1. Before a student can receive an MSc or be considered for transfer into the PhD program in Medical Microbiology, the student must successfully complete MMIC 7050 (Microbial Pathogenicity) and a minimum of 6 more credit hours of graduate level courses.
2. All graduate students in the Department must attend and participate in the Medical Microbiology seminar/journal club program.
3. A minimum overall grade point average of 3.0 must be obtained in all courses with no letter grade below C+ in any single course.

1. a) The PhD program requires an additional 6 credit hours beyond the requirements of the MSc degree.
   b) In addition, for students beginning the PhD program who have obtained an MSc degree from an institution other than the University of Manitoba Department of Medical Microbiology, the requirement to enroll in Microbial Pathogenicity (MMIC 7050) will be at the discretion of the Department GSC in determining if a course equivalent to MMIC 7050 has been successfully completed in their MSc program.
2. All graduate students must attend and participate in the Medical Microbiology seminar/journal club series.
3. A minimum overall grade point average of 3.0 must be obtained in all courses with no letter grade below C+ in any single course.

Coordinators: Drs. Blake Ball, Matthew Gilmour, and Alberto Severini 
Co-coordinator:  Drs. Keith Fowke, Xiaojian Yao
Administrative Assistant: Cheryl Reimer

When? and Where?
In this year, our journal club/research seminar course for each group will be held once a month.  This means each group will have a 3 hours journal club for 4-6 students in each month. Coordinators for each course will determine the time and place for their journal club.

Three Themes:

• Host-Pathogen Interactions Journal Club.  
  Time and Place: to be determined by the the coordinator (Dr. Ball)
  This literature review will focus on the relationship between innate and adaptive host immune responses to infectious agents in humans and other mammals and the mechanisms pathogens utilise to escape these responses.
• Molecular Virology Journal Club:
  Time & Place: to be determined by the coordinator (Dr. Severini)
  Topics for discussion in this journal club can include the fundamental molecular mechanisms that control viral replication, the molecular analysis of viral genes and their products and subsequent interactions with host cells.
• Bacteriology Journal Club: 
  Time & Place: to be determined by thecoordinator (Dr. Gilmour).
  Topics for discussion in this journal club can include the virulence, genomics, proteomics, surveillance, or antimicrobial resistance of bacterial pathogens.

Objectives:
For students to learn how to

• critically evaluate scientific work
• communicate scientific ideas and concepts effectively  

• The Journal Club Presentations will not be offered for credit but it is a mandatory aspect of the graduate program in this Department and is required for graduation.

• All graduate students must register with and regularly attend one of the journal club series.  The students are able to attend other series as the topics and their interests allow.  
  • The absentia students (except for medical or other emergent situation) will be required to provide a 3-5 page written analysis of a new, high-ranking paper (Impact factor of above 4) and report to coordinator, and consistent lack of attendance could affect continuation in the graduate program.
  All post-doctoral fellows are encouraged to attend but it is not a requirement.
• All Med Micro faculty are encouraged to attend.  Supervisors are advised of when their student is presenting and are strongly encouraged to attend.   This Department views this as a key part of the mentoring process and helping the students improve.

Who has to present?

• All of MSc and PhD level graduate students will be required to present one presentation in each year of their graduate studies in this Department. The evaluation form of each student will be recorded each week as the indication of your attendance.

Format:

• 20 min presentation
• 10 minutes for questions
• 5-6 students will present per session

• Articles must be pre-approved by your Journal Club series coordinator at least 3 weeks in advance.
• There are three general thematic areas that form the basis for the three Journal club series; Molecular Virology, Bacteriology, Host-Pathogen Interactions.
• You may choose any paper that falls within the general theme of the Journal Club series in which you are presenting.  Articles must be a primary scientific publication (no review articles) in first-rate journals.
• Articles should not be from someone’s own laboratory.
• The chosen paper should be with higher impact factor. It should be emphasized that the student’s responsibility is to provide an environment where everyone in the audience will take away something. 
• Articles should be from the last 12 months.
• The article must be available in electronic form.  If it isn’t in a PDF from the journal then you must scan the article in yourself.  There are scanners in the Department that you can use.

