The project will be focused on identifying and understanding the bacterial cell factors that enable Rhodobacter capsulatus to receive genes transferred by a virus-like gene transfer agent, RcGTA. The cells have receptors to be able to receive and incorporate RcGTA-borne genes in their genome. The approach is to create mutants and test these mutants for the ability to acquire an RcGTA-borne antibiotic resistance marker. We hypothesize that cell surface polysaccharides are crucial for RcGTA to be able to bind to target cells. To test this, in one approach we are analyzing the genome sequence to identify genes that might encode proteins needed for lipopolysacharide (LPS) biosynthesis, and targeting these genes for disruption (creation of knockout mutants). In a second approach, we are selecting for mutants that survive infection with a phage known to bind LPS (Bardy et al. 2025. "Penton blooming, a conserved mechanism of genome delivery used by disparate microviruses". mBio 16:e03713-24. https://doi.org/10.1128/mbio.03713-24). These mutants will be screened for their ability to acquire genes transferred by RcGTA, and characterized in terms of the genes mutated, to reveal the genetic basis of recipient capability.
Research area, student roles & skills
Research area: We study a variety of things relating to bacterial horizontal gene transfer, using the model system of a bacteriophage-like gene transfer agent (RcGTA) in Rhodobacter capsulatus. We are interested in the regulation of RcGTA gene expression, and the interaction of RcGTA protein domains with bacterial cell surface receptors leading to injection of DNA into the cell. Our research is guided by the high resolution structure of RcGTA, as described by Bárdy et al. "Structure and mechanism of DNA delivery of a gene transfer agent". Nat Commun. 2020 Jun 15;11(1):3034. doi: 10.1038/s41467- 020-16669-9.
Student roles: Student Activities The student will design PCR primers for amplification of sequences flanking potential LPS biosynthetic genes, and use the primers to amplify these sequences from R. capsulatus genomic DNA. These flanking sequences will be combined in a suicide plasmid, using FastCloning methods (Li, et al. https://doi.org/10.1186/1472-6750-11-92) in E. coli. The plasmid will be transferred into R. capsulatus by conjugation, with gene knockouts obtained using the sacB counter-selection method. Mutants will then be evaluated for LPS composition and recipient capability using an established gene transfer agent protocol.
Deliverables 1. Isolation of mutant strains. These strains are the first deliverable. 2. Characterize mutant strains in terms of LPS composition and gene transfer agent recipient capability. These data are the second deliverables.
Interaction The student and the professor will interact on a daily basis, and the student will also interact at greater length with other students and research associates each day. The student will be asked to present their research at a lab meeting, at least once during the summer. Lab members are eager and enthusiastic in their support in these meetings. When attending presentations, the student will be strongly encouraged to engage in constructive criticism, and questioning. The relaxed and friendly group meeting atmosphere is highly conducive to open questioning, debate, and discussion.
Skills required: General knowledge of bacterial cell structure, function, and physiology. Experience with bacterial cultivation, DNA purification and analysis, and protein purification. Gel electrophoresis methods, gene cloning and expression techniques, PCR. Familiarity with computer text and image applications is required. It would be helpful if the student is familiar with BLAST sequence alignments and other genome sequence analysis software.
The laboratory of Prof. Tarek Rouissi at the Eau Terre Environnement Research Centre (INRS) is currently seeking a highly motivated intern to join its research team. The selected candidate will contribute to an innovative project focused on the biodegradation of PFAS (per- and polyfluoroalkyl substances).
Research area, student roles & skills
Research area: Environmental Chemistry and Biotechnology
Student roles: The intern will actively participate in experimental research activities and contribute to the preparation of scientific publications in collaboration with the research team.
Skills required: We are looking for passionate and creative individuals who thrive in a collaborative and dynamic research environment. The ideal candidate will demonstrate: • Strong planning and organizational skills • Scientific rigor and persistence • Excellent communication and teamwork abilities
3. Caractérisation de microorganismes provenant de biofilms agroalimentaires.
The presence of spoilage bacteria and pathogens is a potential issue, especially when these microorganisms can form biofilms. The source of these microorganisms is often associated with the food, the water used for rinsing and/or the biofilm. In addition to posing a risk to food safety, biofilms are a complex microbial ecosystem that can damage equipment.
As part of this internship project, biofilm samples from the food industry will be received and added to the collection. IT management will be necessary to orchestrate everything. Subsequently, the microorganism(s) will be identified by various classical microbiological methods and sequencing methods. After its isolation, the microorganism will be characterized (Gram, morphology, etc.). In addition, its ability to form biofilms will be evaluated, to test new antibiofilm control strategies. The antibiofilm effect will be assessed by various analytical methods (e.g., absorbance measurement, bacterial counting on selective agars, and electron and/or confocal microscopy).
The results obtained during this internship will be decisive since they will allow us to expand the collection of microorganisms responsible for biofilms. Ultimately, this collection will facilitate the development and application of new control strategies in the agri-food industry.
Research area, student roles & skills
Research area: The presence of spoilage bacteria and pathogens can be a major problem in the food industry by affecting the quality and safety of the products. Biofilms remain one of the most important sources of unwanted microorganisms.
Dr. Julie Jean's research team is currently working to set up a unique collection of microorganisms that can produce biofilm the agri-food industry. It will speed up the development of antibiofilm control methods.
Student roles: Firstly, the student will be brought to read scientific literature to become familiar with his internship project. Secondly, he or she will be brought to prepare and organize the scientific experiments related to his project by using or adapting pre-existing tools and methods with the help of his supervisor to be able to carry them out in the best conditions. Finally, he or she will have to collect and analyze all the data from the different experiences that he or she will have realized in the laboratory. In parallel with its project, the student may be asked to provide technical support to the research team of the laboratory by carrying out various tasks associated with other projects of the laboratory.
Skills required: The successful candidate must have a BSc degree in microbiology, molecular biology, food science or other related disciplines. He or she will have practical skills in the microbiology and/or cell biology fields. The student should also have a special interest for research in food sciences and microbiology. He or she should also have to be independent, organized and have the ability to work with a team. Mastering French (written and spoken) will be considered a particular advantage.
A major goal of our lab is to understand how cell-wall insertion and ell-wall growth (spatial expansion) are coordinated, and how they lead to stable cell shape. This project will tackle this question experimentally, with live-cell fluorescence microscopy, combined with genetic and chemical perturbations, to study the role of enzymes synthesizing, cutting, or remodeling the peptidoglycan cell wall. We aim to study where in the cell these processes happen, whether they happen at the same location, at the same time, whether they are localized to common signals or whether one of the two processes attracts the respective other. We are using fluorescent proteins to label enzymes and cytoskeletal proteins involved in cell wall insertion, and we study the location of cell-wall growth/expansion by using fluorescent dyes that are bound to the peptidoglycan cell wall.
Research area, student roles & skills
Research area: Our interdisciplinary lab uses approaches from physics and biology to understand how bacteria control their cell shape during growth. Cell shape is physically determined by the cell envelope and notably by the peptidoglycan cell wall. To learn how cells control envelope geometry, architecture, and physical integrity we combine experiments (microscopy, microfluidics, genetics, and cell biology) and theory (computer simulations). We measure and perturb processes and variables ranging from cell-cycle progression, mechanical forces, and biomass growth, to single-protein movement. Since the cell envelope is a major target for antibiotics, our work ultimately helps to develop better antibacterial strategies.
