Bmb Qualifying Exam

Bmb Qualifying Exam

BMB Qualifying Exam Guidelines (04/21/2015)

QUALIFYING EXAMINATION

VERNA AND MARRS MCLEAN

DEPARTMENT OF BIOCHEMISTRY

AND MOLECULAR BIOLOGY

BAYLOR COLLEGE OF MEDICINE

Revised 04/21/2015

TABLE OF CONTENTS

Topic Page

Overview3

Abstract4

Written Proposal5

Resources and Assistance6

Plagiarism7

Oral Examination7

Rules for Conduct of the Oral Examination8

Evaluation of the Oral Examination9

Possible Outcomes10

Appendix 1: How to Write a Specific Aim12

Appendix 2: Elements of Hypothesis-Based Research13

Appendix 3: General Description of an NIH Grant Proposal15

OVERVIEW

GOAL

  • Assess student’s qualifications for pursuing PhD research

GENERAL FORMAT

  • Examine students over proposed thesis project
  • Students prepare a Written Proposal over their thesis topic
  • Faculty evaluate students in an Oral Examination

BENEFIT

  • Forces students to think deeply about their research at the beginning

TIMELINE

  • Select thesis committee by July 1
  • Meet with thesis committee before September 1 to discuss abstract
  • Turn in Written Proposal by March 1 (or April 1, if making up third term classes)
  • Defend proposal in an Oral Examination before April 1 (or before May 1, if making up third term classes)

ABSTRACT (4-page limit, excluding figures and references)

  • Hypothesis and 2-3 Specific Aims (1 page)
  • Background and Significance (3 pages)
  • References

WRITTEN PROPOSAL (15-page limit, excluding figures and references)

  • Hypothesis and Specific Aims, including one ‘novel’ Aim (1 page)
  • Background (2-3 pages)
  • Significance (0.5-1 page)
  • Innovation (0.5-1 page)
  • Preliminary Results (1-3 pages)
  • Research Design and Methods (7-10 pages)
  • References

ORAL EXAMINATION

  • Student will defend the written proposal in an oral examination
  • BMB Program Director will chair the oral examination committee
  • Members of the exam committee will include the full thesis committee
  • One additional BMB faculty will serve as a member
  • The advisor will be present as a silent observer

EVALUATION

  • Preliminary Results (25%)
  • Written Proposal (25%)
  • Oral Presentation (25%)
  • Fielding Questions (25%)

OUTCOMES

  • Pass (above 80%)
  • Incomplete (60-80%)
  • Fail (below 60%)

ABSTRACT

The purpose of the Abstract is to summarize the student’s proposed thesis research for discussion with the thesis committee.

The Abstract must be submitted to the thesis committee—and to the Director of Graduate Studies—one week before the scheduled thesis committee meeting. The thesis committee meeting must be completed before September 1.

The Abstract is a written document that must not exceed 4 pages, excluding references and figures. Use 12-point Arial font, 1½-line spacing, 1-inch top and bottom margins, and 1.25-inch left and right margins.

Page 1 should present an overview of the proposed research. It should provide a brief context for the research, including its significance, and state the main Hypothesis being tested. It should include 2 or 3 Specific Aims whose goals are to test the main hypothesis or related sub-hypotheses. This section should include a brief description of the research design and procedures to be used to accomplish each Specific Aim.

Pages 2-4 should describe the Background and Significance of the proposed research. The Background should summarize the literature that is relevant to the proposed research, and provide a critical evaluation of the current state of knowledge. The Significance should state clearly why the proposed research is important. In this section, describe the critical gaps in our current knowledge that will be addressed, along with the medical relevance, if any. Relevant literature should be cited in the text, and clarifying illustrations—with figure legends—should be included.

The reference list, which is not included in the page limit, can be in any format, so long as the FULL TITLE is included and ALL the authors (up to 10) are listed.

NOTE: The Abstract, as described above, is required, but it will not be evaluated as part of the Qualifying Examination grade. It is the starting point for the examination process. The Abstract is meant to serve as a basis for discussion with the thesis committee, to allow the student to get initial feedback from the committee on the proposed research.

The student should plan to present the Abstract at the first thesis committee meeting. The student should prepare a PowerPoint presentation that will last no more than 30 minutes. The goal of the presentation is to explain the proposed research to the committee (remember, they might not have read the Abstract). The student should give sufficient Background and Significance to set the stage for the proposed research, and should present the overview of the research, including the hypotheses and rationale for each Specific Aim, and the results.

