Physical Sciences and Mathematics Commons^™

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 …

Short-Term Versus Long-Term Effects Of Nitrogen Addition And Warming On Ecosystem N Dynamics In A Grass-Dominated Temperate Old Field, Benjamin F. A. Souriol

Electronic Thesis and Dissertation Repository

Increased atmospheric nitrogen (N) deposition and climate warming are both anticipated to influence the ecosystem N dynamics of northern temperate ecosystems substantially over the next century. Nevertheless, in field experiments with N addition and warming treatments, temporal scale can play an important role in determining the extent of treatment effects on N dynamics, and it is unclear to what extent the results of short-term studies can be extrapolated to responses over longer time scales. I compared the short-term versus long-term effects of N addition and warming on net N mineralization, N leaching, and N retention in a grass-dominated old field. …

Protein Stability In Solution And In The Gas Phase., Yousef Haidar

Electronic Thesis and Dissertation Repository

Electrospray Ionization mass spectrometry (ESI-MS) is widely used for probing proteins, yet many aspects of this technique remain elusive. Using MS, ion mobility spectrometry (IMS), and circular dichroism (CD) spectroscopy, this thesis sheds light on the stability differences of proteins in the gas phase and solution. After a general introduction (Chapter 1), Chapter 2 scrutinizes some aspects of native ESI. Our data highlight the significance of cone voltage in maintaining a native-like fold and show the advantage of using NH₄Ac in protein experiments. Chapter 3 focuses on hydrogen/deuterium exchange (HDX)-MS. Several studies have reported that D₂O …

Towards Clinical Microscopic Fractional Anisotropy Imaging, Nico Jj Arezza

Electronic Thesis and Dissertation Repository

Microscopic fractional anisotropy (µFA) is a diffusion-weighted magnetic resonance imaging (dMRI) metric that is sensitive to neuron microstructural features without being confounded by the orientation dispersion of axons and dendrites. µFA may potentially act as a surrogate biomarker for neurodegeneration, demyelination, and other pathological changes to neuron microstructure with greater specificity than other dMRI techniques that are sensitive to orientation dispersion, such as diffusion tensor imaging. As with many advanced imaging techniques, µFA is primarily used in research studies and has not seen use in clinical settings.

The primary goal of this Thesis was to assess the clinical viability of …

Decoy-Target Database Strategy And False Discovery Rate Analysis For Glycan Identification, Xiaoou Li

Electronic Thesis and Dissertation Repository

In recent years, the technology of glycopeptide sequencing through MS/MS mass spectrometry data has achieved remarkable progress. Various software tools have been developed and widely used for protein identification. Estimation of false discovery rate (FDR) has become an essential method for evaluating the performance of glycopeptide scoring algorithms. The target-decoy strategy, which involves constructing decoy databases, is currently the most popular utilized method for FDR calculation. In this study, we applied various decoy construction algorithms to generate decoy glycan databases and proposed a novel approach to calculate the FDR by using the EM algorithm and mixture model.

Addressing The Impact Of Time-Dependent Social Groupings On Animal Survival And Recapture Rates In Mark-Recapture Studies, Alexandru M. Draghici

Electronic Thesis and Dissertation Repository

Mark-recapture (MR) models typically assume that individuals under study have independent survival and recapture outcomes. One such model of interest is known as the Cormack-Jolly-Seber (CJS) model. In this dissertation, we conduct three major research projects focused on studying the impact of violating the independence assumption in MR models along with presenting extensions which relax the independence assumption. In the first project, we conduct a simulation study to address the impact of failing to account for pair-bonded animals having correlated recapture and survival fates on the CJS model. We examined the impact of correlation on the likelihood ratio test (LRT), …

The Synthesis And Characterization Studies Of Modified Nucleobase In Pna And Dna, Gyeongsu Park

