Biology

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This is the collection for the University of Waterloo's Department of Biology.

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Examining the Effects of Traits on Early-Establishment Tree Communities Under Different Soil Water Conditions
(University of Waterloo, 2025-11-12) Galarneau, Magalie
Studies have demonstrated the existence of a positive relationship between species richness and productivity in forests around the world. This positive relationship is thought to be explained by two mechanisms: complementarity effects and selection effects. Both mechanisms rely on species’ traits, whereby the diversity of traits (under complementarity effects) or the presence of specific trait values (under selection effects) can increase productivity. However, while it has been clearly established that species richness increases productivity, few studies have tested the implicit assumption that traits underpin the established species richness-productivity relationship. To address this gap, this study examined which traits are responsible for the species-productivity relationship in temperate tree communities during the early stages of stand development, and whether they act via complementarity effects or selection effects. In addition, this study aims to determine how the observed relationship and its underlying traits change in environments with different water availabilities by assessing which traits are associated with productivity in each environment. These questions were answered using an experimental plantation of temperate tree communities in the early stages of stand development, in which water exclusion treatments were implemented. Six temperate tree species were planted in this experiment, either in a monoculture or in a three-species mixed community. To separate the effects of species and trait diversity, the mixed tree communities had a fixed species richness but varied in trait diversity. The species compositions of the mixes were selected to create a trait diversity gradient. Leaf area, leaf mass per area, stomatal density, chlorophyll concentration, specific root length, root tissue density, and root diameter were measured in each community. Community productivity was measured both as aboveground biomass and as belowground biomass. The most consistent pattern of selection in the press treatment was for leaf area, as it was under selection in combination with leaf mass per area and with stomatal density. Pairs of traits including specific root length were also under selection in the pulse and the control treatments. Selection for these traits resulted in three to fivefold increases in aboveground biomass. These results demonstrate that selection effects are the driving force of community productivity during stand establishment. Here, selection acted upon traits related to tree architecture, thermoregulation, photosynthetic rate, and water use, which illustrate the mechanisms by which selection effects drive increases in the productivity of early-establishment communities across varying soil water conditions.
Stream periphyton response to phosphorus loading events is constrained by antecedent conditions
(University of Waterloo, 2025-11-06) Schneider, Natalie
Phosphorus (P) loadings to streams often occur in short duration events associated with runoff from human activities. Although it has been shown that stream periphyton can uptake and assimilate event-based P, the role of antecedent P concentrations in modulating P uptake from event-based loadings and resulting effects on periphyton structure and function is not known. To assess effects of antecedent P concentration on stream periphyton response to short-term P loading events, we completed two 26-day artificial stream experiments at the Thames River Experimental Stream Sciences (TRESS) Centre in London, Canada. Experiments consisted of exposing periphyton communities in nine artificial streams to a range of 48-hour P loading event concentrations (15 to 690 μg P/L) under low (10 μg P/L) or high (50 μg P/L) antecedent P concentrations. Periphyton was sampled one day before, one day after and 10 days after P loading events to quantify periphyton structure (ash free dry mass (AFDM), chlorophyll a (chl a), P content) and function (P uptake, benthic metabolism, cellulose decomposition, biomass growth, chl a accumulation). Under low antecedent P conditions one day after the P event, P content and P uptake had a positive linear relationship with event concentration and this was similarly seen in biomass and chl a ten days after the P event. One day after the P event in high antecedent streams, P content and P uptake showed a positive linear response with P event concentration, but this additional P in periphyton did not lead to increases in biomass and chl a. Whereas, a negative linear relationship with event concentration and P uptake was seen ten days after the P event. Measures of periphyton function (benthic metabolism and cellulose decomposition) were unaffected by P event size and regardless of the antecedent condition. These findings suggest that high antecedent P concentrations caused cellular saturation of periphyton limiting the assimilation of P from event-based P loads. Therefore, streams with high antecedent P may deliver reduced water purification benefits with regards to attenuating P transport to downstream ecosystems at risk of eutrophication. Management actions to reduce antecedent P concentrations will be needed to rehabilitate ecosystem service provision in streams chronically enriched in P.
Microbial Diversity and Potential for Biogeochemical Cycling in Heavy Metal Contaminated Environments
(University of Waterloo, 2025-09-18) Chen, Xiang
Heavy metal contamination arising from resource extraction and wastes poses a threat to natural ecosystems and public health. Microorganisms influence the mobility and toxicity of metals through various resistance mechanisms and metabolic pathways. This thesis investigates microbial diversity and functional capacity across multiple metal-contaminated systems, integrating environmental sequencing data with experimental observations. The overall objective was to better understand the microbial processes involved in metal cycling, focusing on As, Fe, Cu, Ni, and Pd. Using 16S rRNA amplicon and metagenomic sequencing, I profiled microbial communities from aquifers associated with thermally mobilized arsenic, as well as from mine tailings derived from nickel/copper ores. Sampling across a wide range of spatial and geochemical conditions revealed considerable variation in microbial taxonomic and functional diversity. Although community diversity correlated with many factors, including arsenic (in aquifers) and iron (in tailings) concentrations, metal concentrations alone were not predictive of the abundance and localization of specific populations. Metal resistance genes were widespread in all communities across sites and geochemical conditions, suggesting that metal tolerance is regulated at the gene expression level. In contrast, the distribution of taxa and genes associated with iron- and sulfur- cycling was more closely linked to environmental factors such as redox potential, pH, and/or temperature, where these variables were more selective for specific microbial guilds. Additional results from metaproteomic analyses of tailings samples complemented the metagenomics data by confirming the expression of predicted metal and sulfur-related genes. In both environments, ‘-omics’ approaches identified many uncultivated lineages with the potential for metal and sulfur redox transformations. Sulfate-reducing bacteria were predicted to be especially relevant in heavy metal remediation, due to their ability to precipitate dissolved metals as insoluble sulfides. Building on this insight, I experimentally evaluated the ability of a model sulfate-reducing bacterium, Oleidesulfovibrio alaskensis G20, to selectively recover metals from simulated mining waste. O. alaskensis G20 was shown to form nickel sulfide and palladium nanoparticles from mixed-metal solutions, demonstrating a viable method of biologically mediated metal recovery. Collectively, the research presented in this thesis advances our understanding of microbial diversity and biogeochemical cycling in heavy metal-contaminated environments, and highlights the potential to harness microbe-metal interactions for bioremediation and metal recovery technologies.
