Graduate Program in Biochemistry. Department of Biochemistry and Molecular Genetics. Rules for the Comprehensive Examination

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1 Graduate Program in Biochemistry Department of Biochemistry and Molecular Genetics Rules for the Comprehensive Examination Application for Candidacy Completing the required courses for the program does not automatically admit a student to candidacy for the degree. Each student must complete the Application for Admission to Candidacy form (available in the Ph.D. Comprehensive Examination packet from the Graduate School Office). This application for candidacy must be completed, reviewed by the graduate student academic advisor, Dr. Paul Megee, and approved by the Graduate School two weeks prior to scheduling of the Comprehensive Examination (see below for details). Once the Graduate School approves candidacy, the student will be sent notification by mail and . Please refer to the Graduate School Handbook for specific details for application to candidacy. Comprehensive Examination The primary goal of the comprehensive exam is to determine whether or not a student should be admitted to Ph.D. candidacy, based upon his or her general knowledge in Biochemistry and Molecular Genetics, and the candidate s ability to formulate a hypothesis and design reasonable experiments to test it. Therefore, students are expected to take the exam seriously, and present the written portion of the exam to their committee as a sample of their very best work. The faculty expect and hope that the process of completing the comprehensive exam will also be a learning experience for the student, but its primary goal is to establish whether the student meets or exceeds a minimum standard before being allowed to continue working towards a Ph.D. It therefore can and will be used to eliminate students who cannot demonstrate that they meet this standard. The Ph.D. comprehensive exam is an oral exam. After completion of the coursework in the first year of study and some introductory research in the dissertation laboratory, the student will be required to prepare a research grant proposal using the formal of an NIH grant. Defense of this proposal provides the basis of the oral exam. The comprehensive examination should be taken within 1.5 years of passing the preliminary examination, usually by the end of February of the third year. 1

2 The exam will be conducted by a faculty committee chosen by the student. Students should start organizing their committees early, usually in later half of their second year. It is a good idea to have a meeting of your committee after your Departmental seminar in the second year and a short, organizational meeting before the comprehensive examination in the third year. A. Scheduling The student is responsible for scheduling the exam, including all paperwork for the Graduate School (instructions are in the Graduate School Handbook available from the Graduate School Office). The scheduling of the exam should be completed at least four weeks prior to the exam date. The examination can be in any room on campus, but usually the conference rooms on 9 th or 10 th floors are used [see Diane Ross or Jean Sibley (Molecular Biology Program) about reserving these rooms]. The student should notify the graduate advisor, Dr. Paul Megee, and the Committee chairperson of the final schedule. B. Guidelines for Choosing a Comprehensive Exam Committee 1. The Committee should consist of five members, not including your mentor. At least three members must be from the Biochemistry Program (see Appendix for a list of Biochemistry Program Members). At least one member must be from "outside" the Department, that is, they should not have a graduate appointment in Biochemistry (Dr. Megee can be consulted about possible outside members). 2. All Committee members must have Graduate Faculty status. If a faculty member does not have Graduate Faculty status, please ask them to contact the Department Office to begin the paperwork. It takes several months for the Graduate School to approve a faculty member for Graduate Faculty status. Should a member not be approved at the time of your defense, your defense could be voided. 3. The Examination Committee chair must be a member of the Biochemistry Program or an adjunct member. 4. The student's thesis advisor may not be a member of the examination committee. However, he/she should be present during the exam. Please note that after the successful completion of the comprehensive exam, your thesis advisor will become a full member of your thesis committee. Consequently, you may retire one member of the comps committee to maintain the number of committee members at five. The makeup of the committee should be as follows: at least three members from the 2

3 Biochemistry Program, one member from outside the program, and another faculty member of your choosing. 5. Committee Responsibility: The committee will administer the comprehensive examination, guide the student throughout their thesis project, and conduct the thesis defense examination. The committee will have its first meeting with the student immediately following the seminar presentation, or as soon as possible thereafter, during the student s second year in the program. The first charge of the committee is to guide and evaluate the student s research progress to this point, and set the guidelines and a tentative date for the comprehensive examination. Students must meet with their committee at least annually; more frequent is advisable as they move further into their research. It is the responsibility of the student to arrange annual committee meetings, to inform the members and the Biochemistry program administrative assistant or the graduate student advisor in writing of the date and place of the meetings, at least 2 weeks in advance, and to submit a short written summary of progress to the committee before the meeting. 6. Committee Chair Responsibility: It is the responsibility of the committee chair to write a brief summary of each committee meeting and submit this to the Program student advisor. This should include: 1) the student s progress since the last committee meeting; 2) planned studies for the immediate future; 3) indication of how student s progress relates to the specific aims of the thesis proposal presented in the comprehensive exam; 4) manuscripts published, in press or in preparation; and 5) number of years in the Program as well as anticipated date of completion. Written summaries should be signed by the student and the committee chair, and turned in to the Biochemistry office within 1 week following the committee meeting. C. Writing the Comprehensive Exam Proposal Topic choice: The examination will consist of two written proposals. The first proposal (major) is a detailed proposal in NIH-grant format (see below). The topic of this proposal is similar to your dissertation research. The second proposal (minor) is in a similar, but simpler format and must be on topic remote from the first proposal. Remoteness means the topic must be very different from your field of study. For example, if you are studying yeast Cdc7 kinase, you cannot propose to study DNA replication or cell cycle control, but T- cell receptor structure is fine. You may want to use a project you became familiar with during your rotation. The minor proposal is important because it allows the committee to judge your thinking independent of your dissertation advisor. Before you begin writing, 3