It is expected that the student will develop the Specific Aims and approaches much more fully in the Written Proposal, based on the feedback from the thesis committee; discussions with the PI and lab members; discussion with other students, postdocs, and faculty; outcomes of preliminary experiments; and their own deepening understanding of the literature, the system, and experimental approaches. The Specific Aims of the final Written Proposal do NOT need to match those of the Abstract.

WRITTEN PROPOSAL

The purpose of the Written Proposal is to provide a detailed elaboration of the student’s thesis project, which will then serve as the basis for the Oral Examination.

The Written Proposal must be submitted to the Program Administrator by March 1. If the deadline of March 1 falls on a Saturday or Sunday, the Written Proposal will be due the following Monday. Turning in the Written Proposal late results in an automatic grade of FAIL on the Qualifying Exam. As is true for a failure due to poor performance on the exam, a FAIL due to lateness is the first strike and a student gets just one more chance. The FAIL becomes a permanent part of the student’s record, and the student is put on Academic Probation until it is resolved.

In the case of a FAIL due to a missed deadline, the date for submission of the Written Proposal will be extended by three weeks, and the exam will be rescheduled to take place as soon as possible, but not sooner than two weeks after the submission deadline.

Students are expected to work on experiments and the QE in parallel and should not be out of the lab for more than two weeks to prepare the final Written Proposal. (If a student is re-taking classes in the third term such as Regulation of Gene Expression, the deadline for submission of the Written Proposal will be delayed to April 1.)

The Written Proposal must not exceed 15 pages, excluding references and figures. Use 12-point Arial font, 1½-line spacing, 1-inch top and bottom margins, and 1.25-inch left and right margins. Students are required to submit two copies of the Written Proposal: one with figures and one without.

The Written Proposal, which is modeled on the NIH grant format, should contain the following six sections in the order listed below.

(In addition to the brief information provided below, students should read the material in the Appendices, which give a more comprehensive perspective. Appendix 1 gives specific examples of specific aims and their associated hypotheses and experimental approaches. Appendix 2 presents a concise description of the elements of hypothesis-based research and relates them to the sections of a research proposal. Appendix 3 talks about the same elements in the context of preparing an actual NIH grant proposal. Finally, we will give each student examples of a funded NIH grant and a successful student proposal.)

Hypothesis and Specific Aims: Present a concise overview that places the proposed research in context, briefly describes its significance, and states the main hypothesis to be tested. List two or three Specific Aims. Each aim should state the objective of the research in that aim, the specific hypotheses that are being tested, and summarize the experimental approach and expected outcomes. At least one aim should be a novel aim that was conceived by the student.Innovative approaches will be rewarded. Please identify the novel aim(s) in the Written Proposal. One page is recommended.

Background: Briefly discuss the literature relevant to the proposal. This section of the proposal should provide a critical evaluation of the current state of knowledge, including relevant published and unpublished experiments from the PI’s laboratory. References to literature should be cited in the text. It is expected that the student will have read the cited papers. Two to three pages are recommended.

Significance: This section should make clear why the thesis project is worth doing. The student should show the importance of the proposed research by relating the Specific Aims to previous knowledge. Will the proposed research fill in critical gaps in current knowledge? Will it solve an important problem in the field? Will it aid in the understanding, diagnosis, or treatment of a disease? One half to one page is recommended.

Innovation: Describe what is innovative about the proposed research. Does it challenge or seek to shift current research paradigms? Does it propose new concepts, approaches, or methodologies? Does it refine or improve theoretical concepts, approaches, or methodologies, or apply them in a new way? Although proposals need not be innovative to be good, the most creative ones usually are. One half to one page is recommended.

Preliminary Results: Briefly describe the work that you have accomplished on the thesis project. Relevant work by other members of your lab should be included in the Background section. Clearly indicate who did the work, if it was not you; for example, you can state who did the work in a figure by citing that person in the figure legend. Relate your work to the Specific Aims. It is understood that different projects proceed at different rates; however, this section will allow the committee to evaluate quality of experimental design and effort expended. If you have done substantial work that is not directly related to your proposal topic, you may summarize it in this section. Up to three pages is recommended.

Research Design and Methods: Describe in detail the design of the proposed research and the procedures that will be used to accomplish it. When possible, refer to published protocols for standard methods (molecular biology techniques, raising antibodies, DNA sequencing, etc.). Discuss how the data will be collected, analyzed, and interpreted. Indicate how the potential outcomes will test the hypothesis. Discuss the potential difficulties and limitations of the proposed procedures and indicate what alternative approaches could be used to achieve the aims. Seven to ten pages are recommended.

Reference List: The reference list, which is not included in the page limit, can be in any format, so long as the FULL TITLE is included and ALL the authors (up to 10) are listed.