Student roles: The student will conduct her/his own experiments under the supervision of a senior member of the lab. Depending on the background of the student the project can involve different activities listed below. The precise project will also be chosen depending on research progress prior to the start date, and depending on the preferences of the candidate. However, all students will conduct quantitative live-cell microscopy as a major part of the research project. - Live-cell microscopy, sample preparation - Computational image analysis - Construction of bacterial mutants through cloning, notably gene deletions, protein overexpression, and the construction of mutants, for proteins implicated in cell-envelope growth. - Construction and test of fluorescent-protein fusions to proteins of interest
Skills required: This project is open to students from backgrounds in both biology or quantitative sciences such as physics and engineering. However, it requires a keen interest in interdisciplinary science at the interface of physics and biology. Independently of background, basic experience in computer coding is desired. For students from biology, prior experience with cloning, molecular biology, or cell biology is helpful but not strictly required.
In this project you will work with model filter systems that use fungal tissue materials. The aim of this project is to study the absorption of various substances and ions (including pollutants) by fungi.
Research area, student roles & skills
Research area: I am a mycologist interested in fungal biodiversity, fungal ecology and mycoremediation.
Student roles: You will
1. Prepare filter systems 2. Measure chloride concentrations before and after fungal exposure. 3. Record results using different parameters 4. If time permits prepare vital stains and fungal cultures.
Skills required: A good background in biological sciences, biodiversity and related fields is required.
The ideal candidate would have had some prior experience in a mycological or microbiological laboratory.
6. Coarse-grained molecular-dynamics simulations of the bacterial cell wall
A major goal of our lab is to understand how cell-wall insertion and ell-wall growth (spatial expansion) are coordinated, and how they lead to stable cell shape. This project will tackle this question mostly theoretically, with coarse-grained molecular-dynamics computer simulations, however with a a potential experimental component for testing the computation-model assumptions.
The cell wall is a covalent meshwork of sugars and peptides that withstand the high osmotic pressure in the cell. During growth, the network must be cut by certain enzymes while other enzymes insert new material, all the while not perturbing cell integrity and shape. We are simulating the process of cell-wall growth using a molecular dynamics computer code that is to be further developed and who’s results are to be compared with experiments from our lab and experiments found in the literature.
Facultatively, these computational 'experiments' will be tested with experiments using live-cell light microscopy.
Research area, student roles & skills
Research area: Our interdisciplinary lab uses approaches from physics and biology to understand how bacteria control their cell shape during growth. Cell shape is physically determined by the cell envelope and notably by the peptidoglycan cell wall. To learn how cells control envelope geometry, architecture, and physical integrity we combine experiments (microscopy, microfluidics, genetics, and cell biology) and theory (computer simulations). We measure and perturb processes and variables ranging from cell-cycle progression, mechanical forces, and biomass growth, to single-protein movement. Since the cell envelope is a major target for antibiotics, our work ultimately helps to develop better antibacterial strategies.
Student roles: The student will further develop and explore the parameter landscape of an already existing molecular dynamics computer simulation code written in both python and C. There are different avenues for development (speed-up, extension to different geometries, (force-dependent) enzymatic activities) and conducting in silico experiments, i.e., measuring the results in the simulation and comparison to previous or current experiments. Tasks may involve - Coding in python and/or C - Data anlysis of simulation runs - Potentially live-cell microscopy including bacterial (sterile) culture, sample preparation, microscope handling, computational image analysis
Skills required: This project is for students with a background in quantitative sciences such as physics, engineering, chemistry. However, it requires a keen interest in interdisciplinary science at the interface of physics and biology. Independently of background, prior experience in computer coding beyond a mere programming courses is strictly required.
7. Copper-based nanoparticles as potential antifungals and antibiofilm agents for Pestalotiopsis clavispora blueberry infection.
Berry production (strawberries, raspberries, blackberries, and blueberries) holds immense economic importance for Mexico and Canada, generating significant revenue for both countries (SIAP, 2025; Agriculture and Agri-Food Canada, 2025). However, the industry faces a severe threat from the fungus Pestalotiopsis clavispora, which causes disease in the roots, crowns, vascular system, leaves, and fruits of these berry bushes, resulting in devastating economic losses, particularly in Mexico. In Canada, this is an emerging pathogen, already appearing and infecting berry crops in Ontario. P. clavispora persists by using several crops as biological bridges and is easily spread by wind, water, and agricultural practices. Its emerging resistance to conventional fungicides hinders its effective control, severely impacting export competitiveness, food security, and the livelihoods of farming families. In the context of plant pathology, fungal plant pathogens can form biofilms, highly structured microbial communities that are embedded within a self-produced extracellular polymeric substance (EPS), on plant surfaces, and in some cases, within host tissues. This EPS matrix, composed of polysaccharides, lipids, proteins, and extracellular DNA, provides structural stability and protection to fungal cells. The fungal biofilm cycle, beginning with initial attachment, irreversible adhesion, microcolony formation, maturation, and eventual dispersion, enhances pathogen persistence, host colonization, dissemination, and tolerance to fungicides.
Copper oxide nanoparticles (CuO-NPs) have gained significant attention as potent antifungal agents based on their broad-spectrum activity. Their efficacy is primarily driven by their ultra-small size, high surface area, and ability to interact with microbial cells, making them promising candidates for sustainable agricultural strategies. Many crops require low concentrations of copper to thrive, but at high concentrations it is damaging to both crops and soil, making the slow release of copper from nanoparticles an effective strategy. The proposed research will synthesize the CuO-NPs and evaluate their impact on P. clavispora and its biofilm structural integrity.
Research area, student roles & skills
Research area: My group studies how cells respond to environmental contaminants and antibiotics using biochemistry, microbiology and advanced microscopy. Of special interest to us is the mechanisms of antifungal agents, the impact of pesticides and how cells cope under these stresses during growth, differentiation, and biofilm formation.
My research group is developing new nanoscale tools to assess the impact of antifungals to prevent and combat fungal infections in human and plant hosts.
Student roles: The student will learn to do routine cell culture, prepare copper nanoparticles, minimum inhibitory concentration (MIC) assays and advanced microscopy. The MIC assays will assess the antifungal activity of the copper-based nanoparticles on the plant fungus Pestalotiopsis clavispora. Advanced microscopy (atomic force, confocal, scanning electron) will assess the impact of the copper-based nanoparticles on P. clavispora growth and biofilm formation. The student will be taught to collect, analyze and interpret data to present at weekly group meetings, and will be invited to attend our annual research retreat. Students are encouraged to write a full final report of their work that will ultimately contribute to a publication on which they would be co-authored.
Skills required: The student should have basic biochemical (accurate pipetting skills) and microbiological expertise, and basic computer skills. Knowledge of statistics, plant biology, and a theoretical and experiential understanding of light and fluorescence microscopy would be an asset. Students will have the opportunity to gain experience with atomic force microscopy and laser scanning confocal microscopy during the internship. Dahms group members are highly cooperative and helpful. Applicants are expected to be hard-working, motivated, persistent, and must be able to work in a team. This project will involve Dahms’ Biosafety Containment Level 2 laboratory for which the applicant would receive training.