Electronic Thesis and Dissertation Repository

Nucleic acids have been extensively studied not only for their importance in biological systems as the medium of genetic information but also for their potential uses in therapeutic, diagnostic and other biological applications. As such, modified oligonucleotides and oligonucleotide analogues have drawn the attention of researchers from various disciplines. Modification of oligonucleotides can enhance their desired characteristics and engender unique properties, such as fluorescence, giving rise to a variety of applications. Peptide nucleic acid (PNA) is an oligonucleotide mimic with a pseudo-peptide backbone based on N-(2-aminoethyl)glycine that is renowned for high target binding affinity and resistance to enzyme degradation. …

On The Spatial Modelling Of Biological Invasions, Tedi Ramaj

Electronic Thesis and Dissertation Repository

We investigate problems of biological spatial invasion through the use of spatial modelling. We begin by examining the spread of an invasive weed plant species through a forest by developing a system of partial differential equations (PDEs) involving an invasive weed and a competing native plant species. We find that extinction of the native plant species may be achieved by increasing the carrying capacity of the forest as well as the competition coefficient between the species. We also find that the boundary conditions exert long-term control on the biomass of the invasive weed and hence should be considered when implementing …

Conformational Dynamics And Aggregation Of Thermally Stressed Proteins Studied By Hydrogen/Deuterium Exchange Mass Spectrometry, Nastaran Nosrat Tajoddin

Electronic Thesis and Dissertation Repository

Proteins perform various biological functions, e.g., as enzymes or transporters. In addition to naturally occurring proteins, the use of protein therapeutic drugs for treating cancer and other diseases is a rapidly growing area. A thorough biophysical characterization of proteins and protein therapeutics opens the door to a more comprehensive understanding of their role in health and disease. This dissertation aims to expand the capabilities of an existing technique (Hydrogen Deuterium Exchange Mass Spectrometry, HDX-MS), which is widely used for probing protein structure and dynamics. Conventionally, HDX-MS experiments are performed as a function of labelling time. Here we aim to establish …

An Implementation Of Integrated Information Theory In Resting-State Fmri, Idan E. Nemirovsky

Electronic Thesis and Dissertation Repository

Integrated Information Theory (IIT) is a framework developed to explain consciousness, arguing that conscious systems consist of interacting elements that are integrated through their causal properties. In this study, we present the first application of IIT to functional magnetic resonance imaging (fMRI) data and investigate whether its principal metric, Phi, can meaningfully quantify resting-state cortical activity patterns. Data was acquired from 17 healthy subjects who underwent sedation with propofol, a short acting anesthetic. Using PyPhi, a software package developed for IIT, we thoroughly analyze how Phi varies across different networks and throughout sedation. Our findings indicate that variations in Phi …

A Generative-Discriminative Approach To Human Brain Mapping, Deepanshu Wadhwa

Electronic Thesis and Dissertation Repository

During everyday behaviours, the brain shows complex spatial patterns of activity. These activity maps are very replicable within an individual, but vary significantly across individuals, even though they are evoked by the same behaviour. It is unknown how differences in these spatial patterns relate to differences in behavior or function. More fundamentally, the structural, developmental, and genetic factors that determine the spatial organisation of these brain maps in each individual are unclear. Here we propose a new quantitative approach for uncovering the basic principles by which functional brain maps are organized. We propose to take an generative-discriminative approach to human …

Coevolution Of Hosts And Pathogens In The Presence Of Multiple Types Of Hosts, Evan J. Mitchell

Electronic Thesis and Dissertation Repository

How will hosts and pathogens coevolve in response to multiple types of hosts? I study this question from three different perspectives. First, I model a scenario in which hosts are categorized as female or male. Hosts invest resources in maintaining their immune system at a cost to their reproductive success, while pathogens face a trade-off between transmission and duration of infection. Importantly, female hosts are also able to vertically transmit an infection to their newborn offspring. The main result is that as the rate of vertical transmission increases, female hosts will have a greater incentive to pay the cost to …

Investigation Of Shocked Basalts From Vargeão Dome And Vista Alegre: Implications For The Search For Life On Mars, Nikol Posnov

Electronic Thesis and Dissertation Repository

Impact craters represent excellent astrobiological targets for planetary exploration missions to Mars. The impact of an asteroid or comet into a crystalline, H₂O-bearing target may result in development of a hydrothermal system and increase the habitability of the substrate for the colonization of endolithic microorganisms. Given that Mars’ surface is covered by cratered basaltic rock, this study investigated target rocks and impact breccias from Vargeão Dome and Vista Alegre impact structures that formed in basalt in the Paraná Basin of Brazil.

