Biological Sciences - Theses, Dissertations, and other Required Graduate Degree Essays

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Quantitative in vitro-in vivo extrapolation of biotransformation rates for bioaccumulation assessment: Focus on organic sunscreen agents in rainbow trout

Author: 
Date created: 
2019-08-26
Abstract: 

An improved understanding of chemical biotransformation has been identified as a key requirement for the bioaccumulation assessment of commercial chemicals. In vitro biotransformation assays, in combination with in vitro-in vivo extrapolation (IVIVE) represents one initiative to generate chemical biotransformation rates for use in bioaccumulation modeling efforts. However, rigorous evaluation of the IVIVE approach requires studies with well-matched animals to ensure in vitro tests adequately predict in vivo biotransformation potential. Therefore, the overarching objective of this thesis was to evaluate factors that may influence the extrapolation of hepatic in vitro biotransformation rate constants (kdep) using well-matched studies with rainbow trout. Hydrophobic organic ultraviolet filters (UVFs) 4-methylbenzylidene camphor, 2-ethylhexyl-4-methoxycinnamate (EHMC), and octocrylene (OCT) represented model chemicals in this investigation. The first study showed that measured kdep values for UVFs were highly dependent on the selected assay concentration. Modeled bioconcentration factors (BCF) derived from kdep measured at concentrations well below corresponding Michaelis-Menten constants (KM) were closer to empirical BCFs than those calculated from kdep measured at higher test concentrations. A corresponding in vivo study demonstrated that during standardized dietary exposures that measured UVF concentrations in trout were well below the previously derived KM values This demonstrated that biotransformation pathways in trout operate under first-order conditions and that working at an appropriate concentration range in in vitro assays (i.e., C0 << KM) can be expected to improve estimates of in vivo biotransformation potential. In a final study, an existing IVIVE model was expanded to consider biotransformation in both the intestinal epithelia and liver. For chemicals biotransformed at higher rates by hepatic S9 fractions (e.g., EHMC), the ‘liver only’ IVIVE model was sufficient in estimating whole-body biotransformation rate constants (kMET). For chemicals biotransformed at higher rates in intestinal S9 fractions (i.e., OCT), the inclusion of both hepatic and intestinal activities improved estimates of kMET relative to the in vivo data generated here. The results of this study indicate that current ‘liver only’ IVIVE approaches may underestimate kMET for chemicals that undergo substantial intestinal biotransformation. The presented findings suggest that the future use of quantitative IVIVE methods for bioaccumulation assessment require greater consideration of extrahepatic biotransformation.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Frank Gobas
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Sea lice in the North Pacific: from sub-lethal effects on wild salmon to parasite management and policy

Author: 
Date created: 
2018-09-07
Abstract: 

Since wild-capture fisheries production plateaued in the early 1990s, the world’s dependence on aquaculture has grown steadily. This ‘blue revolution’ may have helped the conservation of some wild aquatic species by decreasing fishing pressure, but for others it has depleted their populations through habitat degradation, harvest for feed, and the spread of infectious disease. This thesis examines how parasites from aquaculture facilities can indirectly influence wild host survival and assesses how improvements to policy could limit these effects. I explore these topics in British Columbia, Canada, where wild Pacific salmon (Oncorhynchus spp.) are commonly infested with parasitic sea lice (Lepeophtheirus salmonis and Caligus clemensi) from open-net salmon farms. In Chapter 2, I use a field experiment to demonstrate that heavy sea louse infestation is associated with decreased competitive foraging ability for juvenile sockeye salmon (O. nerka). In Chapter 3, I show that this louse-associated reduction in competitive ability leads to decreased foraging success for juvenile sockeye in the wild. In Chapter 4, I analyse the otoliths (i.e., ear stones) of juvenile sockeye to reveal that highly infested fish grow more slowly than uninfested individuals. Each of these responses – competitive ability, foraging success, and growth – has major implications for salmon survival. In Chapter 5, I then investigate the ways in which parasite control policy could be improved on salmon farms to limit transfer of sea lice to wild salmon. I demonstrate that there is considerable underestimation bias in self-reported sea lice counts from industry, which determine when delousing treatments are used to control sea lice outbreaks on farms. I also show that current parasite control policy is not resilient to changing environmental conditions and I assess the potential effectiveness of alternative policies. Ultimately, the sustainability and success of the blue revolution will depend on our understanding of the full impacts of disease on wildlife and our ability to limit them.

