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

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Contributions to the Molecular Biology of Kelp

Peer reviewed: 
No, item is not peer reviewed.
Date created: 
1999
Abstract: 

Genetic relatedness between various kelp (Order Laminariales, Class Phaeophyceae, Division Heterokontophyta) taxa was investigated using DNA sequencing and PCR-typing. The rDNA ITS1 region of gametophytes generated by a naturally occurring apparent kelp hybrid of Macrocystis C. Agardh and Pelagophycus Areschoug were sequenced to determine parentage. All gametophytes examined had only Macrocystis rDNA suggesting either a non-hybrid, or more complicated hybridization than pure equal parental contribution occurred. Laboratory-generated intergeneric hybrids of Alaria Greville and Lessoniopsis Reinke were examined for parentage based on rDNA regions amplified using PCR. Both parental rDNA types were visible in one identified possible hybrid and non-hybrids were easily distinguished. Actin introns in both Alaria and Nereocystis Postels & Ruprecht were characterized and sequenced, representing the first actin intron sequences examined in the Heterokontophyta. The second actin intron fiom individuals of three Alaria species, spanning a geographic range of hundreds of kilometres, were sequenced to quantify variation and to examine individual relatedness for usage in studies of gene flow and population subdivision. Relatedness seemed to correlate with oceanographic distance but not with accepted species boundaries.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Louis D. Druehl
Department: 
Dept. of Biological Sciences - Simon Fraser University
Thesis type: 
(Thesis) Ph.D.

The evolution, ecology, and restoration of anadromy in rainbow trout/steelhead Oncorhynchus mykiss

Date created: 
2014-09-02
Abstract: 

Evolution can occur on ecologically relevant timescales, creating the potential for a bidirectional link between evolution and ecology. For example, migrating species provide important pulses of resources to recipient ecosystems, but are increasingly subject to intense selection due to ongoing global change. If heritable variation underlies migration, then contemporary evolution may increase non-migratory life histories, thereby increasing population persistence, but at the expense of important ecological processes. I examine contemporary evolution and its consequences of migration in an economically and ecologically important species, the resident and migratory ecotypes of the species Oncorhynchus mykiss. In Chapter 2, I show that a stream barrier has driven the evolutionary loss of the migratory ecotype in only ∼25 generations. I estimated the genetic contribution to variation in traits underlying the expression of migration and show that in the above-barrier population there has been a 30% decrease in expression of the migratory ecotype relative to the below-barrier population of origin. In Chapter 3, I examine the ecological consequences of this contemporary evolution. I show that the density decreases associated with loss of anadromy consistently had a greater effect on mesocosm ecosystems than the per-capita effects of the ecotypes. In Chapter 4, I use an analytical model to explore whether a population of O. mykiss would evolve toward greater residency in response to increased costs of migration. I find that evolution can rescue isolated populations; populations that persist are those that evolve in response to the changing selection regime on timescales that prevent population extinction. However, when conditions are restored to the pre-disturbance state, the rate of recovery of the migratory ecotype was unpredictable and generally slower than its loss. Finally, in Chapter 5 I review pathways for restoring the migratory ecotype, and how restoration of a life history may differ from restoring a species. Effective restoration of this life history will entail understanding the ecological and genetic mechanisms underpinning the expression of migratory behavior. Together, these chapters highlight that migratory barriers can drive contemporary evolution of the non-migratory ecotype that increases population persistence, but decreases their ecological impacts. More generally, this research highlights the importance of incorporating evolutionary perspectives in manage- ment, conservation, and restoration.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jonathan Moore
Department: 
Science:
Thesis type: 
(Thesis) Ph.D.

The effects of natural and anthropogenic disturbance in lotic ecosystems

Date created: 
2014-09-03
Abstract: 

