Policies and Guidelines – Ph.D.
THIS INFORMATION IS for Graduate Students who entered the MMG program in 2010 or earlier. Ph.D. CANDIDATES THAT ENTERED THE CMB PROGRAM IN 2011 AND LATER SHOULD SEE THE POLICIES FOR CMB STUDENTS LISTED UNDER “CURRENT STUDENTS“.
MMG admits students into the Ph.D. program and the Ph.D. portion of the M.D.-Ph.D. program. All policies described below apply equally to Ph.D. candidates and M.D.-Ph.D. candidates, except for minor differences in the Core Curriculum (see section II below.)
Prerequisites for admission to the Ph.D. program require that the candidate have a baccalaureate degree prior to the date of first enrollment; one year of Biology; one year of organic Chemistry; one year of inorganic Chemistry; one year of Physics; Mathematics through Calculus; and satisfactory scores on the general aptitude portion of the Graduate Record Examination. Subject GRE tests are recommended but not mandatory. Students who have not taken all of the prerequisite courses as undergraduates but have a good academic record may be admitted to the program and required to make up any deficiencies early in the program.
The Graduate Admissions Committee will review applications and make recommendations to the faculty. Candidates may be invited to the University for an interview. All students who are accepted into the Ph.D. degree program will be awarded a Graduate Fellowship. This is a full-time position that currently (2010-2011) pays $20,300 per calendar year, plus full tuition waiver and health benefits. Once a candidate is accepted into the program, s(he) will be assigned to a temporary advisor until a thesis advisor is chosen.
Graduate College requirements: All Ph.D. candidates must earn at least 30 course credits; research credits (up to 45) generally account for the remainder of the 75 credit total that is required by the Graduate College. M.S. candidates must accumulate at least 24 course credits; research credits (up to 6) generally account for the remainder of the required 30 credit total. Both Ph.D. and M.S. candidates must earn a GPA of 3.00 (B) or higher to remain in good academic standing. Students whose GPA’s fall below 3.00 may, at the discretion of the MMG Graduate Policy Committee, be given a limited length of time to make up this deficiency, but may also be subject to dismissal from the graduate program.
The core curriculum: To demonstrate basic competency in the areas of microbiology, cell biology, genetics, and biochemistry, both Ph.D. and M.S. candidates must earn a grade of B or higher in courses that make up the Department’s core curriculum. The core curriculum includes:
- Six credits of Biochemistry (BIOC 301 and BIOC 302), usually taken during the student’s first year.
- Three credits of Cell Biology (CLBI 301), usually taken during the student’s first year.
- Three credits in Methods in Bioinformatics (MMG 296), offered in alternate Spring semesters.
- One credit in Colloquium in Bioethics (MMG 295), usually taken during the student’s first year.
- At least four credits in Seminar courses. The Department generally offers one two-credit Seminar course each semester.
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Microbiology and Microbial Pathogenesis Track
Required track specific requirements:
- Six credits of Genetics, to include MMG 211 (Prokaryotic Molecular Genetics, usually taken in the student’s first year) and MMG 312 (Eukaryotic Molecular Genetics; offered in alternate years and usually taken during the student’s second or third year).
- Four credits in Cellular Microbiology (MMG 320), offered in alternate Spring semesters.
Other potential courses (electives) to meet the 30 course credit minimum:
- Immunology (MMG 223)
- Virology (MMG 225)
- Cell Biology: Specialized Cells & Cell Processes (CLBI 302)
Protein-Nucleic Acid Transactions and Structural Biology Track
Required track specific requirements:
- BIOC 371 Physical Biochemistry (taught in alternate Fall semesters)
- MMG 352 Protein-Nucleic Acids Interactions (taught in alternate Spring semesters)
Other potential courses (electives) to meet the 30 course credit minimum:
- MMG 312 Eukaryotic Genetics (taught in alternate Spring semesters; usually taken during the second or third year)
- BIOC 351 Proteins I: Structure and Function
- BIOC 353 Proteins II: Enzymology
- BIOC 372 Cancer Biology
- BIOC 307 & 308 Special Topics in Biochemistry
Preparation for core courses: Occasionally, students are admitted to the MMG Graduate Program without the academic background they need to excel in MMG 312 (Eukaryotic genetics). Students in this position must take BCOR 101 (Introductory Genetics) during their first year. Similarly, students who have never had a college-level course in microbiology must take MMG 101 during the Fall semester of their first year. Students who are unsure about whether their preparation for MMG 312 and MMG 320 is adequate, or who may need additional preparation to succeed in BIOC 301 and BIOC 302 should consult with their first year advisor or the Graduate Program Director. Students who have taken either BCOR 101 or MMG 101 can petition the Graduate College to have credits earned in those courses apply toward the graduate course credit requirements.
