Plant Biology

University of California, Berkeley

This is an archived copy of the 2015-16 guide. To access the most recent version of the guide, please visit http://guide.berkeley.edu.

About the Program

The Graduate Program in Plant Biology is designed to train students in modern research areas of plant biology. Students' courses of study are designed individually, in light of their interests and career goals. The graduate program features an introductory seminar (Faculty Research Review), six five-week core course modules, and additional special topic courses and seminars in areas of faculty specialties. The department has research expertise in the following areas: molecular, cellular, genetic, biochemical, physiological, developmental, and structural biology, and plant-microbe interactions. The core courses cover plant developmental genetics, genomics and computational biology, plant diversity and evolution, plant cell biology, plant biochemistry, and plant systems biology.

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Admissions

Admission to the University

Minimum Requirements for Admission

The following minimum requirements apply to all graduate programs and will be verified by the Graduate Division:

  1. A bachelor’s degree or recognized equivalent from an accredited institution;
  2. A grade point average of B or better (3.0);
  3. If the applicant comes from a country or political entity (e.g., Quebec) where English is not the official language, adequate proficiency in English to do graduate work, as evidenced by a TOEFL score of at least 90 on the iBT test, 570 on the paper-and-pencil test, 230 on the computer-based test, or an IELTS Band score of at least 7 (note that individual programs may set higher levels for any of these); and
  4. Sufficient undergraduate training to do graduate work in the given field.

Applicants Who Already Hold a Graduate Degree

The Graduate Council views academic degrees not as vocational training certificates but as evidence of broad training in research methods, independent study, and articulation of learning. Therefore, applicants who already have academic graduate degrees should be able to pursue new subject matter at an advanced level without need to enroll in a related or similar graduate program.

Programs may consider students for an additional academic master’s or professional master’s degree only if the additional degree is in a distinctly different field.

Applicants admitted to a doctoral program that requires a master’s degree to be earned at Berkeley as a prerequisite (even though the applicant already has a master’s degree from another institution in the same or a closely allied field of study) will be permitted to undertake the second master’s degree, despite the overlap in field.

The Graduate Division will admit students for a second doctoral degree only if they meet the following guidelines:

  1. Applicants with doctoral degrees may be admitted for an additional doctoral degree only if that degree program is in a general area of knowledge distinctly different from the field in which they earned their original degree. For example, a physics PhD could be admitted to a doctoral degree program in music or history; however, a student with a doctoral degree in mathematics would not be permitted to add a PhD in statistics.
  2. Applicants who hold the PhD degree may be admitted to a professional doctorate or professional master’s degree program if there is no duplication of training involved.

Applicants may apply only to one single degree program or one concurrent degree program per admission cycle.

Any applicant who was previously registered at Berkeley as a graduate student, no matter how briefly, must apply for readmission, not admission, even if the new application is to a different program.

Required Documents for Applications

  1. Transcripts:  Applicants may upload unofficial transcripts with your application for the departmental initial review. If the applicant is admitted, then official transcripts of all college-level work will be required. Admitted applicants must request a current transcript from every post-secondary school attended, including community colleges, summer sessions, and extension programs. Official transcripts must be in sealed envelopes as issued by the school(s) attended. 
    If you have attended Berkeley, upload your unofficial transcript with your application for the departmental initial review. If you are admitted, an official transcript with evidence of degree conferral will not be required.
  2. Letters of recommendation: Applicants may request online letters of recommendation through the online application system. Hard copies of recommendation letters must be sent directly to the program, not the Graduate Division.
  3. Evidence of English language proficiency: All applicants from countries or political entities in which the official language is not English are required to submit official evidence of English language proficiency. This applies to applicants from Bangladesh, Burma, Nepal, India, Pakistan, Latin America, the Middle East, the People’s Republic of China, Taiwan, Japan, Korea, Southeast Asia, most European countries, and Quebec (Canada). However, applicants who, at the time of application, have already completed at least one year of full-time academic course work with grades of B or better at a US university may submit an official transcript from the US university to fulfill this requirement. The following courses will not fulfill this requirement: 1) courses in English as a Second Language, 2) courses conducted in a language other than English, 3) courses that will be completed after the application is submitted, and 4) courses of a non-academic nature. If applicants have previously been denied admission to Berkeley on the basis of their English language proficiency, they must submit new test scores that meet the current minimum from one of the standardized tests.

