Bioinformatics

The study examines the phytochemical and phytohormone profiles of two ecotypes of Doliocarpus dentatus (Capadulla) from Guyana with an emphasis on their potential therapeutic applications, particularly in the context of erectile dysfunction. The research concentrates on the red and white ecotypes, which are visibly differentiated by the colouration of their inner and outer bark; moreover, the red ecotype is widely regarded by traditional knowledge to be more efficacious in treating erectile dysfunction. The study seeks to provide much-needed scientific evidence to support the traditional medicinal uses of D. dentatus and aims to accomplish this by providing semi-targeted and targeted analysis of its bioactive compounds.The thesis employs a multi-faceted approach, commencing with Chapter 2, an examination of the international and national frameworks that govern natural product research in Guyana, thereby ensuring ethical and sustainable practices. Chapter 3, Liquid chromatography-mass spectrometry-based metabolomics was utilized to analyze the phytochemical profiles of the red and white ecotypes of D. dentatus. Approximately 847 compounds were identified, with 138 tentatively classified as potentially therapeutic, particularly polyphenols exhibiting antioxidant properties. Chapter 4 focus on the phytohormone profiling revealed that the red ecotype generally exhibited higher levels of active cytokinins, particularly trans-zeatin (tZ) and cis-zeatin (cZ), compared to the white ecotype. A strong correlation was identified between specific cytokinins and secondary metabolites such as flavonoids and alkaloids, suggesting complex interactions that may enhance the therapeutic potential of D. dentatus. Chapter 5 further analysis of total phenolic content, flavonoid content, and their antioxidant capacities demonstrated differences between the red and white ecotypes, with the red ecotype generally showing higher levels of these compounds. Both ecotypes demonstrated significant antioxidant activity, with the red ecotype showing enhanced radical scavenging capacity. The study also revealed a diverse range of bioactive compounds, including flavonoids, terpenoids, and alkaloids, which may contribute to the plant's reported medicinal properties. This semi-targeted and targeted analysis provides novel insights into the phytochemical and phytohormone profiles of D. dentatus ecotypes, offering a scientific basis for their traditional medicinal uses and potential therapeutic applications. The findings suggest that D. dentatus, particularly the red ecotype, may have significant potential for developing new drugs, especially in the context of erectile dysfunction therapy.

Author Keywords: antioxidant, Bioactive compounds, liquid chromatography-electrospray ionization tandem mass spectrometry, metabolomics, secondary metabolites, therapeutic properties

Crop losses due to pathogens, pests, and weeds account for 20–40% of global production, with fungal pathogens responsible for the most significant yield reductions and economic impact. The diseases caused by fungi spread through dormant spores, which protect its genetic material under adverse conditions. Dormancy is maintained until favorable germination conditions are met. Despite their importance in the fungal lifecycle, the molecular transitions from dormancy to germination remain poorly understood. The research presented uses the basidiomycete Ustilago maydis, the causal agent of Common Smut of Corn, to investigate fungal spore dormancy and germination. It aims to 1) identify the molecular transitions and stages of teliospore germination and 2) the roles of RNA helicases during teliospore germination. RNA-seq and respiration analyses were used to propose teliospore germination stages and a microdissection technique was developed for studying these stages. Transcriptomic analysis identified patterns of gene transcript level changes during germination, with GO term enrichment identifying genes involved in cell morphogenesis, metabolism, and RNA metabolism. Several RNA helicases were identified with potential roles during dormancy and germination. Previous work in the Saville Laboratory proposed that mRNAs are stored as dsRNA in dormant teliospores. I hypothesized that RNA helicases function to make these mRNAs available for translation upon germination. Forty-six RNA helicases were identified in U. maydis, and 28 RNA helicases were proposed to have roles in growth, pathogenesis, stress response, and teliospore dormancy and germination. The RNA helicases udbp3 and uded1 were selected for functional analysis by creating mutant strains. The results suggest that udbp3 negatively regulates osmotic stress response, potentially modulating stress-responsive genes during dormancy. The altered uded1 expression in mutant strains leads to slow and polarized growth and dsRNA formation. This suggests uded1 represses translation by stabilizing sense/antisense transcripts in dormant spores and then reactivates translation during germination. These findings increase our understanding of the molecular events during teliospore germination and offer insights into factors contributing to disease progression in fungal plant pathogens.

Author Keywords: gene expression, genome annotation, RNA helicases, RNA-seq, teliospore germination, Ustilago maydis

Hybridization contributes to the genetic diversity and can impact speciation. This study investigates the genetic evidence of recent hybridization under climate change in sympatric populations of northern and southern flying squirrels in Ontario. Using low-coverage whole-genome sequences, my research examines the existing population structure and measures the genomic variation of the Glaucomys species. The global estimates of FST (0.308) and DXY (0.141) are indicative of substantial differentiation between the species. Measures of genetic diversity (π), differentiation (FST), and divergence (DXY) across the genome reveal insights into the divergent selection driving speciation. Results indicate an absence of contemporary hybridization or introgression at a site with longstanding sympatry. Across both species' genomes, signatures of selection align with four different scenarios for the formation of genomic landscapes of differentiation, shedding light on the complex speciation history of these flying squirrels. These findings enhance understanding of evolutionary dynamics, adaptation, speciation, and genetic differentiation.

Author Keywords: Genomic differentiation, Glaucomys, northern flying squirrel, southern flying squirrel, speciation