Honours Theses/Papers

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A comparison of drought tolerance in two conifers with contrasting mycorrhizal associations
(2023) Robson, Bethany
Drought events are increasing in frequency, severity, and distribution as a result of climate change. Plants have a variety of adaptations to water stress, including symbioses with mycorrhizal fungi. Little is known about how the type of mycorrhizae (arbuscular or ecto-) may affect drought tolerance, especially in conifers that are restricted in what association they can make. Research suggests that there may be an effect of mycorrhizal type on drought tolerance, and that mechanisms for this may be different in arbuscular and ecto- mycorrhizae. The objective of this study was to determine how the type of mycorrhizae may affect drought tolerance in Pinus contorta and Thuja plicata, species that make contrasting mycorrhizal associations. Three experiments were performed using both aeroponics and traditional soil culture to explore the effects of mycorrhizal association on drought tolerance. P. contorta performed consistently better in all experiments when compared to two populations of T. plicata from different ecozones in British Columbia. Quantum yield declined linearly with increasing drought stress in both treatments with mycorrhizal colonization, and non-linearly in the treatment with no colonization. These trends were consistently shown across all seedling populations, which suggests that both types of mycorrhizal symbioses are important in the drought tolerance of these species. Further investigation is needed to determine how mycorrhizae may influence recovery after drought in these species, as well as the mechanisms mycorrhizae may use to improve drought tolerance in host plants like P. contorta and T. plicata.
A comparison of Saprolegnia parasitica gene expression in the presence and absence of a host
(2018) May, Emily
As the importance of aquaculture increases globally, determining the infection strategies of opportunistic fish pathogens like Saprolegnia parasitica grows increasingly vital. Saprolegnia parasitica, a hemibiotrophic oomycete, has an initial biotrophic stage in which it suppresses host defences to facilitate infection, but the molecular mechanisms behind this infection strategy are largely unknown. In this study, I tested the hypothesis that expression of two S. parasitica virulence genes differs in the presence and absence of a host. The studied genes were: SpHtp1, a putative RXLR-like effector gene and SPRG_13235, a potentially horizontally transferred disintegrin gene with no known oomycete analogs. To test my hypothesis, I exposed pure S. parasitica zoospore cultures either to water imbued with Salmo salar effluents or to sterile water; then, I extracted RNA from experimental samples and measured expression differences with polymerase chain reactions (PCR). I successfully used nested PCR with gene-specific primers to qualitatively analyze expression, but quantitative analyses with real-time PCR (qPCR) were unsuccessful. Based on qualitative analyses, I concluded that SPRG_13235 was expressed in low amounts in both host presence and host absence, implying that factors other than host presence mediate gene expression variance. I was unable to determine whether SpHtp1 expression varied. Future studies should consider both studied genes but should focus on SPRG_13235, which remains largely uncharacterized. Disintegrin proteins inhibit vital cell functions by blocking integrin ligand-binding domains, potentially making them vital for host infection. The SPRG_13235 primer sets designed in this study can be used to facilitate future research in this area and can also be used to effectively detect S. parasitica propagules in environmental samples.
