Member Scientists

Antibiotics that cause damage to the bacterial genome do so in an effort to kill bacteria. However, like humans, bacteria are able to repair DNA damage and survive. In addition to promoting survival, these repair pathways may introduce mutations that lead to antimicrobial resistance. The Andres Lab is pursuing three major questions to understand how to combat antimicrobial resistance: 1. What is the molecular mechanism of DNA repair? 2. What differences exist in repair between bacterial species? 3. Can repair be inhibited to improve antimicrobial therapies? To answer these questions, researchers in the Andres Lab combine multiple approaches, integrating structural biology techniques with biochemistry and bacterial genetics. Some of their favourite structural techniques include small-angle x-ray scattering (SAXS), atomic force microscopy (AFM) and x-ray crystallography.

Antibiotics that cause damage to the bacterial genome do so in an effort to kill bacteria. However, like humans, bacteria are able to repair DNA damage and survive. In addition to promoting survival, these repair pathways may introduce mutations that lead to antimicrobial resistance. The Andres Lab is pursuing three major questions to understand how to combat antimicrobial resistance: 1. What is the molecular mechanism of DNA repair? 2. What differences exist in repair between bacterial species? 3. Can repair be inhibited to improve antimicrobial therapies? To answer these questions, researchers in the Andres Lab combine multiple approaches, integrating structural biology techniques with biochemistry and bacterial genetics. Some of their favourite structural techniques include small-angle x-ray scattering (SAXS), atomic force microscopy (AFM) and x-ray crystallography.

The overall goal of our research program is to develop strategies that exploit the ability of our innate defense to fight viral infections and cancers. Over the last 10 years our laboratory has focused on 2 central research questions: 1) How do IFNs and NK cells provide early innate protection against viral infections while controlling the immune cells to avoid overactivation and immunopathology, and 2) Why are human NK cells dysregulated in the tumor microenvironment (TME). and how can we overcome this to harness the anti-tumor potential of human NK cell.

1- Innate antiviral immunity

Successful host defense requires tight control of inflammation to mount an effective immune response while limiting damage to the host. Loss of such inflammatory control can result in a pathological dysregulated immune response characterized by immune cell hyperactivity and mass production of inflammatory cytokines (cytokine storm) that causes tissue damage. In fact, mortality from most acute infections, including bacterialsepsis, hemorrhagic fevers, seasonal influenza, and more recently SARS-CoV-2, is rarely due to the pathogen itself, but rather to such hyperinflammation by the host’s immune system, causing organ damage and subsequent failure. There is a critical need to develop therapies that effectively target hyperinflammation without compromising host resistance. However, a major limitation to this end is that the cellular mechanisms that initiate and propagate the cytokine storm remain poorly understood. Our research aims are to elucidate the mechanism(s) and pathways by which our innate immune system, particularly IFNs and NK cells, excerpts their immunoregulatory functions.

2- NK cell-based cancer immunotherapy

A major goal of our research is developing efficacious and safer treatments for hard-to-treat solid tumors. To do this, we are harnessing the tumor killing ability of Natural Killer (NK) immune cells, which have an intrinsic ability to distinguish between healthy and malignant cells. Advances in the ex vivo expansion of human NK cells has enabled the adoptive transfer of NK cells to treat patients, showing clinical success against hematologic malignancies. However, there are still two major limitations to overcome in order to successfully combat solid tumors: 1) efficient homing of the adoptively transferred immune cells to the solid tumor microenvironment (TME), and 2) the hostile and immunosuppressive TME. Our lab aims to overcome these two limitations to enhance NK cell-based cancer immunotherapy for solid tumors.

The overall goal of our research program is to develop strategies that exploit the ability of our innate defense to fight viral infections and cancers. Over the last 10 years our laboratory has focused on 2 central research questions: 1) How do IFNs and NK cells provide early innate protection against viral infections while controlling the immune cells to avoid overactivation and immunopathology, and 2) Why are human NK cells dysregulated in the tumor microenvironment (TME). and how can we overcome this to harness the anti-tumor potential of human NK cell.

1- Innate antiviral immunity

Successful host defense requires tight control of inflammation to mount an effective immune response while limiting damage to the host. Loss of such inflammatory control can result in a pathological dysregulated immune response characterized by immune cell hyperactivity and mass production of inflammatory cytokines (cytokine storm) that causes tissue damage. In fact, mortality from most acute infections, including bacterialsepsis, hemorrhagic fevers, seasonal influenza, and more recently SARS-CoV-2, is rarely due to the pathogen itself, but rather to such hyperinflammation by the host’s immune system, causing organ damage and subsequent failure. There is a critical need to develop therapies that effectively target hyperinflammation without compromising host resistance. However, a major limitation to this end is that the cellular mechanisms that initiate and propagate the cytokine storm remain poorly understood. Our research aims are to elucidate the mechanism(s) and pathways by which our innate immune system, particularly IFNs and NK cells, excerpts their immunoregulatory functions.

2- NK cell-based cancer immunotherapy

A major goal of our research is developing efficacious and safer treatments for hard-to-treat solid tumors. To do this, we are harnessing the tumor killing ability of Natural Killer (NK) immune cells, which have an intrinsic ability to distinguish between healthy and malignant cells. Advances in the ex vivo expansion of human NK cells has enabled the adoptive transfer of NK cells to treat patients, showing clinical success against hematologic malignancies. However, there are still two major limitations to overcome in order to successfully combat solid tumors: 1) efficient homing of the adoptively transferred immune cells to the solid tumor microenvironment (TME), and 2) the hostile and immunosuppressive TME. Our lab aims to overcome these two limitations to enhance NK cell-based cancer immunotherapy for solid tumors.

The Bishop Lab’s research on the structure and function of membrane proteins attacks one of the most important and challenging problems in contemporary biochemistry. Their most recent work focuses on an outer membrane enzyme called PagP from pathogenic Gram-negative bacteria. PagP transfers a palmitoyl group from a phospholipid molecule to the lipid A (endotoxin) component of lipopolysaccharide (LPS). This simple modification provides bacterial resistance to host antimicrobial peptides and attenuates the inflammatory response signaled through the human toll-like receptor 4 pathway. By understanding how the structural and dynamic properties of PagP relate to its biological function, the Bishop Lab aims to design inhibitors that are useful for the treatment of infections and to synthesize novel endotoxin antagonists for the treatment of septic shock.

The Bishop Lab’s research on the structure and function of membrane proteins attacks one of the most important and challenging problems in contemporary biochemistry. Their most recent work focuses on an outer membrane enzyme called PagP from pathogenic Gram-negative bacteria. PagP transfers a palmitoyl group from a phospholipid molecule to the lipid A (endotoxin) component of lipopolysaccharide (LPS). This simple modification provides bacterial resistance to host antimicrobial peptides and attenuates the inflammatory response signaled through the human toll-like receptor 4 pathway. By understanding how the structural and dynamic properties of PagP relate to its biological function, the Bishop Lab aims to design inhibitors that are useful for the treatment of infections and to synthesize novel endotoxin antagonists for the treatment of septic shock.

Research interests in the Bowdish Lab include:

1) Understanding how macrophage phagocytosis changes with age and during acute and chronic inflammation, particularly in response to the pulmonary pathogen Streptococcus pneumoniae;

2) Determining how age-associated inflammation changes monocyte and macrophage development and function and increases susceptibility to infection;

3) Elucidating how age-associated inflammation changes immune function and alters the aging trajectory; and

4) Understanding how the microbiota contributes to healthy or unhealthy aging and how microbiome-host interactions can be harnessed to prevent infections.

Research interests in the Bowdish Lab include:

1) Understanding how macrophage phagocytosis changes with age and during acute and chronic inflammation, particularly in response to the pulmonary pathogen Streptococcus pneumoniae;

2) Determining how age-associated inflammation changes monocyte and macrophage development and function and increases susceptibility to infection;

3) Elucidating how age-associated inflammation changes immune function and alters the aging trajectory; and

4) Understanding how the microbiota contributes to healthy or unhealthy aging and how microbiome-host interactions can be harnessed to prevent infections.

Antibiotic resistance has reached crisis proportions, principally because modern industrial drug discovery efforts have failed to provide new antibiotics. The reasons for failure are manifold; however, a lack of understanding of the basic biology has played a large part. Where modern drug discovery emphasizes reductionist approaches, there is a profound risk of failure if the complexity of the target, indeed the system, is underestimated. Brown Lab researchers are investigating enigmatic processes that are essential for the survival of bacterial pathogens and are working to understand these processes in the context of complex cell systems. Dr. Eric Brown’s research group is also developing creative chemical-biology platforms to enable the discovery and characterization of new chemical probes with utility as tool compounds in exploring complex biology. Efforts to date have resulted in exciting new knowledge, platforms, chemical probes and lead compounds for antibacterial research.