8. Development of a real-time quantification system to study phage-bacteria interaction
Supervisor: Yuan Fang
University: University of Saskatchewan (Saskatoon campus)
It has been an age-old battle between phage and bacteria on microbial ecology. However, the real-time quantification methods to study the phage-bacteria interaction is lacking. Using an infusion protein green fluorescence protein (GFP) to report promoter activity has advanced system biology by allowing a real-time measurement of transcription kinetics in living cells. The approach has successfully determined the kinetic parameters of gene expression by measuring GFP activity under the control of different promoters in parallel using a fluorometer. The system, which allows analysis in an intact regulatory system, would provide a valuable tool for studying transcriptional interactions between bacteria and prophage regulation, which are independent but interactive regulation systems, particularly upon bacterial stress response. For instance, the prophage is an integrated DNA to bacterial genome during phage (bacterial virus) transduction; the expression of prophage remains dormant until host bacteria are stressed and trigged with specific stress response to repair cellular damages caused by stress. During stress response, the particularly stress-regulated protein (RecA) is overly produced and interact with prophage repressor, resulting autocleavage of prophage repressor and activation of prophage genomes.
Because the prophage-bacteria interaction occurs at specific condition and time, to qualify the extend of interaction between prophage and bacteria is challenging. To measure the transcriptional activity of the bacterial host and the prophage in real time, we will develop a dual-fluorescent quantification method using green and red fluorescent proteins (RFP) to report promoter activity and prophage expression, respectively. The reporter systems aim to include 19,000 GFP infused promoters of E. coli, each contain an RFP-labelled prophage.
The novel dual-fluorescence reporting system will be provides an advanced tool to study the dynamics of prophage and E. coli under environmental stress. This approach enables real-time, multiplexed measurement of the regulation and response of both bacterial host and phage.
Research area, student roles & skills
Research area: The research program specializes in linking fundamental mechanisms of bacterial physiology, genetic regulations, genomic diversity with microbial persistence, adaptation and survival in stress environments. The research integrates basic microbial assays, advanced molecular approaches and functional genomics to understand stress response and resistance mechanisms of foodborne pathogens to environmental changes and evaluate the intervention strategies to control their prevalence in Agri-food systems.
Student roles: Students will work closely with graduate students and postdoc in the program to facilitate technology and method development and conduct routine microbiological and molecular lab work . Students are responsible to execute research activities, collect, analysis and interpret data, report and present the results by the end of the internship. Lastly, as a member in the team, each students works collaborative to support the group and maintain the clean and safe lab environments.
Skills required: Ideal candidate is expected to have background in Food microbiology, Microbiology, Environmental microbiology, or related disciplines.
Antimicrobial resistance (AMR) has reached global disaster status, where existing antibiotics fail to treat infections. By 2050, 10 million people a year could die worldwide due to AMR, up from around 700,000 today. Infectious diseases pose a severe problem to health worldwide with a considerable social and economic burden. However, most research addressing this problem relies on testing isolated microbes under conventional lab conditions, which do not adequately represent the infection situation. These discrepancies likely lead to failure to capture the entire arsenal superbugs deploy during infection.
The proposed research project addresses these knowledge gaps by uncovering the microbial weapons unleashed only during infection but not in traditional lab conditions, which will enable the discovery of novel therapeutics that disarm microbes from these weapons. The student will explore the microbial responses to antibiotics under conditions that mimic different infection situations. Factors that will be examined include host-derived molecules and interactions between co-infecting bacteria. The observed microbial responses will be characterized through interdisciplinary studies using microbiology, biochemistry, molecular biology, chemical biology, and advanced chemogenomics methodologies. This work will uncover new clinically-relevant antibiotic resistance targets for the development of novel antimicrobials. Therefore, the goal is to exploit the newly identified targets to discover drugs that cripple microbes' ability to resist antibiotics under clinically-relevant conditions, using state-of-the-art high-throughput screening campaigns, providing new potential treatments for infectious diseases.
Together, the proposed research project will work towards providing new antibiotic leads for clinical development and help healthcare professionals optimally use currently available antibiotics in the clinic. Thus, this research will contribute to global efforts to fight antimicrobial resistance and alleviate the burden of infectious diseases worldwide.
Research area, student roles & skills
Research area: Dr. Omar El-Halfawy is a Canada Research Chair in Chemogenomics and Antimicrobial Research and an Associate Professor of Biochemistry. The El-Halfawy Lab is actively working towards solutions for the current antibiotic crisis. The research group uses a wide range of approaches spanning microbiology, biochemistry, molecular biology, chemical biology, and chemogenomics. Current efforts aim to uncover novel antibiotic resistance and microbial virulence mechanisms and discover new antimicrobial strategies under clinically-relevant infection-mimetic conditions. Previous work revealed previously unknown mechanisms of intrinsic antibiotic resistance mediated by metabolites and other bacterial small molecules and discovered novel solutions to target multi-drug resistant bacteria.
Student roles: The student will engage in cutting-edge research in a vibrant and interdisciplinary research setting using a state-of-the-art robotic high-throughput infrastructure. The student will undertake various training activities and perform experiments independently and under the mentorship of other senior lab members. The student will also survey and read some of the relevant literature, analyze and present the generated data in the form of lab presentations, written reports, or both as appropriate, and attend and actively participate in group meetings and individual meetings with Dr. El-Halfawy. Additional training opportunities outside the lab may be available through the university or in the form of science seminars, among others. The El-Halfawy lab endeavors to participate in various science outreach activities such as organizing and delivering science activities to school-age children that attend summer camps at the University of Regina. The student will be invited to participate in these science outreach events should they be organized during the student’s internship.
Skills required: Applicants are required to have taken an introductory microbiology theoretical course. A course in molecular biology, chemical biology, or biochemistry is an acceptable alternative. Background information in molecular biology, microbial biochemistry, medical microbiology, and/or topics related to infectious diseases, antibiotics, and microbial resistance to antibiotics is desirable. Similarly, prior knowledge of laboratory skills in bacteriology and aseptic technique is beneficial but is not required.
Antimicrobial resistance (AMR) has reached global disaster status, where existing antibiotics fail to treat infections. By 2050, 10 million people a year could die worldwide due to AMR, up from around 700,000 today. Infectious diseases pose a severe problem to health worldwide with a considerable social and economic burden. However, most research addressing this problem relies on testing isolated microbes under conventional lab conditions, which do not adequately represent the infection situation. These discrepancies likely lead to failure to capture the entire arsenal superbugs deploy during infection.
The proposed research project addresses these knowledge gaps by uncovering the microbial weapons unleashed only during infection but not in traditional lab conditions, which will enable the discovery of novel therapeutics that disarm microbes from these weapons. The student will explore the microbial virulence phenotypes under conditions that mimic different infection situations. Virulence phenotypes include biofilm formation and response to host innate immune system and may involve testing under various in vivo infection models. The observed microbial responses will be characterized through interdisciplinary studies using microbiology, biochemistry, molecular biology, chemical biology, and advanced chemogenomics methodologies. This work will uncover new clinically-relevant virulence targets for the development of novel antimicrobials. Therefore, the goal is to exploit the newly identified targets to discover drugs that cripple microbes' ability to cause severe infections under clinically-relevant conditions, using state-of-the-art high-throughput screening campaigns, providing new potential treatments for infectious diseases.
Together, the proposed research project will work towards providing new antibiotic leads for clinical development and help healthcare professionals optimally use currently available antibiotics in the clinic. Thus, this research will contribute to global efforts to fight antimicrobial resistance and alleviate the burden of infectious diseases worldwide.
