Theses, Dissertations, and other Required Graduate Degree Essays

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This collection contains digitized SFU theses except for those theses submitted within the last 12 months. If you cannot find the thesis you are looking for please search Recently Submitted Theses as it may be a recently submitted thesis and thus not yet available in Summit.

Advances in fluorogenic RNA aptamer systems for live cell imaging: Towards orthogonality and multicolour applications

Author: 
Date created: 
2018-10-25
Abstract: 

Recent developments in the field of RNA biology continue to demonstrate the importance of RNA in regulating cellular processes. However, directly imaging biologically important RNAs has been hindered by a lack of live cell fluorescent tools. As such, aptamers that bind and enhance the brightness of fluorogenic dyes are promising tools to improve fluorescent RNA imaging. The Unrau laboratory developed RNA Mango I, a small, 39-nt aptamer that binds to a modified thiazole orange fluorophore (TO1-Biotin) with nanomolar affinity. This binding is accompanied by an 1,100-fold increase in its green channel fluorescence. To further improve the Mango aptamers, in collaboration with the Ryckelynck laboratory, we used microfluidics-based selection methods to isolate three brighter, high affinity RNA Mango fluorogenic aptamers (Mango II, III and IV). Together with the Rueda laboratory, we show that these new Mangos can accurately image the sub-cellular localization of three small non-coding RNAs in fixed and live mammalian cells. These new Mangos are unique in structure. Unlike Mango I and II, Mango III rigidly connects its ligand binding core to an external helix. As the Spinach/Broccoli aptamer family, which binds GFP-like chromophores (DFHBI, DFHBI-1T), also share this property, the Broccoli/DFHBI-1T aptamer complex was used as a FRET donor paired with the far red-shifted Mango III/YO3-Biotin complex as a FRET acceptor. Interestingly, the high affinity Mango I, II, III aptamers can discriminate between TO1/YO3-Biotin and DFHBI/DFHBI-1T by at least a 102-fold difference in affinity. In contrast, Spinach binds many fluorophores indiscriminately and weaker. With this, concentrations could be determined to obtain appropriate binding for Mango III/YO3-Biotin and Broccoli/DFHBI-1T when in the same system. FRET efficiency was measured using an RNA duplex of variable length between the two aptamers. FRET signal depended on the length of the duplex, and oscillated in intensity precisely with the predicted twist of the helix, demonstrating strong orientation dependence. While this pair of aptamers enable in vitro FRET studies, there are no truly orthogonal fluorescent aptamer systems. To that end, I discuss an in vitro selection to develop orthogonal aptamers for a red fluorophore, TO3-Biotin, that can potentially be paired with existing Mango aptamers.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Peter Unrau
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) Ph.D.

Sedimentological and ichnological characterization of small- and large-scale channel IHS in the Middle McMurray Formation of the Central-C area, McMurray Sub-Basin, Alberta

Author: 
Date created: 
2018-12-11
Abstract: 

The Lower Cretaceous McMurray Formation is interpreted as a brackish-water, tidally influenced estuarine complex. The study area encompasses Townships 90-95, Ranges 10-14W4 in northeast Alberta. Facies analysis of 41 cored wells led to the identification and differentiation of large- and small-scale lateral accretion IHS associated with tidal-fluvial channels. Five sedimentary facies are assembled into four recurring facies associations to characterize these channel systems. Sedimentological and ichnological characteristics point to elevated physico-chemical stress in most large-scale channel successions, interpreted to be the consequence of carrying the bulk of the fluvial discharge through these trunk channel systems. By contrast, small-scale channels display less evidence of physico-chemical stress indicating they carried little fluvial flow. Abandoned channel deposits likewise show reduced paleoenvironmental stress. This study suggests that the deposits of small-scale channels and abandoned channels are the most suitable for assessing the degree of marine influence in the study area.

Document type: 
Thesis
Senior supervisor: 
James MacEachern
Department: 
Science: Department of Earth Sciences
Thesis type: 
(Thesis) M.Sc.

Heat and electron conduction in microporous catalyst layers of polymer electrolyte membrane fuel cells

Author: 
Date created: 
2018-11-28
Abstract: 

