Program and Abstracts

Oral presentations (20)

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The biodiversity of Microfungi isolated from the bark of the Sugar Maple (Acer saccharum)
Jonathan Mack (Graduate student – Smith Lab – Carleton University)
The diversity of microfungi occurring on the bark of the Sugar Maple (Acer saccharum) has never been documented. This study examine the biodiversity of microfungi from the bark of ten different dead trees from three distinct forests using traditional (direct observation and moist chamber) and high-throughput (particle filtration with dilution to extinction) culture methods. Commonly isolated species are presented. Three species were found to be new and are compared to closely related taxa based on morphology and phylogeny. Caveats and recommendations for future studies are discussed.
Two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis
Gokalp Yildirir (Graduate student – Corradi Lab – University of Ottawa)
We combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome and epigenetic diversity in a group of obligate plant symbionts: the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within-species variability in size, as well as in gene and repeat content. Strain-specific Hi-C contact maps reveal a ‘checkerboard’ pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments.
A systematic approach to developing new Antimicrobial Peptides
Ali Shukri (Graduate student – Biggar & Wong Labs – Carleton University)
Antibiotic resistance is a growing concern that threatens global healthcare systems around the world. Antimicrobial peptides (AMPs) are a diverse group of biomolecules that have been shown to have substantial inhibitory activity against pathogens. Here, we use systematic evolution of two known AMPs Indolicidin and UyCT3, and through generations of peptide evolution, our predicted peptides can inhibit growth of Escherichia coli in comparison to its wild-type counterpart.
Examining nuclear transfer between homokaryotic and dikaryotic strains of Rhizophagus irregulari
Bianca Turcu (Graduate student – Corradi Lab – University of Ottawa)
Anastomosis between compatible fungal strains results in nuclear transfer, creating spore progeny with new combinations. To assess if nuclear exchanges occur in arbuscular mycorrhizal fungi, I examined anastomosis frequencies between 12 crosses of homokaryotic and dikaryotic strains of the model AMF species R. irregularis using microscopy and droplet digital PCR. Evidence of nuclear transfer was observed between the crosses. Future crossings between closer relatives may result in more successful nucleotype transfers which could further confirm the creation of new nuclear combinations.
Achieving hypoxia/ischemia tolerance through Ca2+ management in Naked mole-rat brain mitochondria
Hang Cheng (Graduate student – Pamenter Lab – University of Ottawa)
Most adult mammal brains are highly sensitive to reduced oxygen availability (i.e., hypoxia/ischemia). Naked mole-rats (NMRs, Heterocephalus glaber) are among the most hypoxia-tolerant mammals and there is evidence that NMR brain is tolerant of in vivo and in vitro hypoxic/ischemic challenges. However, our understanding of the underlying neuroprotective mechanisms is in its infancy. Of particular interest are mechanisms that regulate mitochondrial Ca2+ homeostasis since Ca2+ dysregulation is central to hypoxia/ischemic cell death in hypoxia-intolerant mammal brain. The goal of my study is to uncover mechanisms via which mitochondria maintain cellular Ca2+ homeostasis, and the impact of these mechanisms on hypoxia/ischemia tolerance in NMR brain. Using high-resolution respirometry, I found that NMR brain mitochondria better retain oxidative phosphorylation (OXPHOS) capacity than mouse following serial external Ca2+ challenges: the half-maximal inhibitory concentration (IC50) at which Ca2+ inhibits OXPHOS capacity was 81.65±4.49 in NMR versus 34.13±3.35 µM in mouse. Additionally, NMR brain mitochondria maintained outer-mitochondrial membrane integrity until relatively higher dose of Ca2+, (100 µM in NMR versus 20 µM in mouse). Moreover, the phosphorylation system control ratio was regulated by Ca2+ in a dose dependent manner in NMR but not mouse brain mitochondria. Finally, I examined the relationship between mitochondrial membrane potential (Δψm) and Ca2+ uptake using fluorescence measurements. The results suggested that Δψm significantly regulates Ca2+ uptake in NMR but not mouse brain (Koff (1/sec) = 1.3±0.12 E-3 in NMR versus 1.4±0.2 E-4 in mouse). Correspondingly, the IC50 at which Ca2+ decreases Δψm was 36.11 ± 0.51 in NMR versus 8.25 ± 0.14 µM in mouse. These abilities may permit uptake of and tolerance to large amounts of Ca2+ during hypoxia in NMR brain mitochondria, which may help explain the remarkable tolerance to hypoxic/ischemic stress in NMR brain.
