Plant and Microbial Biology (PLANTBI)
PLANTBI 10 Plants, Agriculture, and Society 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 2 hours of Lecture per week for 15 weeks.
Changing patterns of agriculture in relation to population growth, the biology and social impact of plant disease, genetic engineering of plants: a thousand years of crop improvement and modern biotechnology, interactions between plants and the environment, and effects of human industrial and agricultural activity on plant ecosystems. Knowledge of the physical sciences is neither required nor assumed.
Instructors: Staskawicz, David Zilberman
PLANTBI 11 Fungi, History, and Society 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of lecture, 1 hour of discussion/demonstration, and 3 optional weekend field trips.
Fungi have interacted with humans in both positive and negative ways throughout history. These interactions have included production of foods, medicines, fuels, plant and animal diseases, decay, allergies, and mind-altering drugs.
Instructors: Bruns, Taylor
PLANTBI 13 Genetic Revolutions 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
Genetic discoveries have changed our lives. All are controversial. Especially changed are human physical and mental health, agriculture, social systems, and worldviews. Having many DNA-sequenced genomes, including human, accelerates discovery. This course will study the science, history, and philosophical implications behind past discoveries and will contemplate future genetic revolutions.
Instructor: Freeling
PLANTBI 20 Introduction to the Plant Sciences at Berkeley 1 Unit
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Offered for pass/not pass grade only.
Hours and format: 1 hour of lecture/discussion per week plus field trips.
This course will include discussions on the academic path (courses) needed for the Genetics and Plant Biology major; an introduction to resources and facilities for studies of the plant sciences at Berkeley, such as the University Herbarium and the Botanical Garden; an exploration of plant science related careers, including presentations from guest speakers who work in organic farming, government, and Cooperative Extension; talks by faculty about their current research, and information about how to do research in a lab.
Instructor: Feldman
PLANTBI 22 Microbes Make the World Go Around 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Although often unseen, microbes are everywhere! This course covers the role that microbes, including archaea, bacteria, protists and fungi, play in terrestrial, marine and extreme environments and their effect on the geochemistry of the earth. In addition, we will explore the profound effects of microbes on human and plant health and how microbes have changed the course of human history.
Instructor: Glass
PLANTBI 24 Freshman Seminar 1 Unit
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall and spring
Grading: Offered for pass/not pass grade only.
Hours and format: 1 hour of seminar per week.
Reading and discussion with Plant and Microbial Biology faculty on current research and topics in plant and microbial biology. Topics which may be discussed include microbial biology, plant genetics, plant development, plant pathology, agricultural biotechnology, and genetic engineering. Ideal for students who are considering a major in the Department of Plant and Microbial Biology. Enrollment is limited to 20 freshmen.
PLANTBI 39E Freshman/Sophomore Seminar 2 - 4 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall and spring
Grading: The grading option will be decided by the instructor when the class is offered.
Hours and format: 1 hour of lecture per week per unit.
Freshman and sophomore seminars offer lower division students the opportunity to explore an intellectual topic with a faculty member and a group of peers in a small-seminar setting. These seminars are offered in all campus departments; topics vary from department to department and from semester to semester. Enrollment limits are set by the faculty, but the suggested limit is 25.
Course may be repeated for credit when topic changes. Instructor: Lindow
PLANTBI 40 The (Secret) Life of Plants 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
Covers contemporary topics in plant biology. Examines how plants grow, reproduce, and respond to the environment (e.g., to light) in ways distinct from animals. Presents basic principles of genetics, cell, and molecular biology. Basics of genetic engineering and biotechnology reveal how they are used to modify plants, and these socially relevant issues are assessed. Includes visit to modern plant biology research laboratory, and aspects of plant disease and diversity. Knowledge of the physical sciences neither required nor assumed.
Instructor: Zambryski
PLANTBI 84 Sophomore Seminar 1 or 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall, spring and summer
Grading: The grading option will be decided by the instructor when the class is offered.