• Choose an article (MUST be in electronic form) At least 3 weeks before your presentation email the PDF of the paper to the responsible coordinator.  Please note there are large numbers of graduate students in our Department so when you send your article please state
  • Your name
  • Your supervisor's name
  • What your lab's research focuses on in general
  • What is your specific research topic
    I will not approve the article without that information
• All papers should be approved by the appropriate coordinators, Drs. Blake Ball, Matthew Gilmour, and Alberto Severini, who are responsible for the Host-Pathoen Interactions,  Bacteriology and Molecular Virology respectively,  Journal Club series.  If the coordinator is not available at the time, Dr. Yao and Fowke may approve papers at http://130.179.18.117/cms/ioEditor/yao2@cc.umanitoba.ca or fowkekr@cc.umanitoba.ca
• When the coordinators have approved your selection they will request that you forward the article to Ms. Cheryl Reimer. Cheryl may be contacted directly at cheryl.reimer@med.umanitoba.ca.
• Cheryl will put notice of your presentation onto the Med Micro Seminar schedule and place the paper on the Med Micro web page. She'll also forward the article to the student's supervisor.
• If presenting in 540 BMSB, bring your USB and pick up the cordless keyboard and mouse (for use with the Samsung Screen in Room 540) from Cheryl in Room 530 BMSB. If presenting at CSCHAH please arrive early to make sure you know how to load your presentation into the built-in system.  It is the presenter’s responsibility to make sure everything is hooked up and working properly. IF YOU ARE USING YOUR OWN COMPUTER YOU MUST ENSURE THAT IT IS COMPATIBLE WITH THE PROJECTOR, DON’T ASSUME IT WILL BE.
• All students will download the articles and the appropriate evaluation form and bring a copy of each to the Journal Club. Without an evaluation sheet you don't get credit for having attended.

• Evaluation forms.  All students will provide a numerical score assessing how the presenter performed (a score and written comments that will be summarized and relayed to the presenter). You will be expected to give thoughtful comments on the strengths and weaknesses of each presentation.  The intent is for constructive advice.  Don’t forget to mention the good points also.
• DURING OPEN DISCUSSION TIME, STUDENTS WILL BE EXPECTED TO ASK QUESTIONS.  Each participant of the journal club series should be prepared with a couple of questions.  The questions will start with the assigned questioners, followed by other students, then open to all.
• The comments and marks will be summarized and provided as written feedback to the presenter.
• Marking will be based on 50% students’ average mark and 50% faculty mark.
• Top two presentations and top rookie receive awards at the end of the year

What to focus on this year?

One weakness of some presentations last year was a lack of critical evaluation of the paper.  People conveyed what was done in the paper very well but many did not provide their opinion whether the study was valid and has science move forward because of it.  Remember you don’t always have to be correct, but you do have to have thought about it and have an opinion.

*If a schedule change is required, it is the student's responsibility to arrange that and inform Cheryl Reimer email: cheryl.reimer@med.uanitoba.ca

New students, with the assistance of their supervisor, are to select and meet with their advisory committee within three months of starting their graduate program.  The graduate program assistant will follow up to ensure this meeting has taken place. 

No later than three days prior to all committee meetings, a Medical Microbiology Graduate Student Research Progress Report (MMGSRP), 2 pages single-spaced long, is to be emailed to the advisory committee (in the case of a new student, this report is emailed to the supervisor). 

The Report will consist of the following, or similar, sections:

Background, Gaps in Knowledge, Rationale, Hypothesis, Objectives, Approach or Results, Progress since last meeting.

Upon completion of the meeting, a Graduate Studies Progress Report and Graduate Student Annual Advisory Committee Checklist are to be completed and submitted to the graduate program assistant along with a copy of the MMGSRP  as a record of the meeting and the appointment of the committee members. 

M.Sc. committees shall consist of a minimum of 3 Faculty of Graduate Studies members (the list of these Faculty members can be found on the U of M website at http://umanitoba.ca/faculties/graduate_studies/admin/index.html):

• The student’s supervisor
• A Faculty member of the Departmental Graduate Studies Committee*:
       Dr. Keith Fowke (Chair)
       Dr. Michelle Alfa
       Dr. Blake Ball
       Dr. Kevin Coombs
       Dr. Mike Drebot
       Dr. John Wylie
       Dr. Xi Yang
       Dr. Xiaojian Yao
       Dr. Joanne Embree (ex officio)

A Faculty member from another department.  This person may be cross-appointed in the Department of Medical Microbiology but if they are, at the time the thesis is examined, a faculty member from another department not cross-appointed in the Department of Medical Microbiology is required (Advisory Committee versus Examining Committee).