Impact of Temperature on the Antigen Presentation pathway in VHSV-infected Rainbow Trout (𝘖𝘯𝘤𝘰𝘳𝘩𝘺𝘯𝘤𝘩𝘶𝘴 𝘮𝘺𝘬𝘪𝘴𝘴)
(University of Waterloo, 2025-09-17) Wong Benito, Valentina Andrea
Sudden water temperature shifts are increasing in frequency and altering aquatic ecosystems, where small water bodies are especially vulnerable. These rapid temperature drops can severely impact fish immune system, and can also influence host-pathogen interactions, particularly during viral infections. Rainbow trout (Oncorhynchus mykiss) is economically important in aquaculture and is highly susceptible to disease outbreaks such as viral hemorrhagic septicemia virus (VHSV). A key process during antiviral immunity is the antigen presentation by the major histocompatibility complex class I receptor (MHC-I) and its chaperone β2- microglobulin (β2m). These proteins form a trimeric complex with viral peptides that can be presented to and recognized by CD8+ T cytotoxic cells, which activate adaptive immunity. Although transcriptional responses of antigen presentation molecules to low temperatures during VHSV infection have been reported, little is known about the folding and stability of MHC-I complexes, the antigen processing and presentation pathways, and T cell activation under thermal stress. This thesis investigates how suboptimal temperatures modulate the antigen presentation pathway in rainbow trout infected with VHSV, integrating bioinformatic analyses, in vitro refolding of the MHC-I complexes, in vitro cellular responses and T cell activation using a novel antigen presentation assay. Initially, the thermostability of the rainbow trout MHC-I UBA molecule complexed with β2m and VHSV-derived peptides was evaluated. Peptide candidates derived from VHSV nucleoprotein (Protein N), and glycoprotein (Protein G) were selected using a combination of bioinformatic tools and then, the predicted structure of the MHC-I/β2m/VHSV-peptide complex vi was analyzed using AlphaFold2. Temperature influenced the structural behavior of the MHC-I complexes according to a computational simulation program revealing potential molecular mechanisms of thermal stress on the antigen presentation pathway. To validate these in silico analysis, MHC-I and β2m recombinant proteins were successfully purified using E. coli expression systems, and in vitro refolding with the selected VHSV peptides was optimized. These results provided experimental evidence of rainbow trout MHC-I complexes refolding with VHSV peptides for the first time. Differential scanning fluorimetry confirmed that the stability of these complexes was sensitive to temperature and dependent on both peptide binding and biochemical characteristics. Continuing with the molecular characterization of this pathway, the functional effects of temperature on antigen processing, trafficking and presentation was assessed using a controlled in vitro system with VHSV-infected rainbow trout cell lines; RTGill-W1, RTS11, and RTGut-GC. These cells were infected and exposed to suboptimal temperatures, 4°C and 14°C, for nine days and, 20°C-exposed cells were used as control group . Flow cytometry analysis showed that the cell surface expression of MHC-I/β2m was reduced during infection at 14°C, compared to other temperatures. In addition, these results correlated with the release of β2m to the extracellular space. On the contrary, proteasomal activity and the secretion of the antiviral cytokine IFN-I were not impaired at suboptimal temperatures, highlighting the specificity of temperature-sensitive antigen presentation disruption. Finally, an antigen presentation assay using dorsal fin cells as antigen presenting cells was developed and validated to analyze the impact of temperature in antigen recognition and T cell activation. To perform this, primary fin cell cultures were exposed to heat-killed VHSV and co- vii cultured with VHSV-sensitized splenocytes. Cytotoxicity was evaluated with the release of lactate dehydrogenase (LDH), resulting in an antigen-specific and MHC-I-dependent cytotoxic response from the activated splenocytes. In addition, this cytotoxic response was negatively affected by lower temperatures, once again, supporting the idea that suboptimal temperatures impair the antigen presentation pathways at different levels during a viral infection in rainbow trout. Altogether, this thesis offers a comprehensive and integrated approach into understanding how temperature regulates antigen presentation during viral infections in rainbow trout. It highlights not only the thermal sensitivity of antigen presentation and viral antigen processing but also contributes to the immense knowledge gap about fish immunity. Importantly, these findings provide in silico and in vitro methodologies for studying antigen presentation and T cell cytotoxicity, with direct application for vaccine design and maintaining fish health, especially during thermal stress.
Development of a novel assay for the characterization of germination responses in microsporidian parasites: An investigation into the biology of Spraguea americanus
(University of Waterloo, 2025-09-17) Rogozynski, Noah
The microsporidia are a widespread group of intracellular parasites which infect a broad range of hosts across the animal kingdom. In particular, the microsporidian Spraguea americanus has received considerable attention in recent years due to its role as an endemic pathogen in American anglerfish (Lophius americanus); a species of highly valued finfish currently at risk due to overfishing. However, like many species of microsporidia, the germination responses of S. americanus remain poorly described. This study outlines a novel in vitro germination assay for microsporidia, which is then used to comprehensively survey the germination responses of S. americanus under a variety of conditions. The results of this investigation indicate that S. americanus is responsive to mechanical pressure, hydrogen peroxide, sodium carbonate/bicarbonate and divalent cations, but not to mucin proteins as seen in closely related species. These observations provide evidence to refute the predominant hypothesis that members of Spraguea enter their hosts via the subcutaneous mucosal glands. In addition to providing much needed insight into the transmission of Spraguea spp., this study is among the first to extensively assess the germination responses of a single species of microsporidia; data which may lend itself to a more complete understanding of the mechanisms underlying the initiation of germination in microsporidia or support the establishment of new in vitro models for economically relevant species.
Impact of phosphorus enrichment patterns on stream periphyton microbial communities
(University of Waterloo, 2025-09-17) Skrobonja, Anja
Delivery of excess nutrients, such as phosphorus (P), to nearby surface waters due to intensified agricultural and urban land use activities has resulted in the degradation of aquatic ecosystems such as lakes, coastal areas, and flowing waters. In stream ecosystems, excess P can influence the diversity and composition of periphyton communities. However, P enrichment can vary over time and in intensity according to the source of P and there is limited knowledge of the impacts of event-based loadings on the microbial community composition of stream periphyton. To address this knowledge gap, two related stream mesocosm experiments were conducted. The first objective of my research was to evaluate whether P delivery patterns that are commonly associated with human land use practices influence the microbial community composition of stream periphyton. I achieved this objective by conducting a 25-day mesocosm experiment using nine artificial streams subjected to one of three P enrichment loading patterns in triplicate: unenriched, continuously enriched, or event-based enriched. Periphyton samples were collected at six time points and underwent high throughput sequencing of 16S and 18S rRNA genes to profile prokaryotic and eukaryotic microbial assemblages. Results showed that microbial community composition could not be differentiated among enriched delivery patterns, indicating the P load magnitude was more important than the P loading pattern. Thus, management of P enrichment in streams should prioritize targeting the most efficient way to reduce P loads, regardless of source. The second research objective was to assess how stream periphyton microbial community composition responded along an increasing gradient of P event concentrations and test whether antecedent P availability influenced this response. Two artificial stream experiments were conducted under low or high antecedent P conditions, with each stream receiving one of nine different P event concentrations. Periphyton were collected one day before and 10 days after the event and high throughput sequencing of the 16S and 18S rRNA genes were used to characterize prokaryotic and eukaryotic members of stream periphyton communities. The results indicate that small levels of P enrichment from P events can lead to a common enriched stream periphyton community. Thus, bioassessments of periphytic communities in anthropogenic landscapes may underestimate the extent of enrichment in streams with high baseflow P concentrations.
Hydrological responses of critical aquatic habitat in Wood Buffalo National Park for the world’s only naturally reproducing migratory population of whooping crane to past climate variation
(University of Waterloo, 2025-09-16) Anderson, Laura
The only wild, self-sustaining population of endangered whooping crane (Grus americana) breeds within a remote, pond-rich, groundwater discharge region in and adjacent to Wood Buffalo National Park where there is concern for habitat degradation by climate change. Due to their small area and volume, shallow ponds respond rapidly to changes in climate and are vulnerable to desiccation, which can reduce breeding success by altering food availability and encounters with predators. Hydrological information is scant in this remote region, and longer time-series of data are needed to anticipate how shallow water breeding habitat will respond to future climate warming. Here, contemporary measurements (2022-2023) at three shallow ponds that range from weakly to strongly connected to groundwater are integrated with paleolimnological analyses, which span the past ~300-400 years and capture the cold, arid Little Ice Age and subsequent warming, to improve understanding of hydrological responses to climate variation. Correspondence of pond water ẟ18O inferred from sediment carbonate (carbonate-inferred ẟ18Opw) with contemporary measurements of pond water ẟ18O indicates that carbonate-inferred ẟ18Opw provides a reliable methodology to reconstruct past variation in pond water ẟ18O. Evidence suggests two of the three ponds desiccated during the mid- and late 1700s when the climate of the Little Ice Age was arid. At pond SK 31, where connectivity to groundwater is weak, carbonate-inferred ẟ18Opw increased during this interval and exceeded the contemporary estimate of the terminal basin steady-state isotope composition, indicating strongly negative water balance prevailed due to evaporation. Similar strong net evaporation and near-desiccation has been detected during the same time interval from a record of cellulose-inferred lake water δ18O at a shallow upland lake located ~175 km to the south (Wolfe et al., 2005), which provides confidence in the interpretations based on carbonate-inferred δ18Opw at SK 31. At pond SK 58, where connectivity to groundwater is strong but desiccation occurred in 2023 and 2024 likely by vertical seepage, the stratigraphic record of carbonate-inferred δ18Opw reveals no evidence of enrichment by evaporation during the mid- and late 1700s. A distinctive peak in C/N ratios in sediment deposited ~1790 suggests, however, that an apparently rare desiccation, or near-desiccation, event may have occurred by vertical seepage when SK 31 and PAD 5 also nearly desiccated by evaporation. Smaller C/N-ratio peaks in ~1908 and ~1998 may capture two other short-lived near-desiccation events at SK 58. Recent observed desiccation at SK 58 in 2023-2024 occurred when unusually arid climate conditions resulted in a decline in water level of 60 cm in Great Slave Lake to the lowest levels recorded by the 84-year-long record. At pond SK 26, low carbonate-inferred ẟ18Opw values throughout the ~280-year record provide no evidence of drawdown by evaporation and suggest there may have been shifting sources and discharge of groundwater, which may be indicative of the spatial and temporal variability of past hydrological conditions across this complex landscape. Overall, pond desiccation, including the recent drying of SK 58, appears to be a largely rare occurrence since 1800 but may become increasingly common with ongoing climate change.