A mouse model of Rett syndrome shows a cell-autonomous reduction of α4* nicotinic receptors in dopaminergic neurons of the substantia nigra pars compacta
(2018) Le Gratiet, Keyrian
Rett syndrome (RTT) is a neurodevelopmental disorder due to spontaneous mutations in a gene (MECP2) on the X chromosome. With the mutations typically found in the paternal germline, female RTT patient are more common than males and manifest a constellation of severely debilitating symptoms after birth. Development is mostly normal during the first 6 months but then stalls and regresses resulting in individuals that lack motor coordination, have impaired speech, and exhibit Parkinsonian symptoms often accompanied by seizures. Mice with the same mutation have many neuronal dysfunctions including poor neural communication, some of which is due to improper signaling by the transmitter acetylcholine (ACh). The cholinergic system is critically involved in the generation of purposeful behaviours including voluntary motor acts, which correlate with some of the conditions seen in RTT patients. The present study investigated whether mutant (Mecp2-) dopaminergic (DAergic) cells have downregulated α4-containing (α4*) nicotinic acetylcholine receptor (nAChRs) expression compared to wild-type (Wt) (Mecp2+) DAergic cells in the substantia nigra pars compacta (SNc) of a RTT female mouse and whether this downregulation was cell-autonomous. Spectral confocal imaging was used to quantify the YFP-tagged α4* nAChRs in five-week-old Mecp2EGFP/+/ α4YFP/+, Mecp2+/- / α4YFP/+, and Mecp2+/+ / α4YFP/+ female mice. Imaging confirms that mutant DAergic neurons have reduced expression of α4* nAChRs compared to spatially colocalized Wt DAergic neurons in the SNc of a young RTT female mouse. Furthermore, the reduction in nAChR expression in DAergic neurons was found to be cellautonomous with Wt DAergic neurons from the RTT female and DAergic neurons from Wt females displaying similar amounts of α4* nAChRs on their soma. Finally, there was convincing evidence for spatially-modulated reduction in nAChR expression in mutant DAergic neurons with the lateral SNc showing a greater reduction in levels of nAChR expression compared to the medial SNc. To our knowledge, this is the first study to provide anatomical evidence for a cellautonomous downregulation of α4* nAChR expression in DAergic neurons in the SNc of a young RTT female mouse.
A novel 3D bioprinted model of Alzheimer's disease using patient derived hiPSC derived neurons in a fibrin-based hydrogel bioink
(2021) Walters-Shumka, Jonathan
Alzheimer's Disease (AD) is an age-related neurodegenerative disease that does not yet have any disease modifying treatments. Because there is a high cost associated with the disease and because the prevalence of AD is increasing, the need for new drugs to treat AD is high. Many drugs have passed pre-clinical trials only to fail in clinical trials. Most of the pre-clinical trials have been conducted on 2D monolayer cell culture and animal models. The failure of these drugs in clinical trials indicates that these two kinds of models do not accurately model AD. A 3D bio printed hydrogel model of AD which uses familial AD (fAD) patient derived human induced pluripotent stem cells (hiPSCs) can provide a more accurate model. Here we describe the first steps in creating a novel 3D bio printed model of AD using hiPSCs derived from a patient with a fAD mutation on the APP gene and a healthy control hiPSCs line. We 3D printed ring-shaped constructs 8mm high and 1cm wide containing fAD and healthy patient derived hiPSC derived neural progenitor cells (NPC's). The 3D printed constructs were then differentiated for 45 days in a cortical neuron differentiation medium. We have shown that both the AD and healthy cell lines are able to produce neurite extensions and stain positive for the early neuronal cytoskeleton marker ß tubulin III in our bioink. This indicates that the cells have successfully differentiated into neurons within our bioink. We have also observed axonal boutons, and dendritic spines on both cell lines and an axonal swelling on an AD neuron which is associated with early AD pathology. These findings confirm past work that healthy and diseased patient derived hiPSC derived neurons can be differentiated in hydrogel scaffolds. This is however, the first time this has been done in 3D printed hydrogel scaffolds. This is also the first time that dendritic spines and axonal swellings have been observed in a 3D hydrogel model of AD.
A survey of meiofaunal communities in beaches of Victoria, B.C.
(2021) Dundas, Amanda
Meiofauna are an understudied category of beach biodiversity worldwide, even though they are highly abundant. Factors that control the distribution of meiofauna, such as those related to sediment characteristics, are unclear. This study aimed to categorize the abundance and taxonomical diversity of meiofauna, the median grain size (Q50), the sediment sorting coefficient (Q25/Q75), and the organic matter content at 18 beaches in Victoria, B.C. It also investigated if those characteristics differed between two beach types, muddy and sandy, and whether meiofauna abundance was correlated with sediment characteristics. To test the hypothesis that meiofauna would be more highly abundant in fine sediment beaches (mudflats) than in coarse sediment beaches (sandy beaches), nine mudflats and nine sandy beaches were chosen based on visual inspection of the sediment. Then, sediment cores and meiofauna samples were taken at each of the 18 different beaches. Sediment size was determined using sieving, and organic matter of the sediment was quantified using loss on ignition. Meiofauna were enumerated and quantified using microscopy. The data were analyzed using two-sided t-tests and regression analyses. Meiofauna were found to be extremely abundant (on average 835 animals per 15cc of sediment) across all sample beaches. Median sediment size and sediment sorting (heterogeneity) did not vary significantly between muddy and sandy beaches, although the overall trends were in line with the prediction that muddier beaches had lower median particle size and higher sediment heterogeneity than sandy beaches. Organic matter was significantly higher in mudflats compared to sandy beaches. Meiofaunal abundance and total number of taxa were not significantly different among the beach types, and were not correlated with sediment characteristics. Based on my study I make several recommendations for future sampling programs. More research, especially time-series data collection, is needed to understand variation in these communities, as it is difficult to observe patterns from a single time point. My results illustrate how vast meiofaunal communities are (millions per square meter), yet how little we understand them. As the world changes, it is important to understand all aspects of beach biodiversity, and these tiny animals account for most of the non-microbiotic portion of it.
