POLICIES AND PROCEDURES. Revised September 2015 DEPARTMENT OF MICROBIOLOGY AND INFECTIOUS DISEASES

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1 POLICIES AND PROCEDURES Revised September 2015 DEPARTMENT OF MICROBIOLOGY AND INFECTIOUS DISEASES 1

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3 TABLE OF CONTENTS 1.0 General Faculty Research Interests Microbiology and Infectious Diseases Graduate Program Degrees and Specializations Offered Admission Requirements Application Procedures Registration Advanced Credit Financial Information Competitive Scholarships/Studentships Program Requirements Research Integrity Day Policy Time Limit Supervisory Status Supervisory Committees Research Proposal Requirements Course Information Courses Candidacy Examination Master and Doctoral Thesis 13 3

4 A GUIDE TO THE DEPARTMENT OF MICROBIOLOGY AND INFECTIOUS DISEASES GRADUATE PROGRAM 1.0 General The Department of Microbiology and Infectious Diseases administers graduate programs leading to the degrees of MSc or PhD in Microbiology and Infectious Diseases. The objectives of this graduate program are to provide educational opportunities in microbiology and infectious diseases with emphasis on molecular approaches and microbial pathogenesis and therapy. The Department of Microbiology and Infectious Diseases is comprised of individuals who carry out research on the pathogenesis, epidemiology, host response to, diagnosis and therapy of microbial infections. Departmental research groups have been formed to focus on such areas as lung infections in cystic fibrosis, role of viruses and autoimmunity in diabetes mellitus, molecular diagnostics and therapeutics, and pathogenesis and vaccine development against pathogens. 1.1 Faculty Research Interests Antimicrobial Resistance Mechanisms - Resistance of bacteria to antimicrobial agents; mechanisms of antibiotic transport and action; mechanisms of bacterial persistence under antibiotic pressure; antiviral therapy of HIV infection. Bacterial Pathogenesis - Molecular analysis of bacterial virulence factors; gene expression during infection and in response to environmental regulators; mechanisms of iron acquisition; bacterial exotoxins and proteases; development of vaccines Clinical Infectious Diseases - Clinical trials involving assessment of antimicrobial and immunotherapy; pediatric and adult infectious diseases; new treatments for sexually transmitted diseases; infections and therapy of HIV infected/aids patients. Epidemiology - Molecular epidemiology of verotoxin production in E. coli, hospital acquired infections; sexually transmitted diseases; viral gastroenteritis; monitoring pathogens during outbreaks and clinical trials, development of molecular typing schemes, molecular epidemiology of environmental pathogens. Immunology - Regulation of T cell responses in protozoan infections; the immunologic response to infectious agents in immunosuppressed subjects. Parasitology - Immunology of parasitic infections; pathogenesis of amoebae, malaria, giardiasis, cryptospordiosis. Virology - Mechanisms of viral persistence; viral invasion; viral pathogenesis; emerging viral infection; interactions of viruses with cellular growth factor receptors; generation of recombinant viruses to target cancer cells; role of viruses in autoimmunity, viruses and insulin-dependent diabetes mellitus. 4

5 2.0 Microbiology and Infectious Diseases Graduate Program 2.1 Degrees and Specializations Offered The Department of Microbiology and Infectious Diseases offers graduate work leading to the MSc and PhD degrees. A joint MD/MSc and MD/PhD program is also offered under the title "Leaders in Medicine". 2.2 Admission Requirements: Admission to the Microbiology and Infectious Diseases graduate program (MDMI) is granted by the Faculty of Graduate Studies, based on the recommendation of the Graduate Education Committee (GEC) and the Graduate Director for Microbiology and Infectious Diseases. The minimum qualifications required by the MDMI Graduate Program are as follows: 1. Approval of a Potential Supervisor in the Department of Microbiology and Infectious Diseases. A list of potential supervisors can be found on the program website: 2. A baccalaureate degree from a recognized institution with a minimum grade-point average of 3.3 (on a 4-point system) equivalent to a B+, based on the degree work for the last two years and consisting of at least 10 full-course equivalents. 3. Proficiency in the English language: The Test of English as a Foreign Language (TOEFL) is required from applicants whose native language or language of instruction in the institutions from which they obtained their qualifying degrees is not English. The minimum acceptable score is 92 - internet-based. The test of International English Language Testing System (IELTS) where the minimum acceptable score is 7.0. Pearson Test of English with a minimum score of 64. By writing the Michigan English Language Battery (MELAB) test and obtaining a score of 82. The MELAB test includes a written composition, a listening test, and a test of grammar, vocabulary, and reading comprehension. An optional speaking test is also available. The MELAB test is offered once a month at the University of Calgary by the Effective Writing Program. By successful completion of Level 3 of the English for Academic Purposes (EAP) program. The department may waive the English proficiency testing requirement in certain circumstances and with the support of the student s prospective supervisor. 5