Figures and figure legends should be included in all sections to clarify the descriptions in the text. It is preferable that they be incorporated in the text near their descriptions. Figures and legends do not count toward the 15-page limit for the Written Proposal.

RESOURCES AND ASSISTANCE

Students are expected to take full advantage of all available resources, including the research literature, online databases, the advisor’s grants, and experts. Students are encouraged to discuss the proposed research with their advisor, the members of the lab, as well as other students, postdocs, and faculty. The preparation of the proposal is intended to model the preparation of an actual NIH grant, where all resources are fair game. In contrast to writers of NIH grants, however, students are expected to be able to defend their proposal orally. Students are responsible for the preparation of the Abstract, Written Proposal, and Oral Presentation; they may get suggestions and feedback from anyone, but the students carry the final responsibility for content. Students should understand their proposal in great depth, including the rationale for experimental design, the experimental procedures, the methods for analysis and interpretation, and be able to explain them to the committee’s satisfaction. Students may include their mentor in their practice talks, if they wish, but should not include members of their examination committee.
PLAGIARISM

Plagiarism—to pass off the words of another as one’s own without citing the source—is grounds for Failure. Under no circumstances should material be copied verbatim from a published paper, manuscript, grant, or any other work written by an author other than the student. When the essence of a particular sentence must be included in a proposal, the sentence should be re-written in the student’s own words. If the student feels a compelling need to use published material, it should be included in quotation marks and given an appropriate citation. Students should also refrain from copying the organization of the introduction or discussion of a published paper or the flow of ideas in a grant. Students can assume that the examination committee will have read literature relevant to the proposal.

Oral Examination

The purpose of the Oral Examination is to assess the student’s understanding of their thesis project, as described in the Written Proposal, and to determine their fitness to pursue the PhD degree in BMB at BCM.

The Oral Examination will take place during March. The Program Administrator will schedule the date and time of the Oral Examination. (If a student is re-taking classes from the third term, the Oral Examination will be scheduled during the month of April.)

Students should prepare an oral presentation that summarizes the Written Proposal. The oral presentation will take place in two parts. In the first, the student will present a general overview of the proposal. It should include background information, significance and innovation of the project, and the main hypothesis being tested. A summary of key preliminary results should be included in the overview of the Specific Aims. The overall presentation should last no more than 25 minutes. As a rough guide, 10-15 minutes should be spent on the background, significance and innovation, and main hypothesis, and 10-15 minutes should be spent on the overview of the Specific Aims and the preliminary results.

Following the initial presentation, the members of the examination committee will ask questions covering the background, significance, and preliminary results you have presented. Students should expect that these questions will test not only their knowledge of the thesis project, but also their broader knowledge both in the area of research and in the general areas covered by their coursework.

After a break during which the examination committee will decide the order in which they wish to hear the Specific Aims, the student will be asked to present detailed description of the proposed experiments. The student should prepare a 10-15 minute presentation for each Specific Aim that includes the rationale for doing the proposed experiments, the preliminary results that have been obtained, the design of the experiments, expected outcomes. It is important for the student to consider the possibility that the actual results may differ from the expected outcomes: How will that affect their hypothesis or model? What alternative hypotheses or models can they propose? During this part of the exam, the committee will ask detailed questions during the student’s presentation. (Because it is unusual for the committee to get through all three specific aims before the end of the exam, the student may wish to ensure that all key preliminary results are incorporated into the overview presentation.)

It is the student’s responsibility to arrange to have an appropriate data projector available the day of the exam.

Students should aim to become an expert in the area of the proposal. Good preparation for the exam includes reading relevant literature in the field, especially papers from your advisor’s lab, paying particular attention to the details of the experiments performed and the reasons why these experiments were done.

In general, do not prepare slides strictly for the purpose of answering anticipated questions, unless they involve complex chemical structures, intricate diagrams, or complex figures. For simple diagrams and structures, the student should be prepared to draw pictures on the board. Notes should not be referred to in order to answer questions on general knowledge.

The student should be prepared to answer questions dealing with:

  1. Details of the experimental techniques to be used for the proposed research.
  2. The biological significance of the project.
  1. The existing body of knowledge, including work done in different organisms and different experimental systems relevant to the project.
  1. Relevant details of any literature cited in the proposal.
  1. How the experimental outcomes will test the hypothesis and distinguish between it and other related hypotheses.
  2. The difficulties and limitations of the proposed procedures.
  1. Alternative approaches to achieve the specific aims.
  1. Possible outcomes of the proposed experiments and the next steps to be taken in each case.
  1. Specific details of the biochemical or biological process being studied.
  1. Future directions of the proposed research beyond the specific aims.

It is the experience of the faculty that students have the most difficulty with questions concerning numbers five, six, and seven.

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