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

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A molecular investigation of the dynamics of piscine orthoreovirus in a wild sockeye salmon community on the Central Coast of British Columbia

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-09-11
Abstract: 

Many Pacific salmon (Oncorhynchus sp.) populations are declining due to the action of multiple stressors, possibly including microparasites such as piscine orthoreovirus (PRV), whose host range and infection dynamics in natural systems are poorly understood. First, in comparing three methods for RNA isolation, I find different fish tissues require specific approaches to yield optimal RNA for molecular PRV surveillance. Next, I describe PRV infections among six fish species and three life-stages of sockeye salmon (O. nerka) over three years in Rivers Inlet, BC. Screening reveals a 3% overall prevalence of PRV in this system, along with the first evidence of PRV in Dolly Varden (Salvelinus malma) and eulachon (Thaleichthys pacificus). Among sockeye, the prevalence declined by 4% from the fry to smolt stages for the 2014 and 2015 cohorts.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Richard Routledge
Jim Mattsson
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Juvenile salmon use of estuaries: investigating food web ecology, growth, and residency

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

Estuaries are valuable nursery and stopover habitats that support mobile consumers during their ontogenetic migrations such as juvenile anadromous salmon. My first data chapter was an extensive field study that examined how two salmon and two small pelagic fish integrate with key prey across the estuary of the Skeena River. The different fishes selected different prey that were unevenly distributed across the estuary seascape in time and space; however, some prey were associated with biophysical factors like salinity and eelgrass. My next chapter compiled empirical published data on five species of juvenile salmon growth rates and residency durations. Several species had poor coverage of these aspects, but it was evident that different salmon species and life history strategies have different growth rates and residency durations in estuaries. Collectively, this work adds and organizes empirical support for valuing estuaries as important habitat for juvenile salmon.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jonathan Moore
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

The environmental fate and persistence of sea lice chemotherapeutants used in Canadian salmon aquaculture

Author: 
Date created: 
2018-05-23
Abstract: 

In Canada, five formulations have been used to treat sea lice infestations in salmon aquaculture. This research investigated the environmental partitioning, persistence, and acute toxicity to marine organisms of Slice® (AI: emamectin benzoate [EB]), Salmosan® (AI: azamethiphos [AZ]), Alphamax® (AI: deltamethrin [DM]), Excis® (AI: cypermethrin [CP]), and Interox® Paramove 50 (AI: hydrogen peroxide [HP]). EB, CP and DM partitioned mainly to the sediment in sediment-water microcosms; AZ and HP remained mainly in the water. The persistence of chemicals in water was reported: CP > DM > AZ > HP. In sediment, CP > EB > DM was observed. Toxicity tests indicate a lack of trends however the information is useful for identifying risks. Some reported values for echinoderms, kelp, and topsmelt toxicity are below the recommended treatment concentrations. This research provides insight into the environmental fate and associated risks to non-target marine organisms in the vicinity of salmon aquaculture sites.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Chris Kennedy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Project) M.E.T.

Identification and characterization of proteins involved in the cytoskeletal rearrangements caused by bacterial pathogens

Date created: 
2024-08-21
Abstract: 