Hours and format: 1 hour of seminar per week per unit for 15 weeks. 1 and 1 half hours of seminar per week per unit for 10 weeks. 2 hours of seminar per week per unit for 8 weeks. 3 hours of seminar per week per unit for 5 weeks.
Prerequisites: At discretion of instructor.
Sophomore seminars are small interactive courses offered by faculty members in departments all across the campus. Sophomore seminars offer opportunity for close, regular intellectual contact between faculty members and students in the crucial second year. The topics vary from department to department and semester to semester. Enrollment limited to 15 sophomores.
Course may be repeated for credit as topic varies. Course may be repeated for credit when topic changes.
PLANTBI C96/INTEGBI C96/MCELLBI C96 Studying the Biological Sciences 1 Unit
Department: Plant Biology; Integrative Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Offered for pass/not pass grade only.
Hours and format: 2 hours of Lecture per week for 15 weeks.
Prerequisites: Consent of instructor.
Freshmen will be introduced to the "culture" of the biological sciences, along with an in-depth orientation to the academic life and the culture of the university as they relate to majoring in biology. Students will learn concepts, skills, and information that they can use in their major course, and as future science professionals. Restricted to freshmen in the biology scholars program.
Instructor: Matsui
PLANTBI 98 Directed Group Study 1 - 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall and spring
Grading: Offered for pass/not pass grade only.
Hours and format: 1 to 3 hour of Directed group study per week for 15 weeks.
Lectures and small group discussions focusing on topics of interest, varying from semester to semester.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 99 Supervised Independent Study and Research 1 - 4 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall, spring and summer
Grading: Offered for pass/not pass grade only.
Hours and format: Individual meetings.
Prerequisites: GPA of 3.4 or higher; lower division status.
Lower division independent study and research intended for the academically superior student. Enrollment only with prior approval of faculty advisor directing the research.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 101L Experimental Plant Biology Laboratory 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 6 hours of Laboratory and 1 hour of Discussion per week for 15 weeks.
Prerequisites: Biology 1A-1B; Plant and Microbial Biology 135, 150, and 160 (may be taken concurrently).
Students will perform state-of-the-art research to address an important question in modern plant biology. The experimental progression exposes students to a variety of modern molecular approaches and techniques. Experimental design, data acquisition, and analysis of the student's real experimental data is emphasized. Research results will be presented in written and oral formats similar to those used in research laboratories.
Instructor: Wildermuth
PLANTBI C103/MCELLBI C103/PB HLTH C102 Bacterial Pathogenesis 3 Units
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology; Public Health
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: 100, 102 or consent of instructor.
This course for upper division and graduate students will explore the molecular and cellular basis of microbial pathogenesis. The course will focus on model microbial systems which illustrate mechanisms of pathogenesis. Most of the emphasis will be on bacterial pathogens of mammals, but there will be some discussion of viral and protozoan pathogens. There will be an emphasis on experimental approaches. The course will also include some aspects of bacterial genetics and physiology, immune response to infection, and the cell biology of host-parasite interactions.
Instructor: Portnoy
PLANTBI C107L/INTEGBI C107L Principles of Plant Morphology with Laboratory 3 Units
Department: Plant Biology; Integrative Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 1 hour of lecture and 3 hours of laboratory and 1 hour of discussion per week.
Prerequisites: Biology 1A-1B.
An analysis of the structural diversity of land plants plants with emphasis on the developmental mechanisms responsible for this variation in morphology and the significance of this diversity in relation to adaptation and evolution.
Instructor: Specht
PLANTBI C110L/INTEGBI C110L Biology of Fungi with Laboratory 4 Units
Department: Plant Biology; Integrative Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 2 hours of lecture and 6 hours of laboratory per week. Several field trips are offered, including day trips to a mushroom farm and winery, and a weekend mushroom foray.
Prerequisites: Biology 1B
Selected aspects of fungi: their structure, reproduction, physiology, ecology, genetics and evolution; their role in plant disease, human welfare, and industry. Offered even fall semesters.
