Requirements for the Ph.D. Degree

Courses

Formal Coursework

(See Appendix 5, Ph.D. Calendar of Deadlines; Appendix 6, Ph.D. Student Schedule) Normally, all entering students take three core courses in their first year: BIOCHEM 623 - Advanced General Biochemistry, MOLCLBIO 641 - Advanced Cell Biology, and MOLCLBIO 642 - Advanced Molecular Biology. Exemption from core courses can be granted at the time of admission by the Admissions Committee. At other times, exemptions can be granted by the Graduate Operations Committee. In addition to the three core courses, all students must complete a minimum of 9 credits in graduate-level elective courses. To be considered an eligible elective, the course must be taught by MCB Program faculty or the student must receive permission to take the course from his/her thesis adviser and the Graduate Operations Committee. Training at such places as Woods Hole, Cold Spring Harbor, etc., can count towards one course (3 credits). Students must submit a course syllabus and proof of course completion to the MCB Office for your student file. Students who receive a grade of C in any core course or required elective course will ordinarily be required to re-take the course and earn a grade of B or better. Grades of B- or C+ will require remedial work, to be specified in individual cases by the Graduate Operations Committee. Students must maintain an average grade of B or better for core courses and required electives (Laboratory Rotation grades are excluded from this average).

Laboratory Rotation

1. Purpose: Individual laboratory rotations allow the student to become acquainted with areas of current research within the program through work on specific laboratory projects and participation in other activities of the research groups. They also provide an important opportunity for the student to gain a working knowledge of techniques commonly used in contemporary research in molecular and cellular biology. In addition, rotations give faculty an opportunity to evaluate the student's performance in a research setting.
2. Description: Each first-year student participates in three laboratory rotations, the first extending from September through December, the second from December through February, and the third from February through the last day of the spring semester in May. The Director of the program must approve all arrangements made between a faculty member and a student on the basis of the student's research interests and his/her need for experience in techniques in one or more area. To assist students in their laboratory choices, interested faculty will provide a written description of the rotation project(s) available in his/her lab, and will participate in Rotation Receptions in mid-September. In addition, the Graduate Operations Committee will meet with each new student at the beginning of the fall semester of their first year and during intercession. The student is expected to devote a minimum of 10 hours per week to the rotation project during the semester. The student should discuss more specific expectations related to their project with his/her rotation adviser at the start of the rotation.
3. Presentation of Rotation Work: At the end of the first rotation period, students will participate in a poster session at which each will present a summary of his/her rotation project to the MCB community. Following the second and third rotation periods, students will present brief (5 minute) talks to the MCB community, normally during the regular Colloquium and Seminar series. MCB Program Redbook Page 7 of 39
4. Grading: Upon completion of each rotation, the faculty member will write an evaluation of the student's performance and assign a letter grade. A copy of the written evaluation will be given to the student. Rotation grades will be interpreted as follows: A Excellent performance in majority of important areas. Shows potential to become a first-rate, independent, highly motivated and highly productive researcher. Likely to overcome any weaknesses. A-/B+ Good performance in most areas. Shows potential to perform capable, effective, independent research. B Adequate, but not much beyond adequate performance in most areas. Potential to become a solid but perhaps not fully independent researcher. Some weaknesses in ability or motivation. B-/C+ Serious weaknesses in important areas. Adviser has reservations about whether candidate has potential to do Ph.D. level work. C Serious inadequacies in important areas. Adviser believes candidate lacks potential to do Ph.D. level work.
5. Exemptions: Students entering the program with an M.S. degree, or substantial research experience, may be excused from one laboratory rotation at the discretion of the Admissions Committee or the Graduate Operations Committee. Requests for exemption, in the form of a petition by the student to the Graduate Operations Committee, should be documented as fully as possible by the inclusion of an M.S. thesis, reprints of published papers, and the like.
6. Laboratory Affiliation: Students choose a laboratory for their dissertation research upon completion of the third rotation. This selection should be made only after a thorough discussion of goals and expectations with the intended faculty adviser. All choices are subject to approval by the Program Director, who should be informed of each student's intentions in mid-March. Students are expected to provide a more in-depth (15 minute) presentation about their dissertation laboratory project to the MCB community in early September (the beginning of the students' second year).

