Plant Biology Ph.D. Policies and Procedures

Research Rotations

Most doctoral students in the Plant Biology Graduate Program enter the program with their graduate adviser already identified; i.e., they do not “rotate.” However, students who are awarded departmental teaching assistantships, university fellowships, or hold other fellowships may opt to rotate. Generally, this will involve identifying 2-3 faculty members with whom the student will work during the fall semester and possibly part of the spring semester.

Rotations give students the opportunity to gain sufficient familiarity with research operations and goals in laboratories of faculty members so that they can choose and pursue a research topic of high interest. Faculty members also become familiar with the student. After the final rotation, the student must consult with the DGP to identify their graduate adviser. Students enroll in PB 893 during their rotation period (with the DGP as the adviser). Student performance during each rotation is evaluated by the principal investigator of the laboratory. Evaluation will include an assessment of laboratory performance and a written or oral report by the student on their rotation experience. Satisfactory performance in the laboratory rotations conducted will be required to receive credit for PB 893.

Students supported with a stipend funded from a faculty member’s grant or targeted resources are not required to participate in the laboratory rotations but may do so by arrangement with the principal investigators. Students are encouraged to review the faculty research pages and to meet with faculty members before deciding upon the specific labs in which the rotation is carried out.

Doctoral Preliminary Exam Procedures

Before the first day of spring semester classes in the third year in the Plant Biology Ph.D. program, students will have ideally completed the requirements of the preliminary exam. Students have two options for their preliminary exam; which option a student pursues is a joint decision of the student and their committee.

It is advisable that the student meet in person with their committee to discuss the preliminary exam. This means the student should be holding a committee meeting in the spring semester of their second year or fall semester of their third year to discuss the preliminary exam with their committee. They would then be taking their preliminary exam sometime during their third year. The options are as follows:

(1) a traditional subject-matter exam, whereby each committee member submits questions that the student must answer in a defined time, followed by an oral exam that may follow the topics of the written exam or range elsewhere; or

(2) a research proposal, whereby the student proposes to the committee a research proposal idea subject to their approval, after which they write and submit the proposal for committee evaluation and ultimately defend the proposal as the oral part of the examination (which may also include general plant biology subject matter questions).

The procedures for the traditional written exam are as follows:

Each member of the advisory committee prepares a set of questions for the student’s response, and the answers to each set are returned to the appropriate faculty member for grading. The student and committee should establish the plan for the exam, i.e., how and to whom the committee members will submit the questions (usually to the committee chair who then conveys them to the student on the scheduled days for each set); the specific dates the student will be working on each committee member’s questions (this should be written down and approved by all parties); how the student will submit the answers (usually to the committee chair, who then conveys them to the committee member); the specific rules for each set of questions (some may be open-book or allow use of web resources, others may not; the specific format and rules for each set of questions is at the discretion of the individual committee member); any variance on the time limit (the norm is 48 hours per set of questions, but the committee may agree that one or more of its question sets can have longer time); and a timeline for committee member evaluation of the answers.

The committee members submit their evaluations of the student’s answers to the committee chair together with whether or not they authorize “permission to proceed” to the oral examination. The committee must be unanimous that the student has permission to proceed. If there is unanimous consent, then the committee chair notifies the student and the DGP of that result and the student proceeds with the oral examination as outlined below. If there is not unanimous consent, then the committee chair must work with the committee to determine the next steps. The committee may recommend a reexamination, may issue a conditional permission to proceed, the conditions of which must be met before the student can proceed to the oral exam, or the committee may indicate that the student has failed the exam and should no longer participate in the graduate program. Each of these options requires consultation with the DGP and provision of documentation to the student, DGP, and the Graduate School. The DGP will also inform the student of their options regarding appeals and grievances.

If the student has received permission to proceed to the oral exam, they work with their committee (including the Graduate School Representative) to identify a time and date for the oral examination. It is a good idea to have established a tentative oral exam date at the beginning of the examination process (making sure to include sufficient time between the written exam and the proposed oral exam date for the committee to evaluate the student’s answers. Once a date has been confirmed by all committee members, the student prepares and submit to the DGP the Request to Schedule an Oral Examination. Note that the form must be submitted no later than 10 working days prior to the proposed date. If the student is submitting the form close to the 10-day deadline, they should confirm that the DGP will be available to review and submit the form to the Graduate School. If any committee members will be participating remotely (this cannot be the Graduate School Representative), another form is required and is also subject to the 10 working day deadline. Request to conduct Remote Oral Examination.

In the oral exam, committee members may question the student on any phase of the course work taken by the student during graduate study or any subject logically related to an understanding of the subject matter in the major and minor areas of study. The questions are designed to measure the student’s mastery of his/her field and the adequacy of preparation for research, to test the student’s ability to relate factual knowledge to specific circumstances, to use this knowledge with accuracy and promptness, and to demonstrate a comprehensive understanding of the field of specialization and related areas.

The outcomes of the preliminary oral exams can be an unconditional pass, a conditional pass, or a fail. The outcome is formally reported to the Graduate School on an exam report form. Conditional passes require a specific statement of what the student must do in order to pass. This should include dates by which those benchmarks will be accomplished. The report requires that a Fail be accompanied by the committee’s judgment of what comes next: either a reexamination (include an estimate of the date when that would occur) or termination from the program. The DGP must be involved in discussing options for failed exams. The DGP will also inform the student of their options regarding appeals and grievances.