Antibiotic resistance has reached crisis proportions, principally because modern industrial drug discovery efforts have failed to provide new antibiotics. The reasons for failure are manifold; however, a lack of understanding of the basic biology has played a large part. Where modern drug discovery emphasizes reductionist approaches, there is a profound risk of failure if the complexity of the target, indeed the system, is underestimated. Brown Lab researchers are investigating enigmatic processes that are essential for the survival of bacterial pathogens and are working to understand these processes in the context of complex cell systems. Dr. Eric Brown’s research group is also developing creative chemical-biology platforms to enable the discovery and characterization of new chemical probes with utility as tool compounds in exploring complex biology. Efforts to date have resulted in exciting new knowledge, platforms, chemical probes and lead compounds for antibacterial research.

Type IV Pili

Many species of bacteria produce long, thin, flexible appendages called type IV pili (T4P). T4P can be rapidly and repeatedly extended and retracted, allowing bacteria to capture DNA and stick to different surfaces. T4P allows bacteria to ‘feel’ surface contact, which then turns on the expression of surface-associated genes, such as those involved in biofilm formation. Further, T4P are receptors for bacteriophages, and can even act as wires to conduct electricity in some species. The Burrows Lab investigates multiple aspects of T4P and has many ongoing projects ranging from studying the machine that makes T4P, the motor that extends and retracts them, the diversity of the subunits that make up T4P and its relationship to phage escape, and the regulatory pathways involved in surface sensing, among other projects.

Biofilms

Biofilms are communities of bacteria that grow on surfaces. They make cells more tolerant of disinfectants and antibiotics, making biofilm infections difficult to treat. The Burrows Lab studies how biofilms develop in response to chemical cues, particularly antibiotics. Sub-lethal concentrations of antibiotics stimulate biofilm formation – they study how this phenotype is induced, and exploit it to identify new antimicrobials in complex mixtures or compound libraries.

Type IV Pili

Many species of bacteria produce long, thin, flexible appendages called type IV pili (T4P). T4P can be rapidly and repeatedly extended and retracted, allowing bacteria to capture DNA and stick to different surfaces. T4P allows bacteria to ‘feel’ surface contact, which then turns on the expression of surface-associated genes, such as those involved in biofilm formation. Further, T4P are receptors for bacteriophages, and can even act as wires to conduct electricity in some species. The Burrows Lab investigates multiple aspects of T4P and has many ongoing projects ranging from studying the machine that makes T4P, the motor that extends and retracts them, the diversity of the subunits that make up T4P and its relationship to phage escape, and the regulatory pathways involved in surface sensing, among other projects.

Biofilms

Biofilms are communities of bacteria that grow on surfaces. They make cells more tolerant of disinfectants and antibiotics, making biofilm infections difficult to treat. The Burrows Lab studies how biofilms develop in response to chemical cues, particularly antibiotics. Sub-lethal concentrations of antibiotics stimulate biofilm formation – they study how this phenotype is induced, and exploit it to identify new antimicrobials in complex mixtures or compound libraries.

Molecular diversity is an important and recurring theme in modern organic and biological chemistry, whether it be for the medicinal chemist wishing to develop a new class of pharmaceutical based on an original structural template, or the organometallic chemist looking at catalyst design and wanting to move beyond the currently available ligands. The Capretta research team addresses this issue in their laboratory by developing synthetic methods and catalytic systems that allow for facile and direct access to compounds with new molecular structures and architectures.

Molecular diversity is an important and recurring theme in modern organic and biological chemistry, whether it be for the medicinal chemist wishing to develop a new class of pharmaceutical based on an original structural template, or the organometallic chemist looking at catalyst design and wanting to move beyond the currently available ligands. The Capretta research team addresses this issue in their laboratory by developing synthetic methods and catalytic systems that allow for facile and direct access to compounds with new molecular structures and architectures.

Dr. Zain Chagla is an M.D. specializing in internal medicine, tropical medicine, and infectious diseases. He is a Consultant Physician at St. Joseph’s Hospital and Hamilton Health Sciences, Associate Professor of Medicine at McMaster University, and adjunct faculty at the University of Namibia in the Department of Medicine. Dr. Chagla’s research and clinical interests include global health and tropical medicine, education and antimicrobial stewardship, infections in renal transplantation, and ultrasound in infectious diseases.

Dr. Zain Chagla is an M.D. specializing in internal medicine, tropical medicine, and infectious diseases. He is a Consultant Physician at St. Joseph’s Hospital and Hamilton Health Sciences, Associate Professor of Medicine at McMaster University, and adjunct faculty at the University of Namibia in the Department of Medicine. Dr. Chagla’s research and clinical interests include global health and tropical medicine, education and antimicrobial stewardship, infections in renal transplantation, and ultrasound in infectious diseases.

Host-Pathogen Interactions

Bacteria secrete virulence factors in order to commandeer host cells and evade our immune system. Coombes Lab researchers use cutting-edge technologies in quantitative proteomics, functional genomics, and structural biology to understand the molecular mechanisms of bacterial pathogenesis and the actions of virulence factors. This knowledgebase creates opportunities for innovative drug target discovery with tangible impacts on public health.

Harnessing Immunity to Combat Superbugs

Pathogens use sophisticated strategies to overcome the innate immune system in order to colonize, establish a host niche, and transmit to new hosts. The Coombes Lab has embarked on a line of research to understand the components of the innate immune system involved in protection against enteric pathogens such as Salmonella, pathogenic E. coli, and bacteria associated with Crohn’s disease.

Crohn’s Disease

It is now accepted that Crohn’s disease is an inflammatory disease driven by microbes in our gut. However, mechanisms by which pathogenic or commensal microbes work in concert with each other and with host factors to drive this inflammation are not well known. Coombes Lab scientists are conducting basic research and working with the private sector to understand the microbes that drive chronic inflammation during Crohn’s disease, with a particular focus on adherent- invasive E. coli that are linked to Crohn’s disease in humans.

Host-Pathogen Interactions

Bacteria secrete virulence factors in order to commandeer host cells and evade our immune system. Coombes Lab researchers use cutting-edge technologies in quantitative proteomics, functional genomics, and structural biology to understand the molecular mechanisms of bacterial pathogenesis and the actions of virulence factors. This knowledgebase creates opportunities for innovative drug target discovery with tangible impacts on public health.

Harnessing Immunity to Combat Superbugs

Pathogens use sophisticated strategies to overcome the innate immune system in order to colonize, establish a host niche, and transmit to new hosts. The Coombes Lab has embarked on a line of research to understand the components of the innate immune system involved in protection against enteric pathogens such as Salmonella, pathogenic E. coli, and bacteria associated with Crohn’s disease.

Crohn’s Disease

It is now accepted that Crohn’s disease is an inflammatory disease driven by microbes in our gut. However, mechanisms by which pathogenic or commensal microbes work in concert with each other and with host factors to drive this inflammation are not well known. Coombes Lab scientists are conducting basic research and working with the private sector to understand the microbes that drive chronic inflammation during Crohn’s disease, with a particular focus on adherent- invasive E. coli that are linked to Crohn’s disease in humans.

Currie and his lab members study the ecological and evolutionary dynamics of symbiotic associations, with a particular focus on the interactions that occur between insects and microbes and the role of beneficial microbes in mediating infectious diseases through the production of antimicrobials. His research, including extensive work with the charismatic leaf-cutter ants, has potential applications in fields as diverse as bioenergy development and drug discovery.

Currie and his lab members study the ecological and evolutionary dynamics of symbiotic associations, with a particular focus on the interactions that occur between insects and microbes and the role of beneficial microbes in mediating infectious diseases through the production of antimicrobials. His research, including extensive work with the charismatic leaf-cutter ants, has potential applications in fields as diverse as bioenergy development and drug discovery.

The vision of the Didar Lab is to design and develop bio-inspired technologies for applications in diagnostics, therapeutics, drug discovery and other biomedical related areas. They focus on engineering the physical and chemical interface between the biological and non-biological matter (i.e. the bio-interface) as a means for designing innovative, highly functional platforms for biomedicine. More specifically, they focus on developing effective bio-interfaces by minimizing non-specific binding of undesired biomolecules and cells (i.e. bacteria, plasma proteins) while enhancing the specificity and selectivity of the bio-interface towards desired biotargets and in effect, assuring reliability and performance of the final biomedical platform.

