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Biochemistry and Molecular Biology PDF of the "Handbook of the Graduate Program" - For Students Admitted Fall 2008 and later
TABLE OF CONTENTS I. ENTRY TO THE GRADUATE PROGRAM
B. Academic and Professional Standards
C. Ph.D. Candidacy and Dissertation
III. THE MASTERS DEGREE PROGRAM B. Masters to Ph.D. Candidacy Change IV. SAMPLE COURSE SCHEDULE V. SIGNATURE SHEET GOALS AND OBJECTIVES OF THE PROGRAM This Handbook developed by the Faculty of the Graduate Program in Biochemistry and Molecular Biology outlines the requirements for graduate training leading to a degree in Biochemistry and Molecular Biology. This program adheres to the standards set forth by the American Society of Biochemistry and Molecular Biology (ASBMB) and the International Union of Biochemistry and Molecular Biology (IUBMB). IUBMB Standards for the Ph.D. Degree in the Molecular Biosciences*
*This list is adapted from the publication "Ph.D. Degree in the Molecular Biosciences".http://www.asbmb.org/CareersAndEducation.aspx?id=256&linkidentifier=id&itemid=256 In addition to the information contained in this handbook, the student is urged to also consult the current Graduate School Catalog for additional information regarding the requirements of the Graduate Council at West Virginia University. I. ENTRY TO THE GRADUATE PROGRAM Graduate students join the graduate program in Biochemistry and Molecular Biology by electing to do their dissertation research with a faculty member affiliated with this program. The graduate program in Biochemistry and Molecular Biology is able to accommodate students with diverse backgrounds and wide ranges of interests. Any student admitted to the undifferentiated first year curriculum is eligible to join the graduate program. Students with MS degrees desiring direct entry into the program must still apply through the school-wide admissions committee and may need to complete portions of the first year curriculum. Students are encouraged to have a strong academic preparation in qualitative/quantitative chemical analysis, organic chemistry, calculus, physics, and physical chemistry. For students with demonstrated abilities, course deficiencies can be corrected after enrollment with the guidance of their graduate advisory committee. A sample curriculum is provided at the end of this document. The Ph.D. program averages 5 years in length. The first year of study, the student takes the undifferentiated core curriculum. Students who did not take the module offered by this graduate program as part of the first year curriculum will be required to take it in the second year. In the second year, the students will take a 2 credit course in protein chemistry and enzymology, this course will be offered for the first time in the fall of 2006. The remainder of the student's plan of study is designed under the guidance of the student’s advisor and will ultimately need to be approved by the student’s advisory committee. The student is required to take two advanced courses, one of which must be one of the program’s advanced courses:
and the other course is an elective . The elective should be a graduate level course to complement the student's background as well as research interests. The student must consult with their advisor when choosing an elective. Suggested electives include:
Additional coursework is optional but many students will find that they desire the additional enrichment. A.2. Seminars and Research Forum The student will present three seminars during their graduate study. One seminar will be the dissertation proposal which is the background and proposed research for the student's dissertation project. This seminar should be given by the end of the first semester of the third year in graduate school. A second seminar will be on a subject unrelated to the student’s research. The topic is selected by the student, with the approval of his/her advisor and the seminar coordinator. Students may choose to present from the topic of their written exam. This seminar should be given during the spring semester of the third year. A list of guidelines in preparing this seminar should be obtained from the seminar coordinator once the topic is selected. The final seminar will be the student’s dissertation defense. Students should avail themselves of all opportunities to present their research in an oral presentation. The Departmental Research Forum is a less formal mechanism for presenting one's research and students will be asked to participate in this. It is designed to keep members of the department abreast of new developments, provide a forum to address complex experimental problems, and to permit students an opportunity to develop their skills at presenting and defending their research results. A schedule for this is developed in August of each year and the advisor selects the dates for presentations by the lab personnel. Students may also present as part of retreats, research forums in Centers, the Van Lierre student research convocation, and at national meetings. Any opportunity to practice these skills is strongly encouraged. The Department also hosts a weekly seminar series to include faculty, students and invited speakers from outside the University. Time is allotted for the students to meet with invited seminar speakers generally at a lunch following the seminar. Each semester, the graduate students as a group are encouraged to invite a speaker of their choosing. The Graduate Student Representatives will coordinate this effort with the seminar coordinator. The students should attend all student seminars, research forums and the Departmental seminar series. Experiments and other obligations should be planned to allow attendance of these very important educational opportunities. Repeated absences from these events may result in the required enrollment in a credit of graduate seminar that will be graded based on attendance. All