distribution of these …

Learning And Growth: My Experiential Learning With Metatherapy And Western Heads East, Naomi So

SASAH 4th Year Capstone and Other Projects: Publications

This paper provides a reflective analysis of my experiential learning opportunities with Meta Therapy and Western Heads East (WHE). At Meta Therapy, I acquired practical and professional skills as a physiotherapist assistant, putting my scientific knowledge to the test and refining my clinical proficiency. The paper delves into the challenges faced, particularly navigating a workplace conflict, and discusses the strategies employed to overcome it. In contrast, my internship with Western Heads East took me to Rwanda for four months, where I played a role in enhancing community health, fostering economic development, and empowering women through probiotic yogurt production. The experience …

Investigating The Soil Mycobiome Of American Ginseng, Rachel Amelia Rajsp

Electronic Thesis and Dissertation Repository

American ginseng (Panax quinquefolius L.) is a perennial herbaceous plant cultivated for its medicinal properties. Growers report that when ginseng is replanted in a field previously used to cultivate ginseng, it soon succumbs to disease, known as ginseng replant disease. I examined changes in composition in the ginseng mycobiome throughout cultivation in a newly planted garden and beyond (i.e., 3–14 years post-harvest) with a third-generation metabarcoding approach (Pacific Biosciences, single-molecule real-time sequencing). Amplicons of about 600 nucleotides from the nuclear ribosomal internal transcribed spacer (ITS) region and translation elongation factor 1-α gene were chosen to help discriminate between closely …

Freezing Tolerance Of Herbaceous Legumes Within Southwestern Ontario: Evidence Of Disproportionate Freezing Sensitivity, Samuel L. Rycroft

Electronic Thesis and Dissertation Repository

Legumes (Fabaceae) represent a diverse and ecologically significant plant taxon; most described legumes form mutualisms with diazotrophic rhizobia, potentially fixing substantial quantities of nitrogen within habitats where they are well-established. Stressors causing lethal or sub-lethal impacts in legumes or rhizobial symbionts may therefore impact the nitrogen dynamics of such habitats. In recent decades, variability of winter temperatures, precipitation, and soil freeze-thaw cycling has increased in temperate regions. Without adequate snow cover to insulate roots and shoot bases, herbaceous plants will likely be exposed to more frequent or severe freezing. In southwestern Ontario, a pattern of disproportionate freezing sensitivity relative to …

Sufu In Shh Signalling Mediated Myogenesis, Suleyman Abdullah

Electronic Thesis and Dissertation Repository

Myogenesis is defined as the formation of skeletal muscle tissue during embryonic development and involves a multitude of cellular signalling pathways. Among these include the Sonic hedgehog (Shh) signalling pathway which must be deactivated for differentiation into muscle cells to occur. However, less is known regarding the pathways operation during cell differentiation and whether Suppressor of Fused (SUFU), the protein inhibitor of Shh signalling, plays a role. To address this, mouse C2C12 myoblast cells were utilized as a model and differentiated into muscle cells to identify the presence of SUFU during this time. Experiments in qRT-PCR show a decrease in …

Elucidating The Relationships Between Spider Size, Joint Stiffness, And The Mechanical Frequency Response Of The Body, Reese L. Gartly

Electronic Thesis and Dissertation Repository

Spiders use vibrations to sense their surroundings. It has been suggested that the vibration perception in spiders may be altered by the mechanics of the body. I studied the biomechanics of spiders, at the level of leg joints and the whole body. To study joints, I quantified the allometry of leg joint stiffness in spiders. I found that the stiffness of spider joints increased nearly isometrically with increasing body mass, partly by having shorter and thicker leg segments and also by other unknown means. Using these data, I developed empirically validated biomechanical models which predicted the effects of mechanics on …

Sex Comparisons Of External, Anatomical And Methodological Factors On Motor Unit Firing Behavior, Michael James Marsala

Electronic Thesis and Dissertation Repository

Motor unit (MU) recruitment and firing rate (MUFR) modulation are the primary factors governing force control. Differences in the anatomical distributions of α-motoneurons, muscle properties, and perception of fatigue between males and females may cause sexually dimorphic MU firing behaviors. The purpose of this dissertation was to further examine external, anatomical, and methodological factors that may influence observations of sex-related differences in neuromuscular function. In chapter 2, sex differences in how mental fatigue may influence MU firing behaviors were examined. Mental fatigue did not significantly alter MU firing behavior, maximal force, or force tracing ability in either males or females. …

Characterizing The Spatial Distribution Of Inhibitory Interneurons Across Early Sensory And Association Areas In Callithrix Jacchus, Nika Khajehdehi

Electronic Thesis and Dissertation Repository

The prefrontal cortex (PFC) is one of the cortical areas responsible for complex cognitive abilities, a function that is believed to arise from increased persistent activity within its microcircuits. Activity within microcircuits is regulated by parvalbumin-containing (PV), calbindin-containing (CB), and calretinin-containing (CR) inhibitory interneurons (INs). It remains unclear how the distribution of activity-regulating INs differs across cortical areas such that persistent activity increases specifically within association areas, allowing for their complex functions. This thesis aims to address this gap by characterizing the spatial distributions and differences in relative proportions of INs across early sensory areas and association areas of the …

The Introduction Of Nursery Seedlings And Their Fungi To A Spruce-Fir Forest In Newfoundland, Alicia G. Banwell

