Life as a Second-Year Student

In your second year, you will continue to make progress by meeting siginificant milestones in your graduate degree along with completing required classes. In this year, you will begin teaching,  preparing for and taking the qualifying exam and close out the year by advancing to become an official Ph.D. candidate. 

Coursework | Teaching | Qualifying Exam | Advancement to Candidacy 


During your second year in the program, you will take several courses to help you prepare for teaching as a graduate student instructor (GSI) and for your qualifying exam, and you will  receive course credit for your individual research and participation in lab group meetings.

View the Berkeley Academic Guide for class numbers, full course descriptions, and scheduling details.

  • PLANTBI 375, Workshop on Teaching 
    This course has two goals: discussion of questions and problems relating to the GSI's teaching, and learning how to design and execute a whole course. Effective teaching methods will be introduced by experienced GSIs and faculty. Students will participate in reciprocal classroom visits, visitation and critique of faculty lectures, course design, lecture preparation, sample lecture presentation, and discussion of current literature on teaching.This is required for all first time GSIs to be taken concurrently with or before the first semester teaching. 
  • PLANTBI 602, Individual Study for Graduate Students
    Individual study in consultation with the major field advisor, intended to provide an opportunity for qualified students to prepare for examinations required of Ph.D. candidates. This is to be taken during the semester in which you are scheduled for your qualifying exam, which for most students will be the spring semester of your 2nd year or 4th semester. 
  • PLANTBI 292, Research Review in Plant and Microbial Biology
    Lectures, reports, and discussions on current research in plant and microbial biology. Sections are operated independently and directed toward different topics. This course formalizes the group lab meetings and provides credit for your work. 
  • PLANTBI 298, Plant Biology Group Studies
    Advanced study of research topics which will vary semester to semester. Enrollment in more than one section permitted. 
  • PLANTBI 299, Independent Research Student
    This course provides you course credit for the dissertation research and work you do individually with your respective labs.


Students are likely to be a Graduate Student Instructor (GSI) during one of the two semesters of their second year. Students are required to teach twice prior to graduation and must teach two different types of classes in order to fulfill the requirement. Students are required to teach in two distinctly different classroom settings; specifically, teaching in a large enrollment course (100+) and small upper division, lab, or low enrollment (< 100) course. Second year students usually teach lab or discussion sections of large undergraduate courses, primarily Biology 1A and Biology 1B. GSI Application information is available in April of each year. 

The PMB GSI Application form can be found on the Student Resources page on PMB website. An email announcement is typically sent mid-Spring semester to notify students that the application form is open. We encourage students to also apply to other departments, and instructions may require students to fill out applications in multiple departments.

If so inclined, students may teach two semesters in their second year. Generally, teaching positions are more difficult to get in the Fall as more graduate students want to teach in the Fall and take their Qualifying Exam in the Spring. Be aware that you are not guaranteed a teaching position in any year. It is the student’s responsibility to acquire a teaching position.

You will also need to review the campus requirements, rules, and regulations around GSI teaching positions, which can be found in the GSI Teaching and Resource Center with the Graduate Division. First-time GSIs have the following requirements: attend the Fall Semester Teaching Conference, complete the GSI Ethics Online Course before interacting with students, and enroll in a required 300-level pedagogy course for first-time GSIs.

Qualifying Exam

The Purpose of a Qualifying Examination

All students are expected to take the qualifying exam by the end of the second year and advance to doctoral candidacy before the beginning of the third year. The Qualifying Examination assesses the candidate's broad knowledge of microbial biology and/or plant biology and determines in-depth knowledge in the proposed area of research. The examination consists of a dialog between the student and the examiners to provide a forum for the student to demonstrate an ability to integrate and extrapolate from information obtained in the classroom and laboratory. The examination provides a way to evaluate the student's preparation to complete an individual research project. It stresses breadth, depth, and sophistication of knowledge. During the examination the student will demonstrate:

  1. Mastery of a significant body of relevant knowledge
  2. The capacity to think and write critically
  3. The ability to apply information learned in the classroom and laboratory to the solution of relevant biological problems.