Activation of the Hippo Pathway in Rana sylvatica: Yapping Stops in Response to Anoxia
Aakriti Gupta (Graduate student – Storey Lab – Carleton University)
Regulation of glucose signaling in naked mole-rats during hypoxia
Mohammad Ojaghi (Graduate student – Pamenter Lab – University of Ottawa)
Does cannabis inhibit an endocannabinoid degradation enzyme?
Ryan Pusiak (Graduate student – Harris Lab – University of Ottawa)
This presentation will tease apart the effects of cannabis samples on the inhibition of an endocannabinoid degradation enzyme. I will walk the audience through cannabis, cannabinoids, interactions with the endocannabinoid. The results will explore differences between groups of cannabis and inhibition, followed by correlating inhibition to levels of THC (tetrahydrocannabinol – the high compound) and CBD (cannabidiol: calm back down). There might even be explanation on codes I ran in R.
Introgression of early maturity alleles from wild soybean to domesticated cultivars
Simon Lackey (Graduate student – Samanfar Lab – Carleton University)
Wild crop relatives are being investigated for potential genes in numerous economically important crops. Plant breeders will need to look to the soybeans wild crop relative, Glycine soja Sieb. & Zucc., for added diversity and adaptability. Examples of G. soja have been found with increased salt tolerance, novel resistance mechanisms to soybean cyst nematode, greater resilience in poor soil conditions, and elevated seed protein content. This study aims to investigate early maturity found in a G. soja accession that may harbor novel alleles not found in cultivated G. max.
Insights into a cancer-target demethylase: substrate discovery avenues for lysine demethylase 3A
Anand Chopra (Graduate student – Biggar & Willmore Labs – Carleton University)
Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the removal of methyl groups from lysyl residues. Several JmjC KDMs promote cancerous properties, of which KDM3A is relevant to tumour progression. To uncover the mechanism(s) by which KDM3A imparts its oncogenic function(s), we unraveled KDM3A substrate specificity to then predict and validate novel KDM3A substrates. Notably, this led to the identification of three in vitro substrates which are relevant to cancer progression. These findings may be further explored to decipher the avenues by which KDM3A imparts cancerous phenotypes.
CYP1A1 induction as a biomarker of pollutant-induced β-cell dysfunction
Myriam Hoyeck (Graduate student – Bruin Lab – Carleton University)
Human studies report an association between exposure to persistent organic pollutants (POP), such as dioxin, and increased diabetes risk. We have recently shown that ex vivo exposure to dioxin activates cytochrome P450 1a1 (CYP1A1) and supresses insulin secretion in human islets. However, the magnitude of these effects varied considerably amongst donors, indicating donor-specific responses to dioxin. We are investigating the cause for this variability to better understand factors that are driving pollutant-induced β-cell dysfunction in human islets.
Predicting the severity of COVID-19 with Machine Learning approaches
Matthieu Vilain (Graduate student – Aris-Brosou Lab – University of Ottawa)
To date, predicting the outcome of epidemics is essentially based on epidemiological modeling, which proved limited in the case of COVID-19. To circumvent this, we propose to resort to genomics and Machine Learning algorithms. As a proof of concept, we recoded SARS-CoV2 complete genomes using tools from Natural Language Processing (k-mer / Term Frequency Inverse Document Frequency), and trained both Random Forests and Feedforward Neural Networks. Result show we can predict case numbers, as well as the 2-week incubation period, and identify parts of the genome affecting virulence.
