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Graduate supervisors

Name Area(s) of interest
Trevor C. Charles We use molecular genetics to probe the interactions of bacteria with their host organisms, focusing on the model Sinorhizobium meliloti / alfalfa interaction. We study soil and human microbiomes using functional metagenomics.

For more information view the profile page of Charles.
Simon Chuong Plant cell and molecular biology: Cellular and molecular characterization of mechanisms controlling the structure and function of single-cell C4 photosynthesis in terrestrial plants. Major interests include characterizing the role of the cytoskeleton and its regulatory proteins in the movement of organelles and localization of macromolecules resulting in the establishment of cellular polarity in plant cells. We use a combination of approaches such as biochemistry, molecular biology, physiology, and cell biology including standard immunofluorescence and immunogold electron microscopy as well as the latest imaging techniques involving fluorescent-tagged proteins of living cells to investigate the research questions.

For more information view the profile page of Chuong.
Kim Cuddington Theoretical and terrestrial ecology: Current ecological theory does a poor job of linking the physical environment to community processes. As a result there is a gap between ecosystem ecology and population/community ecology. This linkage is investigated in various systems of interest for conservation and management, such non-native forest pests, using both mathematical models and experiments. Current projects include development of new theory to predict the effects of species which modify the physical environment (ecosystem engineers), and production of accurate models of climate variability to predict extinction risk.

For more information view the profile page of Cuddington.
Brian Dixon Molecular and functional characterization of fish immune systems, particularly Major Histocompatibility (MH) receptors and chemokines. Studying MH gene evolution through the molecular characterization of various fish populations. Effects of toxic chemicals on immune systems of aquatic organisms.

For more information view the profile page of Brain Dixon.
D. George Dixon Effects of toxic chemicals on aquatic organisms, principally fish. Biotic modifying factors of toxicity. Development of methods for environmental effects monitoring. Physiologically based pharmacokinetic modelling of contaminant levels in fish.

For more information view the profile page of George Dixon.
Andrew Doxey

Research in the Doxey Lab seeks to understand how biological function is encoded by DNA sequences, proteins and ultimately entire genomes. 

We develop and apply computational methods to analyze, predict, and design molecular functions using genomic and bioinformatic data. Our work spans multiple disciplines including computational biology, molecular evolution, structural biology, protein design, and genomics.

For more information view the profile page of Doxey.

Bernard P. Duncker Cancer-related cell cycle studies. My research is focused on characterizing protein factors that regulate the initiation of DNA replication, a key step in cell proliferation. The budding yeast Saccharomyces cerevisiae, is being used as a model organism, as it is one of the few eukaryotes for which numerous origins of replication have been identified. Many origin-associated protein factors have now been isolated from budding yeast. Human homologues of replication proteins originally identified in yeast have recently shown great promise as markers for potentially cancerous cell proliferation. Current work in the lab includes studying the Dbf4/Cdc7 kinase, which helps to trigger DNA replication by associating with origins and phosphorylating other origin-bound proteins, characterizing ORC (the origin recognition complex), and identifying novel origin-associated replication factors.

For more information view the profile page of Duncker.
Bernard R. Glick Isolation, characterization and manipulation of microbial genes which encode products that are involved in the microbial stimulation of plant growth. Biochemical and physiological consequences of genetically lowering plant ethylene levels. Microbial siderophore and phytohormone biosynthesis.

For more information view the profile page of Glick.
Bruce M. Greenberg Photobiology and Photochemistry of xenobiotic contamination and ultraviolet radiation. The work addresses the impacts of sunlight on environmental biology and chemistry. The focus is on two projects: Photoinduced toxicity of environmental contaminants and effects of Ultraviolet (UV-B) radiation on plants. These projects involve molecular, biochemical, photochemical, photobiological and whole organism techniques. The toxicology project deals with the impact of structural modification of contaminants after release into the environment. The environmental chemistry and toxicology of polycyclic aromatic hydrocarbons (PAHs) are under investigation as a model system to address these problems. The UV-B project is to assess the impact stratospheric ozone layer depletion on plants. The long range goal is the development of crop plants that are tolerant to elevated UV-B radiation and to probe the mechanisms of tolerance.