Basic Elements of the Exam

  1. Assemble a committee
  2. Write a proposal on your thesis project
  3. Write a proposal on an unrelated system
  4. Orally defend your proposals to a committee of senior scientists 

The Qualifying Exam Committee

It is the student’s responsibility to contact faculty to request their service on the student’s Qualifying Exam committee. All committee members must be members of the Berkeley Division of the Academic Senate, including those holding titles of Professor, Associate Professor, Assistant Professor, and more (note: Please check with GSAO with questions regarding potential committee members not listed here as some accepted titles such as Professor of Cooperative Extension held by Professor Lemaux have not yet been added). These requirements are set by the Graduate Division

Composition of the Committee

  • Committee Member 1 (Chair)
    The Chair should be a tenured faculty member from either the department of Plant & Microbial Biology (PMB) or the Graduate Group in Microbiology (GGM), which includes faculty in other departments. The Chair should be familiar with the field in which the student proposes research.
  • Committee Member 2 (ASR)
    One member of the committee must be an Academic Senate Representative (ASR) to serve as the representative of the Graduate Division to ensure the integrity of the exam. The ASR may not be an adjunct faculty member. The ASR is permitted to be from the student’s program (major) or outside of the program (major).
  • Committee Member 3 &4
    The rest of the committee should be constructed of scientists who are able to assess the proficiency of the student. That is, committee members need not be experts in the student’s proposed topic, but should have peripheral knowledge of the proposed research area such that they can challenge the student’s hypotheses and approaches.

Committee Responsibilities

  • Any examiner may ask questions in any subject area. Thus, we strongly recommend that the student meet with each committee member before the examination to discuss the proposal and the committee member’s expectations. The professor and student may choose to focus on topics within a particular subject area and may meet regularly to discuss these topics.
  • As long as the committee adequately assesses the student's broad knowledge of microbial biology or plant biology, the committee may discuss additional areas by mutual agreement between the student and the examiners.
  • The Chair of the committee and the student should meet in advance of the exam to review expectations as well as the format of the exam.
  • Following the exam, the Chair should email the GSAO a pass/fail notification as well as any feedback from the committee. This should then be shared with the student and student’s advisor.

Important Details for Committee Selection

  • Plant Biology students can consult the faculty list on the PMB site:
  • Microbiology students can consult the faculty list on the GGM site:
  • Adjunct Professors may serve as members of the committee, by exception, but not as the committee chair or ASR. There can be only one such non-senate committee member per committee and requires approval from the Head Graduate Advisor and Dean of the Graduate Division.
  • Non-Senate members and faculty from other campuses may serve upon approval of the Head Graduate Advisor and Dean of the Graduate Division. 

Thesis Advisor Role and Involvement

The thesis advisor is expected to advise their student on developing proposals and adequately preparing for the exam. As such, the student is encouraged to work directly with the advisor (and lab members) to craft the proposals and practice the oral portion of the exam. It is not unusual for the student to give multiple practice exams, some of which will include peers from outside of the lab without attendance by the thesis advisor.

The student will also write an outside proposal which should be distinct from the thesis project in its topic and approaches. The goal of the outside proposal is for students to independently develop a hypothetical thesis project. The qualifying exam chair (not the thesis advisor) approves the topic and general approaches of the outside exam. However, students can still receive feedback and suggestions from their advisors and lab members on the written and oral portions of their outside proposals.

It is highly encouraged that the student and advisor meet early in the process to discuss:

  1. Potential committee members
  2. Tentative exam date (suggestion: agree on a general time frame to accommodate committee scheduling conflicts, i.e. “mid April”)
  3. Potential projects, aims, and experiments
  4. Advisor’s experience with more senior graduate students’ QEs and from serving on qualifying exam committees themselves
  5. Labwork hiatus for quals prep

It is critical that the student and advisor arrive upon a mutual agreement of the advisor’s involvement in the writing and preparing process. Some students rely more heavily on their Committee Chair, while others meet regularly with their advisor during their QE preparation.