Life history and migration patterns of Arctic Char (Salvelinus alpinus) and Dolly Varden (Salvelinus malma malma) in the Coppermine River and Coronation Gulf
(University of Waterloo, 2025-09-15) Smith, Rosie
Arctic Char (Salvelinus alpinus) and Dolly Varden Char (Salvelinus malma malma) are of vital importance to Indigenous communities in Arctic Canada. Both species are facultatively anadromous and anadromous individuals exhibit remarkable diversity in migration tactics. Both species are also iteroparous and relatively long-lived, which allows migration patterns of individuals to be studied over multiple years. The Coppermine River, near Kugluktuk, Nunavut, is the only freshwater location where anadromous individuals of both Arctic Char and Dolly Varden have been confirmed to occur in sympatry, thereby providing a unique opportunity to compare habitat use and migration patterns between species. The overarching goal of this thesis was thus to investigate the diverse life history and migration tactics of Arctic Char and Dolly Varden that use the Coppermine River. To achieve this goal, I used an acoustic telemetry dataset from tagged Arctic Char and Dolly Varden that was collected over six years (2018–2023) in the Coppermine River and nearby marine environment of Coronation Gulf. Acoustic telemetry is widely used in aquatic environments to study animal movement, behaviour, and ecology, but many studies that employ acoustic telemetry neglect to consider the possibility that some detections may be from mortalities or expelled tags, and this can result in biased results. To assist acoustic telemetry practitioners in identifying detections from potential mortalities or expelled tags in a simple and reproducible manner, I developed the R package mort. In Chapter 2, the methods and package are described, and application is demonstrated using three diverse acoustic telemetry datasets that represent: 1) a mobile freshwater fish ((Arctic Grayling (Thymallus arcticus)) in a river network; 2) a relatively sedentary marine fish (Greenland Cod (Gadus ogac)); and, 3) a highly mobile marine fish (Atlantic Salmon (Salmo salar)). Detections flagged by mort were reviewed and removed from the acoustic telemetry datasets that were analyzed in subsequent thesis chapters (Chapter 3, Chapter 4, and Chapter 5). Marine feeding is of critical importance for anadromous Arctic Char and Dolly Varden; individuals of both species must acquire sufficient resources for growth and reproduction during the brief ice-free seasons. In Chapter 3, I used network analysis and local spatial statistics to identify and describe high use locations and movement patterns in the marine environment for char (Arctic Char or Dolly Varden; species was unknown at the time of writing) that overwintered either above or below Kugluk or Bloody Falls (“the falls”; a large cascade). Char exhibited preference for coastal habitats (relative to offshore or island habitats) and habitat use did not appear to be associated with overwintering location. Timing of return to fresh water was associated with overwintering location, however; char that overwintered above the falls returned to fresh water earlier than char that overwintered below the falls, which suggests that length and difficulty of the migratory pathway was associated with migration timing. Timing of return migration to fresh water was earlier in years when the river froze earlier; this indicates that the timing of char returning to fresh water is responsive to environmental conditions in the system. Environmental influences on timing of return migration to fresh water are largely unknown for both Arctic Char and Dolly Varden. In Chapter 4, I investigated how environmental variables were related to: 1) timing of return to fresh water by both Arctic Char and Dolly Varden; and, 2) ascension of the falls by Dolly Varden (no Arctic Char were observed ascending the falls in any year). The primary environmental cue for return to fresh water was sea surface temperature (SST); all char returned to fresh water as SST increased. Dolly Varden that overwintered above the falls returned to fresh water at colder SST (earlier) than Arctic Char and Dolly Varden that overwintered below the falls. For Dolly Varden that overwintered above the falls, river temperatures were warm and potentially stressful at the time of return. It is possible that these individuals experienced decoupling between the cue to return to fresh water (SST) and suitable conditions for migration (river temperature). Tide may have facilitated ascension of the falls but was not associated with timing of return to fresh water for Dolly Varden that overwintered above the falls. In contrast, tide was associated with timing of return to fresh water for Arctic Char and Dolly Varden that overwintered below the falls. Together, these results suggest that Dolly Varden that overwintered above the falls made directed return and upstream movements, whereas fish that overwintered below the falls returned to fresh water more passively. Differences in threshold (SST) for return migration and influence of tide between Dolly Varden that overwintered above and below the falls suggests that there may be an underlying physiological cue for migration timing and/or overwintering location. Fluvial overwintering habitats used by both Arctic Char and Dolly Varden below the falls in the Coppermine River are unusual in that there are no known groundwater inputs. In Chapter 5, I assessed evidence for several potential mechanisms that could explain overwintering below the falls: spawning status, foraging opportunities in the marine environment, and failure to ascend the falls. I found no evidence of foraging from stomach contents, although spatial and temporal coverage of samples was limited. Consistent with intent to overwinter below the falls, Arctic Char staged longer at the river mouth and moved upstream more slowly than Dolly Varden that overwintered above the falls. Dolly Varden that overwintered below the falls exhibited inconsistent movement patterns and I suggested that some Dolly Varden may thus intend to overwinter below the falls, whereas others may fail to ascend the falls. I found no confirmed evidence of spawning activity below the falls for either Dolly Varden or Arctic Char. Telemetry data indicated that Arctic Char overwintered in alternate rivers in some years, which suggests that spawning could occur in alternate rivers and that the lower reaches of the Coppermine River represent easily accessible overwintering habitat in non-spawning years. Dolly Varden that overwintered below the falls were smaller and younger than Dolly Varden that overwintered above the falls, and I suggested that it is likely that Dolly Varden migrate above the falls in spawning years. Spawning locations and frequency remain unknown for both species that use the Coppermine River. The research presented in this thesis describes the life history and migration tactics of anadromous Arctic Char and Dolly Varden that use the Coppermine River, the only freshwater system that is known to support anadromous life history types of both species. Similarities in marine habitat use and movement patterns between Arctic Char and Dolly Varden and between overwintering groups (above or below falls) of Dolly Varden may present challenges for fisheries management if conservation concerns are identified in future. I observed inter individual and inter-annual (within individual) diversity in migration tactics in Arctic Char and Dolly Varden that use the Coppermine River and Coronation Gulf, as well as influences of environmental conditions on migration timing. The observed plasticity in responses