Graduate Theses & Dissertations

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Fingerprinting of dissolved organic matter and copper ligands in the Canadian Arctic and North Pacific Ocean
Dissolved organic matter (DOM) in oceans provides nutrients and ultraviolet radiation protection to microbes. Some DOM compounds can chelate with metals, including copper, controlling their transport and bioavailability in marine systems. As copper functions as both a nutrient and toxicant, studies into the chemical structures of Cu-ligands is important, however currently limited. In this thesis, the chemical composition of total and Cu-binding DOM is investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in the Canadian Arctic and North Pacific. Chapter 2 reveals chemical differences in DOM composition between the southern and northern Canada Basin, revealing the influence of terrestrial and biological sources. Chapter 3 shows the uniqueness of Cu-binding ligands found in the Canadian Arctic and North Pacific Ocean. Studying the composition of DOM gives insight into the chemical diversity of marine DOM, helping to predict the effects of a changing climate on marine ecosystems. Author Keywords: biological, dissolved organic matter, fluorescence, immobilized metal-ion affinity chromatography, mass spectrometry, terrestrial
Expression optimization and NMR spectroscopy of Giardia intestinalis cytochrome b5 isotype III
The parasitic protist Giardia intestinalis does not synthesize heme and lacks many common eukaryotic heme proteins, yet it expresses four cytochrome b5 (gCYTB5) isotypes of unknown function. These have low reduction potentials and distinct subcellular locations that are consistent with structural features and biological functions that differ from their mammalian counterparts. Isotype III (gCYTB5-III) is particularly fascinating for its unusual location in the nuclei of Giardia. This thesis reports the optimization of recombinant gCYTB5-III overexpression for structural studies by NMR spectroscopy. Vital optimization factors for isotope labelling were first identified, finding that auto-induction promotes the optimization of many other conditions, such as colony selection, starter cultures, media components, temperature, pH and aeration. Optimized conditions were then applied to the expression and NMR spectroscopy of isotope-labelled gCYTB5-III and bovine cytochrome b5 as a control. These results can be extended to other heme proteins and will expand our biochemical knowledge of Giardia. Author Keywords: Auto-induction, Cytochrome b5, Giardia intestinalis, Isotope Labelling, Nuclear Magnetic Resonance Spectroscopy, Recombinant Protein
Detectability and its role in understanding upland sandpiper (Bartramia longicauda) occurence in the fragmented landscape of southern Ontario
Upland Sandpipers (Bartramia longicauda), like many grassland birds, are undergoing population decline in parts of their range. Habitat fragmentation and change have been hypothesized as potential causes of decline. I used citizen-science occurrence data from Wildlife Preservation Canada’s Adopt-A-Shrike Loggerhead Shrike (Lanius ludovicianus) program in conjunction with validation surveys, using similar point-count methods, to examine detectability and determine if landscape level habitat features could predict occupancy of Upland Sandpipers in Southern Ontario. In a single season detectability study, I used Wildlife Preservation Canada’s survey protocol to determine detectability in sites that were known to be occupied. Detectability was low, with six surveys necessary to ensure detection using a duration of at least 18 minutes early in the breeding season. The proportion of open habitat did not affect detection on the landscape. Using a larger spatial and temporal scale, with five years of citizen-science data, I showed that Annual Crop Inventory data could not effectively predict Upland Sandpiper occupancy. Model uncertainty could be attributed to survey protocol and life history traits of the Upland Sandpiper, suggesting that appropriate survey methods be derived a priori for maximizing the potential of citizen-science data for robust analyses. Author Keywords: Bartramia longicauda, citizen-science, detection, landscape, occupancy, Ontario
Modelling the Lanthanum Aluminate-Strontium Titanate Interface with a Modified Transverse Ising Model
In 2004 it was discovered that a two-dimensional electron gas (2DEG) forms at the interface between lanthanum aluminate (LAO) and strontium titanate (STO). This 2DEG exhibits a variety of electronic and magnetic phenomena, motivating intense research into its applicability to electronic devices. Over the years several models have been developed in theoretical exploration of this system. Here, the transverse Ising model is applied to the LAO/STO interface for the first time. It is shown that the model as it is traditionally formulated cannot accurately predict the structure of the electron density at the interface. I show that this can be fixed with a simple modification of the model, and discuss how this modification affects both the polarization distribution in ferroelectric thin films and the electron density at the LAO/STO interface. The importance of including the depolarizing field when modelling spatially inhomogeneous ferroelectric systems is also explored. Author Keywords: ferroelectric thin film, lanthanum aluminate, strontium titanate, transverse Ising model, two-dimensional electron gas
Support Vector Machines for Automated Galaxy Classification
Support Vector Machines (SVMs) are a deterministic, supervised machine learning algorithm that have been successfully applied to many areas of research. They are heavily grounded in mathematical theory and are effective at processing high-dimensional data. This thesis models a variety of galaxy classification tasks using SVMs and data from the Galaxy Zoo 2 project. SVM parameters were tuned in parallel using resources from Compute Canada, and a total of four experiments were completed to determine if invariance training and ensembles can be utilized to improve classification performance. It was found that SVMs performed well at many of the galaxy classification tasks examined, and the additional techniques explored did not provide a considerable improvement. Author Keywords: Compute Canada, Kernel, SDSS, SHARCNET, Support Vector Machine, SVM
