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Microbiology and Immunology (PhD)

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The Department of Biochemistry, Microbiology and Immunology is located in the Faculty of Medicine and offers graduate programs leading to the degrees of master of science (MSc) and doctor of philosophy (PhD) in microbiology and immunology.

The objective of the program is to refine critical and scholarly skills in fields and areas of specialization and to prepare students for a career in a research and/or in a governmental, clinical, or industrial setting. Graduates are expected to have acquired autonomy in conducting research, in preparing scholarly publications, through a training that includes course work, research seminars, and independent research leading to a thesis.

Members of the Department are engaged in two main research fields: microbiology and host biology. Additional information is posted in the departmental website.

The Department is a participating unit in the following collaborative programs: the bioinformatics program (at the master’s level) and the pathology and experimental medicine program (at the master's and doctoral levels).

Most of the courses in these programs are offered in English. Research activities can be conducted either in English, French or both, depending on the language used by the professor and the members of his or her research group.

The programs operate within the general framework of the general regulations of the Faculty of Graduate and Postdoctoral Studies (FGPS) of the University of Ottawa, which are posted on the FGPS website.

Search all research fields for members of the teaching staff

The professors included in the list below are members of the Faculty of Graduate and Postdoctoral Studies. This means that they are authorized to supervise or co-supervise theses. A complete list of the faculty and staff members associated with the program can be found at http://www.med.uottawa.ca/grad/eng/departments.html

ALLAN, David, Cross-appointment

ALLEN, David, Associate Professor

ANGEL, Jonathan, Cross-appointment
HIV; immunology; cellular immunity

BROWN, Earl, Full Professor
Viruses: genetics; evolution; pathogenesis; Reovirus, Influenza; Hepatitis C; oncolytic viruses; pneumonia

CAMERON, William, Cross-appointment
Clinical epidemiology

DIAZ-MITOMA, Francisco, Full Professor
Development of vaccines for RNA viruses; pathogenesis of herpes viruses and hepatitis C

DIMOCK, Ken, Full Professor
Virus receptors, virus entry

FAIRHEAD, Todd, Cross-appointment

FARBER, Jeffrey, Adjunct Professor
Food safety; food microbiology; foodborne pathogens

FILION, Lionel, Associate Professor
Immunology of multiple sclerosis; antigen presentation; regulation; flow cytometry

FREEDMAN, Mark, Cross-appointment
Multiple sclerosis; neuroimmunology; Gamma Delta T cells; immune mediated CNS damage

KORNELUK, Robert, Cross-appointment
Modulation of programmed cell death (apoptosis) for therapeutic benefit in disease

KRISHNAN, Lakshmi, Adjunct Professor
Vaccine adjuvants; reproductive immunology; cellular immunology

KUMAR, Ashok, Cross-appointment
HIV; CD44; cytokines; IL-10; IL-12; TNF-alpha; monocytic cells; signal transduction

LANGLOIS, Marc-André, Assistant Professor

LEE, Jonathan, Associate Professor
Breast and ovarian cancer; oncogenes; apoptosis; actin; cytoskeleton

LEE, Seung-Hwan, Assistant Professor
Natural Killer Cell; Cytokines; Virus Infection; Immunoregulation

LI, Xuguang (Sean), Adjunct Professor
Genetically modified viral vectors for vaccine and gene delivery; mechanistic study of SARS viral assembly; pathogenesis of prion diseases

LIN, Min, Adjunct Professor
Bacterial pathogenesis; immunology

LOGAN, Susan, Adjunct Professor
Bacterial pathogenesis; prokaryotic protein glycosylation systems

MACFARLANE, Amanda, Adjunct Professor
Folic acid metabolism; Inflammation and cancer; Fetal origins of disease; Epigenetics

MAH, Thien-Fah, Assistant Professor
Understanding of the molecular mechanisms utilized by bacteria to increase their resistance to antimicrobial agents once they become part of a biofilm, Mutants of Pseudomonas aeruginosa; bacterial biofilms

MAKRIGIANNIS, Andrew, Assistant Professor

MATTISON, Kirsten, Adjunct Professor
Food borne hepatitis A virus and noroviruses; develop detection methods for isolating these viruses from food samples

NADIN-DAVIS, Susan, Adjunct Professor
Phylogenetic evaluation of collections of lysaviruses (rabies and rabies-related viruses); generation and use of novel monoclonal antibody panels for epitope analysis of viral proteins, development of sheep genotyping methods in support of scrapie control programmes; application of quantitative PCR methods to detect recombinant viruses in viruses in vaccine safety trials