among individuals and years may promote resilience of the two species, but future research on spawning locations and spawning frequency is necessary to provide a comprehensive assessment of potential stressors that could affect the species’ persistence and inform fisheries management. Nainaakhimayok Unipkangat (Inuinnaqtun translation of Abstract) Ikalukpiit (Salvelinus alpinus) tahapkualu Dolly Varden-mik attiktaohimayot Ikaluit ihuukit (Salvelinus malma malma) pimagioyot ikaluit nunakakaktot nikkigingmatjuk tahamani Ukkiuktaktumi Kanatami. Tahapkua tamakmik ikaluit ilangit hittuvaktut tagiokmut ilangitaok aullayuitot tattini. Ikaluit hittuvaktut tagiokmut ajikingitot iliitkuhiit hittugangamik, ilangit kakkugungugangat nammutlu hittuvaktot. Tamakmik hapkua ikaluit iglingmingni igniokpaktot kakkugungagangat tatvalu innughaakataktot, taimatot naunaiyaikatagungnaktavut kanok iliitkuhiitnik hittunahuagangata kaffiktaklugit ukkiuni. Tatvani kugluktumi Kuukmi, kanninganiitok Kugluktuk, Nunavut, tatvatuanguyok kaoyimayavut immagiktok hittuviat tahapkua ikalukpiit tatvalu tahapkua ikaluit ihuukit attiktaohimayot Dolly Varden, una Kuuk nayugagiyat attaotikut. Tukkikaktok tahamna Kuuk atjikutakangitok nayugagiyat hittuvigivakhutjuk tahapkua ikaluit. Taimatot ihomagiloaktavut tahamna naunaiyaiyot havagiyomavlutjuk kanok allangayaghaita hittuvigikatakhutjuk tahapkua ikalukpiit tatvalu hapkua Dolly Varden ikaluit ihuukit nayogagiyat tahamna Kugluktumi Kuuk. Tatva taimatot havagiyomavlutjuk, tahapkua ikalukpiit Dolly Varden ikaluit ihuukit attaataliktoktaovaktot nallauhiktokhugitlo tauktoktaovaktot namungaokatakmangata 6-sinik ukkiunik havagivlutjuk (2018-min 2023-mut) tahamani Kugluktup Kuukmi tatvalu kaningani tahamani tagiokmi Coronation Gulf-mi. Ataataktuinik tatvalu tammalaitkutinik nallauhiktoinik atogaokataktot imakmi nauyaiyaotigivlutjuk ikaluit namungauningitnik, iliitkuhiitnik tatvalu nayogagiyaitnik, kihiani ammihuyut tahapkua tammalaitkutinik nallauhiktoinik ihomagingitait immakak illangit hapkua naunaiyaotait pihimayungnakhiyat ataatakhimayunit ikalunit tukkuhimayunit uvalunin ataatait kattaktitaonikata, taimatot nallukhaotaungmiyot. Ikkayotaongmat inuknun naunaiyaiyunot ummayunik immakak tahapkua ataatait tukkuhimayuningakhimayot ikalunit uvalunin kattakhimayonik ataatanit, ihuaghaihimaliktunga naunaitkutikhamik kagitaoyakukutimik attikaktok mort-mik. Tatvani unipkat Naunaipkutani 2-mi, naunaiyakhimayaga unipkagivlugo kanok atoktaoyagiakaktok una kagitaoyakut naunaiyaotaoyok, ayogiktoitjutigiyaga kano kuna kagitaoyakut naunaiyaotaoyok atoktaoyungnaktok pingahut allatkit naunaipkutini: 1) tattiniotak una ikaluk (Hulukpaugak (Thymallus arcticus)) kukanikataktok; 2) tagiokmiotak ikaluk una hangukatangitok (Uugak (Gadus ogac)); tatvalu, 3) ungahiktoliakataktok una tagiokmiotak ikaluk (Atlantic Salmon (Salmo salar)). Tahapkua naunaipkutaoyot naunaiyaktaohimayot kagitaoyakut ahivaktaokataktot tahapkunanga naunaiyaotaoyonit takkuktaohimayot ahianit unipkangita naunaipkutaitni (Naunaipkutani 3, Naunaipkutani 4, tatvanilo Naunaipkutani 5). Tagiokmi nigginiakviat tahapkua ikaluit pimagioyok; tahapkua ikaluit allatkiit nikkikatiagiakaktot akliyamingnik tatvalu igniugiamingnik hikkukangititlugo. Tatvani unipkami Naunaipkutani 3, naunaiyakhimayatka titigakhugit tahapkua nayogagiloaktaitnik namungaokatakningitiklo tahamani tagiokmi hapkua ikalukpiit ikaluitlo ihuukit hapkua Dolly Varden; kanogitungmangata tahapkua ikaluit nallukhaotaoyut titigakpalialiktitlugo tahamna unipkalioktaoyok, tahapkua ukkikataktot nalliakni kullani uvalunin natkani tahaffuma Kugluk-mik attikaktuk Kuuk. Ikalukpiit nayogagiyakaktot hinnanikhiokhutik takkunakpalangitot ittinikmi uvalunin kikiktani. Tahapkua nayogagikataktait ikaluit ihomagiyaovalangitat nannikatakmangata ukkiumi. Uttigangata tagiokmit tahamunga tattinut immagiktunut ihomanaktok nanikatakmangata ukkiumi, kihianitaok; hapkua ikalukpiit ukkikataktot kulani tahaffuma kukluakviani Kuukmi uttikataktut immagiktunut tattinut pinnagikataktot ikalukpiitnit ukkihimayunit natkanit haffuma kukluakviani Kuukmi, ihomannaktok tatva hivituninga tatvalu ayoknautigikataktat tahamna ingilgayatik mayogahualigangamik kinguvautivagungnakhiyok. Kakugu mayokvikikataktat tattinut immagiktunut pinnagikatakhimayot ukkiuni kinguani tahamna Kuuk hikkunagikatagaluakmat; taima naunaikhimaliktok tatva kakugo mayokvighaat tahapkua ikalukpiit tattinut immagiktunut hillap kannugininganik nayogiyagiakaliktok. Hillap kanogininga pitjutaokatakmat kakugo mayokvighaatnik tahapkua ikalukpiit tatvalu ikaluit ihuukit Dolly Varden nallukhaotaoyut. Tatvani unipkami Naunaipkutani 4, naunaiyaihimayunga kanok tahamna hillap kanogininganik pitjutaokataka tahapkuninga: 1) Kakugo mayokatakat tattinut immagiktunut tahapkua ikalukpiit tatvalu ikaluit ihuukit Dolly Varden; tatvalu, 2) mayokpakhutik kullanut kukluaktup Kuukmi tahapkua ikaluit ihuukit Dolly Varden (naunaiyakhimangitot mayoktunik kullannut Kuukmi huli). Ihomagiluaktavut hilla allangugangat mayokvikhaat tattinut immagiktunut tagiok niklakpalialigangat; tahapkua ikalukpiit mayokataktot tattinut immagiktunut tagiok unnakpaliatitlugo. Tahapkua ikaluit ihuukit ukkikataktot kullani kukluaktumi kuukmi mayokatakmiyot tagiok niklakpalialigangat tahapkuataok ikaluit ihuukit Dolly Varden ukkikataktot natkani tahaffuma kukluaktumi kuukmi. Tahapkua ikaluit ihuukit Dolly Varden ukkikataktot kullani kuukmi, kuukap unnakninga unnatkiyaokatakmat ummilgungnaktokhaoyok mayokpalianiaktitlugit. Immakak tahapkua ikaluit ayughaotigikataktat mayokvikhatik tattinut uttakivagungnakhiyat unnakninganik kukkap. Immaokaomagangat ikkayotaovagungnakhikmiyok kihiani pitjutaovalangituyaaktok mayokvikhaatnik tahapkua ikaluit ihuukit Dolly Varden ukkikataktot kullani kuukmi. Kihianitaok, immaokagangat pitjutaungmiyok mayokvikhaitnik tahapkua ikalukpiit tatvalu ikaluit ihuukit Dolly Varden ukkikataktot natkani kuukmi. taimaitkaluaktitlugit, naunaiyakhimayavut ihomangnaktok tahapkua ikaluit ihuukit Dolly Varden ukkikataktot kullani kukluakviani kuukmi ayoghakhimaitomik mayokataktot tattinut, tatvataok tahapkua ikaluit ukkikataktot natkani kuukmi mayokatakmiyot tattinut immagiktunut kayumiitunuamik. Ikaluit ihuukit Dolly Varden ukkikataktot kullani kukluakviani Kuukmi ahianik tagiop unnakpalianinganik pitjutikakmiyot mayokvighait tattinut immagiktunut immaokaknialo allangangmiyok tahapkunanganin ikaluit ihuukit Dolly Varden tatvanganin ukkikataktunit kullani kukliaviani kuukmi. Ihomanaktok immakak ahianik pitjutikakpagungnakhiyot mayokvikhaat tatvalu/uvalunin ukkiumi namungaovikhaitnik inmingnik ikpigiyakagangamik tahapku tamaita ikaluit taima ihomanaktok. Tahamna Kuuk ikalukaknik atogagiyat tahakmik hapkua ikalukpiit tatvalu ikaluit ihuukit Dolly Varden ukkiukmi natkani tahaffuma Kukluktumi Kuukmi allangayok pitakangituyaakmat tahamna mannigak immak nakingaakmangata illitugingitnamku. Tatvani unipkami naunaipkutani 5-mi, takkukhimayaga kaffiit ihomagivlugit huok ilangit tahapku ikalukpit ukkikatakat natkani tahaffumja kukkiktuk kuukani: igligiyaitlu igniokvigikataktaitniklo naunaiyagahuaklugit, nigginiakvigiyataktaitlo naninmangata tagiokmi, huoklo maayokatangitpat kuukiktumi kuukmit. Tahapkuataok ikaluit ukkiukataktot natkani tahaffuma kuukiktumi kuukmi, takkuhimangitunga hunnanik igginiakatakmangata akkiagoit illuhikangitmata, kihianitaok naunaiyaihimangitnamta ammihunik ikaluknik nannilunin takkukhimangitnaptigo huli. Taima illiitkuhiktuyaaktot tahamaninaakniaktok ukkiugalok naatkani tahaffuma kukluakviani Kuukmi; tahamaniikhatkiyaongmiyot kukkap pannani tatvalu maayoknahaatkiyaovakhutik tatvanganin ikaluit ihuukit Dolly Varden mayoknagikataktot ukkikatakhutik kulani tahaffuma kukluakviani