Core course exemptions and substitutions: Students who enter the MMG graduate program with strong academic preparation in either biochemistry or cell biology may be exempted from taking the corresponding courses in the core curriculum, at the discretion of the Graduate Program Director. Students who fail to earn a grade of B or better in a core curriculum course may make up this deficiency by either re-taking the course or taking another graduate-level course in the same area. Students may obtain a list of approved substitute courses from their Advisors or the Graduate Program Director.
Transfer credits: Students who have earned grades of B or better in relevant graduate-level courses prior to entering the MMG graduate program may consult with the Graduate Program Director to determine if these courses qualify for transfer credit that will help them meet the graduate course credit requirements.
Other coursework: Students who have fulfilled the core curriculum requirements (totaling 24 and 19 credits, respectively, for Ph.D. and M.S. candidates) may satisfy their remaining course credit requirements by taking other 200- or 300- level courses that are appropriate to their particular research interests. Students are encouraged to consult with their advisor or studies committee in choosing appropriate courses.
A. Laboratory Rotations
First-year Ph.D. degree students are required to perform at least two laboratory rotations within the department before a decision on a thesis advisor is made. These rotations will be at least two months in duration with the selection of a thesis advisor usually occurring by the end of the student’s second semester. The scheduling of an adequate amount of research time within a given lab will be necessary for successful completion of a lab rotation.
The rotation advisors will provide written evaluations of the student’s performance, indicating both strengths and weaknesses, to the student, the Department Chair, and the Chairs of the Student Affairs and Graduate Policy Committees.
B. Studies committee
Once a prospective candidate for the Ph.D. degree has been accepted into the program and a thesis advisor has been selected, an interdepartmental Studies Committee will be assigned. This committee will guide the student through the program. The committee will help the student plan appropriate course work and research, and periodically review the student’s progress. The committee will be chaired by the thesis advisor. All Studies Committees must satisfy the following criteria:
- The members of the Studies Committeewill be chosen by the thesis advisor in consultation with the student and DepartmentChair.
- The Studies Committee will consist of at least 4 members, withat least two from the Department and one from outside the department.
- The Studies Committee will meet atleast once each year, usually following presentation of the student’s annual researchseminar (described below). It will be the student’s responsibility to notify themembers of the Studies Committee to attend the seminar.
C. Qualifying exam
Ph.D. candidates shall write an NRSA-format research proposal, and defend the proposal in an oral exam. The subject of the research proposal should substantially differ from the students’ own research area or experimental approach, and must be approved in advance by the Graduate
Education Committee. The Graduate Education Committee will acquaint students with the basic form a grant proposal takes and provide them reasonable guidance in the writing of the proposal. However, the student is expected to assume final responsibility for the proposal, to independently seek expert advice if necessary, and to acquire sufficient mastery of his/her chosen subject area to defend the proposal.
Students will present their written proposal to the Graduate Education Committee. The Committee will determine if the written proposal is satisfactory and, if it is, schedule an oral defense. During the oral defense, the Committee shall be free to explore the knowledge of students on a range of subjects related to the proposal, much as occurs during a thesis defense.
At its discretion, the Graduate Education Committee may ask up to two outside scientific advisors to help review the written proposal or participate in the oral defense. However, the permanent Committee members will be responsible for deciding whether the student’s proposal and oral defense are satisfactory.
GRADING, SECOND CHANCES, AND FAILURES. If the written proposal is deemed unsatisfactory, the candidate will be given one opportunity to rewrite the proposal. If a student fails the oral defense, s/he will be given one opportunity to re-defend the proposal. If the student fails a second time, s/he will be dismissed from the Ph.D. program. However, The Graduate Education Committee (in consultation with the Policy Committee) may decide that the student has passed at a level commensurate with the requirements of the M.S. program (described below) and give the student an opportunity to switch to the M.S. program. Students who enter the M.S. program by this route shall be exempted from the normal M.S. qualifying exam described below.
