Microbiology Handbook

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Section 1: Handbook

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This handbook describes and presents the guidelines, rules of operation, and policies of the Graduate Program in Microbiology. It serves as the central source of information for both graduate students and faculty for the operation of the Program.

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The Graduate Program in Microbiology conforms to University rules as published in the Graduate School Handbook. It follows the policies, rules and guidelines found in the Graduate School Bulletin.

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Section 2: Graduate Studies Committee

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The Graduate Studies Committee is the executive committee of the Graduate Faculty of the Program. It conducts routine matters related to graduate work and monitors the functioning of the Program. It coordinates graduate work in the program, assists members of the Graduate Faculty and represents the Program in performing specific functions related to operations of the Graduate School as defined in the Graduate School Bulletin and the Graduate School Handbook. Actions proposed by the Graduate Studies Committee are approved by the Graduate Program Faculty.

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The Graduate Studies Committee is composed of at least three Graduate Faculty, one of whom serves as Chairperson, and one graduate student. All members are appointed by the Microbiology Department Chairperson, in consultation with the Graduate Faculty, for terms designated by the Department Chairperson.

Current Graduate Studies Committee:

• Dr. Chad Rappleye (Chair)

• Dr. Juan Alfonzo

• Dr. Patrick Bradley

• Dr. Irina Artsimovitch

• Peter Brechting (graduate student representative)

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The Graduate Studies Committee is responsible for the Graduate Admissions activities of the department. Specific duties of the Graduate Studies Committee include:

  • Publishes a graduate program handbook containing the policies, rules, and procedures of the Graduate

Program

  • Establishes rules and procedures for the conduct of the Candidacy Examination
  • Establishes rules and policies for the selection of advisory committees
  • Determines eligibility of students to hold GTA appointments
  • Recommends action on curricula, graduate courses, and program changes
  • Specifies criteria and credentials for admission to the graduate program in addition to those required by the Graduate School
  • Reviews applications to the Graduate Program and nominates applicants for admission
  • Reviews requests from students for changes in program, registration, and credits
  • Nominates faculty to the Graduate School for category P status
  • Appoints faculty to the Graduate Program for category M status
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Category P Qualifications

Qualifications

  • The faculty member holds appointment as a tenure-track or research track faculty member
  • The faculty member holds a Ph.D., D.M.A, Ed.D., or equivalent
  • The faculty member is engaged in an active program of research or demonstrates significant promise of establishing such a program

Process

  • The candidate faculty member provides members of the Graduate Faculty with a CV and Summary of Research.
  • The candidate faculty member gives a seminar to the department on their research
  • The Graduate Program faculty approve nominations to Category P status
  • The Graduate Studies Committee Chairperson nominates the candidate through Grad Forms using the Graduate Faculty Form

Category M Qualifications

Qualifications

  • The faculty member holds a tenure-track or clinical faculty appointment
  • The faculty member holds a master’s degree or higher, or equivalent

Process

  • The Graduate Program faculty approve nominations to Category M status
  • The Graduate Studies Committee Chairperson notifies the Graduate School of the appointment

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Section 3: Advisors and Advisory Committees

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3.1    First Year Students and Laboratory Rotations

First Year Students and Laboratory Rotations

 3.1.1    Advising for First-Year Students

The Graduate Studies Committee Chairperson serves as a temporary advisor for incoming Ph.D. students and assists the students in choosing courses and in initiating their graduate program during the first year of study.

3.1.2    Laboratory Rotations and Selection of Advisor

Students admitted to the program are required to do three seven-week rotations in laboratories of interest. Students are strongly encouraged to contact and/or visit faculty members they are considering for rotations or permanent location to obtain additional information, prior to the faculty agreeing to allow the student to rotate. Students will be required to initiate and complete a Rotation Agreement Form prior to beginning each rotation. Rotation assignments are made by the Graduate Studies Committee Chair based on ranked choices by the students and available space in research laboratories. One week prior to the end of the three    rotations (and not before), students submit a ranked list of  three  potential  advisors  to  the  Graduate Studies Committee Chair, who will consult with the potential advisors. Funding  and the training capacity of a particular lab will also be considered  before  the  Graduate Studies Committee approves final laboratory assignments. Students may inquire of faculty if they have an available position, but faculty and students should not make independent prior arrangements or agreements regarding the student’s dissertation lab.