The procedures for the research proposal option are as follows:

This option requires even more extensive communication with your committee. Again, a student is urged to meet in person with their committee as a whole to discuss the specifics of their preliminary exam. The student need to work hard to determine the expectations of each committee member and make sure that they make every effort to meet those expectations. External committee members and committee members from other departments may not be familiar with the proposal option (their department may only have a question option preliminary exam). Make sure they understand the process and our program expectations. Take nothing for granted and make sure you know in advance what the committee members are expecting. This includes such mundane matters as the format of the research proposal. Generally, the committee will expect the student to follow a specific granting agency’s proposal guidelines (i.e., National Science Foundation, US Department of Agriculture, National Institutes of Health). Confirm with the committee which of these is expected and whether or not all components of a standard grant proposal are to be included (i.e., a budget, current and pending support, facilities statement, etc.) Be sure you know if you are to adhere to the strict page limits of the agency or if the committee will impose a higher page limit.

The research proposal exam consist of two parts, the written proposal and an oral defense by the student before the members of the Advisory Committee.

The Written Preliminary Examination – A Research Proposal (Part A)

You must have met with your committee and received their approval to pursue the research proposal option. That meeting should result in an agreed-upon written understanding of the format to be followed and the establishment of a schedule for the various steps of the process. This agreed-upon written understanding should include which research-granting agency format you will use and which components of a proposal to that agency you should include in your proposal. There should have been extensive discussion of possible proposal topics, but final approval of the topic of the research proposal follows a process that is outlined below.

You will choose a topic for this proposal that encompasses new research. The topic must be distinct from your research if that research is part of funded or other ongoing research in the lab, although the topic may encompass experimental approaches that are familiar to the student. Alternatively, the topic may be directly related to your research if the advisory committee unanimously agrees that it is not part of funded or other ongoing research in the lab.

You should start this process several months before you plan to write the proposal. Read papers in an area that you are thinking about choosing. Once you have an idea of a general topic of importance to plant research, develop a hypothesis and contact your committee members individually to see if they think this is a reasonable area to explore. This preliminary step helps to avoid spending a lot of time on something that a committee member thinks is too related to your research. Your advisor and committee will have suggestions relevant to your particular area of research. If you take the time to do this advance preparation, it will help you work efficiently as you go through the proposal writing.

The next step is to write a one page abstract that you submit to your advisor for feedback. After revising the abstract to your advisor’s satisfaction, you should then submit the abstract to your committee members, requesting their feedback and approval of the abstract as the subject of your grant proposal. This is a critical step: interacting with your committee members about the topic and scope of the proposal now will help to ensure that your proposal is something that can be defended in the oral examination. You will find your committee members to be invaluable in pointing out major problems with your research approach: perhaps it is not hypothesis-driven, perhaps it is overly ambitious, perhaps there are pitfalls to the techniques of which you are not aware, perhaps you have made assumptions that will not pan out. puts you in a position to write something that can be defended at the orals. It is up to you to take all of the comments from the committee members into consideration and then either write the original proposal, modify the original aims or present a new abstract to the committee.

The goal of this process is to give you advance warning that a faculty member thinks you might have problems defending the proposed work. Our goal is to guide your independence, but to save you from a wasted effort. In many ways, this preliminary exercise is one of the most valuable aspects of the preliminary exam.

Once your abstract has been approved (or at least vetted as being appropriate in scope and subject) then you may proceed with writing your proposal. At this point, you are entirely on your own for the writing of the proposal. This is, after all, an examination. You will have four weeks to write your proposal. Once it is completed, you submit it to your major professor, who will then convey it to the committee members. The committee members will evaluate the proposal and send their feedback and evaluation to the major professor, who will then inform the student of the outcome.

The possible outcomes are:

•Pass: the student has satisfactorily completed the written examination and has permission to schedule the oral exam;
•Conditional Pass: the committee will provide the student with a written set of expectations of what must be accomplished and by what date in order for them to earn a pass on their preliminary exam. The DGP should be involved in this process;
•Fail: the advisory committee will either recommend a reexamination (with a proposed deadline by which that should occur) or that the student no longer participate in the graduate program. The DGP must be involved and will inform the student of their options regarding appeal and grievance.

The Oral Preliminary Examination – Defense of the Proposal (Part B)

Once you are given permission to proceed to the oral examination, you should consult with your committee (including the Graduate School Representative) to identify a time, date, and place for the oral exam. Once that is determined, you should complete a Request to Schedule a Doctoral Oral Examination and send it to your major professor, who will forward it to the DGP indicating that the committee has unanimously granted permission for you to proceed to the oral exam.

You should have already determined the committee’s expectations for the oral exam in your initial planning meeting of the preliminary exam. If not, then be sure to discuss this with your major professor and contact the committee members to make sure you understand their expectations.

A typical exam would start with your giving a brief (20-30 minute) presentation of your research proposal. You will then respond to questions from the advisory committee. The questions will focus on the research proposal but may include any question relevant to it or to the expected proficiency in plant biology.

Immediately following the examination, the advisory committee will decide its outcome, which can be one of the following:

•Unconditional pass.
•Conditional pass. The committee must indicate on the exam report form what conditions the student must satisfy to earn an unconditional pass and the date by which that must occur.
•Fail. The committee must indicate on the exam form whether they recommend a reexamination (and the date by which that should occur) or that the student be separated from the program. The DGP must be consulted regarding this decision and will inform the student of their options regarding appeal or grievance.


Once the student has passed the preliminary examination (written and oral) they will have achieved candidacy status.