Molecular Biology and Genetics Track Policy and Curriculum (Prior to June 2002)

This document is only applicable to students who matriculated before June 2002. Students who matriculated during or after June 2008 should view the current Molecular Biology and Genetics documents.

The prospective student must meet all general requirements for the M.S. or Ph.D. degree in the Department of Biological Sciences. The curriculum described below was developed to ensure that students achieve breadth of knowledge, written and oral communication skills, and proficiency in the practice of research expected of individuals holding an advanced degree with a specialization in Molecular Biology and Genetics. All students are expected to have basic competency in biochemistry and molecular biology upon admittance to the program since these fields underpin the training provided in this track. This competency can be demonstrated by the grade of B or better in a biochemistry course from another institution or by completing CHEM 641 (Biochemistry) with a B or better in the first semester of graduate enrollment. Acceptance of biochemistry courses from other institutions is subject to approval by the Track coordinator. Alternatively and with approval of the Track coordinator, biochemistry competency can be demonstrated by satisfactory performance on a written examination administered by the Track preliminary examination committee.

Graduate Curriculum

Electives

All students also are required to complete at least one of the following:

• BISC 605 - Advanced Mammalian Physiology
• BISC 612 - Advanced Cell Biology
• BISC 615 - Vertebrate Developmental Biology
• BISC 648 - Bioremediation
• BISC 656 - Evolutionary Genetics
• BISC 673 - Advances in Immunology
• BISC 679 - Virology
• BISC 693 - Human Genetics
• ANSC 644 - Bioinformatics
• CHEM 667 - DNA-Protein Interactions
• PLSC 635 - Plant Developmental Biology
• PLSC 646 - Plant Cell Biology
• PLSC 655 - Pollution Microbiology
• PLSC 666 - Plant Physiology
• PLSC 804 - Plant Molecular Biology

If any graduate courses equivalent to those listed above have been taken in previous degree programs, the requirements can be waived with the approval of the Track coordinator.

Other courses in addition to those listed above may be taken upon the advice of the student's advisor and thesis/dissertation committee.

All students in the program are expected to register for BISC 867, graduate research seminar, every semester in which they are enrolled full time.

Masters students must complete 24 credits of course work/research credit in addition to 6 credits of BISC 869 - Master's Thesis, prior to public defense of the research based Master's thesis.

Doctoral students must pass a qualifying examination in order to advance to candidacy for the Ph.D. degree.

The Preliminary Examination

In order to be eligible to take the preliminary exam, students must have completed first year core courses (including CHEM 641 Biochemistry, if applicable) with a grade of B or better. In all cases, the student is expected to correct all deficiencies in their performance in the first year curriculum by the end of the semester after the deficiency was created but no later than the end of their third semester in the program. If the applicable course is not offered, a suitable substitute will be determined by the Track coordinator. Failure to obtain a B or better in a required course in the second attempt will result in termination from the Track. Students are expected to take the preliminary exam within six weeks after the first year curriculum has been successfully completed. If the student fails to complete the preliminary exam by this time, the student with be terminated from the Track.

Graduate students in Molecular Biology and Genetics are expected to possess a fundamental body of knowledge in genetics and molecular/cellular biology, and the ability to critically analyze scientific literature. To ensure that this is the case, an oral preliminary examination will be administered to all graduate students (M.S. and Ph.D.) in the Track at the end of their first year of study.

Procedure

Students will be provided with at least four sets of papers from the primary literature selected by Track faculty from which they must choose one set as the basis for their oral examination. These papers will be available at least six weeks before the exam, usually no later than May 1, so that the exam can be administered the second or third week of June. Four weeks prior to the exam, the student should inform the Track coordinator of the chosen paper set and arrange the time of the exam. Prior to the exam, the student should prepare transparencies or computer graphics of all of the figures and tables presented in the papers so that they will available for discussion during the exam.

During the exam, the student will be tested by a committee of four to six Track faculty on his/her comprehension of all aspects of the paper including background and related information. Students present a 10 minute synopsis of the primary paper, then the examination committee will ask questions pertaining to background material, methodology, experimental results and their significance, as well as the article's overall significance to the field. It therefore is imperative that the student searches and reads the literature for background and related information. While a good starting point is the bibliography at the end of the chosen paper set, it is likely that other primary literature sources will need to be consulted. Prior to the exam, students are encouraged to contact faculty to discuss the topics they are responsible for and to clarify difficult concepts.

