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

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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.

Semiochemical communication between yellowjacket wasps and their yeast symbionts

Author: 
Date created: 
2018-07-03
Abstract: 

My research investigated whether (i) symbiotic yeasts isolated from the digestive tract of social wasps, (ii) commercial yeasts, or (iii) the volatiles these yeasts produce can be used as trap baits for capturing yellowjackets. I found that adding brewer’s yeast to dried fruit and fruit powder enhanced attraction of yellowjackets in Argentina. I also found that the two yeast species Hanseniaspora uvarum and Lachancea thermotolerans, isolated from North American yellowjackets and grown on grape juice-infused agar, attract yellowjackets. Lachancea thermotolerans in admixture with fruit powder was also attractive and expressed an additive effect when combined with a commercial wasp lure. Synthetic analog blends of the volatiles produced by H. uvarum growing on grape juice-infused media and L. thermotolerans growing on fruit powder were both attractive to western yellowjackets, but not to other yellowjackets. In summary, symbiotic yeasts and their semiochemicals, respectively, show potential as yellowjacket trap baits or lures.

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

Hepatic gene profile analysis for chronic exposure of clothianidin in early life stage sockeye salmon (Oncorhynchus nerka)

Date created: 
2018-06-25
Abstract: 

This study investigated the effects of the neonicotinoid insecticide clothianidin on hepatic gene expression in juvenile sockeye salmon. Four genetically distinct pairs of wild sockeye salmon were collected and fertilized in clean water, and were subsequently exposed to 0.15, 1.5, 15, 150 μg/L clothianidin from 1 hour post-fertilization through to the swim-up fry developmental stage. Individual swim-up fry livers from all genetic crosses and each treatment were collected and various genes of interest were quantified using quantitative PCR. The genes of interest evaluated in this study were estrogen receptor alpha and beta 2, cytochrome P450 1A, suppressor of cytokine signaling 3, and glucocorticoid receptor 2. The glucocorticoid receptor 2 showed a significant 4-fold downregulation at 150 μg/L compared to the control treated fish (p <0.05). This study indicates the utility of quantitative PCR in these early life-stage studies and potential impacts on the stress axis after prolonged exposure to clothianidin.

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

Effects of the aquatic herbicide, Reward®, on the Fathead minnow and Northwestern Salamander

Date created: 
2018-05-24
Abstract: 

In this study the commercial formulation of the aquatic herbicide Reward® (active ingredient diquat dibromide [DB]) was tested. In larval and adult Fathead minnows (Pimephales promelas; FHM) after two 24 h pulse exposures spaced two weeks apart the LC50’s of 4.19 mg/L and 6.71 mg/L were obtained, respectively. A lowest observed effect concentration of 1.18 mg/L for larval growth in FHMs during a 7 d continuous exposure was also derived. An acute 96 h LC50 of 71.5 mg/L DB was obtained for Northwestern salamander (Ambystoma gracile) larvae, while a 21 d continuous exposure LC50 was dramatically lower (1.56 mg/L DB) for these larvae. Few reports of environmental concentrations of this pesticide could be found for Canadian waters. Whether aquatic and/or terrestrial applications and/or DB’s persistent nature in sediments translate into acute or sub-chronic toxicity exposure scenarios in Canadian aquatic systems is unknown and should be the focus of future studies.

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

River network structuring of climate and landscape effects in salmon watersheds

Author: 
Date created: 
2019-01-09
Abstract: 

Climate change is altering historic patterns of temperature and precipitation worldwide with significant implications for the abiotic and biotic dynamics of river ecosystems. Flowing downhill, precipitation aggregates into creeks, streams and eventually rivers, forming a branching network over the landscape architecturally similar to the branches, limbs and trunk of a tree. Linking disparate locations, these river networks integrate the varied expressions of climate within a watershed. Thus, the river network offers a framework for understanding how spatial patterns of climate are organized and become manifest in rivers. By considering the river network's structuring of climate and landscape interactions, we might better understand how climate and land-use change impact river ecosystems and more clearly identify particularly vulnerable biota. In chapter 2, I examine how river networks dampen signals of climate change in hydrologic flow by integrating varied flow trends from upstream. I demonstrate that by integrating a diverse climate portfolio, the network accumulates changing flow regimes of different volatility, direction and magnitude, such that on average downstream climate change trends are moderated. In chapter 3, I consider the match-mismatch potential of juvenile salmon migrating towards the springtime zooplankton resource pulse in the estuary. I show that populations further from, and whose climate is more dissimilar to, the estuary, are more likely to miss the peak zooplankton bloom. These findings suggest migratory distance influences phenological mismatch risk among populations. My fourth chapter develops an unsupervised machine learning method for cleaning stream temperature data to facilitate big data studies. In chapter 5, I gathered temperature data at over 100 locations throughout a watershed the size of Ireland, over 4 years at 2-hour intervals resulting in over 1 million data points. These data informed a spatial stream network model that quantified how landscape features and river connectivity control seasonal temperature dynamics. These temperature dynamics across space and time revealed that different adult salmon migrations have very different exposures to warm temperatures. Collectively, these findings illustrate that river networks: 1. integrate and dampen signals of climate change, 2. structure phenological match-mismatch patterns and 3. organize thermal exposure potential of biota.

