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

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Investigations into the roles of thyroid hormone and retinoic acid on opsin expression in juvenile rainbow trout

Author: 
Date created: 
2019-03-27
Abstract: 

Thyroid hormone (TH) and retinoic acid (RA) are powerful modulators of photoreceptor differentiation during vertebrate retinal development. In the embryos and young juveniles of salmonid fishes and rodents, TH induces switches in opsin expression within individual cones, a phenomenon that also occurs in adult rodents following prolonged (12 week) hypothyroidism. The ability of TH to modulate opsin expression in the differentiated retina of fish, and the role of RA in inducing opsin switches, if any, is unknown. Here I investigate the action of TH and RA on single cone opsin expression and the absorbance of visual pigments in juvenile rainbow trout. Prolonged TH exposure increased the wavelength of maximum absorbance (λmax) of the rod, and the medium (M, green) and long (L, red) wavelength visual pigments, and affected single cone opsin expression in the alevin. RA did not induce any opsin switches nor change the visual pigment absorbance of photoreceptors.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Inigo Novales Flamarique
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Microbiome analysis at a proposed northern Canadian mine site

Author: 
Date created: 
2019-04-11
Abstract: 

Copper is a metal that can persist in the environment following anthropogenic activities. The toxic effects of metals such as copper in aquatic environments can be decreased through bioremediation efforts. Prior to proposed mining operations, upstream sites in a Canadian watercourse showed elevated copper concentrations in conjunction with low pH values. Downstream sites showed low copper concentrations and higher pH values. Natural bioremediation has possibly occurred in the area resulting in reduced copper concentrations. Microbial populations were sampled at five sites along the watercourse to determine their community profiles through 16S rRNA gene sequencing and assess the natural bioremediation process. Results showed the Gallionellaceae family dominated the community at the high copper concentration sites. Metagenome sequencing of the site with the highest copper concentration and one site upstream indicated an enrichment of metal tolerance genes, revealing microbial tolerance to this acidic metals-rich environment and suggesting possible mechanisms of bioremediation.

Document type: 
Graduating extended essay / Research project
Supervisor(s): 
Christopher Kennedy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Project) M.E.T.

The influence of predation danger on the distribution of non-breeding shorebirds in a tropical estuary system

Date created: 
2019-04-05
Abstract: 

I studied non-breeding shorebirds in the extensive mangrove-mudflat system of Northern Nariño, Colombia. I asked how the non-breeding distributions of 18 species are influenced by functional traits, the interplay between food and danger attributes of landscapes, and interactions with other species. I found that almost all the area’s ~8000 Whimbrels (Numenius phaeopus) roost together on just one of the hundreds of available mangrove islands. Much smaller numbers occasionally roost on a few other islands. The larger roost site is distinguished by its location, having a larger amount of Whimbrel feeding habitat (mudflat) within a 12 km radius than almost any other mangrove island, and being more isolated from the mainland and thus from terrestrial predators, but not more isolated from villages or shipping channels than other islands. Within a subset of nine shorebird species, an increase in body mass predicted an increase in wing load both within and between species. Contrary to expectations, wing load did not correlate strongly with escape performance (take off speed), but as expected, heavier wing loads did correlate with stronger escape responses (flight initiation distances) across species. Species with higher escape performance use habitats that are more productive, but also more dangerous, while species with lower escape performance reacted sooner to predator stimulus. Tactile and gregarious species show stronger responses to safety gradients. An analysis of co-occurrence of species pairs demonstrated that non-random patterns were prevalent within communities of non-breeding shorebirds. Species pairs tracking same or opposing environmental gradients explain some positive and negative associations, but a large proportion of the associations was due to residual variation linked to the species themselves. Positive associations could be explained by heterospecific attraction associated with reducing predation danger and public information about resources. The fewer negative associations could indicate competitive interference. Alternatively, other sources of environmental variation not captured in this study could explain these “species only” associations. Our results contrast with previous studies of avian communities for which shared environmental responses play a larger role and suggest that social interactions are as important in structuring shorebird communities. This thesis demonstrates how using distribution models informed by species’ morphology, behavior, and interactions with other species, we will be better equipped to understand the effects of habitat conversion on the conservation of migratory shorebirds.

