title: THE LIVING AMONGST THE DEAD: THE ROLE OF HALIFAX CEMETERIES AS GREENSPACE AND THEIR POTENTIAL FOR EXPANSION OF THE URBAN FOREST

contributor: School for Resource & Environmental Studies

subject:
urban forest
cemeteries
Canada

abstract: Urban forests provide cities with a multitude of benefits but face many survival challenges. This thesis sought to determine the potential for cemeteries to expand the urban forest in Halifax, Nova Scotia through tree planting. Inventories of existing cemetery trees and potential plantable spots were conducted. Interception surveys with cemetery users and interviews with cemetery managers were used to determine the importance of cemetery trees and identify concerns and barriers to planting trees in cemeteries. The results indicate that Halifax cemeteries have relatively high canopy covers primarily composed of older non-native trees, and that the number of cemetery trees could be nearly doubled. Cemetery users highly value cemetery trees and have very few concerns about them. Cemetery managers also value cemetery trees but cited barriers to planting such as a lack of space, financial constraints, and potential for damage. For current canopy cover to be maintained (and expanded), these barriers need to be addressed.


title: ORNSTEIN-UHLENBECK PROCESS AND OPTIMAL SAMPLING FOR ANALYSIS OF MICROBIOME DATA

contributor: Department of Mathematics & Statistics - Statistics Division

subject:
ORNSTEIN-UHLENBECK PROCESS
OPTIMAL SAMPLING
MICROBIOME DATA
FISHER INFORMATION MATRIX

abstract: The Ornstein–Uhlenbeck (OU) process is a widely used model for stochastic processes, where the value drifts towards a fixed stable value. We examine how well the OU process fits the data by using likelihood ratio tests to compare models of temporal dynamics of OTUs. Then, we derive the Fisher information of the OU process and show how it can be used to maximize the temporal efficiency of sampling. We apply this to parameters estimated from real data to determine optimal sampling schemes for human microbiomes. We use simulations to show that the asymptotic theory applies to typical finite sample cases.


title: Assessing Gender: An Exploration of Transgender Individuals' Experiences of Assessments for Hormone Therapy or Surgery in Nova Scotia

contributor:
School of Social Work
Master of Social Work
Dr. Margaret Robinson
Dr. Catrina Brown
Dr. Marion Brown
Dr. Cassandra Hanrahan
Dr. Catherine Bryan
Received
Not Applicable
Not Applicable

subject: transgender health

abstract: Transgender individuals living in Nova Scotia and wishing to undergo gender-confirming hormone therapy or surgery must participate in a mandatory mental health assessment to determine whether they meet the diagnostic criteria for gender dysphoria. This project explores the experiences of eleven transgender individuals in Nova Scotia who had received an assessment for gender-confirming hormone therapy or surgery. It considers these experiences in light of a framework of medicalization, examines the range of experiences by considering the role of private and public systems, the experiences of the standard WPATH (World Professional Association for Transgender Health) model versus the emerging model of Informed Consent for access to care, and explores areas for change. This work presents an opportunity to listen to first-voice accounts of the experiences of trans Nova Scotians, and to use these to advocate for a more equitable and anti-oppressive healthcare system for transgender individuals wishing to access transition-related care.


title: Looking to the Future with the Burdens of the Past: Exploring the Systems of Mental Health Treatment for War-Affected Youth in Northern Uganda

contributor: Department of International Development Studies

subject:
Mental Health
Conflict
International Development Studies
War-Affected Youth
Former Child Soldiers
Health Systems
Uganda
Northern Uganda
LRA Insurgency

abstract: This thesis explores the NGO-led sector of mental health treatment for war-affected youth (aged between 15 and 35 years old) in Northern Uganda.

abstract: Conflict-related trauma is linked intrinsically to mental health. This reality remains ever-present in Northern Uganda, as war-affected youth continue to suffer from the lingering effects of the LRA insurgency. With struggling health infrastructure, little capacity exists to address the magnitude of this issue. In place of hospitalized treatment, many local NGOs provide a variety of mental health services. These programs range from PTSD counselling to art-based therapies. This thesis asks, how do these services help war-affected populations and how can the system be strengthened? Based on the qualitative findings from grassroots practitioners, additional funding and attention is needed to combat challenges of coordination, apathy, participation, and gaps between policy and practice. Societal issues impacting scale, stigma, and poverty must be addressed. For a working holistic model of psychological care, infrastructure, capacity and finances must be strengthened and concentrated to heal the wounds of trauma which left from decades of conflict.


title: THE NATURE AND DYNAMICS OF CHANGES IN LIPIDS AND FATTY ACIDS DURING POSTHARVEST NEEDLE ABSCISSION, THEIR ROLE IN COLD ACCLIMATION, ULTRA-STRUCTURAL CHANGES, AND NEEDLE ABSCISSION RESISTANCE IN BALSAM FIR, ABIES BALSAMEA, L.

contributor:
Department of Biology
Doctor of Philosophy
Dr. Don Smith
Dr. Don Smith
Dr. Sophia Stone
Dr. Claude Caldwell
Dr. Chibuike Undenigwe
Dr. Rajasekaran Lada
Not Received
Yes
No

subject:
postharvest
lipids and fatty acids
balsam fir
needle abscission

abstract: Balsam fir is an important species of Atlantic Canada’s Christmas tree and greenery industries that is suffering due to excessive needle loss postharvest. A series of investigations were carried out to: (i) characterize and establish links between polar lipid and fatty acids  (FA) and postharvest needle loss;  (ii) uncover the differences in the nature and quantity of polar lipid and fatty acids in contrasting genotypes with high and low needle retention duration (NRD); (iii) explore temporal changes in polar lipids and fatty acids; (iv) establish the genotypic differences in polar lipids and FA during temporal changes, and (v) confirm the ultrastructural changes of cells of balsam fir postharvest using scanning and transmission electron microscopy. Polar lipids decreased significantly postharvest in all studies (p < 0.001). The mean percentage of monogalactosyldiacylglycerol (MGDG) decreased significantly postharvest (p < 0.0001), caused mostly by a decrease in MGDG 36:6 and 36:7. There was also a significant decrease in the MGDG: DGDG (digalactosyldiacylglycerol) ratio in all studies (p < 0.05), earlier in the poorer needle retaining clone. During cold acclimation, Clone 506 was identified as a high needle abscission resistant (NAR) clone, while Clones 9, 37, and 566 all proved to be lower. MGDG decreased during the fall and early winter in all clones, with a subsequent increase in DGDG and a significant decrease in the MGDG: DGDG ratio in all clones tested (p < 0.001). There was a significant decrease also in the GL: PL ratio (p < 0.001). There was significantly less DGDG in Clone 506 than in Clone 9 (p < 0.05). LPG 16:1 was eight times higher in Clone 506. In balsam fir, there was a significant reduction (p < 0.001) in α – linolenic acid in all clones postharvest. During cold acclimation, there was an increase in α – linolenic acid in one of the lower clones, Clone 566, but an increase in Δ5-UPIFA, 18:3 (pinolenic acid) in the other clones, suggesting different metabolism (p < 0.001). Chloroplast disorganization was confirmed. In addition, most of all stoma were closed in both clones, however, there was more fungal hyphae associated with the poorer NRD clone.


title: Impacts of Trade Openness with China on Labour Market Outcomes for Canadian Women in the Manufacturing Sector

contributor:
Department of Economics
Master of Arts
Mutlu Yuksel
Christos Ntantamis
Shelley Phipps
Teresa Cyrus
Not Applicable
Not Applicable
Not Applicable

subject:
Canadian trade openness with China
Effects on Canadian women
Weekly hours worked;
Real hourly wages

abstract: Trade liberalization between Canada and China has increased drastically since the 2000s, which could imply change in outcomes for Canadians in the labour market. This thesis looks at the consequences of increased trade openness with China on Canadian women across the manufacturing sector by assessing the effects on weekly hours at work and real hourly wages. The results suggest that there is a total negative effect by import and export exposure with China on weekly hours worked for females for the years of 1997 and 2005, and a positive impact in 2015. Meanwhile, there is a total negative effect from import and export exposure with China on real hourly wages by for all three years for females.


title: INVESTIGATION OF CARCINOGENIC PESTICIDE-ASSOCIATED  N-NITROSO COMPOUNDS IN HUMAN SERUM AND URINE IN  PRINCE EDWARD ISLAND

contributor:
Interdisciplinary PhD Programme
Doctor of Philosophy
Dr. Brian Wagner
Dr. Lynne Robinson
Dr. Ellen Sweeney
Dr. Wenda Greer
Dr. Cathryn Ryan
Dr. Jong Sung Kim
Received
Not Applicable
Not Applicable

subject: pesticides

subject: QuEChERS

subject: UHPLC/HRAM Orbitrap MS

subject: pesticide-associated N-nitroso compounds

subject: serum

subject: urine

abstract: N-nitroso compounds form during acid-catalyzed reactions between certain nitrogen-containing compounds and nitrite. Approximately 90% of over 300 N–nitroso compounds have shown evidence of carcinogenicity. Pesticide-associated N-nitroso compounds (PANNs) may form endogenously from nitrosatable pesticide residues in food or water and may be detected in serum and urine. The objectives of this doctoral dissertation were to (i) develop analytical methods using ultra-high pressure liquid chromatography (UHPLC) high-resolution accurate mass (HRAM) orbital ion trap mass spectrometry (MS) for measuring 10 PANN precursors in serum and urine; (ii) investigate PANN formation in water by combining nitrosatable analytes with nitrite under environmentally-relevant conditions; and (iii) analyze serum and urine from a sample population in Prince Edward Island, the province with the highest pesticide-use intensity, and an urban control population (Halifax, Nova Scotia) for target analytes and PANNs. Three sample preparation methods were evaluated for extraction of target analytes from biomatrices. Deproteinization by methanol resulted in excessive ion enhancement of some analytes and complete loss of others. Solid-phase extraction showed less ion enhancement than did deproteinization; however, analyte loss remained an issue. The Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) approach resulted in a novel method for extraction of target analytes with mean initial recoveries in serum ranging between 74 and 120% (% relative standard deviation, RSD <12) and 96% to 116% (%RSD 10) in urine. To assess PANN formation, nine nitrosatable precursors were individually reacted at environmentally-relevant concentrations with sodium nitrite and hydrochloric acid in water. Ethylenethiourea (ETU) produced carcinogenic N-nitrosoethylenethiourea (N-ETU) in several experiments and at initial ETU concentrations as low as 7.5 µg L-1. Finally, serum and urine from 64 healthy individuals in PEI and NS were analyzed for 10 PANN precursors. ETU and 3,5,6-trichloro-2-pyridinol were detected in serum while atrazine and ETU were detected in urine with no significant differences in detection frequency in either biomatrix between provinces. Six and 10 PANNs were tentatively identified in serum and urine, respectively, in both provinces. Based on these findings, endogenous N-ETU formation may be a concern for individuals exposed to ETU and PANNs may be utilized as biomarkers of pesticide exposure.