A Time for Recollection: Exploring the Temporality of Victoria’s Sea-To-Sea Green Blue Belt Campaign
(2024) Lefort, Audrey
The rapid growth of our Earth's population has increased the demand for development and urban sprawl, consequently endangering the protection of the natural world. To ensure the future of functioning ecosystems, recreational spaces, and agricultural land, many have turned to green belts as planning strategies. Specific to Vancouver Island in British Columbia, Canada, the collaboration between different organizations, community members, and levels of government successfully protected the lands connecting Tod Inlet, Sooke Basin and Sooke River. This Sea-to-Sea Green Blue Belt is the subject of this research, and semi-structured interviews, modified photovoice activities, and secondary data were used to understand the timeline and temporal experiences of nine participants who were actively involved from 1988 to the early 2000s. The article explains that the campaign was catalyzed by an algae bloom in the drinking water which led to a court case against the Greater Victoria Water District’s (GVWD) illegal logging activities in 1994, and the eventual creation of the Sooke Hills Wilderness Regional Park in 1997. This was followed by a 2000 Regional Park Acquisition Fund used to secure private lands for the green belt, which has resulted in the acquisition of over 4,900 hectares of parkland as of 2024. In addition, the anthropological theoretical frameworks of future orientation and social ecology revealed that participants’ identity influenced how their expectations, anticipation, and hope propelled the Sea-to-Sea Green Blue Belt campaign towards success, but that they now rely on speculation to envision the future of global environmental protection. This research contributes to current green belt academic literature by providing a deeper look into the human experience of advocating for this green infrastructure.
A trait-based assessment of the functional diversity of marine Cetacea in the Canadian Offshore Pacific Bioregion
(2025) Tuck, Matthew
The identification of biodiversity hotspots is a critical step in the protection and conservation of wildlife, and the ecosystems they depend upon. Recently, the identification of numerous highly diverse benthic seafloor and seamount habitats in the Canadian Offshore Pacific Bioregion (OPB) has prompted the establishment of large marine protected areas (MPAs) which target the protection of these sensitive benthic habitats. This region has high productivity due to eddy associated upwelling of nutrients, and contains numerous unique environments, including the continental slope, cold water seamounts, hydrothermal vents, and the open ocean. Elevated productivity supports a number of Cetacea species, which take advantage of seasonal windows of productivity. Cetaceans provide ecological functions related to nutrient transfer (e.g., the whale pump), food web processes (e.g, suppression of lower trophic levels), and the creation of unique seafloor habitats (i.e., whale falls). Despite the functional importance of these species, present conservation measures in the OPB and its associated MPAs do not legislate protections targeting the surface waters Cetacea species depend on. Here, I assess whether the OPB hosts a functionally diverse subset of the global marine Cetacea species pool through comparative analyses based on the global functional space of Cetacea spp., using seven traits related to species roles in food web processes and nutrient cycling. I also identify unique features of the species found in the OPB by comparing their trait distribution to the global Cetacea species pool. The OPB hosts 28% of the known marine Cetacea species but encompasses 70% of the global marine cetacean functional space. The functional dispersion and functional redundancy of the OPB mirrors values obtained from randomly subsampling the global species pool, indicating that the region is a representative sample of functional diversity present in the global species pool. Species using the OPB are distinguished by increased body sizes, likely due to the increased richness of large-bodied, baleen feeding Mysticeti species. The functional roles of large bodied species are fundamental for ecosystem health and stability, but are being eroded around the world as human activities continue to down-size the populations of the largest megafauna on Earth. Thus, the OPB is critical for protecting a high proportion of the global cetacean functional diversity, and the ecological roles of large cetaceans.