In the event a student does not find a laboratory for their dissertation research, the student can complete a fourth rotation to try to find an advisor. If a student has not found a research laboratory for their dissertation research, the student will meet with the Graduate Studies Committee chairperson to discuss options for a master’s degree.

3.1.3    Direct Admission

Students who have made contact with an individual faculty member prior to arriving on campus, and only after the faculty member’s approval, can petition the Graduate Studies Committee to waive the rotations. In this latter case, both the student and faculty member must write a letter of petition; this is to ensure that all parties are aware of the decision and are in agreement. Advisors who agree to accept a student without rotations must provide the first year of support for the student.

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3.2    Research Advisor

Only Microbiology Graduate Program faculty are eligible to serve as the dissertation advisor. Ph.D. Advisors must have Category P status within the Microbiology program. Currently, all Microbiology Graduate Faculty hold Category P status. A Master’s degree advisor must have at least Category M Graduate Faculty status; Category M Faculty members can serve as Ph.D. Advisors under the supervision of a Category P faculty member.

After rotations, the choice of an advisor must be the result of mutual agreement between student and advisor. The advisor for a Ph.D. candidate makes a commitment to the student to oversee progress of the student's laboratory research and class work. The student makes a commitment as an apprentice scientist to undertake laboratory research on a project to which they mutually agree. This association of student and advisor is a substantial commitment of time and resources by both parties. The obligation between both parties should compel students and faculty to seriously consider their choices in this regard. The advisor has the primary responsibility of overseeing the graduate student's choice of coursework and provides guidance on the student's conduct of study and research.

Financial Responsibility

Advisors assume financial responsibility for the student after the first year. Funding of graduate students

as graduate research associates (GRAs) can be through grant support, fellowships, etc. Support for students as graduate teaching associates (GTAs) is provided to faculty members based on the availability of positions to the department. Salaried, non-tenured faculty are given first priority and positions are subsequently offered to salaried, tenured faculty of the department on a limited basis. If GTA positions are still available, they can be provided to non- salaried, courtesy-appointed faculty of the program however, there is no guarantee that students advised by non-salaried courtesy-appointed faculty will be provided GTA positions.

3.2.1    Changing Advisors

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Each student must have an Advisory Committee consisting of the advisor and at least three other graduate faculty members, two of whom must be from the Department of Microbiology graduate program. All members of the dissertation committee for PhD students must be category P faculty. Students are expected to have formed their Advisory Committee prior to the Summer Semester of their first year and no later than the beginning of the second year of graduate study. The student and advisor select suitable committee members based on the student’s research direction(s). The advisor will be Chair of the committee. All members of the dissertation committee for PhD students must be category P faculty.

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Section 4: Degree Programs

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Section 5: The Ph.D. Program

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5.2 Course Requirements

Students will complete a total of at least 80 credit hours. Of these, at least 18 credits must be graded courses (i.e., not S/U grading) in which a B or higher grade is required. These graded credits are typically completed during the first two years with core and elective courses.

The remaining hours are comprised of seminar courses and research credit hours. Pre- candidacy students will enroll in 8-18 hours (Autumn and Spring) or 3-8 hours (Summer) per term. Post-candidacy students enroll in three credit hours per term.

5.2.1 Microbiology Core Courses

Students entering the Ph.D. program will complete a four-course, 11 credit-hour graded core curriculum during the first year of study. In the Autumn Semester students will take:

  • 6010 (2 credits): Principles of Microbiology
  • MICRBIOL 6020 (3 credits): Microbial Physiology and Biochemistry

In the Spring semester, students will select two from three course options:

  • MICRBIOL 5161 (3 credits): Bioinformatics and Molecular Microbiology
  • MICRBIOL 6155 (3 credits): Microbial Ecology and Evolution
  • MICRBIOL 6080 (3 credits): Advanced Microbial Genetics
  • Elective Courses

In addition to the core courses, students are required to complete at least 7 hours of graded electives, typically taken during the second year of study. Selection of electives appropriate to the student’s research are chosen by the student in consultation with the Advisor and the Advisory Committee. A list of approved elective courses is provided here. Students may take other elective courses as appropriate for their dissertation research; these courses must be approved in advance by their Advisory Committee.

The student’s Advisor, in consultation with the Advisory Committee, will provide guidance for the selection of courses needed to meet the requirements for Microbiology course distribution and the overall credit hour requirements.