title: Benchmark and Earth-Abundant Electrocatalysts for Acidic Water Oxidation

contributor:
Department of Chemistry
Master of Science
Dr. Peng Zhang
Dr. Heather Andreas
Dr. Mark Stradiotto
Dr. Mita Dasog
Not Applicable
Yes
Yes

subject:
water oxidation
iridium dioxide
water electrolysis
earth-abundant

abstract: Solar-mediated hydrogen technology is a promising candidate for the low-carbon production of chemical fuels. Solar-mediated water electrolysis is a mature form of H2 technology that functions by rupturing water molecules to release H2 and O2 gas. Water electrolysis can be performed at any pH, but presently only acidic conditions offer sufficient gas separation and solution conductivity. Large-scale integration of solarmediated acidic water electrolysis is limited by the oxygen evolution reaction (OER), which requires oxidatively stable catalysts to proceed at appreciable rates and energies. The only materials known to possess acceptable levels of activity, stability and selectivity for acidic OER are iridium oxide (IrOx)-based systems.  IrOx serves as a “benchmark” material against which other OER catalysts are compared. The performance of IrOx is largely determined by its method of preparation and the conditions under which it is tested, neither of which are controlled for in the literature. To catalogue the impact of fabrication and electrolyte conditions on IrOx OER performance, IrOx films were prepared using common literature techniques and evaluated under equivalent electrolyte conditions. Further, the OER performance of IrOx films was evaluated in different electrolytes and molarities. The results of this study revealed preparation-dependent OER performances and film-dependent sensitivities to electrolyte composition. Identification of fabrication- and electrolyte-dependent properties for IrOx films allows for better comparison between literature electrocatalyst systems. The scarcity and cost of Ir limits the sustainability and scalability of water electrolysis. Earth abundant (EA) alternatives are required for this technology to be an economical large-scale energy solution. The current repertoire of EA materials for acidic OER all show poor stability and/or activity compared to analogous IrOx-based systems. Titanium diboride (TiB2) is a corrosion-resistant material with theorized and demonstrated catalytic behaviour. Its suitability as an acid-stable electrocatalyst for OER was investigated. It was found to have the highest chemical stability of known active EA materials for acidic OER and superior activity relative to other electrochemically-stable EA systems. However, TiB2 films showed limited mechanical stability and delaminated after ~ 10 h operation.


title: INNOVATIVE APPLICATIONS OF TIRE DERIVED AGGREGATE (TDA) FOR BURIED PIPES AND CULVERTS

contributor:
Department of Civil Engineering
Doctor of Philosophy
Dr. Nicholas Vlachopoulos
Dr. Hany El Naggar
Dr. John Newhook
Dr. Farid Taheri
Dr. Hany El Naggar
Not Applicable
Not Applicable
Yes

subject:
Tire Derived Aggregate
Shallow foundations
buried pipes
CSP culverts
Geocell
Seismic analysis
CHBDC

abstract:
Social well being and economic prosperity are tied together in a mutually supportive and interdependent scheme. Achieving prosperity is highly related to the socio-economic well being and cannot be achieved without strong and supportive civil infrastructures. Soil-metal structures including buried bridges, culverts, and pipelines are key supporting pillars for the economic prosperity of developed communities.
In densely populated and congested urban centers, the interaction between surface structures and buried utilities are unavoidable. For instance, placing the pipe at a shallow depth attracts substantial additional earth pressures and loads causing overstressing and/or unacceptable deformations of the buried pipe. There are several alternatives that may be used to mitigate this situation. These alternatives include using induced trench construction, using lightweight fill material to reduce the imposed loads, and finally relocation of utilities which is the most expensive and less desirable alternative. The characteristics of the used backfill material control the pipe-soil interaction mechanism and sequentially the amount of exerted pressures. Using lightweight compressible materials above buried structures has long been investigated to reduce the stresses above buried pipes.
In this thesis innovative applications for using tire derived aggregates (TDA) as a lightweight backfill material to protect and improve the performance of buried structures under static and seismic loading conditions were investigated experimentally and numerically. Exploring useful uses for TDA (produced from recycled scrap tires) in civil engineering applications helps to reduce the environmental impacts that could be caused by disposing the tires in landfills which is becoming a scares resource by time. Full-scale field tests were carried to examine the feasibility of protecting pre-existing pipes, located underneath shallow foundations, by using TDA as an engineered stress-reduction fill above the pipes and underneath a concrete footing. Additionally, the study was extended to investigate the behaviour of rigid footings resting on a surface of conventional backfill materials overlying a TDA layer with different thicknesses. Furthermore, a comprehensive three-dimensional modelling exercise using the finite element (FE) code PLAXIS 3D was conducted to study the effect of changing various key parameters, i.e., the thickness of the TDA layer, the shape and configuration of the TDA cross-section, etc., on the performance of the system.
Another four full-scale tests were executed in the lab to investigate the feasibility of using TDA around corrugated steel culverts to enhance their performance under service loading. Afterward, 3D finite element models were developed for the different tested configurations to investigate crucial parameters affecting the culvert performance and to optimize the design of the proposed TDA system. In addition, a coupled TDA Geocell stress bridging system was developed utilizing three additional full-scale tests and a comprehensive 3D modelling component. The developed system uses a geocell reinforced top granular backfill layer over the TDA layer to induce a stress arching mechanism capable of reducing the imposed stresses on the underneath pipe and control the surface settlement.
Finally, the last part of this research focuses on evaluating the seismic design of open bottom large span metal arch culverts in the Canadian Highway Bridge Design Code (CHBDC) and developing an innovative system using TDA to mitigate the seismic hazards in high seismicity regions. Based on the results of the conducted study, a set of recommendations for the analysis and design of buried structures are proposed.


title: The Post-Spawning Ecology of Iteroparous Salmonids: Basis of Variability in Migratory Behaviour and Survival, Ecological Importance and Conservation Implications

contributor:
Department of Biology
Doctor of Philosophy
Ian A. Fleming
Sophia L. Stone
Frederick G. Whoriskey
Jan G. Davidsen
Christophe Herbinger
Ramón Filgueira
Glenn T. Crossin
Received
Yes
Not Applicable

subject:
Ecophysiology
Acoustic Telemetry
Salmonids
Iteroparity
Population Dynamics

abstract: The overarching objective of my thesis is to shed light on a poorly understood life history stage of salmonid fish species, by quantifying spatio-temporal variation in the ecological importance of iteroparity (i.e. repeated breeding), as well as the factors influencing the movement ecology and survival of post-spawners, in freshwater, estuaries, and at sea. To do so, I used a variety of methods, including the analysis of long-term empirical data series, in addition to acoustic telemetry and physiological sampling, which I applied at various spatial and temporal scales and for two different but related iteroparous salmonid species – Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). The work identified some of the potential causes of inter-individual variation in migratory decisions and success, as well as the consequences for population-level processes. Throughout my studies, I consistently observed that, after spawning, nutritionally depleted (i.e. low body condition factor and/or plasma triglyceride concentration) or highly stressed individuals (i.e. high plasma cortisol and glucose concentrations) opted for riskier migratory tactics, which might reflect their higher energetic requirements and the necessity to accept greater risks in trying to offset these and recondition for future spawning attempts. While I showed that post-spawning migratory decisions, survival, and ultimately the degree of iteroparity are at least partly mediated by endogenous constraints related to the costs of reproduction, I also documented the consequences of additional anthropogenic stressors that are likely limiting repeat spawning potential in some regions. Collectively, my thesis provides valuable biological insights into the factors currently limiting repeat spawning ability and highlights the potential for increases in iteroparity to occur when anthropogenic threats are mitigated, with quantified benefits to population resilience. Moreover, considering that iteroparity is a bet-hedging strategy allowing individuals to spread the risk of reproductive failure over multiple years, addressing these issues is of particular importance for the management of declining salmonid populations, especially under increasing environmental variability associated with climate change.


title: EFFECT OF NEWLY CONSTRUCTED STRUCTURES SUPPORTED ON RAFT FOUNDATIONS ON EXISTING CONCRETE TUNNEL LININGS

contributor:
Department of Civil Engineering
Doctor of Philosophy
Dr. Mohamed Meguid
Dr. Hany El Naggar
Dr. Craig Lake
Dr. Nouman Ali
Dr. Zoheir Farhat
Dr. Hany El Naggar
Not Applicable
Not Applicable
Yes

subject:
tunnel
exclusion zone
stage  construction
three-dimensional analyses
shallow foundation

abstract: In densely populated areas, there is increasing construction of high-rise buildings adjacent to existing tunnels. The interactions involved are complex and unavoidable. Based on experience and field monitoring, many tunnel owners impose exclusion zones for construction close to their tunnels. This research studies the effect of a newly constructed building supported by a shallow foundation on a pre-existing tunnel. With the aid of the PLAXIS software, a detailed three-dimensional finite element analysis is used to conduct a parametric study showing the interaction between the burial location of the pre-existing tunnel and the new shallow foundation. The concrete lining is modelled by using the newly developed concrete model included in the PLAXIS user-defined library. The model considers the non-linearity of the material behaviour and the distinction between strength in tension and compression. The constitutive soil where the tunnel system is constructed is simulated by using a hardening soil model with small-strain stiffness, which accounts for increased stiffness at small strains. The construction of the tunnel is divided into several phases, where each phase is simulated with the advancement of the shield boring machine. Accordingly, new design guidelines can be developed for shallow foundations in close proximity to pre-existing tunnels.


title: Winter Distribution of the Black Guillemot (Cepphus grylle) in Atlantic Canada

abstract: Environmental Science Undergraduate Honours Thesis

abstract:
An understanding of animal movements contributes important knowledge on the spatial and temporal distribution of these animals. In particular, research on the distribution of seabirds, which are important ecological indicators, can provide new insights and understanding of the physical and biological aspects of the marine environment. Information on distribution can also be used to delineate marine protected areas and oil spill response strategies. Black Guillemots (Cepphus grylle) are particularly susceptible to various threats in the marine environment such as vessel disturbance, tidal energy development and oil spills due to their drifting and diving foraging behaviour. As tidal energy development and oil exploration increase, the effects on Black Guillemots may go unobserved due to our limited understanding of their at-sea distribution. Little is known about Black Guillemot distribution in Atlantic Canada, particularly in the winter (nonbreeding) season. To examine the winter distribution Black Guillemots, Global Location Sensing (GLS) tags were deployed and recovered on seven individuals at two breeding colonies in Nova Scotia, Canada, and New Brunswick, Canada, during 2017-2018. Guillemots dispersed from breeding colonies throughout the region (Scotian shelf, Gulf of St. Lawrence, Bay of Fundy, Gulf of Maine) with both populations overlapping in the Bay of Fundy. Most bird locations (82%) were associated with the continental shelf, with 8% associated with pelagic waters and 10% associated with the shelf break (25 km buffer around the 200 m shelf break). Birds moved an average of 167 km from colony and 70 km from shore, with maximum offshore distances of 470 km and maximum depths of 4830 m. The application of GLS tagging methods on Black Guillemots enhances our ability to examine seabird distribution and to use seabirds as ecological indicators of the marine environment.