The vision of the Didar Lab is to design and develop bio-inspired technologies for applications in diagnostics, therapeutics, drug discovery and other biomedical related areas. They focus on engineering the physical and chemical interface between the biological and non-biological matter (i.e. the bio-interface) as a means for designing innovative, highly functional platforms for biomedicine. More specifically, they focus on developing effective bio-interfaces by minimizing non-specific binding of undesired biomolecules and cells (i.e. bacteria, plasma proteins) while enhancing the specificity and selectivity of the bio-interface towards desired biotargets and in effect, assuring reliability and performance of the final biomedical platform.

Dr. Jonathan Dushoff is a theoretical biologist with a wide variety of interests, but with a primary focus on the evolution and spread of infectious diseases, particularly in human health. Diseases that the lab works on include HIV, syphilis, canine rabies, and Ebola. They apply theoretical, statistical and computational approaches to understanding disease data, with a special focus on methods that combine dynamic mechanisms with statistical inference.

Dr. Jonathan Dushoff is a theoretical biologist with a wide variety of interests, but with a primary focus on the evolution and spread of infectious diseases, particularly in human health. Diseases that the lab works on include HIV, syphilis, canine rabies, and Ebola. They apply theoretical, statistical and computational approaches to understanding disease data, with a special focus on methods that combine dynamic mechanisms with statistical inference.

Dr. David Earn develops and analyzes mathematical models of biological systems, primarily for applications in epidemiology, ecology and animal behaviour.

One of the main themes of his research is understanding and controlling extinctions. In the ecological context, he investigates strategies for the conservation of endangered species. In the epidemiological context, he studies strategies for the eradication of parasites that cause infectious diseases. From a mathematical point of view, these are very similar problems.

Another area of Dr. Earn’s research concerns the application of game theory to the evolutionary dynamics of behavioural traits. This work clarifies the adaptive significance of animal behaviour, ranging from cooperation and parental care to foraging and cannibalism.

Dr. David Earn develops and analyzes mathematical models of biological systems, primarily for applications in epidemiology, ecology and animal behaviour.

One of the main themes of his research is understanding and controlling extinctions. In the ecological context, he investigates strategies for the conservation of endangered species. In the epidemiological context, he studies strategies for the eradication of parasites that cause infectious diseases. From a mathematical point of view, these are very similar problems.

Another area of Dr. Earn’s research concerns the application of game theory to the evolutionary dynamics of behavioural traits. This work clarifies the adaptive significance of animal behaviour, ranging from cooperation and parental care to foraging and cannibalism.

The streptomycetes are Gram-positive, soil-dwelling bacteria renowned for their metabolic diversity and morphological complexity. They produce a vast array of compounds (known collectively as ‘secondary metabolites’) having profound medical benefits, including anti-cancer agents, immuno-suppressants, and more than 80% of commercially important antibiotics. In addition, Streptomyces have a multicellular life-cycle, differentiating into distinct tissue types in response to environmental stimuli, and provide a unique opportunity to explore cell differentiation in a simple, bacterial system. Intriguingly, differentiation and antibiotic production are intricately connected and share many regulatory links. Using genetic, biochemical, cell-biological and post-genomic technologies, the ultimate goals of Dr. Marie Elliot’s research program are:

1. To understand how cellular differentiation is achieved in a multi-Cellular bacterium;

2. To understand how newly discovered RNA regulators act to control differentiation, metabolism, and environmental adaptation; and

3. To develop ways of stimulating new antibiotic production, helping to overcome resistance to existing antibiotics and treat infectious disease.

The streptomycetes are Gram-positive, soil-dwelling bacteria renowned for their metabolic diversity and morphological complexity. They produce a vast array of compounds (known collectively as ‘secondary metabolites’) having profound medical benefits, including anti-cancer agents, immuno-suppressants, and more than 80% of commercially important antibiotics. In addition, Streptomyces have a multicellular life-cycle, differentiating into distinct tissue types in response to environmental stimuli, and provide a unique opportunity to explore cell differentiation in a simple, bacterial system. Intriguingly, differentiation and antibiotic production are intricately connected and share many regulatory links. Using genetic, biochemical, cell-biological and post-genomic technologies, the ultimate goals of Dr. Marie Elliot’s research program are:

1. To understand how cellular differentiation is achieved in a multi-Cellular bacterium;

2. To understand how newly discovered RNA regulators act to control differentiation, metabolism, and environmental adaptation; and

3. To develop ways of stimulating new antibiotic production, helping to overcome resistance to existing antibiotics and treat infectious disease.

The Gillgrass Lab’s primary research focus is on immunology and infectious disease. Globally, 37% of deaths in people with HIV are from co-infections with tuberculosis. The combination of the two pathogens can be lethal since each negatively affects the disease progression of the other. The Gillgrass Lab is currently focused on exploring a humanized mouse model of HIV/TB co-infection to better understand how this affects immune responses, treatment, prophylaxis, and disease outcome.

The Gillgrass Lab’s primary research focus is on immunology and infectious disease. Globally, 37% of deaths in people with HIV are from co-infections with tuberculosis. The combination of the two pathogens can be lethal since each negatively affects the disease progression of the other. The Gillgrass Lab is currently focused on exploring a humanized mouse model of HIV/TB co-infection to better understand how this affects immune responses, treatment, prophylaxis, and disease outcome.

Dr. Shariq Haider is an infectious disease specialist with research interests including infections in immunocompromised hosts such as HIV, cancer patients, and bone marrow transplant patients. Much of Dr. Haider’s research includes studies on: 1) novel antiretroviral therapy in naïve and experienced HIV patients; 2) the epidemiology, diagnosis, and treatment of HCV coinfection in HIV infected patients; 3) antifungal therapies in neutropenic hosts; 4) improving diagnostic methods in invasive fungal infections; and 5) novel antibacterial therapies. He is a co-investigator for the CIHR Canadian HIV Trials Network (CTN 264), which is investigating the relationship between access to food for people co-infected with HIV and HCV and behavioural outcomes, and CTN 222, which is examining the reasons for more rapid progression of liver disease in people co-infected with HIV and HCV.

Dr. Shariq Haider is an infectious disease specialist with research interests including infections in immunocompromised hosts such as HIV, cancer patients, and bone marrow transplant patients. Much of Dr. Haider’s research includes studies on: 1) novel antiretroviral therapy in naïve and experienced HIV patients; 2) the epidemiology, diagnosis, and treatment of HCV coinfection in HIV infected patients; 3) antifungal therapies in neutropenic hosts; 4) improving diagnostic methods in invasive fungal infections; and 5) novel antibacterial therapies. He is a co-investigator for the CIHR Canadian HIV Trials Network (CTN 264), which is investigating the relationship between access to food for people co-infected with HIV and HCV and behavioural outcomes, and CTN 222, which is examining the reasons for more rapid progression of liver disease in people co-infected with HIV and HCV.

The Hosseinidoust Lab addresses the global AMR crisis by using bacteriophages. Current research endeavors include the discovery and design of: Phage Antimicrobials The team uses bacteriophages for their inherent property: as bacterial killers. Specifically, they focus on understanding the interaction of bacteriophages with bacterial biofilms with the ultimate goal of designing bacteriophage cocktails that can be used independently or in combination with antibiotics to tackle biofilm infections medical implants. Phage Biomaterials In their simplest form, phages are bionanoparticles that can propagate themselves and self-assemble. These properties make them more powerful than synthetic nanoparticles. The Lab packs bacteriophages into solid form to design antimicrobial hydrogels, microgels and coatings. Phage Diagnostics Bacteriophages are very effective at finding and specifically targeting their host bacteria in nature. The team uses this property to design high throughput and point-of-care diagnostics for infectious diseases.

The Hosseinidoust Lab addresses the global AMR crisis by using bacteriophages. Current research endeavors include the discovery and design of: Phage Antimicrobials The team uses bacteriophages for their inherent property: as bacterial killers. Specifically, they focus on understanding the interaction of bacteriophages with bacterial biofilms with the ultimate goal of designing bacteriophage cocktails that can be used independently or in combination with antibiotics to tackle biofilm infections medical implants. Phage Biomaterials In their simplest form, phages are bionanoparticles that can propagate themselves and self-assemble. These properties make them more powerful than synthetic nanoparticles. The Lab packs bacteriophages into solid form to design antimicrobial hydrogels, microgels and coatings. Phage Diagnostics Bacteriophages are very effective at finding and specifically targeting their host bacteria in nature. The team uses this property to design high throughput and point-of-care diagnostics for infectious diseases.

Bacteriophages (“phages”) are bacteria-specific viruses. They outnumber their hosts 10:1 and are thought to be responsible for the death of 40% of bacteria every day. The Hynes Lab studies the role of phages in shaping bacterial communities, such as those of the gut microbiome, and leverages this information to exploit the activities of phages for therapeutic purposes.