Cyp1a1/1a2 deletion protects female mice from high-fat diet induced glucose intolerance
Angela Ching (Graduate student – Bruin Lab – Carleton University)
Type 2 diabetes (T2D) incidence has been increasing in recent years. A high-fat diet (HFD) and exposure to environmental pollutants are risk factors for T2D. Cytochrome P450 1A1/1A2 (CYP1A1/1A2) enzymes are mainly involved in breaking down xenobiotics, but they are also involved in fatty acid metabolism. In mice, HFD activated CYP1A1/1A2 enzymes in the endocrine pancreas, which contains insulin-producing cells. I performed a long-term HFD study on Cyp1a1/1a2 knockout (CypKO) mice and littermate controls to investigate the role of CYP1A1/1A2 on glucose regulation.
Exploring biological traits of Common Carp to inform the use of barriers for selective fragmentation
Morgan Piczak (Graduate student – Cooke Lab – Carleton University)
We examined biological traits that can be exploited to exclude non-native common carp from spawning habitat using barriers, while also minimizing impacts on native fish species. The four biological traits that can be used to implement this selective fragmentation include phenology, sensory capabilities, morphology and ethology. This approach with common carp can be applied to other aquatic non-native species to assess the potential for barriers to minimize impacts on native species.
Reproductive roles of the nonapeptides AVT and IT in Danio rerio: using a Crispr/Cas9 approach
Divya Ramachandran (Graduate student – Mennigen Lab – University of Ottawa)
Arginine vasotocin (AVT) and oxytocin (OXT) are nonapeptides that are well conserved across all vertebrate species with notable roles in sociosexual behaviors and reproduction. I created two zebrafish knockout lines for AVT and OXT respectively to test that these nonapeptides are determinants of reproductive success in zebrafish. Mating assays revealed that homozygous AVT -/- lines exhibited reduced reproductive success. Probing mechanistic basis for this phenotype, I found that the HPA-controlled ovary develops less eggs compared to wild type controls.
Latitudinal trends in Lobelia mating system inferred from Citizen Science
Matthew Coffey (Graduate student – Andrew Simons – Carleton University)
Lobelia inflata is obligately selfing at the northern extent of its species range. We used images uploaded to iNaturalist to study geographic trends in selfing behaviour in L. inflata and four North American congenerics. The visibility of the floral stigma, inferred from observation photos, was used as a proxy measure for outcrossing capability. We found that for L. inflata, evidence of outcrossing increased at southern latitudes which followed traditional trends of selection for selfing at range margins and high latitudes.
Cisplatin impairs β-cell function in immortalized cell lines and mouse islets
Lahari Basu (Graduate student – Bruin Lab – Carleton University)
Diabetes incidence is rising rapidly, suggesting that unidentified environmental factors are contributing to diabetes risk. Previous research has shown increased rates of metabolic syndrome and diabetes risk in cancer patients following cisplatin treatment. In our studies, cisplatin exposure leads to impaired glucose-stimulated insulin secretion, altered mitochondrial function, and increased cell death in primary mouse islets and immortalized β-cell lines. These findings suggest that cisplatin-induced β-cell dysfunction could contribute to increased diabetes risk in cancer survivors.
Disruption of DROSHA in HCT116 cells favours death by apoptosis in response to actinomycin D
Gavin Sharpe (Graduate student – McKay Lab – Carleton University)
MicroRNAs (miRNAs) are short non-coding RNAs that function as sequence-facilitated post-transcriptional inhibitors of gene expression. The cellular response to actinomycin D (ACT-D) was examined in genetically modified cell lines that differ in their ability to produce miRNAs. While miRNA-deficient cells are more susceptible to ACT-D-induced apoptosis, they are equally sensitive to the effects of ACT-D on DNA, RNA and protein synthesis. Our results suggest that these cell lines are equally sensitive to ACT-D but are differentially susceptible to distinct modes of ACT-D-induced cell death.
Investigating Diabetogenic Activity of The Flame Retardant, Dechlorane Plus, on Pancreatic β-Cells
Kyle Van Allen (Graduate student – Bruin Lab – Carleton University)
My research investigates diabetogenic activity of flame retardants such as Dechlorane Plus (DP) using INS1E cells, human islets, and stem cell-derived (SC) β-cells exposed to DP (1, 10, 100 nM) in vitro for 48-hours. DP exposure increased basal insulin secretion in INS1E cells and human islets from non-diabetic donors. However, diabetic donor islets and SC β-cells showed impaired stimulated insulin secretion, although results varied between human donors. These data suggest DP-exposed β-cells have impaired function that may differ depending on the initial metabolic health of the cells.