Key words: Black Guillemot, Cepphus grylle, distribution, geolocator, migration, seabird tracking


title: An examination of the distribution, abundance, and habitat preferences of soft corals (Octocorallia: Alcyonacea) in offshore Nova Scotian waters

abstract:
Cold-water corals have been observed in Atlantic Canada since the 1800’s and to date, there are 31 confirmed species. Although research on cold-water corals in Atlantic Canada has increased over the last two decades, knowledge gaps remain, especially surrounding soft corals (Octocorallia: Alcyonacea). In light of Canada’s recent efforts to protect significant and representative marine ecosystems, more detailed information pertaining to soft corals is needed. This study aimed to increase our knowledge of the various species of soft corals, and specifically their distribution, abundance, and habitat preferences offshore Nova Scotia by using coral samples, interpolated geospatial surfaces, and environmental data collected between 2001-2011 and in 2017 by Fisheries and Oceans Canada during their annual multi-species bottom trawl surveys. The trawl surveys were conducted on the Scotian Shelf, Scotian Slope, and Bay of Fundy. Eight species, Gersemia rubiformis, Gersemia fruticosa, Drifa glomerata, Drifa sp.2, Duva florida, Anthomastus grandiflorus, Heteropolypus sol, and Pseudoanthomastus agaricus belonging to two families, Nephtheidae and Alcyoniidae, were identified. The majority, 62%, of sampled colonies were Gersemia rubiformis. The spatial distribution of all soft coral species displayed a strong affiliation with the northeastern portion of the Scotian Shelf and Scotian Slope. However, the Nephtheidae species are most common on the shelf while the Alcyoniidae species are most common on the shelf edge. This northeastern affiliation may be attributed to the colder temperatures, 1.8–4.3°C, exhibited on the northeastern Scotian Shelf and Scotian Slope compared to the warmer temperatures, 5.8–10.4°C, exhibited on the southwestern portions, and may indicate a preference of soft corals to colder temperatures.

Keywords: Soft corals, distribution, abundance, habitat preferences, Northwest Atlantic Ocean


title: An Examination of 4th and 5th Grade Children’s Conceptualization of Neighbourhoods in Halifax Nova Scotia

abstract: ENVS 4902 Environmental Science Undergraduate Honours Thesis

abstract: This study utilizes artistic expression, written description and verbal communication through interviews to better understand children's conceptualizations of neighbourhood. This conceptualization is used to determine how children define a neighbourhood, what children value in a neighbourhood, and whether aspects of nature are currently a part of their understanding of the area that they live in. Results from this study indicate that conceptualization of neighbourhood is primarily grounded in the children’s sense of home, and opportunities for socializing or play, as seen through the importance of built play areas, parks and abundant references to familiar houses. The aforementioned combination infers a sense of community throughout the analysis. This adds to the body of knowledge in the area of children’s perception of neighbourhoods as well as some understanding in terms of their biophilic relationship with nature.


title: A NEW METHOD FOR PRIORITIZING CATCHMENTS FOR TERRESTRIAL LIMING IN NOVA SCOTIA

abstract:
Freshwater acidification is a chronic issue in South Western Nova Scotia (SWNS). Despite reductions in emissions causing acid deposition in SWNS, water quality in the region is not predicted to improve for another 60 years (Clair et al., 2004). Acidification is the primary factor limiting the Southern Upland (SU) Atlantic salmon (Salmo salar) designatable unit which was evaluated as endangered by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) in 2010. The SU salmon have declined from 88-99% since the 1980’s and have a high probability of extirpation in the next 50 years if habitat quality is not improved (DFO, 2013).
  Liming, the addition of base cations to an acidified system, is the only mitigation method for acidification. Terrestrial liming is the addition of buffering material to the catchment of an acidified river and is a promising mitigation method for rivers in SWNS as it is sustainable and requires no maintenance (Olem, 1991). The effectiveness of terrestrial liming varies by location therefore an assessment of potential liming catchments is necessary to identify the top priority sites for terrestrial liming. The federal government and community groups are interested in terrestrial liming in SWNS to improve water quality and help support the SU salmon population but unfortunately a method for identifying and prioritizing catchments for terrestrial liming does not exist. I have developed a comprehensive and quantitative GIS decision model to prioritize catchments for terrestrial liming in Nova Scotia. The model identifies catchments that best support effective liming and the SU population; these catchments are the primary units of SU conservation when using terrestrial liming mitigation methods. Additionally this research identifies key information needs required for improved terrestrial liming catchment selection.


title: Employee Behaviour and Sustainability in a Dining Hall at Dalhousie University

abstract:
Due to the volume of food production, commercial-sized foodservice facilities are more energy and water-use intensive than office and classroom spaces. In addition, foodservices utilize large quantities of food and material inputs and impact waste diversion rates of these resources. Resource waste can be reduced by installing upgrades, such as water and energy efficient equipment, efficient lighting and improved heating, ventilation, and air conditioning systems; however, as operators of the kitchen, employees also have control over resource use. Little literature exists on employee behaviour and the sustainability of foodservice operations. This study explores sustainability issues at the Sherriff Hall Residence dining hall and kitchen areas at Dalhousie University. This study attempts to answer: 1) What behaviors in the dining hall impact sustainability objectives?; 2) What are the barriers that dining hall employees face in meeting sustainability objectives?; 3) What changes or programs could be implemented in order to reduce resource use and enhance waste diversion in the dining hall? Qualitative research methods employed include interviews with dining hall staff from the Sherriff Hall Residence, Aramark management at Dalhousie University and stakeholders from Facilities Management, Ancillary Services and Environmental Services. In addition, guided tours of the dining hall were completed with three key participants. A variety of behaviours which impact the sustainability of dining hall operations were documented, including behaviours that contribute to resource waste and improper waste diversion as well as behaviours which reduce these. Barriers to implementing sustainable behaviours in the dining hall were also identified, including: motivation, time, customer service, health and safety, knowledge, resistance to change, equipment and facilities, as well as external factors that are beyond employee control. Recommendations are made on training, enforcement, and changes in operational procedures.

Key words: sustainable, green, employee behaviour, university, dining hall, foodservice, kitchen


title: N and O isotope ratios of NO3- as a tracer for nitrogen cycling and water mass distribution

contributor:
Department of Oceanography
Doctor of Philosophy
Dr. Roberta C. Hamme
Dr. Markus Kienast
Dr. Carolyn Buchwald
Dr. Katja Fennel
Dr. Helmuth Thomas
Dr. Markus Kienast
Not Applicable
Not Applicable
Yes

subject:
Nitrogen cycling
Stable isotopes
biogeochemistry

abstract: Nitrogen plays a central role in marine biogeochemistry. Its distribution, chemical speciation and ratio relative to other nutrients governs the presence and abundance of microbial communities, and of large scale ocean production. In this respect, my thesis examines how biochemical and physical processes regulate the distribution of different nitrogen (N) species and their transformation in various marine environments by evaluating the spatial distribution of nitrogen and oxygen isotopes of nitrate (NO3-), in combination with a varying set of complementary biogeochemical tracers. Chapter 2 examines the isotopic composition of NO3- and total dissolved inorganic carbon (DIC) to elucidate the hydrography of the Western Equatorial Pacific (WEP) and biogeochemical evolution of water masses that contribute to the Equatorial Undercurrent (EUC). Based on isotope data and water mass mixing estimates, I highlight the different biogeochemical histories of nutrients feeding the northern and southern WEP, and provide support for the theory of a predominantly Southern Ocean source of NO3- to the EUC. Chapter 3 focuses on Baffin Bay, which represents a major link between the high Arctic and the northwestern Atlantic, owing to its effect on the salt and nutrient budgets of the adjacent Labrador Sea and the wider Atlantic Ocean. I combine NO3- isotope ratios with nitrous oxide (N2O) isotope measurements to identify the origin of the pronounced N-deficit and N2O supersaturation prevalent in deep Baffin Bay. The set of isotopic tracers used in this study allows the identification of different, yet complementary, N transformation processes. NO3- isotopes reflect substantial in situ remineralization of organic matter originating from surface productivity fueled by Pacific-derived nutrients, whereas N2O isotopomer abundances point to sedimentary denitrification as a potential source of the N-deficiency observed in the deep basin. In chapter 4, I use NO3- isotope ratios measured in the Canada Basin and in the Baffin Bay together with hydrographic data and nutrient ratios as a baseline to evaluate the distribution of Pacific- and Atlantic-derived water masses throughout the Arctic Archipelago. With this work, I highlight the importance and applicability of dual isotope measurements as water mass tracers and provide insights into individual processes within the N cycle.


title: Channel bodies of the lower Sydney Mines Formation (Carboniferous), Sydney Coalfield, Atlantic Canada

abstract:
This is a scanned MSc thesis from 1997. Could you please submit this to the person in charge of the FGS collection.

The supervisor was Martin Gibling.


title: SYNAPTOPODIN-2, AN ACTIN-BINDING PROTEIN, IS A PROMYOGENIC FACTOR FOR MYOBLAST FUSION AND MYOFIBRILLOGENESIS IN MOUSE AND ZEBRAFISH

contributor:
Department of Microbiology & Immunology
Doctor of Philosophy
Dr. Douglas Millay
Dr. Brent Johnston
Dr. Craig McCormick
Dr. James Fawcett
Dr. Victor Rafuse
Dr. Roy Duncan
Received
Not Applicable
Not Applicable

subject:
Myoblast fusion
Muscle development
Actin
Cell motility
Zebrafish
Myofibrillogenesis
Synaptopodin-2

abstract: Myogenesis is a differentiation-dependent process involving migration and fusion of uninucleated myoblasts to form multinucleated myotubes, the building blocks of striated, contractile muscle fibers. Several actin-binding proteins are involved in remodeling the actin cytoskeleton and one such protein is synaptopodin-2 (synpo2). Synpo2 binds and polymerizes actin and is upregulated during myogenesis, however, its functional role in the multistep myogenic program is unknown. My objective was to use cell culture and in vivo models of myogenesis to determine the roles of SYNPO2 isoforms during myogenesis. The first model used ectopic expression of the three mouse SYNPO2 isoforms (SYNPO2A, SYNPO2B and SYNPO2As) in stably transduced mouse C2C12 myoblasts or shRNA knockdown of endogenous synpo2, and the effects of these isoforms on migration and fusion was assessed using various approaches. Results indicated that only SYNPO2As is upregulated following differentiation and that knockdown of endogenous SYNPO2As inhibits myotube formation. Ectopic overexpression of SYNPO2As increased myotube formation and pharmacological inhibition of the Rho effector kinase ROCK resulted in loss of the enhanced fusion phenotype. Conversely, ectopic expression of SYNPO2A or SYNPO2B inhibited myotube fusion, consistent with the lack of upregulated expression of these isoforms following differentiation. All three isoforms increased C2C12 migration independent of ROCK inhibition indicating SYNPO2As utilizes two different pathways to promote myoblast migration and fusion. To understand the function of synpo2 in vivo, studies were carried out using zebrafish embryos. Zebrafish Synpo2 expression was restricted to the musculature of developing embryos and inhibiting Synpo2 expression using morpholino knockdown or CRISPR knockout resulted in abnormal muscle development. Morpholino-injected embryos showed a dramatic curved tail phenotype and immunostaining and electron microscopy revealed disorganized actin fibers, reduced myotube formation and disorganized Z-disk filaments. CRISPR knockout embryos did not show a curved tail phenotype but electron microscopy revealed immature myofilaments and reduced I band width.  Loss of the curved tail phenotype and abnormal myotube formation did not reflect upregulated genes that could be compensating for the absence of Synpo2, as assessed by RNAseq analysis, but numerous genes associated with myofibril organization were significantly downregulated. Together, these results identify synpo2 as a new promyogenic factor.