Bacteriophages (“phages”) are bacteria-specific viruses. They outnumber their hosts 10:1 and are thought to be responsible for the death of 40% of bacteria every day. The Hynes Lab studies the role of phages in shaping bacterial communities, such as those of the gut microbiome, and leverages this information to exploit the activities of phages for therapeutic purposes.

Dr. Charu Kaushic’s lab focuses on understanding the microenvironment of the female genital tract and its interaction with sexually transmitted pathogens and the immune system. They currently focus on two sexually transmitted viral pathogens: herpes simplex virus type 2 (HSV-2) and human immunodeficiency virus type 1 (HIV-1).

Using a mouse model of genital herpes, the Kaushic Lab has shown that the female sex hormones estradiol and progesterone have a profound effect on the outcome of primary infection with HSV-2, as well as in vaccinated mice following challenge with wild type virus. Current efforts focus on examining the mechanism by which hormones affect the local environment and initiation of immune responses to alter changes in susceptibility and the outcome of infection.

The Kaushic Lab has developed an in vitro model using primary cell cultures from the reproductive tracts of women that mimics the conditions in vivo. Using this model, they examine the interactions of genital epithelial cells to HIV-1. They are now developing this system as an ex-vivo model of heterosexual transmission, using semen from HIV-infected men to infect the primary genital epithelial cells. Concurrently, they are trying to understand how sex hormones and other co-infections may affect the interaction of HIV with genital tract cells. They are also initiating clinical studies in HIV-infected women to examine the effect of co-infection with HSV-2 on genital viral shedding and its influence on the menstrual cycle.

Dr. Charu Kaushic’s lab focuses on understanding the microenvironment of the female genital tract and its interaction with sexually transmitted pathogens and the immune system. They currently focus on two sexually transmitted viral pathogens: herpes simplex virus type 2 (HSV-2) and human immunodeficiency virus type 1 (HIV-1).

Using a mouse model of genital herpes, the Kaushic Lab has shown that the female sex hormones estradiol and progesterone have a profound effect on the outcome of primary infection with HSV-2, as well as in vaccinated mice following challenge with wild type virus. Current efforts focus on examining the mechanism by which hormones affect the local environment and initiation of immune responses to alter changes in susceptibility and the outcome of infection.

The Kaushic Lab has developed an in vitro model using primary cell cultures from the reproductive tracts of women that mimics the conditions in vivo. Using this model, they examine the interactions of genital epithelial cells to HIV-1. They are now developing this system as an ex-vivo model of heterosexual transmission, using semen from HIV-infected men to infect the primary genital epithelial cells. Concurrently, they are trying to understand how sex hormones and other co-infections may affect the interaction of HIV with genital tract cells. They are also initiating clinical studies in HIV-infected women to examine the effect of co-infection with HSV-2 on genital viral shedding and its influence on the menstrual cycle.

Dr. Adam Komorowski is a Canadian-Italian medical microbiologist and part-time Assistant Professor in the Department of Pathology and Molecular Medicine at McMaster University, with a cross-appointment to the Division of Infectious Diseases, Department of Medicine. Adam completed his medical training in Ireland, finishing his medical microbiology residency training at McMaster in 2024. Adam is a master’s student in health research methodology focused on whole genome sequencing of AmpC-producing Enterobacterales with Drs. Dominik Mertz and Marek Smieja through a Ministry of Health-funded Clinician-Investigator Program fellowship. He has published over 30 peer-reviewed papers, including guidelines co-authored with the Ontario COVID-19 Science Advisory Table. Adam is also the 2024 editorial mentee for the journal Clinical Infectious Diseases, and a 2024-2026 research fellow in non-pharmacologic pandemic interventions at Kellogg College, University of Oxford.

Research interests: bacteriology, mycology, antimicrobial resistance, vaccines, research methodology

Dr. Adam Komorowski is a Canadian-Italian medical microbiologist and part-time Assistant Professor in the Department of Pathology and Molecular Medicine at McMaster University, with a cross-appointment to the Division of Infectious Diseases, Department of Medicine. Adam completed his medical training in Ireland, finishing his medical microbiology residency training at McMaster in 2024. Adam is a master’s student in health research methodology focused on whole genome sequencing of AmpC-producing Enterobacterales with Drs. Dominik Mertz and Marek Smieja through a Ministry of Health-funded Clinician-Investigator Program fellowship. He has published over 30 peer-reviewed papers, including guidelines co-authored with the Ontario COVID-19 Science Advisory Table. Adam is also the 2024 editorial mentee for the journal Clinical Infectious Diseases, and a 2024-2026 research fellow in non-pharmacologic pandemic interventions at Kellogg College, University of Oxford.

Research interests: bacteriology, mycology, antimicrobial resistance, vaccines, research methodology

Dr. Yingfu Li’s research group works at the interface between chemistry and biology. Their overall research interest is to examine the unusual functions of nucleic acids and to be creative about them. The molecules that they are interested in studying include artificial or natural single-stranded DNA or RNA molecules with often surprising properties.

Their study on DNA or RNA has several distinct features. First, they examine DNA or RNA, not for its well-recognized role as the genetic material to store and transmit genetic information for living organisms, but rather for its less-known utility as a simple polymer to carry out catalytic and binding functions. Second, they study DNA or RNA, not in their rigid double-stranded form, but in their flexible single-stranded configuration. Third, as usually there is no natural source to fetch the DNA or RNA molecules for their study, they create their own molecules using a technique called “in vitro selection”. This is a simple yet powerful combinatorial approach that allows simultaneous screening of up to 1016 different DNA or RNA molecules in a single mixture for rare sequences with unusual functions.

It has been well demonstrated that nucleic acids, in addition to their roles in the storage and transmission of genetic information, can also act as enzymes (ribozymes and DNAzymes) and receptors (aptamers and riboswitches). The Li group is interested both in the study of basic functions of these molecules and in the exploration of these molecules as novel molecular tools for therapeutics, biomolecular detection, drug discovery, and nanotechnology.

Dr. Yingfu Li’s research group works at the interface between chemistry and biology. Their overall research interest is to examine the unusual functions of nucleic acids and to be creative about them. The molecules that they are interested in studying include artificial or natural single-stranded DNA or RNA molecules with often surprising properties.

Their study on DNA or RNA has several distinct features. First, they examine DNA or RNA, not for its well-recognized role as the genetic material to store and transmit genetic information for living organisms, but rather for its less-known utility as a simple polymer to carry out catalytic and binding functions. Second, they study DNA or RNA, not in their rigid double-stranded form, but in their flexible single-stranded configuration. Third, as usually there is no natural source to fetch the DNA or RNA molecules for their study, they create their own molecules using a technique called “in vitro selection”. This is a simple yet powerful combinatorial approach that allows simultaneous screening of up to 1016 different DNA or RNA molecules in a single mixture for rare sequences with unusual functions.

It has been well demonstrated that nucleic acids, in addition to their roles in the storage and transmission of genetic information, can also act as enzymes (ribozymes and DNAzymes) and receptors (aptamers and riboswitches). The Li group is interested both in the study of basic functions of these molecules and in the exploration of these molecules as novel molecular tools for therapeutics, biomolecular detection, drug discovery, and nanotechnology.

Dr. Brian Lichty has extensive expertise in oncolytic viruses and related immunotherapies as well as vaccine development. He has been a professor in the Department of Medicine, the Centre for Discovery in Cancer Research (CDCR), the McMaster Immunology Research Centre (MIRC) and Institute for Infectious Disease Research (IIDR) at McMaster University since 2004. He is also a co-founder of Turnstone Biologics, AeroImmune Biotechnologies and Esphera SynBio Inc. Dr. Lichty’s expertise includes influence research in the identification of strategies to leverage viral vectors and exosomes to harness the patient’s immune system in a sustainable manner, including vaccine design and engineering to directly engage the adaptive immune system tumour-specific and/or to enhance combinations with other immunotherapies. He is also director of the Robert E. Fitzhenry vector lab at McMaster where clinical grade viral vaccines are manufactured for human clinical trials. Dr. Brian Lichty received his PhD from the University of Toronto and holds a BSc from the University of Guelph.

Dr. Brian Lichty has extensive expertise in oncolytic viruses and related immunotherapies as well as vaccine development. He has been a professor in the Department of Medicine, the Centre for Discovery in Cancer Research (CDCR), the McMaster Immunology Research Centre (MIRC) and Institute for Infectious Disease Research (IIDR) at McMaster University since 2004. He is also a co-founder of Turnstone Biologics, AeroImmune Biotechnologies and Esphera SynBio Inc. Dr. Lichty’s expertise includes influence research in the identification of strategies to leverage viral vectors and exosomes to harness the patient’s immune system in a sustainable manner, including vaccine design and engineering to directly engage the adaptive immune system tumour-specific and/or to enhance combinations with other immunotherapies. He is also director of the Robert E. Fitzhenry vector lab at McMaster where clinical grade viral vaccines are manufactured for human clinical trials. Dr. Brian Lichty received his PhD from the University of Toronto and holds a BSc from the University of Guelph.