Adorning the Dead A Bio-Archaeological Analysis of Ochre Application to Gravettian Burials
(2017-02-20) McKinney, Sierra
“Am I Japanese? Am I Nikkei?” An exploration of the identities of Yonsei and Gosei Japanese Canadians
(2024) Nagasaki, Djuna
In February 2024, I received a conspicuous text message from my grandmother asking me to call her as soon as possible. “You will not believe what I found,” she exclaimed as I picked up the phone. It was a postcard from my great-grandfather, John Nobuo Nagasaki, sent to my grandparents in 1974, almost 50 years prior. My great-grandfather was born in Vancouver on the 22nd of April, 1922. He was Canadian-born. However, he was also of Japanese descent and, despite never setting foot in Japan, was still considered ‘alien’ on so-called ‘Canadian’ soil. In 1942, when John Nobuo was 20 years old, he and his family were forcibly uprooted from the West Coast along with thousands of other Japanese Canadians and incarcerated in internment camps. Their family home in Vancouver was dispossessed and lost to them forever. In 1974, John Nobuo visited Vancouver for the first time since his uprooting, a trip during which he wrote this postcard. As my grandma read it out loud over the phone, I felt my heart beat erratically in my chest. This postcard is the only piece of writing I have ever found from my great-grandfather, a figure in my ancestry who is somewhat of a mystery while simultaneously holding so much influence over my life and identity. The postcard read: “Hi, It sure has changed a lot here. I am getting lost every time I go out, But it sure is beautiful, and has it ever grown. Our old home is still here, and it’s the nicest on the block (remodeled). See you all soon, Dad.” I felt chills. “It’s practically a family artifact,” my grandmother went on, “look at how he calls it a home and not a house…really shows how they lost so much more than just a house, so much more than just things.” I felt tears well up in my eyes. This postcard offered a rare connection to the past, a short missive which briefly outlined the emotion behind what my great-grandfather went through in the 1940s. Today, my family is mixed, assimilated, and disconnected, a broad tapestry of trauma trickling down through the generations. In reading this short postcard, I form a relationship with my heritage and the intergenerational trauma within my family, coming closer to understanding what it means for me to be Japanese Canadian, what it means to be a descendant of internment.
Ammonium, nitrate, and proton flux in fern gametophytes
(2024) Creasy, Em
Total net NH4+, NO3-, and H+ fluxes were investigated in three species of fern gametophytes: Polystichum munitum, Christella dentata, and Cyrtonium falcatum. Flux measurements were performed with a microelectrode ion flux measurement (MIFE) system. Overall, net NH4+ influx was seen in all gametophytes. Net NO3- efflux and net H+ influx was seen in most gametophytes. The gametophyte generation of C. dentata and C. falcatum displayed greater NO3- efflux than the sporophyte generation. On average, male P. munitum gametophytes displayed greater per-unit-area NH4+ uptake than female/hermaphrodite gametophytes, though the latter showed greater NH4+ uptake at the whole-organism level. This finding suggests that fern gametophytes may conform to the expectations of nutrient-based sex determination. This study was the first to perform precise ion flux measurements at discrete positions on fern gametophytes and sporophytes. This research provides greater insight into the nutrient ecology of fern gametophytes, an under-studied field.
