Guidelines for Graduate Students in Biochemistry and Molecular Biology

Prerequisites: All entering students are expected to have developed competence in fundamental areas of basic science. For all students, these minimal requirements include a two semester course in organic chemistry theory and mechanisms as a prerequisite for admission. Students are also strongly encouraged to have completed a calculus-based physical chemistry course and a one semester course in cell biology. Students entering the program with a graduate level degree may be allowed to apply credit for courses previously taken to their collateral requirement. Qualified students should submit a request to the Graduate Committee, summarizing the credit desired and accompanied by a copy of their transcript listing the courses previously taken. A final decision concerning credit will be made by the Graduate Committee.

Course Requirements: The graduate program of study requires course work in biochemistry. The following classes are required:

1. Biochemistry I (BICM 705)
2. Biochemistry II (BICM 706)
3. Molecular Biology I (BICM 731)
4. Biochemical Techniques (BICM 707)
5. Introduction to Biochemical Research (BICM 702, 703)
6. Scientific Communication (BICM 700, 701) (3 semesters)
7. Special topics in biochemical literature (BICM 715/716) (4 semesters)
   

Sequence of Courses and Requirements (required courses are underlined)

FirstYear

August
Biochemical Techniques
Introduction to Faculty Research Interests
Choose Laboratory for First Rotation

Fall Semester
Biochemistry I
Molecular Biology I
Scientific Communication
Introduction to Biochemical Research
Choose a different Laboratory for the Second Rotation

Spring Semester
Biochemistry II
Scientific Communication
Introduction to Biochemical Research
Collateral course(s) based on interest
Choose Advisor by March 15

Second Year

Fall Semester
Scientific Communication
Special topics in biochemical literature
Collateral course(s) based on interest
Choose Advisory Committee

Spring Semester
Special topics in biochemical literature
Submit Outline for the Preliminary Exam Proposal

Summer
Preliminary Exam must be completed by August 1

Third Year

Special topics in biochemical literature
Research Seminar, once per year
Committee meetings, once per year
Tutorials, depending on interests and as recommended by Advisory Committee

Subsequent Years

Research Seminar, once per year
Committee meetings, once per year

Collateral Courses: In the second semester of the first year, collateral (elective) courses may be chosen by the student based on research interest and in consultation with the Program advisor. In subsequent years, additional elective courses may be selected by the student with the advice of his/her advisor and committee. These collateral courses are not required, but are encouraged as a means to augment the student’s education in selected areas of focus. Collateral courses may also be used to provide additional background in areas identified by the student’s committee.

Laboratory Rotations: Introduction to Biochemical Research (BICM 702, 703) is taken both semesters of the first year and consists of individualized laboratory projects carried out under the supervision of a full faculty member in the department. The student is assigned to a different laboratory each semester in order to enhance the research experience. The laboratory assignment is based upon the students preference and the availability of a position in the chosen laboratory.

Seminars: All students will attend the Biochemistry departmental and student seminar series. Students are also encouraged to participate in tutorial programs and symposia sponsored by the graduate school and various basic science departments.

Special topics in biochemical literature: All second and third year students will participate in Special Topics in Biochemical Literature, a class devoted to examination of the primary literature. Participation in this class is intended to develop skills required for critical reading and interpretation of the scientific literature.

Academic Standing: The faculty will review each student's progress at the end of every semester to determine whether he/she will be permitted to continue. To remain in the Ph.D. program, a student must maintain a grade-point average of at least 2.5, unless an exemption is granted by the faculty. If a decision is made to terminate a student in the Ph.D. program, the individual may be given the option to complete the M.S. degree program. The requirements for the M.S. degree are defined in the Graduate School Bulletin.

Class mentor: Each class is assigned a mentor, who is a faculty member in the Department of Biochemistry. The role of the class mentor is to maintain contact with the students in that class and their advisors and assure that progress is being made towards timely completion of programmatic requirements. The Program Director will serve as mentor to first year students.

Choice of Faculty Advisor and Advisory Committee: The student will be assigned an advisor before the end of the second semester. This assignment will be based on a ranking of choices submitted by the student to the Graduate Program Director by March 15. In preparation for making these choices, the student should attend the faculty research presentations and consult with faculty individually about specific research problems. In addition, the student may use the course Introduction to Biochemical Research to evaluate prospective laboratories. All full faculty members in the department are eligible to be the thesis advisor if adequate time and resources are available to devote to the student. These criteria will be determined by consultation between the student, the proposed advisor, the Graduate Program Director and the Department Chair.

After choosing a faculty advisor, an advisory committee will be appointed by consultation between the advisor, the student, and the Graduate Program Director. The advisory committee should consist of the advisor, two other members of the department, a member of the graduate faculty from outside the department, and a fifth member, from within or outside the department, representing a related area of research. If desired by the student and the advisor and approved by the Graduate Dean, additional faculty-level scientists may be appointed as committee members. The committee should be appointed by the beginning of the student's third semester and will subsequently meet with the student once a year to assess his/her progress. The chair of the preliminary examination committee should be a departmental faculty member other than the faculty advisor. It is the responsibility of the chair of the preliminary examination committee to determine that the student has met all departmental requirements. This committee generally serves as the final examination committee. The committee member from outside the department serves as chair of the final examination committee and determines that all graduate school requirements are fulfilled.

Preliminary Examination

The Ph.D. preliminary examination must be completed by August 1 of the second year, after the student has passed the required biochemistry courses. The Ph.D. examination consists of (1)passing all the required biochemistry courses with a final grade of B or better, (2) oral defense of a written research proposal.