6 4. Two reference letters and forms from individuals that can attest to the student s academic experience. Admission into the program is conditional on confirmation of funding from the supervisor. This must be secured before admission can be granted. All graduate programs have a limited enrollment capacity. Meeting the minimum requirements does not guarantee admission. 5. Endorsement by the Graduate Director proving the applicant is acceptable and has adequate supervision for the proposed program. It will be the responsibility of all graduate students to be familiar with the regulations and deadlines of the Faculty of Graduate Studies as stated in the Faculty of Graduate Studies Policies Application Procedures Applications for admission can be made on-line through the Faculty of Graduate Studies at Contact the MDMI Graduate Program Administrator for further information on the admission process if necessary. The Graduate Director will consider an application for admission when: 1. The online application and application fee has been submitted. 2. A potential supervisor has been identified and the applicant has made some type of contact with that supervisor. 3. The applicant supplies one copy of all official transcripts that must be sent from the issuing institution in a sealed and stamped envelope. 4. The applicant has met the minimum requirements - acceptable GPA of 3.3 over the last two full years or equivalent and where applicable. 5. Two references from individuals that can attest to your academic experience. 6. English Language Proficiency Prospective graduate students are encouraged to apply as early as possible. Application Deadlines The deadlines for the submission of the completed application forms are as follows: June 1 st for September admission October 1 st for January admission March 1 st for May admission May 1 st for July admission 6

7 International Student deadlines for admission are: April 1 st for September admission August 1 st for January admission December 1 st for May admission February 1 st for July admission 2.4 Registration The normal dates for first registration in the Faculty of Graduate Studies are listed in the Academic Schedule for January, May, July and September. A continuous standing in the MDMI program requires an annual registration; failure to reregister will result in the withdrawal of the student. All students are required to reactivate their annual registration on their anniversary date of admission through the online Student Centre: Each registration is for a 12-month period. For students who have missed the deadline to reactivate their annual registration, forms are available from the Graduate Program Office. Any changes require a Change of Registration and Status form, signed by the student, the student's supervisor, and the Graduate Director. It is the responsibility of the graduate student to ensure that annual registration is completed. 2.5 Advanced Credit The applicant must make advanced credit requests as part of the admission process. Credit will not be given for course work taken as part of another completed degree/diploma or for courses taken to bring the grade point average to a required level of admission. 3.0 Financial Information The general policy of the Microbiology & Infectious Diseases Graduate program is: All students shall be full-time students All students will receive financial support for the entire 12-month period of their annual registration. All supervisors must provide a minimum stipend as follows: $21,000 per year for MSc students $23,000 per year for PhD students 7

8 The sources of financial support include: Scholarships. Graduate Research Scholarships support from the Faculty of Graduate Studies. Supervisor trust funds The University of Calgary's Faculty of Graduate Studies Calendar provides details regarding other awards. In addition, the Graduate Science Education Office also provides information regarding financial assistance and scholarships specific to MSc and PhD students within the Faculty of Medicine. The Faculty of Graduate Studies also has an Open Scholarship competition. 3.1 Competitive Scholarship/Studentships It is the responsibility of the student, with their supervisor, to identify and apply for all relevant scholarship support. Details are available from the Faculty of Graduate Studies, Graduate Scholarship Officer. Please note that many applications to external agencies must be signed by the Dean or an Associate Dean of Graduate Studies. As Deans and Associate Deans are very busy people, it will take time for these papers to be signed. It is a general rule that it takes at least 24 hrs to obtain a signature on applications left at the offices of the Dean and Associate Deans of the Faculty of Graduate Studies. Major External Funding Agencies: Alberta Innovates- Health Solutions Canadian Institutes of Health Research Studentships (CIHR) Alberta Ingenuity Fund Studentships icore Natural Sciences and Engineering Research Council of Canada (NSERC) Social Sciences and Humanities Research Council (SSHRC) Other Possible Funding Agencies and application deadlines: Alberta Lung Association studentships- Jan 15 Alberta Cancer Board Studentships - May 1 Alzheimer Society of Canada - Oct 31 Canadian Cystic Fibrosis Foundation - Oct 1/Apr 1 Canadian Diabetes Association - Dec 1 Canadian Liver Foundation - Mar 15 Canadian Lung Association - Nov 1 Canada Millennium Scholarship Foundation Heart and Stroke Foundation - Sep 8 Huntington Society of Canada - Nov1/May 1 Kidney Foundation of Canada - Oct 15 8