Kuukmi. Tahapkua ikaluit ihuukit Dolly Varden ukkikataktot naatkani kukluakviani Kuukmi ajikingitut ingilgayangit, ilangit tahapkua ikaluit ihuukit ukkikataktot naatkani kukuakviani Kuukmi, ilangitaok ammukatangitot naatkanit haffuma kukluakvianin Kuukmi. Illiitkugingitatka pikagiaghaita igliitnik naatkani tahaffuma kukluakviani Kuukmi tahapkua ikaluit ihuukit uvaluni ikalukpiit. Tahapkua ikaluit naalautait naunaipkutigivlugit illiitugihimayavut ukkikataktutaok ahinni kukkani ilangitni ukkiuni, taima ihomanaktok iglikakpagungnaghiyok tahapkua ikaluit ahinni kukkani tatvalu ukkiyaktokpakhutik tahamunga Kuglumtumi Kuukmit ukkiuni igliliungitagangamik igniukvikhamingnik, ayungnaitkiyaoyungnakhingmat. Tahapkua ikaluit ihuukit Dolly Varden ukkiktaktaktot tahamani naatkani Kuukmi mikitkiyaovakhutik ikalukpiakjuit tatvanganin tahapkuninga ikaluit ihuukitnit Dolly Varden ukkikatakmata kullani tahaffuma kukluakviata Kuukmi, ihomanaktok immakak tahapkua ikaluit ihuukit Dolly ammukpagungnakhiyot kullanut kukluakviani Kuukmi igliliogiaktokhutik igniokvikhamingnik. Igliliokviit tatvalu kanovalaak igliliokatakmangata tammakmik tahapkua allatkik ikaluit nalluyaoyut huli tahamani Kugluktumi Kuukmi. Tahamna naunaiyaktaohimayok unipkalioktaovluni tahapkuninga ikaluit hiitokataktot iliitkuhiitnik ikalukpiit tatvalu hapkua Dolly Varden ikaluit ihuukit nayogagiyat tahamna Kugluktuk Kuukmi, ahiani taima pittakangitok immagiktumik Kuukmik hittuviovaktumik tahapkuninga allatkinguyunik ikalungnik. Ajikiiktoktut tagiokmut hiitovakhutik namungaokatakmangatalo tahapkua ikalukpiit tahapkulo ikaluit ihuukit Dolly Varden tatvalu ammugangata ukkiukhivikhamingnut (kullanut uvalunin natkannut tahaffuma Kuukmi kuukikningani) tahapkua ikaluit ihuukit Dolly Varden ayungnavakniaktot tatva hapkua ikaluknik naunaiyaiyiit havagiyaitnik hivunighami ihomalutaovaliaklikatjuk ikkilivalianingit. Hapkua ikalukpiit tatvalu hapkua ikaluit ihuukit Dolly Varden hiitukataktot Kugluktuni Kuukmit tatvalu tagiokmut Coronation Gulf-mut, uvanga takkukhimayatka tahapkua allatkit ikaluit ajitkingitot hiitugangat ingilgayangit ajikikatangitot ukkiuni. Takkukhimangmiyaga tahamna nuna manigaak hulitjutaongmiyok hittuniahaaktitlugit ikaluit tagiokmut. Taima atjikikatangitmata ikaluit hittuviat namungaukatakniitlo ikkayutaoniakuktat tahapkua ikaluit annaumatjutaitnik hila kannugininganik. Kihiani hivunikhami naunaiyainik pivaligiakaktok naninmangata tahapkua ikaluit igliliokviit tatvalu kannuvaklaak igliliokatakat kaoyivaliotiginahuaklugit kanok hunaniklo ullugiangaktomitjutait tatvalu kanok annaomatjuktikaohighaitnik tahapkua allatkik ikaluit tatvalu tuhaktinahuakutikhaitnik tahapkua ikaluhikinikut ataniktoiyot.
Assessing the Waterfowl Forage Value of Wetland Plant Communities
(University of Waterloo, 2025-08-27) Kramarenko, Andrii
Invasive Phragmites australis continues to threaten wetland biodiversity and reduce food availability for waterfowl across North America. Assessing how vegetation responds to suppression efforts, and how these changes influence forage quality, is essential for informing management. In this study, I adapted the Vegetation Forage Quality Index (vFQI) for use in southern Ontario by developing updated forage value coefficients through expert elicitation. I also introduced a new tool, the Weighted Mean Waterfowl-forage Coefficient (WMWCs), modified to reduce the influence of species richness on the index score. I tested both indices in wetlands of the Long Point and Big Creek National Wildlife Areas, where P. australis suppression was conducted to evaluate the impact of suppression on waterfowl forage value. Field surveys (2022-2023) revealed that the WMWCs, but not the vFQI, successfully distinguished among invaded, treated, and reference sites, detecting improved forage quality in treated areas two years post-treatment. However, neither index was strongly correlated with empirical seed mass data from sediment cores, suggesting that seed biomass alone may not fully reflect foraging value. This study highlights the limitations of richness-sensitive indices like the vFQI and demonstrates the potential of WMWCs as a more robust indicator of wetland forage quality for waterfowl. Recommendations for future work include validation with bird observations and long-term monitoring to better capture temporal recovery dynamics.
The C117D and C145D Variants Elucidate Oxidation-Induced Functional and Conformational Changes in the SARS-CoV-2 Main Protease
(University of Waterloo, 2025-08-15) Andress, Samuel
The main protease (Mpro) of SARS-CoV-2 is essential for viral replication. Its proteolytic mechanism relies on a catalytic dyad formed by the C145 and H41 residues. Recent studies have focused on understanding how Mpro defends itself against oxidative stress as the C145 side chain is susceptible to oxidative damage, which can irreversibly inactivate the enzyme. Oxidative conditions, such as those induced by the immune response, are known to trigger structural changes in Mpro, including the formation of a disulfide bond between C145 and the proximal C117, as well as a shift toward an inactive, monomeric state. It has been proposed that non-catalytic cysteines may act as redox-sensitive switches, or as oxidative sinks that reduce harmful oxidants before reaching the catalytic C145. In this study, functional assays (kinetic analysis and thermal shift assays) combined with structural methods (small-angle X-ray scattering and X-ray crystallography) reveal that mimicking oxidation at C117 via a C117D point mutation drives Mpro toward an inactive monomeric conformation. This transition involves changes in the substrate-binding pocket, rigidification of the dimerization domain, and increased disorder at the N-and C-termini. In contrast, a C145D mutation, designed to mimic oxidation at the catalytic residue, had no impact on the enzyme’s conformation or oligomeric state. These findings present the first solved structure of the monomeric form of Mpro and reveal a novel role for C117 as a redox sensor that mediates oxidative regulation of the protease’s structure and function.
Population trends and behaviours of bats in Maritime Canada
(University of Waterloo, 2025-08-11) Golestaneh, Sepidar
In a rapidly changing world with many drivers of extinction, monitoring wild populations has become of increasing priority to researchers. For many bats (order Chiroptera) in North America, population assessments have become critical in monitoring population trends following disease disturbance, specifically White Nose Syndrome. White Nose Syndrome is a fungal disease that has resulted in mass mortality of many hibernating bat species in eastern North America since its detection in 2006. Given the time elapsed for many areas since White Nose Syndrome introduction, many affected populations have reached an established state where disease-associated mass mortality is not currently observed. As such, the motivation for population assessments has shifted more towards describing patterns of recovery in White Nose-affected populations. However, population assessments for bats, like for other taxa, may be biased and consequently impact the inferences made by researchers. This thesis aims to describe population trends of species affected by White Nose Syndrome in Maritime Canada and assess the impacts of research techniques on study findings. The specific objectives of this thesis were to (1) assess population trends of resident hibernating bats with respect to White Nose Syndrome detection in Maritime Canada, and (2) assess the potential biases of capture surveys on bats, a standard research method used to conduct population assessments and study bat activity.