Utilizing petrography and micro-X-ray diffraction (μXRD), the degree of shock metamorphism in plagioclase was quantitively determined. Measuring …

The Analysis Of Ginsenosides In Ginseng Garden Soil, Karina Marie Kaberi

Electronic Thesis and Dissertation Repository

American ginseng (Panax quinquefolius L.) produces natural products called ginsenosides. The biggest challenge Ontario commercial ginseng farmers face is ginseng replant disease. To understand the function of ginseng root exudates, ginsenoside accumulation and persistence over time were investigated. Currently, no reliable ginsenoside specific extraction method, characterizing the changes in soil chemistry exists. Ginsenoside extraction protocol optimization was required to determine how ginsenoside composition changed over time. Overall, protocol optimization resulted in a 30% increase in yield of ginsenosides compared to previous extraction protocols. In the ginseng gardens, ginsenoside accumulation occurs slowly and did not reach significantly measurable amounts until the …

Population And Evolution Dynamics In Predator-Prey Systems With Anti-Predation Responses, Yang Wang

Electronic Thesis and Dissertation Repository

This thesis studies the impact of anti-predation strategy on the population dynamics of predator-prey interactions. This work includes three research projects.

In the first project, we study a system of delay differential equations by considering both benefit and cost of anti-predation response, as well as a time delay in the transfer of biomass from the prey to the predator after predation. We reveal some insights on how the anti-predation response level and the biomass transfer delay jointly affect the population dynamics; we also show how the nonlinearity in the predation term mediated by the fear effect affects the long term …

Reconstructing Carbon Dynamics Of Alpine And Temperate Zone Lakes Using Stable Isotopic Analysis, Rebecca M. Doyle

Electronic Thesis and Dissertation Repository

Lake sediments integrate signals from the catchment, atmosphere and water column, offering a unique window through which to view changes in the carbon cycle. Carbon dynamics in lakes are changing due to nitrogen loading and anthropogenic climate warming (ACW), threatening the water quality of lakes. This thesis identifies how the carbon dynamics of lakes have responded to anthropogenically-driven forcings by comparing pre- and post- AD 1850 records preserved in lake sediments. First, the carbon dynamics of Barry Lake (Ontario, Canada), a low-elevation temperate lake, are investigated. Effective moisture (the net of water inputs and evaporation) is reconstructed using the carbon …

Effects Of Oxidative Modifications On The Structure And Non-Canonical Functions Of Cytochrome C Studied By Mass Spectrometry, Victor Yin

Electronic Thesis and Dissertation Repository

The peroxidase activity of the mitochondrial protein cytochrome c (cyt c) plays a critical role in triggering programmed cell death, or apoptosis. However, the native structure of cyt c should render this activity impossible due to the lack of open iron coordination sites at its heme cofactor. Despite its key biological importance, the molecular mechanisms underlying this structure-function mismatch remain enigmatic. The work detailed in this dissertation fills this knowledge gap by using mass spectrometry (MS) to decipher the central role that protein oxidative modifications and their associated structural changes play in activating the peroxidase function of cyt c …

Computational Methods For Predicting Protein-Protein Interactions And Binding Sites, Yiwei Li

Electronic Thesis and Dissertation Repository

Proteins are essential to organisms and participate in virtually every process within cells. Quite often, they keep the cells functioning by interacting with other proteins. This process is called protein-protein interaction (PPI). The bonding amino acid residues during the process of protein-protein interactions are called PPI binding sites. Identifying PPIs and PPI binding sites are fundamental problems in system biology.

Experimental methods for solving these two problems are slow and expensive. Therefore, great efforts are being made towards increasing the performance of computational methods.