Instructors: Bruns, Taylor
PLANTBI C112/MCELLBI C112 General Microbiology 4 Units
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall and summer
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1 hour of Discussion per week for 15 weeks. 4.5 hours of Lecture and 1.5 hours of Discussion per week for 10 weeks.
Prerequisites: Biology 1A and 1B.
This course will explore the molecular bases for physiological and biochemical diversity among members of the two major domains, Bacteria and Archaea. The ecological significance and evolutionary origins of this diversity will be discussed. Molecular, genetic, and structure-function analyses of microbial cell cycles, adaptive responses, metabolic capability, and macromolecular syntheses will be emphasized.
Instructor: Ryan
PLANTBI C112L/MCELLBI C112L General Microbiology Laboratory 2 Units
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall and spring
Grading: Letter grade.
Hours and format: 4 hours of laboratory and 1 hour of discussion per week.
Prerequisites: C112 (may be taken concurrently).
Experimental techniques of microbiology designed to accompany the lecture in C112 and C148. The primary emphasis in the laboratory will be on the cultivation and physiological and genetic characterization of bacteria. Laboratory exercises will include the observation, enrichment, and isolation of bacteria from selected environments.
Instructors: Komeili, Taga
PLANTBI 113 California Mushrooms 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall. Offered alternate odd years.
Grading: Letter grade.
Hours and format: 3 hours of laboratory and 1 hour of discussion per week and 3 weekend overnight field trips.
Prerequisites: Consent of instructor.
This is a hands-on class in identification of macro fungi. Emphasis will be on laboratory work with fresh and dried fungi. Short lectures at the beginning of labs focus on mushroom systematic, collection techniques, and identification. Three weekend field trips are required in addition to the weekly laboratory. Previous course experience with fungi is recommended, but not required. Grades are based on tests and a collection.
Instructor: Bruns
PLANTBI C114/ESPM C138/MCELLBI C114 Introduction to Comparative Virology 4 Units
Department: Plant Biology; Environ Sci, Policy, and Management; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Introductory chemistry (Chemistry 1A or 3A-3B or equivalent) and introductory biology (Biology 1A, 1AL, and 1B or equivalent) and general biochemistry (Molecular and Cell Biology C100A or equivalent--preferably completed but may be taken concurrently).
This course will provide a comparative overview of virus life cycles and strategies viruses use to infect and replicate in hosts. We will discuss virus structure and classification and the molecular basis of viral reproduction, evolution, assembly, and virus-host interactions. Common features used during virus replication and host cellular responses to infection will be covered. Topics also included are common and emerging virus diseases, their control, and factors affecting their spread.
Instructors: Glaunsinger, Jackson
PLANTBI C116/MCELLBI C116 Microbial Diversity 3 Units
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
Prerequisites: Upper-division standing. C112 or consent of instructor and organic chemistry (may be taken concurrently).
This course for upper-division and graduate students will broadly survey myriad types of microbial organisms, both procaryote and eucaryote, using a phylogenetic framework to organize the concept of "biodiversity." Emphasis will be on the evolutionary development of the many biochemical themes, how they mold our biosphere, and the organisms that affect the global biochemistry. Molecular mechanisms that occur in different lineages will be compared and contrasted to illustrate fundamental biological strategies. Graduate students additionally should enroll in C216, Microbial Diversity Workshop.
Formerly known as 116. Instructor: Coates
PLANTBI 120 Biology of Algae 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A-1B; Integrative Biology 101 recommended. Must be taken concurrently with 120L.
General biology of freshwater and marine algae, highlighting current research and integrating phylogeny, ecology, physiology, genetics, and molecular biology.
Instructor: Niyogi
PLANTBI 120L Laboratory for Biology of Algae 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 4 hours of laboratory per week plus field trips.
Prerequisites: Biology 1A-1B; Integrative Biology 101 recommended. Must be taken concurrently with 120.
Laboratories include study of representative types, identification of specimens collected during several field trips, and experiments on development, physiology, and molecular genetics.
