Department of Biology Graduate Theses

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    Field assessment of Vincetoxicum rossicum secondary metabolites and their effects on species richness and V. rossicum invasion
    (2024-05-17) Le, Andrew; Biology; Colautti, Robert
    Vincetoxicum rossicum is an invasive vine in North America that impacts native biodiversity and ecosystem services. One of the leading hypotheses to explain the rapid proliferation of V. rossicum is its ability to produce phytotoxic chemicals that directly inhibit the growth of native plants or act indirectly by altering soil fungal communities. Although (-)-antofine, septicine, and tylophorine have been shown to exhibit antifungal properties in vitro, it is unclear whether these chemicals are biologically active and ecologically relevant under natural field conditions. In this thesis, I test the ecological relevance of (-)-antofine and other phytochemicals using field survey data from the Rouge National Urban Park, Canada. First, I test the hypothesis that plots with higher densities of V. rossicum will have higher soil concentrations of (-)-antofine, septicine, and tylophorine. Second, I test the hypothesis that species richness will be lower in plots with higher concentrations of these allelochemicals. Finally, I test the hypothesis that plots with higher allelochemical concentrations will have a direct negative effect on species richness in the following year, and an indirect positive effect on V. rossicum abundance. Soil cores were collected from twelve meadow and nine forest understory sites. In total 168 soil samples were analyzed using ultra-performance liquid chromatography with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-Q-TOF-MS) to measure the concentration of all three secondary metabolites. The impacts of soil allelochemicals produced by V. rossicum were compared using linear and structural equation models. Overall, the concentrations of soil allelochemicals were all positively correlated with the density of V. rossicum, and species richness was negatively correlated with allelochemical concentrations. Furthermore, our structural equation model provides empirical evidence that these allelochemicals impact V. rossicum abundance but not species richness in the following year. In addition, my findings suggest that allelochemicals produced by V. rossicum varied across habitat-type and allelochemical type, with only (-)-antofine impacting meadow habitat. My research indicates that (-)-antofine may be an important factor, but it is not sufficient, to fully account for the success of V. rossicum.
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    Effects of artificial climate warming and competition on growth of Alliaria petiolata and Vincetoxicum rossicum
    (2024-05-10) Sherise Vialva; Biology; Colautti, Robert; Antunes, Pedro
    Climate change and exotic invasive species are both major threats to global biodiversity. Experimental studies typically treat these as separate phenomena, but their impacts may be antagonistic. For example, studies investigating the ecology of invasive species usually focus on interactions with invasive species even though habitats often include many competing invaders. In this thesis, I study competition between two invasive species in southern Ontario, Vincetoxicum rossicum and Alliaria petiolata, where they threaten local biodiversity. First, I investigate the extent of co-existence between V. rossicum and A. petiolata at different spatial scales, using observational records and targeted field surveys. Second, I set up a field experiment conducted at the Queen’s University Biological Station (QUBS) using artificial warming chambers to test how future climate warming may affect future co-existence. Results from the field survey show that V. rossicum and A. petiolata frequently co-exist locally in southern Ontario, as close as 0.5 m2. In the QUBS experiment, A. petiolata was a stronger competitor than V. rossicum, having no significant difference in size between individuals growing in the two competition treatments. Conversely, V. rossicum was, on average, 20 % shorter when grown with A. petiolata than grown with other V. rossicum. Additionally, climate warming appears to benefit A. petiolata more than V. rossicum with A. petiolata height, number of leaves, and leaf area all becoming significantly larger under warming conditions. On the other hand, only V. rossicum height increased under warming conditions while leaf number and leaf area were unaffected. Based on these results, I predict that A. petiolata is more of a threat than V. rossicum and will become more so in the future, and therefore the former should be a higher priority for control when both species are present in an area.