Dr. Mark Loeb’s research interests largely focus on epidemiologic and genomic population-based studies on viral infections such as influenza, West Nile, and dengue. His current projects include an NIH population genetics research program, a CIHR-funded cluster randomized controlled trial to reduce the spread of influenza by immunizing children in Hutterite colonies, and a CIHR-funded influenza pandemic team grant to establish the natural history, as well as immunologic and genetic determinants, of influenza infection. Dr. Loeb’s clinical focus encompasses general infectious diseases.

Dr. Mark Loeb’s research interests largely focus on epidemiologic and genomic population-based studies on viral infections such as influenza, West Nile, and dengue. His current projects include an NIH population genetics research program, a CIHR-funded cluster randomized controlled trial to reduce the spread of influenza by immunizing children in Hutterite colonies, and a CIHR-funded influenza pandemic team grant to establish the natural history, as well as immunologic and genetic determinants, of influenza infection. Dr. Loeb’s clinical focus encompasses general infectious diseases.

Dr. Lesley MacNeil’s lab works with the model organism C. elegans to study how the environment impacts health and development. Current research themes in the MacNeil Lab include:

1. Environmental influence on neuronal health & neurodegeneration – The MacNeil Lab examines the effects of environmental factors on neuronal function and age-related neuronal decline and uses models of Alzheimer’s and other neurodegenerative diseases to study the impacts of the environment on neurodegeneration.
2. Metabolic & dietary regulation of developmental processes – In response to low nutrient diets, C. elegans slows its developmental rate, taking more time to reach maturity. The MacNeil Lab examines how animals sense and respond to diet and metabolic changes to understand these mechanisms at a molecular level.
3. Gene-environment interactions – The lab uses C. elegans to examine gene-environment interactions. They examine how the penetrance and severity of phenotypes in various genetic mutants are altered by dietary and microbiotal factors.
4. Identifying factors that reduce bacterial virulence – In collaboration with Dr. Mike Surette and Dr. Lori Burrows, the MacNeil lab uses C. elegans as a pathogenesis model to identify factors that reduce virulence of P. aeruginosa.
5. Insect microbiota collection – The team is constantly trying to isolate new and exciting bacterial strains to feed their worms. One of their current projects involves isolating bacteria from insects.

Dr. Lesley MacNeil’s lab works with the model organism C. elegans to study how the environment impacts health and development. Current research themes in the MacNeil Lab include:

1. Environmental influence on neuronal health & neurodegeneration – The MacNeil Lab examines the effects of environmental factors on neuronal function and age-related neuronal decline and uses models of Alzheimer’s and other neurodegenerative diseases to study the impacts of the environment on neurodegeneration.
2. Metabolic & dietary regulation of developmental processes – In response to low nutrient diets, C. elegans slows its developmental rate, taking more time to reach maturity. The MacNeil Lab examines how animals sense and respond to diet and metabolic changes to understand these mechanisms at a molecular level.
3. Gene-environment interactions – The lab uses C. elegans to examine gene-environment interactions. They examine how the penetrance and severity of phenotypes in various genetic mutants are altered by dietary and microbiotal factors.
4. Identifying factors that reduce bacterial virulence – In collaboration with Dr. Mike Surette and Dr. Lori Burrows, the MacNeil lab uses C. elegans as a pathogenesis model to identify factors that reduce virulence of P. aeruginosa.
5. Insect microbiota collection – The team is constantly trying to isolate new and exciting bacterial strains to feed their worms. One of their current projects involves isolating bacteria from insects.

Dr. Nathan Magarvey’s lab defines new ways to realize the next generation of antibiotics and other natural products that kill or modulate drug-resistant pathogens. The modes of discovery stem from the convergence of disciplines of chemistry, microbiology, medicine, and computer science to mine beneficial microbes for evolved drugs. The platform technologies created in this pursuit seek to accelerate the discovery of new therapeutic agents from environmental microbes and those from the human

Dr. Nathan Magarvey’s lab defines new ways to realize the next generation of antibiotics and other natural products that kill or modulate drug-resistant pathogens. The modes of discovery stem from the convergence of disciplines of chemistry, microbiology, medicine, and computer science to mine beneficial microbes for evolved drugs. The platform technologies created in this pursuit seek to accelerate the discovery of new therapeutic agents from environmental microbes and those from the human

The Magolan Lab specializes in hit-to-lead medicinal chemistry, which is a key part of the complex and interdisciplinary process of discovery and development of new medicines. They synthesize small organic molecules with drug-like structural features including natural products and their derivatives. Working closely with biologists who evaluate these new compounds, they refine their chemical structures to achieve optimal biological properties and pharmaceutical potential, ultimately aiming to advance promising drug candidates into clinical trials.

Synthetic Methods

The Magolan Lab develops new reactions and synthetic strategies that enhance the capacity of chemists to produce valuable specialty compounds from simpler, inexpensive building blocks. They focus mainly on three areas: 1) using sulfoxides and vinyl sulfides as versatile synthetic intermediates, 2) using environmentally benign heterogeneous reagents to simplify reactions and 3) efficiently preparing nitrogen-rich heterocyclic scaffolds with drug-like structural properties.

The Magolan Lab specializes in hit-to-lead medicinal chemistry, which is a key part of the complex and interdisciplinary process of discovery and development of new medicines. They synthesize small organic molecules with drug-like structural features including natural products and their derivatives. Working closely with biologists who evaluate these new compounds, they refine their chemical structures to achieve optimal biological properties and pharmaceutical potential, ultimately aiming to advance promising drug candidates into clinical trials.

Synthetic Methods

The Magolan Lab develops new reactions and synthetic strategies that enhance the capacity of chemists to produce valuable specialty compounds from simpler, inexpensive building blocks. They focus mainly on three areas: 1) using sulfoxides and vinyl sulfides as versatile synthetic intermediates, 2) using environmentally benign heterogeneous reagents to simplify reactions and 3) efficiently preparing nitrogen-rich heterocyclic scaffolds with drug-like structural properties.

The McArthur Lab’s research program is rooted in bioinformatics, functional genomics, and computational biology. It spans complex informatics approaches to the functional genomics of microbial drug resistance, development of biological databases, next-generation sequencing for genome assembly and molecular epidemiology, automated literature curation approaches, controlled vocabularies for biological knowledge integration, and functional genomics approaches in environmental toxicology. A major part of the McArthur research program involves their Comprehensive Antibiotic Resistance Database (card.mcmaster.ca) and a national consortium of academic & government researchers developing software and data standardization tools for genomic surveillance of virulent or antimicrobial-resistant bacterial pathogens. They additionally research the use and generation of ‘Big Data’ in the biomedical sciences, with the goal of integrating biomedical research and clinical healthcare.

The McArthur Lab’s research program is rooted in bioinformatics, functional genomics, and computational biology. It spans complex informatics approaches to the functional genomics of microbial drug resistance, development of biological databases, next-generation sequencing for genome assembly and molecular epidemiology, automated literature curation approaches, controlled vocabularies for biological knowledge integration, and functional genomics approaches in environmental toxicology. A major part of the McArthur research program involves their Comprehensive Antibiotic Resistance Database (card.mcmaster.ca) and a national consortium of academic & government researchers developing software and data standardization tools for genomic surveillance of virulent or antimicrobial-resistant bacterial pathogens. They additionally research the use and generation of ‘Big Data’ in the biomedical sciences, with the goal of integrating biomedical research and clinical healthcare.

The McNulty group specializes in synthetic organic chemistry targeting the total synthesis of natural products and analogs with demonstrated biological activities. A major focus is on the development of synthetic methodology allowing access to versatile building-blocks such as functionalized alkenes. A second focus is on the development of catalysts such as late transition metal or organocatalysts that initiate cascade processes that provide access to advanced synthetic intermediates often in asymmetric fashion. We target the development of specific processes that allow access to the core structures found in target molecules of biological importance. Our group has achieved the total synthesis of many complex bioactive natural products including alkaloids, polyketides, meroterpenoids, peptidomimetics and others. The program has allowed for the discovery of potent antiparasitic agents against toxoplasmosis and malaria, a well as potent antivirals. We recently documented the preparation of alkaloids demonstrating potent activity against the SARSCoV2 coronavirus, the causative agent of the Covid19 pandemic.