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

The context-dependent spread and impacts of invasive marine crabs

Author: 
Date created: 
2019-03-15
Abstract: 

Following the establishment of a non-native species, there is often speculation about the potential impacts to the native ecosystem. While these early predictions may be necessary for management, they are often based on a general understanding of invasion ecology rather than context-specific research. The unique nature of each introduction event means these generalizations are prone to over- or under-estimating invasive species impacts. This thesis predicts the impacts of invasive marine true crabs (infraorder Brachyura), with a focus on the invasive European green crab (Carcinus maenas), using both general ‘rules of thumb’ and context-specific research. In Chapter 2, I conduct a meta-analysis to demonstrate that while native and invasive crabs typically have a similar overall impact on prey species, some combinations of prey type and experimental design can favour invasive crabs. In Chapter 3, I examine the geographical variability of green crab impacts worldwide. Using green crabs collected from invasive (South Africa and Canada) and native (Northern Ireland) populations, I conduct a comparative functional response experiment to show how the foraging behaviour of an invasive species varies among regions. In Chapter 4, I use an enclosure experiment to determine how the impact of green crabs on eelgrass (Zostera marina) ecosystems changes with crab density, and conclude that there is the potential for extensive loss of habitat-forming eelgrass in the presence of high densities of green crabs. In Chapter 5, I explore the issue of site-level variability in the abundance, and therefore potential impact, of green crabs on the west coast of Vancouver Island, British Columbia. I develop a species distribution model to identify small-scale biotic and abiotic predictors of ‘hyper-abundant’ populations of green crab. The thesis as a whole explores the generalizations often used to predict invasive impacts and prioritize impact mitigation efforts. I find that, for green crabs, generalizations that rely on the origin or specific invasion history of an invasive species are prone to over-estimating impact. However, measures of density or abundance, paired with an understanding of context-specific behaviours, are more likely to produce reliable impact predictions for these invasive species.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Isabelle Côté
Thomas Therriault
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Plant-pollinator interactions of the oak-savanna: Evaluation of community structure and dietary specialization

Author: 
Date created: 
2019-04-08
Abstract: 

Pollination events are highly dynamic and adaptive interactions that may vary across spatial scales. Furthermore, the composition of species within a location can highly influence the interactions between trophic levels, which may impact community resilience to disturbances. Here, I evaluated the species composition and interactions of plants and pollinators across a latitudinal gradient, from Vancouver Island, British Columbia, Canada to the Willamette and Umpqua Valleys in Oregon and Washington, United States of America. I surveyed 16 oak-savanna communities within three ecoregions (the Strait of Georgia/ Puget Lowlands, the Willamette Valley, and the Klamath Mountains), documenting interactions and abundances of the plants and pollinators. I then conducted various multivariate and network analyses on these communities to understand the effects of space and species composition on community resilience. In addition, I evaluated the pollen composition and floral visit patterns of a mid-sized mining-bee, Andrena angustitarsata, to understand how foraging preferences and dietary specialization may change across space and with varying floral compositions. I found that spatial scales had an effect on species compositions, the interactions between plants and insects, and the foraging preferences of pollinators. I learned that some groups of pollinators may provide stability in networks by increasing generalized interactions and reducing specialization. Additionally, the foraging preferences, A. angustitarsata, were conserved across spatial scales, despite fluctuations in plant compositions and abundances. However, A. angustitarsata is likely not oligolectic, a pollen specialist, because of its ability to facultatively forage on additional plants other than its preferred host plants. Overall, my results show that spatial scales can influence the composition and interactions of plants and pollinators, thus influencing the degree to which species interact and the ability of the community to maintain structure after a disturbance.

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

Fish-mediated nutrients in tropical marine systems

Author: 
Date created: 
2019-02-01
Abstract: 

Animals can mediate biogeochemical processes and drive nutrient availability and productivity in ecosystems. Fish may be a major source of nutrient supply through metabolic processes such as excretion, but their role in influencing primary productivity in nutrient-poor tropical coastal marine systems is not well understood. Broadly, my thesis explores how variations in fish-mediated nutrient provisioning can influence reef primary productivity, and how invasive species can alter fish-mediated nutrient supply in coral reefs and seagrass ecosystems. I quantified excretion rates for several groups of reef fish in The Bahamas, demonstrating that excretion is primarily governed by body size, and that nutrient supply in an area is influenced by fish movements and diel activity levels. I then examined how variations in fish excretion altered three groups of primary producers on reefs using a large manipulative experiment. I demonstrated that increases in fish excretion can result in increased algal biomass and phytoplankton growth and can also lead to higher nutrient content in seagrass blades. I examined natural patterns of seagrass growth in proximity to coral reef fish communities to try and infer how fish communities shape these habitats. I found that while fish communities may have a minor influence on these primary producers through excreted nutrients, other factors such as sand depth likely play a larger role in shaping seagrass in immediate proximity to reefs. Finally, I examined how nutrient supply from native fish communities is altered by an invasive predator, the Indo-Pacific lionfish (Pterois sp). I found that, through their own excretion, these invasive predators replace the nutrient supply of the native fish they consume. Fish-mediated nutrient provisioning is therefore relatively robust to predation from lionfish on short time scales. Overall, my thesis helps to fill critical gaps in our understanding of the role of fish in shaping coral reef productivity. Bottom-up processes such as nutrient provisioning from reef fish may be a key aspect of reef ecosystem functioning and this specific functional process should be incorporated into future reef management and conservation efforts.