Document type: 
Thesis
File(s): 
Supervisor(s): 
John Reynolds
Lawrence Dill
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

The effects of a high-fat diet and bacterial lipopolysaccharide (LPS) induced inflammation on pregnancy and fetal development in mice

Author: 
Date created: 
2020-06-30
Abstract: 

Inflammation during pregnancy can disturb maternal tolerance of the fetus. In mice, maternal high-fat diet (HFD) induces inflammation without pregnancy complications. I hypothesised that an additional inflammatory insult would exacerbate the immune response, leading to serious complications. To test this, I developed a HFD/LPS model, where female mice were fed a high-fat or low-fat diet prior to mating, and then treated with either bacterial lipopolysaccharide (LPS), an inflammatory stimulant, or a control. Diet, LPS or a diet-LPS interaction had no effect on fetal and placental parameters or maternal levels of TNF-α, an inflammatory marker (p>0.05). Furthermore, fetal and placental parameters did not differ between HFD mice that were prone or resistant to weight-gain. While diet or a diet-LPS interaction did not affect pregnancy, LPS treatment alone caused complete fetal loss in some mice (p<0.05). These findings suggest that LPS does not exacerbate the inflammatory effects of HFD in pregnant mice.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Julian Christians
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Effects of nutrient addition and sheep grazing on tundra rangelands in the Icelandic highlands

Author: 
Date created: 
2020-04-15
Abstract: 

Overgrazing and soil erosion are widespread and chronic environmental problems in the Icelandic highlands. Restoration efforts have included the application of fertilisers and grazing exclusion to increase plant biomass and reduce bare ground, but the effects of fertilisers on plant community composition across ecological conditions remain unresolved. I measured the combined effects of grazing exclusion and fertilisation, including factorial applications of nitrogen (N), phosphorus (P) and potassium (K), in both vegetated and degraded areas at sites with contrasting soil conditions. After four years I found 1) above-ground biomass induced by fertiliser was counteracted by sheep grazing, and 2) joint application of fertiliser and grazing exclusion had contrasting effects on species diversity in vegetated habitats where NPK applications and grazing exclusion reduced species diversity, than in degraded habitats where NPK applications increased species diversity irrespective of grazing. These results contribute to improving restoration efforts in high latitude tundra rangelands.

Document type: 
Thesis
Supervisor(s): 
David Hik
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Studying the foraging and communication ecology of European fire ants

Author: 
Date created: 
2020-04-16
Abstract: 

The European fire ant (EFA), or ruby ant, Myrmica rubra L., is an invasive pest in Greater Vancouver, British Columbia, Canada. EFAs are a nuisance to humans, swarming and stinging aggressively when nests are disturbed. They also cause ecological damage by altering invertebrate communities. The overarching goal of this thesis was to create a control method for EFAs. My specific research objectives were to: (1) develop an effective and affordable food bait; (2) determine trail following of EFAs in response to synthetic trail pheromone; and (3) determine trail following of ants in response to synthetic trail pheromone blends of multiple ant species. Food baits comprising diverse macronutrients such as carbohydrates (apples), proteins and lipids (dead insects) elicited the strongest foraging responses by EFAs. Re-hydrated freeze-dried baits proved as appealing as fresh baits and superior to rehydrated heat-dried baits. Isomerically pure and impure synthetic trail pheromone (3-ethyl-2,5-dimethylpyrazine) prompted similar recruitment responses of ants. The presence of pheromone, irrespective of dose tested, enhanced the recruitment of ants to food baits, with the dose of 200 ant equivalents eliciting the strongest recruitment responses. Trail pheromone applied in a line leading toward the food bait, but not in a circle surrounding it, was effective in recruiting ants, suggesting that 3-ethyl-2,5-dimethylpyrazine has a guiding but not an attractive function to EFAs. The presence of con- and hetero-specific pheromones had additive or indifferent effects on trail-following responses of garden ants, Lasius niger, and carpenter ants, Camponotus modoc, respectively. These data provide key information for the development of a highly functional insecticidal food bait for EFAs and other nuisance ant species.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Gerhard Gries
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.P.M.

