B. MGM Graduate Student Handbook
D. Mentoring
E. Preliminary Examination
F. Thesis Research
G. Varia
A. COURSE REQUIREMENTS
Students need to have 24 credits completed by the end of their second year:
Basic Lecture Courses
One semester of MGM 778 Genetic Solutions to Biological Problems (6 credits), CMB 551 Cell and Molecular Biology core course (6 credits), Core Elective: MGM 552 Virology or MGM 582 Microbial Pathogenesis or MGM 732 Human Genetics (3 credits), BIOTRAIN 720 Scientific Writing/ Writing Grant Proposals (3 credits) and two courses of choice (5 credits total); A total of 12 modules are taken in a combination of UPGEN 778 and CMB 710. At least 6 need to be UPGEN 778 except for 2nd year entering students in which case, 4 must be UPGEN 778; All students supported by the Viral Oncology Training Grant are required to take MGM 552 (Virology and Viral Oncology).
Student Seminar Courses
MGM 790S: Topics in Molecular Genetics and Microbiology, required for first six semesters (1 credit/semester = Total of 6 credits). MGM 701: Foundations of MGM for the first year students (1 credit).
MGM students attend the MGM-sponsored Thursday Seminar Series, the Monday Department Research Seminars and our annual MGM Scientific Retreat. MGM students are highly encouraged to attend the UPGG-sponsored Tuesday Seminar Series when a MGM faculty member is hosting or speaking.
Suggested Electives
PHARM 733 Biostastics (2 credits), IMMUNOL 601 Immunology of Human Diseases (3 credits), IMMUNOL 544 Principles of Immunology (3 credits, if no prior background), MGM 778 Genetic Solutions to Biological Problems (4 credits, additional semester of genetic modular course), MGM 522 Critical Readings in Genetics (3 credits), MGM 703 Infection Biology (3 credits), MGM 720 NGS Computational Tools (3 credits).
Responsible Conduct of Research (RCR)
All Molecular Genetics and Microbiology matriculating PhD students are required to complete 18 contact hours of RCR training in the first four years of their study. The RCR Requirements can be found on The Duke Graduate School website.
MGM Course Requirements PowerPoint
You can view the MGM course requirements PowerPoint here: https://mgm.duke.edu/sites/default/files/2023-03/2022-2023%20Course%20Requirements%20for%20MGM_1.pdf
B.MGM HANDBOOK
You can access the MGM Graduate Student Handbook here:
C. LAB ROTATIONS
Each MGM student is required to conduct three laboratory rotations. Students may begin rotations in the summer, prior to the start of the first semester. If you are interested in a summer rotation, please contact the DGS for assistance in identifying a suitable laboratory.
Duration
Each rotation is 10-12 weeks long. The rotations are time-coordinated, i.e. all rotations begin and end at the same time:
First rotation: early September – mid November
Second rotation: mid-November – early February
Third rotation: early February – mid April
Students should schedule their first rotation prior to the start of classes. The summer rotation can be shorter, but needs to be at least eight weeks in length. All exceptions to these guidelines should be discussed with the DGS or DGSA.
Labs
Students are encouraged to select at least two rotations in labs of PIs with an MGM affiliation. The students must have their rotation plans approved by the MGM Graduate Student Advisory Committee (GSAC) or the DGS. The first rotation should preferably be with a primary MGM faculty member to familiarize each student with the culture of the department. For rotations with faculty not associated with MGM, permission from the DGS is required. Faculty are encouraged to host no more than two rotation students from any program at a time to ensure sufficient guidance by the PI.
Evaluation
First year students must submit a one-page summary of the research performed during the lab rotation or a copy of slides of any oral presentation of their rotation work given at the PI’s research group meeting. In addition, each PI will provide a written evaluation of the student’s performance during the lab rotation. Both evaluations are done within T3. This information will help the MGM DGS monitor the student’s performance.
D. MENTORING
The students will meet with the DGS each semester of their first two years. These meetings are an opportunity for students to obtain information regarding electives, to discuss progress in the classroom, and to discuss rotations and progress in the laboratory.