Where to Apply

Visit the Berkeley Graduate Division application page . 

Admission to the Program

Prospective students for the graduate program in plant biology are expected to demonstrate academic excellence and potential for independent scientific research. Students are expected to have a basic background in chemistry, physics, mathematics, and biology equivalent to those in the undergraduate program. An admissions committee composed of nine to ten members of the department will review applications and make recommendations to the full department on admissions matters. Recommendations for admission will be based on a demonstration of academic excellence and potential for independent scientific research as shown by grades in university-level undergraduate and graduate courses, letters of recommendation, written statements of academic and professional goals, and other evidence of academic accomplishment. Scores on standardized tests, such as the Graduate Record Examination (GRE), will be required of all applicants. Students seeking detailed information about matters such as admission, curriculum, and courses of financial support should contact the student affairs adviser or the graduate adviser.

Doctoral Degree Requirements

Normative Time Requirements

Normative Time to Advancement

Normative time to advancement to PhD candidacy is two years.

Year 1
Students perform three laboratory rotations in order to explore areas of research interest and identify a faculty mentor, dissertation project, and laboratory. Students undertake required core classes and attend seminars of interest.

Year 2
Students attend seminars, perform their first teaching assignment, and prepare for the PhD qualifying exam which consists of two research proposals and an oral examination. With the successful passing of the qualifying exam, students select a dissertation committee and advance to candidacy for the PhD degree prior to the start of the fifth semester.

Normative Time in Candidacy 

Years 3–5/5.5
Students attend seminars of interest and perform their second teaching assignment. Students conduct original laboratory research for the PhD dissertation with the guidance of their faculty mentor and a self-selected 3 to 4 person dissertation committee. Students are required to meet annually with the dissertation committee. Students write the dissertation based on the results of their research. Upon approval of the dissertation by the dissertation committee and Graduate Division, students are awarded the doctorate. There is no formal defense of the completed dissertation; however, students are expected to publicly present a talk about their research in the final year.

Total Normative Time

Total normative time to degree is 5–5.5 years.

Time to Advancement

Curriculum

Courses Required
PLANTBI 200APlant Developmental Genetics1.5
PLANTBI 200BGenomics and Computational Biology1.5
PLANTBI 200CPlant Diversity and Evolution1.5
PLANTBI 200DPlant Cell Biology1.5
PLANTBI 200EPlant Biochemistry1.5
PLANTBI 200FPlant-Environment Interactions1.5
PLANTBI 201Faculty Research Review2
PLANTBI 210Scientific Reasoning and Logic1
PLANTBI 290Seminar (or equivalent)2
PLANTBI 299Graduate Research (multiple)1-12
PLANTBI 298Plant Biology Group Studies1-6
PLANTBI 375Workshop on Teaching2

Professional Development

Research Presentations

All plant biology graduate students attend the Plant and Microbial Biology (PMB) department retreat at least once during their graduate studies. Students are encouraged to attend both the Plant and Microbial Biology department retreat and the Graduate Group in Microbiology retreat and present their research. Students are highly encouraged to present during the PMB department student/post-doc seminar series. They are also encouraged to attend national and international conferences to present research. 

Teaching

Plant biology graduate students are required to teach two semesters. Students are required to teach in two distinctly different classroom settings; specifically, teaching in a large enrollment course (100+) and a small upper division, lab, or low enrollment (< 100) course.

Grant Writing

Students are encouraged to take PLANTBI 297.

Courses

Plant Biology

PLANTBI 200A Plant Developmental Genetics 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will be provided with both the basic framework and current topics of plant developmental genetics.

