Ph.D. Program

Dissertation Plan

The Plant Biology Graduate Group operates under Plan B, as described in the Davis Division Regulation 520(C). Plan B specifies a three member (minimum) dissertation committee, a final oral examination (decision to hold at the discretion of the Dissertation Committee on an individual student basis), and an exit seminar is required of all candidates.

Course Requirements (41 units minimum)

The student will complete his/her degree in one of 4 areas of specialization in (a) Cell and Developmental Biology; (b) Environmental and Integrative Biology; (c) Molecular Biology, Biochemistry and Genomics; or (d) Systematics and Evolutionary Biology. The area of specialization determines the nature of the student’s elective coursework and the topics covered in the qualifying examination. The student chooses his/her area of specialization. A change in a student’s area of specialization requires approval from the Ph.D. program’s Master Adviser (the student submits a written email request to the Master Adviser).

a) Core Courses (15 units total):

PBI 200A Core Course Series – Fall Quarter (5 units) *taken the first year
PBI 200B Core Course Series – Winter Quarter (5 units) *taken the first year
PBI 200C Core Course Series – Spring Quarter (5 units) *taken the first year

b) Required Seminars (17 units):

3 units of PBI 290A (1 unit each) - Fall, Winter, Spring of the second year
6 units of PBI 290B (1 unit each) - Fall, Winter, Spring of both the first and second years
5 units of PBI 291 (1 unit each) – Fall and Winter of both the first and second years
3 units of PBI 292 (1 unit each) - Fall, Winter, Spring of the first year

Students may request exception to the seminar requirements if there is a scheduling conflictwith an especially important specialization course.Such requests are subject to approval by the student’s Graduate Adviser and the Master Adviser. If the request is approved, the minimum number of required seminars will also be changed accordingly.


c) Courses in Specialization Area (9 units):

A minimum of three additional courses (for a minimum of 9 units), taken from the student's specialization area course list. (See the Advising Course Lists for more information.) Alternatively, a student may take two courses from the course list for their area of specialization and one course not on the list. All courses must be approved by the Graduate Adviser.

The expectation is that all three courses will be at the graduate level; however, one of the three may be an upper division undergraduate course from the course lists upon approval by the student's Graduate Adviser.

d) Summary

No single course may be used to satisfy more than one degree requirement (for example, the same course cannot be used to fulfill an undergraduate deficiency and satisfy the elective course requirement). All courses taken to fulfill degree requirements for which a letter grade is offered must be taken for a grade (and not Passed/ Not Passed or Satisfactory/ Unsatisfactory). A grade of C- or better is required to satisfy the degree requirement for an advanced undergraduate level (100) course and a grade of B- or better is required to pass a graduate (200) level course.

40 units are required at a minimum: 15 units of core courses, 9 units of specialization/elective courses, and 16 units of seminar courses. A minimum course load is 12 units per quarter. Per UC regulations, students cannot enroll in more than 12 units of graduate level coursework (200) or more than 16 units of combined upper division and graduate level coursework (100, 200, 300) per quarter.

Special Requirements

As part of the their annual evaluation of progress, students after they advance to candidacy are required to present at least one oral presentation on their dissertation work at the Tuesday noon seminar series (PBI 291). This "in progress" seminar is in addition to the required exit seminar (which is given following completion of their dissertation research). Typically, the "in progress" presentation will occur in the students' third or fourth year, more than a year before completion of the dissertation. Students may present more than one time. An additional objective of this requirement is to provide students with an opportunity to practice giving oral presentations on their own area of research and practice placing their work in the broad context of plant biology research. In addition, it is expected that the students' dissertation committee members will attend this seminar to assess the students' research progress as part of their annual evaluation. These presentations do not require completion of a large body of work. The expectation is that students present the background of the research problem, the questions asked, approaches taken, the results obtained to date and future experiments to be undertaken.

In addition, all advanced students are encouraged to regularly attend these seminars to learn about other research on campus and to learn to evaluate their peers' presentations and research. The Tuesday noon seminar series is also reserved for the exit seminar. All students are required to present their dissertation work through a public exit seminar, and it is highly recommended that they present in this course, but not required.


Qualifying Examination Committee

The student, in consultation with his/her Major Professor and Graduate Adviser, nominates five faculty to serve on the Qualifying Examination Committee, and chooses two areas of plant biology outside their specialization area for examination. Neither the Major Professor nor others deemed to have a conflict of interest with the student or the Major Professor (for example, close collaborators) shall serve on the committee. A PBI faculty with expertise in the specialization area will serve as Chair of the committee. Two members will examine in one of the two additional areas, one member will examine in general plant biology and one member and the chair will examine in the specialization area. The student nominates a first and second choice for each of the members, including the chair. These nominations are submitted to the Master Adviser. At a meeting of all the advisers, typically in the winter quarter, the nominations for qualifying examination committee are generated. These nominations are submitted to the Office of Graduate Studies for formal appointment in accordance with Graduate Council policy.