PAGOTTO, Franco, Adjunct Professor
Bacterial pathogens ; Microbiological safety and control of fresh-cut produce ; Hazard identification and risk assessment in foods ; Molecular typing and genomic characterization of foodborne bacterial pathogens and foodborne viruses, Pathogenesis and virulence determinants of foodborne pathogens, molecular diagnostics using DNA microarray technology, and DNA chip technology for detection of genetically modified organisms and foods

PARKS, Robin, Cross-appointment
Development and characterization of adenoviral vectors deleted of all viral protein coding sequences for use in gene therapy; characterization of host immune responses to gene therapy vectors and foreign (therapeutic) proteins, investigating novel therapeutics for the treatment and correction of muscular dystrophies and cancer

PEZACKI, John P., Adjunct Professor
Biology and Virology Research

PICKETTS, David, Cross-appointment
Genetics diseases

RAMIREZ, Sandra, Adjunct Professor
Bacterial contamination in blood products; bacterial cell division and cell growth; cell division mechanisms of Staphylococcus epidermidis

SAD, Subash, Adjunct Professor
Cell immunology; T cell memory; lymphocyte biology; host-pathogen interactions

SANDHU, Jagdeep, Adjunct Professor
Cell biology; immunology; techniques - immunohistochemistry; confocal microscopy; cell culture; biochemistry; molecular biology

STEWART, Alexandre, Cross-appointment
Inherited cardiovascular disorders; genetic risk factors for Coronary Artery Disease

STINTZI, Alain, Associate Professor
Microbial genomics, campylobacter jejuni; iron acquisition and metabolism; and stress responses

STOJDL, David, Cross-appointment

TANHA, Jamshid, Adjunct Professor

TESSON, Frédérique, Cross-appointment
Idiopathic dilated cardiomyopathy, genetic predictors of weight loss in obese women

WALLACE, Valerie, Cross-appointment
Retinal and optical nerve development; Sonic Hedgehog protein signaling

WANG, Lisheng
Cellules souches embryonnaires; médecine regénérative; cellules immunitaires

WOULFE, John, Cross-appointment
Neurodegenerative dementias; (Alzheimer's disease and non-Alzheimer's frontotemporal dementias); Parkinson's disease and the synucleinopathies; pathogenesis of certain neurodegenerative disorders

WRIGHT, Kathryn, Associate Professor
Viruses; pathogenesis; immunology

PhD in Microbiology and Immunology

The following requirements must be met:

Successful completion of compulsory course MED8166 Professionalism and Professional Skills .

Six credits of MIC graduate courses including at least 3 credits at the 8000-level, approved by the Department.

Enrollment in the seminar course MIC8366, which involves the presentation of a seminar and regular attendance at the departmental seminars.

Successful completion of a comprehensive examination (MIC9998).

Presentation of a pre-thesis seminar (MIC9997) in the eight months preceding the submission of the PhD thesis.

Presentation and defense of a thesis (MIC9999) based on original research carried out under the direct supervision of a research faculty member in the Department.

NOTE: The Department may require students to take additional courses, depending on their backgrounds.

Collaborative Program in Pathology and Experimental Medicine

The requirements of both the primary program and those of the collaborative program must be met.

The requirements specific to the collaborative program are as follows:

One course (3 credits) in the primary program.

One Pathology and Experimental Medicine specialization course (3 credits).

Successful completion of the Pathology and Experimental Medicine seminar course.

Successful completion of the Comprehensive Examination as required by the respective primary program.

Preparation and defense of a thesis under the supervision of a professor who is a member of the Pathology and Experimental Medicine program. The thesis must be relevant to the focus of the Pathology and Experimental Medicine program. At least one of the examiners must be a member of the Pathology and Experimental Medicine collaborative program.

The passing grade in all courses is C+. Students who fail two courses (equivalent to 6 credits), the thesis proposal, or the comprehensive exam or whose research progress is deemed unsatisfactory are required to withdraw.

Transfer from Master's to PhD Program

Following the transfer, all of the rquirements of the doctoral program must be met:

doctoral seminar (MIC8366)

six credits of course work

comprehensive examination (MIC9998)

pre-thesis seminar (MIC9997)

thesis (MIC9999)

Duration of the Program

The requirements of the program are usually fulfilled within four years. The maximum time permitted is six years from the date of initial registration in the program, or seven years in the case of the students transferring from the master’s to the doctorate.

Residence

All students must complete a minimum of six sessions of full-time registration. In the case of transfer students, the residency period is nine full-time sessions from the initial registration in the program.

Minimum Standards

Thesis Advisory Committee

During the first session of the program, a thesis advisory committee (TAC) is formed for the candidate. The Committee’s membership will be determined by the specific interests of the candidate. It will be composed of the supervisor and 2-3 additional professors. At least one member of the thesis committee, in addition to the supervisor, must be form the Faculty of Medecine. The TAC is responsible for guiding the student throughout the program, including course selection, the comprehensive examination, thesis proposal, and thesis defense.