Research area, student roles & skills
Research area: Dr. Omar El-Halfawy is a Canada Research Chair in Chemogenomics and Antimicrobial Research and an Associate Professor of Biochemistry. The El-Halfawy Lab is actively working towards solutions for the current antibiotic crisis. The research group uses a wide range of approaches spanning microbiology, biochemistry, molecular biology, chemical biology, and chemogenomics. Current efforts aim to uncover novel antibiotic resistance and microbial virulence mechanisms and discover new antimicrobial strategies under clinically-relevant infection-mimetic conditions. Previous work revealed previously unknown mechanisms of intrinsic antibiotic resistance mediated by metabolites and other bacterial small molecules and discovered novel solutions to target multi-drug resistant bacteria.
Student roles: The student will engage in cutting-edge research in a vibrant and interdisciplinary research setting using a state-of-the-art robotic high-throughput infrastructure. The student will undertake various training activities and perform experiments independently and under the mentorship of other senior lab members. The student will also survey and read some of the relevant literature, analyze and present the generated data in the form of lab presentations, written reports, or both as appropriate, and attend and actively participate in group meetings and individual meetings with Dr. El-Halfawy. Additional training opportunities outside the lab may be available through the university or in the form of science seminars, among others. The El-Halfawy lab endeavors to participate in various science outreach activities such as organizing and delivering science activities to school-age children that attend summer camps at the University of Regina. The student will be invited to participate in these science outreach events should they be organized during the student’s internship.
Skills required: Applicants are required to have taken an introductory microbiology theoretical course. A course in molecular biology, chemical biology, or biochemistry is an acceptable alternative. Background information in molecular biology, microbial biochemistry, medical microbiology, and/or topics related to infectious diseases, antibiotics, and microbial resistance to antibiotics is desirable. Similarly, prior knowledge of laboratory skills in bacteriology and aseptic technique is beneficial but is not required.
11. Harnessing interbacterial competition to improve biocontrol of plant pathogens
Supervisor: Sean Booth
University: University of Manitoba (Winnipeg campus)
Bacterial pathogens that infect crop plants must compete with other bacteria present. By inoculating the surface of crops with protective biocontrol bacteria, pathogens can potentially be kept away, preventing the need to use pesticides or the loss of the crop. However, in order to establish themselves and protect the plant, the biocontrol bacteria must also compete with any other bacteria that are present. Pseudomonas chlororaphis PA23 is a biocontrol bacterium which can inhibit the growth of the pathogen Xanthomonas translucens. Strains of Pseudomonas engage in interstrain competition using molecular weapons, especially protein bacteriocins called S pyocins. It’s possible that in trying to use PA23 to protect from X. translucens, native strains of Pseudomonas use their S pyocins to repel PA23, preventing it from establishing itself and providing protection. Conversely, PA23 could potentially use its S pyocins to combat any established strains and establish itself. To understand S pyocin mediated competition in plant biocontrol bacteria, we have generated mutant strains of PA23 which are susceptible to its own S pyocins, and will use these strains to test whether they can facilitate invasion and defence of plant surfaces. Most S pyocins enter target cells via iron importers, which are expressed in response to low environmental iron availability. The receptors for PA23’s S pyocins are unknown, and may be for other required metals than iron. To investigate the use of S pyocins for invasion and defence, wild-type attacker and susceptible strains will be co-cultivated in lab media and on experimental plants with differing levels of metal availability. The effectiveness of the pyocins will be measured by counting the number of cells of each type at the start and end using fluorescence microscopy, as the susceptible cells have also been tagged with constitutively-expressed fluorescent protein genes.
Research area, student roles & skills
Research area: Bacterial communities influence human well-being in myriad ways: those in our agricultural soils help us grow the plants we eat, and those in our bodies help us digest our food and protect us from pathogens. Controlling the composition of bacterial communities will allow us to increase crop yields and prevent infections. Bacteria attack and kill their rivals using nano-scale molecular weapon systems. By better understanding how bacterial warfare, we could use bacterial weapons as a lever to control the composition of communities.
Student roles: In this project, the students role will be to carry out competition assays between wild-type Pseudomonas chlororaphis and mutants susceptible to its own S pyocins. For these assays, cultures of both strains must be normalized to the same optical density, then mixed at defined ratios and diluted to set initial densities. These co-cultures will then be grown either in liquid cultures, static pellicle biofilms, as colonies on agar plates or on the surfaces of live plants. At the beginning and end of the cultivation period, the student will serially dilute the culture and plate them to determine how many cells of each strain are present. To distinguish the two strains, the susceptible strain has been tagged with fluorescent protein and antibiotic resistance genes, so a combination of antibiotic containing plates and fluorescence microscopy will be used to get accurate counts. Once the data have been collected, the student will be taught how to plot and analyze the data using the statistical computing program ‘R’. To investigate what kind of environmental conditions influence these interbacterial interactions, the student will make media with different compositions to try to replicate the chemical conditions present on plants. The student will also be responsible for making all the media they use throughout the experiments and will contribute to general preparation tasks for all the materials they will use in their experiments. The student will also grow plants from seed, then inoculate competitions directly onto the surface of the plants then recover the culture to determine how competitions play out in realistic conditions.
Skills required: The ideal candidate will be enthusiastic about investigating how bacteria interact with each other, and excited about the prospect of working with plant-associated bacteria. They should have basic skills in streaking cultures, pipetting, carrying out serial dilutions, and counting colonies. Experience weighing and measuring chemicals would also be beneficial. The project may also involve growing and handling plants, so experience or enthusiasm and patience for growing plants is needed.
12. Host-phage interaction in environmental adaptation
Supervisor: Yuan Fang
University: University of Saskatchewan (Saskatoon campus)
Shiga-toxin Escherichia coli (STEC) are major foodborne pathogens that are naturally adapted to cattle and frequently contaminate the beef processing environment in North America. Shiga toxins (Stx), the cardinal virulence factor of STEC, are encoded and well retained on prophages in STEC. Phage regulation encodes phage gene-specific regulatory components that interact with host regulatory systems in bacterial pathogens; however, their function is largely unexplored in STEC. Despite its importance as a zoonotic pathogen, a significant gap remains in understanding the function and benefits of Stx prophage for bacterial survival in drastically different environments, ranging from animals to food processing.
This research project aims to study the interaction of prophage and E. coli at stress environments and further the understanding of how prophage regulation impacts the bacterial response to stress. The project will focus on in vitro characterization of physiological changes and genetic responses using novel fluorescence-transcription systems developed by my research program. The development of the fluorescence transcription systems involves genetic editing and engineering to construct the fluorescence encoding gene to the targeted regions of host chromosome and prophage regions. The constructed mutant will express fluorescent proteins as a quantitative indicator of regulator activity of prophage and host bacteria. The novel molecular systems enables the real-time quantification of the interaction between prophage and bacterial host to advance the knowledge of the ecological relationship between bacteriophages and their bacterial host.
Research area, student roles & skills
Research area: The research program specializes in linking fundamental mechanisms of bacterial physiology, genetic regulations, genomic diversity with microbial persistence, adaptation and survival in food and food processing environments, to solve practice food safety related issues in various foods and food ingredients. The research integrates basic microbial assays, advanced molecular tools, applied bioinformatics to understand the mechanisms of stress response and resistance to environmental changes, and evaluate the novel and green preservation technologies to control the prevalence of foodborne pathogens during food processing.
Student roles: Students will be assigned with short project and will working closely with the graduate student in the lab as research assistant Students are responsible to execute research activities, collect, analysis and interpret data, present the results and prepare a report by the end of the internships.
Skills required: Ideal candidate is expected to have background in molecular microbiology, microbiology, food/environmental microbiology. Students should have experience working in the microbiology lab for over 6 months, and have hands on experience with bacterial inoculation, basic enumeration methods, and worked with molecular equipments, including PCR, qPCR, and etc. Able to and have experience working in a team.