The prevalence of large-scale anthropogenic and natural disturbance has increased in recent decades around the world. For example, over 50% of the world’s large rivers are currently dammed and the frequency of large wildfires has nearly quadrupled in western North America since the mid-1980s. Disturbances such as these are principal drivers of change in lotic ecosystems and we seek to improve our understanding of how they affect recipient ecosystems in the context of fisheries management and conservation. My thesis research combines empirical studies and modeling to improve our ability to predict and measure the effects of several major types of natural and anthropogenic disturbance in lotic ecosystems. In Chapter 1 I improved the accuracy of hydrodynamic habitat models for juvenile salmon by up to 10% by applying Akaike information criterion and model averaging. In Chapters 2 and 3 I applied multiple regression and bioenergetic models to illustrate how wildfire, by burning riparian vegetation, can elevate stream temperatures by up to 0.6°C adding ~5 kJ of metabolic costs to salmonids. As well, I found concentrations of food web resources such as nitrate and fine particulate organic matter increased in burned compared to unburned regions by 244% and 44%, respectively, and I found significantly greater seasonal changes in terrestrial and aquatic invertebrate abundance than changes attributable to wildfire. Despite similar regional invertebrate prey abundance, Bayesian stable isotope mixing models revealed seasonal and regional differences in salmonid diets, with higher trophic level prey contributing more to diets in the burned compared to a reference region. Lastly, in Chapter 4 I found that forest harvest and rising air temperatures are warming waters in the Fraser River basin at 0.07°C per decade on average by applying Spatial Stream Network models. In total, my thesis research builds on previous work and illuminates how disturbance can affect abiotic and biotic responses in lotic ecosystems at spatial scales ranging from less than 10 m2 to over 200,000 km2. Thus, results from my thesis research will aid fisheries management and conservation by improving our understanding of how natural and anthropogenic disturbance may alter streams and rivers in our future.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jonathan W. Moore
Department: 
Science:
Thesis type: 
(Thesis) Ph.D.

The modulation of abcb4 and cyp3a65 gene expression and multidrug/multixenobiotic resistance (MDR/MXR) functional activity in the model teleost, Danio rerio (zebrafish)

Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2014-08-28
Abstract: 

The multidrug/multixenobiotic resistance (MDR/MXR) mechanism is a cellular response involving the induction and coordinated action of the ATP-binding cassette (ABC) transporter, P-glycoprotein (P-gp), and the phase I metabolizing enzyme, cytochrome P450 3A (CYP3A), which confers protection against potentially cytotoxic exposures of various drugs and environmental contaminants. In mammals, ligand-mediated pregnane X receptor (PXR) transcriptional activity regulates the induction of P-gp and CYP3A but this mechanism is not well characterized in fish species. In this study, zebrafish treated with the Pxr (PXR) agonist PCN co-modulated P-gp (Abcb4) and CYP3A (Cyp3a65) mRNA expression and this co-modulation was associated with increased hepatic MDR/MXR functional activity in vivo. Consistent with a mammalian-like MDR/MXR mechanism regulated by PXR, zebrafish co-treated with PCN and the mammalian PXR antagonist, ketoconazole (KTC) attenuated the PCN-mediated modulation of hepatic abcb4 and cyp3a mRNA levels, as well as attenuated the PCN-mediated modulation of MDR/MXR functional activity. These results suggest abcb4 may be involved with the MDR/MXR response in the adult zebrafish liver, and that Pxr (PXR) may regulate this dynamic process. Finally, the lack of Cyp3c1 mRNA modulation by PCN suggests that Cyp3c1 and Cyp3a65 may be regulated by separate transcriptional pathways.

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

Nutrient enrichment, trophic exchanges and feedback loops: effect of spawning salmon-derived nutrients on juvenile coho salmon

Date created: 
2014-07-11
Abstract: 

The movement of nutrients across ecosystem boundaries can affect recipient ecosystems at individual, population, and community levels. This is particularly the case when more productive systems subsidize less productive ones, where subsidies can sustain and enhance populations in nutrient-poor recipient environments. One prominent example of this is the annual migration of salmon from the marine environment into low-productivity freshwater streams for spawning. This thesis uses data collected from 47 near-pristine streams on the central coast of British Columbia to study spawning chum (Oncorhynchus keta) and pink (O. gorbuscha) salmon and the ecological implications of their nutrient subsidy, focusing on stream-rearing juvenile coho salmon (O. kisutch). While considering a broad suite of habitat characteristics, the strongest predictors of juvenile coho size and abundance were spawning chum and pink salmon abundance. Streams with more spawning chum salmon had larger coho, while streams with more spawning pink salmon had higher coho populations. Further, the evidence suggested the negative association between juvenile coho and their intraguild predators/competitors, sculpin (Cottus aleuticus and C. asper), may be reduced as more spawning salmon nutrients became available. Altogether, this thesis shows strong impacts of marine-derived nutrient subsidies to freshwater ecosystems at multiple ecological scales. In general, it provides insights into the ecological mechanisms by which species interact with their environments, the potential for nutrient subsidies to affect recipient populations through changing food supply and predator-prey dynamics, and the role of multi-trophic interactions in subsidized trophic cascades. In specific, this research improves our understanding of the potential positive feedback between different species of salmon while incorporating the importance of multiple habitat characteristics. This has the potential to inform conservation and ecosystem-based management, particularly in light of the drastic decline in spawning salmon abundance in northern Pacific regions.