students are required to enroll in Biochemistry and Molecular Biology Journal Club each semester they are in residence. This course involves the presentation and discussion of current research papers. It is also the time for students to become acquainted with the variety of methods used in scientific research. The journal club is facilitated by the faculty. Students may participate in other journal clubs at the discretion of their advisor. Teaching experience is a valuable part of Ph.D. training. Every effort will be made to provide the student with training in this area. Students with a particular interest in teaching should make this known to both their advisor and the Graduate Program coordinator so that amble experience can be planned. Possible experiences include a teaching practicum taught in combination with other graduate programs and presenting a lecture in a course. The student should discuss their goals in this area with their advisor. The dissertation advisor is the student’s sole advisor for his/her time in the graduate program. Most of the student's time will be taken up with this research. Students register for research credits each semester as BIOC 797, and their performance is graded satisfactory or unsatisfactory by their dissertation advisor. A critical aspect of this is for the student to learn to continue to make progress on their research while engaging in course work, journal club, teaching, and seminar attendance. This time should be used wisely as the student may not defend their dissertation until they have first authorship on at least one paper submitted to a peer-reviewed journal. A.6. Vacations, Sick Leave, and Work Schedules Once in the second year of graduate study, the student no longer adheres to the vacation schedule of the undergraduate University calendar. If the student is sick for a journal club or seminar, they should inform the faculty member in charge of that activity of their absence. Please note any policies regarding absenteeism in the syllabi of courses. This can be by phone or email and should be done prior to the time of the class or meeting. Do not assume that informing your advisor or a single course director of your absence will result in that absence being communicated to all other faculty. Each faculty member with whom you have a class or other obligation must be informed individually each time an absence is going to happen. The student should discuss vacation and sick policies with their advisor. The student is cautioned that the degree is granted based on completion of the dissertation research and not based on length of time in the program. The general University guideline for sick leave is 1 day per month. Vacation time varies with appointment; 1 day per month for research staff and 2 for faculty. Most faculty advisors find that they do not use all of the allotted 2 vacations days per month or their sick leave. Graduate students should have a similar expectation. The University does not have policy for maternity/paternity leave for graduate students. Students who need this leave should discuss expectations with their advisor. A general guideline would be 6 weeks maternity leave and 2 weeks paternity leave and University policy is that this time is deducted from sick and vacation leave. Many women and men find that they can return to some activity prior to this time. Remember, time spent away from the laboratory either due to illness or vacation will hamper the student’s progress on their research. The student should discuss the expectations for total hours of work as well as the days of service (weekends/holidays) with their dissertation advisor. These expectations are likely to vary between laboratories so it is important to establish what these are upon entry into a laboratory. The student should be aware that these decisions are made in the best interest and safety of the student and for the efficient conduct of the experiments. B. Academic and Professional Standards It is expected that students will perform satisfactorily on all required courses. To remain in good standing in the Ph.D. program a student is required to maintain the following standards:
Failure to comply with these standards will result in the student being placed on academic probation and may result in dismissal from the graduate program. B.2. Evaluation of the Student's Progress The progress of each student will be reviewed by the faculty once each year; generally at the end of the second semester. Each major advisor will be responsible for presenting the progress of their respective student(s). The Graduate Studies committee will monitor that program requirements are being met in a timely fashion. When a student is overdue for the completion of a requirement, the committee will first contact the advisor. Failure to complete the requirement within a reasonable time thereafter may result in action by the committee, to set timelines for its completion. B.3. Student Code of Academic and Professional Integrity Developing and practicing high standards for professional conduct are critical for the scientist. Both the University Graduate Council and the Graduate Faculty consider maintaining scientific integrity to be of utmost importance. All students are required to take a course in Scientific Ethics as part of the integrated first year curriculum. These standards are to adhere to throughout the student's graduate education and into his or her career. All students are directed to be familiar with the University's policy on this subject. This can be found at: http://www.arc.wvu.edu/admissions/integrity.html Students should pay particular attention to the avoidance of plagiarism in all scientific writing. The University's definition and position on plagiarism is: "Plagiarism is defined in terms of proscribed acts. Students are expected to understand that such practices constitute academic dishonesty regardless of motive. Those who deny deceitful