5.2.3 SEMINAR COURSES

All graduate students will enroll in Microbiology seminars each Autumn and Spring semester throughout their program:

  • MICRBIOL 8899 (1 credit): Seminars in Microbiology (Student Seminars)
  • MICRBIOL 7899 (1 credit): Microbiology Colloquium (Departmental Seminar Series)

All students are required to attend each seminar throughout the year in both Micro 7899 and 8899; students failing to do so, and not receiving approval to miss a seminar, will receive a grade of U.

Ph.D. students are required to complete a minimum of two presentations in MICRBIOL 8899. In addition, students must complete MICRBIOL 7600 (1 credit; First-year Student Orientation), typically during the first semester.

5.2.4 RESEARCH CREDITS

First year students will do three 7-week laboratory rotations during their first year. For these, students will enroll in MICRBIOL 6789 (Research Principles and Techniques in Microbiology) in the Autumn and Spring semesters of their first year with the Graduate Studies Committee Chair serving as the temporary advisor.

After joining a laboratory for their dissertation research, students will enroll in either MICRBIOL 7899 Research in Microbiology (pre-candidacy students) or MICRBIOL 8999 (post-candidacy students) each term (including Summer term) under their Advisor.

5.2.5 REGISTRATION

The number of credit hours attempted each semester is mutually determined by the student and the advisor and reflects faculty and student effort and the extent to which University resources are utilized. Course loads for full-time students can vary, as noted below. A student may not enroll for more than 18 credit hours per semester, 8 hours in Summer Session, without Advisor and Graduate School approval. This includes audited courses.

Post Candidacy & Continuous Enrollment

All students who successfully complete the doctoral Candidacy Examination (“post-candidacy”) are required to be enrolled in every semester until graduation. These students must be enrolled for at least 3 credits per semester. This policy is effective for all students who were admitted to the Graduate School Autumn Semester 2012 and after (Section 7.8).

Graduate Associates (GA)

Graduate associates, either graduate teaching associates (GTAs) or graduate research associates (GRAs), holding 50 percent or greater appointments must register for at least eight (8) credit hours per semester, except in summer when the minimum is four credits. (Microbiology pre-candidacy students are encouraged to register for 12 credit hours per semester, four in summer session.) GAs holding a 25 percent appointment must register for at least four credit hours per semester, two credit hours in summer session. Post-candidacy doctoral students must register for at least three credit hours each semester an appointment is held, including summer term.

Fellows (Students on Fellowships)

Pre-candidacy doctoral students holding the title of graduate fellow, regardless of the source of the funds, must register for a minimum of 12 credit hours each semester the appointment is held (six credit hours during Summer Session). Graduate fellows who are post-candidacy doctoral students must register for at least three credit hours per semester, including Summer Semester.

5.2.6 Leave and Partial Enrollment
5.2.6.1 Short-term Leave

Funded graduate students requesting to take time off must complete a short-term leave form; this does not apply to weekend-only travel or holiday breaks during which campus is closed.

Any absence during academic breaks (e.g., Spring break or Winter break) requires completion of a short-term leave form. Short-term leave must be approved in advance by the student’s advisor and the student’s TA supervisor (if the student is a GTA) and the form turned into the into the Graduate Studies Committee.

5.2.6.2 Partial Enrollment

Part time registration is permitted only with approval of the Graduate Studies Committee. Students are expected to complete all required graded coursework (core and electives) within 5 semesters of initial enrollment.

Graduate students who take a leave of absence or who do not enroll in the Graduate School for longer than one year, at any time during their Ph.D. program, are considered to have left the Program and are not eligible for any financial support. Students who elect to take a leave of absence for extenuating personal circumstances should meet with the Graduate Studies Committee Chair to discuss the situation and establish expectations to be done during the leave of absence. Students must petition the Graduate Studies Committee for re-enrollment, unless prior arrangement has been made with the Advisor and Graduate Studies Committee.

5.2.7 Sample Course Schedule
5.2.8 Transfer Students

Students who are transferring to the program from another institution with their advisor will not be required to participate in rotations. These transfer students are expected to establish their Advisory Committees no later than completion of the first term in the program. This committee, in consultation with the Graduate Studies Committee, will determine which core and elective courses are required to supplement the student’s prior coursework. Doctoral students must complete 80 credit hours to qualify for the degree; students transferring to OSU from another university must complete at least 30 credit hours at OSU.

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5.6 Review of Students’ Progress

To assist the development of each student, a review of progress will be made by the student's Advisory Committee. These reviews should occur at least annually. It is the responsibility of the student and his/her advisor to plan review meetings and to ensure that reports of the meetings (Annual Review Form) are sent to the Program Coordinator (micro.grad@osu.edu (mailto:micro.grad@osu.edu)) for placement in the student's file each year.