Work in the dissertation laboratory begins in March. Students who are undecided by this time may carry out a fourth rotation during March and April to assist them in the selection of a suitable laboratory. It is understood that an MCB faculty member is expected to provide support for dissertation students throughout their MCB careers, and faculty and their department heads/chairs are asked to sign a Memorandum of Understanding to this effect. Faculty members who lose funding and wish to request MCB support for a dissertation student must do so no later than one month prior to the start of the semester or summer in which funding is requested. Faculty members who wish to request a Teaching Assistantship for their student should indicate as such when appointment information is solicited.

Journal Clubs

All students are expected to enroll in a Journal Club each semester from their second to fifth year. Journal Clubs covering various topics in the current scientific literature are offered by the various participating departments. Students must register for Journal Clubs in at least two different scientific areas during their residency.

Seminars

All students are expected to attend the weekly MCB Colloquia (MOLCLBIO 691A), which feature MCB faculty, as well as Special Topics Workshops held throughout the year. Students are also expected to attend one seminar per week sponsored by the MCB Program (BIO 891-02 or MOLCLBIO 692) or the participating departments. PhD students should register for Seminar and Colloquium every semester until their fifth year.

Teaching Assistantship Requirement

Every MCB student is expected to have some teaching experience during his/her residency. This is usually, but not always, accomplished through a teaching assistantship in the first year. Evaluations of the student's performance as a Teaching Assistant will be made in writing to the Director by the TA's faculty supervisor and will become part of the student's file.

Implicit Bias workshop

As part of the action items identified to sustain and increase diversity within MCB, the Implicit Bias workshop is included in the orientation for incoming students. In addition, this workshop is open to all current students, and all are encouraged to participate.

Responsible Conduct of Research (RCR)

All MCB PhD students are strongly encouraged to attend RCR training. Students in their first or second year are particularly encouraged to enroll. Every MCB student who matriculated in 2020 or later will be required to take this training while at UMass. Workshops will be offered regularly, so everyone will have a chance to participate.

Evaluation of Student Progress in First Year

If performance was unsatisfactory during the first semester in residence, the student will be notified in February in writing that s/he is on probation, and performance standards will be specified which must be met during the second semester in order for the student to remain in the program. Students who fail to perform satisfactorily during both the first and second semesters may be dismissed from the program, with financial support being terminated in May.

When a student has made satisfactory progress in some areas and shows some promise for graduate work, but has serious deficiencies in other areas, the student may be formally transferred to the M.S. track. This action may result in a terminal M.S. degree, or the student may be invited to re-apply to the Ph.D. Program after completing substantial M.S. work. Students transferred from the Ph.D. track to the M.S. track at the end of the first year have not met the requirements for an M.S. degree (see Appendix 8).

Continuation in the program toward completion of an M.S. will normally require that the student secure the agreement of a faculty adviser willing to provide laboratory space and financial support for work on a laboratory project. Students who are unable to make such an arrangement will be dismissed from the program without completion of the M.S.

Evaluation of Student Progress After the First Year

Brief written evaluations of student progress are prepared each year by the dissertation adviser and submitted to the Graduate Operations Committee for review. These evaluations normally become part of the student's file, and a copy is sent to the student. Any student who wishes to examine his/her file should make an appointment at the MCB Program office to do so. However, the files may not be removed from the office.

Fellowship Application

In the summer of their first year, after dissertation labs are selected, MCB PhD students will prepare a proposal application on their research topic modeled after the NSF GRFP. Students will first meet with the Office of Professional Development for guidance on crafting a proposal. The purpose of the proposal development is to enable students to immerse themselves in relevant literature, to help with future success with ORP and prospectus preparation, and to familiarize students with the application process for funding from external agencies. A review panel will provide feedback about the proposals; eligible students are encouraged to submit the proposals to NSF, and ineligible students are encouraged to apply for alternative external funding. All students will be eligible for an internal award for the strongest proposal application.

Comprehensive Examination

1. The comprehensive examination consists of an oral defense of an original research proposal (ORP). The research proposal must take the form of a formal written document that is approved by the Examining Committee and kept in the student's official MCB file. The oral defense of this proposal must be passed before the end of the spring semester of the second year in residence unless special permission for an extension is granted by the Curriculum Committee.