Analysis of synaptic plasticity events concerning the endocannabinoid system in the young adolescent (YA) rat media perforant pathway (MPP) following repetitive mild traumatic brain injury (r-mTBI)
(2025) Zejnulahovic, Emir
Traumatic brain injury (TBI) is a widespread health issue, with mild TBIs (mTBI) making up to 85% of cases, often underdiagnosed due to subtle symptoms. Young adolescents are most at risk for repetitive mTBI (r-mTBI), which compounds mTBI symptoms and outcomes. These injuries can impair synaptic plasticity, including short-term potentiation (STP) and long-term potentiation (LTP), both crucial for cognition. Acute neuronal damage and chronic apoptosis underlie these deficits, especially in the dentate gyrus (DG) and its medial/lateral perforant pathways (MPP/LPP) substructures, whose electrical inputs are essential for adult neurogenesis. Cannabinoid one receptors (CB1Rs) and Transient Receptor Vanilloid Protein 1 (TRPV1), part of the endocannabinoid system (EC), regulate synaptic plasticity in MPP/LPP due to the high concentrations each receptor has in the DG. Altered EC signaling in mTBI models contributes to excitotoxicity. Pharmacological tools for targeting CB1Rs (AM251) and TRPV1 (AMG9810) reveal the receptor’s effects indirectly before and after r-mTBI. 53 Sprague Dawley rats were used for recordings, with ninety-nine slices used. Animals were split across six groups (Sham/r-mTBI controls, plus corresponding drug groups). Sham/r-mTBI controls only showed differences in LTP induction, with mechanistic properties of the synapse appearing unchanged via paired pulse and short-term potentiation (STP) recordings. Both AMG9180 and AM251 restored LTP deficits seen between Sham/r-mTBI controls, while TRPV1 also significantly enhanced STP levels, and removed paired-pulse facilitation effects seen in Shams. This suggests that both receptors can be pharmacologically manipulated to aid in synaptic plasticity deficits following r-mTBI, as well as suggesting that both receptors are downregulated following r-mTBI.
Analysis of the female reproductive secretions of Cycas revoluta
(2019) Morrison, Nora S.
Gymnosperms produce sexual fluids for reproduction. Cycads ovules produce both pollination drops and a fluid from their megagametophytes. The latter pools in the archegonial chamber and mediates fertilization. Megagametophyte fluid from Cycas revoluta was analyzed by various techniques and, where suitable, was compared to the pollination drop of Taxus x media, yew, a commonly analyzed gymnosperm ovule secretion. Osmolarity was found to be 672 ± 66 mOsm from four individual plants, which was similar to the osmolarity of yew pollination drops. Of the 661 proteins revealed by mass spectrometry using an Orbitrap Fusion, 372 were of plant origin, and 220 were of bacterial origin. These results differ from yew in that the proteins in Cycas are almost entirely degradome, as opposed to Taxus in which are almost entirely secretome. The presence of bacteria in cycads suggests that the reproductive system of Cycas revoluta is not a closed system. In Cycas revoluta, the fluid that causes pollen tubes to burst and provides a medium in which sperm can swim has solutes that are released by the megagametophyte, indicating that the female controls major events prior and during fertilization.
Anatomical and ultrastructural characterization of the frog accessory olfactory bulb and vomeronasal nerve
(University of Victoria, 2026) Merx, Xander
The accessory olfactory bulb (AOB) serves as the central relay for vomeronasal chemosensory information and has been implicated in activity-dependent synaptic plasticity in frogs. Activity-dependent enhancement (ADE), observed at the vomeronasal nerve (VNN)–mitral cell synapse, has been described in Rana pipiens and hypothesized to involve neuropeptide co-release from dense-core vesicle (DCV)-containing afferent terminals. Bimodal compound action potential recordings from the Lithobates catesbeiana VNN suggest the presence of two morphologically distinct axon populations. The present study employed light microscopy, transmission electron microscopy (TEM), and horseradish peroxidase (HRP) anterograde tracing to characterize the anatomy and ultrastructure of the AOB and VNN in adult L. catesbeiana. Light microscopy revealed a laminated AOB with glomerular and mitral cell layers; a notably sparse periglomerular cell population was identified, consistent with the frog AOB being less elaborated than its mammalian counterpart. TEM of the glomerular neuropil identified likely dendrodendritic synapses and gap junctions, features documented in the mammalian olfactory bulb but not previously reported in the frog AOB. Large vesicular profiles with electron-dense cores were observed in HRP-DAB labeled VNN afferent terminals; however, the evidence is insufficient to confirm the presence of dense-core vesicles, and these observations do not provide anatomical support for the neuropeptide co-release hypothesis. Quantitative axon diameter analysis identified two morphologically distinct fascicle types: Type A fascicles with a unimodal small-axon distribution and Type B fascicles with a bimodal distribution with a sparse large-profile subpopulation, consistent with the bimodal CAP profile. These structural observations support ongoing functional investigations and warrant further study using biochemical and volumetric imaging approaches. Supervisor: Dr. Kerry Delaney