Bacterial pathogens have evolved to alter the cytoskeleton of their hosts during their respective infection processes. The extracellular bacterium, enteropathogenic Escherichia coli (EPEC), generates an actin-rich pedestal to “surf” along the host cell surface. In contrast, L. monocytogenes (L. monocytogenes) invades its host and polymerizes actin filaments to generate a comet tail for movement within and among host cells of epithelia. Salmonella enterica serovar Typhimurium (S. Typhimurium) induces actin-rich membrane-ruffles to invade its host cell. These bacteria have evolved to generate their respective actin-rich structures to colonize the intestinal epithelia. To further characterize the actin-rich structures generated by these bacteria, I selected four proteins from a mass spectrometry analysis of EPEC pedestals previously conducted in our laboratory. I found that the known actin-bundling proteins calponin 1 and calponin 2 decorated all the actin-rich structures formed by these three bacteria. Another actin-stabilizing protein transgelin (SM22) also decorated EPEC pedestals and L. monocytogenes comet tails. Moreover, the formation of pedestals and comet tails were dependent on SM22 protein levels. Aside from these three members of the calponin family, I found that a ubiquitin conjugating enzyme Ube2N was enriched at the invasion events and at the plasma membrane-bound comet tails formed by L. monocytogenes. This novel association of Ube2N with actin structures at the plasma membrane led to my discovering that Ube2N binds directly to actin, and that Ube2N function influences actin-based whole cell motility. Another bacterial pathogen, Klebsiella pneumoniae (K. pneumoniae), has been shown by others to alter the host actin cytoskeleton. I have found that the disassembly of the host microtubule networks precedes these actin cytoskeletal alterations in lung epithelial cells, and show that the Klebsiella pneumoniae gene ytfL (Kp ytfL) initiates this microtubule disassembly and that the katanin catalytic subunit A like 1 protein (KATNAL1) as well as the katanin regulatory subunit B1 protein (KATNB1) are activated to cause microtubule severing. Through this, I identified the bacterial initiator and the host cell effector proteins responsible for K. pneumoniae-induced microtubule disassembly. From these, I identified proteins that are novel to the actin structures of EPEC, L. monocytogenes and S. Typhimurium as well as effector proteins that are crucial for the novel host microtubule alterations of K. pneumoniae.

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

Trophic magnification of legacy persistent organic pollutants and emergent contaminants within a terrestrial food-web of an avian apex predator, the Cooper’s Hawk (Accipiter cooperii)

Author: 
Date created: 
2018-08-24
Abstract: 

Several types of legacy and lipophilic persistent organic pollutants (POPs), such as organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs), and emergent proteinophilic POPs like perfluorinated compounds (PFCs) are released from multiple sources into the environment and negatively impact endocrine functions within exposed wildlife. Protocols to assess bioaccumulation of these persistent chemicals within terrestrial systems are far less developed compared to aquatic systems. Consequently, regulatory agencies in Canada, the United States, and the European Union use only aquatic information to assess bioaccumulation potential of chemicals. However, recent studies have shown that some chemicals that are not bioaccumulative in aquatic food-webs do biomagnify in terrestrial food-webs. To better understand the bioaccumulation behaviour of chemicals in terrestrial systems, we assessed the biomagnification of lipophilic and proteinophilic POPs in a terrestrial food-web that included an avian apex predator, the Cooper’s Hawk (Accipiter cooperii). Over 100 samples were collected from various trophic levels of the food-web including hawk eggs, songbirds, invertebrates, and berries. We estimated the trophic position of each organism using stable isotope analysis of δ13C and δ15N signatures of the hawks, songbirds, invertebrates, and berries. We analyzed the biota samples for concentrations of 38 PCB congeners, 20 OCPs, 20 PBDE congeners, 7 other brominated flame retardants (BFRs), and 18 PFCs listed on the Government of Canada's Chemicals Management Plan. We used censored regression by maximum likelihood estimation to assess the relationship between the natural logarithm of each contaminant concentration and trophic position. Trophic magnification factors (TMFs) were determined as the antilog of the regression slope. We determined TMFs for contaminants that were detected at appreciable levels in all of the biota samples (i.e. had 50% or greater detection frequency) and compared these terrestrial TMFs to those observed in aquatic systems. TMFs of legacy and lipophilic POPs ranged from 0.77 to 15.66, indicating that the majority of those POPs are biomagnifying. TMFs of PFCs ranged from 13.02 – 86.19, indicating PFCs are also readily biomagnifying and perhaps at a greater extent than lipophilic POPs. Terrestrial TMFs for legacy POPs were comparable or higher than aquatic TMFs; whereas, terrestrial TMFs for PFCs were considerably higher than aquatic TMFs.