Grading

After the oral examination, the examination committee will determine an appropriate grade. Four grades are possible: unconditional pass, conditional pass, re-examination or failure. If the student receives an unconditional pass, the exam was completed satisfactorily and no conditions are applied. In a conditional pass, the student performed marginally in one or more areas and may be asked to complete (with a grade of B or better) one or more courses as a condition for changing the grade to pass. The examination committee may prescribe conditions in addition to, or in lieu of, course enrollment. Once the condition is fulfilled, the student is responsible for informing both the graduate program director and the Track coordinator so that the grade can be changed officially. If the student receives a re-examination, the student's performance was unsatisfactory and the exam must be repeated with a new set of papers before the beginning of the following semester. If the student does not perform satisfactorily in the re-examination, the student will be terminated from the Molecular Biology and Genetics Track. If the student receives a failure, the student's performance strongly indicated an inability to complete an independent research project and the student will be terminated from the Molecular Biology and Genetics Track without the possibility of a retest.

Once a Master's degree student passes the preliminary examination, he/she becomes eligible to defend their thesis as soon as appropriate.

Once a Ph.D. student passes the preliminary examination, he/she becomes eligible to take the qualifying examination for advancement to Ph.D. candidacy.

The Ph.D. Candidacy Examination

The purpose of the oral candidacy examination is to give the student the opportunity to demonstrate:

• an understanding of the research area in which he or she is interested;
• the ability to formulate a research problem and to comprehend its significance; and,
• the ability to design appropriate experimental approaches to solve the problem.

A student's performance will be regarded as satisfactory only if the student:

• demonstrates an adequate knowledge of the field in general as well as the research specialty in which he or she is interested;
• formulates a research problem, the solution of which will make a substantial contribution to our existing knowledge;
• demonstrates that the experimental design and methods proposed are appropriate to solving the problem.

Ph.D. Research Proposal

At the end of the student's third year, the student is expected to have spent at least two years working on a research project in the laboratory of the dissertation advisor. At this time, the student, in consultation with the dissertation advisor, will prepare a proposal in a format similar to an NIH grant proposal that outlines the background of the project, the hypothesis to be tested, the research accomplishments to date and the research to be completed to fulfill the requirements of a Ph.D. in Biological Sciences. It is the student's responsibility to submit the Research Proposal to each member of the dissertation committee at least two weeks prior to the oral exam date.

The Research Proposal must be double-spaced and should include:

• Specific Aims: State concisely and realistically what the research is intended to accomplish and what hypothesis is to be tested. Do not exceed two pages.
• Background and Significance: Briefly sketch the background to the present proposal, critically evaluate existing knowledge, and identify gaps that the proposed research is intended to fill. State concisely the importance of the research by relating the specific aims to longer term objectives. Four to eight pages.
• Research Design and Methods: Briefly summarize the experimental design and the procedures to be used to accomplish the specific aims of this research. Include a description of the types of data to be obtained and how they will be analyzed to accomplish the specific aims. Students must be prepared to discuss potential pitfalls in the experimental design and contingency plans in the event that the data run counter to expectations. Fifteen to twenty pages.
• Literature Cited: All citations must include all author names as well as article titles. A suggested format (the standard for Journal of Cell Science for EndNote users) is:

Mazaki, Y., Uchida, H., Hino, O., Hashimoto, S. and Sabe, H. (1998). Paxillin isoforms in mouse. J. Biol. Chem. 273, 22435-22441.

The Proposal also may contain a concise Preliminary Results section. However, the candidacy examination is not meant to be a defense of the student's previous laboratory work, but rather it should be an evaluation of the student's ability to construct a hypothesis and to design the means by which to test it.

Exam for admission into candidacy for the Ph.D. (Qualifying exam)

The exam will be administered by the student's dissertation committee excluding the student's primary research advisor. Since the primary advisor for the dissertation will not be present during the examination, the student must choose an examination committee chair from among the four remaining members. The chair will be responsible for the conduct of the exam and the completion of a detailed report outlining the student's strengths and weaknesses, as well as any suggestions for alterations to the research proposal after the defense.

Prior to the exam, the student should meet with each committee member to clarify which topics that member feels are relevant for the background knowledge portion of the exam. At the oral defense, the student will present the background and significance of the work, the hypothesis to be tested and the preliminary data collected. The majority of the presentation should be devoted to explaining the experiments to be performed in the two years remaining in the student's degree program. Students should plan on a 30-45 minute presentation during which the committee will not ask questions except to clarify very specific issues (graph axes, incubation times, etc.). At the conclusion of the formal presentation the committee will evaluate the student's scientific background as well as the scientific validity of the proposed research project. It also is essential that the student demonstrates the ability to make a significant intellectual contribution to their project.

If the student receives a grade of unconditional pass, the student will be admitted into candidacy and should arrange for the appropriate paperwork to be filed with the graduate school. If the student receives a grade of conditional pass, deficiencies were found in the student's preparation that need to be rectified by completion of the "condition(s)" before the student is admitted into candidacy. The student is responsible for informing the graduate program director when any such conditions are fulfilled so that the student can be admitted into candidacy. If the student receives a re-examination, deficiencies in the written proposal and/or the student's scientific background will need to be corrected and the defense repeated. If the student fails the qualifying exam on the second attempt, the student may be either recommended for a terminal Master's degree or for termination from the Ph.D. program by the examining committee.