9 Multiple Sclerosis Society of Canada - Oct 1 Muscular Dystrophy Association of Canada - Jan 15 National Cancer Institute of Canada Research Studentships - Feb 1 National Institutes of Health Research Training Opportunities varies 4.0 Program Requirements Students in the MSc and PhD degree programs may specialize in the Research Groups (Bacterial Pathogenesis, Infectious Diseases, and Gastrointestinal) that comprise the Department of Microbiology & Infectious Disease. Other options are the combined MD/Master's and MD/PhD programs offered under the title "Leaders in Medicine". Graduate students pursue original research with a faculty member serving as supervisor and additional academic support provided by a supervisory committee. Master of Science Requirements: Attend and complete research integrity day (see below). The completion of a minimum of one full course equivalent (see below). The presentation of an annual seminar in the applicable research group. The completion of an original research project. The completion and successful defense of a written thesis which normally leads to one or more publications. The presentation of a seminar on the results of the student's research. Doctor of Philosophy Requirements: Attend and complete research integrity day (see below). The completion of a minimum of one and one-half full course equivalents (see below). The presentation of an annual seminar in the applicable research group. The completion of an original research project. The successful completion of the Candidacy Examination. The completion and successful defense of a written thesis. The thesis normally leads to one or more publications. The presentation of a seminar on the results of the student's research. 4.1 Research Integrity Day Policy All graduate students in the Faculty of Medicine are required to attend the Research Integrity Day workshop once during their program as part of their course requirements. 9

10 PhD students must meet this requirement prior to their candidacy exam. Any student not meeting this requirement will not be able to proceed with their program until they have attended the session. MSc students must meet this requirement prior to defending their thesis. Any student not meeting this requirement will not be able to proceed with their defence until they have attended the session. It is the shared responsibility of the student and supervisor to ensure that this requirement is met. The Research Integrity Day is offered twice a year, in January and April. Students will be advised by their graduate program administrators when the next upcoming session will be offered. 4.2 Time Limit Expected completion time for students in: The Master of Science (MSc) program - Two years (maximum four years) The PhD program - Four years (maximum six years) The Leaders in Medicine program - MD/MSc - Four to five years (maximum six years) - MD/PhD - Six to seven years (maximum eight years) 4.3 Supervisory Status Faculty members with continuing Board Appointments in the Professional ranks in the Faculty of Medicine may request supervisory privileges in the department based on the criteria specified below. New Faculty Appointments with an MD degree: Initial supervision of MSc students only, with the number of students specified by the Graduate Coordinator. Following successful completion of mentorship of a Masters student, the Faculty member may reapply to extend supervisory privileges to both MSc and PhD students. New faculty members will be encouraged to sit on the supervisory and examination committees of other graduate students to gain experience. New Faculty Appointments with a PhD: Unrestricted supervision for both MSc and PhD students. It is recommended that for doctoral students, the students committee must be made up of one or more senior/experienced members until the first PhD student successfully completes the program. 4.4 Supervisory Committee Students in thesis-based programs will normally have identified a supervisor at the time of admission. Both MSc and PhD students, in consultation with their supervisors, must select a 10