For more information view the profile page of Greenberg.
Roland I. Hall

Applied aquatic ecology, paleolimnology, diatom algae. My research combines fields of aquatic ecology, paleoecology, hydrology and multivariate statistics to assess effects of multiple stressors (periodic floods & droughts, acidification, climatic variability & change, nutrients, species invasions) on lakes, wetlands and reservoirs. A focus is to improve our understanding of factors that regulate aquatic ecosystems at a multi-annual, whole-system scale. An additional focus is to quantify and predict ecosystem responses during degradation and recovery phases due to human disturbances and natural phenomena. Ongoing research projects assess effects of:

  • climatic variability and river impoundment on hydro-ecological conditions of sensitive lakes and wetlands in the Mackenzie Basin Deltas (Peace-Athabasca Delta, Slave River Delta, MacKenzie River Delta) over the past 1,000 years. (Collaboration with Dr. Brent Wolfe [Natural Sciences and Engineering Research Council (NSERC) Northern Research Chair, Wilfrid Laurier University], Dr. Tom Edwards [Earth Sciences, University of  Waterloo], Dr. Peter Leavitt [U. Regina]; Dr. Bill Last [University of Manitoba] );

  • interactions among acid deposition, climatic variability (drought) and wetlands on recovery of Ontario lakes from effects of acid rain (collaboration with Dr. Peter Dillon [NSERC Industrial Research Chair, Trent University], Dr. Andrew Paterson [Ministry of the Environment (MOE), Dorset Environmental Science Centre] );

  • human land use and climate on Lakes in Africa during the past 200 years (collaboration with Dr. Bob Hecky, Biology, University of Waterloo)

For more information view the profile page of Hall.

John J. Heikkila Our research goals are to understand the function and developmental regulation of small heat shock proteins (shsps) during early development. Shsps are molecular chaperones that are involved in stress resistance and cellular differentiation. Their synthesis has been associated with various disease states such as multiple sclerosis, Alzheimer’s disease and muscle myopathy. Recent studies in my lab using amphibian embryos have shown that members of the shsps are differentially expressed during development and that recombinant shsp can act as a molecular chaperone by inhibiting heat-induced protein aggregation. Examples of the methods used in our laboratory include gene cloning, Reverse Transcription Polymerase Chain Reaction (RT-PCR), in situ hybridization, immunhistochemistry, microinjection of modified genes into embryos, molecular chaperone assays, site-specific mutagenesis, protein analysis etc.

For more information view the profile page of Heikkila.
Todd Holyoak

Dr. Holyoak’s research group is interested in examining the connections between the structural plasticity of enzymes and their ability to function as biological catalysts. This work relies heavily on determining the three-dimensional structures of enzymes of interest using X-ray crystallography. Beyond the structural studies, research projects encompass the kinetic and biophysical characterization of enzymes of interest in order to more fully understand the relationship between structural plasticity and enzyme function and regulation. Enzymes under current study in the laboratory include phosphoenolpyruvate carboxykinase, an essential metabolic enzyme with a key role in the maintenance of blood sugar levels, as well as a family of large, extracellular proteases secreted from pathogenic bacteria.

For more information view the profile page of Holyoak

Zoya Leonenko

Biophysics of lipids and lipid-protein interactions, the role of structural changes and physical properties of lipid monolayers and bilayers in controlling biological processes and diseases, and application of lipid films in biomedical nanotechnology. Methods: optical, fluorescence and scanning probe microscopy such as atomic force microscopy (AFM), Kelvin probe force microscopy (KPFM), AFM based force measurements, as well as Langmuir-Blodgett monolayer technique.

For more information view the profile page of Leonenko.

Susan Lolle Non-mendelian inheritance in plants: Molecular and genetic approaches are employed to understand how individual Arabidopsis thaliana plants can give rise to offspring that have distinct molecular profiles from those of the parent plant. Our research shows that the inheritance of non-parental markers occurs through a completely novel mechanism and suggests that these plants sequester a cryptic copy of ancestral genomic information. Research efforts focus on elucidating how Arabidopsis plants can give rise to this de novo genetic variation and whether these inbreeding plants harbor a genomic sequence cache.

For more information view the profile page of Lolle.
Kesen Ma Physiology and enzymology of hyperthermophilic archaea and bacteria: anaerobic and sulfur-dependent metabolism; function of dehydrogenases and flavoproteins; alcohol metabolism; relationship between structure and function of thermostable enzymes; protein engineering.

For more information view the profile page of Ma.
Mungo Marsden My research interests are centered around the molecular mechanisms that mediate changes in biological form. In particular I am interested in the modulation of cell adhesion states that allow for the complex three dimensional rearrangements that characterize early embryogenesis. These changes in adhesive state are under strict spatial and temporal control, and in many cases stem from extra-cellular signals that cells perceive in their immediate environment. My major line of research involve two families of cell adhesion molecules, the integrins, and the cadherins. Recent evidence indicates the regulation of adhesive states is through a direct cross-talk between these molecules, indicating a coordination between cell-matrix and cell-cell adhesion. This regulation of cell adhesion is not only found during early development but is also of fundamental significance to a wide variety of health related issues such as cancer and wound healing.