The massive increase in antibiotics resistant bacteria has become a global health concern. In the near future even last resort antibiotics may not be effective against infections anymore. Some predictions indicate more people will eventually die from these infections than from cancer. Although we know the cellular targets of antibiotics, in most cases the precise mechanism how and under what circumstance the antibiotics actually leads to bacterial death is unclear.
This is especially concerning as bacteria are frequently exposed to antibiotics in the environment at levels that are far below therapeutic concentrations. In order to develop new means to control bacterial infections it is therefore crucial to improve our understanding of mechanisms leading to bacterial death. Recent studies have shown that the lethality of antibiotics is dependent on the activity of the bacterial metabolism during the time of exposure. Thus, there is an underappreciated connection between bacterial metabolic activity and efficacy of antibiotics.
The goal of this study is to identify this connection and pinpoint how antibiotics cause cellular collapse. Top this end, state-of-the-art quantitative proteomic techniques will be employed to investigate cellular activity of the human pathogen Salmonella enterica serovar Typhimurium in presence of antibiotics. This approach allows the large scale-monitoring of protein contents in the cell, which will be used to reconstruct the metabolic activity of the bacterium. Moreover, we will manipulate cellular metabolism by altering growth conditions and investigate how the cell reacts to antibiotics under these altered conditions. This investigation will provide insights into which processes are crucial for effective killing by antibiotics, how cells can potentially evade these effects, and how environmental conditions could affect antibiotics efficiency.
Research area, student roles & skills
Research area: My research aims to understand the molecular basis of cellular adaptations. Bacteria, react to environmental challenges by synthesizing proteins in response. The study of the bacterial proteome, i.e. the complete protein complement of the cell, therefore provides functional insights into how bacteria survive challenging conditions and, conversely, may allow the development of means to control them. In my laboratory we combine traditional molecular techniques with high-throughput quantitative proteomic approaches in order to dissect complex cellular adaptations of pathogens related to survival and infection processes.
Student roles: The candidate will perform antibiotic assays with the pathogen Salmonella wildtype, as well as mutant strains with modified metabolic activities. These analyses will identify the effect of altered energy or carbon metabolism to resilience to antibiotics. Additionally, the student will test how changing media conditions, such as increasing or decreasing nutrient levels affects antibiotics survival in Salmonella. Furthermore, from selected conditions cells will be harvested and proteins will be isolated. The student will then learn how to prepare protein samples for mass spectrometric analyzes and how to perform quantitative proteome studies. Within the project the student will gain familiarity in performing global “omics” analyses, including the handling and analysis of large molecular data sets. Depending on progressed the students are, the project will either focus more on technical skills or introduce more complex concepts such as the the impact of carbon and energy metabolism for bacterial stress survival.
Skills required: Ideally the student will have a background or interest in microbiology and/or molecular biology and be eager to learn and execute molecular biological experiments. Prior practical experience in basic laboratory work (e.g., aseptic cultivation techniques, molecular biological or bioanalytical methods, cloning) would be an asset. Specific training will be offered on-site.
14. Identifying mechanisms of persistence in hospital-associated isolates of Acinetobacter baumannii
Supervisor: Jessica Sheldon
University: University of Saskatchewan (Saskatoon campus)
Due to its frequent resistance to multiple drugs, the World Health Organization recently declared Acinetobacter baumannii a “priority critical” pathogen for research into novel treatment strategies. The design of new antimicrobials against A. baumannii is hampered by a lack of knowledge regarding the mechanisms it uses to survive and proliferate. The spread of A. baumannii not only within hospitals but globally is thought to be facilitated by a strategy known as “persist and resist.” Here, the prevalence of the bacterium is attributed to its ability to endure unfavorable conditions such as nutrient limitation, desiccation, pH extremes, and disinfection. One mitigation strategy to reduce the burden of A. baumannii would thus be to reduce or eliminate its environmental persistence. Although the “persist and resist” strategy is often cited to explain the establishment of A. baumannii reservoirs, rarely is the capacity of contaminating isolates to withstand various stressors directly assessed. This project, designed to provide students with technical skills in microbiology and molecular genetics, will evaluate hospital-associated isolates of A. baumannii for their ability to resist metal starvation, desiccation, acidic and alkaline pH, and common disinfectants. The resistance of these modern isolates will be compared to historical and laboratory strains of A. baumannii to determine if their increased prevalence can be explained by enhanced tolerance to these insults. Further, comparative genomics will be used to identify unknown mechanisms of persistence and resistance. Together this research will provide valuable insight into how A. baumannii thrives in harsh nosocomial environments.
Research area, student roles & skills
Research area: Our lab is broadly interested in studying the molecular pathogenesis of multidrug resistant bacteria. In particular, we are focused on how various stressors impact the outcome of infection, as well as persistence of these organisms in the environment. Current research within the lab focuses on Acinetobacter baumannii, an emerging opportunistic pathogen that causes a wide range of diseases, from wound and urinary tract infections, to more serious illnesses such as pneumonia and sepsis. We use techniques in bacteriology, molecular genetics, transcriptomics, and infection modeling to identify mechanisms used by A. baumannii to survive and proliferate under different conditions of stress.
Student roles: The student(s) will phenotypically characterize hospital-derived A. baumannii isolates by exposing bacteria to metal limitation, desiccation, extremes of pH, ethanol, and bleach, and comparing their growth to that of known type strains. Where discrepancies exist, whole genome sequencing will be performed to identify possible mechanisms of resistance. Time permitting, deletion mutants in putative “hits” will be produced to assess their role in resistance to a given stress.
Attendance at a responsible conduct in research meeting to discuss considerations of sex, gender, and EDI (equity, diversity, and inclusion) will be required of all employees.
Skills required: The student(s) should have basic bacteriology and molecular genetics experience, but more importantly, enthusiasm and motivation to perform basic science research. Beneficial skills include knowing strategies for culturing different bacteria and a knowledge of aseptic techniques, gel electrophoresis, PCR, and cloning/mutagenesis. Individuals with theoretical knowledge but without hands on experience are encouraged to apply. The student(s) is expected to be engaged, enthusiastic, resilient, and willing to work as member of a diverse scientific team.
15. Investigating how Crohn’s disease-associated bacteria form biofilms and cause inflammation
Supervisor: Wael Elhenawy
University: University of Alberta (Edmonton campus)
Inflammatory bowel diseases, like Crohn’s disease (CD), result from a dysregulated immune response towards the microbiome. Pathogenic bacteria like adherent-invasive Escherichia coli (AIEC) strains are known to drive gut inflammation. However, the mechanisms used by AIEC to promote disease are unknown. We have recently identified a role for type IV secretion system (T4SS) in biofilm formation by AIEC strains known to contribute to the development of CD (Wong et al., Nature Communications, 2025). These strains employ biofilm formation to persist in the gut and promote inflammation. Importantly, we have recently found that AIEC strains upregulate their T4SS upon adhering to the epithelial cells. This finding led us to hypothesize that these strains carry regulatory elements that link the expression of T4SS to the host cells. Thus, the following questions emerge:
1-What are the host cues responsible for activating T4SS in AIEC strains? (Aim1)
2-How are the host cues sensed by AIEC to initiate biofilm formation? (Aim2)
Answering these questions will inform the design of drugs that prevent biofilm formation by AIEC, and hence, decrease inflammation
Research area, student roles & skills
Research area: My research focuses on studying the perpetually complex interactions between gut bacteria and the host, and how this intricate ecological network affects human health. My primary research interest is to understand the molecular mechanisms that drive the pathogenesis of bacteria during Crohn’s disease (CD). My work focuses on using animal infection models and genomics to identify the components of bacterial virulence in the CD environment. The aim of this research is to unravel the genetic elements that allow CD-associated bacteria to propel inflammation, and evade antimicrobial therapy.