Regular meetings between the student and thesis committee members will take place at least once per session. The thesis examining board may include members who are not part of the TAC.

Tous les cours ne sont pas nécessairement offerts chaque année. Les cours sont offerts dans la langue dans laquelle ils sont décrits.

Not all of the listed courses are given each year. The course is offered in the language in which it is described.

MED8166 PROFESSIONALISM AND PROFESSIONAL SKILLS
Basic professional skills related to academic integrity, proper referencing techniques, avoidance of plagiarism, professional etiquette, public speaking, time and stress management, conflict management, teamwork, knowing when and how to access student support services. Compulsory for all students enrolled in master’s or doctoral programs at the Faculty of Medicine. Graded S/NS (Satisfactory/Not satisfactory).

MED8566 ATTITUDE ET COMPÉTENCES PROFESSIONNELLES
Compétences professionnelles de base en matière d’intégrité scolaire, d’usage des références, de vigilance face au plagiat, d’étiquette professionnelle, de présentations orales, de gestion du temps et du stress, de gestion des conflits, de travail d’équipe et de savoir faire à l’égard de l’accès aux services d’appui aux étudiants. Obligatoire pour tous les étudiants inscrits aux programmes de maîtrise ou de doctorat de la Faculté de médecine. Noté S (satisfaisant) ou NS (non satisfaisant).

MIC5100 HOST/PATHOGEN INTERACTIONS AND MOLECULAR IMMUNOLOGY (3cr.)
This course will examine current issues in microbiology/immunology. Topics to be chosen to allow discussion across the broad areas of virology, immunology and bacteriology. Within each of the modules, the focus will be on host-pathogen interactions at the molecular level, how microorganisms utilize, modify or disrupt host cell functions, including immune cell functions and immune responses, to establish infection and cause diseases, or on immunological diseases which may have an infectious component. Prerequisite: At least one undergraduate course in microbiology and/or immunology and one course in molecular biology, or permission of the course coordinator.

MIC5366 MSc SEMINAR (3cr.)
Attendance at two half-day symposia with guest speakers, attendance and participation in the annual BMI Student Symposium and BMI Poster Day, attendance at BMI seminars relevant to Microbiology and Immunology. Students must present at least one poster and one oral presentation during the course of their program. Graded S/NS

MIC7999 THÈSE DE MAÎTRISE / MSc THESIS
Avant la soutenance de sa thèse, il faut que chaque étudiant donne un séminaire portant sur ses recherches au Département / Prior to defending their thesis, each student will be required to present a formal seminar about their research to the department.

MIC8122 ADVANCED TOPICS IN IMMUNOLOGY (3cr.)
Focus on cellular immunology, including thymocyte maturation, induction and regulation of cellular responses, immune responses to pathogens, immunological memory, tolerance. Student assessments to be conducted by two methods: Weekly assessment of student presentations and participation in class discussions; assessment of take-home assignments such as completion of a research grant on a topic covered in the course. To be offered alternate years subject to sufficient demand. Prerequisite: MIC 4125 or equivalent.

MIC8124 / BCH8109 ADVANCED TOPICS IN CELL DEATH (3cr.)
Molecular mechanisms of cell death. Particular attention to be paid to role of aberrant cell death in human disease. Offered in the Fall of odd numbered years.

MIC8125 SPECIAL TOPICS IN MICROBIOLOGY AND IMMUNOLOGY (3cr.)
Discussion of current topics in Microbiology and Immunology. Topics to vary from year to year depending on the interest of faculty members offering the course and students. Student assessments to be conducted by two methods: Weekly assessment of student presentations and participation in class discussions; assessment of take-home assignments such as completion of a research grant on a topic covered in the course. Prerequisite: Permission of the course coordinator.

MIC8126 IMMUNOCHEMISTRY (3cr.)
Focus is on antigen structure of protein and carbohydrate antigens, receptor structure of B cells and T cells, structure of MHC molecules, accessory molecules and cytokine receptors and cell signalling pathways induced by the antigen and cytokine receptors. Student assessments to be conducted by two methods: Weekly assessment of student presentations and participation in class discussions; assessment of take-home assignments such as completion of a research grant on a topic covered in the course. To be offered alternate years subject to sufficient demand. Prerequisite: MIC 4125 or equivalent.

MIC8129 CURRENT TOPICS IN STEM CELLS AND IMMUNE DEVELOPMENT (3cr.)
This course will focus on the haematopoietic system that gives rise to the many cell types of the immune system. Topics to be covered include the developmental processes of embryonic stem cell differentiation into mesoderm and then into haematopoietic and non-haematopoietic progenitors; development of adult haematopoietic and immune systems; symmetric and asymmetric division of cells; intrinsic transcription factors and extracellular microenvironment factors regulating cell fate; immunological aspects of stem-cell based therapy; new technologies and their use in the field, and experimental design. Prerequisite: At least one undergraduate course in immunology or cell biology, or permission of the course coordinator.