For more information view the profile page of Marsden.
Brendan J. McConkey Protein structure and function; bioinformatics and proteomics. Current research involves development of methods for the prediction of protein structure from amino acid sequence, using a combination of computational and biochemical techniques. Cross-linking data obtained from mass spectrometry is integrated into predictive algorithms, greatly reducing the problem complexity. Target structures include bacterial proteins inducible by antibiotic stress, and membrane proteins of unknown structure.

For more information view the profile page of McConkey.
Barbara A. Moffatt Plant molecular biology: isolation and molecular genetic analysis of mutants of Arabidopsis thaliana that are deficient in adenosine/adenine recycling some of which lead to defects in methylation. The role of these enzymes in plant development is being examined by genetic and biochemical analysis, metabolic profiling, protein interaction studies, immunolocalization, in situ hybridization, light and electron microscopy and creation of transgenic plants.

For more information view the profile page of Moffatt.
Kirsten M. Müller

Biogeography, evolution and ecology of eukaryotic algae and the prediction of RNA secondary structure. My research is focused on the evolution, biogeography and ecology of marine and freshwater eukaryotic algae (primarily the Rhodophyta). These organisms play an important role in both freshwater and marine ecosystems. In particular, the rhodophyte subclass, Bangiophycidae, has been a primary focus in my laboratory. This subclass is believed to be the ancestral group from which the more morphologically complex red algal taxa have arisen and have played a pivotal role in the origin of plastids through secondary symbioses in the Cryptophyta, Haptophyta and Heterokonta. More recently we have been examining the invasion of eukaryotic algae (Bangia atropurpurea) and the distribution of green algae (Cladophora glomerata and Ulothrix zonata) within the Laurentian Great Lakes. My research program uses a combination of techniques to address biogeographic and taxonomic questions: analysis of conserved DNA sequences (nuclear and plastid SSU rRNA and rbcL genes), analysis of ultrastructural and morphological characteristics, karyology, seasonality studies, population genetics (Inter Simple Sequence Repeats ISSRs, RAPDs and Amplified Fragment Length Polymorphism AFLPs). In addition, my research focuses on the use and prediction of rRNA structure from sequence (covariation analysis) and the use of structure in taxonomic delineation.

For more information view the profile page of Müller.

Josh D. Neufeld

Microbial communities are responsible for the biogeochemical cycling of trace gases, fertility of soils and aquatic environments, healthy function of the human body, metabolic production for the food industry, and countless applications in biotechnology. Despite a profound influence of microorganisms on human life and the global climate, very little is known about the distribution and diversity of microorganisms in natural communities, the vast resource of genes associated with the majority of uncultured microbial life, and the identities of most microbial species on earth: those adapted to life at low abundance.

My lab seeks to understand the causes of microbial diversity, the importance of diversity for ecosystem function, and the relationship between taxonomic and functional diversity. We discover new organisms and pathways involved in carbon and nitrogen cycling in soil and aquatic environments. We are developing new molecular methods to identify and characterise low-abundance organisms. Please contact me if you are interested in graduate work or postdoctoral opportunities in these areas.

For more information view the profile page of Neufeld.

Michael Power Research activities focus on the conduct of inter-disciplinary programs in the areas of freshwater fisheries ecology and management and risk assessment. There is a special emphasis on the application of stable isotope techniques to the study of such issues. Current projects include collaboration with: [1] the Department of Fisheries and Oceans on an analysis of possible climate change effects on anadromous and lacustrine stocks of Arctic char, the analysis of trophic polymorphisms in Arctic char and comparative analysis of impacted lake foodwebs; [2] the University of Plymouth on the analysis of fish and invertebrate community structure change in British estuarine environments; [3] the Shannon regional Fisheries Board, Ireland, on a comparative trophic analysis sympatric Arctic char and brown trout populations; and [4] the Ontario Ministry of Natural Resources on telemetry studies of brow trout in the Credit River. Graduate students are currently working on aspects of caribou ecology using stable isotopes, validation of defensible methods for determining habitat alteration impacts on fish populations, determination of the impacts of water abstraction from small headwater streams on resident brook trout populations and macro-invertebrate communities and the use of stable isotopes to track contaminant impacts in aquatic foodwebs in northern Alberta.