Poster presentations (13)

VO2max decreases in Heterocephalus glaber during continuous strenuous exercise in hypoxia
Sidney Abar (Undergraduate student – Pamenter Lab – University of Ottawa)
Hypoxia-tolerant naked mole-rat experience intermittent and severe hypoxia while performing energetically expensive tasks in their natural burrows. NMRs have been seen to decrease their metabolic rate by up to 85% in severe hypoxia, in part through decreases in thermoregulation and physical activity. However, previous experiments have studied resting animals and how hypometabolism impacts VO2max in exercising animals remains unknown. Therefore, we explored the interactions between hypoxia, thermoregulation, and exercise on metabolic rate in NMRs during exercise in a sealed running wheel.
Uncovering Substrates of Lysine Methyltransferase G9a
Feras Balbous (Undergraduate student – Biggar Lab – Carleton University)
G9a is an H3K9 methyltransferase and a regulator of gene expression. G9a has been associated with human health and disease, however, this association has also been linked to the enzyme’s ability to methylate non-histone proteins. The aim of the study is to identify G9a substrates outside of histones. Towards this goal, two approaches are implemented to determine potential substates of G9a:(1)a de novo approach of shared specificity where substrates of other H3K9 modifying enzymes are examined and (2)scoring of the methylome, ubiquitinome, and acetylome by K-OPL globally normalized array data.
Lost in translation: exploring microRNA biogenesis and messenger RNA fate in anoxia-tolerant turtles
Sarah Breedon (Graduate student – Storey Lab – Carleton University)
Red-eared slider turtles often face changes in oxygen levels, including long-term anoxic hibernation. Anoxia-tolerance is underlaid by regulatory mechanisms such as mRNA transcript silencing via miRNA. Hepatic miRNA biogenesis was appeared downregulated in early processing steps, while later steps were upregulated. These contradictory findings indicate either overall decreased miRNA biogenesis, or increased biogenesis if sufficient pre-miRNA stores were produced in early anoxia. Conversely, muscle showed clear upregulation of multiple biogenesis steps indicating increased miRNA production.
Glutathione depletion disrupts ROS homeostasis during hypoxia in cortex of naked mole rats
Liam Eaton (Graduate student – Pamenter Lab – University of Ottawa)
Oxidative damage during hypoxia/reoxygenation is linked to reactive oxygen species (ROS) flux. This is thought to be mitigated in brains of hypoxia-tolerant naked mole rats (NMRs) through attenuated production or enhanced scavenging. We hypothesized that ROS does not fluctuate in NMR cortex in hypoxia(1% O2)/reoxygenation, primarily due to enhanced ROS scavenging. ROS flux in NMR cortex remained unchanged during hypoxia/reoxygenation. CDNB application during hypoxia induced ROS flux. NMRs may maintain hypoxic ROS homeostasis through attenuated production and enhanced scavenging of ROS.
Uncovering the Basic Helix-Loop-Helix Transcription Factors Involved in Suberin Deposition
Kassandra Fugard (Graduate student – Rowland Lab – Carleton University)
The projected impacts of climate change may dramatically affect the growth and development of plant species across the world. The formation of specialized cell wall-associated barriers, such as suberin, is critical in maintaining water and solute movement in the root. We are exploring the molecular interactions of several suberin-associated transcription factors (TFs) in the plant species Arabidopsis thaliana. My research focuses on the role of basic helix-loop-helix (bHLH111 and bHLH112) TFs, as regulators of suberin synthesis and lateral root development under abiotic stress conditions.
Let’s talk plant-microbe interactions
Alicia Halhed (Graduate student – Rowland Lab – Carleton University)
Plant-microbe interactions contribute to the success of agricultural crops. A plant’s microbiome is a community of plant-associated microbes, such as bacteria and fungi. The primary objective of my research is to identify how plants communicate with the soil microbiomes in healthy or stressed conditions. I am currently developing analytical techniques to identify chemical cues in the plant roots and surrounding soil, including suberin and phytohormones. Continued research on plant-microbe interactions contributes to efforts in sustainable agriculture to feed a growing global population.