PBI has been approved for an exception to the policy requiring a member outside of the graduate group on the PBI qualifying examination committees, so all qualifying examination committee members may be from the PBI membership (approved by the Graduate Council in July 2006).

Dissertation Committee

After successful completion of the qualifying examination, the student is eligible for advancement to candidacy. In consultation with the Major Professor and Graduate Adviser, the student nominates two faculty members to serve on the dissertation committee; the third member and Chair is the Major Professor. These nominations are submitted to the Office of Graduate Studies for formal appointment in accordance with Graduate Council policy. The dissertation committee will advise the student on the dissertation research and pass on the merits of the dissertation. The PBI group requires yearly dissertation committee meetings.

Advising Structure and Mentoring

Each student has a Graduate Adviser who serves as an adviser in planning the coursework program, approves the program of study, and is a resource for information on academic requirements, policies and procedures, and registration information. The student is expected to meet with the Graduate Adviser before the first, and during the third and fourth quarters. During the first quarter meeting, the Graduate Adviser will assist with coursework and career planning. The purpose of the third quarter meeting will be to evaluate progress (via the student progress report) and discuss future coursework. The fourth quarter meeting will verify the completion of coursework and will discuss qualifying examination requirements and issues; additionally, students will submit nominations for their qualifying examination committees during this fourth quarter meeting.

The Major Professor is the faculty member who supervises the student's research and dissertation; this person serves as the Chair of the Dissertation Committee. The Master Adviser is a resource for other Graduate Advisers and oversees the nominations of faculty to serve on examination committees. The Graduate Program Staff assists students in identifying appointments, and is a resource regarding program policies and requirements, and general university policies. In addition, to assist faculty in defining mentoring responsibilities, a Mentoring Guideline document can be found here.

Advancement to Candidacy

The student is eligible for Advancement to Candidacy after successful completion of all graduate program degree requirements, must have maintained a 3.0 GPA in all coursework (except those courses graded S/U), and after passing the Qualifying Examination; this is typically in the 7th quarter. The student must file the appropriate paperwork with the Office of Graduate Studies and pay the candidacy fee in order to be officially promoted to Ph.D. Candidacy.

According to university policy, a graduate student cannot hold an academic title (e.g., GSR/TA/AI) for more than 9 quarters before passing their Qualifying examination. After passing the Qualifying Examination, the student is eligible for advancement to candidacy and should complete the paperwork promptly. The expectation is that advancement to candidacy will occur within one month after successful passing of the Qualifying examination. The student, after consultation with his/her Major Professor and Graduate Adviser, selects the members of the dissertation committee and submits their names to Graduate Studies for approval.

Qualifying Examination and Dissertation Requirements

a) Qualifying Examination

1. General Information on the QE
PBI students are required to pass an oral qualifying examination before being advanced to candidacy for the Ph.D. in Plant Biology. The QE is to be held before the end of the seventh quarter in residence and after the student has completed all PBI course requirements, which is verified by the student's Graduate Adviser.

PBI students are strongly advised to meet with committee members to discuss their expectations for the Qualifying Examination. The purpose of the exam is (1) to evaluate the breadth and depth of the student's knowledge and understanding of Plant Biology, and (2) to assess the student's intellectual capability and preparedness for conducting a productive dissertation research, which should identify and address a significant question in Plant Biology and culminate in a dissertation of high quality.

2. The Written Component of the Qualifying Examination
Students are required to prepare a dissertation proposal that will be evaluated by the Qualifying Examination Committee. The candidate will be expected to distribute a written dissertation research proposal to the chair of the Qualifying Examination Committee at least two weeks prior to the oral examination. If necessary, the chair may make recommendations on improving the quality of the proposal before it will be distributed by the student to the other members of the committee at least one week prior to the examination.

The purpose of the dissertation proposal is to concisely introduce, describe and justify the proposed research. The scope and format of the proposal should be similar to that of a formal application for funding (e.g., application for a doctoral fellowship). The student is expected to show mastery in scientific writing, in the critical analysis of preliminary data, and in the synthesis of information derived from the relevant literature. The dissertation research proposal (single-spaced, 12 pts font size, 1 in. margins) should be organized into five sections and should not exceed 5 pages for sections 1-4, including figures.

(1) General objective and specific aims. State briefly the overall objective of your dissertation research in its broad context and list the specific aims to achieve this goal. (less than half a page).

(2) Background and significance. Describe the background and rationale for your thesis research. Critically evaluate the existing knowledge relevant to your research and identify an important question or unsolved problem that your thesis research will address in order to advance the field. State concisely the significance of the proposed research and relate the specific aims to the long-term objective. (approx. one page).

(3) Preliminary data. Briefly describe research that has been conducted and that is relevant to the proposal. Clearly state your contributions to this research (approx. one page).