Instructor: Niyogi
PLANTBI 122 Bioenergy 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A and 1B; Chemistry 3B.
Offers an assessment of global energy supply and demand, addresses the chemistry of climate change, examines the response of plants and microbes to changes in the environment, and emphasizes the role of biology and photosynthesis in offering solutions to related energy and societal problems. Bioenergy is examined from the point-of-view of potential biofuels, including aspects of the biological generation of hydrogen, hydrocarbons, fatty acids, lipids, and bio-oils, polymers and related materials.
Instructors: Melis, Pauly
PLANTBI C124/BIO ENG C181/CHEM C138/CHM ENG C195A The Berkeley Lectures on Energy: Energy from Biomass 3 Units
Department: Plant Biology; Bioengineering; Chemical & Biomolecular Engineering; Chemistry; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Chemistry 1B or Chemistry 4B, Mathematics 1B, Biology 1A.
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 placed 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-the-art research.
Repeatable when topic changes with consent of instructor. Instructors: Bell, Blanch, Clark, Smit, C. Somerville
PLANTBI C134/MCELLBI C134 Chromosome Biology/Cytogenetics 3 Units
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
Survey of behavior, structure, and function of chromosomes with emphasis on behavior in model organisms. Topics include mitosis, meiosis, chromosome aberrations, genome function, dosage compensation, transposons, repetitive DNA, and modern cytological imaging.
Instructors: Cande, Karpen
PLANTBI 135 Physiology and Biochemistry of Plants 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A-1B.
A study of physiological and biochemical processes in higher plants, including water relations, ion transport, and hormone physiology; photosynthesis (light utilization and carbon assimilation), nitrogen and sulfur metabolism, and plant-specific biosynthetic pathways.
Instructors: Melis, Terry
PLANTBI 142 Plant Genomics and Bioinformatics 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 1 hour of Lecture and 1 hour of Discussion per week for 15 weeks.
Prerequisites: Any lower division biology class. Genetics and Plant Biology majors in the Plant Genetics, Genomics, and Bioinformatics concentration must take this course concurrently with Plant and Microbial Biology C144L in order to receive credit toward the major.
This course is designed as a companion course to Plant and Microbial Biology C144L and will equip students with the minimal skills required to use the main bioinformatics webservers and databases. Each lecture will present one or more webservers or databases and explain how to use that webserver as part of a protein function or structure prediction/analysis.
Instructor: Sjolander
PLANTBI C144/BIO ENG C144 Introduction to Protein Informatics 4 Units
Department: Plant Biology; Bioengineering; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
This course will introduce students to the fundamentals of molecular biology, and to the bioinformatics tools and databases used for the prediction of protein function and structure. It is designed to impart both a theoretical understanding of popular computational methods, as well as some experience with protein sequence analysis methods applied to real data. This class includes no programming, and no programming background is required.
Instructor: Sjolander
PLANTBI C144L/BIO ENG C144L Protein Informatics Laboratory 2 Units
Department: Plant Biology; Bioengineering; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 6 hours of Laboratory per week for 15 weeks.
This course is intended to introduce students to a variety of bioinformatics techniques that are used to predict protein function and structure. It is designed to be taken concurrently with C144 (which provides the theoretical foundations for the methods used in the laboratory class), although students can petition to take this laboratory course separately. No programming is performed in this class, and no prior programming experience is required.
Instructor: Sjolander
PLANTBI C148/MCELLBI C148 Microbial Genomics and Genetics 4 Units
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
Prerequisites: Molecular and Cell Biology C100A/Chemistry C130 or Molecular and Cell Biology 102.
Course emphasizes bacterial and archaeal genetics and comparative genomics. Genetics and genomic methods used to dissect metabolic and development processes in bacteria, archaea, and selected microbial eukaryotes. Genetic mechanisms integrated with genomic information to address integration and diversity of microbial processes. Introduction to the use of computational tools for a comparative analysis of microbial genomes and determining relationships among bacteria, archaea, and microbial eukaryotes.