PLANTBI 200B Genomics and Computational Biology 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
Principles of computational and genomic biology. Covers evolutionary, algorithmic, and statistical foundations of sequence analysis, allowing students to understand concepts underlying modern computational methods. Practical applications wil be pursued in student-coordinated sessions. Combined lecture with 220B.

PLANTBI 200C Plant Diversity and Evolution 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
This course will introduce the students to the diversity of plant form and function and provide them with a basic understanding of the tools and techniques used to study plant diversification and evolution. Molecular and morphological data will be discussed and plant diversity will be introduced at molecular, population, organismal, and ecological levels.

PLANTBI 200D Plant Cell Biology 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The course will describe the conceptual framework of plant cell biology followed by in-depth discussion of several active areas of research including cell wall biology, membrane transport, cellular trafficking, and cell signaling.

PLANTBI 200E Plant Biochemistry 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The aim of this course is to augment the student's knowledge of key plant-specific (or particularly relevant) biochemical processes focusing on the underlying experiments used to deduce key cycles coupled with current areas of exploration and debate surrounding a given topic area. In addition, this section will broaden and deepen the student's knowledge of biochemistry in general including basic enzyme kinetics, assessment of enzymatic (biochemical) function, and modes of regulation.

PLANTBI 200F Plant-Environment Interactions 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
Students will be provided with both the historical framework and current topics in the molecular mechanisms underlying plant dynamic responses to external signals and stresses.

PLANTBI 201 Faculty Research Review 2 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
Presentation and discussion of faculty research in the areas of plant and microbial biology. Faculty speakers review recent advances in their area of expertise and present an outlook of current research activities in their laboratories. The format of the class is designed to stimulate a dialogue between instructor and students in the course of each presentation.

PLANTBI 202 Faculty Research Review 2 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
Presentation and discussion of faculty research in the area of microbial biology. Faculty speakers review recent advances in their area of expertise and present an outlook of current research activities in their laboratories. The format of the class is designed to stimulate a dialogue between instructor and students in the course of each presentation.

PLANTBI 205A Introduction to Research 2 - 12 Units

Terms offered: Fall 2017, Fall 2016
Closely supervised experimental work under the direction of an individual faculty member; an introduction to experimental methods and research approaches in particular areas of plant and microbial biology.

PLANTBI 205B Introduction to Research 2 - 12 Units

Terms offered: Spring 2017
Closely supervised experimental work under the direction of an individual faculty member; an introduction to experimental methods and research approaches in particular areas of plant and microbial biology.

PLANTBI 210 Scientific Reasoning and Logic 1 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The objectives of this class are to teach students to critically read and interpret scientific papers. Students will read and discuss strongly and poorly reasoned papers. At the end of the class the student should understand the logic and reasoning which make a paper strong, often classic, contribution.

PLANTBI C216 Microbial Diversity Workshop 1 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
This workshop for graduate students will parallel C116, Microbial Diversity, which should be taken concurrently. Emphasis in the workshop will be on review of research literature and formulation of paper pertinent to research in microbial diversity.

PLANTBI 220A Microbial Genetics 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will learn fundamental principles and advanced techniques in microbial genetics. The use of genetics in deducing biochemical pathways, protein interactions, and signal transduction pathways will be explores through reading and discussion of current and classic papers from the primary literature. Experimental design and interpretation will be the focus of problem sets solved in student-coordinated sessions.

PLANTBI 220B Genomics and Computational Biology 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
Principles of computational and genomic biology. Covers evolutionary, algorithmic, and statistical foundations of sequence analysis, allowing students to understand concepts underlying modern computational methods. Practical applications will be pursued in student-coordinated sessions. Combined lecture with 200B.

PLANTBI 220C Microbial Diversity and Evolution 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
The students will be provided with both the basic framework and current topics of microbial diversity and evolution.

PLANTBI 220D Cell Structure and Function 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will be provided with both the basic framework and current topics of cell structure and function.

PLANTBI 220E Microbial Physiology 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will be provided with both the basic framework and current topics of microbial physiology.

