Graduate Theses & Dissertations

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Advanced broadband CARS microscopy based on a supercontinuum-generating photonic crystal fiber
I have developed and improved a coherent anti-Stokes Raman scattering (CARS) microscope based on the spectral focusing (SF) technique. The CARS microscope uses an 800 nm oscillator and a photonic crystal fibre module to generate the supercontinuum Stokes. The photonic crystal fibre was originally designed to generate light beyond 945 nm which is useful for CARS microscopy in the CH/OH frequencies but essentially prevents access to the important fingerprint region at lower frequencies. With expert and nontraditional approaches to generating supercontinuum with sufficient power at wavelengths below 945 nm, I substantially extend the usefulness of the module for SF-CARS microscopy deep into the fingerprint region. Moreover, with the invention of a dynamic supercontinuum generation scheme we call "spectral surfing," I improve both the brightness of the CARS signal and extend the accessible CARS frequency range to frequencies as low as 350 cm$^{-1}$ and as high as 3500 cm$^{-1}$---all in a single scan-window. I demonstrate the capabilities of our broadband SF-CARS system through CARS and four-wave mixing hyperspectroscopy on samples such as astaxanthin, lily pollen and glass; liquid chemicals such as benzonitrile, nitrobenzene and dimethyl sulfoxide; and on pharmaceutical samples such as acetaminophen, ibuprofen, and cetirizine. Furthermore, In search of more useful Stokes supercontinuum sources, I compare the performance of two commercial photonic crystal fibre modules for use in SF-CARS applications, ultimately finding that one module provides better spectral characteristics for static supercontinuum use, while the other provides improved characteristics when spectral surfing is implemented. Author Keywords: coherent anti-Stokes Raman scattering, nonlinear microscopy, scanning microscopy, spectroscopy, supercontinuum generation, vibrational spectroscopy
History of Canada's UFO Investigation, 1950-1995
From 1950-1995, the Canadian government investigated the phenomenon of unidentified flying objects (UFOs), amassing over 15,000 pages of documentation about, among other matters, nearly 4,500 unique sightings. This investigation was largely passive and disconnected, spread across a number of federal departments and agencies that infrequently communicated about the subject. Two official investigations, Project Magnet and Project Second Storey, were initiated in the early 1950s to study the topic. The government concluded that the UFO phenomenon did not “lend itself to a scientific method of investigation,” and terminated the projects. After this point, the investigation entered a state of purgatory, with no central communication, and every government department eager to pass the responsibility onto someone else. As such, Canadian citizens writing to the government for straight answers to the UFO enigma were often on the receiving end of what they called “doublespeak.” Citizens were seeing things in the sky and wanted the government to simply tell them what they were. The government was unable and unwilling to do this, and over time frustration grew on both sides. What began for the government, in its own words, as an irritating intrusion into more important matters, became the catalyst for a dynamic of mutually-reinforced mistrust between state and citizen during the postwar period. This dissertation offers a chronological history of the efforts that the Canadian government and citizens made to investigate UFOs, and when and why these efforts came into conflict. The main argument is that the Canadian state attempted to use UFOs as a site to assert its modernity during a time of uncertainty and anxiety over its legitimacy, by drawing on the cultural authority of the scientific community. The project was one of ridding the public of ignorance and creating instead a more rational citizen. This attempt ran up against beliefs and attitudes that some citizens shared, that tapped into a spirit of anti-authoritarianism present during the 1960s and even earlier. These citizens considered themselves to be iconoclasts, unmoved by claims of expertise, and accused the government of conspiracy theory. These approaches fed into one another, contributing to further misunderstanding and conflict. The history of Canada’s UFO investigation is thus more broadly a history of changing attitudes toward authority and expertise in the postwar era. Author Keywords: Canada, citizenship, history of science, scientific object, state, UFO
Indirect Effects of Hyperabundant Geese on Sympatric-Nesting Shorebirds