Document type: 
Thesis
Senior supervisor: 
David J. Green
John Elliott
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Wintering and breeding distributions of Black Oystercatchers (Haematopus bachmani): Long-term trends and the influence of climate

Date created: 
2018-08-03
Abstract: 

Black Oystercatchers (Haematopus bachmani) are argued to be at risk from global climate change as rising sea levels could threaten their coastal habitat. However, population estimates have doubled to ~15 000 since 1994. This has been attributed to improvements in survey methods rather than to population trends, which remain uncertain. I assessed trends and climatic influences on winter abundance (Christmas Bird Counts, 1975/1976 – 2015/2016) and numbers of breeding pairs (British Columbia breeding surveys, 1962 – 2014). Winter counts were stable or increasing across the species' range. Numbers of breeding pairs were stable in British Columbia, but were lower following the warm phase than the cool phase of the El Niño Southern Oscillation. Although new challenges may arise as the climate continues to change, Black Oystercatcher populations appear resilient to current environmental and anthropogenic challenges.

Document type: 
Thesis
File(s): 
Senior supervisor: 
David Green
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Protocols for measuring in vitro and in vivo biotransformation rates of hydrophobic substances in fish

Author: 
Date created: 
2018-07-31
Abstract: 

The effective management of commercial chemicals is important for achieving sustainable development goals while reducing risks to human and ecological health. National and international practices for the management of chemicals involve identifying substances with bioaccumulative properties which can lead to elevated chemical concentrations in organisms and associated toxic effects. Current metrics for identifying bioaccumulative properties of chemicals are the fish-water bioconcentration factor (BCF) and the octanol-water partition coefficient (KOW). The currently recommended method for measuring the BCF is expensive, difficult, time consuming, and requires the use of many animals. The objective of this research is to develop and test alternative methods for assessing the bioaccumulation of substances. Methods include a dietary in-vivo bioaccumulation test, in-vitro biotransformation tests and in-vitro to in-vivo extrapolation. The research involved the development and testing of a dietary bioaccumulation test for determining the BCF as well as biotransformation rates in the intestines and the body of the fish that involved the use of non-metabolizable reference chemicals. The results show that gastro-intestinal biotransformation plays a dominant role in the bioaccumulation of a large number of the tested hydrophobic organic chemicals when fish are exposed via the diet; while somatic biotransformation (including hepatic biotransformation) plays a dominant role in the bioaccumulation of tested chemicals in fish exposed via the water. The results demonstrate that the BCF can be measured in a dietary bioaccumulation tests and that biotransformation pathways and rates differ between aqueous and dietary tests. The research also involved the development and testing of an in-vitro fish liver S9 biotransformation testing method. The results show that biotransformation rates using fish liver fractions are highly dependent on the concentration of the test chemical in the test. As a result, the recommended 1 µM initial substrate concentration may underestimate the in vitro biotransformation rate constant and, therefore, an overestimation of the whole fish BCF. To avoid challenges presented by concentration dependence, multiple solvent delivery based depletion experiments at a range of initial concentrations are recommended for determining the maximum depletion rate constant. Meanwhile, a single sorbent phase dosing experiment may also provide reasonable approximations of maximum depletion rates of very hydrophobic substances. Lastly, the research involved extrapolating in vitro maximum depletion rate constants to somatic biotransformation rate constants and comparing the results with those measured from in vivo dietary tests. The results show a good agreement with empirical measurements from various in vivo experiments for the majority of test chemicals. However, a significant underestimation of the in vitro-extrapolated somatic biotransformation rate constant for 9-methylanthracene may suggest that the fish liver S9 in vitro system may not contain all of the enzymes and/or co-factors to biotransform the chemical compared to the whole fish. Overall, the results demonstrate potential for fish liver S9 extracts to assess in vivo biotransformation potential in the fish body. Both in vivo and in vitro research indicate that extrahepatic may not be considered using standardized in vivo (BCF) and liver S9 in vitro testing. For gastro-intestinal biotransformation to be considered, streamlined in vivo dietary bioaccumulation tests are recommended. Meanwhile, in vitro S9 protocols may be best supplemented with in vitro gastro-intestinal biotransformation tests in future research, especially when extrapolating to endpoints such as BMF and BAF where the diet is a significant route of exposure.