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    Understanding the Regulation and Function of CDK8 Using Saccharomyces Cerevisiae
    (2024-02-28) Anbalagan, Bhuvan; Biology; Aristizabal, Maria
    Cdk8 is a conserved protein kinase and a member of the Mediator transcription co-activator complex. Accumulating evidence highlights CDK8 as an oncogene in colorectal cancer, emphasizing the need to understand its function and regulation. Notably, CDK8 amplification or overexpression is observed in approximately 60% of colon cancer tumours and has been detected in melanoma, leukemia, as well as breast, pancreatic, and prostate cancer. Collectively, this evidence has stimulated efforts to develop Cdk8 inhibitors for cancer therapy. Despite a growing interest to target Cdk8 for anti-cancer treatment we have limited information about Cdk8 regulation, a knowledge gap that may complicate efforts to block its activity. To understand the function and regulation of Cdk8, I used the budding yeast model system and leveraged disease-associated variability and recent insight from structural and biochemical analyses. Specifically, using information from primary cancer studies and ClinVar I identified a cluster of CDK8 missense mutations that localize to the kinase ATP binding pocket and sites of interaction with proteins known to regulate Cdk8 kinase activity, that affect CDK8 function. Careful examination of these mutants suggests the existence of a feedback mechanism that regulates Cdk8 protein and mRNA levels. In addition, my work also showed that the interaction between Cdk8 and Med12 regulates CDK8 function in a condition-specific manner. Collectively, this research sheds light on the function and regulation of Cdk8, work that will inform the development of targeted therapies and enhance our understanding of the mechanisms by which Cdk8 contributes to cancer development.
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    Identifying Candidate Genes for Flowering Time and Floral Development in Genome and Transcriptome Assemblies of the Non-Model Plant Lythrum salicaria.
    (2024-02-06) Fuentes-Vergara, Mabel S.; Biology; Colautti, Robert
    Climate change is leading to environmental shifts, challenging the survival of many organisms. Some invasive species like Lythrum salicaria (purple loosestrife) can rapidly adapt to new conditions and thrive in human-altered habitats, offering a valuable model for studying the ecological and genetic factors that enable species survival under global change. While the ecological factors promoting the invasion and spread of L. salicaria are well-studied, the genetic basis for ecologically important traits is less understood. The aim of this thesis was to develop an annotated genome and transcriptome to investigate the genetic architecture of L. salicaria and the genetic basis of adaptive traits. A draft genome of a diploid ancestor from the native range was assembled using paired-end and mate-pair libraries sequenced on the Illumina HiSeq and MiSeq platforms. Ten transcriptomes were sequenced, representing four tetraploid individuals from the introduced range, and included different samples from the stem, floral meristem, flowers, and fruits of early and late-flowering phenotypes. Additionally, the genome assembly was annotated using the transcriptome as well as sequence-based predictions. The genome assembly was approximately 0.8 Gb in size across 648 scaffolds with 60,656 potential genes. A re-assembly of the transcriptome using the annotated genome resulted in 120,565 transcripts derived from 66,445 potential genes, including isoforms. An enrichment analysis identified 1,946 genes potentially involved in flowering processes, with 1,399 showing protein matches to 124 reviewed flowering-related proteins in the UniProtKB database. Additionally, matches were identified for genes related to stress response and defense metabolites. A key focus was the differential expression analysis of transcripts related to flowering time and floral tissues, providing insights into the genetic factors influencing these traits in L. salicaria. This research enhances the understanding of the genetic architecture of L. salicaria and identifies candidate genes for future investigations into plant genomics and adaptation strategies in changing environments.
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    Assessing the Toxic Effects of “Eco-Friendly” Road De-Icer Alternatives on Freshwater Plankton Communities
    (2024-01-12) Martin, Troy A.; Biology; Arnott, Shelley
    Increasing use of de-icing salt on roads and paved surfaces is contributing to rising salinity in freshwater, threatening aquatic ecosystems. In response, novel road de-icers advertised as “eco-friendly” have been developed and are widely used in cities across North America. Despite this, testing of the toxicity of road salt alternatives rarely extends beyond individual aquatic species, and community and ecosystem-level testing remain limited. We used outdoor mesocosms at the Queen’s University Biological Station to test how zooplankton communities, important primary consumers in aquatic systems, responded to multiple levels of three de-icers: road salt (NaCl), an organic alternative (beet-juice & salt-brine), and an inorganic alternative (NaCl, CaCl2, MgCl2). We found that both alternatives were toxic to zooplankton and decreased total abundance and affected community indices. Cladocerans and copepods were more sensitive than rotifers to all de-icers. We saw various impacts at the zooplankton species level, indicating differential sensitivities that could impact community composition, species interactions, and ecosystem function. However, the mechanisms of toxicity among de-icers may have differed; a decline in oxygen in the organic alternative correlated with the decline in zooplankton abundance not observed in the other de-icers tested. The inorganic and road salt de-icers also increased the chlorophyll a concentration at the end of the chloride gradient, while the organic de-icer decreased it. These results suggest that some de-icer alternatives might not be as environmentally friendly as advertised despite their recommended and growing use across North America, although more research is needed in impacted lakes.