If a student does not pass a required biochemistry course with a grade of B or better, the faculty may decide to allow him/her to retake the course to make up the deficiency and remain in the Ph.D. program. A failure to pass the retake with a grade of B or better disqualifies a student from continuing in the Ph.D. program. In this situation, the student has the option of requesting a hearing with the Biochemistry faculty. The chairman of the graduate committee meets with the student to discuss the case and presents the case to the faculty at this hearing. After all pertinent information on the student's past performance in didactic and laboratory work is heard, the faculty votes to determine if special action will be taken to allow the student to try again for candidacy. A two-thirds positive vote by the faculty permits this special action to proceed. Remedial studies and subsequent performance requirements for the student are established by the faculty on a case-by-case basis.

Research Proposal: Each student will submit a proposal of the research that will be performed for the Ph.D. thesis. The proposal will be in the form of a NIH research grant as outlined in detail below. Students are encouraged to seek assistance from their advisor, the advisory committee, and other faculty during the preparation of the proposal. The mentor or other faculty should offer suggestions if the proposal is unclear or needs expansion (more background, references, illustrations, etc.). Approaches to achieving the specific aims should be discussed. However, it is inappropriate to tell the student in detail how to correct deficiencies or to detail specific technical approaches.

Examination Committee: The examination committee for the preliminary examination will consist of the members of the student's advisory committee. The function of the committee is to determine acceptability of the student for advancement to degree candidacy by critically evaluating the scientific quality of the project, the clarity of the written proposal, the completeness of the literature survey, and the student's originality and understanding of relevant biochemical concepts.

Dates and Deadlines: The Preliminary Examination must be completed by August 1 of the second year, but may be completed as early as the Spring semester of the second year if the student and his/her committee agree. If the student is unable to complete the Ph.D. examination by August 1, she/he may request a hearing prior to August 1 of the Graduate Program Committee. The student will explain the reason for the inability to meet the deadline. If the Committee decides that the student’s explanation is insufficient to warrant an extension, the student will receive a grade of Unsatisfactory for research in that semester, and will be placed on academic probation. The student will be given a new deadline for completion of the examination. If this second deadline is not met, a recommendation for dismissal will be made. If at the initial hearing the Committee decides that the student has provided sufficient reason for an extension, one extension may be granted. Subsequent procedures will be as described above. If the examination is not completed by August 1 and an extension has not been requested, the student will receive a grade of Unsatisfactory for research in that semester.

The date set for the oral exam (prior to August 1) will determine when all other deadlines fall. Eight weeks before the date of the oral exam (prior to June 1), the student will submit an outline of the proposal. One week later, the examining committee will meet briefly with the student to discuss the acceptability of the outline and to make suggestions. The purpose of this meeting is to guide the student in preparing for the oral examination. It is appropriate to give examples of the issues that will be raised. However, detailed questioning and defense of the proposal should be reserved for the oral examination. If there are no major problems, the student may proceed to complete the written proposal.

Two weeks before the oral exam, the student will submit the completed written proposal. Within 1 week, the examining committee will inform the student if the written proposal is acceptable for oral defense. If not, the committee will provide a detailed written critique and set a date for receipt of a revised proposal, usually within 2‑3 weeks. If a revision is recommended by the examining committee, this will be considered an acceptable reason for extension of the August 1 deadline. The Chair of the examining committee will notify the Graduate Program Committee for the new deadline. If the revised proposal is unacceptable, the examining committee will recommend to the Biochemistry Graduate Committee whether the student should be terminated from the Ph.D. program.

If the proposal is judged acceptable, the oral exam will proceed as scheduled. Following the exam, a decision on acceptability of the student for admission to degree candidacy will be made by the committee. In the event that a student does not pass the oral exam, the examining committee can recommend that the student be refused admission to candidacy for the Ph.D. program or that reexamination be allowed no earlier than six months from the date of the first exam. A student may be reexamined only once. If the committee does not recommend the student for advancement to Ph.D. candidacy, the student may, at the discretion of the faculty, have the option to complete the M.S. degree program. The chair of the committee will inform the Graduate Program Director of the outcome of the preliminary exam. The Graduate Program Director then informs the graduate office.

Format: The outline and the final proposal will be patterned after NIH guidelines. The student should consult with the examining committee on questions of format during the preparation of the proposal. Typing will not be done by departmental secretaries on department time. The proposal should be clearly written in the student's own words and should be carefully proofed for spelling and grammatical errors.

Outline Format

The outline should be no longer than two pages (single-spaced) and should consist of the following sections.

Specific Aims: A concise statement of the specific research objectives, including the hypotheses to be tested.

Justification: Explain the significance of the project and its originality, placed in the context of a brief summary of previous work done in the area.

Research Plan: Summarize experimental design to be used to address the specific aims, including methods to be used.

Final Proposal Format

The final proposal should be patterned after the NIH guidelines, with a limit of 20 single-spaced pages. The student should consult with his/her examining committee on questions of format during the preparation of the proposal. Typing width should be no smaller than 15 characters per inch and type height should be 10-12 points. The final proposal should consist of the following sections:

Abstract: (1/2 page). A short summary of the problem and the goals of the project.

Specific Aims: (1 page). A concise statement of the specific research objectives, including the hypotheses to be tested.

Background and Significance: (3-4 pages). A summary of the literature describing the present status of the field. The background section should place the proposed research in proper context. The significance and value of the proposed research should be included in this section.

Preliminary Studies: (0-6 pages). A description of any significant progress already made by the student toward the goals of the proposal. Graphs and charts should be computer-generated and of sufficient size to be clearly readable. Some of the preliminary data can be presented in a short appendix, if the page limitation is a problem.

Research Plan: (8-15 pages, depending on size of other sections). Experiments and methods to be used to address the specific aims with a description of the results expected. This section should identify any special problems that are anticipated and describe alternatives.

References: Techniques to be used and all work and ideas of others should be properly referenced. References should include titles and follow a format approved by the committee.