Recent movement toward zero-emission mobility has propelled significant technological advancements in commercialization of polymer electrolyte membrane fuel cells (PEMFCs). PEMFCs provide electricity by reacting hydrogen with oxygen through two half-reactions occurring inside two respective anodic/cathodic microporous catalyst layers (CLs) with thicknesses of ~2-8 µm. Other products of the overall reaction include water and waste heat. All the electricity generation/consumption and most of the heat generation modes occur inside the CLs through a set of highly coupled multi-physics phenomena (a coupling between the electrochemical reactions, transport of species, electron conduction, and heat conduction). This necessitates knowing thermal and electronic conductivities of CLs for optimizing the fuel cell performance in various operating conditions. In this thesis, novel procedures are developed to measure thermal and electronic conductivities of CLs at low error rates. The procedures are based on novel methods to increase the amount of catalyst in the testbeds for enhancing the signal to noise ratio while ensuring complete deconvolution of the CL bulk signal. Further, a comprehensive platform is developed to characterize microstructure of CLs from different aspects, including a complete scheme for characterizing cracks for the first time. Separate measurements of in-plane and through-plane electronic conductivities, for the first time, uncovers anisotropic microstructure of CLs. CL designs with various compositions and structures are made and characterized. Observed trends in the conductivity data are linked to various structural properties of the CLs to understand structure-property correlations. A complete set of closed-form multi-scale structural models are developed for the conductivities in different directions to understand the underlying physics and provide tools for development of CLs with desired conductivities. The developed models agree well with the experimental data and precisely predict the structural trends. The models also explain and predict effects of different operating conditions. Using the developed tools, design guidelines are proposed for fabricating CLs with desired thermal and electronic conductivities, whose proof of concepts were made and successfully tested in the experimental phase of this research. Order of magnitude analyses show significant potentials for enhancing the fuel cell performance by tuning the conductivities through engineering the microstructure.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Majid Bahrami
Department: 
Applied Sciences: School of Mechatronic Systems Engineering
Thesis type: 
(Thesis) Ph.D.

Readers in the margins: Texts, paratexts, and reading audiences in Romantic-era fiction

Author: 
Date created: 
2018-10-19
Abstract: 

Readers in the Margins: Texts, Paratexts, and Reading Audiences in Romantic-era Fiction investigates how the form of the book influenced literary form in the Romantic period—not just how readers read and how publishers marketed, but how pre-existing paratextual norms shaped how writers conceived of and composed their writing. To do so, this project draws on a combination of book history and narratological strategies to explore how the material and historical realities of the Romantic-era book industry shaped fiction during the period. Contextualizing the narrative strategies of authors including Maria Edgeworth, Jane Austen, and Frances Burney within the early nineteenth-century material culture of the book reveals how Romantic-era cultural conceptions of genre, audience, and gender are encoded in the physical manifestations of their fiction. This argument builds on three critical discourses in the study of the period’s fiction: discussions of eighteenth-century and Romantic-era paratexts and the book as technology, by Janine Barchas, Christina Lupton, Andrew Piper, and Alex Watson; scholarship that engages with the commercialization of print, historical reading practices, and their relationship to the construction of Romantic-era reading audiences in the popular imagination, by Stephen Colclough, Jan Fergus, Michael Gamer, Jon Klancher, and William St. Clair; and studies of the gendering of audiences, genres, and authors, by Adriana Cracuin, Ina Ferris, and Jacqueline Pearson, among others. Bringing together these disparate strands of criticism demonstrates how the paratext is a necessary context for understanding literary innovation in the Romantic period. The first two chapters explore what kinds of explicit and implicit information paratexts conveyed to readers during the Romantic period and what kinds of implications those had for readers who had to navigate an increasingly overwhelming number of books by looking at title page design and Maria Edgeworth’s use of genre, respectively, while the third and fourth chapters take as case studies two authors, Jane Austen and Frances Burney who make use of their readers’ paratextual expectations to experiment with narrative for political ends.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Michelle Levy
Department: 
Arts & Social Sciences: Department of English
Thesis type: 
(Thesis) Ph.D.

Fully hydrocarbon ionomer catalyst layers in proton- and anion-exchange membrane fuel cells

Author: 
Date created: 
2018-09-17
Abstract: 