Comparative Effect of Herceptin and Its Biosimilar: Transcriptomic and Proteomic Insights from HER2-Positive Cancer Cell Lines
(University of Waterloo, 2025-07-31) Karsten, Rinas
The first patent for the therapeutic monoclonal antibody Herceptin expired in 2019, opening the door for the development of biosimilars. Biosimilars are copies of the originator product that must demonstrate biosimilarity for regulatory approval. This is a very difficult task. Antibodies are large molecules that undergo extensive post-translational modifications (PTMs), which affect their potency, stability, binding affinity, and immunogenicity. Batches of the originator products often vary in their PTM patterns, making structural similarity very difficult to prove. Despite these challenges, most biosimilar development workflows rely on targeted wet-lab assays to assess structural similarity, purity, and efficacy, often without addressing the full complexity of the task. Herceptin targets the surface receptor HER2 (human epidermal growth factor receptor 2) on breast cancer cells, inducing global cellular changes including cell arrest, programmed cell death, reduced motility, and angiogenesis. The complete mode of action is under investigation, and the development of resistance to Herceptin is common and complex. Due to these gaps in knowledge and complexity of Herceptin’s effect, untargeted omics techniques, such as transcriptomics and proteomics, are ideally suited for functionally comparing biosimilars to their originator product. Therefore, the primary goal of this thesis is to evaluate whether transcriptomics and proteomics experiments are useful for investigating the impact of the biosimilar on target cells compared to the originator product. To this end, Herceptin’s effect on the breast cancer cell lines BT474, SKBR3 and MCF7 will be compared to a biosimilar, called Apotex- Trastuzumab (ApoTras), provided by Apobiologix (Toronto, Canada). This analysis will allow us to investigate the sensitivity of the methods in detecting differences and determining how many of the known effects can be identified. This work will provide valuable insights into the use of untargeted omics approaches for investigating the functional similarity of a biosimilar to its originator product.
Exploring the Dominant Negative Potential of 𝘊𝘖𝘟11 Mutants in 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦
(University of Waterloo, 2025-07-07) Coletta, Genna
Cytochrome 𝘤 oxidase (COX) is the terminal enzyme of the electron transport chain and plays a crucial role in cellular respiration. As a multisubunit enzyme, COX consists of catalytic core subunits encoded by the mitochondrial genome and requires the coordinated action of more than 30 nuclear-encoded assembly factors for proper biogenesis and function. Human COX deficiencies have been associated with mutations in both nuclear and mitochondrial genes and are thus characterized by immense genetic heterogeneity and a vast spectrum of clinical phenotypes. 𝘊𝘖𝘟11 is a nuclear-encoded copper chaperone that is required for COX assembly. Beyond this well-characterized role, COX11 has an additional, uncharacterized role in cellular redox homeostasis. Caron-Godon et al. reported a patient with compound heterozygous mutations in 𝘊𝘖𝘟11, whose homologous mutations were studied in haploid yeast. When grown on non-fermentable carbon sources, one of the mutant alleles, P238T, demonstrated robust growth, indicative of respiratory competence, in contrast to the truncation mutants, Y250* and R254*, which exhibited a complete and partial respiratory deficiency, respectively. Given that COX deficiencies are inherited in an autosomal recessive manner, this finding adds an unexpected complexity to the patient’s phenotype, which may suggest the possibility of a hypomorphic or dominant negative allele. To better recapitulate the patient’s genotype, I employed a pseudodiploid system in 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦, which involves the stable co-expression of two mutant 𝘊𝘖𝘟11 alleles in a single haploid background. Functional assays, including growth on non-fermentable carbon and COX enzymatic activity, as well as immunoblotting of core COX subunits, demonstrated that the pseudodiploid double mutants, representative of the patient, supported robust respiration and maintained COX assembly at levels comparable to those of wild-type. In contrast, evaluation of oxidative stress markers revealed defects in cellular redox balance. Double mutant strains, particularly P238T/R254*, exhibited significantly elevated superoxide dismutase activity, a pronounced decrease in mitochondrial aconitase activity, and increased sensitivity to hydrogen peroxide. These data indicate that the redox equilibrium is compromised even when cytochrome 𝘤 oxidase function is preserved.
Investigating Changes in Mercury Concentrations in Small-Bodied Fishes Following Mine-Related Flooding in the Canadian Arctic
(University of Waterloo, 2025-06-19) Soogrim, Noel
Mercury (Hg) is a globally distributed contaminant that, in its methylated form (methyl mercury (MeHg)), is a potent neurotoxin that bioaccumulates and biomagnifies in aquatic food webs. At high enough exposures, Hg can pose risks to wildlife and human health. While Hg concentrations in aquatic ecosystems have been relatively well-studied in boreal systems, less research has been conducted in Arctic freshwater ecosystems, particularly in Barrenland tundra lakes that are increasingly affected by industrial activity and climate-driven change. This thesis examined the effects of a mine-related flooding event at the Amaruq project site in Nunavut, Canada, on aqueous and biological concentrations of Hg in a series of shallow Arctic lakes. Concentrations of total mercury (THg) and methyl mercury (MeHg) in water, indicators of organic matter (OM) quantity and quality in water, including concentrations of dissolved organic carbon (DOC), humification index (HIX), and specific ultraviolet absorbance (at 254 nm; SUVA) and concentrations of Hg in the tissues of Slimy Sculpin (Cottus cognatus) and Ninespine Stickleback (Pungitius pungitius), were compared: 1) before and after flooding in impacted lakes; and, 2) between flooded and reference lakes in the post-flood years. A series of potential covariates of fish Hg concentrations, including fish age, condition, C: N, δ13C, and δ15N, were also compared between pre- and post-flood years and between flooded and reference lakes. Aqueous concentrations of THg and MeHg were significantly higher in flooded lakes compared to reference lakes (THg filtered: p = 0.01; MeHg filtered: p < 0.001) in post-flood years. In flooded lakes, concentrations of THg and MeHg were significantly higher in post-flood years compared to pre-flood years (p < 0.05) whereas there were no significant differences among years in reference lakes (p > 0.28). Concentrations of DOC were significantly higher in flooded lakes than in reference lakes in post-flood years (p < 0.001), suggesting increased terrestrial OM inputs. Higher MeHg concentrations and higher % MeHg in water in flooded lakes relative to reference lakes in post-flood years may indicate that terrestrial OM inputs increased net Hg methylation rates, but there was no difference in % MeHg between pre- and post-flood years in the flooded lakes (p < 0.05). Evidence for enhanced methylation post-flood is thus mixed, and more research is necessary. Fish tissue Hg concentrations were significantly higher in flooded lakes than in reference lakes in the post-flood years for both Slimy Sculpin (p < 0.001 in 2020 and 2021) and Ninespine Stickleback (p = 0.002 in 2021). Within flooded lakes, tissue Hg concentrations in both species were significantly higher in the post-flood years relative to pre-flood years (Slimy Sculpin: F₃,₂₆₁.₇₁ = 14.53, p < 0.001; Ninespine Stickleback: F₃,₁₁.₀₆ = 33.96, p < 0.001). Flooding-induced increases in fish Hg concentrations appeared to be most closely related to concomitant decreases in δ¹³C; δ¹³C ratios were significantly more depleted in post-flood years (Slimy Sculpin: F₃,₃₁₅.₂₈ = 20.11, p < 0.0001; Ninespine Stickleback: F₃,₃₆₇.₃₃ = 5.38, p = 0.001) compared to pre-flood years, and were negatively correlated with fish Hg concentrations (Slimy Sculpin: r = -0.72; Ninespine Stickleback: r = -0.63). These results suggest a shift in basal carbon sources, likely reflecting increased reliance on terrestrially derived, allochthonous OM. The strong correlation between δ¹³C and Hg concentrations indicates that OM dynamics played a central role in driving Hg bioaccumulation in the food web. Other potential covariates of fish Hg concentrations, including relative condition, C:N ratio, and length-at-age, explained less variation in Hg concentrations and/or did not appear to be affected by flooding, although weak negative correlations between Hg concentrations and condition were observed. While the general patterns observed in this study align with findings from boreal systems subjected to flooding, it is possible that Arctic lakes are uniquely vulnerable to flooding-induced Hg mobilization and increases in fish Hg concentrations due to their low productivity and catchments with permafrost. These characteristics may increase the release of OM and Hg during flooding and increase bioaccumulation of newly released Hg. Despite limitations in sampling design and data availability, results of this study provide the first empirical evidence linking industrial flooding to increases in Hg concentrations in Arctic lakes. Results underscore the need for long-term contaminant monitoring in remote tundra regions where climate warming, industrial development, and permafrost degradation are expected to intensify. Given the cultural importance of fish for northern communities, understanding how environmental disturbances affect Hg bioaccumulation is critical for protecting both ecosystem and human health in the Arctic.