Rising populations of Lesser Snow and Ross’ geese (hereafter collectively referred to as light geese) breeding in the North American Arctic have caused significant environmental change that may be affecting some populations of nesting shorebirds, which in contrast to geese, have declined dramatically. In this thesis I examine the indirect effects of light geese on sympatric-nesting shorebirds. I first conduct a literature review of the effects of light geese on northern wildlife and outline multiple mechanisms in which geese may affect shorebirds in particular. Using bird survey data collected in plots situated across the Canadian Arctic from 1999 to 2016, I then identify spatial effects of light goose colonies on shorebird, passerine, and generalist predator densities. The densities of cover- nesting shorebirds and passerines were depressed near goose colonies while the densities of open-nesting shorebirds were less so. Next, using habitat data collected at random sites and shorebird nest sites situated at increasing distances from a goose colony on Southampton Island, Nunavut, I outline the effects of geese on shorebird nest site selection. I found that the availability of sedge meadow and amount of lateral concealment increased as a function of distance from goose colony; cover-nesting shorebirds selecting nest sites with less concealment and sedge meadow near the colony. Then, to characterize spatial effects of light geese on predators and risk of predation I used time-lapse cameras and artificial shorebird nests placed at increasing distances from the goose colony. Activity indices of gulls, jaegers, and foxes were all negatively correlated with distance from the goose colony while the reverse was true for artificial nest survival probability. Finally, I relate changes in ground cover to goose use and link these changes to variation in invertebrate communities. I then use DNA metabarcoding to characterize the diet of six shorebird species across study sites and identify inter-site variation in the biomass of dominant shorebird prey items. Prey item biomass was elevated at the two study sites near the goose colony potentially indicating an enhancing effect of goose fecal deposition. Overall, I show that light geese interact with shorebirds in multiple ways and negatively affect their habitat availability, nest site selection, and risk of predation, effects that likely outweigh the positive effects of enhanced prey availability. Author Keywords:
Effect of Nitrosative Stress on Heme Protein Expression and Localization in Giardia Intestinalis
The parasitic protist Giardia intestinalis has five heme proteins: a flavohemoglobin and several isotypes of cytochrome b5. While the flavohemoglobin has a role in counteracting nitric oxide, the functions of the cytochromes (gCYTb5s) are unknown. In this study, the protein level and cellular localization of three gCYTB5 isotypes (gCYTb5-I, II and III) and flavohemoglobin were examined in Giardia trophozoites exposed to three nitrosative stressors at two different concentrations: nitrite (20 mM, 0.5 mM); GSNO (2 mM, 0.25 mM) and DETA-NONOate (2 mM, 0.05 mM). An increase in protein levels was observed for gCYTb5-II with all stressors at both concentrations. However, the effects of these nitrosative stressors on gCYTb5-I and III were inconclusive due to the variation among the replicates and the poor detection of gCYTb5- III on western blots. The protein level of the flavohemoglobin also increased in response to the three stressors at the low concentrations of stressors that were tested. Only the cellular localization of gCYTb5-I changed in response to nitrosative stress, where it moved from the nucleolus to the nucleus and cytoplasm. This response was extremely sensitive and occurred at the lower doses of the three stressors, suggesting that gCYTb5-I may be involved in a nucleolar- based stress response. Author Keywords:
Contemporary adaptive shifts in the physiology and life history of Pumpkinseed (Lepomis gibbosus) introduced into a warm climate
Contemporary evolution has the potential to help limit the biological impact of rapidly changing climates, however it remains unclear whether wild populations can respond quickly enough for such adaptations to be effective. In this thesis, I used the introduction of native North American Pumpkinseed (Lepomis gibbosus) into the milder climate of Europe over 140 years ago, as a 'natural' experiment to test for contemporary evolution to a change in climate in wild populations. In 2008, four outdoor pond colonies were established in central Ontario using adult Pumpkinseed from two native Canadian populations, and two non-native populations from northeastern Spain. By raising native and non-native Pumpkinseed within a common environment, this design minimized the impact of phenotypic plasticity on differential trait expression, and allowed me to interpret differences in the phenotype among pond-reared Pumpkinseed as evidence of genetic differences among populations. I demonstrated that Canadian and Spanish Pumpkinseed have similar thermal physiology except when acclimated to seasonally warm temperatures; trait differences are consistent with Spanish Pumpkinseed being better adapted to a warmer climate. Populations also had similar overwintering ecology, however some differences, such as higher survival under starvation conditions and greater energetic benefits associated with winter feeding, indicated that Canadian populations are better adapted to harsh winter conditions typical of the native range. Finally, I determined that the relatively fast life history expressed in wild European Pumpkinseed is largely driven by plastic responses to the local environment; however, the higher reproductive investment by European populations has a genetic basis. Most climate change research considers taxa that are expected to be negatively impacted by warming: my research demonstrates that even warm-tolerant taxa that are unlikely to experience strong climatic selective forces can respond to a warming environment through evolutionary changes. The potential for adaptive contemporary evolution in warm-tolerant taxa should be taken into account when predicting future ecosystem effects of climate change, and when planning management strategies for species introduced into novel climates. Author Keywords: climate change, contemporary evolution, fish, non-native species, thermal biology, winter ecology