Application of the derivative and van der Kamp methods: Enhancing the interpretation of pumping tests for fractured bedrock aquifers on Vancouver Island, BC
(2025) Abel, Malakye
Interpreting pumping test responses for fractured bedrock aquifers is challenging, particularly when estimating the transmissivity of an aquifer and the long-term sustainable yield of a well. This study applies the derivative method (e.g., Renard et al., 2009) on the pumping and recovery phase of six pumping tests from bedrock wells on Vancouver Island and the Gulf Islands, sourced from local consultants, to characterize flow regimes to determine how transmissivity calculations can be improved. The van der Kamp method (van der Kamp, 1989) was also tested for its effectiveness in the extrapolation of pumping responses and its potential for improving the ability to estimate a sustainable pumping rate for a 100-day dry season (Q100) that is often prescribed when licencing a well. Two pumping tests studied were for fractured sedimentary bedrock aquifers while four were for fractured crystalline bedrock aquifers. The tests lasted 12-72 hours and were followed by recovery monitoring of a similar duration. The results showed that for the fractured sedimentary bedrock aquifers, linear flow may precede infinite-acting radial flow for several hundred minutes. For the tests that exhibited infinite-acting radial flow as the final derivative response, the duration was approximately 0.3 log cycles of time, cut off when pumping ended. Infinite-acting radial flow identified using the recovery phase derivative often matched the pumping phase derivative in symmetry, though was sometimes different in magnitude. Identifying periods of radial flow from the pumping and recovery phases facilitated the calculation of transmissivity using various analytical solutions. Transmissivity values calculated using the Theis curve-matching (Theis, 1935) and Cooper-Jacob (Cooper & Jacob, 1946) methods, from the same radial drawdown data, were similar (within 0.5 log transmissivity values). For three pumping tests, transmissivity values calculated from the symmetrical recovery phase using the Theis recovery method (Theis, 1935) were noticeably different (over 0.19 orders of magnitude smaller or larger) than those calculated from the pumping phase. The van der Kamp method did not work for all pumping tests analyzed. The extended drawdown calculated using the van der Kamp method for the same three tests exhibited various non-ideal responses. Two tests exhibited a rising static water level, where the water level in the well at the start of the pumping test was erroneously assumed to be not changing. An unaccounted-for rising static water level induces a drift in the drawdown and subsequent recovery data, causing a discrepancy in the transmissivity calculated from the pumping and recovery phase, evident by a difference in the magnitude of the pumping and recovery derivative plots. The third test may have been subject to dewatering or a falling static water level late in the recovery phase which caused a steepening of the extended drawdown. When the “static” water level is not static, the extended drawdown does not improve the extrapolation of the drawdown to 100 days, which is required when estimating Q100. When the static water level was stable, as for the three other pumping tests, it lent confidence to the extrapolation of drawdown to 100 days to calculate Q100, reducing the reliance on an empirical straight-line extrapolation of drawdown to 100 days. A rising static water level, if not identified before pumping, negatively affects Q100 estimates; especially for high-yield wells where the drawdown rate is slower and may be more sensitive to static water level shifts. The drawdown rate drifts do not as negatively alter transmissivity calculations because transmissivity values are log-normally distributed. Minor drifts in drawdown rate have less impact on the relative accuracy. To enhance test reliability and facilitate the application of the van der Kamp method, future tests should confirm a “static” water level before proceeding with testing. Additionally, to extract maximal utilization of the van der Kamp method and recovery derivative, the recovery phase should last at least as long as the pumping phase, rather than ending at 90% recovery as is currently recommended by the B.C. Ministry of Environment (MoE, n.d.). Supervisors: Mike Wei and Lucinda Leonard
Are there bacteria in the ovules of Cycas revoluta? An exploratory study
(2021) Antony, Madeline
The presence of bacteria in the ovules of Cycas revoluta was examined in three individuals and five tissues via DNA extraction and qPCR. The five tissues examined were: integument, apex of megagametophyte, interior of megagametophyte and chalazal end of the megagametophyte. The extraction process used a modified CTAB method. The average extraction concentrations were 5.13 ng/?L for the nucellus, 206.22 5.13 ng/?L for the apex of the megagametophyte, 83.15 ng/?L for interior, and 249.98 ng/ul for the chalazal end. The integument samples had an extraction average concentration of 190.3 ng/ul. qPCR was done using the Ncl-I, niH, 16S and Cycas LFY primers. Each tissue type displayed amplification products for LFY, and none of the tissue types displayed significant amplification for NCI or niH. The apex and interior sections of the megagametophyte were the only two tissues to display 16S amplification. It was concluded that there were unidentified bacteria in the apex and interior sections of the megagametophyte of Cycas revoluta ovules.