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

The bird who kicked the wasp's nest: Red-throated Caracara predation, nesting and territorial behaviour

Date created: 
2014-07-10
Abstract: 

Red-throated Caracaras are enigmatic but seldom studied raptors of tropical American forests. They are known to prey on social wasps and exhibit cooperative breeding, but little quantitative data have been published. We investigated Red-throated Caracara nesting, predation and social behaviour in the field in French Guiana from 2008 to 2013. We closely studied two nests with automated camera systems and found a high level of cooperative behaviour among adults tending nests. Seven individuals were involved in bring prey to and guarding a nest in 2009. Our observations of caracaras nesting in bromeliads confirmed that the majority of their diet was comprised of the brood of social wasps, although they also brought millipedes and fruits to the nest. The social behaviour of the caracaras included intense territorial behaviour, including specific vocalizations and displays in response to conspecifics or playback of caracara calls. Caracaras also attacked conspecific decoys, and we observed them attacking members of other groups on two occasions in 2011. The caracaras provided their chicks with nests of a diverse assortment of wasp genera, including Polybia, Pseudopolybia, Leipomeles, Apoica and Parachartergus, and the proportional abundance of these taxa is not congruent with published studies on generic abundances. In addition, while army ants had previously been considered top predators of social wasps, we calculated that the caracaras, as specialist predators, could rival or exceed army ants as a mortality factor for social wasps. It had been hypothesized that these caracaras rely on a powerful chemical repellent to protect themselves from the stings of their defensive prey, but we found no evidence of such a repellent. We used a video recording arena to observe caracara predation behaviour on nests of various species of Polybia. We observed that the caracaras are indeed stung by some species of wasps, but the caracaras mount high-speed aerial strikes against such nests, knocking them to the ground or striking them repeatedly until the adult wasps depart in an absconding swarm. The caracaras exploit this absconding response when attacking highly defensive wasp species in order to minimize stings while obtaining the wasp brood.

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

Size-based insight into the structure and function of reef fish communities

Author: 
Date created: 
2014-07-15
Abstract: 

What would reef fish communities look like without humans? Effective ecosystem management and con- servation requires a clear understanding of community structure and the processes that drive it. Relatively undisturbed reef fish communities appear to be inverted biomass pyramids (IBPs) with greater biomass of large-bodied predatory fishes compared to smaller fishes at lower trophic-levels. However, the processes that might give rise to IBPs are subject to debate. In this thesis I show that biomass pyramids and size spectra are equivalent and interchangeable representations of community structure. Key constraints on the slopes of size spectra – particularly mean community predator-to-prey-mass ratio (PPMR) – also constrain the shapes of biomass pyramids, meaning that IBPs are unlikely for closed communities. There are surprisingly few quantitative descriptions of biomass pyramids, and PPMR has not been estimated on reefs. I undertook a detailed case-study and quantify fish community size-structure using underwater vi- sual surveys and empirically estimate PPMR using stable isotopes at a relatively undisturbed island chain in Haida Gwaii, BC. I observe an IBP, but the PPMR estimate suggests that the community should be a stack or bottom-heavy. There is 4-5 times more biomass at the largest body-sizes than would be expected given observed PPMR. I hypothesise that the most plausible explanation is energetic subsidies. Using the same fish assemblage I show how two foundational components of habitat complexity (substrate rugosity and kelp canopy characteristics) shape fish community size-structure. Higher kelp canopy cover and den- sity leads to more biomass across all size classes, whereas higher substrate rugosity boosts the biomass of smaller-bodied fishes and leads to a more even distribution of biomass across size classes. Finally, I step back to the global scale and estimate baseline biomass spectra for the world’s reef fishes, accounting for local ecological variation. Current reef fish biomass is less than half of the baseline expectation and 90% of the largest (> 1 kg), most functionally-important, individuals are absent. In addition to providing the first global description of how humans have shaped reef biomass pyramids, my thesis gives new insight into how size-based processes underlie the structure and function reef fish communities.

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

Why did the Carabid Cross the Fence?

Author: 
Date created: 
2014-08-14
Abstract: 

Physical barriers and biological control can be used to manage pests, but they have the potential to interfere with each other’s effectiveness. Exclusion fencing, which targets Delia radicum, could also create a barrier for poor-flying carabid beetles, polyphagous predators, from entering Brassica fields. I performed field and laboratory experiments to determine the permeability of exclusion fencing to the carabids Pterostichus melanarius and Bembidion lampros. The results show that the fence is permeable to both species, that as mesh size decreases, fence permeability decreases for B. lampros, and that B. lampros accumulates at the fence. A simulation model and cost-benefit analysis combined the results from the experiments with parameters from the literature to explore how carabids move across a field when a fence is present, and the fence’s cost to growers. Combining exclusion fence use with carabids and conservation biological control does not interfere with either tool’s effectiveness in controlling D. radicum.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bernard Roitberg
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.P.M.