Molecular Composition of Dissolved Organic Matter Controls Metal Speciation and Microbial Uptake
Aquatic contaminant mobility and biological availability is strongly governed by the complexation of organic and inorganic ligands. Dissolved organic matter (DOM) is a complex, heterogeneous mixture of organic acids, amino acids, lipids, carbohydrates and polyphenols that vary in composition and can complex to dissolved metals thereby altering their fate in aquatic systems. The research conducted in this doctoral dissertation addresses 1) how DOM composition differs between phytoplankton taxa and 2) how DOM composition affects metal speciation and its subsequent microbial bioavailability in laboratory and field conditions. To accomplish this, a series of analytical methods were developed and applied to quantify thiols, sulphur containing DOM moieties, and the molecular composition of DOM. The works presented in this thesis represents one of the first comprehensive and multipronged analyses of the impact of phytoplankton metabolite exudates on microbial metal bioavailability. This dissertation demonstrated the analytical versatility of high-resolution mass spectrometry as a tool for compound specific information, as well as having the capabilities to obtain speciation information of organometallic complexes. The work presented in this PhD strengthens the understanding compositional differences of both autochthonous and allochthonous DOM and their effects on metal biogeochemistry. Author Keywords: Dissolved Organic Matter, Mercury, Metal Accumulation, Phytoplankton, Spring Melts, Thiol
An Investigation of Rare Earth Element Patterns and an Application of Using Zn and Cd Isotope Ratios in Oysters to Identify Contamination Sources in an Estuary in Southern China
Environmental monitoring and investigation of metal biogeochemical cycling has been carried out in the Pearl River Estuary (PRE), an important and complex system in Southern China. In this study, rare earth element (REE) patterns as well as isotope ratios (i.e., Zn and Cd) were evaluated as tools to identify contamination sources in environmental compartments (i.e., water and suspended particles (SP)) as well as in oysters collected from estuarine sites. Results show elevated concentrations (also called anomalies) of Pr, Nd, Dy and Ho, relative to other REE elements, in water samples, potentially from REE recycling and other industrialized activities in this area. Unlike water samples, no REE anomalies were found in SP or oysters, suggesting that the dominate REE uptake pathway in oysters is from particles. Secondly, site to site variations in Zn isotope ratios were found in water and SP, showing the complexity of the source inputs in this area. Also, in estuarine locations, larger spatially differences in Zn isotope ratios were found in water collected in wet season than those in dry season, which may due to mixing of different source inputs under the water circulations in different seasons. A series of laboratory experiments were conducted during which changes in Zn isotope ratios were measured during uptake under varying salinity and Zn concentrations and during depuration. Neither in vivo Zn transportation among the various tissues within the oysters nor water exposure conditions (i.e., different salinities or Zn concentrations) caused Zn isotopic fractionation in the oysters. Cd and Zn isotope ratios were also determined in oysters obtained from the PRE. Large variations in Cd and Zn isotope ratios suggest that oysters were receiving contaminants from different input sources within the PRE. A consistent difference (approximately 0.67‰) was observed for Zn isotope ratios in oysters collected from the east side of the PRE compared to those from sampling locations on the western side of the PRE, suggesting different Zn sources in these two areas. Ultimately, by combining biogeochemistry with physiology, this study represents a first attempt to assess pollution status, monitor contaminants using oysters and model/identify contamination sources using both REEs and metal isotope ratios. Author Keywords:
Socioloegal Mediation of Rave Sound System Technologies