TIMING. Students must complete both the written and oral parts of the qualifying exam (including second tries if necessary) by the end of their fifth semester in graduate school. Therefore, students are strongly advised to write and defend their proposals during the summer after their second year.
All Ph.D. degree candidates in the Program must teach a minimum of two semesters in partial fulfillment of their degree requirements. At the end of each assignment, the student will be evaluated follows. The Director of Student Laboratories and course instructors will write an evaluation of the student’s performance, indicating both the student’s strengths and weaknesses. Evaluations will be submitted to the Chairperson, to members of the student’s Studies Committee, and to the student. Evaluations will be reviewed by the Department Faculty at the end of each semester. A student who receives a poor evaluation will usually be teamed with a different instructor on his/her next assignment. The faculty will assist students who wish to improve their teaching skills. Students who have serious deficiencies and fail to correct them on subsequent assignments may be dismissed from the position of teaching assistant at the discretion of the faculty
Candidacy for the doctoral degree requires at least one full year of graduate study in residence at the University of Vermont. Decisions regarding advancement to candidacy must be made by the end of the third year of residency. A doctoral student will be accepted to candidacy upon approval of the student’s thesis advisor and Studies Committee, the Faculty of the Department, and the Dean of the Graduate College.
In order to be admitted to candidacy a student must have:
- a minimum overall grade point average of 3.0;
- completed core course requirements;
- performed satisfactorily on teaching assignments; and
- successfully completed the departmental qualifying examination (see above).
Students who are not admitted to candidacy for the doctoral degree will be permitted to complete studies for the master’s degree if requirements for that program are met.
Each candidate, while in residence at the University of Vermont, must complete an acceptable original research project which contributes new knowledge or techniques in his/her academic field. A thesis describing the research project and the results obtained must be submitted in compliance with the detailed instruction sheet which is obtained in the office of the Graduate College.
- A copy of the current instruction sheet,issued once each semester, can usually be obtained from the Graduate College oryour thesis advisor or the Department Chairperson.
- A completed thesismust be submitted at least 7 weeks prior to commencement.
- In order touse the manuscript format in place of the traditional format the following isrequired: inclusion of two or more peer reviewed full length research articleswhich have been accepted for publication or published in (an) appropriate scientificjournal(s); 2) a comprehensive literature review to precede the individual articlesto provide an integrated perspective to the total body of research and literature;3) a comprehensive “Results and Discussion” or “Results and FutureProspects” section which provides an intergration and expansion of thosesections in the individual articles; and 4) a comprehensive bibliography or “ReferenceCited” section.
- The Thesis Defense Examination Committee will beappointed by the Dean of the Graduate College upon recommendation from the candidate’sadvisor. The committee will usually include members of the studies committee asdescribed above. An additional outside member will be designated chairperson bythe Graduate Dean.
- Dissertation Defense (Oral). The date of the thesisdefense must be at least 2 weeks from the date the completed thesis is submitted.One re- examination only is permitted. Candidates for the degree of Doctor ofPhilosophy will not be permitted to schedule their dissertation defense untilthey have submitted a draft of at least one manuscript that describes their dissertationresearch to an appropriate scientific journal for publication.
Each student is encouraged to read the Graduate College Catalogue and is responsible for obtaining a copy of the current “Guidelines for Thesis Writing” from the Office of the Dean of the Graduate College. This document outlines the current deadlines for prospective graduates. (The Department Chairperson usually will have copies of the Guidelines and a current list of deadlines.)
COMMITTEE MEETINGS, RESEARCH SEMINARS. Students will submit written progress reports and a statement of future plans to their advisor and other members of their Studies Committee at least one week prior to each scheduled committee meeting. The reports may be written in an informal style, without details of methods and procedures, but should contain sufficient information to enable committees to evaluate each student’s progress. Beginning in their second year, every student will present at least one research seminar each year.
Candidates for the Ph.D. degree must remain in residence until completing all degree requirements, including successful defense of the dissertation.
The Department of Microbiology and Molecular Genetics (MMG) requires that graduate students demonstrate proficiency in computer skills. Computer skills are divided into three types (I-III below), each of which is subdivided into categories. All departmental graduate students must demonstrate proficiency in Category (A) skills which are considered essential for scientific work in Microbiology and Molecular Genetics. Category (B) skills are in some cases more advanced skills and in other cases skills that would be helpful to know. Departmental graduate students must demonstrate proficiency in all category A skills, and a total of three skills in category B (e.g. IB1, IIB1 and IIIB1).