5.6.1 First-Year Review

The First Year Review, which should occur at the start of the second year, provides the first official opportunity for the student to meet with the Advisory Committee. The student should bring a summary of his/her coursework and grades, and prepare a short oral presentation of his/her research project. The committee will review the academic record and plan of the student and provide advice on the design and implementation of his/her research.

The advisor will submit an Annual Review Form to the Graduate Studies Committee Chairperson; if the advisor feels there are deficiencies, a letter addressing these deficiencies will be provided to the Graduate Program Chairperson and the student. The Graduate Studies Committee Chairperson reviews these summaries, and if necessary will discuss any problems with the advisor, the student, and the Graduate Studies Committee..

5.6.2 Second-Year Review

 

Near the end of the second year of graduate study, all graduate students are required to schedule a committee meeting. This Second Year Review serves as an evaluation of the student’s progress toward the degree and as a planning meeting for the Candidacy Exam proposal.

The Second Year Review is intended to be an interactive discussion of student’s research progress and his/her plan for the Candidacy Exam proposal. The student should provide a summary of his/her coursework and grades, which will be reviewed by the committee to ensure that the curriculum requirements have been adequately met. Then, the student will present his/her research progress and an outline of proposed Aims for the Candidacy Exam document. The student should plan an approximately 30-minute oral presentation and be prepared for an active discussion.

5.6.3 Reviews After the Second Year

Students are required to have annual committee meetings, to provide updates on research progress and modifications of the research plan, and to obtain input from the Advisory Committee. Students should prepare a short progress report (1-2 pages) which should be given to the Committee members before the meeting. This document should be placed in the student’s file as an appendix to the Annual Review.

An Advisory Committee meeting will be held one semester before the anticipated semester of graduation. During this meeting the student will summarize the research accomplished to date. The committee members will review the material to be included in the Dissertation and will make specific recommendations concerning the completion of the Dissertation.

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5.7 Candidacy Examination

Advancement to candidacy requires successful completion of a written proposal (the Candidacy document) and an oral defense (the Candidacy Examination). The student will have four weeks to prepare the written document (described below). After passing the written portion, the student will defend their document in the Oral Examination, which normally occurs two to three weeks after passing the written portion. The Advisory Committee becomes the Candidacy Examination Committee.

5.7.1 Candidacy Examination Topic

The Candidacy Exam proposal should include three Specific Aims. Two of the Aims will focus on research that is planned for the dissertation. The remaining Aim (the independent Aim) can be on a related topic but cannot address a question currently under investigation in the advisor’s laboratory. The third aim is developed in consultation with the advisory committee during the Second Year review. The student is required to come to the Second Year Review meeting with 2-3 suggestions for the independent Aim. Ideas for this Aim must originate from the student and may be discussed with the advisor prior to the meeting. By the close of the Second Year Review, the Specific Aims of the proposal should be agreed upon (by the committee members and student). The advisor will submit an Annual Review form to the Graduate Program Chairperson that summarizes the meeting and includes a list of the Aims decided upon.

The Candidacy Exam must be taken by the end of Autumn Semester of the third year of enrollment; students who fail to meet this requirement will be denied enrollment (exceptions are by petition to the Graduate Studies Committee, and will be granted only under extreme extenuating conditions such as serious illness).

As OSU faculty serve on many candidacy examination committees within and outside of the Microbiology department, students should provide their committee members information on Microbiology policies regarding Candidacy (i.e., by providing them with a copy of section 5.7 describing the Candidacy Examination).

5.7.2 Candidacy Examination Timeline                        

Task                                                          Allowed time Elapsed time

2nd Year Review & assignment of specific aimsstart

 

week 0

Completion of Written Proposal

4 weeks

week 4

Committee review and approval of Proposal

1 week

week 5

Oral Examination

2-3 week

week 7-8

 

5.7.3 Candidacy Document

After the Second Year Review, the student will have four weeks (28 days) to prepare his/her Candidacy Exam proposal. This proposal follows that of an NIH R01 application. The scope of the proposal should include sufficient work to occupy the full-time efforts of a single researcher for a two-year period. The proposal must have the following sections: Abstract, Specific Aims, Research Strategy, and References. The Research Strategy section has subsections titled Significance, Innovation, and Approach. The document must not exceed one page each for the Abstract and Specific Aims, and 12 pages for the Research Strategy. It is suggested that roughly half of the Research strategy be on the two aims of the student’s dissertation research and half be on the independent Aim. The References section does not count toward any page limits.