Making eDNA count
Environmental DNA (eDNA) is rapidly becoming an established method for the detection of species in aquatic systems and has been suggested as a promising tool to estimate species abundance. However, the strength of the relationship between eDNA concentrations and taxon abundance (density/biomass) can vary widely between species. I investigated the relationship between eDNA concentration and species abundance using two common and closely-related amphibians in eastern North America, the wood frog (Rana sylvatica) and northern leopard frog (Rana pipiens). I manipulated tadpole density in 80 L mesocosms and documented the relationship between tadpole density, biomass, and eDNA concentration. Species were comparable in biomass but differed in the amount of detectible genetic material produced; density and biomass were the superior abundance metric correlated with eDNA concentration for wood frogs and leopard frogs, respectively. However, increases in eDNA concentration reflected increasing tadpole biomass, therefore biomass is likely a better metric of abundance than density. Overall my findings support that eDNA concentration can be used as an index of species abundance, but that species-specific calibration may be needed before eDNA concentration can be effectively translated to an abundance metric. Future research should refine our understanding of how biotic and abiotic factors influence eDNA production, degradation, and recovery across species, before the method can receive widespread use as a monitoring tool in natural settings. Author Keywords: abundance estimates, environmental DNA, mesocosm, Rana pipiens, Rana sylvatica
Observation-based assessment of atmospheric sulphur surrounding a major aluminum smelter in British Columbia, Canada
Recent developments at an aluminum (Al) smelter in Kitimat, BC resulted in a permitted increase of 27 to 42 tonnes of sulphur dioxide (SO2) emissions per day. Gaseous SO2 is a pollutant known to contribute to acidic deposition through processes of wet and dry deposition and can additionally react in-atmosphere to form particulate sulphate (pSO42-). Between June 2017 to October 2018, an extensive network consisting of ion exchange resin (IER) column, passive-diffusive, and active filter-pack samplers was established to provide an estimate of total annual S deposition and pSO42- variation throughout the Kitimat Valley. Filter-pack sampling determined the relative concentration of pSO42- increased downwind of the smelter. Comparison of observation-based and modelled total annual deposition suggested CALPUFF was accurate in representing the spatial viability of S deposition (R2 = > 0.85). However, the model appeared to overpredict near-field deposition suggesting the potential of underestimation further downwind of the smelter. Author Keywords: aluminum smelter, atmospheric deposition, filter-pack sampler, ion-exchange column sampler, pSO42-, SO2
Seasonal habitat use and movement of native brook trout (Salvelinus fontinalis) in urban headwater streams
Coldwater streams are becoming increasingly impacted due to urbanization. Using environmental surveys, mark-recapture and telemetry, I assessed factors influencing seasonal brook trout (Salvelinus fontinalis) habitat use and movement in urban headwater streams in central Ontario between 2017-18. Generalized additive models were used to assess which habitat variables best explained seasonal yearling and older brook trout abundance, while generalized least squares models were used to assess overall trends in radio-tagged brook trout movement. My research demonstrated dynamic patterns in habitat use and movement by urban stream-dwelling brook trout. Yearlings were primarily influenced by water quality (stream temperature, conductivity), while older brook trout were most strongly influenced by stream morphology (depth, undercut bank). Movement occurred disproportionately around the spawning season and was more limited in the smaller, more altered stream. These findings may be used to inform fisheries managers on crucial timing and location of brook trout habitat refugia within urbanized environments. Author Keywords: Brook trout, coldwater stream, groundwater, habitat use, radiotelemetry, urbanization
Effects of Invasive Wetland Macrophytes on Habitat Selection by Turtles
Invasive species that alter habitats can have significant impacts on wildlife. The invasive graminoids Phragmites australis (Cav.) Trin. ex Steud, hereafter Phragmites, and Typha × glauca Godr. are rapidly spreading into North American wetlands, replacing native vegetation. Invasive Phragmites is considered a potential threat to several species-at-risk (SAR), including some turtle species. My study wetland contained large stands of Phragmites, as well as Typha spp. (including invasive T. × glauca) that have similar structural traits to Phragmites. To explore the hypothesis that Phragmites and Typha spp. do not provide suitable habitat for turtles, I tested the prediction that turtles avoid Phragmites- and Typha-dominated habitats. I used VHF-GPS transmitters to follow Blanding’s turtles (Emydoidea blandingii, n = 14) and spotted turtles (Clemmys guttata, n = 12). I found that both turtle species did not avoid Phragmites- or Typha-dominated habitats when choosing a home range, or while moving within their home range. I also tested whether the microhabitat selection of Blanding’s turtles and spotted turtles is affected by shoot density of Phragmites, Typha spp., or both. I compared shoot densities of Phragmites and Typha spp. in 4 m2 plots, from locations used by tracked turtles