title: Enhanced tools to model preleukemia to leukemia transformation

contributor:
Department of Microbiology & Immunology
Doctor of Philosophy
Trista E North
Brent Johnson
Graham Dellaire
Jan Rainey
Jason N Berman
Roy Duncan
Received
No
No

subject:
Hematology
Stem cell biology
Leukemia
Microenvironment
Preleukemia

abstract: Preleukemia to leukemia transformation is one of the least well-understood processes in the hematopoiesis field, which is in no small part due to the lack of models that faithfully recapitulate this phenomenon. In this thesis, I provide three novel model systems that help to elucidate crucial factors that contribute to leukemia progression. First, I developed a zebrafish model that expresses human hematopoietic cytokines, which critically preserves the clonal diversity present in the original patient-derived leukemia. These human cytokine fish enhance the self-renewal capacity of transplanted human hematopoietic stem cells and also lead to multi-lineage differentiation. Secondly, I developed a tet2 loss-of-function zebrafish to mimic clonal hematopoiesis. TET2 mutations are seen in older individuals and significantly increases the chance of acquiring leukemia. I observed that tet2-deficient zebrafish had restrictive hematopoiesis resulting in fewer cells across multiple blood lineages. Induction of emergency hematopoiesis in these zebrafish resulted in a proliferative phenotype with increased blasts and progenitors. A key translational finding from the tet2 zebrafish is that growth factor treatment may accelerate leukemia in the subset of patients with acute myeloid leukemia and a TET2 mutation. Finally, I examined the KIT D816V mutation commonly seen in a preleukemic neoplasm called systemic mastocytosis, which can evolve into aggressive mast cell leukemia. Upon examination of the mutant D816V KIT receptor, I discovered that dimerization does not occur as it does in the wild type in the presence of ligand, and downstream signalling is activated independently of dimerization. Phosphoproteome analysis highlighted increased activity of the pro-survival mTOR axis, revealing that mTOR inhibiting agents (rapamycin and its analogues) may have a previously unrecognized therapeutic benefit in preleukemic conditions associated with mutant KIT. These models will provide useful preclinical tools for future candidates and unbiased drug screens to identify prospective drugs and effective drug combinations to improve the outcome of human preleukemic diseases.


title: A study of the inorganic carbon cycling on the Scotian Shelf

contributor:
Department of Oceanography
Master of Science
Owen Sherwood
Markus Kienast
Christopher Algar
Markus Kienast
Helmuth Thomas
Not Applicable
Not Applicable
Not Applicable

subject:
stable carbon isotopes
Scotian Shelf
inorganic carbon cycling

abstract: The stable carbon isotopic composition (d13CDIC) of dissolved inorganic carbon (DIC) can be used as an effective indicator of biological processes in carbon cycling, however, so far, few, if any, studies have been conducted on Scotian Shelf (NW Atlantic) waters focusing on (d13CDIC). In this study, the spatial and temporal distribution of DIC and d13CDIC in Scotian Shelf waters and their governing processes are investigated. Samples were collected on the Scotian Shelf during April and October of 2014 on the Canadian Coast Guard Ship Hudson. Throughout the research period, a combination of biological processes such as photosynthesis and respiration, and the freshwater input resulted in the changes of DIC concentration and d13CDIC values in the Scotian Shelf waters. The monthly NCP on the surface water of the study region ranges from -0.76 to 0.57 molC m-2 month-1, with an average NCP of 0.06 molC m-2 month-1. The Scotian Shelf reveals both autotrophic and heterotrophic regions in its mixed layer, with most of the offshore region presenting a heterotrophic system.


title: Developing a Sustainable Bioprocess for Chitin Extraction from Atlantic Lobster Shell Waste

contributor: Department of Process Engineering and Applied Science

subject:
Chitin
Fermentation
Lactic Acid Bacteria
Lobster shells

abstract: The goal of this research was to develop a fermentative chitin extraction method from Atlantic lobster shell waste. Results showed initial inoculum ratio was the most statistically significant variable in chitin extraction efficiency at a 5% shell ratio. Novel pre-treatments (MAE and UAE) were not found to have a significant influence on extraction efficiency under the tested conditions regardless of the presence of lactose in the pre-treated slurry. As determined by degree of decalcification and deproteinization as well as further measurement of fermentation dynamics, the most efficient of the tested formulations was 5% shell: 5% lactose: 5% inoculum (w/v) without a pre-treatment. The fermentation achieved 95.0% decalcification and 72.7% deproteinization when maintained at 37°C for 5 days with constant stirring. This fermentative approach using lactose and lactobacilli inoculum successfully yielded high levels of mineral and protein removal however further studies are required to optimize the process.


title: Ireland's New Losers: Contemporary Irish Fiction and the Ethos of Failure

contributor:
Department of English
Doctor of Philosophy
Danine Farquharson
Kathy Cawsey
Carrie Dawson
Alice Brittan
Bart Vautour
Gerald White
Not Applicable
Not Applicable
Not Applicable

subject:
Ireland
Contemporary Literature

abstract: The figure of the “loser” has become something of a staple in recent Irish fiction, especially fiction dealing with the major sociocultural transformations and crises that have taken place in Ireland in the last quarter century—namely, the Celtic Tiger, the economic crash, the clerical abuse crisis, and the end of the Troubles in Northern Ireland. This dissertation examines why. In reading recent novels by Donal Ryan, Peter Cunningham, Paul Murray, Claire Kilroy, Roddy Doyle, John Boyne, Paul McVeigh, and Garbhan Downey, I contend that the loser figure proves particularly valuable in assessing the difficulties of self-evaluation and self-definition within the transitioning social matrix of contemporary Ireland.Following an introduction in which I define “loserdom” and establish the social, national, and gendered contexts in which the loser figure typically operates, I offer four chapters, each examining a specific sociocultural transformation. In the first two chapters, I analyse the economic boom and bust, respectively, and consider the ways in which Irish novelists use the loser to respond to Irish society’s problematic embrace of neoliberal ideologies as well as to challenge the narratives of blame that circulated after the economic downturn. In the later chapters, I explore Ireland’s clerical abuse crisis and the post-conflict period in Northern Ireland, respectively. In the first case, I argue that novelists deploy loser characters as a way of emphasizing the degradation of Irish society resulting from the abuse scandal and as a means of indicting the nation’s culture of inaction and uncritical deference to the Church. Finally, I contend that novelists dealing with the post-conflict North deploy the loser figure as a means of representing productive dissidence. The losers in these texts, I suggest, embody a potential alternative to identities rooted in those tribal narratives of ethnic pride that perpetually threaten to undermine an already tentative peace in Northern Ireland. Taken together, these chapters explore the various ways in which Irish fiction imagines contemporary Ireland as defined by an ethos of failure.


title: Associations of Perceived Risk of Regular Cannabis use With Cannabis-Related Driving and Passenger Behaviours Among Canadian High School Students

contributor: Department of Community Health & Epidemiology

abstract:
Objective: Employing a sample of 33,915 high school students, the present study aimed to examine the association of perceived risk of regular cannabis use with driving under the influence of cannabis (DUIC) and riding with a cannabis-impaired driver (RWCD).
Methods: Participants were drawn from the 2016-2017 Canadian Student Tobacco, Alcohol and Drugs Survey. Multinomial logistic regression techniques were employed in the analysis of adjusted and unadjusted models. Stratified analyses were also performed assessing effect size differences between males and females, and urban and rural students.
Results: Greater perceived risk of regular cannabis use was associated with reduced risk of DUIC and RWCD in a dose-response manner. Associations were consistent for both males and females, and urban and rural students.
Conclusions: Given the strong role played by youth perceptions in shaping cannabis-related driving and passenger behaviours, efforts must be placed on disseminating appropriate information regarding cannabis risks to high school students.


title: RALOXIFENE SENSITIZES GLIOBLASTOMA CELLS TO HYPOXIA -INDUCED DEATH THROUGH INHIBITION OF STRESS GRANULE DISSOLUTION

contributor:
Department of Medical Neuroscience
Master of Science
Barbara Karten
Kazue Semba
Sultan Darvesh
Sean Christie
Adrienne Weeks
Craig McCormick
Not Applicable
Not Applicable
Not Applicable

subject:
Glioblastoma
Hypoxia
Stress granules
Raloxifene

abstract: Glioblastoma multiforme (GBM) is the most common primary malignant brain tumour and carries a uniformly poor prognosis.  Despite aggressive therapy, median survival is only 14 months.  Death typically results from treatment failure and local recurrence.  Hypoxia is a feature of the GBM microenvironment, and previous work has shown that cells residing in hypoxic regions resist treatment.  Hypoxia can trigger formation of stress granules (SGs), sites of mRNA triage that promote multiple cell survival mechanisms.  We hypothesize that SGs play a role in hypoxia-induced resistance to therapy.  A screen of 1120 FDA-approved drugs (the Prestwick Drug Library) was conducted, and 98 candidates were identified that inhibited hypoxia-induced SG formation whereas 127 candidates inhibited SG dissolution following return to normoxia. The screen identified the selective estrogen receptor modulator raloxifene as a potent inhibitor of SG dissolution in a dose-dependent manner.  When raloxifene was administered to U251 astrocytoma cells prior to hypoxia, the combination achieved synergistic killing of tumour cells that correlated with the activation of apoptosis and autophagy pathways.  Taken together, this data suggests that raloxifene induces apoptotic and autophagic death in GBM cells by disrupting normal SG dynamics.  As raloxifene is a currently approved drug already used in the treatment of estrogen receptor-positive breast cancer and osteoporosis, promising pre-clinical data could inform the development of a phase III clinical trial in GBM patients.