intent, claim not to have known that the act constituted plagiarism, or maintain that what they did was inadvertent are nevertheless subject to penalties when plagiarism has been confirmed. Plagiarism includes, but is not limited to: submitting, without appropriate acknowledgement, a report, notebook, speech, outline, theme, thesis, dissertation, or other written, visual, or oral material that has been copied in whole or in part from the work of others, whether such source is published or not, including (but not limited to) another individual's academic composition, compilation, or other product, or commercially prepared paper." (from: http://www.arc.wvu.edu/admissions/integrity.html ) Students who have any questions regarding what constitutes plagiarism should request clarification from the faculty before embarking on any writing assignment. Failure to adhere to these standards of scientific integrity will result in disciplinary action by the graduate faculty and may jeopardize the student's status in the graduate program. C. Ph.D. Candidacy and Dissertation Admission to candidacy occurs following successful completion of the qualifying exams. Consistent with University requirements, the qualifying exam has both written and oral components. C.1. Written Qualifying Examination Students who have received all A’s in their graduate coursework will be exempt from the written exam. The qualifying examination is given in May of the second year of graduate study. The student shall select, in consultation with their dissertation advisor, any topic in the broad area of Biochemistry and Molecular Biology, which will be the subject for the exam. The student shall prepare an abstract outlining the current understanding of that topic, limited to two pages and a maximum of 10 literature citations. This will be submitted to the student’s examination committee by the end of the first week in May. The exam committee will be the student’s advisory committee with a member of the graduate faculty substituting for the student’s advisor. All exam committees will have this same faculty member to provide consistency between exams and they will function as the chair of the committee. The committee will meet within one week of receiving the topic and prepare questions relating to the topic and which address general areas of biochemistry and molecular biology such as protein structure and function, enzymology, intermediary metabolism, molecular biology and genetics, cell structure and function, and signal transduction. The student shall have 2 weeks to write essay answers to the questions. These may be completed in an open book format but in the student’s own words and without consultation with other students. The student small meet with the advisory committee one week after submission of their answers to discuss the answers and approve or disapprove continuation to the oral exam. Failure to pass the exam may result in either placement of the student in the Master’s track or dismissal from the program. C.2. Oral Qualifying Examination The oral qualifying examination involves the preparation and defense of a written proposal of the student's dissertation research project. The purpose of this portion of the exam is to demonstrate that the student is prepared to undertake doctoral research. The presentation should include background information, rationale for the proposed experiments and available preliminary data. Most students revise their proposals at some point in their graduate work. Thus, this exam should not be delayed so as to include yet one more experiment. The dissertation proposal shall be submitted to the student’s advisory committee and the Graduat e Program coordinator by the first day of classes of the fall semester of the third year. Every effort should be made to defend the proposal by September 30 of that semester. Failure to pass this exam by the end of March of the third year unless prior approval is provided by the graduate program steering committee will result in dismissal from the doctoral program. To accomplish these goals, the student will prepare a written dissertation research proposal to be submitted to their advisory committee (see section C.3 below). The written report is to be prepared in NIH format, as per the directions for the application for a Public Health Service Grant (PHS 398), to include:
The page limitation of 25 pages will be strictly enforced. The student should determine the aims of the project in conjunction with their advisor, and should consult with their advisor on writing style and grantsmanship issues. The proposal must not be a copy and paste effort from the advisor’s grants. The written proposal should be given to the advisory committee at least two weeks before the meeting to allow them sufficient time to evaluate the project. The dissertation proposal will be presented as a public seminar to the Biochemistry graduate faculty. Following the seminar, the student will meet with the advisory committee to evaluate the proposal in depth. During this meeting, the advisory committee will be charged with examining the student in broad areas of Biochemistry and Molecular Biology including an understanding of the techniques used in the proposal and the student’s ability to use deductive reasoning. During the proposal defense, all subsequent advisory committee meetings, and the dissertation defense, the student’s advisor must not speak for the student or answer questions directed at the student. The proposal defense must be completed following the time line delineated above. In extenuating circumstances, such as a change of advisor, the student may petition the Biochemistry steering committee to delay their proposal defense for a period not to exceed six months. C.3. Student Advisory Committee A student advisory committee will be chosen during the second year of study to evaluate the student's progress in research, to provide a sounding board for