We present DELPHI, a deep learning based program for PPI site prediction and SPRINT, an algorithmic …

Mathematical Modelling Of Prophage Dynamics, Tyler Pattenden

Electronic Thesis and Dissertation Repository

We use mathematical models to study prophages, viral genetic sequences carried by bacterial genomes. In this work, we first examine the role that plasmid prophage play in the survival of de novo beneficial mutations for the associated temperate bacteriophage. Through the use of a life-history model, we determine that mutations first occurring in a plasmid prophage are far more likely to survive drift than those first occurring in a free phage. We then analyse the equilibria and stability of a system of ordinary differential equations that describe temperate phage-host dynamics. We elucidate conditions on dimensionless parameters to determine a parameter …

Spatial And Temporal Variation Of Nutrients In The Great Lakes-St. Lawrence Basin: Implications For Primary Production In Stream Ecosystems, Nolan Pearce

Electronic Thesis and Dissertation Repository

Growing human populations and associated land use activities has increased the amount of nutrients delivered to surface waters. Eutrophication from the over-enrichment of nitrogen and phosphorus has degraded ecosystem conditions in streams, lakes, and coastal areas worldwide. Thus, the management of anthropogenic nutrient loading is a global concern. This thesis employed a combination of field and experimental research to provide watershed managers with information on the spatial and temporal patterns in stream nutrient enrichment, and the associated ecological effects of anthropogenic nutrient loading in the Great Lakes-St. Lawrence basin. Four studies were completed to address this research goal. First, I …

Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa

Electronic Thesis and Dissertation Repository

In the field of bioinformatics, taxonomic classification is the scientific practice of identifying, naming, and grouping of organisms based on their similarities and differences. The problem of taxonomic classification is of immense importance considering that nearly 86% of existing species on Earth and 91% of marine species remain unclassified. Due to the magnitude of the datasets, the need exists for an approach and software tool that is scalable enough to handle large datasets and can be used for rapid sequence comparison and analysis. We propose ML-DSP, a stand-alone alignment-free software tool that uses Machine Learning and Digital Signal Processing to …

Contraction Analysis Of Functional Competitive Lotka-Volterra Systems: Understanding Competition Between Modified Bacteria And Plasmodium Within Mosquitoes., Nickolas Goncharenko

Electronic Thesis and Dissertation Repository

We propose and analyze an extension to the classic Competitive Lotka-Volterra (CLV) model. The goal is to model competition between species, with a response from the environment. This response is a function of the population of all species and can represent numerous physical phenomena including resource limitation and immune response of a host due to infection. We name this new system a Functional Competitive Lotka-Volterra (FCLV) model. We mainly use the construction of contraction metrics, to determine global properties of the model. We use this result to analyze the competition between Plasmodium sp. and genetically engineered bacteria within the midgut …

Phage-Bacteria Interaction And Prophage Sequences In Bacterial Genomes, Amjad Khan

Electronic Thesis and Dissertation Repository

In this investigation, we examined the interaction of phages and bacteria in bacterial biofilm colonies, the evolution of prophages (viral genetic material inserted into the bacterial genome) and their genetic repertoire. To study the synergistic effects of lytic phages and antibiotics on bacterial biofilm colonies, we have developed a mathematical model of ordinary differential equations (ODEs). We have also presented a mathematical model consisting of a partial differential equation (PDEs), to study evolutionary forces acting on prophages. We fitted the PDE model to three publicly available databases and were able to show that induction is the prominent fate of intact …

The Stability Of Temperate Lakes Under The Changing Climate, Aleksey Paltsev

Electronic Thesis and Dissertation Repository

There is a collective prediction among ecologists that climate change will enhance phytoplankton biomass in temperate lakes. Yet there is noteworthy variation in the structure and regulating functions of lakes to make this statement challengeable and, perhaps, inaccurate. To generate a common understanding on the trophic transition of lakes, I examined the interactive effects of climate change and landscape properties on phytoplankton biomass in 12,644 lakes located in relatively intact forested landscapes. Chlorophyll-a (Chl-a) concentration was used as a proxy for phytoplankton biomass. Chl-a concentration was obtained via analyzing Landsat satellite imagery data over a 28-year period (1984-2011) and using …