This examination is intended to test the student's ability to develop a feasible research project, to conceive scientifically valid hypotheses, to work out experimentally sound means for their proof, and to defend these ideas in front of an examining committee. The scientific objective of the proposal may be in the general area of the thesis research, although it may not overlap significantly with the thesis project. The proposal must be based on original ideas and certified as such by the dissertation adviser.

The oral examination is designed to test the competence of the doctoral candidate in skills not evaluated by previous examinations. The skills to be tested include the ability to become expert in a limited area of the current research literature; to conceive an original research project; to apply newly learned tools to the investigation; to envision the possible results of planned experiments; to set criteria by which the data and results will be assessed; to establish reasonable priorities among possible approaches to the problem.

Not all research projects that are reasonable are equally suitable for this examination. For example, it may be interesting to identify all the volatile components of human blood. One could propose to use a combination of gas chromatography and mass spectrometry to do this. However, for an oral exam this topic may not provide evidence of creativity or the other attributes listed above. Borderline proposals may be given the benefit of the doubt, but in such cases the student should expect to be examined in detail on the methods to be used.

In short, the more interesting and original the central concept, the more questioning will focus on that concept. This generally provides the most satisfactory examination and the most valuable experience for the student. However, it is particularly important that the student state a clear-cut hypothesis that can be directly tested.

In starting work on a proposition, a student will usually find it most efficient to read deeply on a few limited topics rather than to read volumes of reviews hoping for an idea to strike. Good ideas usually come more readily when the current work is well understood.

2. Role of Faculty (See Appendix 2, The Role of Faculty in Preparation of the Comprehensive Examination)

The adviser’s input should be limited to providing general guidelines about proposal development. Although other faculty may guide a student by asking questions, it is not appropriate to suggest ideas or provide answers outright. The faculty member, in so far as possible, should help the student find the way to prepare a proposal and not give them such direct advice as to share in the development of the idea. It is also not acceptable for any faculty member to participate in a practice examination. Instead, students should be encouraged to give presentations of their proposition to groups of other graduate students who can then advise on matters of presentation and provide practice in an oral defense. The adviser may be present at the final examination, though (s)he does not vote on the outcome. For a complete description of the role of the student's faculty adviser and any other faculty in preparation of the comprehensive examination, see Appendix 2.

3. Detailed Guidelines (See Appendix 1, Deadlines for Comprehensive Examination)

A preliminary meeting for students and advisors to review ORP guidelines will be held in the fall semester prior to the abstract submission deadline.

Step One: On the first day of class in the fourth semester of residence, the candidate will submit an abstract of the proposed research project and a statement of independence to the MCB Program office. The abstract document should start with a carefully worded title, the student's name, the date due, and the statement: “Abstract of a research proposal submitted to the Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, in partial fulfillment of the requirements for the Oral Comprehensive Examination.”

The abstract should begin with an introductory paragraph, which summarizes succinctly the background and relevance of the proposed research. This should be followed by a direct and lucid statement of the problem, the hypotheses to be tested, the objectives, and the experimental approaches to be employed. Not more than two thirds of the text should be devoted to background and introduction; not less than one third should be devoted to the specific experiments proposed. The abstract should be one or two pages in length and should contain about five literature references most pertinent to the problem.

In addition to the abstract, the student must provide a statement of independence, which will be a separate document that summarizes the research proposal and summarizes the research in the laboratory where the student is performing experiments. If there is overlap between the ORP and the current research being done in the laboratory, including the work of others, the student must describe how the proposal differs. The abstract will then be forwarded to the adviser with a request to describe the overlap between the ORP and any current research in the lab. One of the goals of the ORP exercise is for the student to identify a novel and tractable question in the field, and then to propose experiments to answer the question.

Step Two: Within two weeks following receipt of the Abstract and Statement of Independence (February 15 or September 15) the Chair of the Curriculum Committee will appoint a three-member Examining Committee; one of these three will be Chair. Members of the committee will generally be drawn from the program faculty, although non-MCB examiners may be included. A representative of the Curriculum Committee will also be appointed, if the candidate so desires. The MCB Program office will notify Examining Committee members of their appointment and distribute copies of the abstract. Within ten days of receiving the abstract, the Examining Committee Chair will notify the student, the Chair of the Curriculum Committee and the MCB Program office whether it is approved. If disapproved, the Examining Committee Chair will discuss the remedy with the student, and provide a deadline for the submission of the revised abstract.