The McNulty group specializes in synthetic organic chemistry targeting the total synthesis of natural products and analogs with demonstrated biological activities. A major focus is on the development of synthetic methodology allowing access to versatile building-blocks such as functionalized alkenes. A second focus is on the development of catalysts such as late transition metal or organocatalysts that initiate cascade processes that provide access to advanced synthetic intermediates often in asymmetric fashion. We target the development of specific processes that allow access to the core structures found in target molecules of biological importance. Our group has achieved the total synthesis of many complex bioactive natural products including alkaloids, polyketides, meroterpenoids, peptidomimetics and others. The program has allowed for the discovery of potent antiparasitic agents against toxoplasmosis and malaria, a well as potent antivirals. We recently documented the preparation of alkaloids demonstrating potent activity against the SARSCoV2 coronavirus, the causative agent of the Covid19 pandemic.

Dr. Dominik Mertz is the Medical Director of Infection Control and is practicing Infectious Diseases at McMaster University and Hamilton Health Sciences. He has a special interest in Antimicrobial Stewardship and is chairing the Antimicrobial Stewardship Working Group at Hamilton Health Sciences. Dr. Mertz’s main research interest is the identification of risk factors for infection or colonization by organisms that are antimicrobial resistant, the prevention of transmission and control of outbreaks by AMR in a hospital setting, and antimicrobial stewardship as a preventive measure to slow down the spread of AMR and to optimize antibiotic treatment of patients with AMR infections.

Dr. Dominik Mertz is the Medical Director of Infection Control and is practicing Infectious Diseases at McMaster University and Hamilton Health Sciences. He has a special interest in Antimicrobial Stewardship and is chairing the Antimicrobial Stewardship Working Group at Hamilton Health Sciences. Dr. Mertz’s main research interest is the identification of risk factors for infection or colonization by organisms that are antimicrobial resistant, the prevention of transmission and control of outbreaks by AMR in a hospital setting, and antimicrobial stewardship as a preventive measure to slow down the spread of AMR and to optimize antibiotic treatment of patients with AMR infections.

Research in the Miller Laboratory is divided into three main areas of focus: Innate & Adaptive Immunity Upon infection, both the innate and adaptive immune system is mobilized to protect the host from virus-mediated pathologies. The Miller Lab focuses on understanding both the protective and harmful qualities of immune responses – essential information for developing novel vaccines and therapeutics. Influenza Virus Influenza A virus (IAV) presents a particularly formidable challenge to the adaptive immune system. The virus has specific properties that allow it to cause seasonal epidemics and periodic pandemics, which leads to current- generation IAV vaccines having to be administered seasonally, while providing optimal protection against only a very limited number of IAV strains. However, a new class of antibodies has recently been discovered which is capable of providing much more broad protection across multiple IAV subtypes. The Miller group is focused on understanding the immunobiology of these antibodies, how they are elicited, and how they may be useful for the generation of “universal” influenza virus vaccines and therapeutics. ALS Abnormal inflammation is a signature of many neurodegenerative diseases, yet the way in which inflammation contributes to the pathology of these diseases is poorly defined. The Miller Lab is working to understand the role of inflammation in the etiology of neurodegenerative diseases, with a specific focus on its role in amyotrophic lateral sclerosis (ALS).

Research in the Miller Laboratory is divided into three main areas of focus: Innate & Adaptive Immunity Upon infection, both the innate and adaptive immune system is mobilized to protect the host from virus-mediated pathologies. The Miller Lab focuses on understanding both the protective and harmful qualities of immune responses – essential information for developing novel vaccines and therapeutics. Influenza Virus Influenza A virus (IAV) presents a particularly formidable challenge to the adaptive immune system. The virus has specific properties that allow it to cause seasonal epidemics and periodic pandemics, which leads to current- generation IAV vaccines having to be administered seasonally, while providing optimal protection against only a very limited number of IAV strains. However, a new class of antibodies has recently been discovered which is capable of providing much more broad protection across multiple IAV subtypes. The Miller group is focused on understanding the immunobiology of these antibodies, how they are elicited, and how they may be useful for the generation of “universal” influenza virus vaccines and therapeutics. ALS Abnormal inflammation is a signature of many neurodegenerative diseases, yet the way in which inflammation contributes to the pathology of these diseases is poorly defined. The Miller Lab is working to understand the role of inflammation in the etiology of neurodegenerative diseases, with a specific focus on its role in amyotrophic lateral sclerosis (ALS).

Dr. Mossman’s group focuses on understanding how viruses evade host immune defenses. When a virus infects a host, the host mounts an impressive immune response aimed at preventing the virus from multiplying and spreading. Viruses have evolved strategies to block this response in order to ensure their survival. Probably the most important aspect of the host immune response to virus infection is the production of an immune modulator called interferon. Interferon has a great impact on host defense mechanisms, and as a result, viruses have evolved multiple strategies to overcome its activities.

The Mossman Lab studies the mechanisms of interferon inhibition and the countermeasures taken by different viruses. These studies have led them to develop viruses for use in gene therapy and cancer therapy. They focus on herpes simplex virus type 1 (HSV-1), a human pathogen that causes cold sores, and have found that by disabling the virus through the removal of particular genes, the virus can grow in cancer cells and kill them while having no effect on healthy cells. Such viruses, called “oncolytic viruses”, are currently being tested as a novel approach to cancer therapy in the hopes of eliminating tumors without the toxic side effects associated with many current treatments. HSV-1 is also being studied as a tool for gene therapy, since it is easy to manipulate, can be targeted to specific tissues, and can house several therapeutic genes in a single vector.

Thus, the overall goal of the Mossman Lab is to understand how viruses and their hosts interact with each other so they can use viruses as tools for the treatment of multiple diseases.

Dr. Mossman’s group focuses on understanding how viruses evade host immune defenses. When a virus infects a host, the host mounts an impressive immune response aimed at preventing the virus from multiplying and spreading. Viruses have evolved strategies to block this response in order to ensure their survival. Probably the most important aspect of the host immune response to virus infection is the production of an immune modulator called interferon. Interferon has a great impact on host defense mechanisms, and as a result, viruses have evolved multiple strategies to overcome its activities.

The Mossman Lab studies the mechanisms of interferon inhibition and the countermeasures taken by different viruses. These studies have led them to develop viruses for use in gene therapy and cancer therapy. They focus on herpes simplex virus type 1 (HSV-1), a human pathogen that causes cold sores, and have found that by disabling the virus through the removal of particular genes, the virus can grow in cancer cells and kill them while having no effect on healthy cells. Such viruses, called “oncolytic viruses”, are currently being tested as a novel approach to cancer therapy in the hopes of eliminating tumors without the toxic side effects associated with many current treatments. HSV-1 is also being studied as a tool for gene therapy, since it is easy to manipulate, can be targeted to specific tissues, and can house several therapeutic genes in a single vector.

Thus, the overall goal of the Mossman Lab is to understand how viruses and their hosts interact with each other so they can use viruses as tools for the treatment of multiple diseases.

Dr. Mukherjee is an Assistant Professor in the Division of Respirology, Department of Medicine, and a translational scientist affiliated with the Research Institute of St. Joe’s, Hamilton. She has demonstrated expertise in investigating inflammatory mechanisms of chronic respiratory diseases, in particular autoimmunity, response to treatment and developing/validating clinical biomarkers. Dr Mukherjee has identified the presence of localized autoimmune responses in the airways of patients with complex airways disease, and determined their pathogenic role in driving disease severity. Of recent, she has identified autoimmune responses in acute-severe COVID and linked autoimmunity with post-acute COVID-19 sequelae (or Long COVID).

Dr. Mukherjee’s research program thus focusses on “Lung autoimmunity and biomarkers”. She is the current recipient of the Emerging Researcher Award in Allergic Asthma awarded conjointly by the Canadian Institutes of Health Research (CIHR) and the Canadian Asthma, Allergy and Immunology Foundation (CAAIF). Her lab is funded by federal and non-federal sources including CIHR-ICRH and industry. Current ongoing projects span from investigating mechanisms of disease to validating biomarkers in asthma, eGPA, COVID-19 and lung cancer.

Dr. Mukherjee is an Assistant Professor in the Division of Respirology, Department of Medicine, and a translational scientist affiliated with the Research Institute of St. Joe’s, Hamilton. She has demonstrated expertise in investigating inflammatory mechanisms of chronic respiratory diseases, in particular autoimmunity, response to treatment and developing/validating clinical biomarkers. Dr Mukherjee has identified the presence of localized autoimmune responses in the airways of patients with complex airways disease, and determined their pathogenic role in driving disease severity. Of recent, she has identified autoimmune responses in acute-severe COVID and linked autoimmunity with post-acute COVID-19 sequelae (or Long COVID).