Electronic Thesis and Dissertation Repository

A few species of boreal trees form symbiotic relationships with many ectomycorrhizal (ECM) fungi that allow trees to thrive on nutrient poor soils in Canada. A small number of ECM species grow on tree seedlings raised in nurseries for reforestation of clearcut sites. The native ECM fungal community composition of a mixed spruce-fir forest in Newfoundland was determined through next generation sequencing. With the introduction of nursery seedlings, the transfer of native ECM fungi to seedlings and nursery-established ECM fungi to roots was investigated over 20 months. ECM community composition was found to be similar to that of other boreal …

Investigating Task-Free Functional Connectivity Patterns In Newborns Using Functional Near-Infrared Spectroscopy, Homa Vahidi

Electronic Thesis and Dissertation Repository

Robust functional connectivity in sensorimotor resting-state network (RSN) has been linked to positive neurodevelopmental outcomes in neonates. In the current study, we aimed to map the developmental trajectory of sensorimotor RSN in awake neonates using functional near-infrared spectroscopy (fNIRS). We acquired fNIRS resting-state data from 41 healthy newborns (17 females, gestational age range=36+0 to 42+1 weeks) within the first 48 hours after birth. At the group level, we observed robust positive connectivity in numerous channel-pairs across the sensorimotor network, especially in the left hemisphere. Next, we examined the relationship between functional connectivity, gestational age and postnatal age, while controlling for …

Differential Migration Timing And The Form And Function Of Avian Wings, Jessica E. Deakin

Electronic Thesis and Dissertation Repository

A common differential migration strategy in birds is protandry, whereby males arrive earlier than females. The probable causes of protandry are well studied from the perspective of innate and physical environmental cues, but the influence of the social environment and wing morphology are less known. Theoretical models propose that sex ratio influences protandry; male-biased sex ratios are predicted to advance timing in males due to increased intrasexual competition. To empirically test this, I investigated the spring migration traits of male Yellow-rumped Warblers Setophaga coronata under differing sex ratios. An integrated automated telemetry approach was used, where locomotor movement of captive …

The Adaptor Protein P66shc Governs Central Nervous System Cell Metabolism And Resistance To Aβ Toxicity, Asad Lone

Electronic Thesis and Dissertation Repository

Alzheimer’s disease (AD), a progressive and irreversible neurodegenerative disorder, and is the leading cause of dementia worldwide. It has been posited that AD is caused by the gradual deposition of toxic amyloid-b (Ab) plaques in the brain- that cause oxidative stress and eventually leads to neuronal death and synaptic loss. However, multiple therapies that either interfere with the production, or enhance the removal of Ab from the brain, have ultimately failed to slow or prevent AD. With the ever-increasing burden of AD worldwide, there exists an urgent need for novel therapeutic targets. The adult human brain is an energy demanding …

Neural Responses To Magnetic Orientation Information In Songbirds, Madeleine Ir Brodbeck

Electronic Thesis and Dissertation Repository

Effective navigation and orientation is essential for animals to survive. The study of migratory birds provides insights into these processes, particularly through mechanisms like the geomagnetic compass, which uses Earth's magnetic field for directional information. A brain region in songbirds relevant to this is cluster N, known for its potential role in processing geomagnetic information. Notably, cluster N appears exclusive to nocturnally migratory birds, being active solely at night, and lesion studies reveal that an intact cluster N is necessary for geomagnetic compass orientation. However, given the scarcity of empirical data concerning cluster N, substantial questions persist regarding its function. …

Identification Of Early Diagnostic And Predictive Biomarkers Of Cisplatin-Induced Acute Kidney Injury Using Metabolomics, Yong Jin Lim

Electronic Thesis and Dissertation Repository

Cisplatin is an effective chemotherapeutic agent used for the treatment of a wide variety of solid tumors and hematologic cancers. Despite its effectiveness, cisplatin is associated with several toxic effects to non-cancerous tissues. Nephrotoxicity is the main dose-limiting toxicity in cisplatin therapy, manifesting as acute kidney injury (AKI) in approximately one-third of patients receiving cisplatin. AKI is defined as an abrupt decline in kidney function and is associated with several short- and long-term adverse outcomes, including chronic kidney disease, cardiovascular disease, and mortality. AKI is currently diagnosed by increased serum creatinine (SCr) concentrations. However, SCr is a marker of functional …

Acetylation Regulates Thioredoxin Reductase Activity And Oligomerization, David E. Wright

Electronic Thesis and Dissertation Repository

The Thioredoxin (Trx) system provides the cell with robust defense against oxidative stress and regulates the function of nearly every cellular process through the reduction-oxidation (redox) regulation of proteins. The Trx system is involved in the development of many diseases ranging from cancer to cardiovascular disorders. Thioredoxin reductase (TrxR) is the key enzyme in the Trx system and contains the 21^st genetically encoded amino acid, selenocysteine (Sec). There were multiple experimentally identified TrxR acetylation sites with an unknown effect on TrxR activity. My thesis tested the hypothesis that programmed protein acetylation will enhance the activity of TrxR1. I used …

Aging Effects On The Motivational Consequences Of Unsuccessful Memory Recall, Rachel Sargeson

Electronic Thesis and Dissertation Repository

The present thesis addressed whether experiences of failed recall for names of familiar faces could induce states of curiosity and drive memory benefits. Experiment 1 investigated whether older adults exhibit the same familiarity preference in information seeking, following an unsuccessful recall attempt for names of previously studied faces, as seen in younger adults. Experiment 2 considered whether acting on the curiosity induced by unsuccessful recall of names associated with familiar faces could provide benefits for the relearning of those names in both age groups. The older adults displayed a similar, if not more pronounced, positive relationship between familiarity and subsequent …