Impacts of temperature variation on duckweed population growth and distribution in a changing climate
(University of Waterloo, 2025-06-16) Andrade-Pereira, Debora
Understanding the impacts of climate change on aquatic plants involves examining how temperature fluctuation patterns influence their temperature-dependent vital rates and distribution. Duckweeds, small aquatic plants with both economic significance and ecological concern, can pose challenges due to overgrowth and the spread of invasive species. The impact of climate-induced temperature changes on aquatic plants remains poorly understood, as many studies use constant conditions that do not account for natural variability in temperature. Research focused on increased average temperatures has shown general ectotherm responses tied to geographic location, such as enhanced growth in temperate regions. However, when temperature fluctuations are considered, responses differ from those under constant conditions due to nonlinear and asymmetrical thermal performance. Increased autocorrelation, with prolonged sequences of unusually high or low temperatures, can affect population growth rates, while nighttime warming alters diel temperature variation and potentially influences time-sensitive processes like photosynthesis and respiration. This thesis investigates the thermal performance and distribution of duckweed species under varying temperature regimes associated with climate change, incorporating both controlled experiments and predictive modeling. The second chapter uses a Maxent species distribution model to predict the potential range expansion of Landoltia punctata (dotted duckweed), an invasive, herbicide-resistant species. Habitat suitability is modeled under current and future climate scenarios, using satellite-derived water temperature data and constraining model features to match the shape of thermal performance curves obtained from laboratory experiments. Results indicate high suitability for this species in Western Europe and Southern Canada, with the Great Lakes region becoming increasingly suitable in the future due to climate warming. These projections underscore the importance of climate-informed management strategies to mitigate the ecological impact of invasive species. The third chapter investigates how diel temperature variability and climate change affect the reproduction of Lemna minor (common duckweed) during spring and summer. Experimental results highlight the importance of temperature variance as opposed to the timing of warming. While increased mean spring temperatures enhance duckweed performance, reduced temperature variance during high summer temperatures in regions such as Canada helps mitigate the negative impacts of otherwise excessively hot fluctuating conditions. These findings emphasize the varying effects of climate change on duckweed's thermal performance across different seasons. The fourth chapter examines the effects of temperature autocorrelation on both common and dotted duckweed reproduction and survival. Experiments show that strongly autocorrelated sequences result in mortality due to heat stress when hot temperature sequences begin with elevated heat. In contrast, autocorrelation has limited impacts under cooler average conditions, likely due to slower physiological responses. These findings align with broader predictions of increased extinction risks for ectotherms under persistent and extreme temperature patterns caused by climate change. This work is a step towards a more realistic understanding of aquatic plant responses to climate change by considering thermal performance responses, diverse temperature fluctuation patterns, and water temperatures. Our results can be used in population dynamics models to make more realistic predictions of climate change responses. The experimental and modeling findings in this thesis advance our understanding of aquatic plant responses to climate change and support the development of informed strategies to manage their ecological impacts and sustainable production in a warming world.
A Biophysical Study on the Effects of Bacterial Infection and Neuroprotective Molecules in Relation to Alzheimer’s Disease
(University of Waterloo, 2025-06-10) Filice, Carina Teresa
Alzheimer’s disease (AD) is a prominent health concern among the aging population. This disease impairs neuronal cells, in part, through the accumulation of amyloid-β(1-42) peptide (Aβ1-42) and its various toxic mechanisms. With the advent of controversial anti-amyloid drugs, the efficacy of newly developed treatments is still not high. Investigations into novel treatment strategies highlight the potential protective abilities of natural products; one of which is melatonin, a hormone produced by the pineal gland. Due to its inherent lipophilicity and interaction with membranes, melatonin is investigated in this work as a novel membrane-protection strategy. The difficulty in discovering effective anti-amyloid drug targets may be related to Aβ1-42’s physiological role as an antimicrobial peptide. Several hypotheses suggest microbial infections as a causative risk factor of AD through the stimulation of Aβ1-42 and neuroinflammation. This work specifically focuses on the contributions of bacterial functional amyloids, known as ‘curli fibers’, to Aβ1-42 processes. The basis for this investigation into curli fiber-amyloid interactions lies in multiple established instances of cross-seeding with other amyloidogenic peptides. Recently published studies demonstrate this interaction but many questions still remain as to the nature and effect that this interaction will have on other AD processes. In this work, we intend 1) to elucidate the molecular mechanism of melatonin membrane protection against amyloid toxicity and 2) to investigate the interaction of infection-establishing bacterial curli fibers with Aβ1-42 and the effect of these complexes on AD-associated mechanisms. To explore these mechanisms, we used multiple methods in biophysics, molecular biology, and computational chemistry to provide an interdisciplinary perspective. Previously published lipid models mimicking various AD-afflicted neuronal membranes were pre-treated with melatonin prior to Aβ1-42 and resulting damage was assessed via atomic force microscopy (AFM) imaging and black lipid membrane electrophysiology. In this work we demonstrated melatonin’s ability to inhibit peptide binding and promote membrane repair after Aβ1-42 exposure is dependent on its fluidic nature working in combination with lipid composition of target membranes. Similarly, high speed-AFM, AFM, and BLM studies evaluated the differences in antimicrobial and toxic mechanisms of Aβ1-42 in comparison to a known antimicrobial peptide. These evaluations revealed that anionic bacterial membranes repel Aβ1-42 indicating antimicrobial activity is not likely related to the same non-specific membrane binding as is its toxicity. Next, curli-amyloid interactions and the identification of participating aggregation states were evaluated through molecular dynamics simulations, transmission electron microscopy and AFM, as well as a novel biomolecular condensate assay. We confirmed that not only do curli fibers and Aβ1-42 interact and form peptide complexes, but also identified that this interaction is solely carried out by early aggregation species such as monomers and oligomers. Additionally, the effects of curli fibers on Aβ1-42 toxicity were first modelled by MD simulations and experimentally confirmed through measurements of damage on simple eukaryotic-based models by AFM and BLM, cell viability assays of murine microglial cell cultures, and immunogenicity evaluations using enzyme-linked immunosorbent assays. We also established that these curli-amyloid complexes reduce toxicity directly related to membrane perforation mechanisms but still negatively affect cell viability, presumably due to a heightened immunogenicity of the peptide complexes. Our findings lead us to propose a novel membrane-centric neuroprotection strategy against Aβ1-42 toxicity. This proposed mechanism intends to expand our knowledge of melatonin’s effect on membranes in AD and could inform therapeutic development. Furthermore, our investigations into curli-amyloid interactions and their effect on AD processes highlights the important role of Aβ1-42 in physiology and how this can relate to AD onset. These findings can reinforce the current research paradigm shift to microbial infections, the gut-brain axis, and the role of microbial products as potent initiators of AD onset pathways. Therefore, this entire body of work aims to develop knowledge of important AD mechanisms to guide new research, diagnostics, and treatment avenues.
Artificial selection of Stutzerimonas stutzeri MBI-RS3 towards enhanced nitrogen fixation in presence of ammonia and oxygen
(University of Waterloo, 2025-05-27) Tello Yepes, David Felipe
Food security is a primary concern for every region of the world. Today, the agricultural sector relies heavily on artificial fertilizers to maintain crop production and yield. This has an unsustainable dependency that has exceeded the planetary boundary for nitrogen fertilizer usage for decades. Biologically, nitrogen nutrition can be provided by nitrogen fixation carried out by bacteria in the rhizosphere of crops. Nitrogen fixation is done by an enzyme called nitrogenase. This enzyme converts biologically inaccessible N2 from the atmosphere and into NH4, which is then readily available in the soil. Nitrogenase expression and activity are heavily downregulated by oxygen and biologically available nitrogen, making it challenging for bacteria to balance respiration, proliferation, and nitrogen fixation when subject to levels of oxygen and nitrogen. Bacteria capable of nitrogen fixation can be endosymbiotic or free-living. Endosymbiotic nitrogen-fixing bacteria interact specifically with legume plants by triggering nodulation. Free-living nitrogen-fixing bacteria can colonize legume and non-legume rhizospheres, opening possible environments where free-living nitrogen-fixing bacteria can survive and fix nitrogen. Free-living nitrogen-fixing bacteria are exposed to a wide range of oxygen and nitrogen concentrations, forcing them to adapt more extensively than endosymbiotic nitrogen-fixing bacteria. The genetic modification of free-living nitrogen-fixing bacteria can give an advantage in the race against artificial fertilizers, contributing to a more sustainable and resilient agriculture. Stutzerimonas stutzeri MBI-RS3 is a free-living bacterium that is capable of fixing nitrogen. This thesis focuses on exposing strain MBI-RS3 to UV energy, targeting a 99% kill rate and generating random mutations in the 1% survivors. A plasmid construct carrying a fusion of nif promoter and gus was developed. The UV-irradiated culture was recovered, transformed with a reporter gene plasmid pFT1NP and screened for blue colonies. Forty-three isolates were recovered and cryopreserved. Six candidates (FT11, FT16, FT22, FT34, FT38, FT40) were characterized by β-Glucuronidase assay, identifying mutant FT11 as the sample with the strongest nif gene expression. MBI-RS3 wildtype and mutants were inoculated in tomatoes, soybeans, and canola to assess their plant growth-promoting activity in different conditions. This showed a stronger performance of the mutant groups (FT11, FT16, FT22, FT38) compared to the wild-type in tomatoes, with higher shoot dry weight production. Mutant FT11 and FT22 showed some potential to make up for the decrease in nitrogen fertilizer use while maintaining yield. Mutants FT16 and FT 40 showed more pod and shoot dry weight in soybeans than wildtype in the presence of Bradyrhizobium sp. The MBI-RS3 wild-type was the best performer in terms of dry weight production of canola pods and shoots. These results demonstrate that not only MBI-RS3 wild-type but also some mutants exhibit plant growth-promoting activity, with a particular focus on nitrogen nutrition. Furthermore, in the tomato and soybean rhizosphere, the mutants induce higher yields and biomass production compared to the wild-type. All MBI-RS3 6 mutants and wild type were assessed by acetylene reduction assay to confirm nitrogenase activity, but only the MBI-RS3 wildtype strain showed ethylene production.