Formerly known as Plant and Microbial Biology 118. Instructors: Brenner, Glass
PLANTBI 150 Plant Cell Biology 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
Prerequisites: Biology 1A-1B.
An introduction to the structure, dynamics, and function of plant cells: organelle structure and development; intracellular trafficking of small and macromolecules; cellular signaling; cell division and specialization.
Instructors: Luan, Sung
PLANTBI 160 Plant Molecular Genetics 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A-1B.
A consideration of plant genetics and molecular biology. Principles of nuclear and organellar genome structure and function: regulation of gene expression in response to environmental and developmental stimuli; clonal analysis; investigation of the molecular and genetic bases for the exceptional cellular and developmental strategies adopted by plants.
Instructors: Fischer, Fletcher
PLANTBI 165 Plant-Microbe Interactions 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of lecture per week.
Prerequisites: Biology 1A-1B, Statistics 2 or 20 or 131A or Public Health 142. Completion of an upper division plant biology and an upper division microbiology course is recommended.
This course will cover topics in molecular plant-microbe interactions ranging from how microbes cause disease to how plants defend themselves. A second goal of the course is to engage students in state-of-the-art research in the area of plant-microbe interactions.
Instructors: Somerville, Baker, Lewis
PLANTBI 170 Modern Applications of Plant Biotechnology 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A-1B.
This course is designed to introduce students to the principles and applications of modern plant biotechnology. Basic concepts of modern agriculture will be reviewed in light of emerging biotechnology applications. Emphasis will be placed on understanding the tools and strategies involved in optimizing plant productivity.
Instructors: Baker, Somerville
PLANTBI 180 Environmental Plant Biology 2 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A-1B.
An integrated and multidisciplinary approach to the study of interactions between plants and the environment. Introduces physical parameters in the global and micro-environment that affect plant function; and molecular, cellular, and developmental aspects of plant response to suboptimal/adverse conditions. Underlying biochemistry, physiology, and molecular biology of plant adaptation and acclimation mechanisms. Examines consequences of industrial activity on plant growth and productivity.
Instructor: Terry
PLANTBI 185 Techniques in Light Microscopy 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of lecture and 3 hours of laboratory per week.
The course will be a detailed overview of the practice of light microscopy as applied to scientific investigation. The emphasis of the course will be on the correct and appropriate use of the light microscope for biological scientists; however students of other disciplines are welcome. The course will cover optical microscope theory, microscope components and mechanics, and optical techniques including detailed descriptions, demonstrations, and use of all the modern light microscope contrast methods. Students will receive hands-on experience in all microscope and digital imaging techniques via direct instruction and use of instrumentation in the College of Natural Resources Biological Imaging Facility.
Instructor: Ruzin
PLANTBI 190 Special Topics in Plant and Microbial Biology 1 - 4 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall, spring and summer
Grading: Letter grade.
Hours and format: 1 to 4 hour of Lecture per week for 15 weeks. 2.5 to 10 hours of Lecture per week for 6 weeks.
Prerequisites: Upper division standing or consent of instructor.
This class is designed to develop skills in critical analysis of specific plant and/or microbial biology issues. Topics may vary from semester to semester.
Course may be repeated for credit as topic varies. Course may be repeated for credit when topic changes.
PLANTBI H196 Honors Research - Plant and Microbial Biology 4 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall, spring and summer
Grading: Letter grade.
Hours and format: 1 to 4 hour of Independent study per week for 15 weeks. 1.5 to 7.5 hours of Independent study per week for 8 weeks.
Prerequisites: Upper division standing and minimum GPA. See College of Natural Resources Honors website for current minimum GPA. http://nature.berkeley.edu/site/honors_program.php.
Supervised independent honors research specific to aspects of the plant and microbial biology major, followed by an oral presentation and a written report. Honors students must complete two semesters of research.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 198 Directed Group Studies in Plant Biology 1 - 3 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall and spring
Grading: Offered for pass/not pass grade only.
Hours and format: 1 hour of discussion per unit per week.