4 prepare an abstract and a draft of the specific aims section of your proposals (including hypotheses) and submit to the committee chair for approval. Document Guidelines: 1. The proposal should not exceed 25 pages, not counting the literature cited, using margins of at least 1 inch, 12 point type, and single spacing. It should be organized into the following sections: Specific Aims, Background and Significance, Preliminary Studies, Research Design and Methods. While page restrictions are not imposed, the Research Design and Methods section should constitute about 2/3 of your proposal. Do not feel compelled to use all 25 pages. Shorter, better focused proposals often fare better than proposals using the entire 25 pages. 2. The Specific Aims section will be expected to include testable hypotheses, based on experimental evidence already existing in the field. The specific aims are the ways you will address general hypotheses, and should briefly explain your experimental approaches. An Aim is not a single experiment, but a series of experiments designed to accomplish one goal. You will probably have 2-3 specific aims. 3. The Background section should contain enough information to make the proposal readable and understandable by other scientists. "Significance" means you should answer the question of why this research is important. 4. Preliminary Studies should include any work you have done on the project in the dissertation laboratory. 5. Research Design and Methods. We recommend that you write out the experiments you propose for each specific aim one-by-one, and for each aim, and include a section that covers the following: Rationale. Why is this a logical experiment to do? Sometimes this will just be a reminder of background information, but it could also be a discussion and your interpretations of conflicting data in the literature, or could include very specific data not given in the background section. Experimental Design. Describe in detail the experiments planned. You may include methods here or list them after. Describing methods with which most investigators in the field would be expected to be familiar with is not necessary or desirable, but the specifics should be addressed. For instance, if you're doing a Southern blot, what is your probe? What restriction enzymes will you use? How will you interpret your results? Or, if you're doing flow cytometry, what antibodies will you use? How will they be labeled, etc.? 4

5 Limitations. What things might be expected to go wrong? Have you made any assumptions that could turn out to be pitfalls? What will you do if this happens? Can any of this be avoided? Note - in the past, some students have designed specific aims that were mutually dependents, for example, Aim 2 could not be undertaken if Aim 1 did not turn out as expected. This should not be! Mutually dependent experiments within an aim are okay, but you must point out that this is the case, and discuss alternatives if the outcome is not what you expect it to be. 6. The minor proposal will also include Specific Aims, Background and Significance, Preliminary Studies, Research Design and Methods sections, but the Research Design and Methods section should be very brief without much detail and the Preliminary Studies section is optional. Usually, the minor proposal is about seven to ten pages long. Proposals must be provided to the committee at least 2 weeks before the date of the oral exam. Because no exceptions are permitted, any problems will require you to re-schedule the exam. Prepare for your oral exam! You will be expected to make a short (15-20 minute) presentation of your proposal before defending it, so you might want to bring overheads and make sure an overhead projector is available in the examining room before your exam starts. Remember that your proposal is only the basis for your oral exam! You may be asked questions about other areas of biochemistry, molecular genetics or even general biology by members of your committee. Evaluation of the Exam: The student will be informed by the committee chair of the performance. The exams are assessed as: Pass, without conditions; Pass, with conditions; or Fail. The program may allow a retake of the examination in cases where the student fails. In cases where the performance of the student is generally considered satisfactory but certain deficiencies exist, the committee may grant a conditional pass. Additional effort is required to make up a deficiency, and must be completed in as short a time as possible after the exam is held. In the case of a failing grade, the student must leave the program as required by University of Colorado Graduate rules. 5

6 APPENDIX Biochemistry Program List of "In" Graduate Faculty (See the Department al webpage for faculty listings at Richard Spritz, M.D. (HMGP) Lori Sussel, Ph.D. Jessica Tyler, Ph.D. Dennis Voelker, Ph.D. (NJH) Rui Zhao, Ph.D. Primary departmental affiliations other than Biochemistry or locations offcampus of members are indicated in parenthesis. Students can select any of these faculty for their candidacy examination either as chair or as internal members. Biochemistry Program Members: Natalie Ahn, Ph.D. (Biochem. Boulder) David Bentley, Ph.D Andy Bradford, Ph.D. (Ob/Gyn) Thomas Campbell, Ph.D. (PEDS) Thomas Cech, Ph.D. (Biochem. Boulder) Mair Churchill (Pharmacology) Richard Davis (Pediatics) James DeGregori, Ph.D. Sonia Flores, Ph.D. (Webb-Waring Inst.) Heide Ford, Ph.D. (Ob/Gyn) Jacob Friedman, Ph.D. (PEDS) Arthur Gutierrez-Hartmann, M.D. (MED) James Hagman, Ph.D. (NJH) Robert Hodges, Ph.D. Mingxia Huang, Ph.D. Jeffrey Kieft, Ph.D. Les Krushel, Ph.D. Changwei Liu, Ph.D. Philippa Marrack, Ph.D. (NJH) Paul Megee, Ph.D. David Patterson, Ph.D. (ERICR) David Pollock, Ph.D. David Quissell, Ph.D. (DENT) David Riches, Ph.D. (NJH) Robert Sclafani, Ph.D. Nicholas Seeds, Ph.D. Thomas Slaga, Ph.D. (AMC Cancer) 6