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

Physiological basis of aerobic capacity and workload ability in birds

Author: 
Date created: 
2018-07-30
Abstract: 

Many behaviours exhibited by free-living animals that are crucial for survival and reproduction involve elevated levels of activity or “workload”. Individuals with higher workload ability should be able to cope with the high metabolic demands imposed by these behaviours better and consequently would have higher fitness. High workload could also result in costs such as impaired reproduction or reduced survival. However, the underlying physiological mechanisms that allow individuals to have higher workload ability, and the mechanisms underlying costs of high workload remain poorly understood. This thesis took an exercise perspective and investigated the physiological basis of aerobic capacity and workload ability in birds, using both a comparative, phylogenetic approach, as well as various laboratory-based experimental approaches. In surveying the literature, we identified several potential common physiological markers underlying individual variation in exercise performance and costs of exercise. We also found that hematological traits co-vary with life-history variables, and to a certain extent, energy metabolism in birds at the interspecific level. Additionally, we provided experimental evidence for physiological responses to flight at high attitude and showed that the relationship between hematocrit and flight performance is dependent on altitude. Lastly, we provided experimental evidence for behavioural and physiological adjustments to high workload and demonstrated that physiological adjustments to high workload can negatively impact reproduction. Taken together, this thesis uncovered several physiological mechanisms underlying workload ability and costs of high workload in birds. Future work should consider and integrate multiple physiological systems when studying the physiological basis of workload ability, and more generally, life-history trade-offs in animals. Ultimately, we hope that the knowledge we gain from this thesis can be used to complement studies in free living animals and aid in the design of field experiments.

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

Beyond the reef: How risk of predation shapes fish movement over sand

Author: 
Date created: 
2018-06-22
Abstract: 

On naturally fragmented coral reefs, the reluctance of small-bodied fishes to cross sand is widely considered a predator-avoidance response, but the extent to which distance from safety and how specific predators mediate off-reef movements is unclear. Here, I use video-generated estimates to assess the degree to which sand acts as a barrier to reef-associated fish movement, and I use novel translocations to test how the presence of standardized models of native and invasive predators over sand affects the homing probability of a Caribbean damselfish, Stegastes partitus. The frequency of fish observed over sand fell non-linearly with distance from the nearest reef, and fish were often observed when < 50 m away (~90 fish per hour, 33 species). However, only the native predator model reduced damselfish homing probability over sand. The invasive lionfish (Pterois sp.) did not affect homing, suggesting damselfish are naïve to the threat of predation posed by lionfish.

Document type: 
Thesis
Senior supervisor: 
Isabelle Côté
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Altered mitochondrial dynamics in a novel cellular model of Leber Hereditary Optic Neuropathy (LHON)

Author: 
Date created: 
2018-07-11
Abstract: 

Leber Hereditary Optic Neuropathy (LHON) is a disease that is caused by mutations in mitochondrial DNA resulting in vision loss due to retinal ganglion cell (RGC) degeneration. The exact pathophysiological mechanism causing RGC degeneration is poorly understood. This is partly due to a lack of a suitable model system. We created a novel cellular model for investigating mitochondrial dynamics in LHON by treating human dermal fibroblasts carrying the most prevalent G11778A LHON mutation with staurosporine (STSP). This treatment induced cytoplasmic protrusions resembling neurites. Mitochondrial movement was impaired in LHON fibroblasts compared to wild-type fibroblasts under conditions that induce oxidative phosphorylation (OXPHOS) but could not be attributed to reduced cytosolic ATP levels. Furthermore, LHON fibroblasts displayed altered mitochondrial network remodeling under conditions that induced OXPHOS. Our results demonstrate altered mitochondrial dynamics in LHON fibroblasts which may have implications in the pathogenesis of LHON in RGCs.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Gordon Rintoul
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.