Student roles: Under direct supervision from Dr. Elhenawy, the student will execute high-throughput assays to identify the factors that promote biofilm formation in bacteria. This project also involves using next-generation sequencing to map the hits from the screening assays. In this regard, the student will learn how to analyze these datasets using pipelines developed in the laboratory (R language). Follow-up work entails making bacterial mutants to validate the hits and pursue the mechanisms underlying biofilm formation. The student will learn how to grow biofilms on epithelial cells and to use immunofluorescence to stain these structures. Importantly, the student will meet frequently with Dr. Elhenawy to discuss experiments and exchange ideas.
Skills required: Theoretical background of bacterial genetics and general microbiology. How gene regulation in bacteria work. Practical experience is an asset but not essential.
16. Mechanisms of histamine sensing and response in emerging opportunistic pathogens
Supervisor: Jessica Sheldon
University: University of Saskatchewan (Saskatoon campus)
Histamine is gaining recognition as an intra- and inter-species signaling molecule. In bacteria, these molecules often inform them as to their ecological niche, whereas in mammals, histamine is a key immunomodulator. Outside of the mammalian host, an important source of histamine is Gram-negative bacteria, particularly those residing in the gills and gastrointestinal tracts of fish and contributing to food spoilage. Improper storage of fish with naturally high levels of histidine (e.g. tuna, mackerel, and skipjack) can lead to toxic levels of histamine, formed through the activity of a histidine decarboxylase (HDC). HDCs are expressed by bacteria such as Morganella morganii and can result in histamine intoxication (scombroid poisoning), as well as expansive and expensive food recalls. The biological function of histamine in organisms like M. morganii is not well understood and elucidating its role(s) in Gram-negative bacterial physiology is a focus of our research program. Further, M. morganii is emerging as a multidrug-resistant superbug, capable of causing a wide variety of infections from those of the urinary tract and post-operative wounds, to frequently fatal cases of bacteremia and meningitis, where the factors contributing to the establishment of infection are largely unknown. We have identified a locus in M. morganii that is responsible for histamine biosynthesis, and through transcriptomics, targeted mutagenesis, and phenotypic characterization are elucidating how this organism responds to both endogenous and exogenous histamine. Together, these efforts will shed insight into key aspects of the biology of a vastly understudied and highly underappreciated opportunistic pathogen that is important both to global food safety and to human health.
Research area, student roles & skills
Research area: Our lab studies the pathophysiology of multidrug resistant bacteria. Specifically, we are focused on how various stressors impact colonization and infection, as well as persistence of these organisms in niches both inside and outside the host. Current research within the lab focuses on Acinetobacter baumannii and Morganella morganii, two emerging opportunistic pathogens that cause a wide range of diseases, from wound and urinary tract infections, to serious illnesses such as pneumonia and sepsis. We use techniques in bacteriology, molecular genetics, transcriptomics, and infection modelling to identify mechanisms used by these organisms to survive and proliferate under different conditions of stress.
Student roles: The student will phenotypically characterize clinical and environmental isolates of M. morganii, assessing their ability to produce and utilize histamine under various conditions of stress (e.g. nutrient limitation, pH stress, iron restriction, etc.) using commercially available histamine ELISAs. Expression of the histidine decarboxylase gene (hdc) of M. morganii will be assessed by real-time PCR under the aforementioned conditions. Using transcriptomics (RNA sequencing), along with other members of the lab, the student will help to identify histamine-responsive genes in M. morganii and, time permitting, deletion mutants in putative “hits” will be produced to determine their role in histamine sensing and response.
Skills required: The student(s) should have basic bacteriology and molecular genetics experience, but more importantly, enthusiasm and motivation to perform basic science research. Beneficial skills include knowing strategies for culturing different bacteria and a knowledge of aseptic techniques, gel electrophoresis, PCR, and cloning/mutagenesis. Individuals with theoretical knowledge but without hands on experience are still encouraged to apply.
17. Methanol-Based Fermentation for Microbial Biomass and Lipid Production
Supervisor: David Bressler
University: University of Alberta (Edmonton campus)
Methanol-based fermentation is a promising platform for converting low-cost C1 feedstocks into microbial biomass, single-cell protein, and lipid-derived products. These technologies can support the development of more sustainable bioprocesses for animal feed, food ingredients, and renewable bioproducts. The Bressler lab is currently developing fermentation strategies using methanol-utilizing microorganisms to evaluate microbial growth, substrate conversion, biomass productivity, and product formation under controlled bioreactor conditions.
This project will focus on the operation and optimization of aerobic fermentation systems using methanol as the main carbon source. Depending on project priorities, the intern may support research related to single-cell protein production, methanol-to-lipids fermentation, or related methanol-to-bioproduct platforms. Experiments may include batch, fed-batch, or continuous fermentation in bench-scale or 5 L bioreactor systems.
To identify suitable operating conditions, variables such as methanol concentration, feed rate, nutrient composition, aeration, agitation, dissolved oxygen, pH, and fermentation time may be evaluated. The resulting biomass or fermentation products may be analyzed for growth performance, substrate utilization, protein content, lipid accumulation, amino acid composition, and other relevant product-quality indicators.
The project will also provide training in aseptic technique, media preparation, bioreactor setup and operation, sample collection, data recording, and analytical characterization. Depending on the specific experiments completed, the intern may also assist with downstream processing activities such as biomass recovery, centrifugation, freeze drying, spray drying, or preparation of samples for HPLC, GC, or elemental analysis.
Research area, student roles & skills
Research area: The Bressler lab has extensive expertise in microbial fermentation, bioprocess development, and the conversion of low-cost carbon sources into value-added products. The lab is equipped with bench-scale fermenters, twelve 5 L fermenters, four 10 L fermenters, downstream processing equipment including freeze and spray dryers, and an analytical suite that includes HPLC, GC, and elemental analysis. Current fermentation research includes methanol-based bioconversion, single-cell protein production, high-density microbial cultivation, and process optimization for biomass and lipid-derived products relevant to food, feed, and industrial biotechnology.
Student roles: The student will work with the Bressler lab fermentation team to support the development and optimization of methanol-based fermentation processes. The student’s role will include assisting with media preparation, sterilization, inoculum preparation, bioreactor setup, sampling, process monitoring, data collection, and analysis of fermentation performance. The student may participate in batch, fed-batch, and/or continuous fermentation experiments using methanol as the primary carbon source. The work may involve monitoring key process variables such as pH, dissolved oxygen, agitation, aeration, temperature, feed rate, methanol concentration, biomass production, and culture stability. The student will be expected to follow established SOPs, maintain accurate laboratory records, and work under appropriate supervision until they are trained to perform specific tasks more independently. Depending on project needs, the student may also assist with downstream processing and product characterization. This may include centrifugation, biomass recovery, freeze drying, spray drying, crude protein analysis, lipid extraction, amino acid analysis, HPLC analysis, GC analysis, sample preparation, or elemental analysis using existing laboratory protocols. The student will also help organize experimental data, prepare figures and summary tables, and present progress during project or group meetings. By the end of the internship, the student will prepare a final presentation summarizing the project background, methods, results, challenges, and conclusions.