(4) Experimental plan and research methods. Outline the experimental design and the procedures to be used to accomplish the specific aims of your thesis research. Include the means by which data will be collected, analyzed and interpreted. Discuss the potential difficulties and limitations of the proposed procedures as well as alternative approaches to achieve the major objective. Provide a tentative timetable of your research. (two to three pages).

(5) References. Consult a major journal in the field of plant biology and follow its style of citation. Each citation must include the names of all authors, title of the article, name of the journal or book, volume number, page numbers, and year of publication. (no more than two pages or 25 references).

3. The Oral Component of the Qualifying Examination
The oral portion of the Qualifying Examination will consist of three parts: (1) oral presentation and defense of the dissertation research proposal, which will include a broader discussion of questions from the candidate's area of specialization; (2) an oral examination of the candidate's knowledge in general Plant Biology, which will be conducted at a level comparable to content and depth of the undergraduate preparation for the major and of the core course curriculum; and (3) oral examination of two topics from two areas in Plant Biology that will be selected by the student and will be different from the candidate's own area of specialization. These two topics can be selected from a list of suggested topics. All topics must be approved by the advisers. This approval typically occurs at the annual advisers' meeting when QE members are nominated.

The student will prepare an oral presentation for the first part. In addition to the chalk/white board, the student may utilize visual aids to efficiently convey essential information as deemed necessary (limited to the display of information that is difficult to draw on the board). The presentation should not exceed 20 min, excluding intermittent discussions. The exam in total should not last longer than 3 hours.

4. Outcome of the Exam
The committee will reach a decision on the student's performance and inform the student immediately after the oral exam. There are three possible outcomes of the first examination: Pass, Not Pass, and Fail. Pass allows the student to advance to candidacy for the Ph.D. Not Pass means the student is required to retake all or part of the examination or satisfy another requirement (e.g., take a specific class, assist a specific class as a TA, etc.). If requested, the second examination is to be scheduled at the earliest possible date deemed to be appropriate by the committee. The second examination will be administered by the same Qualifying Examination Committee. Only two outcomes are possible for the second examination: Pass or Fail. A Fail on the first or second attempt results the student being recommended for disqualification to the Dean Graduate Studies.

The Qualifying Committee should make every effort to reach a unanimous decision. Split decisions will be referred to Graduate Studies for a final decision.

b) The Dissertation

1. Exit Seminar
The Exit Seminar is a formal public presentation of the student's research before the program faculty and students. Satisfaction of the completion of the Exit Seminar is verified by the Dissertation Committee Chair, who shall not sign the dissertation until this requirement is completed. Adequate scheduling of the exit seminar is the responsibility of the student. The Tuesday noon seminar series (PBI291) is reserved for students to present the exit seminar; it is highly recommended that they present in this course, but not required.

2. Dissertation: General Requirements
Filing of a PhD dissertation with the Office of Graduate Studies is normally the last requirement satisfied by the candidate. The deadlines for completing this requirement are listed each quarter in the General Catalog, and on the Office of Graduate Studies website. A candidate must be a registered student or in Filing Fee status at the time of filing a dissertation, with the exception of the summer period between the end of the Spring Quarter and the beginning of Fall Quarter. The dissertation will be prepared, submitted and filed according to regulations instituted by the Office of Graduate Studies.

3. Dissertation
The research conducted by the student must be of such character as to show ability to pursue independent research. The dissertation reports a scholarly piece of work of publishable quality that solves a significant scientific problem in the field and is carried out under the supervision of a member of program while the student is enrolled in the program. The Major Professor's laboratory is the setting for most of the student's research activities.

Students should meet regularly with their dissertation committee. The dissertation must be submitted to each member of the dissertation committee at least one month before the student expects to make requested revisions; committee members are expected to respond within 4 weeks, not including summer months for nine month faculty. Informing committee members of progress as writing proceeds helps the members to plan to read the dissertation and provide feedback within this time frame. The dissertation must be approved and signed by the dissertation committee before it is submitted to Graduate Studies for final approval.

Normative Time to Degree

The normative time for completion of a Ph.D. program in Plant Biology is six years.

Typical Time Line and Sequence of Events

Course requirements are generally completed by the end of year (2) and the Qualifying exam is normally completed by the end of the seventh quarter.

Year 1

Fall Winter Spring
PBI 200A PBI 200B PBI 200C
PBI 291 PBI 291  
PBI 292 PBI 292 PBI 292
PBI 290B PBI 290B PBI 290B
299 units 299 units 299 units
  Elective Elective

Year 2

Fall Winter Spring
PBI 290A PBI 290A PBI 290A
PBI 290B PBI 290B PBI 290B
PBI 291 PBI 291  
PBI 299 PBI 299 PBI 299

Year 3:
QE examination
Advancement to Candidacy Dissertation Research (299)

Year 4-5:
Dissertation Research (299), 12 units per quarter.
Completion of Dissertation