Dr. Mukherjee’s research program thus focusses on “Lung autoimmunity and biomarkers”. She is the current recipient of the Emerging Researcher Award in Allergic Asthma awarded conjointly by the Canadian Institutes of Health Research (CIHR) and the Canadian Asthma, Allergy and Immunology Foundation (CAAIF). Her lab is funded by federal and non-federal sources including CIHR-ICRH and industry. Current ongoing projects span from investigating mechanisms of disease to validating biomarkers in asthma, eGPA, COVID-19 and lung cancer.

Dr. Pernica’s main research interest is in the diagnosis and management of respiratory and enteric infections in children. He is currently conducting a clinical trial in Botswana investigating whether rapid test-and-treat algorithms and/or probiotic treatment of children with severe gastroenteritis is associated with improved growth, decreased diarrhoea recurrence, and more ‘healthy’ intestinal microbiota. He is also running clinical trials in Canada exploring whether the minimization of antibiotic exposure for children with community-acquired pneumonia and otitis media is associated with less antimicrobial resistance and less disruption of the intestinal microbiome.

Dr. Pernica’s main research interest is in the diagnosis and management of respiratory and enteric infections in children. He is currently conducting a clinical trial in Botswana investigating whether rapid test-and-treat algorithms and/or probiotic treatment of children with severe gastroenteritis is associated with improved growth, decreased diarrhoea recurrence, and more ‘healthy’ intestinal microbiota. He is also running clinical trials in Canada exploring whether the minimization of antibiotic exposure for children with community-acquired pneumonia and otitis media is associated with less antimicrobial resistance and less disruption of the intestinal microbiome.

Dr. Hendrik Poinar is a molecular evolutionary geneticist and biological anthropologist by training, who relies heavily on interdisciplinary research. He uses both chemical and molecular techniques to elucidate the state of preservation within forensic, archeological and paleontological remains. This information is subsequently used to devise novel techniques to extract molecular information (DNA, RNA and/or protein sequences) and use it to address anthropological questions, such as the identification of pathogens responsible for past pandemics (i.e. The Black Death, The Justinian Plague) as well as the evolutionary dynamics of infectious disease (i.e. Vibrio cholera).

Dr. Hendrik Poinar is a molecular evolutionary geneticist and biological anthropologist by training, who relies heavily on interdisciplinary research. He uses both chemical and molecular techniques to elucidate the state of preservation within forensic, archeological and paleontological remains. This information is subsequently used to devise novel techniques to extract molecular information (DNA, RNA and/or protein sequences) and use it to address anthropological questions, such as the identification of pathogens responsible for past pandemics (i.e. The Black Death, The Justinian Plague) as well as the evolutionary dynamics of infectious disease (i.e. Vibrio cholera).

The Rullo “Chemical Immunology” research lab develops synthetic proximity inducing strategies to modulate biological recognition and receptor pharmacology. These strategies include the design and application of novel covalent bi-functional chimeras and multivalent tools with targeted immunotherapeutic function against infectious disease. The lab integrates theory and skill sets spanning organic chemistry, physical biochemistry, and immunology.

The Rullo “Chemical Immunology” research lab develops synthetic proximity inducing strategies to modulate biological recognition and receptor pharmacology. These strategies include the design and application of novel covalent bi-functional chimeras and multivalent tools with targeted immunotherapeutic function against infectious disease. The lab integrates theory and skill sets spanning organic chemistry, physical biochemistry, and immunology.

Dr. Fiona Smaill is a Medical Microbiologist at the Hamilton Regional Laboratory Medicine Program and a consultant in Infectious Diseases at Hamilton Health Sciences. She is actively involved in clinical trials in HIV management, the development of vaccines for tuberculosis, and the management of infections in pregnancy. Her interest in HIV infection includes conducting multi-centre trials to evaluate the efficacy and side-effects of different antiretroviral regimens, management of HIV-related co-morbidities, and work on gender differences in the management of HIV infection. She is also working with Dr. Xing on an adenovirus-based vaccine for tuberculosis, and they are currently running a phase 1 clinical trial to evaluate their novel TB vaccine in healthy volunteers.

Dr. Smaill has an ongoing commitment to keep updated several Cochrane Systematic Reviews related to the management of infections in pregnancy, with a focus on the treatment of asymptomatic bacteriuria and antibiotic prophylaxis for cesarean sections.

Dr. Fiona Smaill is a Medical Microbiologist at the Hamilton Regional Laboratory Medicine Program and a consultant in Infectious Diseases at Hamilton Health Sciences. She is actively involved in clinical trials in HIV management, the development of vaccines for tuberculosis, and the management of infections in pregnancy. Her interest in HIV infection includes conducting multi-centre trials to evaluate the efficacy and side-effects of different antiretroviral regimens, management of HIV-related co-morbidities, and work on gender differences in the management of HIV infection. She is also working with Dr. Xing on an adenovirus-based vaccine for tuberculosis, and they are currently running a phase 1 clinical trial to evaluate their novel TB vaccine in healthy volunteers.

Dr. Smaill has an ongoing commitment to keep updated several Cochrane Systematic Reviews related to the management of infections in pregnancy, with a focus on the treatment of asymptomatic bacteriuria and antibiotic prophylaxis for cesarean sections.

Dr. Marek Smieja is a Microbiologist and Infectious Diseases Physician and is Interim Chief of the Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences. His primary research interests are in the diagnosis of respiratory and gastrointestinal infections, and in the role of chronic infections in respiratory and cardiovascular disease. He is involved in the development and evaluation of respiratory diagnostic tests for SARS-coronavirus, influenza, and rhinovirus. His lab develops tests for respiratory and gastrointestinal infections in both Canada and Botswana. Further, Dr. Smieja’s HIV studies have examined the interaction with HIV infection and cardiovascular disease, with current studies focusing on smoking cessation, inflammation, and dental health. His clinical focus encompasses infectious disease and HIV care.

Dr. Marek Smieja is a Microbiologist and Infectious Diseases Physician and is Interim Chief of the Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences. His primary research interests are in the diagnosis of respiratory and gastrointestinal infections, and in the role of chronic infections in respiratory and cardiovascular disease. He is involved in the development and evaluation of respiratory diagnostic tests for SARS-coronavirus, influenza, and rhinovirus. His lab develops tests for respiratory and gastrointestinal infections in both Canada and Botswana. Further, Dr. Smieja’s HIV studies have examined the interaction with HIV infection and cardiovascular disease, with current studies focusing on smoking cessation, inflammation, and dental health. His clinical focus encompasses infectious disease and HIV care.

Biosensors combine biorecognition elements such as nucleic acids, antibodies and their synthetic analogues with signal transduction elements for creating devices for analyzing biologically-relevant targets. In the context of infectious diseases, biosensors can be used for rapid detection of infection, identification of causative agents, and treatment selection, reducing the unnecessary and inappropriate use of antibiotics. At the Soleymani Lab, we study the integration of smart molecular systems such as DNA/antibody assemblies and functional nucleic acids with electrical signal transduction mechanisms to find creative solutions for reagent-less and automated biosensing, in which molecular components are designed to do the work instead of the operator. The knowledge generated through this work has resulted in exciting platforms for the identification of bacterial species in native clinical samples without the need for bacterial growth cultures, target amplification, or addition of reagents, paving the way toward rapid testing.

Biosensors combine biorecognition elements such as nucleic acids, antibodies and their synthetic analogues with signal transduction elements for creating devices for analyzing biologically-relevant targets. In the context of infectious diseases, biosensors can be used for rapid detection of infection, identification of causative agents, and treatment selection, reducing the unnecessary and inappropriate use of antibiotics. At the Soleymani Lab, we study the integration of smart molecular systems such as DNA/antibody assemblies and functional nucleic acids with electrical signal transduction mechanisms to find creative solutions for reagent-less and automated biosensing, in which molecular components are designed to do the work instead of the operator. The knowledge generated through this work has resulted in exciting platforms for the identification of bacterial species in native clinical samples without the need for bacterial growth cultures, target amplification, or addition of reagents, paving the way toward rapid testing.

Jonathan’s current research applies machine learning approaches to discover novel antibacterial therapies with expanded capabilities over conventional antibiotics.

Jonathan’s current research applies machine learning approaches to discover novel antibacterial therapies with expanded capabilities over conventional antibiotics.

Dr. Michael Surette’s research team sheds light on why some microbes keep us healthy while others cause illness. They investigate the role microbes play in chronic diseases, how the microbiome develops and changes over our lifespan, and how these changes affect our susceptibility to disease. Surette and his team combine culturing methods with state-of-the-art sequencing to access and study the diversity of microbes associated with their human hosts. This particular process typically recovers two to three times the diversity of bacteria that molecular profiling alone does. Ultimately, by revealing more about the beneficial properties of the human microbiota, Surette’s research could lead to new microbiome-derived therapies to treat a wide range of conditions, such as cystic fibrosis, asthma, ulcerative colitis, and irritable bowel syndrome.