Skills required: The student is expected to have a background in microbiology, biotechnology, biochemical engineering, chemical engineering, biochemistry, or a related field. A good understanding of microbial growth, fermentation, aseptic technique, and laboratory safety is preferred. Previous experience with bioreactors, methanol-utilizing microorganisms, analytical instruments, HPLC, GC, biomass characterization, protein analysis, lipid analysis, freeze drying, or spray drying would be an asset. The student should be organized, careful with laboratory documentation, comfortable working in a team environment, and willing to learn new fermentation and analytical techniques.
18. Microbial Sources of Natural Products
Supervisor: Kalindi Morgan
University: University of Northern British Columbia (Prince George campus)
The Morgan Lab currently has a library of bacteria isolated from northern forest insects which bioactivity in intial anti-fungal assays. In order to prioritize bacteria for for further investigation a series of tests need to be completed, including biologic assays and PCR analysis.
Mitacs undergraduate students will have the opportunity to engage in hands-on research, learn advanced laboratory techniques, and contribute to meaningful discoveries in natural product chemistry. This project offers a unique blend of organic chemistry and analytical chemistry with some microbiology, providing a well-rounded research experience.
If of interest, this research project will involve growing, completing bioactivity and PCR assays and may utilize PCR to complete 16s rRNA DNA barcoding to evaluate bacteria obtained from environmental samples.
Growing the bacteria previously isolated will involved growing on different media, and completing bioactivity assays against phytopathogens and other organisms. 16s rRNA DNA barcoding involves isolating small amounts of bacteria, then completing PCR with specific primers for identifying the species and ascertaining presence of specific natural product gene clusters to prioritize bacteria for whole genome sequencing (completed out-of-house).
Research area, student roles & skills
Research area: This research focuses on isolating and assaying from microbes obtained from unique northern British Columbian ecologocial sources that will be utilized for natural product discovery. The end goal is the discovery of bioactive natural products from talented microorganisms.
Student roles: The work will be laboratory-based. In a sterile environment, the student will be able to complete experiments towards the identification of various bacteria isolated from environmental samples along with completing several assays. How many bacteria this is completed on is up to the student, although I would estimate 20 bacterial strains would be worked on over the 3 month period.
Skills required: An microbiology background with sterile technique is of great use.
An understanding of the with the application of DNA extraction, PCR work, and primer design is also of great use.
One of the best-studied water-borne bacterial pathogens, in term of its interaction with phagocytic protozoans, is Legionella pneumophila. This species is an important, but often underestimated, cause of community-acquired and nosocomial pneumonia. Transmission occurs primarily by inhalation of contaminated water droplets, but the exact mechanism and other factors influencing virulence remain unclear. Once in the lungs, Legionella infects and replicates inside alveolar macrophages and causes widespread tissue damage. Legionella grows in water system within a wide variety of phagocytic protozoans, such as amoeba and ciliates, that prey on other microorganisms. We have previously studied the microbiome of a few water systems and identified a few species of bacteria and eukarya associated with the presence or absence of Legionella. The goal of this project is to study the interactions of Legionella with the resident microbiota in water systems. To this end, we will use co-culture experiments to test the effect of different isolates on the growth and survivability of Legionella. Then, amplicon sequencing and bioinformatic analysis will be used to identify the isolates.
Research area, student roles & skills
Research area: The Faucher lab focuses on bacterial pathogen in non-clinical environment. Our model pathogens are Legionella pneumophila and Campylobacter jejune. We aimed to understand how they can survive outside the human hosts and how do they evolved in the environment. We are using genetic tools and nest-generation sequencing.
Student roles: The student will perform cultivation of different microorganism and perform counts using flow cytometry and other tools. The student will extract DNA and perform bioinformatic analysis.
Skills required: The candidate should have a background in microbiology and experience with microbial isolation and cultivation. Basic understanding of bioinformatic tools is considered an asset.
20. Mixed microbial bioconversion of agrifood co-products for the generation of value-added biobased products
Prof. Tarek Rouissi’s laboratory at the Eau Terre Environnement Research Centre (INRS) is seeking a highly motivated intern to join its dynamic research team. The selected candidate will contribute to a cutting-edge project focused on mixed microbial bioconversion of agrifood co-products for the generation of value-added biobased products.
Research area, student roles & skills
Research area: Environmental biotechnology and Chemistry
Student roles: The intern will work closely with researchers on experimental activities and actively participate in the preparation of scientific publications.
Skills required: We are looking for individuals who are passionate, creative, and eager to grow within a collaborative research environment. Ideal candidates will demonstrate: • Strong planning and organizational skills • Scientific rigor and perseverance • Excellent communication and teamwork abilities
21. Molecular test development for malaria and arbovirus diagnosis
Supervisor: Stephanie Yanow
University: University of Alberta (Edmonton campus)
Together with our partners at the Universidad de Antioquia in Medellín, Colombia, we propose to develop more sensitive diagnostic tests for malaria and dengue virus, the two major causes of fever in the study region. In our previous work, we developed molecular tests for both pathogens that could be performed directly from a drop of blood, reducing barriers to molecular testing at community health clinics. To build on this work, the interns will compare different platforms for testing to identify those most feasible for a pilot study in Colombia. The project involves testing different diagnostic tools and instruments to compare their sensitivity and specificity. Samples collected from Colombia will be used for validation of these tests.
Research area, student roles & skills
Research area: My research lab studies infectious diseases with a particular focus on malaria. Our projects include developing a vaccine against pregnancy-associated malaria, understanding the pathogenesis of malaria, and designing molecular diagnostics. We conduct in vitro experiments with parasites cultured in the lab and collaborate with partners in Colombia and Kenya to analyze samples from patients with malaria. My expertise is in molecular and cellular biology.
Student roles: The student will learn how to perform qPCR and RT-qPCR to test for Plasmodium and dengue virus in blood samples. They will perform experiments in the lab under the mentorship of a member of my team. They will learn how to analyze the results and determine the performance characteristics of the different diagnostic tests.
Skills required: The student must have a background in microbiology or molecular biology. They should have an understanding of the biology of Plasmodium and dengue virus. Experience with PCR is highly desirable. Students from the Universidad de Antioquia are preferred as this would allow us to build on existing research partnerships and facilitate the transfer of knowledge to support future studies led by our collaborators.
22. Novel azole/protein-based nanoparticles to combat anti-candidal resistance.
The fungi Candida is of medical importance worldwide, associated with approximately 150 million cases of severe fungal infections reported annually and 1.7 million deaths (10.15698/mic2020.06.718). Candida species can cause mucocutaneous infections, endocarditis, bone and joint infections, and even death (10.1111/ijcp.13655). Of the three major classes of antifungal drugs (10.3390/jof10120871), azoles are widely used based on their low toxicity, high efficacy, and ease of administration (10.3389/fmicb.2018.01351). However, their extensive use has led to Candida developing significant resistance through: 1) mutations in the CYP51A enzyme, limiting its ability to effectively bind azoles; 2) overexpression of mdr or cdr genes, coding efflux pumps able to eject azoles (10.3390/cells12222655). This growing resistance underscores the urgent need for new antifungal drugs and delivery strategies.