MIC8134 / BCH8134 STRUCTURE AND EXPRESSION OF EUKARYOTIC AND PROKARYOTIC GENOMES (3cr.)
Sequencing of eukaryote and prokaryote genomes with emphasis on recent technologies, sequence alignments and databases and assembly of genomes from massively parallel sequencing data. Focus on mapping studies, including linkage disequilibrium-based genome-wide association study (GWAS), to characterize functional variants associated with complex traits. Analysis and structure of microbial metagenomes from environmental and human habitats, including structure-function analysis of microbial communities, microbiota-human disease correlations, and molecular phylogeny. Genome expression, including measures of RNA transcripts and proteins and statistical analysis of data. Combination of various -omics data to understand gene-environment interactions.

MIC8236 ADVANCED TOPICS IN VIROLOGY (3cr.)
An in-depth presentation of current topics in virological research. Topics will vary from year to year. To be offered every alternate year subject to sufficient demand. Prerequisite: MIC 4126 or equivalent.

MIC8238 ADVANCED TOPICS IN BACTERIOLOGY - MECHANISMS OF PATHOGENESIS (3cr.)
Recent advances and current topics in selected areas of bacteriology with emphasis on mechanisms of pathogenesis. Students present and discuss journal articles. Offered every alternate year subject to sufficient demand. Prerequisite: MIC 4124 or its equivalent.

MIC8366 PhD SEMINAR (3cr.)
Attendance at two half-day symposia with guest speakers, attendance and participation in the annual BMI Student Symposium and BMI Poster Day, attendance at BMI seminars relevant to Microbiology and Immunology. Students will present a poster in their first and every alternate year, and an oral presentation the second and every alternate year until they have permission to write their thesis. Graded S/NS

MIC8401 ADVANCED TOPICS IN BACTERIAL GENETICS (3cr.)
Microbial genetic and genomic methods: origin, purpose and functioning. Analysis and use of genomes to study bacterial pathogenesis and host-microbe interactions.

MIC8500 SPECIAL TOPICS IN HEALTH-RELATED ENVIRONMENTAL MICROBIOLOGY (3cr.)
Recent advances and current topics in selected areas of health-related environmental microbiology. Topics reflect student interest. Offered in alternate years subject to sufficient demand. Prerequisite: MIC 5500 or equivalent.

MIC8534 / BCH8534 STRUCTURE ET EXPRESSION DES GÉNOMES PROCARYOTES ET EUCARYOTES (3cr.)
Le séquençage des génomes eucaryotes et procaryotes, avec un accent particulier sur les technologies récentes, l’alignement des séquences et les bases de données, et l’assemblage des génomes à partir de données générées par séquençage haut débit. Les études de cartographie comparée incluant les études d’associations pangénomiques basées sur le déséquilibre de liaison pour caractériser les variantes fonctionnelles associées aux traits complexes. L’analyse et la structure de métagénomes microbiens issus d’habitats humains et environnementaux incluant l’analyse structure-fonction des communautés microbiennes, les corrélations entre les maladies humaines et le microbiome ainsi que la phylogénie moléculaire. L’expression génique incluant les mesures de transcriptomes et de protéomes ainsi que l’analyse statistique des données. La combinaison des différentes -données omiques pour comprendre les interactions gène-environnement.

MIC8700 BIOLOGY AND PATHOGENESIS OF HIV INFECTION (3cr.)
Biology and pathogenesis of Human Immunodeficiency Virus (HIV) infection. Genetics, replication, structure, regulation of gene expression, immunopathogenesis, antiviral therapy and vaccine development. Offered in alternate years subject to sufficient demand. Prerequisite: BCH 3170 or equivalent and permission of instructor.

MIC9997 SÉMINAIRE DE RECHERCHE/ RESEARCH SEMINAR
À l'intention des étudiants faisant de la recherche en vue de l'obtention du doctorat. Un séminaire, fondé sur les résultats originaux de leur recherche, doit être présenté par les étudiants au cours de l'avant-dernière ou de la dernière session d'inscription précédant la soumission de la thèse de doctorat / For students doing research leading to the PhD. A seminar based on the student's original results, to be presented during the last two academic sessions prior to submission of the PhD thesis.

MIC9998 EXAMEN DE SYNTHÈSE (DOCTORAT) / COMPREHENSIVE EXAMINATION (PhD)

MIC9999 THÈSE DE DOCTORAT / PhD THESIS

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