Balancing Time Between Research and Exam Preparation

The following statement is from the Department of Molecular and Cellular Biology Qualifying Exam guidelines. Students are expected to effectively balance research with exam preparation. Faculty understand that, for several weeks before the exam, students may need to prioritize exam preparation over research. Individual faculty may have different expectations about balancing these two tasks. It is important that the student discuss their research and exam preparation schedule with their thesis advisor, as well as their expectations. Students should discuss this topic with their thesis advisor in the semester before the exam, before beginning exam preparation.

Exam Failure and Retakes

In the event of a partial fail, the student will perform all edits, amendments, and re-writes suggested by the Committee and submit the revised proposal within one month of the original exam date. IF more time is needed the student and/or the Committee should consult with the advising office.  The Committee, led by the Chair, will meet to discuss whether the edits are sufficient to earn a passing mark. The Committee may or may not ask the student to be present for a portion of this subsequent meeting.

In the event of a total fail, the committee either recommends a second (and final re-examination or does not recommend re-examination leading to dismissal from the program. Students may not retake the exam for at least three months but must retake the exam prior to the end of the following semester. All total fail outcomes must have the unanimous approval of all committee members and be finalized in consultation with the Head Graduate Advisor.

Important Resources, Guides, and Checklist for the Qualifying Exam

In addition to the above information, it is important that all second year students carefully and thoroughly review the PMB Qualifying Exam Guide. It has been written to cover in full all the details and logistics of the exam. Below you will find additional items and checklists that will be crucial in your preparation. For any questions, please feel free to contact the Graduate Advisor and Head Graduate Advisor.

The full PMB Qualifying Exam Guide includes:

  1. Suggested Timeline of Completion
  2. Requirements for the Inside Written Proposal
  3. Requirements for the Outside Written Proposal
  4. Requirements for the Presentation
  5. Remote and Hybrid Participation Formats
  6. Expectations for the Oral Qualifying Exam
  7. Guidelines for Faculty
  8. Instructions on Submitting Forms
  9. Qualifying Exam Checklist
  10. Qualifying Exam Feedback Form

This guide was written by Christine Qabar, M.Sc. with support from Zoila Alvarez Aponte and Rebecca Procknow. Integrated resources were generated by the PMB 2019 Doctoral Cohort and the Departments of Environmental Science, Policy, and Management (ESPM) & Molecular and Cellular Biology (MCB) at the University of California, Berkeley. Special thanks to the core equity team: Rebecca Procknow, Zoila Alvarez Aponte, Dr. Ceci Martinez Gomez, and Christine Qabar, who worked together to tangibly center equity in the qualifying exam process. We in turn thank the teaching team of ESPM290: Critical Engagements in Anti-Racist Environmental Scholarship (Fall 2021) for nucleating this project, and Dr. Arash Komeili and Lyn Rivera for their contributions to this document and process. 

Advancement to Candidacy

Upon passing the qualifying exam, students become eligible to apply for advancement to candidacy. Students are to advance to doctoral candidacy prior to the start of their third year or fifth semester. To apply for advancement to candidacy, you will need to have already configured your thesis committee and complete the online eForm application in CalCentral. Your thesis committee consists of three members: your Faculty Advisor is the chair, another faculty member from your program (major), and any UCB faculty member from inside or outside your program (major). You may have a fourth member if you would like. Similar to the qualifying exam, all members of the committee should be a member of the academic senate. Some exceptions may be allowed. If so, it is important to contact the Graduate Student Services office to help you determine a valid thesis committee.

The deadline to submit and have an approved application by the Graduate Division is the first day of the fall semester, which is typically in mid-August. There is a $90 advancement to candidacy fee that is assessed once the application is approved. This fee will be covered by the PMB department provided that you apply and meet the deadline. The department will issue a $90 refund to you via CalCentral which you can then use to pay the fee balance in your account.

The application is found in CalCentral (similar to the QE eform) and instructions on how to apply can be found here. If you need more time to configure your thesis committee, please contact the Graduate Student Services Office to be considered for an extension to the deadline.

Note to International Students: It is very important that international students advance to candidacy before the start of their 3rd year. Once international students advance to candidacy, they are exempt from paying non-resident tuition for 6 semesters.