The pages are single spaced with font and margin limits as described in the NIH instructions. Students are encouraged to review the candidacy exam guidelines (https://microbiology.osu.edu/gradstudents/examchecklist (https://microbiology.osu.edu/gradstudents/examchecklist)). Students send a copy of the candidacy document and a proposal evaluation form to each member of the Advisory committee.

Within one week of submission of the document, each committee member will complete the proposal evaluation form and submit it to both the advisor and student. The proposal will be graded as High Pass, Pass or Unsatisfactory. A minimum grade of Pass is required from all committee members before the student can schedule the oral portion of the exam. Once the student passes the written portion of the exam, the oral portion of the exam should normally be held within three weeks. Scheduling of this exam, and the completion of the Doctoral Notification of Candidacy Examination form, should begin immediately (see below).

If any committee member finds the proposal to be unsatisfactory, the student will have two weeks to revise and resubmit the document to the committee. The revised document will need simple approval from the committee (via email to the advisor) but will not be re-graded and the student must defend this document in the oral exam. In the circumstance where the Committee decides that the proposal is unacceptable, the student may waive the right to take the oral portion of the examination (per Graduate School rules) by submitting a written statement requesting the waiver to the Committee. The results of the Examination are recorded as “unsatisfactory” with the Graduate School. The Committee will then decide whether the student will be permitted to later take a second Candidacy Exam and must record the decision on the Candidacy Examination Report form.

The student must complete the Notification of Candidacy Examination form with the scheduled date of the oral examination; this must be completed online at Grad Forms. This form must be submitted to the Graduate School at least two weeks in advance of the scheduled oral examination. If this form is not completed, the oral exam will be rescheduled. If this is a second attempt at the Candidacy Exam, the student also provides a copy of the proposal to the Graduate Faculty Representative (who is appointed on second candidacy exam attempts) as soon as the Graduate School informs the advisor.

5.7.4 ORAL EXAMINATION

Two to three weeks after approval of the written document, an oral examination will be conducted in which the student defends the proposal. The Advisory Committee selected for the Second Year Review will evaluate the student in this exam. The advisor serves as the chair of the Examination committee and coordinates questioning during the examination.

At the beginning of the oral exam, the student may give a BRIEF overview of the goals of the proposal, which will be followed by the question and answer period. The student should be prepared to answer questions on the rationale, design, and implementation of the experiments as well as his/her general knowledge of the field. All committee members, including the Advisor, are expected to participate in the questioning of the student. The Advisor is allowed to clarify questions or re-phrase things but is not allowed to help the student with any answers. It is expected that committee will be self-policing so that one committee member does not dominate, or that any committee member’s involvement does not affect the impartiality of the exam. As with the Candidacy document, it is suggested that roughly half of the examination cover the independent aim. The entire exam cannot last more than two hours.

The discussion and decision about the outcome of the candidacy examination is done in the absence of the student (i.e., the student is asked to leave the room while the committee reaches their decision). The committee must unanimously agree that the student's performance was satisfactory for the student to pass. The Advisor participates in the deliberation and the voting. It is recommended that the Advisor allow other committee members to discuss and voice their decisions first before rendering his/her decision. Committee members’ approvals will be entered at Grad Forms (email links are sent to the committee members). The student is brought back into the room and informed of the committee’s decision. Students who pass the written and oral portions of the Candidacy Exam will be advanced to Candidacy.

If the Candidacy Exam is deemed unsatisfactory by the examining committee, the committee may choose one of four options:

  • recommend that the student retake the oral defense portion of the exam, based on the original written proposal
  • recommend that another written proposal and oral examination be given, at a time suggested by the Committee
  • recommend that the student transition to the Master’s program and not be advanced to candidacy
  • recommend that the student withdraw from the graduate program

In accordance with the Graduate School rules, no student is permitted to take the Candidacy Exam more than twice. On the second attempt, the Graduate School will assign a faculty representative to participate in the examination. A student whose performance is Unsatisfactory on two attempts at the Candidacy Exam is not permitted to be a doctoral candidate in the same or in any graduate program at this University.

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Section 6: Completion of the Ph.D degree

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Section 7: Master of Science Program

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Section 8: Satisfactory Progress and Academic Probation

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Section 9: Application to the Graduate Programs