Identification and management of wasabi pathogens in British Columbia

Author: 
Date created: 
2020-03-27
Abstract: 

Wasabi (Wasabia japonica) plants in British Columbia are grown in moist conditions ideal for pathogens, and therefore, are prone to various diseases. Over 3 years, seven wasabi greenhouses were surveyed for pathogens. Prevalence and severity of diseases were documented. Pathogenic species including Phoma wasabiae (Leptosphaeria biglobosa), Botrytis cinerea, and Erysiphe cruciferarum were found in multiple greenhouses. A new disease of wasabi with symptoms of vascular blackening and wilt was discovered. Using morphological and molecular techniques, the causal organism was identified as Verticillium isaacii. Powdery mildew of wasabi caused by E. cruciferarum was prevalent in half the greenhouses surveyed. In order to evaluate management options for powdery mildew, 4 commercially available products, Actinovate®, Cueva®, Rhapsody®, and Regalia® were applied biweekly onto greenhouse plants. Both Cueva® and Regalia® significantly reduced the progression of powdery mildew on wasabi plants.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Zamir Punja
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Ecological consequences of flow regulation by Run-of-River hydropower on salmonids

Author: 
Date created: 
2020-04-02
Abstract: 

Streams are dynamic, disturbance-driven ecosystems, where flow plays a dominant role structuring biological communities. Anthropogenic activities on streams change natural patterns of flow and disturbance, which in turn alters the conditions to which resident fishes are adapted, and their survival and fitness. Run-of-river (RoR) hydropower projects are an example of an anthropogenic activity that may alter stream ecosystems by temporarily diverting a proportion of stream flow to produce electricity. RoR hydropower projects have increased considerably in number and importance in the last three decades in both British Columbia and worldwide. Although there is a perception that RoR hydropower has minimal effects on stream ecosystems due to the small physical footprint of projects, we know surprisingly little about the impacts of RoR hydropower on fish populations. In this thesis, I use a combination of published research, empirical data, and models to evaluate a range of hypotheses regarding how RoR hydropower may affect fish populations, concentrating on salmonid species whose freshwater habitats often overlap with RoR projects. In Chapter 2, I synthesize the impact pathways by which RoR hydropower may influence salmonid populations, inferred from studies of reservoir-storage hydropower and salmonid ecology. In Chapter 3, I use empirical data to quantify increases in water temperature due to RoR flow diversion and explore the possible consequences for resident fish growth with bioenergetics models. In Chapter 4, I evaluate how stranding from anthropogenic flow fluctuations affects the long-term population dynamics of coho salmon (Oncorhynchus kisutch) in RoR-regulated rivers using a matrix model integrating both the strength and timing of freshwater density dependence. Finally, in Chapter 5, I quantify the high level of uncertainty in how much compensation habitat is required to offset chronic mortality incurred by multiple life-stages of coho salmon. The global emergence of RoR hydropower projects emphasizes the importance of understanding their effects on aquatic ecosystems. Overall, our capacity to protect and restore threatened salmonid populations rests upon our ability to not only better understand the pathways of impacts, but also the effectiveness of both natural (density dependence) and human (habitat compensation) interventions that can be used to offset anthropogenic mortality.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Wendy J. Palen
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Survivorship and life history strategies in relation to migration distance in western and semipalmated sandpipers in Perú

Date created: 
2020-03-31
Abstract: 

This thesis explored the relationships between life history, migration distance, survivorship components of fitness, and molt strategies of Western and Semipalmated Sandpipers in one of the most austral non-breeding sites for both species, at Paracas, Perú. I asked how migration distance relates to pre-migratory preparation, survivorship and migratory decisions for different age classes and ecological circumstances between species and within populations. I focused particularly on how timing of first breeding relates to survivorship and thus future overall fitness. I found that adults from both species prepare for northward migration, but no juvenile Western Sandpipers did so, confirming a non-migratory over-summering ‘slow’ life history strategy for more southerly non-breeding populations. Juvenile Semipalmated Sandpipers showed bimodality in migration strategy. Most showed no migratory preparation, but ~30% fattened, molted into breeding plumage, and performed partial post-juvenal wing molt (PPW) during the pre-migratory period. The frequency of PPW is positively related to culmen length (as a proxy for eastern breeding birds with a shorter migration distance). To decompose survivorship between migrant and oversummering (resident) Semipalmated Sandpipers, I used a multi-state model with 5 years of data and found survivorship 8 percentage point higher for oversummering juveniles and 21 percentage points higher for oversummering adults compared to same aged migrant birds, as expected as compensation for the loss of a breeding opportunity. I estimated annual survivorship with an open robust multi state model using 7 years of mark-resighting data from several thousand shorebirds marked at Paracas. As predicted by some migration theories, both species had higher annual survival estimates than those obtained previously at non-breeding sites further north. Western Sandpiper juveniles also had substantially higher annual survival estimates than adults, in line with the predicted survivorship benefits needed to offset their delayed reproduction. I found that the size of the survival advantage in juvenile Semipalmated Sandpipers is migration distance dependent. Western, but not Semipalmated Sandpipers showed a negative relationship in survival with the ENSO warm phase, probably due to the former’s closer association with the Pacific migratory flyway. Finally, I corroborated that the size of the survival advantage is distance dependent. My results provide novel information on non-breeding shorebird survivorship and perspective on the interrelationships that drive avian life history strategies. I confirm that Paracas is also a site with high demographic value.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Ronald Ydenberg
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Morphological and functional characterization of host proteins during infections by actin-hijacking bacterial pathogens