title: N-Phosphinoamidinate Nickel Complexes

contributor:
Department of Chemistry
Doctor of Philosophy
Dr. Cathleen Crudden
Dr. Peng Zhang
Dr. Alexander Speed
Dr. Frances Cozens
Dr. Mark Stradiotto
Dr. Laura Turculet
Not Applicable
Yes
Yes

subject:
Organometallic Chemistry
Inorganic Chemistry
Catalysis

abstract: Society demands cheaper and more abundant metal catalysts to accomplish the tasks previously performed by precious metal catalysts. In turn, chemists have developed ancillary ligands designed to harness the power of first-row metals, such as Mn, Fe, Co, and Ni. In Chapter 1, these design principles are rationalized and summarized, and applied to a variety of important ligand classes. One such class includes N-phosphinoamidinate (PN) ligands. (PN) complexes of first-row metals have been applied as precatalysts for hydrosilative carbonyl reductions (in the case of Fe) and terminally selective alkene isomerization/hydroboration (I-H; in the case of Co). Given a recent surge of advances in homogeneous catalysis using Ni, I began my thesis research with synthetic attempts towards (PN) complexes of Ni. Over the course of my research, I developed a family of related complexes. Ultimately, I was able to harness these complexes to generate the reactive, transient, three-coordinate Ni hydride (PN)NiH, which unlocked three thesis chapters. In Chapter 2, I describe a mechanistic study of alkene I-H via isostructural (PN) Mn, Fe, Co, and Ni precatalysts. The Ni precatalyst performed poorly, and isolable Ni hydride complexes proved unsuitable for the reaction, but the diamagnetism of the Ni complexes afforded in situ monitoring of catalytic intermediates to help determine the origin of terminal selectivity. Chapter 3 contains an analogous study of hydrosilative amide reduction, wherein (PN)NiH instead proved remarkably competent to reduce challenging substrates via optimization of reaction conditions. Iterative optimization of the precatalyst proved the utility of (PN)Ni(OtBu), itself a rare example of a three-coordinate nickel alkoxo complex. Chapter 4 reports the spectroscopic and X-ray characterization of a unique compound conceived by (PN)NiH inserting benzene. It also includes unusual β- or γ- agostic (PN)Ni(alkyl) complexes synthesized in attempts to access (PN)NiH in a controlled fashion via β-hydride elimination.


title: OVERWINTER MORTALITY OF YOUNG-OF-THE-YEAR STRIPED BASS (Morone saxatilis) IN FRESHWATER PONDS IN NOVA SCOTIA

contributor: School for Resource & Environmental Studies

subject:
striped bass
endogenous reserves
freshwater

abstract: Commercial fishing for striped bass (Morone saxatilis) is very limited in Canada, therefore there is potential for pond-based aquaculture to fill the consumer market. One impediment to culture is high overwinter mortality among young-of-the-year (YOY) striped bass. In a culture setting, mortality is restricted to YOY bass transferred to cages in constructed freshwater ponds in November; larger bass (>500 g) typically survive well under the ice. Two trials were completed in consecutive winters (2016-2018) to investigate the effect of body size (range ca. 30-50 g), pre-winter diet, and pond characteristics on overwinter survival in 1m3 cages. Mortality rates varied between ponds and years from 10 to 100 % and was inversely related to body size in some cases but not others. Diet had an insignificant effect on survival. Muscle total lipid and triacylglycerol (TAG) and liver TAG proportions on a wet-weight basis were significantly higher when samples from November and March were compared. Phosphoethanolamine (PE) mass in total muscle phospholipid was higher in striped bass sampled in the winter, but proportions of 18:0 and 22:6n-3 in PE and 18:1n-9 and 22:6n-3 in phosphatidylcholine were lower in March samples. Striped bass appear to rely on other lipid classes or body tissues than those analyzed in this study to survive the winter.


title: Effects of Nitrogen Rate and Planting Date on Growth, Yield and Chemical Composition of Malabar Spinach (Basella alba .L) Under Canadian Maritime Climatic Conditions.

contributor:
Faculty of Agriculture
Master of Science
Dr. Gordon Price
Dr. Samuel Asiedu
Dr. Vasantha Rupasinghe
Dr. Nancy McLean
Dr. Lord Abbey
Not Applicable
Not Applicable
Not Applicable

subject: Malabar Spinach

abstract: Malabar spinach (Basella alba L.) is one of the ethnic leafy vegetables in Canada, which is popular among immigrants of Asian and African origins. However, there are no clearly established production practices for commercial production of Malabar spinach in Canada. Therefore, this research study was conducted to determine the effects of nitrogen (N) rate and planting date on growth, yield and chemical composition of Malabar spinach under Canadian maritime climatic conditions. Our results showed 80 kg N ha-1 is optimal for the greenhouse production of Malabar spinach. Field experiment results indicated 40 kg N ha-1 is optimal for early planting. For mid and late plantings there were no significant differences in the growth and yield of the control and the N applied treatments. Nitrogen rate and planting date had little effect on phenolic and carotenoid content. Nitrate content was found very low regardless of N application rate.


title: Binder Effects on Si-Alloy Electrode Performance

contributor:
Department of Chemistry
Master of Science
Peng Zhang
Michael Freund
Josef Zwanziger
Mark Obrovac
Not Applicable
Not Applicable
Not Applicable

subject:
Li-ion batteries
Si-alloy

abstract:
Si-based anodes have been investigated to improve the energy density of Li-ion batteries due to their high volumetric capacity. However, huge volume changes of Si-based materials can cause severe particle fracture, leading to cell fade. Good binders for Si-based electrodes are expected to inhibit particle disconnection during cycling and simultaneously enhance cell performance.
	This work comprises several binder projects of interest for Si-based materials. For instance, how to improve the Si-alloy cell cycling performance by either chemical or rheological means. Then a feasible way to study the alloy electrode fading mechanism via SEM imaging was investigated. Some new binder systems such as molecular binders and inorganic binders for Si-alloy electrodes were also explored. Finally, future work is introduced.
	As a result of this work, new insights into alloy fade and completely new binder chemistries were discovered. This suggests many new directions in Si-alloy anode research for improving electrode performance.


title: Lake Recovery in Nova Scotia: A Longitudinal Review of Water Chemistry Data

contributor:
Department of Civil Engineering
Master of Applied Science
Dr. Hany El-Naggar
Dr. Peter Duinker
Dr. Rob Jamieson
Dr. Graham Gagnon
Not Applicable
Not Applicable
Not Applicable

subject:
Lake Recovery
Water Resources
Acid Deposition
Trend Analysis

abstract:
Emission control policies aimed at reducing the emission of sulfur oxides have been effective at reducing acid deposition, thereby allowing lakes to recover from acidification (as indicated by decreasing sulfate and increasing pH and alkalinity). In addition to improvements in pH and alkalinity, increasing dissolved organic carbon (DOC) content has also been observed in lakes recovering from acidification.
Using long-term precipitation and lake water chemistry data, this work assessed trends in precipitation and lake water chemistry to evaluate the recovery of NS lakes from acidification. Trend testing revealed that precipitation sulfate decreased by approximately 66% between 1985 and 2016 and that recovery from acidification (decreasing sulfate, increasing alkalinity and pH) has occurred in most of the study lakes. In addition to increasing pH and alkalinity, widespread increases in NOM content (using colour as a proxy) and total phosphorus concentrations were found.


title: DEVELOPING A TWO-PRONGED DRUG SCREEN TO IDENTIFY COMPOUNDS THAT PROTECT AGAINST CISPLATIN-INDUCED OTO- AND NEPHROTOXICITY

contributor:
Department of Microbiology & Immunology
Doctor of Philosophy
David Raible
Brent Johnston
Graham Dellaire
Sidney Croul
Meredith Irwin
Jason Berman
Craig McCormick
Received
Not Applicable
Not Applicable

subject:
Cancer
zebrafish
cisplatin
ototoxicity
nephrotoxicity
drug screening

abstract: Cisplatin is a chemotherapy used to treat a variety of cancers, including several pediatric malignancies. Cancer survivors are plagued by lifelong cisplatin-induced toxicities, including kidney damage and ototoxicity, or hearing loss. In efforts to find adjuvant compounds that can prevent these toxicities, in this study, I employed a two-pronged oto- and nephrotoxicity drug screen. The zebrafish is an excellent model for studying drug toxicities due to conserved genetics and organ systems. Zebrafish have lateral line neuromasts, analogous to clusters of mammalian cochlear hair cells. Similar to hair cell death in humans, cisplatin exposure causes decreases in neuromast viability, visualized with YO-PRO1, a fluorescent dye. Larvae treated with cisplatin (0.001-0.05 mM) demonstrated a dose-dependent reduction in neuromast fluorescence that I was able to measure rapidly using a biosorter. Zebrafish larvae also possess pronephros structures similar to the mammalian nephron. Glomerular filtration rate (GFR) can be measured in larvae by injecting FITC-tagged inulin into circulation. Inulin is renally-excreted, so decreases in vascular fluorescence approximates GFR. Cisplatin-treated larvae exhibited a reduction in GFR, which was also detectable with the biosorter. I employed an in vivo larval neuromast screen to assess the effects of compounds from the Sigma LOPAC®1280 library on cisplatin-induced ototoxicity. I compared these results with an in vitro toxicity test of cisplatin +/- the compound library on human proximal tubule cells, and found 22 drugs that were effective in both assays. I validated the protective capacity of two of these adjuvants, dopamine and L-mimosine, with confocal microscopy of the inner ear and the GFR assay. To determine if these protective compounds impact cisplatin’s cytotoxic effects, I performed an alamarBlueTM viability assay, an apoptosis-based flow cytometry assay, and a Gamma H2AX-based immunohistochemistry assay designed to detect double strand breaks (DBSs) in DNA. In each of these assays, dopamine and L-mimosine did not reduce the cytotoxicity of cisplatin in SK-N-AS and LAN5 neuroblastoma (NBL) cells, or HSC-3 oral squamous cell carcinoma cells. This project provides technological advances in the field of zebrafish-based drug screening, and identifies dopamine and L-mimosine as candidate oto- and nephroprotective compounds.


title: Identification of Factors Regulating Cytoplasmic and Nuclear Lipid Droplets

contributor: Department of Biochemistry & Molecular Biology

subject:
Lipid Droplet
Triglyceride
Phospholipid
Phosphatidylcholine
Kennedy pathway
Lipoprotein
Chylomicrons
Nuclear lipid droplet

abstract:
Lipid droplets (LDs) are cellular metabolic energy reservoirs composed of a neutral lipid
core of triglycerides (TG) and cholesterol esters (CE) that is surrounded by a surface
monolayer of phospholipids and embedded proteins. The most quantitatively significant
phospholipid in eukaryotic cellular membranes is phosphatidylcholine (PC), which is de
novo synthesized by the CDP-choline pathway under the control of the rate-limiting
enzyme CTP:phosphocholine cytidylyltransferase (CCT) α. In the liver and intestine, the
neutral lipids in LDs are hydrolyzed, re-esterified and assembled into lipoproteins for
secretion. Increased PC synthesis is required for LD biogenesis and hepatic lipoprotein
secretion. The aim of this project was to investigate mechanisms involved in regulating
TG and PC biosynthesis during LD biogenesis and cellular lipid metabolism. Knockout
of CCTα in intestinal-derived Caco2 cells (CCTα-KO cells) was used to determine how
PC metabolism controls TG storage in LDs and secretion in chylomicrons. CCTα-KO
cells had significantly decreased de novo PC synthesis and number of cytosolic LDs
(cLDs), but increased droplet size and TG mass. Secretion of chylomicrons was reduced
in differentiated CCTα-KO cells, indicating a specific requirement for the CDP-choline
pathway in intestinal cell TG storage and secretion in lipoproteins. CCTα-KO cells also
had a significant reduction in nuclear LDs (nLDs), which have CCTα and promyelocytic
leukemia nuclear bodies (PML-NBs) coating the surface. Using PML knockout U2OS
cells, we show that PML-NBs are critical for regulating the size and number of cLDs and
nLDs in response to exogenous fatty acids. PML deficiency diminished both cLDs and
nLDs, prevented recruitment of CCTα and LIPIN-1 to nLDs, and reduced PC and TG
synthesis. Our research highlights the importance of coordinated regulation of PC and
TG metabolism for the formation and function of LDs in the cytoplasm and nucleus.