with paired, random locations in these turtles’ home ranges. For both turtle species, the densities of Phragmites and Typha shoots were comparable between used and random locations within the home ranges (generalized linear mixed model; p > 0.05). The use of Phragmites- and Typha-dominated habitats by Blanding’s turtles and spotted turtles suggests that these habitats do not automatically constitute “unsuitable habitats” for turtles. Phragmites and Typha spp. (especially T. × glauca) can replace preferred habitats of some turtle species, and the control of these invasive macrophytes can help to preserve habitat heterogeneity. However, the presence of SAR turtles in Phragmites and Typha spp. stands should inform risk-assessments for invasive plant species control methods that include mechanical rolling of stands, where heavy machinery might encounter turtles. Author Keywords: Blanding’s turtles, compositional analysis, habitat selection, Phragmites australis, spotted turtles, Typha x glauca
Genomic architecture of artificially and sexually selected traits in white-tailed deer (Odocoileus virginianus)
Understanding the complex genomic architecture underlying quantitative traits can provide valuable insight for the conservation and management of wildlife. Despite improvements in sequencing technologies, few empirical studies have identified quantitative trait loci (QTL) via whole genome sequencing in free-ranging mammal populations outside a few well-studied systems. This thesis uses high-depth whole genome pooled re-sequencing to characterize the molecular basis of the natural variation observed in two sexually selected, heritable traits in white-tailed deer (Odocoileus virginianus, WTD). Specifically, sampled individuals representing the phenotypic extremes from an island population of WTD for antler and body size traits. Our results showed a largely homogenous genome between extreme phenotypes for each trait, with many highly differentiated regions throughout the genome, indicative of a quantitative model for polygenic traits. We identified and validated several potential QTL of putatively small-to-moderate effect for each trait, and discuss the potential for real-world application to conservation and management. Author Keywords: evolution, extreme phenotypes, genetics, genomics, quantitative traits, sexual selection
Cluster Approach Applied to the One-Dimensional Anderson-Hubbard Model
S. Johri and R. Bhatt developed a real-space renormalization group approach aimed at extracting the localized single-particle eigenstates of the Anderson model from a large system by identifying clusters of resonant site potentials. E. Campbell generalized this real-space renormalization group approach using standard perturbation theory. Both approaches were intended to approximate the single-particle density of states of the Anderson model. In this thesis, we aimed to test the potential of applying a similar real-space renormalization group approach to calculate the density of states of the interacting Anderson-Hubbard model. Our interest in the density of states of this model is due to a V-shaped zero-bias anomaly in two-dimensional systems. A real-space renormalization group approach is best applied to a one-dimensional system. We found that the zero-bias anomaly is not V-shaped in one-dimension. To test the potential of a real-space renormalization group approach, we used the cluster approach which is the same as the non-interacting renormalization group approach but without the perturbation theory and found that for strong disorder this technique could accurately calculate the density of states over a wide range of energies but deviated from exact results at the band edge, at $\omega=\pm U$ and near $\omega=0$. The first two inaccuracies will be reduced with a proper real-space renormalization group approach. We suspect that the last inaccuracy is associated with long range physics and may be difficult to recover. We also developed a technique that adjusts the identification of clusters in the cluster approach to improve the computation time of the density of states with minimal loss of accuracy in a tunable range around the Fermi level. We found that this technique significantly reduced the computation time and was able to preserve the density of states near the Fermi level, except at the smallest energies near $\omega=0$. Author Keywords: Anderson-Hubbard model, renormalization group, Strong electron correlations, Zero-bias anomaly
Soil Geochemistry and Normative Mineralogy across Canada
Soils play a crucial role in ecosystem functioning, for example, soil minerals provide important provisioning and regulate ecosystem services. This study used major soil oxides from the North American Soil Geochemical Landscapes Project (n=560) to assess elemental associations and infer soil minerals through exploratory data analysis and to determined quantitative soil mineralogy using a normative method, Analysis to Mineralogy (n=1170). Results showed elemental variability of oxides across the provinces of Canada and strong correlations occurred between elements indicative of soil mineral composition (e.g., Silicon and Aluminium). Principal component analysis inferred soil minerals from soil oxides trends on biplots and classified minerals, generally, as carbonates, silicates, and weathered secondary oxides. Spatial variability in minerals (quartz, plagioclase, potassium feldspar, chlorite, and muscovite) was related to the underlying bedrock geology. The use of Analysis to Mineralogy led to a reliable method of quantifying soil minerals at a large scale. Author Keywords: Analysis to Mineralogy, Exploratory data analysis, Normative procedures, North American Soil Geochemical Landscapes Project, Soil geochemistry, Soil mineralogy

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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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1973 - 2033
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