Author: 
Date created: 
2020-04-14
Abstract: 

Cells, much like mammals, possess an internal skeleton. This cellular skeleton (called the cytoskeleton) provides structure to cells, enables their movement within the environment and promotes the internalization of extracellular cargo (endocytosis). Many pathogens have devised strategies to hijack the cytoskeleton and other crucial sub-cellular processes for their disease processes. The bacterium Listeria monocytogenes (L. monocytogenes) utilizes the clathrin endocytic machinery to invade cells, and later, the actin polymerization machinery to generate actin-rich comet/rocket tails to move within and amongst host cells. Salmonella enterica serovar Typhimurium (S. Typhimurium) and Shigella flexneri (S. flexneri) generate actin-rich membrane ruffles at the cell surface to enter cells. Once inside, S. Typhimurium occupies a long-lived vacuole, whereas S. flexneri generates comet/rocket tails. Enteropathogenic Escherichia coli (EPEC) on the other hand remain extracellular and co-opt clathrin and actin to form motile pedestals directly beneath the site of bacterial adherence. In this thesis, I explored the involvement of several host actin- and/or endocytic-associated proteins during bacterial infections and simultaneously used these infections to gain insight into novel roles of the proteins studied. In chapter 2, I discovered that L. monocytogenes co-opts the actin-associated protein palladin during its entry and intracellular motility. Importantly, I revealed that palladin can functionally replace the Arp2/3 complex during bacterial actin-based motility. In chapter 3, I uncovered that the internalization strategy used by L. monocytogenes to transfer between host cells exploits caveolin-mediated endocytosis. In chapter 4, I investigated the host enzyme cyclophilin A (CypA) and found that it is crucial for maintaining the structural integrity of L. monocytogenes membrane protrusions generated during bacterial dissemination events. In chapter 5, I determined that CypA restricts S. Typhimurium invasion but is dispensable for EPEC pedestal formation. Finally, in chapters 6 and 7, I examined the receptor of CypA, CD147, and found that this membrane protein, like CypA, is crucial for the proper formation and function of L. monocytogenes membrane protrusions. In conclusion, my research has 2 major implications: 1) I have uncovered new insight into the mechanisms behind how actin-hijacking pathogens cause disease and 2) I have demonstrated novel cellular functions for host actin-associated proteins.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Julian Guttman
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Microplastics in the Beaufort Sea Beluga Food Web

Author: 
Date created: 
2020-02-06
Abstract: 

Microplastics (MPs, particles <5 mm) represent an emerging global environmental concern and has been detected in multiple aquatic species. Very little is known, however, about the presence of MPs in higher trophic level species, including cetaceans. Working in collaboration with Inuvialuit hunters from Tuktoyaktuk (Northwest Territories, Canada) and researchers from the Department of Fisheries and Oceans, entire stomachs and intestinal sub-sections were collected from seven beluga whales (Delphinapterus leucas) in 2017 (n=4) and 2018 (n=3) for examination. Microplastics were detected in the gastrointestinal tracts in every whale. Each whale contained an estimated 18 to 147 MPs in their GI tract with an average of 97 ± 42 per individual. FTIR-spectroscopy revealed over eight plastic polymer types, with nearly half being polyester. Dominant MP types were equally present, with fragments making up 51% and fibres 49%. The potential source of MPs to beluga via prey items was also determined by examining the GI tracts from five Arctic fish species belonging to the beluga food web (n=116). Species investigated included (Arctic cod (Boreogadus saida), saffron cod (Eleginus gracilis), Arctic cisco (Coregonus autumnalis) four-horn sculpin (Myoxocephalus quadricornis) and capelin (Mallotus villosus). Microplastics were found in 21% of prey. The fish that contained microplastics had a mean abundance of 1.42 ± 0.44 particles per individual and 85% of particles observed were fibres. Particle size and polymer types found in prey were similar to those found in beluga, suggesting that trophic transfer of MPs from prey to beluga may be occurring. The diversity of MP shapes and polymeric identities in all species investigated points to a complex source scenario, and ultimately raises questions regarding the significance and long-term exposure of this pollutant in these ecologically and culturally valuable species.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Leah Bendell
Peter Ross
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.