The central scholarly contribution of this dissertation develops through bringing the theories of Michel Foucault to bear in a sociolegal study of rave culture's criminalization by the United Kingdom's 1994 Criminal Justice and Public Order Act. My methodology develops rave as a cultural keyword. This keyword navigates through a quasi-materialist definition of rave as a cultural codification of sound system technologies. I theorize the way in which sociocultural discourse indexes aestheticized representations and the cultural mythologies that rave sound system's technical mediation generate. These ideas trace the facticity of the legal documentation of rave’s criminalization. I inform this sociolegal history by situating Foucault's work on the genealogy of liberalism as a practical toolkit for associating the legal discourse on rave culture with the genealogy of festival. This opens up a dialogue with the work of Mikhail Bakhtin's theorizing of the festival’s ambivalent political climate. Such ideas are useful in documenting rave as an enduring mimicry of the tension between State and civil society. Pieter Bruegel the Elder’s 1559 painting, “The Fight Between Carnival and Lent”, captures this tension beautifully. The aptness of reading rave's criminalization in relation to Bruegel’s portrayal of landscape is accomplished by returning to Foucault, who defines liberalism's political technologies in relation to Judaeo-Christian precedents. I explore how these political technologies, pastoral power in particular, are helpful in tracing rave's genealogical relation to the festival's sociotechnical cartography. Author Keywords: Bakhtin, Carnival, Christianity, Festival, Liberalism, Materialism
Hoop Dance Project
This dissertation explores a 2017 elementary school Hoop Dance project that was organized by a white music teacher, and taught by an Indigenous artist in Peterborough, Ontario. It aims to respond to the Truth and Reconciliation Commission Calls to Action, numbers 10 and 63, which ask the federal government to sufficiently fund legislation that incorporates the following principles: “… developing culturally appropriate curricula” (p. 2), and “building student capacity for intercultural understanding, empathy, and mutual respect” (p. 7). The dissertation asks the question: In what ways will a seven-week Indigenous Hoop Dance Unit, taught by an Indigenous performing artist and facilitated by a white school teacher, contribute to reconciliation in an elementary school classroom in Ontario? I am the teacher in this study and have worked at this elementary school for five years. Throughout the project, I acted as facilitator, participant, and researcher, while Indigenous dancer and instructor Beany John planned and delivered the Hoop Dance content. Theoretically, the dissertation is organized around the Anishinabek seven grandmother/grandfather teachings, as taught by Ojibwe/Odawa educator and author Pamela Toulouse (2011). I believe that these seven traditional teachings are a meaningful basis upon which to build the project, not only because they inform Indigenous knowledge in the arts, but also because frequent reflection and referral to the teachings help remind me to remain connected to the “higher” purpose of the research throughout the project, which is to further the reconciliation process in Canada, and more broadly, to benefit society. Regarding methodology, I use arts based research (Leavy, 2015) and a constructivist grounded theory analysis, which embraces the subjectivity and positionality of the researcher (Creswell, 2012). The overall conclusion of the dissertation is that although the Hoop Dance project did not significantly address issues of Indigenous sovereignty in education nor our shared inherited legacy of colonial harm, it was a constructive step in the reconciliation project, largely due to the contributions of Beany John, whose teaching gently unsettled conventional educational practice at our school. Author Keywords: Arts Education, Hoop Dance, Indigenous Education, Indigenous Peoples, Settler Colonialism, Truth and Reconciliation
Characterization of Synthetic and Natural Se8 and Related SenSm Compounds by Gas Chromatography-Mass Spectrometry
Elemental selenium has been extensively quantitatively measured in sediments; however, its physical composition is largely unknown, despite it being the dominant selenium species in some reducing environments. Here, for the first time, it is shown that small, cyclic selenium compounds can account for a quantitatively-relevant fraction of the total elemental selenium present. A new method was developed to analyze for cyclooctaselenium (Se8) in both synthetic samples and selenium-impacted sediments. Despite some analytical limitations, this gas chromatography-mass spectrometry (GC-MS) method is the first GC-MS method developed to identify and quantify Se8 in sediments. Once this method was established, it was then applied to more complex systems: first, the identification of compounds in mixed selenium-sulfur melt solutions, and then the determination of SenSm in selenium-impacted sediments. Despite complications arising from pronounced fragmentation in the ion source, assignment of definitive molecular formulae to chromatographically-resolved peaks was possible for five compounds. Developing a fully quantitative method to obtain elemental ratio information can aid in the assignment of molecular formulae to chromatographically-resolved SeS-containing chromatographic peaks. Coupling the existing gas chromatography method to an inductively coupled plasma-mass spectrometer (ICP-MS) system should accomplish this. However, due to a number of complications, this was not completed successfully during the duration of this thesis project. High detection limits for sulfur, retention time discrepancies, and inconsistent injection results between the GC-MS and GC-ICP-MS system led to difficulties in comparing results between both analytical methods. Despite these limitations, GC-ICP-MS remains the most promising method for the identification and quantification of SenSm compounds in synthetic melt mixtures and selenium impacted sediments. Author Keywords: gas chromatography-mass spectrometry, sediments, selenium