Ph.D. committees shall consist of a minimum of 4 Faculty of Graduate Studies members:

• The student’s supervisor
• A Faculty member of the Departmental Graduate Studies Committee* (as above)
• A Faculty member from another department (may NOT be cross-appointed in the Department of Medical Microbiology in any circumstance)
• In addition, please note that a Faculty member from another university must be added to the Ph.D. committee at the time the final Ph.D. Thesis is prepared and examined (Advisory Committee versus Examining Committee)\

  These policies do not prevent the inclusion of additional advisory committee members whose expertise may be of benefit to the student.

  *In cases where a student’s supervisor is a member of the Departmental Graduate Studies Committee, an additional faculty member of this committee is expected to fulfill this requirement.

1. Normally, a student should be considered for transition no less than 18 months from the start date of their MSc program.
2. The student must have completed 12 credit hours of study towards their degree.
3. A transitional seminar is to be given by the student no later than the end of their second year of MSc study.

Topic approval:

The student must indicate to the advisory committee, usually at the advisory committee meeting, that they wish to proceed with the candidacy exam and the committee must approve.  The student, in consultation with their Committee, selects a topic suitable for writing a grant application.  The examination topic may not be directly related to the student’s graduate project or any of their previous projects, as the intent is to test their own ability to design a research project de novo.   While choosing a topic that is completely new to the student is strongly encouraged, the topic may involve a similar scientific question applied to a different organism, or a different scientific question applied to the same organism studied by the student, but not both.  It is at the discretion of the Advisory Committee if the topic is sufficiently distinct from their graduate project or previous work.

Once the general topic is approved, the student then will submit, usually by email, a two-page letter of intent (LOI) to their Advisory Committee.  The LOI will contain the following, or similar, headings: Title, Background, Gaps in Knowledge, Rationale, Hypothesis, Specific Objectives with some experimental detail, and Significance.  Each member of the Advisory Committee must respond to the LOI within one week, either granting the student permission to write the examination or suggesting where major changes need to be made.  The comments from each committee member and the student’s revised LOI must be shared with the whole committee.  Once all members of the committee have approved the LOI the student may then proceed to writing the full grant.

Timing of the process:

At the time the student receives permission to write, the date of the student’s presentation of the grant to the Advisory Committee is to be scheduled.  This is normally 2 months following permission to write and should be no later than three months. All members of the Advisory Committee are expected to attend the Oral Presentation.  Should a committee member be absent for an extended period then provisions should be made to connect that committee member by video or teleconference.  Should that not be possible, the student’s PowerPoint presentation of the grant is to be provided to the committee member at least one week in advance of the oral presentation.  By the time of the oral presentation the absent committee member should provide to the student’s advisor written detailed comments on both the grant and oral defense noting the pass/fail category and any required changes. The advisor will present these to the student and committee following the student’s oral presentation.

Grant writing:

The student will have one (1) month from the date permission is received to write a CIHR-style grant application in the chosen field and submit it to their Advisory Committee.  The grant will take the form of a normal CIHR operating grant.  The grant will be composed of three major modules (CV, research and budget) plus the relevant CIHR pages.  The grant must follow the CIHR guidelines for each module.  The CV Module must be done using the Common CV web page using the CIHR format, including sections such as Most Significant Contributions.  The Research Module must include a Summary page, a Progress to Date page, and an 11-page Research Proposal.  The Summary page and Research Proposal can use section headings similar to the Letter of Intent.  The Budget Module must include a one page budget summary table using the categories identified by CIHR and detailed budget justification.  The budget must be justified for each year of funding requested.   Terms of the grant are to be 3-5 years.  The student should also provide mock letters of collaboration where appropriate. 

The student should assemble the various components of the grant into a single PDF file and distribute to the Advisory Committee by email and hard copy.  

The Committee is normally allowed one month to review the grant.  The timing of the date of Oral Presentation of the grant is to be agreed upon at the time the student is given permission to write the full grant (see above for details).

Oral Presentation and Evaluation:

The student’s presentation consists of a 20- to 30-minute overview of his/her grant to the Advisory Committee, followed by a question and answer period not to last longer than 60 minutes.  The student’s advisor is the Chair of the Oral Presentation proceedings. 

The quality of the proposal and the performance of the student in the candidacy exam will be evaluated based on his/her originality, logical thinking, related knowledge, and the project's feasibility and potential to generate high quality/impact publications. Evaluation is generally verbal, unless a committee member is absent (see above). A student can be given a passing grade without any further modification or, may be passed but asked to make minor modifications to the grant based on the suggestions of the committee members.  The required changes must be agreed upon by the whole committee and submitted in writing to the student. The student’s advisor is tasked by the committee to ensure all of the changes have been made satisfactorily before the Candidacy Examination Form is turned in to the Department Head.