Synthesis Of Crosslinkable Poly(Ester Amide)S For Cell Encapsulation And Delivery, Yu Ting (Natalie) Liang

Electronic Thesis and Dissertation Repository

Tissue engineering using adipose-derived stromal cells (ASCs) shows promise for soft tissue regeneration. Biodegradable polymers are potential biomaterials as they support the growth and delivery of cells. Specifically, poly(ester amide)s (PEAs) are a class of biodegradable polymers with tunable structures that have been shown to exhibit low cytotoxicity and support the growth of various cell types. This thesis involved the development of new water soluble amino acid-based PEAs with crosslinkable moieties to enable formation of hydrogel scaffolds for ASC encapsulation. These hydrophilic phenylalanine-based and alanine-based PEAs were synthesized by solution polycondensation and photo-crosslinked into a series of hydrogels with and …

Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios

Electronic Thesis and Dissertation Repository

F₁-ATPase is a motor protein that can use ATP hydrolysis to drive rotation of the central subunit. The γ C-terminal helix constitutes of the rotor tip that is seated in an apical bearing formed by the α₃β₃ head. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we develop a molecular dynamics (MD) strategy to model the off-axis forces acting on γ in F₁-ATPase. MD runs showed stalling of the …

Calculating The Dimensionality Of The Brain, And Other Applications Of An Optimized Generalized Ising Model In Predicting Brain's Spontaneous Functions, Pubuditha M. Abeyasinghe

Electronic Thesis and Dissertation Repository

Understanding a system as complex as the human brain is a very demanding task. Directly working with structural and functional neuroimaging data has led to most of the understanding we have gained about the human brain. However, performing only the direct statistical comparisons on the empirical function and the structure does not fully explain the observed long-range functional correlations. Therefore, implementations of mathematical models to gain further understanding of the relationship between the structure and function of the brain is critical. Additionally, spontaneous functions of the brain can only be predicted using computer simulated models; which will be pivotal for …

Investigation Of Flow Disturbances And Multi-Directional Wall Shear Stress In The Stenosed Carotid Artery Bifurcation Using Particle Image Velocimetry, Amanda L. Dicarlo

Electronic Thesis and Dissertation Repository

Hemodynamics and shear forces are associated with pathological changes in the vascular wall and its function, resulting in the focal development of atherosclerosis. Flow complexities that develop in the presence of established plaques create environments favourable to thrombosis formation and potentially plaque rupture leading to stroke. The carotid artery bifurcation is a common site of atherosclerosis development. Recently, the multi-directional nature of shear stress acting on the endothelial layer has been highlighted as a risk factor for atherogenesis, emphasizing the need for accurate measurements of shear stress magnitude as well direction. In the absence of comprehensive patient specific datasets numerical …

Performance Impact Of Different Lower-Limb Setup Positions In The Backstroke Swimming Start, Gordon E. Barkwell

Electronic Thesis and Dissertation Repository

The performance impact of different knee extension angles in the setup position for a backstroke start was evaluated using an instrumented starting surface. Ten backstroke swimmers completed maximum-effort starts in each of two setup positions: one with the knees flexed, and one with the knees extended. The start handles and touchpad were instrumented with tri-axial force plates. Activity of major hip and knee extensors was measured using surface electromyography. Body position was recorded throughout the start using two high-speed cameras. There was no difference in time to 10 m between the two conditions, indicating there is likely no advantage in …

Plant Stimuli-Responsive Biodegradable Polymers For The Use In Timed Release Fertilizer Coatings, Spencer Heuchan

Electronic Thesis and Dissertation Repository

The use of nitrogen-based fertilizers continues to accelerate with human population growth and increases in global food requirements. Enhanced efficiency fertilizers (EEFs) have been developed to improve the synchronization between nutrient supply and crop nutrient demand. However, many of the current controlled release fertilizers are coated with non-degradable polymers that contribute to accumulation of microplastics within ecosystems. This thesis describes research towards the development of a new class of fertilizer coatings using a self-immolative polymer known as poly (ethyl glyoxylate) (PEtG). PEtG itself does not have suitable properties to produce a viable coating but once blended with another degradable polyester …