Dr. Michael Surette’s research team sheds light on why some microbes keep us healthy while others cause illness. They investigate the role microbes play in chronic diseases, how the microbiome develops and changes over our lifespan, and how these changes affect our susceptibility to disease. Surette and his team combine culturing methods with state-of-the-art sequencing to access and study the diversity of microbes associated with their human hosts. This particular process typically recovers two to three times the diversity of bacteria that molecular profiling alone does. Ultimately, by revealing more about the beneficial properties of the human microbiota, Surette’s research could lead to new microbiome-derived therapies to treat a wide range of conditions, such as cystic fibrosis, asthma, ulcerative colitis, and irritable bowel syndrome.

Research in the Whitney Lab seeks to understand the molecular mechanisms that underlie microbe-microbe interactions.

Interbacterial Killing – By The Type VI Secretion System The bacterial type VI secretion system is a recently identified protein translocation pathway used by Gram-negative bacteria to deliver toxins to neighbouring bacteria in a cell contact-dependent manner. The Whitney Lab is interested in understanding how these antibacterial proteins are transported from one cell to another and how they exert toxicity once delivered to a target cell.

Type VII Secretion-dependent Interbacterial Antagonism – In contrast to their Gram-negative counterparts, the pathways involved in interbacterial antagonism between Gram-positive bacteria has long remained elusive. In recent work, the Whitney Lab and others have found that the type VII secretion system exports antibacterial toxins that mediate interbacterial competition. Elucidating the mode of action of these toxins will allow for the identification of new vulnerabilities in Gram-positive cells that can be exploited for the development of new antibiotics.

Exopolysaccharide Secretion and Interbacterial Adhesion – Many species of bacteria exist in dense cellular aggregates held together by bacterially produced exopolysaccharides. In this form, bacteria are difficult to eradicate due in part to decreased efficacy of antibiotics. The Whitney Lab is interested in determining how bacterial exopolysaccharides are synthesized and exported from the cell.

Research in the Whitney Lab seeks to understand the molecular mechanisms that underlie microbe-microbe interactions.

Interbacterial Killing – By The Type VI Secretion System The bacterial type VI secretion system is a recently identified protein translocation pathway used by Gram-negative bacteria to deliver toxins to neighbouring bacteria in a cell contact-dependent manner. The Whitney Lab is interested in understanding how these antibacterial proteins are transported from one cell to another and how they exert toxicity once delivered to a target cell.

Type VII Secretion-dependent Interbacterial Antagonism – In contrast to their Gram-negative counterparts, the pathways involved in interbacterial antagonism between Gram-positive bacteria has long remained elusive. In recent work, the Whitney Lab and others have found that the type VII secretion system exports antibacterial toxins that mediate interbacterial competition. Elucidating the mode of action of these toxins will allow for the identification of new vulnerabilities in Gram-positive cells that can be exploited for the development of new antibiotics.

Exopolysaccharide Secretion and Interbacterial Adhesion – Many species of bacteria exist in dense cellular aggregates held together by bacterially produced exopolysaccharides. In this form, bacteria are difficult to eradicate due in part to decreased efficacy of antibiotics. The Whitney Lab is interested in determining how bacterial exopolysaccharides are synthesized and exported from the cell.

Dr. Wissler specializes in biological anthropology, especially bioarchaeology. Her research program encompasses biocultural approaches to health and frailty in historic and archaeological populations by integrating data obtained from human skeletal remains and archival documents to obtain a more holistic picture of past health. She employs epidemiological and demographic methods to explore how inequality, racism, and sexism shape health and survival during major epidemiological events, such as the 1918 influenza pandemic.

Dr. Wissler specializes in biological anthropology, especially bioarchaeology. Her research program encompasses biocultural approaches to health and frailty in historic and archaeological populations by integrating data obtained from human skeletal remains and archival documents to obtain a more holistic picture of past health. She employs epidemiological and demographic methods to explore how inequality, racism, and sexism shape health and survival during major epidemiological events, such as the 1918 influenza pandemic.

Antibiotics are vital components of modern medicine. However, their use is jeopardized by the spread of bacteria that have acquired resistance to their activity. This resistance can take many forms including enzymatic destruction of drugs, efflux, and target modification. To address the problem of antibiotic resistance, Dr. Gerry Wright’s lab is using complementary research strategies:

1 – The direct study of the molecular mechanisms of bacterial antibiotic resistance using chemical biology and chemical genetics;

2 – The identification of new antibiotics and new antimicrobial strategies.

These complementary approaches of fundamental and applied research are being pursued using a multidisciplinary approach, supported by state-of-the-art infrastructure within the Centre for Microbial Chemical Biology.

Antibiotics are vital components of modern medicine. However, their use is jeopardized by the spread of bacteria that have acquired resistance to their activity. This resistance can take many forms including enzymatic destruction of drugs, efflux, and target modification. To address the problem of antibiotic resistance, Dr. Gerry Wright’s lab is using complementary research strategies:

1 – The direct study of the molecular mechanisms of bacterial antibiotic resistance using chemical biology and chemical genetics;

2 – The identification of new antibiotics and new antimicrobial strategies.

These complementary approaches of fundamental and applied research are being pursued using a multidisciplinary approach, supported by state-of-the-art infrastructure within the Centre for Microbial Chemical Biology.

Dr. Zhou Xing’s research team studies mucosal immunity against respiratory infectious diseases including Mycobacterium tuberculosis, Streptococcus pneumoniae, and the influenza virus. They also study the mechanisms of innate immune memory and trained innate immunity, and adaptive T cell memory and immunity. Further, the Xing Lab investigates the mechanistic difference in parenteral and respiratory mucosal vaccine strategies. Together with chemical engineers and medical aerosol specialists, they develop spray drying technologies for improved thermostability (cold chain-free) and aerosol inhalational delivery (needle-free) of virus-based vaccines. They have been working together with clinical infectious disease specialists and respirologists to carry out bench-to-human translational research focused on testing novel tuberculosis vaccine strategies in human volunteers.

Dr. Zhou Xing’s research team studies mucosal immunity against respiratory infectious diseases including Mycobacterium tuberculosis, Streptococcus pneumoniae, and the influenza virus. They also study the mechanisms of innate immune memory and trained innate immunity, and adaptive T cell memory and immunity. Further, the Xing Lab investigates the mechanistic difference in parenteral and respiratory mucosal vaccine strategies. Together with chemical engineers and medical aerosol specialists, they develop spray drying technologies for improved thermostability (cold chain-free) and aerosol inhalational delivery (needle-free) of virus-based vaccines. They have been working together with clinical infectious disease specialists and respirologists to carry out bench-to-human translational research focused on testing novel tuberculosis vaccine strategies in human volunteers.

The overall objective of Dr. Jianping Xu’s research group is to understand how microbes evolve. His lab examines both the patterns of microbial evolution, as well as the mechanisms responsible for the observed patterns of evolution. They study microbial populations from the environment, human hosts, clinics, and the laboratory to address a variety of issues such as the rates and effects of spontaneous mutations, the persistence and spread of mutations in natural environments and human populations, and the origins of novel traits, strains, and species. Their research uses microbiological, molecular, ecological and quantitative genetic tools.

The overall objective of Dr. Jianping Xu’s research group is to understand how microbes evolve. His lab examines both the patterns of microbial evolution, as well as the mechanisms responsible for the observed patterns of evolution. They study microbial populations from the environment, human hosts, clinics, and the laboratory to address a variety of issues such as the rates and effects of spontaneous mutations, the persistence and spread of mutations in natural environments and human populations, and the origins of novel traits, strains, and species. Their research uses microbiological, molecular, ecological and quantitative genetic tools.

Dr. Deborah Yamamura is an Associate Physician and the Head of the Bacteriology and Mycology Laboratory at Hamilton Health Sciences. She has an interest in fungal diagnostics and emerging resistance in both fungal and bacterial pathogens. She is also interested in the evaluation and implementation of technology into the clinical laboratory. Her other main research areas include the epidemiology of invasive candidiasis, diagnostic medical microbiology, quality management and laboratory safety.

Dr. Deborah Yamamura is an Associate Physician and the Head of the Bacteriology and Mycology Laboratory at Hamilton Health Sciences. She has an interest in fungal diagnostics and emerging resistance in both fungal and bacterial pathogens. She is also interested in the evaluation and implementation of technology into the clinical laboratory. Her other main research areas include the epidemiology of invasive candidiasis, diagnostic medical microbiology, quality management and laboratory safety.