If the student is deemed by his/her committee not to be satisfactory in grant writing and/or defense, the student will have failed the exam.  Students who fail will, after consulting their Advisory Committee, either make major modifications to the first application or write another grant. The student's Advisory Committee determines if the application can be improved by modification or whether a new topic must be chosen for the second attempt. The second attempt must be completed and distributed to the advisory committee within one (1) month, and is then followed by a second presentation and question and answer evaluation. Students who fail the exam twice will be required to withdraw from the PhD program by FGS. On successful completion of this examination, the student will be considered a candidate for the PhD degree.

The following reference materials, which are helpful for the grant preparation, are available from the office of the Graduate Studies Coordinator and students are encouraged to consult them:

1.    “CIHR Hints for Research Grant Applicants” (available on the University of Manitoba website)

2.    “Top Tips for Getting Grants” (also available on the website)

3.    Pages 1 and 8 of an actual CIHR grant application.

4.    Guidebook for New Principal Investigators (Institute of Genetics, CIHR), available on the website.

Guidelines for Preparation of Thesis

All graduate students must present their proposed thesis outline to the Advisory Committee for approval prior to writing the thesis (submit the Faculty of Graduate Studies "Thesis Proposal" form to the department following the presentation).

General format of thesis: This information is available from the Faculty of Graduate Studies in a publication entitled "Thesis Guidelines". As a general rule, a Master's thesis is normally less than 100 pages, excluding references and appendices and that of a PhD thesis, 150 pages, also excluding references and appendices.

The thesis shall consist of the following in order as given:

1. Title page
2. Abstract (to conform to National Library and University of Manitoba Library requirements)
3. Acknowledgements
4. Table of Contents (including references, appendices, vitae, etc.)
5. List of Tables
6. List of Figures and Illustrations
7. Text
8. References
9. Appendix(ces)

1. INTRODUCTION
   The introductory chapter must do the following (not necessarily in the order shown):
   1. Broach the subject of the thesis.
   2. Give a brief history of the subject, emphasizing the milestones.
   3. In the light of a brief but critical review of pertinent literature, indicate the state of the subject at the beginning of the investigation and clearly formulate the problem chosen for investigation. Indicate why the problem was chosen and outline logically the approach to the problem. Point out any important aspects of the approach which are unusual and mention any important limitations.
   4. Summarize with a concise STATEMENT OF OBJECTIVES or PURPOSE, which poses the questions to be answered by the research.
   
   
2. MATERIALS AND METHODS
   The Methods sections should be written in the format of a typical paper in a microbiology or molecular biology journal. Standard methods should be referenced without comment but modifications to established methods should be identified in the text. Detailed procedure, especially formulation, etc., may be included in an appendix if desired. The make and model of important major equipment (i.e. centrifuges, scintillation counters, etc.) should be identified in the text; the sources of chemicals, in an appendix. Statistical analyses should be included and details, if necessary (i.e. raw data no included in results), should be provided in the appendix. Discussion of standard methodologies should not be included; however, if new methods were developed and/or if these methods were an essential component of the project, some discussion can be included.
   
   
3. RESULTS
   The results should be stated with no discussion. However, sufficient commentary should be included so that experiments are linked together and the rationale for the experimental procedure is clearly defined.
   
   Tables may be included in the text if small enough. They should include a descriptive title, and sufficient explanation of the experimental protocol in the legend as to be understandable without excessive reference to the text. In the event that the table is not included in the text, it should be treated in the same manner as a figure or illustration (see below). The general format for tables, once selected, should be consistent throughout.
   
   Figures and Illustrations should be located within the appropriate section on the page following first mention in the text and should be placed on the right-hand page with a comprehensive legend on the facing page. The legend to the figure should include a descriptive title, a brief description of the experiment and a key to the symbols and abbreviations used. Either the figure or the legend page should be numbered throughout the thesis.
   
   Any illustration that does not reproduce well must be inserted in its original form (i.e. a photograph) in each copy of the thesis. Direct prints of negatives on 8-1/2" x 11" photographic paper or permanently fixed to a page are acceptable.
   
   Legends of figures and tables should be single-spaced.
   
4. DISCUSSION
   The discussion should be an interpretation of the results. Reference should be made to the literature cited in the introduction, and the relevance of the research should be clearly outlined. A certain amount of speculation is allowable.