I. Document preparation
A. Required Skills
- Word processing
- Graphics: Representation of 1D/2D data (e.g. pie charts, histograms, graphs), scientific illustration.
B. Additional/advanced skills
- Slide making
- Web publishing
II. Information access/management
A. Required Skills
- Familiarity with a computerized literature database
- Ability to find information on the web
- Familiarity with a scientific database
B. Additional/advanced skills
- Spreadsheet use
- Maintaining large amounts of scientific data using computer
- Maintaining a bibliographic database using a computer
III. Scientific methods
A. Required Skills
- Sequence analysis
B. Additional/advanced skills
- Use of a programming language to code an algorithm for analyzing or manipulating data
- 3D visualization/modeling
- Image analysis
ASSESSING PROFICIENCY. A student can meet the above requirements either by taking and earning an A in the computer application course CDAE 85 or by passing a test administered either by the students advisor or the director of the Molecular Modeling Facility (MMF). In the latter case, the advisor or MMF director will then submit a letter to the Chair of MMG, to be included in the student’s file, stating that the student has demonstrated proficiency, and stating the areas of proficiency. In either case, the student should enroll in GRAD 485 so that a grade (S or U) can be reported to the Graduate College.
Graduate students in the Department of Microbiology and Molecular Genetics ordinarily have a twelve-month appointment. They are entitled to the stated University of Vermont Administrative holidays plus 10 days of vacation per year, with additional time to be approved by the mentor and/or the student’s Studies Committee. Unused vacation days may not be carried over into subsequent years, nor do graduate students accrue compensatory time off. Students are expected to discuss their vacation plans in advance with their mentor.
In accordance with the guidelines of the Graduate College students may be dismissed from the program if more than two grades below B, or the designation of U in Thesis or Dissertation Research or Seminar are received. Students whose GPA falls below 3.0 in two consecutive semesters may be dismissed from the program.
B. Grievance procedure
If a Graduate Student in the Department of Microbiology and Molecular Genetics has a grievance, s/he should first meet with his/her mentor to discuss the issue(s). (If the student has not yet chosen a mentor, s/he should first meet with the Chair of the Student Affairs Committee.)If the student is not able to resolve the issue(s) at this meeting, s/he may call a meeting of his/her Studies Committee. If the student and the Studies Committee are unable to resolve the issue(s), the student then may schedule a meeting with the Department’s Grievance Committee. The Grievance Committee in the Department of Microbiology and Molecular Genetics shall include members of the Graduate Policy Committee, an elected Graduate Student Representative, and the Chair of the Department. However, any member of the Grievance Committee who serves either as the Graduate Student’s mentor or on his/her Studies Committee, or has any other conflict of interest, shall be excused from participation (except when their testimony is requested). If the student is dissatisfied with the decision of the Grievance Committee, s/he may appeal the decision to the Dean of the Graduate College, whose decision shall be final.
Academic performance and performance on teaching assignments will be reviewed by the faculty of the Department at the end of each semester. Thesis advisors/supervisors and Studies committees will be responsible for evaluation of progress in research, in accordance with Departmental Guidelines. Studies Committees will meet at least once each year to review academic performance and progress in research. Each student will give at least one research seminar a year. Studies Committee members are expected to attend this seminar and to meet with the student, in committee, following the seminar. The major advisor will keep a record of the committee’s deliberations and recommendations and circulate copies to the student, members of the committee, Department Chairperson, and Director of the Graduate Program.
Recommendations for dismissal from the program can originate from either the Studies Committee or the Graduate Student Affairs Committee. If it is decided that the student’s deficiencies are serious enough to warrant consideration of dismissal, the student will be notified, in writing, by the Chairperson of the Graduate Student Affairs Committee. The student will be invited to respond in writing and a meeting will be scheduled with the advisor and Chairperson of the Subcommittee on Student Affairs. If appropriate, a meeting with the faculty will be scheduled. If, following these deliberations, the recommendation for dismissal is upheld, the student will be dismissed from the program and the Graduate College. Alternatively, the faculty may dismiss the charges, or place the student on probation with recommendations for corrective action. The student’s Studies Committee will be responsible for monitoring the results of implementing the recommendations.