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

Slime, safety and shorebirds: Biofilm production and grazing by migrating western sandpipers (Calidris mauri)

Author: 
Date created: 
2019-04-05
Abstract: 

The quality of stopover sites for migrant shorebirds is thought to be determined by food availability and safety from predators. This thesis investigates this interaction on an estuarine mudflat in British Columbia, where migrant western sandpipers graze biofilm. I measured biofilm concentration and grazing intensity on transects across the mudflat. I found that the concentration of biofilm rose 4.1 mg m-2 hr-1 during tidal emersion periods, with total accumulation matching that removed by sandpipers during grazing visits. During the higher-intensity (10 – 100 fold, based on daily sandpiper counts) northward migration, biofilm concentration increased and grazing decreased with proximity to the shoreline. In contrast, during southward migration biofilm was uniformly high. A danger manipulation experiment supported a trade-off with biofilm concentration: grazing declines with danger, but less so where biofilm is higher. Together the results indicate that dynamic trophic interactions between danger, sandpipers and biofilm create spatial patterns in biofilm concentration.

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

The effects of diluted bitumen on marine intertidal vascular plants

Author: 
Date created: 
2019-01-29
Abstract: 

Canada has the third largest oil reserves in the world, most of which exist in the form of bitumen in the oil sands of the Western Canada Sedimentary Basin. Plans are underway to increase the export of petroleum products including diluted bitumen (dilbit) and crude oil to overseas markets, highlighting the potential risk of a spill into the Canadian marine environment. Understanding and evaluating risk, and the development of chemical management plans require information on the toxicity of dilbit to key marine species. Little information exists regarding the toxic effects of most petroleum products to intertidal vascular plants. The objective of this project was to determine the lethal and sublethal toxicity of environmentally relevant concentrations of dilbit to eelgrass (Zostera marina), an intertidal vascular plant and keystone species in the Pacific Northwest. Eelgrass was collected from the intertidal zone of an uncontaminated site in the Strait of Georgia, near Boundary Bay, British Columbia. A short-term, 9-d exposure and a long-term 28-d exposure of shoots to multiple concentrations of a water-accommodated fraction (WAF) of dilbit were performed. Endpoints assessed in shoots from the short-term exposure included: total reactive oxygen species (ROS), activity of catalase and superoxide dismutase, and protein oxidation. Shoots from the long-term exposure were assessed for biological endpoints including plant growth, chlorophyll-a content, and the effective quantum yield of Photosystem II.

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

The effects of diluted bitumen and the dispersant Corexit 9500A on Pacific marine organisms

Date created: 
2019-03-07
Abstract: 

Canada is expected to significantly increase the production and exportation of bitumen in the next decade. Raw bitumen is diluted with natural-gas condensates to produce diluted bitumen (dilbit), facilitating its flow through pipelines. Few data currently exist on dilbit toxicity to Pacific marine species, either alone or in combination with recently approved chemical dispersant Corexit 9500A. The current study investigated the toxicity of the water-accommodated fraction (WAF) of dilbit, Corexit 9500A, and the chemically enhanced water-accommodated fraction (CEWAF) of dilbit to representative marine species of the west coast of Canada. Oil chemically dispersed by Corexit showed evidence of higher toxicity than dilbit WAF to each test species including juvenile mysids (Mysidopsis bahia), juvenile topsmelt (Atherinops affinis) and adults spot prawns (Pandalus platyceros). Additionally, purple sea urchin (Strongylocentrous purpuratus) fertilization showed high susceptibility to Corexit toxicity, both with and without dilbit present, as nearly 100% of eggs exposed to Corexit remained unfertilized. Overall these results suggest that the use of Corexit as a remediation technique may increase the toxic impacts to Pacific marine species over those caused by a dilbit spill alone.

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

The role of Kdnase (sialidase) in cell wall integrity and virulence of Aspergillus fumigatus

Author: 
Date created: 
2018-08-17
Abstract: 

Aspergillus fumigatus is the leading airborne fungal pathogen worldwide. In immunocompromised individuals, exposure to conidiospores can lead to an infection known as invasive aspergillosis. We have previously shown that A. fumigatus possesses a sialidase that preferentially cleaves the sialic acid, Kdn (3-deoxy-d-glycero-d-galacto-2-nonulosonic acid) and is therefore a Kdnase. The purpose of my research was to characterize a Δkdnase knockout strain. Under hyperosmotic stress, cell wall α-glucan and chitin levels were significantly increased in Δkdnase hyphae compared to wild type (WT). Δkdnase was more susceptible to growth inhibition by amphotericin B and caspofungin but resistant to nikkomycin. Virulence of the Δkdnase strain in neutropenic mice was attenuated compared to WT when mice were also treated with amphotericin B, but not in the absence of the drug. uHPLC-MS analysis showed that WT and Δkdnase conidiospores, and WT hyphae contained Kdn; however, Kdn was not detectable in Δkdnase hyphae.

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