Assaying the role of complement factor D on retinal pigment epithelial cell pathology in a mouse model of Stargardt disease
(2024) Xie, Xiaoya
Stargardt disease (STGD) is a macular dystrophy caused by mutations in ABCA4. ABCA4 loss-of-function leads to the accumulation of bisretinoids, known as lipofuscin, in the retinal pigment epithelial (RPE) cells in the retina. When photoxidized, lipofuscin can become toxic and cause RPE cell damage as well as activating the complement system of innate immunity. Complement factor D (CFD) is necessary for activating a branch of the complement system called the alternative pathway (AP) and is hypothesized to compromise normal RPE homeostasis which in turns promotes RPE lipofuscin accumulation and photoreceptor degeneration in Stargardt disease. This study examined the process of lipofuscin accumulation over time and how the loss of CFD affects STGD development in 6-month and 12-month Abca4-/- mice by quantifying (i) 488 nm RPE autofluorescence as a measure of the accumulation of lipofuscin in paraffin-embedded eye sections, and (ii) the immunofluorescence level of C3 (a critical protein in complement system activation) in the RPE. My results showed that the 488 nm autofluorescence level increased between 6-month and 12-month Abca4-/- mice, and between the 12-month Abca4-/- and the age-matched wildtype mice. However, the autofluorescence levels were unchanged among the 6-month experimental genotypes. The C3 immunofluorescence level in most of the 6-month experimental genotypes was unchanged. Due to the absence of the disease phenotype (i.e., elevated 488 nm autofluorescence) in the 6-month experimental samples, the role of CFD in STGD progression could not be assessed. Since the results of the autofluorescence assay on paraffin-embedded sections in this study are consistent with what has been observed by others in the Chow lab on flat-mounted RPE, cross-section tissue slides may be used as an alternative for examining the progression of STGD.
Assessing diet and nutritional value of small pelagic copepods through lipid analysis
(2021) Gair, Hana
Copepods, a major group of crustacean zooplankton, occupy a central role within marine food webs. Connecting primary producers to higher trophic levels and influencing global biogeochemical cycles, variations in community composition can have lasting impacts on the marine environment. Small marine copepods often greatly exceed the abundance of large-bodied copepods, yet historically they have been overlooked. As the ocean warms, conditions may favour an increasing abundance of smaller copepod species. Therefore, understanding the ecology of small-bodied copepods and their effect on the ecosystem is crucial for estimations of how climate change may affect the marine ecosystem. In June, July, August, and October 2020, copepod samples were collected at five on-shelf stations, two off-shelf stations, one oceanic station, and an intertidal beach along the west coast of Vancouver Island. Through lipid extraction and quantification, and visualization with multivariate non-metric multidimensional scaling, I observed differences in lipid classes and fatty acid profiles among large-bodied oceanic, small-bodied oceanic, and small-bodied intertidal copepod species. Small oceanic copepods all had relatively similar total lipid masses but differed based on their storage lipid. While Aetideus divergens, Pseudocalanus minutus, Pseudocalanus mimus, and Clausocalanus lividus stored wax esters similarly to the large-bodied copepod species, Acartia longiremis and Mesocalanus tenuicornis both stored triacylglycerols, which are associated with more active year-round life cycles and higher metabolic rates. Intertidal copepod Tigriopus californicus had the lowest total lipid mass. Three significantly distinct feeding strategies were observed among species, with the large-bodied copepod species grouping together, and the small-bodied copepod species diverging into two groups that corresponded to the storage lipid distinctions. Almost all small copepod species were observed to have higher proportions of bacterial fatty acid markers than did the large-bodied copepods, indicating they are more connected to the microbial loop than the omnivorous-herbivorous large-bodied copepods. My research contributes to our understanding of the ecology and life strategies of these small-bodied copepod species, and also provides some of the first lipid analysis for certain species.