KDM5 demethylase family substrate preference and identification of potential non-histone substrates
Matt Hoekstra (Graduate student – Biggar Lab – Carleton University)
The KDM5 family of histone demethylases are responsible for the demethylation of histone H3 protein, with recent evidence that their function in disease goes beyond this demethylation event. To help identify non-histone substrates for the KDM5 family, we used a panel of permutated peptide substrates reflective of the WT H3 sequence to characterize recombinant KDM5A/B/C/D substrate preference. Recognition motifs were then developed and used to predict potential substrates for KDM5A/B/C/D. Assessing KDM5 activity with predicted peptide substrates generated a final list of high-ranking substrates
The bun giveth, the hot-dog taketh away: Oxidation state specificity in ALT-type thioesterases
Becky Kalinger (Graduate student – Rowland Lab – Carleton University)
Unlike similar enzymes, ACYL-LIPID THIOESTERASES (ALTs) from plants act on substrates of varied oxidation states, producing medium-chain, 3-hydroxy and β-keto fatty acids. While the products of ALTs have industrial value, little understanding of ALT substrate selectivity limits their biotechnological use. Guided by homology modelling, we identified three motifs in the ALT “hot-dog fold” catalytic domain that affect oxidation state specificity. By mutating these, we were able to broaden or restrict the product profiles of ALTs, a major step toward engineering ALTs for biotechnological purposes.
Metabarcoding aquatic fungi for monitoring environmental health in agricultural watersheds
Phillip Pham (Graduate student – Chen & Aris-Brosou Labs – University of Ottawa)
Aquatic fungi spend part of their life in aquatic environments, so their diversity is expected to reflect watershed quality, but they are seriously understudied. Addressing this knowledge gap, we hypothesize that they are sensitive to environmental perturbations. To test the impact of agricultural land use, weather conditions, and seasonal stream dynamics, we sampled the South Nation River watershed biweekly from 2016-2021 across 9 sites. Using ITS2 metabarcoding, we recovered ~74k barcodes, allowing us to test how land use affects their communities, and hence reflect environmental health.
A Tn-Seq Based Approach to Determining Genetic Background-Dependent Gene Essentiality
Laura Phillips (Graduate student – Wong Lab – Carleton University)
Genetic background may play an important role in determining gene essentiality – that is, whether such genes are essential on all background. We are using a transposon-sequencing (Tn-seq) based approach to determine gene essentiality in various antimicrobial resistance (AMR) strains of Escherichia coli. Comparison of transposon insertion in the presence or absence of antibiotic will allow us to determine what genes are essential uniquely to the AMR strains. This work will thus provide novel insight into the effects of genetic background on gene essentially.
Sub-zero microRNA expression in the liver of the frozen hatchling painted turtle
Anchal Varma (Graduate student – Storey Lab – Carleton University)
Hatchling turtles withstand 53% of total extracellular body freezing. MicroRNAs are a quick and reversible post-transcriptional regulator of biological functions. We found that 30 hepatic miRNAs changed during freezing, mostly affecting cell cycle, focal adhesion, linoleic acid metabolism, and signaling pathways. Overall, miRNA analysis revealed its role in the adaptive strategy that not only enables hatchlings to substantially suppress their nonessential energy needs but also makes them flexible enough to restore and protect their basal organ functions by activating pro-survival processes.
Development and Utilization of Avian ToxChip PCR Arrays for Contaminant Monitoring in the Arctic
Yasmeen Zahaby (Graduate student – Provencher Lab – Carleton University)
High temperatures in the Arctic cause a reduction in sea ice. This leads to more shipping traffic and oil exploration in northern Canada. Wildlife monitoring is needed to document effects of POPs in seabirds. The first chapter documents the development of a tool (ToxChip) to investigate gene expression for Common eider. A ToxChip for Black guillemot will be used for PAC analysis on samples from an oil-spill site and a site of a natural seep. The second chapter will focus on samples collected from a military site with PCB contamination before and after remediation.