Research Area: Microbiology

Cullen Myers

Our current research projects focus on:
- The genetics and enzymology of cell wall glycopolymer degradation and roles in cellular processes including cell division, morphogenesis and the expression of virulence properties.
- The enzymology, structural biology and associated bacterial physiology of lesser-known penicillin-binding proteins, and penicillin-binding protein variants associated with β-lactam resistance.
- The development of activity-independent in vitro platforms to interrogate the flux of xenobiotics across the bacterial cell envelope.

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Matthew Sorbara

Healthy gut microbiota can be disrupted due to antibiotic treatment, intestinal inflammation, or changes in diet. Targeted restoration of the microbiota will require an understanding of how genomic diversity between closely related microbes influences their ability to drive beneficial functions. To address this, our laboratory will use a large collection of whole-genome sequenced isolates to understand how variation between closely related gut isolates alters their ability to prevent pathogen expansion and maintain homeostatic interactions with the mucosal immune system.

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Melanie Wills

My research group focuses on the diagnosis, prognosis and treatment of Lyme disease. I focus on different topics within this research theme, including: 1) the various forms that Borrelia (Lyme bacteria) can adopt and their corresponding role in the expression of the disease; 2) the effects of people and bacteria genetics in the expression of of the disease; 3) the development of new diagnostic tools; and, 4) the interactions that people diagnosed with Lyme disease have with the medical system.

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George van der Merwe

We study the transcriptomic and proteomic adaptation of yeasts to changing nutrient environments, as well as their domestication and fermentation to better understand yeast performance and potentially develop strategies and predictions of fermentation efficiencies and flavour compound production during alcoholic fermentations. We also look at yeast diversity and the unique flavour compounds that could expand product diversity in the wine, beer and cider industries.

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Siavash Vahidi

A key focus of the group is on the protein degradation machinery that helps to maintain proper level of proteins (protein homeostasis) in Mycobacterium tuberculosis, the causative agent of TB, the world's single largest infectious killer that is annually responsible for 1.5 million deaths. The questions we aim to answer are:
1) What is the assembly mechanism of the M. tuberculosis proteasome core particle and its regulatory particles?
2) What is the role of allostery and long-range interactions in the machinery that tags substrates for proteasomal degradation?
3) How are substrates selected for tagging and degradation?
4) What is the molecular basis of antibiotics that operate by disrupting proteasomal protein degradation?

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Baozhong Meng

The ultimate goal of my research is to understand viruses and viral diseases for the betterment of agriculture. Our research involves a number of important viruses that infect plants, which include Grapevine rupestris stem pitting-associated virus (GRSPaV), a ubiquitous and important pathogen of grapes worldwide. Current research directions include: Processing and subcellular localization of polyproteins; structure and cellular localization of viral replication complexes; evolution and bio-informatics of grapevine viruses; development of virus-induced gene-silencing vectors ; and, development and application of technologies for the diagnosis of grapevine viruses.

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Robert Mullen

My research focuses on three main areas of plant cell biology:
1) Characterization of enzymes involved in seed oil biosynthesis.
2) Understanding various aspects of the biogenesis of peroxisomes, including how membrane proteins are targeted to this organelle, and what role the endoplasmic reticulum (ER) serves in the formation of peroxisomes.
3) Identification and characterization of a unique class of integral membrane proteins known as "Tail-Anchored" (TA) proteins.

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Ray Lu

My lab focuses on two main axes of research:
1) Unfolded Protein Response and Human Diseases: We study proteins that play key roles in animal stress responses, specifically the Unfolded Protein Response (UPR), which has been linked to animal development, cell differentiation, as well as a variety of human diseases such as Alzheimer’s, diabetes, cancer and viral infection.
2) Molecular Mechanisms of Aging: We are working to establish planarians as a new aging model to test the hypothesis that longevity requires multiplex resistance to stress. We hope to identify genes or alleles that confer such multiplex stress resistance and/or promote longevity.

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Matthew Kimber

For bacteria, survival requires evading detection. Pathogens must evade their host, but all bacteria need to avoid being targeted by phages. Gram negative bacteria’s survival depends on lipopolysaccharide and capsule – highly complex carbohydrate molecules that coat their outer surface. The enzymes that produce these molecules are complex, drawing on a large set of basic modules but then tweaking and combining them into new organizations that accomplish unique ends. My lab is focused on understanding how the structures and large-scale architectures of these enzymes create the enormous variety of unique custom carbohydrates observed in nature. To this end, we use crystallography, enzymology, and a variety of biophysical assays and bioinformatics tools to better understand these proteins.