Characterization of a Zn(II)2Cys6 transcription factor in Ustilago maydis and its role in pathogenesis
Ustilago maydis (D.C.) Corda is a biotrophic pathogen that secretes effectors to establish and maintain a relationship with its host, Zea mays. In this pathosystem, the molecular function of effectors is well-studied, but the regulation of effector gene expression remains largely unknown. This study characterized Zfp1, a putative U. maydis Zn(II)2Cys6 transcription factor, as a modulator of effector gene expression. The amino acid sequence of Zfp1 indicated the presence of a GAL4-like zinc binuclear cluster as well as a fungal specific transcription factor domain. Nuclear localization was confirmed by tagging Zfp1 with enhanced green fluorescent protein. Deletion of zfp1 resulted in attenuated hyphal growth, reduced infection frequency, an arrest in pathogenic development, and decreased anthocyanin production. This phenotype can be attributed to the altered transcript levels of genes encoding predicted and confirmed U. maydis effectors in the zfp1 deletion strain during pathogenic growth. Complementation of zfp1 deletion strain with tin2, an effector involved in anthocyanin induction, suggested this effector is downstream of Zfp1 and its expression is influenced by this transcription factor during in planta growth. When wild-type zfp1 was ectopically inserted in the zfp1 deletion strain, pathogenesis and virulence were partially restored. This, coupled with zfp1 over-expression strains having a similar phenotype as the deletion strains, suggested Zfp1 may interact with other proteins for full function. These findings show that Zfp1, in conjunction with one or more binding partners, contributes to U. maydis pathogenesis, virulence, and anthocyanin production through the regulation of effector gene expression. Author Keywords: effector, pathogenesis, transcription factor, Ustilago maydis, Zea mays, zinc finger
Effects of Silver Nanoparticles on Lower Trophic Levels in Aquatic Ecosystems
Due to their effective antibacterial and antifungal properties, silver nanoparticles (AgNPs) have quickly become the most commonly used nanomaterial, with applications in industry, medicine and consumer products. This increased use of AgNPs over the past decade will inevitably result in an elevated release of nanoparticles into the environment, highlighting the importance of assessing the environmental impacts of these nanomaterials on aquatic ecosystems. Although numerous laboratory studies have already reported on the negative effects of AgNPs to freshwater organisms, only a handful of studies have investigated the impacts of environmentally relevant levels of AgNPs on whole communities under natural conditions. This thesis examines the effects of chronic AgNP exposure on natural freshwater littoral microcrustacean, benthic macroinvertebrate and pelagic zooplankton communities. To assess the responses of these communities to AgNPs, I focused on a solely field-based approach, combining a six-week mesocosm study with a three-year whole lake experiment at the IISD – Experimental Lakes Area (Ontario, Canada). Our mesocosm study tested the effects of AgNP concentration (low, medium and high dose), surface coating (citrate- and polyvinylpyrrolidone [PVP]-coated AgNPs), and type of exposure (chronic and pulsed addition) on benthic macroinvertebrates in fine and stony sediments. Relative abundances of metal-tolerant Chironomidae in fine sediments were highest in high dose PVP-AgNP treatments; however, no negative effects of AgNP exposure were seen on biodiversity metrics or overall community structure throughout the study. I observed similar results within the whole lake study that incorporated a long-term addition of low levels of AgNPs to an experimental lake. Mixed-effects models and multivariate methods revealed a decline in all species of the littoral microcrustacean family Chydoridae in the final year of the study within our experimental lake, suggesting that this taxon may be sensitive to AgNP exposure; however, these effects were fairly subtle and were not reflected in the overall composition of littoral communities. No other negative effects of AgNPs were observed on the pelagic zooplankton or benthic macroinvertebrate communities. My results demonstrate that environmentally relevant levels of AgNPs have little impact on natural freshwater microcrustacean and benthic macroinvertebrate communities. Instead, biodiversity metrics and community structure are primarily influenced by seasonal dynamics and nutrient concentrations across both lakes. This thesis highlights the importance of incorporating environmental conditions and the natural variability of communities when examining the potential risks posed by the release of AgNPs into the environment, as simplistic laboratory bioassays may not provide an adequate assessment of the long-term impacts of AgNPs on freshwater systems. Author Keywords: Benthic macroinvertebrates, IISD - Experimental Lakes Area, Littoral microcrustaceans, Silver nanoparticles, Whole lake experiment, Zooplankton

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