Prerequisites: Consent of instructor.
Group studies of selected topics.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 199 Supervised Independent Study and Research 1 - 4 Units
Department: Plant and Microbial Biology
Course level: Undergraduate
Terms course may be offered: Fall, spring and summer
Grading: Offered for pass/not pass grade only.
Hours and format: Zero hours of Independent study per week for 15 weeks. 1 to 3 hour of Independent study per week for 8 weeks. 1 to 3 hour of Independent study per week for 6 weeks.
Prerequisites: Consent of instructor; overall GPA of 3.0.
Enrollment restrictions apply; see the Introduction to Courses and Curricula section of this catalog.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 200A Plant Developmental Genetics 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
The students will be provided with both the basic framework and current topics of plant developmental genetics.
Instructor: Hake
PLANTBI 200B Genomics and Computational Biology 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Brenner
PLANTBI 200C Plant Diversity and Evolution 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Specht
PLANTBI 200D Plant Cell Biology 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Luan
PLANTBI 200E Plant Biochemistry 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Scheller
PLANTBI 200F Plant Systems Biology 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
The aim of this course is to highlight the specific hallmarks of systems biology. Students will be informed of the many resources for systems biology available to plant biologists and the recent published work that capitalizes on these resources. Each lecture will focus on fundamental principles followed by discussion of papers that are germane to the topic.
Instructor: Harmon
PLANTBI 201 Faculty Research Review 2 Units
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Consent of instructor.
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
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Consent of instructor.
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 210 Scientific Reasoning and Logic 1 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 1 hour of Lecture per week for 15 weeks.
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.
Instructor: Quail
PLANTBI C216/MCELLBI C216 Microbial Diversity Workshop 1 Unit
Department: Plant Biology; Molecular and Cell Biology; Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 1 hour of Workshop and 1 hour of Discussion per week for 15 weeks.
Prerequisites: Graduate standing; C112 or consent of instructor and organic chemistry (may be taken concurrently).
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.
Instructor: Coates
PLANTBI 220A Microbial Genetics 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Taga
PLANTBI 220B Genomics and Computational Biology 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Brenner
PLANTBI 220C Microbial Diversity and Evolution 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
The students will be provided with both the basic framework and current topics of microbial diversity and evolution.
Instructor: Taylor
PLANTBI 220D Cell Structure and Function 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
The students will be provided with both the basic framework and current topics of cell structure and function.
Instructor: Komeili
PLANTBI 220E Microbial Physiology 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
The students will be provided with both the basic framework and current topics of microbial physiology.
Instructor: Coates
PLANTBI 220F Microbial Ecology 1.5 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1.5 hours of Discussion per week for 5 weeks.
Prerequisites: Consent of instructor.
The students will be provided with both the basic framework and current topics of microbial ecology.
Instructor: Lindow
PLANTBI 222 Biochemistry of Biofuels: Concepts and Foundations 1 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 1 hour of Lecture per week for 15 weeks.
Prerequisites: Consent of instructor.
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.
Instructor: Melis
PLANTBI C224/BIO ENG C281/CHEM C238/CHM ENG C295A The Berkeley Lectures on Energy: Energy from Biomass 3 Units
Department: Plant Biology; Bioengineering; Chemical & Biomolecular Engineering; Chemistry; Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture per week for 15 weeks.
Prerequisites: Biology 1A; Chemistry 1B or 4B, Mathematics 1B.
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.
Repeatable when topic changes with consent of instructor. Instructors: Bell, Blanch, Clark, Smit, C. Somerville
PLANTBI 238 Readings in Environmental Microbiology 1 Unit
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: 1 hour of Discussion per week for 15 weeks.
Prerequisites: Consent of instructor.
Special Topics and Advanced Seminars in Plant Pathology. Seminar/discussion by graduate students of current research in the field of plant pathogenic bacteria.