Characterization of Microbial Communities of the Utikuma Region Study Area (Alberta, Canada)
(University of Waterloo, 2025-05-26) Kwok, Arnold
Understanding the drivers of bacterial communities and the dynamics of boreal ecosystems is critical for safeguarding water quality and ecosystem resilience in the face of environmental change. This study investigates the interplay between cyanobacterial dynamics and ecohydrologic factors in the Utikuma Region Study Area (URSA) of northern Alberta. Cyanobacteria play a pivotal role in oxygenic photosynthesis and nutrient cycling, yet their unchecked proliferation can lead to harmful algal blooms with significant ecological and economic consequences. Field sampling was conducted in 34 URSA ponds using a two-phase filtration process designed to capture both larger microbial and picocyanobacterial cells. DNA was extracted and analyzed through 16S rRNA gene sequencing, with taxonomic assignments derived from the curated CyanoSeq 1.3 database and complementary methods. Advanced bioinformatics pipelines provided high-resolution community profiling, while statistical analyses—including redundancy analysis and PERMANOVA—linked microbial diversity patterns to water chemistry parameters (e.g., pH, nutrients, trace metals) and ecohydrologic variables such as hydrologic relief areas, hydrologic units, and wildfire disturbances. Key findings indicate that environmental factors explain up to 23.9% of the variance in microbial composition based on clr-transformed RDA. Notably, landscape-scale drivers and wildfire history significantly influenced community structure, with their interactions accounting for up to 30.1% of the variance (PERMANOVA). Dominant phyla observed included Pseudomonadota, Bacteroidota, Actinomycetota, Cyanobacteriota, and Verrucomicrobiota, while analysis of 165 cyanobacterial Amplicon Sequence Variants highlighted taxa such as Prochlorococcaceae and Aphanizomenonaceae. These results, while based on a specific sampling period, provide valuable foundational insights into the relationships between ecohydrologic drivers and microbial community structure for a region previously uncharacterized in this regard. This work sets the stage for further research to refine taxonomic methods and inform targeted water quality management strategies in boreal ecosystems.
Characterizing the effects of temperature variation on metabolic capacity in darter fish (Etheostoma spp.)
(University of Waterloo, 2025-05-26) Sinik, Alexandra
With progressive increases in global temperatures from climate change, aquatic ectotherms are particularly at risk, considering they are incapable of maintaining their internal body temperatures. As environmental temperatures increase, metabolic rate rises in ectothermic poikilotherms, with thermal extremes presenting potentially lethal implications. By gaining an understanding of the metabolic functioning of local species, we can draw conclusions on the implications of thermal stress on biochemical responses. Here, we focused on understanding the effect of increased temperatures on enzyme activity in the brain, heart, and muscle tissues of three closely related darter species found in the Grand River of Southern Ontario: Johnny (Etheostoma nigrum: JD), Fantail (Etheostoma flabellare: FTD) and Rainbow darter fish (Etheostoma caeruleum: RBD) to determine whether energetic enzymes are a potential limiting factor in thermal tolerance. Analysis of enzymatic activity of four key metabolic enzymes including lactate dehydrogenase (LDH), pyruvate kinase (PK), malate dehydrogenase (MDH) and citrate synthase (CS) were conducted via enzyme assays through a temperature profile, ranging from 20C to 34C, just past the predetermined critical thermal maximum (CTmax), or upper thermal tolerance, at 30.7C ± 0.9, 31.9C ± 0.6 and 33.3C ± 0.8 for RBD, JD and FTD, respectively (Weber & Craig, 2025). Through modelling enzymatic activity in a segmented regression, breakpoint estimates were found for brain at 22.0C ± 0.8, heart at 22.0C ± 5.0 and muscle at 26.0C ± 4.7 indicating decreases in enzymatic activity at higher temperatures. These results indicate that enzymatic activity in brain and heart tissue is most impacted by increased temperatures as evident by the lower trending breakpoints, suggesting that these tissues may be implicated in defining thermal tolerance limits. Muscle tissue enzymatic activity also decreased at higher temperatures but had a higher trending breakpoint, suggesting compensatory mechanisms. Moreover, breakpoints also occurred far before previously determined CTmax values for these fish, indicating that biochemical processes decline in performance prior to ecological death. Overall, these findings enhance our understanding of the biochemical processes that limit thermal tolerance in these local species, with potential implications for conservational efforts in defining temperatures of concern.
The impact of wastewater effluent and enantiomers of venlafaxine on darters (Etheostoma spp.) in the Grand River
(University of Waterloo, 2025-05-26) Pfeifer, Louis
Aquatic organisms, such as fishes, are in constant contact with various anthropogenic stressors present within their environments, including contaminants from wastewater treatment plant effluents (WWTPE). WWTPE represents a pervasive source of pharmaceutically active compounds (PhACs) in surface waters, with the serotonin and norepinephrine reuptake inhibitor venlafaxine (VEN), frequently detected at elevated concentrations in receiving waters worldwide. VEN is a chiral pharmaceutical administered as a racemic (50:50) mixture of R- and S-enantiomers, which exhibit distinct pharmacological activities and can be selectively degraded or enriched in effluent depending on treatment processes. However, little is known about the stereoselective toxicological effects of VEN in fish, particularly in the context of multi-contaminant WWTPE exposure. This thesis investigates the systemic effects of WWTPE and enantiomer-specific VEN exposure on Etheostoma spp. (darters) using transcriptomic profiling, oxidative stress assays, and biochemical markers of cellular damage. Wild darters (rainbow, greenside, fantail, and johnny darter) were collected upstream and downstream of the Waterloo municipal WWTP outfall (Grand River, ON). Additionally, a laboratory-controlled VEN exposure was conducted using rainbow darters, where liver tissue was analysed for transcriptomic responses and brain tissue was assessed for oxidative stress markers. Findings reveal that WWTPE alters hepatic function and stress responses, with species-specific transcriptional responses. However, key biological pathways related to lipid metabolism, immune regulation, and mitochondrial function were consistently disrupted across species. Laboratory exposure to VEN demonstrated stereoselective effects, where R-VEN primarily influenced amino acid metabolism, vesicle trafficking, and immune pathways, while S-VEN affected chromatin remodelling, epigenetic regulation, and extracellular matrix organization. Despite some overlap in lipid metabolism and inflammatory pathways, few transcripts were shared between VEN-exposed fish and WWTPE-exposed wild populations, highlighting the complex interactions of multi-contaminant mixtures in effluent-exposed fish. In the brain, VEN exposure induced oxidative stress and cellular damage, as evidenced by increased superoxide dismutase (SOD) and glutathione peroxidase (GPX) activity, as well as elevated lipid peroxidation byproducts. S-VEN had a more rapid oxidative impact, suggesting a higher potential for neurotoxicity, which may contribute to behavioural alterations in exposed fish. Overall, this research contributes to the development of biomonitoring practices by identifying molecular markers and key biological pathways disrupted by WWTPE and VEN exposure. Findings support the refinement of Adverse Outcome Pathway (AOP) frameworks for pharmaceutical contaminants and provide high-quality transcriptomic reference data for use in high-throughput ecotoxicological monitoring. These results raise considerations for improving monitoring, regulation, and treatment strategies to better address the potential ecological impacts of effluent-derived pollutants in freshwater ecosystems.

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