PLANTBI 220F Microbial Ecology 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
The students will be provided with both the basic framework and current topics of microbial ecology.

PLANTBI 222 Biochemistry of Biofuels: Concepts and Foundations 1 Unit

Terms offered: Spring 2016, Spring 2015, Spring 2014
This course offers a consideration of genes, enzymes, metabolic pathways and biochemical processes leading to the generation of hydrogen, bio-oils, ethanol, and other biofuels. Discussion of biochemistry is extended to cover product yields and techno-economic analyses of commercial viability of the various biofuel products. Lectures are based on historical and contemporary papers in plant and microbial biochemistry, integrating structure, function and evolution of the molecular, cellular, and organismal levels, and discussing how this knowledge can be applied in the generation of renewable biofuels.

PLANTBI C224 The Berkeley Lectures on Energy: Energy from Biomass 3 Units

Terms offered: Fall 2015, Fall 2014, Fall 2013
After an introduction to the different aspects of our global energy consumption, the course will focus on the role of biomass. The course will illustrate how the global scale of energy guides the biomass research. Emphasis will be places on the integration of the biological aspects (crop selection, harvesting, storage, and distribution, and chemical composition of biomass) with the chemical aspects to convert biomass to energy. The course aims to engage students in state-of-art research.

PLANTBI 238 Readings in Environmental Microbiology 1 Unit

Terms offered: Fall 2014, Spring 2014, Fall 2013
Special Topics and Advanced Seminars in Plant Pathology. Seminar/discussion by graduate students of current research in the field of plant pathogenic bacteria.

PLANTBI 290 Seminar 1 - 2 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
Advanced study in various fields of plant biology and microbial biology. Topics will be announced in advance of each semester. Enrollment in more than one section permitted.

PLANTBI 292 Research Review in Plant and Microbial Biology 1 Unit

Terms offered: Fall 2017, Spring 2017, Fall 2016
Lectures, reports, and discussions on current research in plant and microbial biology. Sections are operated independently and directed toward different topics.

PLANTBI 296 Graduate Supervised Independent Study 1 - 12 Units

Terms offered: Fall 2014, Spring 2014, Fall 2013
Graduate student independent study under the supervision of a faculty member. Sections are operated independently and directed toward different topics.

PLANTBI 297 Grant Writing and Research Presentations 2 Units

Terms offered: Spring 2017, Spring 2016, Spring 2015
Each student will write a grant proposal in three steps: a one page outline, a three-page pre-proposal, and a complete 10-page grant proposal. There will be feedback at each step in the process -- each participant will review the other grant proposals. Some of the scheduled classes will include discussion of the outlines and pre-proposals, and the last class will be organized as a grant panel, with students assigned as primary and secondary reviewers.

PLANTBI 298 Plant Biology Group Studies 1 - 6 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
Advanced study of research topics which will vary semester to semester. Enrollment in more than one section permitted.

PLANTBI 299 Graduate Research 1 - 12 Units

Terms offered: Fall 2017, Summer 2017 8 Week Session, Spring 2017
Graduate student research.

PLANTBI 375 Workshop on Teaching 2 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
Designed for all graduate students. 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.

PLANTBI 602 Individual Study for Graduate Students 1 - 2 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
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

PLANTBI S602 Individual Study for Graduate Students 1 - 6 Units

Terms offered: Prior to 2007
Individual study in consultation with the major field adviser, intended to provide an opportunity for qualified students to prepare themselves for the various examinations required of candidates for the Ph.D.

Contact Information

Department of Plant and Microbial Biology

111 Koshland Hall

Phone: 510-642-9999

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Department Chair

Krishna K. Niyogi

371A Koshland Hall

Phone: 510-643-6602

Fax: 510-642-4995

niyogi@berkeley.edu

Associate Chair and Head Graduate Adviser

Pat Zambryski

Phone: 510-643-9203

zambrysk@berkeley.edu

Graduate Program Coordinator

Rocio Sanchez

Phone: 510-642-5167

rocio_s@berkeley.edu

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