problems encountered or progress made, and to examine the student during the proposal and dissertation defense seminars (see below). The members of this committee will be selected by the major professor and student. The committee will consist of five members: three must be on the faculty of the Graduate program, including the major professor who will act as chair, one must be a faculty member from another program (including adjunct faculty) within the University, and the fifth member can be either from within the program or from another program. In each case, the selection will be based on the nature of the research to be carried out and on the student's interests. In general, the first meeting of this committee will be at the proposal defense. Based upon the advisory committee's recommendation, with satisfactory performance during the proposal defense, the Graduate Program Coordinator will recommend to the Graduate Council that the student be elevated to candidacy for the Ph.D. degree. The committee chair (student’s advisor) will submit to the Graduate Council a completed Qualifying exam form indicating the success completion of both the written and oral exams. C.5. Schedule for Advisory Committee Meetings Following admission to candidacy, the student should have meeting with the advisory committee at least once each year to evaluate progress on the goals of the proposed research. During the yearly meeting, the advisory committee will be charged with examining the student in broad areas of Biochemistry and Molecular Biology including an understanding of the techniques used in the proposal and the student’s ability to use deductive reasoning. It should be emphasized that the biomedical sciences are ever-changing disciplines in which new research information appears at a rapid pace. Consequently, the Ph.D. candidate must keep abreast of these developments, as well as obtain a solid grasp of fundamental biochemical and pharmacological concepts. A written record of this meeting using the “Advisory Committee Evaluation Form” provided on the website must be placed in the student's file. C.6. Dissertation Preparation, Seminar, and Defense When research has progressed to a point considered satisfactory by the major professor and the advisory committee, the student will write their doctoral dissertation describing the work according to Graduate Council guidelines. A copy of these guidelines can be obtained from the Health Sciences Graduate Programs office. A dissertation draft will be read and approved by the major professor and the advisory committee members before the final oral defense. This draft must be given to the committee members one month prior to the defense. Exceptions to this time schedule are strongly discouraged and will require the approval of every member of the advisory committee. The student will not be allowed to defend their dissertation without a minimum of one paper submitted to a peer-reviewed journal, on which the student is first author. Submission of the paper must be approved by the student’s advisor. In some cases, students share first authorship with another member of the laboratory. The use of such papers to fulfill this requirement will be at the discretion of the student's advisory committee. Students are strongly discouraged from leaving the University with only one paper submitted. If this paper requires substantial revision with additional experiments before acceptance by the journal, the student risks the loss of first authorship on the paper. Following this minimal requirement should only be used by students whose projects can not generate data during the course of the degree and should not reflect lack of initiative on the part of the student or laboratory to submit manuscripts more often. The final examination for the Ph.D. degree will consist of presenting a dissertation seminar before the advisory committee, Program and any other interested parties, after which the student will continue with their dissertation defense before their advisory committee. Satisfactory performance in the oral defense as judged by the advisory committee will result in a recommendation for granting of the Ph.D. degree. Following a satisfactory defense of the dissertation, the student must prepare the dissertation for electronic submission to the University. Approval of the written dissertation and the electronic submission, which includes signatures from all committee members, must be completed before the Ph.D. can be conferred. Students should not make firm commitments for start dates in postdoctoral positions or other employment prior to completion of these requirements. C.7. Deadline for completion of the degree The University has 2 deadlines by which the degree must be completed or the student will need to retake introductory coursework. Once a student has been admitted to candidacy, you have 5 years to complete the degree. Overall, the student must complete the degree by the end of the eighth year in graduate school. The expectation is that the student will finish well before this time. To ensure timely progress, the Office of Research and Graduate Studies will send letters to students at the beginning of their sixth year to inquire as to their progress towards completion.
III. THE MASTERS DEGREE PROGRAM
B. Masters to PH.D. Candidacy Change At the approval of the Faculty, the Master's candidate may retake the qualifying examination as a prerequisite for readmission to the Ph.D. program. Such programapproval shall be based on satisfactory and timely progress toward completion of the M.S. degree. Following satisfactory performance on re-examination and defense of the M.S. thesis, the faculty will review the student's status and approve or disapprove admission to the Ph.D. program. Students must be in good academic standing (GPA of 3.0 or better for non-research courses) to re-enter the Ph.D. program. |
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