The structure and morphology of fuel cell catalyst layers and concomitant system properties, particularly mass transport, were investigated through electrochemical and physical characterization techniques. Catalyst layers designed for proton-exchange membrane fuel cells (PEMFCs) incorporated a hydrocarbon ionomer (sP4c) soluble in low-boiling solvents. These were used to probe the property alterations effected by increasing ionomer coverage within the catalyst layer, and also to measure the impact an extremely small quantities (0.38 wt%) of a commonly employed high-boiling solvent, DMF, in the catalyst ink. High-boiling solvents are difficult to eliminate during electrode formation, and resultant solvent-annealed catalyst layers lost electrocatalytic surface area, resulting in markedly greater kinetic losses compared to catalyst layers formed without high-boiling solvents. Catalyst layers designed for anion-exchange membrane fuel cells (AEMFCs) incorporating hydrocarbon ionomer in the catalyst layer (FAA-3) requiring high-boiling solvent (NMP, 2.3 wt% of total solvent) were formed over a broad array of conditions. Catalyst layers formed slowly at high temperatures to drive off high-boiling solvent displayed significantly enhanced mesoporosity, relating to enhanced transport characteristics, over solvent-annealed analogues with low mesoporosity, despite comparable total volumes. The impacts of solvent annealing on AEMFC electrode properties and resultant achievable power density and degradation were disproportionate compared to the similar PEMFC study. A new methodology for fuel cell membrane-electrode assembly construction, direct membrane deposition (DMD), enables lower interfacial resistances and enhanced water transport for a given thickness of membrane. These are desired properties for both PEMFCs and AEMFCs. Initially developed with inkjet printers designed for single-cell biological printing applications, this method was adapted to spray-coating systems in order to address issues with fuel and electrical crossover, suitability for hydrocarbon ionomers, and scalability / large-scale reproducibility. A perfluorinated sulfonic acid ionomer reference material (Nafion D520) was employed for direct comparison to initial methods. Highly reproducible DMDs with low fuel and electrical crossover resulted.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Steven Holdcroft
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

The pollination ecology of highbush blueberry (Vaccinium corymbosum) in British Columbia

Author: 
Date created: 
2018-05-28
Abstract: 

Agricultural systems often support low beneficial insect diversity because they reduce habitat quality. Agricultural management increases landscape homogeneity resulting in low habitat and resource diversity. Crops that rely on wild pollinators for fruit production or predators and parasitoids for pest control may lose access to these services as the agroecosystem becomes increasingly managed. I used yield data from pollination experiments conducted over four years, along with insect surveys, to better understand the dynamics between insect communities in agroecosystems and their use of the agricultural landscape in highbush blueberry (Vaccinium corymbosum) in the Fraser Valley of southern British Columbia, Canada. Regional land use was identified as being an important component in structuring beneficial insect communities. Semi-natural habitat, such as pasture or fallow, was found to support greater abundances and diversity of all beneficial insects. Land use with greater disturbance, like conventional non-flowering agriculture, reduced pollinator species richness but increased the abundance of generalist predators. The differences between groups in their response to land use types might be driven by variability in access to resources (ex. floral resources or pest insects) in the larger agricultural landscape. However, surrounding landscape composition did not affect blueberry yield deficit, which was instead determined primarily by bumble bee visits and minimum daily temperatures. This finding highlights the importance of weather conducive to pollinator foraging for crop production. Despite the importance of bumble bees for reducing yield deficit, experimental introduction of two managed bumble bee species did not mitigate these deficits. Differences in bumble bee species characteristics associated with reproduction predicted pollen forager recruitment, which when coupled with differences in foraging preferences (blueberry pollen comprised 50% of pollen loads in one species, but less than 20% in the other and in managed honey bees) provides some insight into which managed species is best suited for further commercial development. My results highlight the complexity associated with predicting crop pollination levels and demonstrate how the impact of wild insects on production will vary with surrounding land-use, species characteristics, and abiotic factors. In crops highly reliant on wild pollinators, like highbush blueberry, understanding the needs of beneficial insects may allow farmers to modify practices to improve ecosystem services.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Elizabeth Elle
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Three essays on customer-supplier networks and financial markets

Author: 
Date created: 
2018-11-23
Abstract: 

This thesis is composed of three independent essays on customer-supplier networks and financial markets. The first chapter, entitled "Economic Links and Return Volatility", is co-authored with Keyi Zhang and Ramazan Gencay. This study investigates the propagation of stock return volatility along supply chains. Our results show that the effect of customer volatility is approximately 10 times as large as trading volume on supplier's volatility. Our findings are robust to controlling for variables capturing the time-series properties of volatility and a set of idiosyncratic, industry and market factors; tested under various assumptions regarding the activeness of customer-supplier linkages; and to different estimation methods. Our out-of-sample tests provide consistent evidence that incorporating customer channel improves volatility forecasting. Furthermore, the transfer of volatility is more pronounced when investors are more aware of customer-supplier linkages. The second chapter, entitled "Resilience to the Financial Crisis in Customer-Supplier Networks" is also co-authored with Ramazan Gencay and Keyi Zhang. Inspired by the Capital Asset Pricing Model (CAPM) beta, we construct customer and supplier betas to separately investigate potentially different properties of downstream and upstream linkages. With the adjacency matrix acting as a "filter" to extract each company's return covariances with its trading partners, the cross-sectional dependence contained in the customer-supplier network is summarized by our betas. We explore how these two betas are related to a company's resilience to the financial crisis of 2008-2009. We observe that a higher customer beta is generally associated with more resilience during the crisis. The third chapter, entitled "Economic Links and Credit Spreads", is co-authored with Ramazan Gencay, Daniele Signori, Yi Xue and Keyi Zhang. This paper has been published in the Journal of Banking and Finance. This study describes a model of financial networks that is suitable for the construction of proxies for counterparty risk. We find that, for each supplier, counterparties' leverage and option implied volatilities are significant determinants of corporate credit spreads in the period after the 2008-2009 U.S. recession. Our findings are robust after controlling for several idiosyncratic, industry, and market factors.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Ramazan Gencay
Department: 
Arts & Social Sciences: Department of Economics
Thesis type: 
(Thesis) Ph.D.