title: DDOS DETECTION MODELS USING MACHINE AND DEEP LEARNING ALGORITHMS AND DISTRIBUTED SYSTEMS

contributor:
Faculty of Computer Science
Doctor of Philosophy
Dr. Mourad Debbabi
Dr. Michael McAllister
Dr. Vlado Keselj
Dr. Nur Zincir-Heywood
Dr. Srinivas Sampalli
Dr. Peter Bodorik
Not Applicable
Yes
Yes

subject:
Fuzzy logic System
Classification algorithms
Deep Learning
Feature Selection
Spark
Hadoop

abstract: Alsirhani-Amjad-PhD-CSCI-December-2019.pdf

abstract: Distributed Denial-of-Service (DDoS) attacks are considered to be a major security threat to online servers and cloud providers. Intrusion detection systems have utilized machine learning as one of the solutions to the DDoS attack detection problem for over a decade, and recently, they have been deployed in a distributed system. Another promising approach is the deep learning-based intrusion detection system. While these approaches seem to produce favourable results, they also bring new challenges. One of the primary challenges is to find an optimal trade-off between prediction accuracy and delays, including model training delays. We propose a DDoS attack detection system that uses machine learning and/or deep learning algorithms, executed in a distributed system, with four different, but complementary, techniques: first, we introduce a DDoS attack detection framework that utilizes a robust classification algorithm, namely Gradient Boosting, to investigate the trade-off between the accuracy and the model training time by manually tuning the classifier parameters. The results are promising and show that the framework provides a lightweight model that is able to achieve good performance and can be trained in a short time. Secondly, we address the problem of automatic selection of a classifier, from a set of available classifiers, with a framework that uses fuzzy logic. The results show that the framework efficiently selects the best classifier from the set of available classifiers. Thirdly, we develop a framework that utilizes several Feature Selection algorithms to reduce the dimensionality of the dataset, and thereby shortening the model training time. The results are promising in that they show that the approach is not only feasible, but that it reduces the training time without decreasing the accuracy of prediction. Lastly, we introduced a deep learning-based DDoS detection system that uses a Multi-Layer Perceptron (MLP) neuron network algorithm running in a distributed system environment. The results show that the system has a promising performance with deeper architectures trained on the large data sets.


title: Investigating the Design of Bisphosphine Ligands for use in Nickel-catalyzed C(sp2)-N Cross-Coupling

contributor:
Department of Chemistry
Doctor of Philosophy
Dr. Johanna Blacquiere
Dr. Peng Zhang
Dr. Norman Schepp
Dr. Laura Turculet
Dr. Alexander Speed
Dr. Mark Stradiotto
Not Applicable
Not Applicable
Yes

subject:
amination
cross-coupling
ligand design
nickel catalysis

abstract:
Notwithstanding the matured protocol of palladium-catalyzed C(sp2)-N cross-coupling (Buchwald Hartwig Amination, BHA), the development of nickel-based catalysts that carry out analogous transformations is motivated both by the benefits of employing Earth-abundant, cost-effective first-row transition-metals, and the potential for nickel catalysts to unveil new modes of reactivity. Over the past five years, significant advances in nickel-catalyzed amination chemistry have led to a widespread interest and expansion of this methodology. Although nickel catalysts are highly effective in the cross-coupling of ammonia, alkylamine, indole, and primary amide nucleophiles with (hetero)aryl electrophiles, these catalytic systems have yet to contend with palladium analogs in terms of exceedingly low catalyst loadings and the turnover of increasingly challenging substrate classes. Whereas BHA benefits from an unambiguous set of criteria that defines optimal ancillary ligand properties for this palladium-catalyzed transformation, structure-reactivity trends for nickel counterparts are ill-defined. Additionally, complex mechanistic details exist for nickel-catalyzed C(sp2)-N cross-coupling, which may be responsible for the vague guidelines for optimizing ancillary ligands, and the need for higher catalyst loadings.
	My thesis work explores ancillary ligand design criteria for nickel-catalyzed C(sp2)-N cross-coupling by cross-examining top-tier bisphosphine ligand classes with aims of clarifying the apparently divergent properties that exist among state-of-the-art ancillary ligands. Information gathered from the systematic comparisons of these ligand classes results in the development of the new bisphosphine ligand, PAd2-DalPhos, which enables the hitherto unknown nickel-catalyzed C(sp2)-N cross-coupling of primary heteroarylamines with (hetero)aryl chlorides. This chemical transformation is highly sought-after by pharmaceutical chemists for the synthesis of heteroatom-dense molecular structures, and reveals a new mode of reactivity involving challenging substrates in the context of nickel catalysis.


title: “IF YOU COULD SEE THE BIG PICTURE”: CONTEMPORARY CANADA-BASED ARTISTS’ PERSPECTIVES ON THE ROLE OF AN ENVIRONMENTALLY ENGAGED ARTS PRACTICE IN FOSTERING CULTURAL TRANSFORMATIONS

subject:
environmental humanities
ecological humanities
environmental education
environmental art

abstract: Addressing global climate change beyond short-term fixes requires wider cultural change. Artists, as cultural workers, could play a valuable role in attending to questions of social and ecological justice. While there is growing artistic engagement with environmental issues, there are few studies which explore the confluence of art and sustainability within Canada. Through frameworks of poiesis and socioecological transformation, I used a mixed qualitative methodology to understand how an environmentally engaged arts practice could exist as a form of environmental education. I interviewed 24 contemporary Canada-based visual, installation, and performance artists to understand how they could foster a sensibility towards sustainability. I used an inductive thematic coding scheme to analyze transcripts and compared emerging themes to current literature in the environmental humanities. Two theories emerged from the data: the environmental artist-researcher-teacher as facilitator of conviviality, curiosity, and care; and the artist as encouraging socioecological transformation through sympoiesis or self-making-with-environment.


title: Cellular Mechanisms Regulating Neuromuscular Junction Stability and Plasticity in Normal and Diseased Mice

contributor:
Department of Medical Neuroscience
Doctor of Philosophy
Kelvin Jones
Kazue Semba
Turgay Akay
Stefan Krueger
Victor Rafuse
Received
Yes
No

subject:
Amyotrophic Lateral Sclerosis
Nerve crush injury
Schwann cells
BMP4
NMJ

abstract: The stability of the neuromuscular junction (NMJ) is critical for maintaining independence and quality of life. Therefore, understanding the mechanisms that underlie this stability is of paramount importance to be able to recover function lost due to disease or injury. This thesis seeks to investigate these NMJ stability mechanisms in three states: disease, homeostasis, and repair. First, amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by distal neuropathy at the NMJ followed by paralysis and motor neuron (MN) death. I found that terminal Schwann cells (TSCs) at a subset of muscle fibres (type IIb, the most susceptible to disease progression in ALS) vanished from denervated endplates after a partial denervation injury in a mouse model of ALS. These endplates were therefore unable to become reinnervated via a compensatory process called collateral reinnervation. I also found that infiltrating macrophages were interacting with these TSCs, and, when inhibited with masitinib, was able to recover TSC loss and reinnervation in ALS mice. Second, I investigated whether muscular BMP4 in a mouse model had similar roles in NMJ homeostasis as had been previously reported in Drosophila. NMJs lacking BMP4 had impaired synaptic transmission and fragmented acetylcholine receptor clusters. This resulted in mice with locomotor, strength, and proprioceptive impairments. These results correlate with the previous Drosophila literature and provide evidence that the role of this protein at the NMJ is highly conserved. Third, I examined whether muscular BMP4 has a role in neuromuscular reinnervation following Tibial n. crush injury. I found that reinnervated NMJs at muscles lacking BMP4 had impaired reinnervation and delayed withdrawal of polyneuronal innervation. These results were consistent with a delayed maturation phenotype, indicating that BMP4 has similar roles during repair as it does during development. Together, this thesis highlights the complexity of mechanisms that exist at the NMJ to maintain proper function and reveals potential targets to exploit to improve outcomes in ALS as well as following peripheral nerve injury.


title: Study and Development of Synthetic Methodology Towards Pyrrolic Frameworks

contributor:
Department of Chemistry
Doctor of Philosophy
Dr. Robert Britton
Dr. Peng Zhang
Dr. Norman Schepp
Dr. Stephen Bearne
Dr. Alexander Speed
Dr. Alison Thompson
Not Applicable
Not Applicable
No

subject: Chemistry

abstract:
This thesis focuses on the study and development of synthetic methodology towards pyrrolic frameworks. Three projects are discussed: the development of open-air conditions for the synthesis of F-BODIPYs, mechanistic studies in the synthesis of symmetrical dipyrrins, and the development of new reactions for the synthesis of sulfur-bridged pyrroles.
The atmospheric effects of water on the synthesis of F-BODIPYs were explored. A methodology was developed for the high-yielding synthesis of F-BODIPYs involving non-anhydrous reagents and requiring no precautions to exclude moisture. This simple and robust strategy requires the addition of two aliquots of NEt3 and BF3OEt2. The ratio and amounts of NEt3 and BF3OEt2 used in each aliquot are critical to success (6 equivalents of NEt3 and 9 equivalents of BF3OEt2 per each aliquot). Most important is that the protocol can be completed using air-dried bench-top apparatus, without the need to either purchase anhydrous solvents or achieve and maintain anhydrous solvents and conditions.
The synthesis of symmetric α-free meso-H-dipyrrin hydrobromides from 5-unsubstituted 2-formylpyrroles (2-formyl-5-H-pyrroles) was investigated and it was found that the self-condensation produces regioisomeric dipyrrins through adoption of two mechanistic pathways. Through a systematic study involving variously substituted and isotopically labelled 2-formyl-5-H-pyrroles, evidence was provided to suggest that not only does there exist two mechanistic pathways, but that the steric bulk of the substituent adjacent to the 5-unsubstituted position influences which pathway dominates.
There are few synthetic routes to preparing sulfur-bridged dipyrrolyl sulfides, most of which require use of sulfur dichloride, a restricted chemical unavailable within Canada. Towards the preparation of sulfur-bridged di-, tri-, and tetrapyrroles, the first example of electrophilic aromatic substitution of pyrrole using thionyl chloride to produce dipyrrolyl sulfides was developed. The use of thionyl chloride results in an interesting auto-reduction of the sulfoxide centre to produce a sulfide-bridged dipyrrole. The new synthesis was investigated and a mechanism for the auto-reduction reaction was proposed.