Comparative and Genetic Approaches to Placental Evolution and Disease

Date created: 
2014-07-14
Abstract: 

The placenta is an important locus of theory and empirical research in mammalian evolution, physiology, health and disease. Novel comparative approaches to the study of placentation hold great promise in bridging the gap between applied placental research and evolutionary theoretical biology, potentially providing insights into intractable medical conditions affecting the placenta in human beings. This thesis describes genetic and comparative approaches designed for the study of placentation, but which will also prove broadly useful in research at the intersection of human health and evolutionary biology. The thesis begins with a comprehensive investigation into the historical course of evolution of the eutherian placenta, with special focus on identifying the polarity of transformation of interhemal relations, fetal-maternal interdigitation and shape. A range of statistical approaches appear to concur on an early origin of invasive, hemochorial placentation and the existence of repeated independent transitions toward less invasive forms. Tests for positive selection, and assessment of positively selected genes for substitutions of major phenotypic effect, are used to identify genes involved in the evolution of spiral arteries at the origin of the great apes and in the evolution of reduced placental invasion in three independent branches of the euarchontogliran phylogeny. It is shown to be possible to prioritize such genes for investigation into their involvement in diseases of placental vasculature including preeclampsia. The thesis continues with elaboration and discussion of statistical models for the evolution of biological traits that are known to deviate from the neutral, gradualistic assumptions of standard approaches - such as independent contrasts and phylogenetic generalized least squares - that are based on a Brownian motion model of evolutionary change. First, I discuss the use of stable models of continuous character evolution and provide a methodology for estimating ancestral states and characterizing the evolutionary process operating on traits exhibiting occasional rapid bursts of change. Second, I discuss the incorporation of directional tendency into phylogenetically independent contrasts. Simulation studies and application to real biological datasets suggest that such methods may be superior under conditions that deviate markedly from Brownian motion.

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

Development of an in vivo plant-based screen for identifying pharmacological chaperones for treatment of human lysosomal storage diseases

Date created: 
2014-07-08
Abstract: 

Small-molecule- enzyme enhancement therapy has emerged as an attractive approach for the treatment of lysosomal storage diseases (LSDs), a broad group of genetic diseases caused by mutations in genes encoding lysosomal enzymes or proteins required for lysosomal function. Missense mutant lysosomal enzymes normally subjected to rapid disposal by ER-associated degradation (ERAD) can be stabilized by small molecule chaperones that increase residual enzyme activity largely by increasing the transport and maturation of the mutant enzyme. Mucopolysaccharidosis I (MPS I) and Gaucher disease were my research targets – two LSDs caused by a deficiency of alpha-L-iduronidase (IDUA) and β-glucocerebrosidase (GCase), respectively. My goals were two-fold: (1) To determine the proteostasis of a severely defective mutant lysosomal enzyme in plant cells. (2) To develop a plant-cell-based screening system to identify putative LSD therapeutics. For the former goal, post-ER trafficking of the severely malfolded L444P GCase protein, and some aspects of cellular homeostasis, were restored to different degrees by ERAD inhibitors and proteostasis regulators, which increased the steady-state levels of the mutant protein inside the plant cells and rescued a proportion of protein from proteolysis. For goal 2, I developed a plant-cell-screening tool for identifying putative small molecule therapeutics based on selecting for library molecules capable of enhancing the post-ER transport of missense mutant lysosomal enzymes. Since the recombinant variants were equipped with a signal peptide, and the expression cells - transgenic tobacco BY2 cells - possess no lysosomes, the assay was based on increased lysosomal enzyme activity in the secretion media. I first established the proof-of-principle for the assay (i.e. its selectivity and specificity) based on recombinant N370S GCase, and two characterized chaperones - ambroxol and N-(n-nonyl) deoxynojirimycin. Two IDUA mutant proteins that underlie MPS I disease (P533R- and R383H- IDUA), formed the basis of the plant-cell-based assay that was used to screen a library of 1,040 Food and Drug Administration-approved drugs. Downstream validation of the hits identified in the primary screening by secretion and heat denaturation assays resulted in the identification of a potential candidate molecule (‘X-372’) for P533R IDUA. Further development of this molecule may yield a therapeutic for MPS I disease.

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