For more information view the profile page of Power.
Rebecca Rooney For more information view the profile page of Rooney.
Bruce H. Reed Our lab uses green fluorescent protein (GFP)-based methods of live imaging in the model genetic organism Drosophila (the fruit fly) to study how cells are genetically programmed to die when they lose contact with their surroundings. The failure of this type of cell death – known as ‘anoikis’ – contributes to cancer metastasis and tumour invasiveness in humans. As a model system for anoikis we are studying the dynamics and interactions of the amnioserosa and the yolk membrane during embryonic development. One of the players in the interaction of these extraembryonic tissues during Drosophila development is basigin (Reed et al. , 2004: Current Biology 14 , 372-380), also known as EMMPRIN, which is a transmembrane integrin-associated glycoprotein. Mammalian homologues of basigin have established roles in tumour invasiveness but also function as a part of normal embryo implantation.

For more information view the profile page of Reed.
David R. Rose

Structural Studies of Glycoside Hydrolases
This major area of research involves enzymes that recognize and act upon carbohydrates, including especially glycosidases involved in the protein glycosylation pathway and the process of starch digestion.
Current projects include:
- Human intestinal glucosidases involved in deriving glucose from starch. These are potential targets for controlling blood glucose  and insulin levels.
- Glycosidases from bacterial flora, for example from the mammalian gut microflora or from environmental samples
- Mannosidases and other enzymes involved in building the carbohydrate structures on glycoproteins. These are potential therapeutic targets for cancer and infection.

Additional projects are available in collaboration with Dr. Warren Wakarchuk (Adjunct Professor)
Glycobiology is central to many important biological and biochemical processes. In particular, the interaction of surface glycoconjugates of pathogens and their hosts. These interactions are the result of specific interactions with many different binding partners. Fundamental aspects of the function of these glycoconjugates are still not well understood. In order to determine the functions of these complex molecules we must be able to dissect the biosynthetic process, find the control points in these processes, and understand the interactions of glycoconjugates with their receptors. My research has been centred around the investigation of the structure and function of the enzymes involved in making various glycoconjugates. The determination of glycosyltransferase enzyme donor/acceptor specificity as well as contributing to the determination of the 3-dimensional structures has been the major area of research, and will continue to be the focus of my collaborative research program. My research interests also involve similar work on glycosylhydrolase enzymes which are of important to either metabolism of glycoconjugates, or generation of sugars for production of bio-products or of use in synthetic carbohydrate chemistry.

For more information view the profile page of Rose.
Mark R. Servos

The research explores the exposure, effects and remediation of diverse environmental contaminants in aquatic ecosystems. We examine the sources of pollutants and how environmental conditions and processes alter their fate and bioavailability in organisms, especially fish. Using our advanced trace analysis laboratory we quantify exposure and evaluate the influence of water quality and ecosystem structure on uptake into organisms. We link contaminant exposure to observed effects using Effects Directed Assessments that isolate and identify key bioactive components of complex matrices such as municipal effluents. The biological mechanisms starting from gene expression and leading to changes in fish populations are studied to support assessment of risk and the implementation of effective risk management and remediation. We are equipped with leading edge technologies for trace contaminants analysis (LC-MS/MS and GC-MSD) and gene expression through to working with whole organism exposures in our Wet Lab and collections of wild fish (electrofishing, boats, etc). Through extensive collaboration we work in local sites as well as across Canada and internationally.

For more information view the profile page of Servos.

Ralph E.H. Smith Freshwater ecology with emphasis on primary producers and their interactions with natural and anthropogenic environmental factors. Effects of climate change (especially concerning ultraviolet radiation, organic and inorganic contaminants, and invasive species in aquatic ecosystems. Plankton and environmental assessment.

For more information view the profile page of Smith.
J. David Spafford Calcium channels participate in brain functions, such as synaptic transmission, neuronal plasticity, patterned nerve activity underlying rhythmic behaviours, outgrowth of neurons and synapse formation. Actively seeking graduate students.

For more information view the profile page of Spafford.
Heidi Swanson

Using advanced analytical techniques such as stable isotope ratios and otolith (i.e., ear bone) chemistry, I research ecology, life history, and contaminant bioaccumulation in Arctic fishes. My current program includes research on mercury concentrations in fish from the Deh Cho region of the Northwest Territories, trophic ecology of fishes in the Beaufort Sea, life history of Lake trout in Lake Superior, and effects of climate change on ecology and mercury concentrations in lakes on the North Slope of Alaska. I place great value in developing positive collaborative relationships with other academics, government researchers, Aboriginal communities, and industry, and projects in my lab typically involve both laboratory and field components. 

For more information view the profile page of Swanson

Jonathan Witt

Application of molecular markers to address questions related to the ecology and evolution of aquatic organisms. A central theme that is currently being addressed in my lab concerns the reasons for, and consequences of disparities between rates of evolution at the molecular morphological and morphological levels. To address these issues, we employ both population and species level comparative approaches. The lab is also engaged in research related to conservation, and the use of molecular methods for the diagnosis of species boundaries. 

For more information view the profile page of Witt.