Nanotechnology promises to specifically target and deliver drugs, thereby minimizing toxicity while preserving therapeutic impact, enhancing safety and biocompatibility (10.2147/ijn.s596). Albumin has significant potential as a drug carrier and delivery system based on its high biocompatibility, biodegradability, non-immunogenicity, and ability to target specific sites (10.2147/IJN.S467876). The proposed research will evaluate the efficacy of human serum albumin nanoparticles to encapsulate and deliver novel azole derivatives as anticandidals, capable of overcoming resistance. Their impact will be assessed not only for fungicidal activity and host cell cytotoxicity, but also candidal biofilm formation, morphological changes, cytoskeletal and nuclear structure, and other factors related to fungal virulence. We will examine their impact on C. albicans using biochemical, microbiological and advanced microscopy assays.
Research area, student roles & skills
Research area: My group studies how cells respond to environmental contaminants and antibiotics using biochemistry, microbiology and advanced microscopy. Of special interest to us is the mechanisms of antifungal agents, the impact of pesticides and how cells cope under these stresses during growth, differentiation, and biofilm formation.
My research group is developing new nanoscale tools to design antifungals to prevent and combat fungal infections of human and plant hosts.
Student roles: The student will learn to do routine fungal cell culture, prepare protein-based nanoparticles incorporating novel azoles, minimum inhibitory concentration (MIC) assays and advanced microscopy. Once the nanoparticles are synthesized, the student will use MIC assays to assess their efficacy against Candida albicans. The student will be taught to collect, analyze and interpret data to present at weekly group meetings, and will be invited to attend our annual research retreat. Students are encouraged to write a full final report of their work that will ultimately contribute to a publication on which they would be co-authored.
Skills required: The student should have basic biochemical (accurate pipetting skills) and microbiological expertise, and basic computer skills. Knowledge of statistics, and a theoretical and experiential understanding of light and fluorescence microscopy would be an asset. Students will have the opportunity to gain experience with atomic force microscopy and laser scanning confocal microscopy during the internship. Dahms group members are highly cooperative and helpful. Applicants are expected to be hard-working, motivated, persistent, and must be able to work in a team. This project will involve Dahms’ Biosafety Containment Level 2 laboratory for which the applicant would receive training.
23. Studying plant pathogens of economic importance
Supervisor: Xin Li
University: University of British Columbia (Vancouver campus)
Studying soilborne fungal pathogen Sclerotinia scleortiorum using molecular genetics and genomics
Sclerotinia sclerotiorum is one of the most notorious soilborne pathogens on earth. It causes white mold diseases in diverse hosts including canola, soybean, lettuce, peanuts, etc. Its ability to form sclerotia, the overwintering structure, is crucial for its survival in nature. Although this pathogen causes devastating diseases on many plants, our understanding on how it forms sclerotia and how it causes diseases in diverse hosts is limited. During the past few years, our group has developed a novel forward genetic pipeline for gene discovery in this pathogen. The student will be involved in mutant screening to search for mutants that are defective in either sclerotial formation or virulence. Once the mutants are confirmed, the DNA will be extracted for sequencing. Mutations in these mutants will be identified and downstream knockout or complementation tests will be carried out to confirm the exact mutation that is responsible for the observed phenotypes.
Through the Mitacs program, the student will get training in methodologies in molecular biology, genetics, genomics and plant pathology. Genetic pathways will be analyzed, and protein-protein interactions will be assayed. He/She will be required to read original research papers and join group discussion meetings. The student will also meet regularly with the principal investigator for periodic evaluations.
Research area, student roles & skills
Research area: With the human population exceeding eight billions and growing, new solutions are urgently needed to ensure food security for the global community in a sustainable manner. The very active research field of plant‐microbe interaction can help to contribute to this challenge. Our lab specializes in research in plant immunity and fungal pathogens. Although plants have to effectively deal with pathogen infections in nature, we have very limited understanding on how they do it. At the same time, many of the highly damaging fungal pathogens on crop plants are under-studied. Our lab aims to better understand both areas.
Student roles: The student will become a team member of a research group and work closely with the principal investigator and her graduate students. The student will work in a molecular genetics lab to learn skills to solve biological problems. Methods in forward genetics, molecular cloning, biochemistry and plant pathology will be taught to the student. The student will be required to read original research papers and participate in group discussion meetings. He/she will also meet regularly with the principal investigator for periodic progress reflection and evaluation.
Skills required: The intern student is expected to have finished courses in basic genetics, microbiology, molecular genetics, molecular biology, biochemistry, cell biology and plant biology (or equivalents). Most students in the biology program after third year of college education would meet the minimum requirement to be competent for the position.
Students with self-learning capability, high motivation and curiosity in scientific explorations, and high responsibility will be preferably considered. Lab experience is not mandatory, but favored.
24. Using microbial competition to engineer microbiomes to limit antimicrobial resistance
The gut microbiome provides hosts with benefits including defence against the colonization of disease-causing pathogens. Yet, the microbiome can also be a reservoir of antimicrobial resistant (AMR) strains that can spread resistance via plasmid DNA transfer to species within the microbiome, including pathogens. As a result, there is great interest in rationally manipulating the gut microbiome to both slow the spread of AMR and actively target pathogens.
However, this has remained a challenge as the gut microbiome consists of a diverse and variable set of microbes that interact with each other, making it difficult to provide solutions that apply across microbiome compositions. We recently discovered that collective competition in the microbiome limits the ability of newly arriving pathogens to colonize the gut via the mechanism of nutrient blocking. Specifically, when a microbiome can utilize the same nutrients as an invading microbe, it will limit the ability of the new microbe to colonize. However, there is still untapped potential for the rational design of consortia to improve health and limit the burden of AMR.
To fill this knowledge gap, we will leverage a large collection of human gut microbiota strains to test how variation in nutrient blocking affects the colonization of two model gut pathogens of the Enterobacteriaceae family, key problematic pathogens for the spread of AMR: Klebsiella pneumoniae and Escherichia coli.
We will design communities that we predict are protective, leveraging both published genomic-based predictions and empirical metabolic-based predictions. We will then perform challenge experiments with a model gut pathogens in both co-culture experiments and gnotobiotic mice.
Overall, the goal of this project is to provide guiding principles for the rational design of microbial biotherapeutics, allowing us to harness competition in the microbiome for our advantage.
Research area, student roles & skills
Research area: Humans are colonized by trillions of microbes: roughly the same as the number of human cells in the body. These microbes are collectively called the human microbiome and have many beneficial functions to our health. However, the sheer number and diversity of species in the microbiome makes it challenging to understand how they exert their beneficial functions and whether we can influence them to be more helpful. I study the interactions between microbes to understand what drives the composition of a microbiome, how a given composition influences our health, and how we might engineer microbiomes for our own benefit.
Student roles: The student will be paired with a graduate student or postdoctoral researcher. The student’s role in this project is to generate mutants of microbial strains via molecular biology, culture microbes from our laboratory collection of human gut microbiota strains and assemble strains in communities. Via molecular biology, the model pathogens will be labeled and can therefore be quantified from within communities. The pathogens will be added to communities and the level of protection from each community will be tested. Following data collection, the student will also analyze, plot, and interpret data, relating the protective ability of a given community to predictions based on published genomic-based predictions and empirical metabolic-based calculations. The student will also present their result to the peers in the research group and be expected to collaborate with others.
Skills required: The student should have a strong background in working with aseptic technique and basic microbiology methods. Experience with anaerobic microbiology is an asset but not essential. The student should have a strong conceptual background in one or more of the following fields: infection biology, microbiome science, microbiology and immunology, antimicrobial resistance research.