Course may be repeated for credit. Course may be repeated for credit when topic changes. Formerly known as Environmental Science, Policy, and Management 238A. Instructor: Lindow
PLANTBI C244/BIO ENG C244 Introduction to Protein Informatics 4 Units
Department: Plant Biology; Bioengineering; Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 3 hours of Lecture and 1 hour of Discussion per week for 15 weeks.
This course will introduce students to the fundamentals of molecular biology, and to the bioinformatics tools and databases used for the prediction of protein function and structure. It is designed to impart both a theoretical understanding of popular computational methods, as well as some experience with protein sequence analysis methods applied to real data. This class includes no programming, and no programming background required.
Instructor: Sjolander
PLANTBI C244L/BIO ENG C244L Protein Informatics Laboratory 2 Units
Department: Plant Biology; Bioengineering; Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Fall
Grading: Letter grade.
Hours and format: 6 hours of Laboratory per week for 15 weeks.
This course is intended to introduce students to a variety of bioinformatics techniques that are used to predict protein function and structure. It is designed to be taken concurrently with C244 (which provides the theoretical foundations for the methods used in the laboratory class), although students can petition to take this laboratory course separately. No programming is performed in this class, and no prior programming experience is required.
Instructor: Sjolander
PLANTBI 290 Seminar 1 - 2 Units
Department: Plant and Microbial Biology
Course level: Graduate
Terms course may be offered: Fall and spring
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: 1 to 2 hour of Seminar per week for 15 weeks.
Prerequisites: Consent of instructor.
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.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 296 Graduate Supervised Independent Study 1 - 12 Units
Department: Plant and Microbial Biology
Course level: Graduate
Terms course may be offered: Fall, spring and summer
Grading: Letter grade.
Hours and format: 3 hours of independent study per week per unit.
Prerequisites: Graduate standing.
Graduate student independent study under the supervision of a faculty member. Sections are operated independently and directed toward different topics.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 297 Grant Writing and Research Presentations 2 Units
Department: Plant and Microbial Biology
Course level: Graduate
Term course may be offered: Spring
Grading: Letter grade.
Hours and format: 2 hours of Lecture per week for 15 weeks.
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.
Instructor: McCormick
PLANTBI 298 Plant Biology Group Studies 1 - 6 Units
Department: Plant and Microbial Biology
Course level: Graduate
Terms course may be offered: Fall and spring
Grading: The grading option will be decided by the instructor when the class is offered.
Hours and format: 1 hour of lecture/discussion per week per unit.
Prerequisites: Consent of instructor.
Advanced study of research topics which will vary semester to semester. Enrollment in more than one section permitted.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 299 Graduate Research 1 - 12 Units
Department: Plant and Microbial Biology
Course level: Graduate
Terms course may be offered: Fall, spring and summer
Grading: Letter grade.
Hours and format: 3 hours of research/laboratory per week per unit.
Prerequisites: Graduate standing.
Graduate student research.
Course may be repeated for credit. Course may be repeated for credit when topic changes.
PLANTBI 300 Workshop on Teaching 2 Units
Department: Plant and Microbial Biology
Course level: Professional course for teachers or prospective teachers
Term course may be offered: Spring
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: 2 hours of lecture/discussion per week.
Prerequisites: Graduate student status.
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.
Course may be repeated for a maximum of 4 units.Course may be repeated for a maximum of 4 units.
PLANTBI 602 Individual Study for Graduate Students 1 - 8 Units
Department: Plant and Microbial Biology
Course level: Graduate examination preparation
Terms course may be offered: Fall, spring and summer
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: 1 1-hour meeting per week.
Prerequisites: Graduate standing.
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.
Course may be repeated for credit. Course may be repeated for credit when topic changes. Course does not satisfy unit or residence requirements for doctoral degree.
PLANTBI S602 Individual Study for Graduate Students 1 - 6 Units
Department: Plant and Microbial Biology
Course level: Graduate examination preparation
Term course may be offered: Summer
Grading: Offered for satisfactory/unsatisfactory grade only.
Hours and format: Zero hours of Independent study per week for 8 weeks.
Prerequisites: Graduate standing.
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.
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