Step Three: Prior to April 1, the candidate will arrange with the concerned individuals a satisfactory date for the examination. The date should be scheduled prior to May 15 (or December 15 in the fall semester). The candidate will report this information to the MCB Program office, which will then be distributed by memo to the committee and student's adviser.

Step Four: The candidate will prepare the formal research proposal. The ORP Committee and the Chair of the Curriculum Committee may advise the student during its preparation, but the role of the student's thesis adviser (and other faculty) is limited (see Appendix 2). There is often a dialogue between the student and the committee members, typically mediated by the chair, throughout the proposal development process. The proposal should be a carefully written document with a maximum length of twelve single-spaced typewritten pages, excluding references. The cover page of the Proposal should contain the title, the student's name, the date, and the statement: "A research proposal submitted to the Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, in partial fulfillment of the requirements for the Oral Comprehensive Examination." The bibliography should include titles and inclusive pagination of each cited reference. Please see the template in Appendix 3 for formatting guidelines.

The MCB Program office and each member of the Examining Committee will receive from the candidate a copy of the proposal, not less than 10 calendar days before the date of the examination. Members of the Examining Committee have until 5 days before the scheduled examination to move for rejection of the proposal as submitted. To do so, the committee member contacts the chairperson of the Examining Committee. The chairperson, in consultation with all committee members, will decide what steps are necessary to proceed with the examination.

Step Five: The candidate will defend his/her research proposal before the Examining Committee. In general, the candidate will be expected to open the examination with a talk of approximately 30 minutes—illustrated with presentation slides—outlining the salient points of the proposal. During the defense the student must show that the experimental approach proposed is scientifically valid and the techniques to be employed will yield useful and interpretable information. Furthermore, (s)he must demonstrate a familiarity with the background information in the area of research, and with the scientific basis of the methodology to be employed in the proposed investigation.

The remainder of the examination will be devoted to the discussion of questions posed by individual committee members. At the conclusion of the examination the student will leave the room. The candidate's adviser will then be asked if (s)he wishes to make any comments. The adviser will then leave the room. However, both the adviser and the student should remain available to the committee as they deliberate and vote. While the Curriculum Committee representative will not serve as an examiner, (s)he may ask occasional questions during the examination, and may advise the committee on their options and participate in the discussion after the student has left the room. The CC representative does not, however, vote on the final decision.

Step Six: Judgment of the candidate's performance will result in a grade of "Pass," "Conditional Pass," or "Fail." A conditional pass will carry pertinent stipulations for further work including deadlines for revision and redefending, if applicable. The Chair will communicate all comments and concerns of the Examining Committee to the candidate, and transmit the decision and recommendation of the Examination Committee in writing (see Appendix 4: Comprehensive Examination: Final Report) to the Curriculum Committee. A Final Report form will be filled out by the Chair and submitted to the MCB Program office (Appendix 4).

The student will submit a copy of the final proposal to the MCB Program office.

Dissertation and Final Oral Examination/Dissertation Defense

Dissertation Committee

The Dissertation Committee must be formed before the end of the first month of the fifth semester of study (September 30). Names of 4 members (including the dissertation advisor) must be submitted to the MCB Program office and subsequently approved by the MCB Director and the Graduate School. One member must be from OUTSIDE the candidate’s advisor’s home department. One member may be from outside the University, but in that case a copy of his/her C.V. must be submitted to the Graduate School. The dissertation advisor will serve as the Chair of the committee. All MCB dissertation advisors are required to complete the Graduate School’s National Research Mentoring Network (NRMN) training.

It will be the responsibility of the Dissertation Committee to monitor the student's research and progress toward the Ph.D. degree. Meetings of the Dissertation Committee must be held at least once per year. The Dissertation Committee will meet with the student to approve the Dissertation Prospectus, and for the Data Defense (below). The Committee Chair will complete the MCB Dissertation Committee Chair's Report to communicate the results of each meeting, including specific requests made of the student (see Appendix 13). A copy of this report will be given to the student and other committee members.