E. PRELIMINARY EXAMINATION
By the fifth semester, students in the MGM Graduate Program are required to pass a Preliminary Exam that establishes the PhD candidacy of the student. The student must have permission from the DGS and the thesis advisor to take the prelim. Permission is dependent upon adequate performance in both the classroom and the laboratory. Lab performance will be evaluated based on rotation reports and research progress in the laboratory as assessed by the PI. Once the student has permission to schedule their Preliminary Exam, they should set up their profile in T3 and email the DGSA with the names of their committee members along with the date and time of their exam. The DGSA will input the information into T3 prior to the exam.
The Preliminary Exam is conducted in two phases (described in detail below):
•A research proposal (12-pages on a selected topic of your choice, preferably your proposed work thesis)
•An oral presentation and defense of the written proposal. At this stage, the committee also evaluates the student’s general knowledge and understanding of the course work during the first four semesters.
*Please make sure to schedule at least 2.5 hours for the exam. Usually last 2 hours*.
Preliminary Examination Committee
The examination committee consists of four faculty members selected by the student. The thesis advisor is not a member of the examination committee, however, the advisor should be listed on the committee form. The Minor Area Representative (MAR) is a Graduate School requirement for everyone.
Important note: At least three of the faculty members must have primary or secondary appointments in MGM and also be members of the Graduate Faculty.
The composition of the committee requires approval by the DGS and the thesis advisor. One of the examiners will act as chair (appointed by the DGS) of the committee. The committee chair will be responsible for record keeping during and after the exam (see below) and will deliver the final summary of the student’s performance on the exam. The advisor will introduce the student at the beginning of the exam and provide an assessment of the student’s potential as a PhD candidate. The advisor will be present as a silent observer during the examination and should sign the Preliminary Examination Summary within T3.
It is essential that the Committee Approval Form is approved by both the DGS and the Graduate School before the scheduled preliminary exam can take place. Your committee request form, approved by the DGS and thesis adviser can be emailed or given to the Director of Graduate Studies Assistant for online preparation. This form must be approved 30 days prior to the date of the exam.
Written Proposal
The proposal should be written using general NIH guidelines. Although the topic of the proposal may be based on the student’s potential dissertation project, it is expected that the proposed experimental plan constitutes original, independent work. The proposal including Abstract and Specific Aims should be12 single-spaced pages (font: Arial, size 11 pts), including figures and tables. References are not included in the space limit.
Oral Defense
The student will deliver a 30 minute presentation outlining the significance and underlying hypothesis of the proposal. The presentation should clearly cover all specific aims including rationale, preliminary data (if applicable), proposed experiments and interpretation of anticipated results. The student will leave the room for brief discussion among committee members prior to the exam and also after the oral defense. At this time, faculty will discuss and T3 evaluation will be completed. This information is based on the rubric in T3 (in the resources section, which shows what the student is being evaluated on). The average score must be above 3 to yield a pass vote from the faculty member. 4 of 5 faculty members must vote to pass for the student to pass. If the student does not pass, they will have an opportunity to retake the exam after an additional time period has elapsed. The Chair approves the committee results and the T3 result and evaluation is released to the student. Students are encouraged to take the time to look at evaluations, as there can be useful comments.
Important Deadlines
The Preliminary Examination date is scheduled by the student and typically takes place by the Fall semester of the third year. The written portion of the Exam must be completed and turned in at least one week prior to the examination date. Six weeks prior to the prelim, the student should meet with the committee chair to present his/her proposal summary and specific aims. The student is also encouraged to meet with the other committee members. At least five weeks before the beginning of the prelims, the student must have approval from his/her chair that the summary and the specific aims are appropriate. The thesis advisor may provide general guidance and consultation regarding the specific aims before the student begins writing the proposal, however, the advisor should not be involved in any specific aspects of the writing process itself.
Purpose of Preliminary Exam
The purpose of the Preliminary Exam is to:
Test if the student’s basic knowledge in molecular genetics and microbiology is sufficient to successfully complete a PhD in any laboratory of the Department (including primary and secondary faculty of MGM);
Assess whether the student can identify interesting biological problems, conceived of an appropriate experimental design, and write and orally defend a research proposal.
Evaluation of Preliminary Exam
Evaluation of the Preliminary Exam will include these components (click for full list):
Evaluation of the written proposal
The committee will evaluate the student’s knowledge of the relevant literature and the presented methodologies, the feasibility of the experiments, and the overall structure and organization of the proposal.