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

Non-lethal human-shark interactions and their ecological consequences

Date created: 
2018-10-31
Abstract: 

Collapses of predator populations, caused mainly by unsustainable fishing, have been documented in many marine ecosystems. Predators are thought to play critical roles in marine environments where, through direct predation and fear effects, they can shape demographic processes and community structure. My thesis focusses on the effects of two non-lethal anthropogenic impacts on sharks: prey depletion and shark provisioning tourism. Using stable isotopes and a time series of shark vertebrae, I first examine the historical isotope ecology of seven shark species from the southwest Indian Ocean. Two species with generalist diets showed no change over two decades in δ15N or δ13C signatures. Large individuals of five primarily piscivorous species exhibited isotope signatures that deviate from historical baselines, suggesting long-term changes in diet and/or foraging strategy. Next, I measure the effects of tourism-related provisioning on the trophic signatures and movement patterns of Caribbean reef sharks Carcharhinus perezi in the Bahamas. Combining stable isotope analyses, acoustic telemetry and direct observations, I show that individual sharks that are provisioned more frequently have elevated δ15N signatures, but similar residency and movement patterns to un-provisioned conspecifics, suggesting that their broader ecological roles are not affected by long-term provisioning. Finally, I use the gradient of shark abundance generated by provisioning for ecotourism to reveal the wider coral reef community corollaries of reef shark presence. Benthic community structure varied across this gradient, with less macroalgae and more turf algae at sites with more sharks. Herbivorous parrotfish were abundant but fed less selectively and consumed more macroalgae at sites with more sharks, suggesting that fear effects may drive the patterns observed. Teleost fish biomass was almost twice as high near the provisioning site than further away, a pattern driven by fisher avoidance of areas of more sharks. Effective shark conservation may thus deliver broad cascading benefits to coral reef communities. While most marine predator declines are due to direct fishing mortality, my thesis evokes additional mechanisms by which anthropogenic activities may drive change in predator populations and their communities.

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

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

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

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

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

The role of adaptive behaviour in migratory counts of shorebirds

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

Shorebird population status and trends are commonly generated from counts made at migratory stopovers, where large numbers are concentrated at few locations. Shorebirds migrate long distances, encountering changing and unpredictable conditions. The ability to respond with adjustments in behaviours such as site selection, timing and routing, is likely essential. In this thesis I examine how the adaptive behaviour of migrants affects the use of stopover sites, and hence how many shorebirds are counted. I develop a model of mortality-minimizing decisions made by southbound western sandpipers (Calidris mauri) moving through a landscape with large and small stopover sites. I use the model to simulate counts that would be observed under different scenarios, each leaving distinct `fingerprints' on the outcomes. These outcomes were compared to counts made over five years by citizen-scientists across the Salish Sea region. The results support the hypothesis that inter-annual variation in the passage timing of peregrine falcons (Falco peregrinus - the most important sandpiper predator) strongly affects the distribution of sandpipers across small and large stopover sites. Other scenarios appear less parsimonious. An analysis of data collected by the Atlantic Canada Shorebird Survey (2754 surveys, 1974 - 2015) reveals that semipalmated sandpipers (C. pusilla) have steadily shifted their stopover site usage toward larger sites. Surveys of the northbound passage of western sandpipers and dunlins (C. alpina) along the Pacific Flyway show that over recent decades (1985 - 2016), both species passage southern sites, but not northern sites earlier. Each of these approaches demonstrates that the behavioural response of shorebirds to landscape-level conditions affects counts strongly enough that the accuracy of estimated population trends can be poor. Caution should be exerted when using migratory counts to generate trends in populations.

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

Multiple axon guidance pathways asymmetrically distribute axons in the ventral nerve cord of Caenorhabditis elegans

Author: 
Date created: 
2018-11-22
Abstract: 

Early during development neurons project small filamentous processes, axons and dendrites, that extend and eventually connect with other cells and tissues. These processes can grow over long distances and allow for transmission of information between cells. The proper functioning of our nervous system is dependent on these same processes correctly navigating to specific end targets. This is achieved through guidance cues in the environment which interact with receptors on the extending processes allowing them to be steered in the correct direction. Unfortunately, due to the high complexity of most vertebrate nervous systems our understanding of how axons and dendrites use these cues to navigate is still very limited. The aim of this thesis was to discover novel genes regulating axon guidance to shine additional light on how axons navigate during development. Normally axons of the ventral nerve cord in the nematode Caenorhabditis elegans are invariably sorted asymmetrically. Animals with mutations impacting function in individual axon guidance signaling pathways show no or only very low penetrance of disruption of VNC asymmetry. Here genetic screens successfully isolated four mutants in which asymmetry between major longitudinal axon tracts is disrupted. One of these four mutants include a novel allele of the gene col-99 which encodes a previously uncharacterized transmembrane collagen with vertebrate homologs. Detailed characterization of animals lacking COL-99 revealed widespread axon guidance defects impacting longitudinal and lateral axon navigation of a variety of neurons. Of the remaining three mutants two were found to be alleles of unc-52 and unc-34, both previously characterised for roles in axon guidance, while the final mutation remains unidentified. Disruption of any one signaling pathway does not lead to penetrant VNC asymmetry defects suggesting redundancy between parallel signaling pathways here. To better understand how signaling pathways of multiple guidance cues may converge to control guidance at choice points single mutants were crossed into a nid-1 null mutant background and VNC asymmetry phenotypes examined. Previously nid-1 was found to substantially enhance navigation defects of the VNC pioneering neuron AVG when crossed into mutants showing a low penetrance of AVG navigation defects. Double mutants with nid-1 saw defect penetrance significantly increase in several cases indicating parallel signaling pathways. Combination of mutants into triple and quadruple mutant strains showed that UNC-6, SAX-3, and COL-99 represent members of parallel signaling pathways acting redundantly to guide axons in establishment of asymmetry which in addition depends on basement membranes components, including EPI-1. Thus multiple axon guidance signaling pathways, acting in tandem, ensure correct guidance and segregation of axons at the anterior choice point of the VNC establishing VNC asymmetry.

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