Assessing mechanotactic axon pathfinding in induced pluripotent stem cell-derived motor neurons
(2019) Hui, James
In the central nervous system, upper motor neurons and lower motor neurons, alongside spinal cord interneurons, coordinate all muscle contractions within the body. Axon guidance is a crucial process to the development of functional neuronal networks, as well as regeneration of proper neuronal function for treatment of neurological diseases. Biomedical engineering of scaffolds that promote the axon guidance and proper rewiring of neurons is an area being actively studied by many researchers. In this project, the effect of mechanical strength of fibrin-based hydrogel on the growth of spinal motor neuron axons is studied using a gradient fibrin hydrogel assay, combined with light microscopy and mathematical analysis of acquired images. The motor neurons showed no significant preference for softer or stiffer substrate.
Assessing the effect of long-term formalin preservation on zooplankton biovolume estimates
(2023) Fung, Nicole
Energy and carbon transfer from phytoplankton to fish is regulated by zooplankton in marine systems, acting as a link to higher trophic levels and exporting carbon to deeper waters. To determine the relative magnitude of these processes, the biomass and biometrics of zooplankton are often studied. Biomass is generally estimated based on wet mass, dry mass, or carbon mass; however these methods involve a destructive method, ceasing possibilities of future analysis of samples. The alternative method of estimating biomass via measuring biovolume (BV) through image-analysis provides a permanent electronic record of samples. Though an issue with this method is shrinkage observed in formalin-preserved zooplankton, which would provide an underestimated biomass. Therefore, this study investigates the response of different zooplankton taxa when preserved in formalin to determine taxa-specific conversion factors that can provide the means for more accurate biomass estimates. By tracking biovolume changes of different taxa over a two-month period and comparing percent biovolume of taxa in their fresh and preserved state, it was determined that taxa shrink at different rates and by different amounts. Copepods (and specifically Eucalanus sp.), decapod megalops, euphausiids, small hyperiids (BV < 60 mm3), and gastropod veliger larvae had statistically significant differences in the fresh and preserved percent biovolume. Additionally, the acquired conversion factors for several taxa can now be used to correct for the underestimated biovolumes obtained through image-analysis, as a proxy for biomass. This highlights the bias in estimates from previous applications that have investigated ecosystem energy flow or determined how biomass changes in differing oceanographic conditions. While this method has advantages, it is limited to a coarser taxonomic resolution of samples than what could be accomplished with microscopic analysis. Future work could include more taxa to obtain more conversion factors and higher sample size of taxa for more accurate conversion factors.
Calabindin and channelrhodopsin-2 expression in the dopaminergic SNC and VTA of DAT-CRE
(2023) Waller, Olivia
The DAT-Cre::ChR2-EYFP mouse model has recently emerged as a useful tool to investigate the function of the dopaminergic (DA) system, which is known to be involved in motor behaviour, motivation and reward, memory, and cognition. This is accomplished through selective expression of channelrhodopsin-2 (ChR2), a blue light-activated cation channel, in DA neurons. DA neurons that express calbindin (Calb), a calcium-binding protein, make up a discrete subpopulation with unique functional characteristics. Functional and physiological heterogeneity between the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) has been well documented, and past research conducted by the Nashmi lab has observed physiological heterogeneity between DA neurons along the mediolateral axis of the SNc itself. Therefore, there may be potential for Calb to act as a marker for distinct physiological cell phenotypes. Here, we evaluate the DAT-Cre::ChR2-EYFP model’s efficiency in expressing ChR2 within DA neurons and characterize the colocalization of Calb in DA neurons within the VTA and along the mediolateral axis of the SNc. We used confocal fluorescence microscopy of DAT-Cre::ChR2-EYFP brains and quantified tyrosine hydroxylase (TH), ChR2, and Calb expression within regions of interest. No significant difference in Calb colocalization in DA neurons was found between the medial and lateral SNc, although a large difference was observed between the SNc and VTA. We also report a that the DAT-Cre::ChR2-EYFP mouse model is extremely efficient in expressing ChR2 in DA neurons of the midbrain.

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