Lessons learned from the 2013 Calgary Flood: How to prepare for the next disaster

Date created: 
2018-11-08
Abstract: 

Urban centres are constantly exposed to natural hazards. Recovering from natural disasters is a complex process that lacks a grounded theory and an operational definition. This thesis proposed a two-layer conceptual framework that can be helpful when exploring the implementation of recovery efforts. This research project explores the municipal approach of the City of Calgary during the recovery from the 2013 Southern Alberta Flood. The City of Calgary responded to this flood in a partially effective manner. The Calgary case study is a case where the local government had in place the right processes to develop an effective recovery. Nevertheless, the City requires guidance on what a recovery plan should address. Calgary’s approach proposes challenges related to the development of meaningful public participation methods and the slight assistance provided to the business community. Recovery is an action that requires the involvement of the affected and relevant stakeholders to help build governance capacity, which in turn creates a resilient community.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Meg Holden
Department: 
Arts & Social Sciences: Urban Studies Program
Thesis type: 
(Project) M.Urb.

Composition of aquatic microbial communities and their relation to water-column methane cycling among Mackenzie Delta lakes, western Canadian Arctic

Date created: 
2018-11-29
Abstract: 

Seasonal dynamics of water-column microbial communities and methanotrophs were monitored in six lakes of the Mackenzie River Delta using gene sequencing of 16S rRNA gene and qPCR of the 16S rRNA and methane monooxygenase (pmoA) genes. Selected lakes varied in biogeochemistry based on annual river-to-lake connection times, which we hypothesized would impact bacterial community composition and methanotroph relative abundance. River-to-lake and seasonal influences on carbon bioavailability and quantity, nutrients, temperature and flooding correlated with seasonal changes in microbial composition. Methanotroph groups including Methylobacter and methylotrophs Candidatus Methylopumilus and Candidatus Methylophilaceae were detected in all lakes but at higher relative abundance in the winter and spring when lake-water methane concentrations were highest. Open-water methanotroph abundance was highest in spring. In experimental enclosures, methanogenesis was detected in oxygenated lake-water and rates varied by lake type. Nutrient enhancements altered microbial composition and increased rates of methane oxidation with increasing lake isolation.

Document type: 
Thesis
Senior supervisor: 
Lance Lesack
Department: 
Environment: Department of Geography
Thesis type: 
(Thesis) M.Sc.

Empire and dispossession: Coal, communication, and the labour process at the origins of capitalism in British Columbia, 1849 – 1903

Author: 
Date created: 
2018-12-10
Abstract: 

Coal mining on Vancouver Island was a conjunctural point for two complementary systems of dispossession: capitalism and colonialism. Soon after London granted the island and its minerals to the Hudson’s Bay Company in January 1849, industrial mining began to replace the previously non-capitalist organization of the coalfield. The island shifted into industrialization in part through its entanglement in Pacific markets hungry for coal. The tools and capital that returned on homeward voyages hastened mining’s development, while transoceanic maritime networks provided inflows of labour power. As energy capital developed internally, strategies to displace Indigenous organization of the land were matched by efforts to alienate miners from acting as a class in their own interests. Through analysis of archival evidence, this project demonstrates that Vancouver Island mining before 1903 proceeded through a series of compounding deprivations, generally beneficial to islanders occupying dominant economic positions. Toward unpacking this history, “Empire and Dispossession” asks three questions: how did the coal industry support the development of capitalist social relations in the Pacific, north of parallel forty-nine; how did transportation systems sustain the expansion of empires operating on the island; and what social, political, and economic relationships conditioned technical change in the mines? Taken together, the answers to these questions root the development of capitalism in active power relationships of class and race. This project’s original contributions to communication studies include a historical narrative of Western Canadian capitalism, otherwise absent in the field; the development of a transportation-focused approach to communication, rooted in the work of Karl Marx; a history of Indigenous transportation and communication labour at the origins of capitalism on Vancouver Island; and a reinterpretation and application of labour-process theory to the mutually constitutive development of coal-mining machinery, social class, and race in the island’s mines.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Andrew Feenberg
Department: 
Communication, Art & Technology: School of Communication
Thesis type: 
(Thesis) Ph.D.