title: SURPRISING IMPROVEMENTS IN LITHIUM ION AND SODIUM ION BATTERY CYCLE LIFE

contributor:
Department of Chemistry
Master of Science
Peng Zhang
Josef W. Zwanziger
Robert L. White
Mark N. Obrovac
Not Applicable
Yes
Yes

subject:
CYCLE LIFE
LITHIUM ION AND SODIUM ION BATTERY

abstract: Improve the cycle life of lithium and sodium ion battery

abstract:
Lithium ion battery research attracts much attention because lithium ion batteries have such extensive applications. Sodium ion batteries are an emerging field because of the sustainability of Na vs Li. However, issues regarding electrode and electrolyte degradation during cycling have hindered battery performance in both these technologies. In this thesis, thermoelectrochemical activation and ball milling methods were applied to improve the electrochemical performance of inactive CoO in sodium ion batteries. Results show that each method can increase the specific capacity and the combination of both methods can lead to a higher specific capacity and a stable cycling performance.
	CO2 has been shown to have great benefits on the cycle life of silicon alloy anodes. In this thesis, a new method was developed to measure CO2 concentration in electrolyte quantitatively and accurately by FITR. It was shown that the CO2 solubility in 1 M Li+ EC/DEC (1:2 v/v) solutions depends significantly on the salt anion and in a complicated manner. CO2 scavengers like DETA can increase the CO2 solubility effectively at a low concentration, but cause phase separation at higher concentrations.


title: Identification of Roles for Arabidopsis thaliana RING-Type Ubiquitin Ligase XBAT35.2 and its Substrate Accelerated Cell Death11 (ACD11) in Abiotic Stress Tolerance

contributor:
Department of Biology
Master of Science
Sophia Stone
Patrice Côté
Zhenyu Cheng
Sophia Stone
Not Applicable
Not Applicable
Not Applicable

subject:
Ubiquitin Ligase XBAT35.2
Accelerated Cell Death11 (ACD11)
Abiotic stress

abstract: To survive adverse environmental conditions plants utilize various mechanisms including the production of the hormone abscisic acid, which promote cellular changes to ameliorate the negative effects of abiotic stress. The Ubiquitination Proteasome System is used to regulate stress signaling to properly initiate and terminate responses. Ubiquitination involves E3s that govern substrate selection. Here, we demonstrate that the E3 XBAT35.2 and its substrate ACD11 are involved in the abiotic stress tolerance. XBAT35.2 levels, and levels of ACD11 increase in response to stress. Surprisingly, prolonged exposure to stress leads to a decrease in ACD11 abundance. xbat35-1 mutants and plants overexpressing ACD11 display enhanced stress tolerance. Also, XBAT35.2 promotes proteasome-dependent degradation of ACD11 under stress conditions. We propose that while ACD11 promotes tolerance, stress-stabilized XBAT35.2 functions to attenuate/terminate ACD11-mediated responses. This study improves our understanding of XBAT35.2 and ACD11 function and may contribute knowledge to the development of stress tolerant crops.


title: Identification and Aspects of Commercial Production of Anti-Diabetic Peptide(s) from Salmon Protein Hydrolysates

contributor: Department of Process Engineering and Applied Science

subject:
Bioactive Peptides
Atlantic Salmon
Type 2 Diabetes

abstract: A low molecular weight (< 1 kDa) hydrolysate of Atlantic salmon protein has previously been shown to have anti-diabetic effects in vitro and in mouse models. This salmon peptide fraction (SPF) produced using the enzymes pepsin, trypsin and chymotrypsin, contains hundreds of potential bioactive compounds and the identification the functional modulators of this activity may realize novel therapeutic compounds or targets as treatments for type 2 diabetes. The aim of this study was therefore to identify the sequences and characteristics of potential bioactive peptides from the SPF with a functional effect in cultured L6 myotubes. Separation of progenitor proteins by electrophoresis and of SPF by column chromatography with gel filtration and strong anion exchange formats were successful at concentrating bioactive peptides into multiple subfractions. Tandem mass spectrometry of subfractions suggested that di- and tripeptides composed of Ile/Leu, Val, Asp, Glu, Trp, Tyr were common among peptides identified in bioactive fractions. The importance of functional peptide concentration and sequence motifs on bioactivity was tested using the synthetic sequences Ile-Ala-Tyr and Ile-Gly-Tyr and exhibited a stimulating effect at 2.8 nM, but an inhibiting effect at 2.8 pM. Swiss Target Prediction suggested these sequences are peptidomimetics of agonists to mu-type, delta-type and kappa-type opioid receptors. When considering the large total number of peptides and abundance of sequences containing similar motifs in SPF, its bioactivity is likely the result of complex interactions of many peptides.


title: Glycosphingolipid Metabolism and  the Glycosphingolipid-Metabolizing Enzyme Beta-Glucosidase 2:  Biochemical and Cell Biological Studies

subject: Glycosphingolipids

subject: GBA2

subject: Mitochondria

subject: SPG46

subject: Neurodegenerative Diseases

abstract: Glycosphingolipids (GSLs) are constituents of eukaryotic cell membranes and consist of a lipid (ceramide) linked to one or more sugar residues. GSLs occur in many structurally distinct forms, varying in both their lipid and oligosaccharide domains. Most cells contain multiple structurally different GSLs. Different cell types/animal tissues have distinct and consistent GSL profiles, indicating that cellular GSL homeostasis is under strict regulation. Deviations in GSL homeostasis have pathological consequences. Our understanding of the regulation of cellular GSL levels is very limited. In the first part of my project, I have attempted to assess the kinetics of GSL turnover by testing a mathematical model correlating the rates of GSL biosynthesis and degradation. Genetic and pharmacological interventions were made in cellular models to disrupt GSL biosynthetic enzymes. This approach, however, produced inconsistent results. In the second part of the project I investigated cellular and biochemical consequences of the mutations in β-glucosidase 2 (GBA2), a GSL-metabolizing enzyme reported being mutated in SPG46, a complex neurodegenerative disorder. SPG46 (SPastic Gait locus #46) patients present with a combination of spastic paraplegia and cerebellar ataxia and suffer from muscle weakness and spasticity in the upper and lower limbs along with other neurological symptoms. Currently, the cascade of events leading from mutations in the GBA2 gene to SPG46 is largely unexplored. I have characterized ten SPG46-associated GBA2 mutations, five nonsense, and five missense mutations. All ten GBA2 mutants were catalytically inactive. The lack of enzyme activity was not associated with decreased protein expression. Native conformations of all but Gly683Arg mutants were different from the WT GBA2, confirmed by native gel electrophoresis, indicative of different protein-binding behaviors of the mutant proteins. Further, nonsense GBA2 mutants caused mitochondrial depolarization and interfered with mitochondria fusion, resulting in the formation of fragmented mitochondria. I have identified a potential mitochondrial targeting site in GBA2 causing conditional import of GBA2 in the mitochondrial matrix. My research unveils the roles of GBA2 on mitochondrial forms and functions which have not been observed before.


title: A first-principles investigation of the transition between two- and three-dimensional thermal transport in graphene and graphite

contributor: Department of Physics & Atmospheric Science

subject:
first-principles
graphene
graphite
thermal transport
phonons
scattering
thermal conductivity
dimensional transition
dimensional crossover

abstract:
Two-dimensional materials have become a popular research area over the past two decades because of their unique physical properties. The low dimensionality of these materials leads to interesting, and useful, transport properties such as thickness-dependent band gaps and high electrical and thermal conductivity. These materials have applications in nanoelectronics, optoelectronics, and thermoelectric energy generation, the performance of which depends sensitively on understanding and controlling how heat transport occurs.

Most low dimensional materials can be derived by isolating them from their bulk counterparts, which are often comprised of stacks of the two-dimensional layers that are weakly bound together. These layered bulk materials often maintain some of the two-dimensional characteristics of their monolayer form because of the weak interlayer bonds. One common example of such a “quasi-2D” material is graphite, which is made of layered carbon sheets, i.e. graphene. When going from graphite to graphene the room-temperature in-plane thermal conductivity varies from approx. 2000 W/m K to 5800 W/m K, respectively. Both values are exceptionally high, but there is still a large difference between the two. Nevertheless, the majority of studies focus either on the bulk or low-dimensional versions of materials, with little focus on how the transition from 3D to 2D influences the microscopic properties and transport characteristics.

The purpose of this study was to explain how the thermal transport properties of layered materials transition between two and three dimensions. Graphene and graphite were used as simple materials to model this transition. The thermal transport properties were calculated from first-principles using density functional theory (DFT) and iterative solutions to the Boltzmann transport equation (BTE). The transition between two and three dimensions was modelled by systematically moving the layers of graphite apart from each other until they were essentially isolated graphene sheets.

The converged $\kappa$ values of the limiting cases of graphite and graphene agree with experimental measurements and previous calculations, with the stretched cases showing a monotonically increasing thermal conductivity from $\kappa_{\text{graphite}}$ to $\kappa_{\text{graphene}}$. Surprisingly, the largest variation in the thermal transport properties resulted from changes in the phonon dispersion. This is contrary to the previous belief that the difference in $\kappa$ resulted from certain three-phonon selection rules in graphene, which reduce the scattering probability, and do not apply to graphite. The selection rules appear to mostly still apply to graphite and the stretched graphite cases, indicating that the primary mechanism resulting in the differences between $\kappa_{\text{graphene}}$ and $\kappa_{\text{graphite}}$ was the shape of the phonon dispersion, and a corresponding shift in the phonon DOS. This type of analysis could be applied to other layered materials in the future to identify materials with the potential to be exceptional thermal conductors.