Presentation and defense of the proposal
During and after the presentation, the committee will inquire about specific aspects of the proposal to assess the student’s understanding of the methodologies and techniques. The committee may also inquire about specific aspects that were not sufficiently described in the proposal. This might include background information, description of methodology used in the specific aims, difficulties that might be encountered with specific techniques and methods, and possible alternatives that might address such difficulties.
Thorough inquiry by the committee to assess knowledge and understanding of general principles in molecular biology, gene regulation, genetics, virology and/or bacterial pathogenesis.
This part of the examination can test any subject matter discussed in the required course work, especially that covered in the written preliminary document.
Preliminary Exam Outcomes
Two outcomes are possible: Pass or Fail. Re-examination will require pre-approval from the DGS and the Dean of Graduate Studies and should occur at least three months, but not more than five months, after the first exam. Re-examination will require pre-approval from the DGS and the Dean of Graduate Studies. The Preliminary Examination Summary in T3 should be filled out by all committee members and signed by all committee members including the student’s advisor.
F. THESIS RESEARCH
- After successful completion of the Preliminary Exam, the student forms a thesis committee consisting of four to five faculty members, subject to approval by the PI and the DGS. The students must identify a Minor Area Representative (MAR) – this is a faculty member with expertise outside of your research area. The thesis committee does not need to be the same as the Preliminary Examination committee, but any changes must still be approved by the DGS and the Graduate School.
- The role of the thesis committee is to provide regular guidance on the student’s research activities and to ensure that appropriate progress is being made. The first meeting should be scheduled no later than six months after the Preliminary exam, and additional meetings are to be scheduled until the committee determines that the student is qualified to write and defend his/her thesis work. These meetings should occur no later than twelve months from the most recent meeting. Once the student has determined the date and time of their meeting, they should set up their profile (if they haven’t already) in T3 and email the DGSA with the names of their committee members along with the date and time of their meeting. The DGSA will input the information into T3 prior to the meeting.
It is the responsibility of the graduate student to schedule and assemble the committee members. Meetings can be more frequent than one per year. At least three days prior to the meeting, send an updated electronic CV and a 1 page research summary to committee and copy the DGSA. Also, upload those documents into T3.
- A Dissertation Advisory Committee (DAC) Report needs to be filled out within T3 by members of the thesis committee after the meeting. The thesis advisor and the student will discuss the recommendations made in this evaluation form. The form should capture progress, recommendation for timing of next meeting and the date of your most recent IDP meeting.
As you progress in your research toward graduation and your committee has checked the box stating that you may begin writing your dissertation keep in mind that the thesis work must be published in a peer-reviewed journal.
- Important Note: The paper should be published or in press before the thesis defense can be scheduled. Permission to schedule a thesis defense requires approval of ALL committee members.
Thesis Defense
- Once the student has permission to defend, they should set up their profile in T3 (if they haven’t already) and email the DGSA with the names of their committee members, the title of their dissertation along with the date and time of their exam. The DGSA will input the information into T3 prior to the defense. As you prepare for your thesis defense, use the MGM Graduate Checklist. The thesis defense consists of a research seminar (40 to 50 minutes), followed by an oral examination (one to two hours) by the thesis committee. The outcome of the defense examination is Pass or Fail. At least three out of four or four out of five members must pass the student (including the thesis advisor) for the PhD degree to be granted. A Thesis Defense Summary within T3 needs to be filled out by all committee members.
G. VARIA
- CMB and students from other programs joining an MGM lab are required to follow MGM guidelines, but modifications are possible. For example, MGM 790S might be waived for the first two semesters, if a similar course is substituted.
- UPGG students who affiliate with MGM laboratories follow UPGG guidelines.
- MSTP students who affiliate with MGM laboratories should discuss course work, rotations and exams with the GSAC/DGS on an individual basis.In addition to MSTP curricular requirements, MSTP students in MGM will be required to take:
- 1. Spring of first GS year: MGM 552 (Virology) or MGM 582 (Microbial Pathogenesis) or MGM 732 (Human Genetics)
- 2. Fall of second GS year: MGM 702 (Scientific Writing/Writing Grant Proposals)
- 3. One 3-credit or greater elective (e.g. CMB 551, MGM 778, IMM 601, etc) approved by DGS
- 4. Five semesters of 1-credit MGM 790S (student seminar) – this meets every other Friday afternoon and features senior student seminars and practice prelims. Students start this in the spring of their first year.