11 supervisory committee consisting of their supervisor plus two other faculty members within three months of initial registration. The Graduate Director must approve the composition of the supervisory committee. Master of Science students in the Leaders in Medicine program must have a supervisory committee constituted according to the regulations of that particular graduate program. Both MSc of and PhD students in the Leaders in Medicine program will also be evaluated and advised by a Joint Liaison Committee composed of the Associate Dean (Graduate Sciences Education), Associate Dean (Undergraduate Medical Education), and the Director of Admissions and Student Affairs of the Faculty of Medicine. 4.5 Research Proposal Requirements All students are required to prepare a written CIHR-style research proposal of their project and present it to their supervisory committee no later than nine (9) months after their initial registration. The proposal, with an approval form signed by all members of the supervisory committee, must be sent to the Graduate Program Office to be placed in the student's file within 12 months from entry into the program. The research proposal should be about 13 to 17 pages single-spaced in length, excluding references, figures, and tables, and should include: A critical review of the scientific literature pertinent to the proposed area of research. A clear hypothesis and specific aim(s) of the proposal. A detailed experimental plan giving relevant methods and procedures. Preliminary data can be added here. Significance of the proposed research. It is the responsibility of the supervisor and the entire supervisory committee to ensure that the proposal will be critically reviewed and approved by all members of the committee. The objective of the proposal is to ensure that the student has a clear grasp of the proposed research, and to determine if the student has the necessary scientific/scholarly writing skills. It is the responsibility of the entire supervisory committee to carefully ensure that the student meets these requirements, before approving the proposal. All Doctoral students are required to follow the Faculty of Medicine Candidacy Policies for the research proposal which will be a basis for their Candidacy Examination. 11

12 4.6 Course Information Course work is an essential part of every graduate student's program. Courses must be at the graduate level numbered or above, unless approved by the MDMI Graduate Education Committee. No more than one-half of a student's course requirement may be at the undergraduate level (courses numbered ),the minimum being one-half course. The course requirements should be met with courses offered by the Department. If a student wishes to substitute courses, 11 the student must have the approval of the MDMI Graduate Education Committee. Students entering the PhD program with an MSc completed at another institution will be required to complete at least 1 half course. Credit for courses taken during their MSc studies will be evaluated by the MDMI GEC and may at their discretion count as the equivalent of up to 2 half course credits. The supervisory committee can recommend that students take an additional course if their MSc was unrelated to the biological sciences or is necessary for the student s area of research. The minimum passing grade for any course taken by a graduate student is a B-. A grade below Bwill normally result in the student being required to withdraw from the program. An overall GPA of at least 3.0 (B) must be maintained in each year of the program. Students should be aware of the deadline dates for withdrawal with permission from courses. 4.7 Courses The following courses are offered through the Department of Microbiology & Infectious Diseases. Should you wish to view other courses of interest, refer to the Student Master Timetable on line. Medical Science 612 F(3-3) Medical Microbiology The basic principles of medical microbiology and pathogenesis of infectious disease and of clinically important pathogens. Emphasis will be on bacteriology and virology, but will also include parasitology and mycology. Prerequisites: Cellular, Molecular and Microbial Biology 343 or equivalent or consent of the Faculty. Medical Science 613 H(3-0) Advanced Studies in Microbiology Specialized topics including basic principles of infection; spread, prevention and control of infectious diseases; mechanisms of and approaches to study bacterial pathogenesis; mechanism, methodology and modeling of gene expression Epidemiology of Infectious Diseases Pathogenesis of Microbial Disease Regulation of Gene Expression in Bacteria. 12

13 Prerequisite: Medical Science 612 or Cellular, Molecular and Microbial Biology 431 or consent of the Faculty. 4.8 Candidacy Examination All Doctoral students are required to successfully pass the Candidacy Examination. Doctoral candidacy examinations have a written and an oral component. Students who are currently in a PhD program or are considering a transfer to the Ph.D. program should be aware of the requirement to complete the Candidacy Examination. The most up to date policies and procedures for the oral portion of the Candidacy Examination can be found at: The most up to date policies and procedures for the written portion of the Candidacy Examination can be found at: The oral examination, normally two hours long, is governed by the Faculty of Graduate Studies policies at Both the written and oral components need to be satisfactory for successful completion of the exam. The supervisor is a non-voting observer at the doctoral oral candidacy examination. MSc students wishing to transfer to the PhD program are required to follow the Faculty of Medicine transfer procedures. MSc students who successfully transfer to the PhD program are required to follow the Faculty of Medicine Transfer from MSc to PhD procedures for Candidacy Examination Master and Doctoral Thesis All graduate students must write and successfully defend a research based-thesis at the end of their program. The regulations governing the guidelines and examination procedures are set by the Faculty of Graduate Studies and can be found at: 13

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