title: CHARACTERIZATION OF IRON-REGULATED PROTEINS AND THEIR TRANSCRIPTIONAL RESPONSE TO TRANSIENT IRON LEVELS IN THE OPEN OCEAN DIATOM THALASSIOSIRA OCEANICA

contributor:
Department of Biology
Doctor of Philosophy
Dion Durnford
Sophia Stone
Arunika Gunawardena
Claudio H. Slamovits
Julie LaRoche
Not Applicable
Not Applicable
Not Applicable

subject:
Diatom
Iron Starvation-Induced Protein
N-linked Glycosylation
Transgenic Transformation
Targeted Transcriptomics

abstract:
Iron-requiring proteins are essential for numerous cellular processes, but low iron concentrations limit algal growth in over 30% of the ocean’s surface waters. Iron-fertilization experiments induced diatom-dominated blooms, and transcriptional analysis of iron-deprived cultures revealed novel proteins, coined iron starvation-induced proteins (ISIP). The main objectives of this thesis were to study the transcriptional and physiological response of the open ocean diatom Thalassasiosira oceanica to iron addition and to characterize the ISIP proteins.
The first chapter introduces the background, explains the methods, and states the objectives of each chapter.
In the second chapter, the functional characterization of ISIP proteins is explored by reviewing and comparing the iron acquisition strategies in different algal species. Through in-silico analysis and cellular localization experiments, the study reveals differences in iron-uptake proteins, iron-acquisition strategies, and ISIP proteins. Furthermore, this study hypothesizes that ISIP3 is an iron storage protein.
The analysis of the high-resolution temporal response of iron-responsive genes to the addition of iron was the objective of the third chapter. Here, employing targeted transcriptomics, the dynamics of iron-regulated transcripts were followed after the addition of iron to iron-deprived cultures. Iron-uptake related transcripts were downregulated first, followed by an upregulation of transcripts for iron-containing proteins, and photosynthetic parameters recovered within a period of 6 h.
In the fourth chapter, N-linked glycosylated peptides were analyzed under high- and low-iron growth conditions. N-linked glycosylated peptides were captured using the solid-phase extraction of N-linked glycopeptides (SPEG) method and identified via LC-MS/MS, revealing 118 glycosylated peptides with mostly NXT-type motifs. Peptides recovered from low-iron cells confirmed the predicted topology of ISIP1a.
Chapter 5 reports on the development of a transformation system in T. oceanica to identify the cellular localization of YFP-tagged proteins. The transformation vector was designed using the Gibson® cloning technology, and cells were transformed via microparticle bombardment. T. oceanica was genetically transformable, confirmed by the expression of the resistance gene and growth in antibiotic-selective media.
Overall, the findings presented here greatly expand the understanding of the response of diatoms to changes in iron concentrations. The transcription kinetics will be useful for modeling efforts at the cellular and biogeochemical level.


title: The Use of Selected Phytochemicals to Control Listeria monocytogenes; Practical Applications in Food Safety

contributor:
Faculty of Agriculture
Master of Science
Dr. Gordon Price
Dr. Bruce Rathgeber
Dr. Zhenyu Cheng
Dr. Vasantha Rupasinghe
Dr. Rafael Garduno
Not Applicable
Not Applicable
Not Applicable

subject:
Listeria monocytogenes
Phytochemicals
Efflux pumps
Biofilm
Bovine milk

abstract: Listeria monocytogenes is an important foodborne pathogen found in minimally processed foods, such as dairy products. To improve detection methods, phytochemicals were screened against L. monocytogenes and L. innocua. Efflux pump inhibitors promoted the growth for L. monocytogenes strain (FSL-J1-031) over L. innocua strain (2007-663). When tested against multiple strains of Listeria there was no clear differential effect observed. Aiming to control L. monocytogenes, biofilm growth kinetics of 2% Milk Fat pasteurized milk at 4°C was investigated, with a mature biofilm-forming at 74 h. Preformed biofilms were exposed to 20 phytochemicals in vitro with carvacrol, thymol, eugenol, coriander essential oil, and tea tree essential oils removing between 89% and 97% of the biomass. When tested in dispensing pumps, phytochemicals reduced biomass by 17% (thymol) and 32% (thymol) with mechanical force. Further research is needed to identify natural antimicrobial agents and techniques that are more effective for controlling L. monocytogenes.


title: KNEE MECHANICS OF HEALTHY AND OSTEOARTHRITIC JOINTS

contributor:
Department of Biomedical Engineering
Doctor of Philosophy
Dr. Kevin Ford
Dr. Jeremy Brown
Dr. Cheryl Hubley-Kozey
Dr. William Stanish
Dr. Rebecca Moyer
Dr. Janie Astephen Wilson
Received
Yes
Not Applicable

subject: Biomechanics Knee Osteoarthritis MRI Running Basketball PCA Progression

abstract:
Objective: Knee Osteoarthritis (OA) can be the result of both mechanical and biological events that interfere with normal joint function. The aims of this thesis were to (1) quantify the biomechanical factors that differentiated structural OA progression, (2) determine if knee biomechanics changed over time in response to structural changes, (3) identify sex and puberty specific differences that may mechanically predispose females to OA, and (4) determine the response of healthy knee joints to a high dose of sport to assess the contribution of knee mechanics to tissue damage.
Methods: A three-year prospective study of knee OA progression addressed Aim 1 by measuring principal components (PCs) of knee moments and muscle activation patterns that differentiated the progression group, and for Aim 2, identified PC scores that changed with and without knee OA diagnosis and progression. A cross-sectional comparison of PCs between sex and puberty cohorts addressed Aim 3. A five-month prospective study of female varsity athletes addressed aim 4, where the knee joint response to one season of sport was measured with MRI.
Results: (1) The peak KAM was higher prior to structural progression confirming previous findings however greater lateral muscle activity with progression was contradictory. (2) Knee joint moment and muscle activation patterns changed over the three years, with the greatest magnitude of difference occurring in the progression group. (3) Later puberty stages had higher frontal and transverse plane moments when walking and altered patterns of frontal and transverse plane moments when running.  (4) The athletes that had worsening of MRI features had different features of knee joint moments characterizing lower magnitude joint loading.
Conclusions: Higher frontal and altered transverse plane knee moments in the OA progression group highlights the sensitivity of the osteoarthritic knee joint to altered mechanical load. The change in mechanics over time reinforces the dynamic mechanical environment with OA and the sensitivity of gait to this changing structure. The lack of congruence of MRI changes of asymptomatic knees with mechanical features related to knee OA suggests that longer prospective studies are needed to trace mechanical factors in young adulthood to knee OA initiation.


title: LEAD SERVICE LINE REPLACEMENTS: A GEOMATIC APPROACH TO INTEGRATE COST AND WATER QUALITY AND STUDYING THE RELATIONSHIP BETWEEN THEM

contributor:
Department of Civil Engineering
Master of Applied Science
Dr. Hany El Naggar
Dr. Amina Stoddart
Dr. George Jarjoura
Dr. Graham Gagnon
Not Applicable
Not Applicable
Not Applicable

subject:
Lead service line replacements
lead service lines
lead lines
cost estimation
web application
Drinking water--Lead content
Water quality management

abstract:
Lead toxicity has been extensively studied in humans based on blood lead levels (BLLs). Scientists say there is no safe level of lead and that children are especially vulnerable since their bodies can absorb more of the neurotoxin than adults. Infants and children are susceptible to specifically the reduction of Intelligence Quotient (IQ) score and attention-related behaviors. Homes built in the 1950s or earlier have a higher risk of being serviced by a lead service line (LSL). The best way to permanently address sources of lead in drinking water is to remove all components containing lead and to replace all LSLs. North American communities are taking essential steps to accelerate the replacement of LSLs through online tools and financial incentives.
The purpose of the research is to examine the features that were most effective in prompting potential homebuyers or renters to replace LSL through compiling and analyzing information collected for 35 North American utilities.  This study examines the “cost” as one of the significant barriers in all the LSLs and provides a solution through the development of a web application called GIS Cost Estimation portal that will help homeowners know their replacement cost as per the features and location of their house. Over time, the lead content decreases in a service line going to a 100% reduction. However, the cost cannot be correlated with the improvement factor in drinking water quality.


title: Experimental Investigation for the Particle and Sample Size Effect on the Shear Strength Parameters of Tire Derived Aggregate (TDA)

contributor:
Department of Civil Engineering
Master of Applied Science
Dr. Hany El Naggar
Dr. Nouman Ali
Dr. Zoheir Farhat
Dr. Hany El Naggar
Not Applicable
Not Applicable
Yes

subject:
Tire Derived Aggregate
TDA
Particle Size
Sample Size
Scale Effect
Direct Shear
Triaxial

abstract: TDA has been successfully used in different civil engineering projects as a fill material in its pure state or mixed with soils in TDA-soil mixtures. Despite the superior geotechnical properties and successful applications of TDA, the size limitations between the available conventional laboratory testing equipment and the TDA particle sizes commonly used in practice are forcing the researchers and practitioners to conduct their tests on smaller TDA particle sizes rather than the actual sizes used in civil engineering applications. Moreover, several studies are conducted on TDA without due attention to the different sample sizes and their effect on the obtained results. So, the main focus of this research is to investigate the particle and sample size effects on the shear strength parameters of TDA using two commonly used test apparatuses, namely the direct shear and the triaxial.


title: The Feasibility and Impact of a Yoga Intervention on Cognitive and Physical Performance among People Living with HIV

contributor:
PhD in Health
Doctor of Philosophy
Dr. David Kietrys
Dr. Marilyn Macdonald
Dr. Kelly O'Brien
Dr. Jacqueline Gahagan
Dr. Marie-Josee Brouillette
Dr. Marilyn MacKay-Lyons
Received
Yes
Yes

subject:
HIV antibodies
Exercise
Yoga
Cognitive Function
Physical Function
Cognition
Health-related quality of life

abstract:
This dissertation consists of three main projects.
Project 1:
Cognitive impairment is common among people living with HIV (PLWH). Physical activity has emerged as a potential management strategy for cognitive impairment. The study purpose was to map the evidence on exercise and cognition in HIV. We searched 5 databases for exercise and HIV terms. Two authors independently reviewed titles/abstracts for studies addressing physical activity/exercise and cognition in PLWH. Sixteen studies were included. Two of eight interventional studies found exercise benefitted cognition. Eight non-interventional studies showed a positive relationship between physical activity and cognition. These results suggest that physical activity may improve cognition in PLWH.
Project 2:
Although compelling evidence exists about the health benefits of exercise, many PLWH are physically inactive. The study purpose was to use the Theoretical Domains Framework to investigate older PLWH’s exercise barriers and facilitators. This qualitative study involved semi-structured interviews with 12 PLWH≥45 years. Data were analyzed thematically and were coded by two independent investigators. The participants had a working knowledge of exercise but were unfamiliar with specific exercise parameters. Barriers included co-morbidities, injuries, and side effects of HIV and medications. Facilitators included social support and technology. Those designing exercise interventions should incorporate strategies to address these obstacles.
Project 3:
	The purpose of this pilot randomized trial was to assess the feasibility and satisfaction of a tri-weekly 12-week yoga intervention among PLWH. Other objectives included evaluating cognition, physical function, medication adherence, health-related quality of life (HRQoL), and mood among yoga participants versus controls using blinded assessors. We recruited 22 medically-stable PLWH aged≥35 years. A priori feasibility criteria were defined as ≥70% yoga session attendance and ≥70% of participants satisfied with the intervention using a post-participation questionnaire. Two participants withdrew from the yoga group. Mean yoga class attendance was 82% with 100% satisfaction. Intention-to-treat analyses (yoga n=11, control n=11) showed no within- or between-group differences in cognitive and physical function. The yoga group improved over time in HRQoL cognition (p=.047) with trends toward improvements in health transition (p=.063) and depression (p=.055). This pilot study provides preliminary evidence of feasibility and benefits of yoga for PLWH.