Dissertation Prospectus/Outline

Before completion of the third year of study (by August 31 of the summer after the sixth semester) and at least seven months prior to the Final Oral Examination, the student shall submit a Dissertation Prospectus/Outline to the MCB Program office, which will be forwarded to the Graduate School. This is to be approved by his/her Dissertation Committee, as indicated by their signatures on the title page (see Appendix 15). The document should be circulated to the committee prior to the Prospectus meeting. Normally, the Prospectus is no longer than twelve single spaced pages of text, and includes sections for Background, Specific Aims, Preliminary Data, and Conclusion. Examples are available from MCB.

Data Defense

The Ph.D. candidate should receive approval from the dissertation committee to proceed with writing the dissertation. At least two months before the dissertation examination, students are to schedule a data defense with their committee. The successful completion of the data defense gives the student approval to write the dissertation and identifies issues to be addressed prior to the dissertation examination. The Committee Chair will complete the MCB Dissertation Committee Chair's Report to communicate the results of this meeting, including specific requests made of the student (see Appendix 13). A copy of this report will be given to the student and other committee members.

Dissertation and Final Oral Examination/Dissertation Defense

The format of the Ph.D. dissertation document is set by the Graduate School. It is the student's responsibility to learn about and follow the rules governing the dissertation format.

The Final Oral Examination/Dissertation Defense will be administered by the Dissertation Committee after they have read and tentatively approved the dissertation and determined that the candidate has met all other requirements for the doctorate. The Ph.D. dissertation document should be distributed to the committee two weeks prior to the defense date. The time and place of the Defense must be publicly announced by the Graduate School so information about scheduling must be submitted to the MCB Program office at least one month in advance. It is expected the student will arrange for a time when all members of his/her dissertation committee will be present.

At the conclusion of the dissertation defense, the candidate should provide the committee with copies of the face page of the dissertation for their signatures. The candidate should also provide the committee with a filledout copy of Dissertation or Thesis Final Exam Report (Appendix 14). It is the responsibility of the student to ensure that the committee completes the form, including notations about modifications to the dissertation that are required by the committee. All committee members must sign the report, and it is then submitted to the MCB Program Office. The Graduate School must receive formal notification from the MCB Director that the student has successfully passed an oral defense of the dissertation.

It is the student’s responsibility to fill out all necessary forms and meet all requirements set by the Graduate School for graduation. See the Graduate School Handbook and Graduate School Bulletin. For more information, contact the Graduate School at 545-0722.

Publications

The Molecular and Cellular Biology Program at UMass Amherst should be listed as the primary affiliation on MCB students’ publications.

Period of Study

Students in the Ph.D. Program will normally be expected to complete all requirements for their degree within 5 years after admission. Only under exceptional circumstances will financial support be extended beyond 5 years, and this will normally be at the discretion and responsibility of the adviser.

Summary of Required Coursework and Milestone Requirements for the Ph.D. Degree

Courses/Credits

1. Core Courses:
   1. BIOCHEM 623 - Advanced General Biochemistry - 4 credits
   2. MOLCLBIO 641 - Advanced Cell Biology - 4 credits
   3. MOLCLBIO 642 - Advanced Molecular Biology - 4 credits
2. Laboratory Rotations:
   1. MOLCLBIO 696 - Independent Study - 8 credits (3/2/3 credits for three rotations)
3. Advanced Courses:
   1. A minimum of 3 graduate-level elective courses - 9+ credits total
4. Journal Clubs (exempt first year) - 1-2 credits per semester
5. MCB Departmental Seminars - 1 per week minimum
6. MCB Colloquia - 1 per week
7. MOLCLBIO 899 - PhD Dissertation - 18 credits minimum (maximum of 9 dissertation credits per semester)

Fellowship Application

Original Research Proposal/Comprehensive Examination

Prospectus

Data Defense

Dissertation and Final Examination

Total credits, including MCB Seminar and MCB Colloquia - 73 (minimum)

The Graduate School requires no minimum number of credits for a doctoral program, with the exception of dissertation credits. The MCB Program requires a minimum of 18 credits of MOLCLBIO 899 (and the maximum number of dissertation credits allowed per semester is 9). A student can ordinarily register for a maximum of sixteen (16) credits total per semester, but can receive departmental approval to exceed the total credit per semester maximum.