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Krassimir Yankulov

We use the budding yeast S.cerevisiae as a model organism to ask how established chromatin structure is preserved or changed during repetitive rounds of DNA replication, and how these structures are transmitted to daughter cells. We study the activity of chromatin factors that are highly conserved in all eukaryotes. Our specific focus is on cell-to-cell variations in gene expression. Most of these variations are mediated by chromatin. We know little about the mechanisms that confer these changes.

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Rebecca Shapiro

To better study the biology and virulence of fungal pathogens, we are developing new genomic technology platforms for diverse fungal species. We are exploiting CRISPR-Cas9 based technologies to revolutionize the way we do high-throughput functional genomic analysis in fungal pathogens. This is enabling us to map large-scale genetic interaction networks, and uncover genetic factors and pathways that mediate important phenotypes associated with pathogenesis, antifungal drug resistance, and other biological processes associated with fungal infectious diseases.

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Emma Allen-Vercoe

We currently have several projects in various areas that explore aspects of the gut microbiome and beyond:
1) Understanding how gut microbes are involved in the modulation of disease in colorectal cancer, diabetes, infection, and inflammatory bowel diseases
2) Isolation and characterisation of hunter-gatherer people's gut microbiome in an effort to discover novel microbial species and understand their function
3) Characterisation of the non-bacterial microbes of the human microbiome and their functions
4) Building model systems to study human gut microbes in vitro and in vivo
5) The study of 'oncomicrobes' (in particular, Fusobacterium nucleatum), and the development of colorectal cancer.
6) Translation to the clinic - development of 'microbial ecosystem therapeutics'

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Cezar Khursigara

Dr. Cezar Khursigara's research focuses on understanding how bacterial pathogens respond to their environment to cause disease. They are particularly interested in factors involved in biofilm formation and chronic infection. His research group is taking a multidisciplinary approach to answer fundamental questions related to how bacteria form biofilms to cause persistent infections. By combining advanced systems biology and imaging techniques, his goal is to identify potential therapeutics that can target a broad spectrum of disease-causing bacteria.

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Stephen Seah

We are interested in microbial enzymes involved in the steroid and aromatic compounds degradation. These enzymes are important for bioremediation of organic pollutants and are potential targets for development of antibiotics against tuberculosis. In collaboration with Dr. Ting Zhou at Agriculture Agri-food Canada, we are isolating and characterizing enzymes capable of detoxifying the mycotoxins, deoxynivalenol and patulin. These mycotoxins contaminate grains and fruit juices.

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Karl Cottenie

In the next 5 years, I will shift my research strategy by consolidating 4 streams of my past research: temporal dynamics, host-symbiont interactions, small mammal metacommunity dynamics, and DNA-based species identification and bioinformatics. I will focus on a study system that combines my past strengths in metacommunity ecology at multiple scales, but will apply them to a novel system: microbial metacommunities nested within a matrix of metacommunity of different host species.

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Andreas Heyland

Dr. Heyland's laboratory uses novel functional genomics approaches to study the endocrine and neuroendocrine systems of aquatic invertebrates. Specifically he investigates the function and evolution of hormonal and neurotransmitter signaling systems in the regulation of development and metamorphosis. His research includes evolutionary development studies of marine invertebrate metamorphosis, eco-toxicogenomic approached to understand endocrine disruption in aquatic ecosystems and water remediation technologies. These projects are integrated with several national and international collaborations ranging form basic scientific work to industry partnerships.

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Jennifer Geddes-McAlister

We are interested in characterizing the mechanisms of pathogenesis, adaptation, and survival in fungal and bacterial microbes from a systems biology perspective through mass spectrometry-based quantitative proteomics. Specifically, research in the lab centres around the following areas:
1) Systems biology to elucidate microbial proteome dynamics and interactions;
2) Mechanistic characterization of pathogenic proteins; and
3) Mass spectrometry-based proteomics for drug discovery and repurposing.

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Georgina Cox

The Cox lab aims to gain a better understanding of the molecular underpinnings of resistance mechanisms. Specifically, we study bacterial efflux systems, which will provide insight into their physiological functions and origins and will also support future drug discovery efforts and antibiotic stewardship. In addition, recognizing the need for innovation in the search for new antibacterial agents, we are exploring novel approaches to control bacterial infections by investigating the inhibition of bacterial adhesion to host cells.

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