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
At the Intersection Between History and Fiction in Biography and Autobiography; A Repositioning, Using the Quest for the Historical Jesus as a Case Study
The modern sense of historicism developed over time that brought different textures at the intersection between history and fiction. The life of Jesus of Nazareth, prolifically researched after Herman Reimarus (1694-1768) right until today – a phenomenon known as The Quest for the Historical Jesus – provides an instructive case study for a wider discussion about the intersection between history and fiction in biography and autobiography. As a result of these centuries of Jesuanic research, one can identify a set predictable challenges which life-writing may need to confront. Furthermore, interesting historiographical criteria to detect factual authenticity versus factual inauthenticity for life-writing were also developed. Nevertheless, the depth of disagreement about a well-researched narrative such as the Jesuanic chronicle can eventually feel almost insurmountable. Pessimism, in fact, has become widespread. Thus, this dissertation raises the question: Is it but a vain attempt to search for truth by attempting to draw a sharp line between fiction and history? Hence, the discussion moves to Mikhail Bakhtin whose insistence on dialogism rather than truth seeking provides a more relational approach to appreciating the intersection between history and fiction in biography and autobiography. Author Keywords: biography, Copernicanism, dialogism, fiction, historicism, monologism
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
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
Instabilities in the Identity of an Artistic Tradition as "Persian," “Islamic," and “Iranian” in the Shadow of Orientalism
This dissertation is a critical review of the discursive formation of Islamic art in the twentieth century and the continuing problems that the early categorization of this discipline carries. It deals with the impact of these problems on the conceptualization of another category, Persian art. The subject is expounded by three propositions. First, the category of Islamic art was initially a product of Orientalism formulated regardless of the indigenous/Islamic knowledge of art. Second, during the early period when art historians examined different theoretical dimensions for constructing an aesthetic of Islamic art in the West, they imposed a temporal framework on Islamic art in which excluded the non-traditional and contemporary art of Islamic countries. Third, after the Islamic Revolution in 1979, Iranian scholars eventually imposed academic authority over the discipline of Persian/Islamic art, they adopted the same inadequate methodologies that were initially used in some of the early studies on the art of the Muslims. These propositions are elaborated by examples from twentieth-century Iranian movements in painting, The Coffeehouse Painting and The School of Saqqakhaneh, and the incident of swapping Willem de Kooning’s painting Woman III with the dismembered manuscript of the Shahnama of Shah Tahmasp in 1994. The conceptualization of Islamic art as a discipline is also discussed in relation to the twentieth-century cultural context of Iran. The argument is divided into three chapters in relation to three important historical moments in the history of contemporary Iran: The Constitutional Revolution (1905-1911), the modernization of Iran (1925-1975), and the Islamic Revolution (1979-onward). The formation of the discourse of Islamic art is the fruit of nineteenth-century Orientalism. Out of this discourse, Persian art as a modern discourse addressing the visual culture of Pre-Islamic and Islamic Iran came into being. I claim that after the Islamic Revolution, Iranian academics demonstrate a theoretical loyalty to the early theorizations of Islamic/Persian art. By this token, visual signs are given a meta-signified in the narrative of Islamic art. The ontological definition of this meta-signified is subjected to the dominant ideology, which determines how different centers of meaning should come into being and disappear. In the post-Revolution academia, the center is construed as the transcendental signified. Such inherence resulted in a fallacy in the reading of the Persian side of Islamic art, to which I refer as the “signification fallacy.” The dissertation draws on the consequences of this fallacy in the critique of Islamic art. Keywords: Persian art, Islamic art, Iranian art; Persian classical literature, Narrative. Image, Representation, Aniconism, Abstraction, Modernity, Tradition, Orientalism, The Constitutional Revolution, Modernization, The Islamic Revolution. Shahnama of Shah Tahmasp, The Coffeehouse Painting, The School of Saqqakhaneh; Modernism: Woman III. Author Keywords: Iranian Art, Islamic Art, Orientalism, Persian Art, The Constitutional Revolution, The Islamic Revolution
Alien Imaginaries
This dissertation offers a cultural analysis of UFOs and extraterrestrials in the United States. In it I look at what I call real aliens — extraterrestrials believed to be real and interacting with humans on Earth. Beliefs in real aliens are often denigrated and dismissed in official discourse, yet they continue to not only persist, but thrive, in American society. Hence, this dissertation asks: Why do so many people believe that extraterrestrials are visiting our planet? Part One begins by tracing the invasion of real aliens in the United States using Orson Welles’s 1938 radio broadcast “The War of the Worlds” as a starting point. Here, I look at how and why the broadcast registered with listeners’ anxieties and created a fantastic and uncanny effect that made it possible for some to conceive of aliens invading the United States. In Part Two, I trace the rise of ufology, which involves the study of extraterrestrials currently interacting with humans on Earth, and I consider how the social and political climate of the Cold War, as well as the cultural environment of postmodernity, provided the necessary conditions for stories about aliens to be made believable. Part Three explores the case study of the Roswell Incident, a conspiracy theory about the origins of an alleged flying saucer crash and government cover-up. I look at the reasons for why many individuals have come to believe in this conspiracy theory and I reflect on the tensions between “official” and “unofficial” discourses surrounding this case. I also consider how and why Roswell has become such an important site for ufology, and I examine the performances given by ufologists at the annual Roswell International UFO Festival to appreciate how ufologists offers seductive explanations of why things are the way they are; for many, their stories offer a better version of events than the purely rational and positivist explanations offered by official sources, especially since they tap into the disillusionment and mistrust that many Americans feel about contemporary politics. Author Keywords: aliens/extraterrestrials, America, conspiracy, official and unofficial, storytelling, ufology
Role of Dielectric Screening in SrTiO3-Based Interfaces
We build a theoretical model for exploring the electronic properties of the two-dimensional (2D) electron gas that forms at the interface between insulating SrTiO3 (STO) and a number of perovskite materials including LaTiO3, LaAlO3, and GdTiO3. The model treats conduction electrons within a tight-binding approximation, and the dielectric polarization via a Landau-Devonshire free energy that incorporates STO's strongly nonlinear, nonlocal, field-, and temperature-dependent dielectric response. We consider three models for the dielectric polarization at the interface: an ideal-interface model in which the interface has the same permittivity as the bulk, a dielectric dead-layer model in which the interface has permittivity lower that the bulk, and an interfacial-strain model in which the strain effects are included. The ideal-interface model band structure comprises a mix of quantum 2D states that are tightly bound to the interface, and quasi-three-dimensional (3D) states that extend hundreds of unit cells into the STO substrate. We find that there is a substantial shift of electrons away from the interface into the 3D tails as temperature is lowered from 300 K to 10 K. We speculate that the quasi-3D tails form the low- density high-mobility component of the interfacial electron gas that is widely inferred from magnetoresistance measurements. Multiple experiments have observed a sharp Lifshitz transition in the band structure of STO interfaces as a function of applied gate voltage. To understand this transition, we first propose a dielectric dead-layer model. It successfully predicts the Lifshitz transition at a critical charge density close to the measured one, but does not give a complete description for the transition. Second, we use an interfacial-strain model in which we consider the electrostrictive and flexoelectric coupling between the strain and polarization. This coupling generates a thin polarized layer whose direction reverses at a critical density. The transition occurs concomitantly with the polarization reversal. In addition, we find that the model captures the two main features of the transition: the transition from one occupied band to multiple occupied bands, and the abrupt change in the slope of lowest energy band with doping. Author Keywords:

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