Plant and Microbial Biology (PLANTBI)

This is an archived copy of the 2014-15 guide. To access the most recent version of the guide, please visit http://guide.berkeley.edu/.

Courses

PLANTBI 10 Plants, Agriculture, and Society 2 Units

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.

PLANTBI 11 Fungi, History, and Society 3 Units

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.

PLANTBI 20 Introduction to the Plant Sciences at Berkeley 1 Unit

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.

PLANTBI 22 Microbes Make the World Go Around 2 Units

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.

PLANTBI 24 Freshman Seminar 1 Unit

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

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.

PLANTBI 40 The (Secret) Life of Plants 3 Units

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.

PLANTBI 84 Sophomore Seminar 1 or 2 Units

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.

PLANTBI C96 Studying the Biological Sciences 1 Unit

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.

PLANTBI 98 Directed Group Study 1 - 3 Units

Lectures and small group discussions focusing on topics of interest, varying from semester to semester.

PLANTBI 99 Supervised Independent Study and Research 1 - 4 Units

Lower division independent study and research intended for the academically superior student. Enrollment only with prior approval of faculty advisor directing the research.

PLANTBI 101L Experimental Plant Biology Laboratory 3 Units

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.

PLANTBI C103 Bacterial Pathogenesis 3 Units

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.

PLANTBI C107L Principles of Plant Morphology with Laboratory 4 Units

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.

PLANTBI C110L Biology of Fungi with Laboratory 4 Units

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.

PLANTBI C112 General Microbiology 4 Units

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.

PLANTBI C112L General Microbiology Laboratory 2 Units

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.

PLANTBI 113 California Mushrooms 3 Units

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.

PLANTBI C114 Introduction to Comparative Virology 4 Units

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.

PLANTBI C116 Microbial Diversity 3 Units

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.

PLANTBI 120 Biology of Algae 2 Units

General biology of freshwater and marine algae, highlighting current research and integrating phylogeny, ecology, physiology, genetics, and molecular biology.

PLANTBI 120L Laboratory for Biology of Algae 2 Units

Laboratories include study of representative types, identification of specimens collected during several field trips, and experiments on development, physiology, and molecular genetics.

PLANTBI 122 Bioenergy 2 Units

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.

PLANTBI C124 The Berkeley Lectures on Energy: Energy from Biomass 3 Units

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.

PLANTBI C134 Chromosome Biology/Cytogenetics 3 Units

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.

PLANTBI 135 Physiology and Biochemistry of Plants 3 Units

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.

PLANTBI 142 Plant Genomics and Bioinformatics 2 Units

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.

PLANTBI C144 Introduction to Protein Informatics 4 Units

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.

PLANTBI C144L Protein Informatics Laboratory 3 Units

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.

PLANTBI C148 Microbial Genomics and Genetics 4 Units

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.

PLANTBI 150 Plant Cell Biology 3 Units

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.

PLANTBI 160 Plant Molecular Genetics 3 Units

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.

PLANTBI 165 Plant-Microbe Interactions 3 Units

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.

PLANTBI 170 Modern Applications of Plant Biotechnology 2 Units

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.

PLANTBI 180 Environmental Plant Biology 2 Units

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.

PLANTBI 185 Techniques in Light Microscopy 3 Units


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.

PLANTBI 190 Special Topics in Plant and Microbial Biology 1 - 4 Units

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.

PLANTBI C192 Molecular Approaches to Environmental Problem Solving 2 Units

Seminar in which students consider how modern biotechnological approaches, including recombinant DNA methods, can be used to recognize and solve problems in the area of conservation, habitat and endangered species preservation, agriculture and environmental pollution. Students will also develop and present case studies of environmental problems solving using modern molecular methods.

PLANTBI H196 Honors Research - Plant and Microbial Biology 4 Units

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.

PLANTBI 198 Directed Group Studies in Plant Biology 1 - 3 Units

Group studies of selected topics.

PLANTBI 199 Supervised Independent Study and Research 1 - 4 Units

Enrollment restrictions apply; see the Introduction to Courses and Curricula section of this catalog.

PLANTBI 200A Plant Developmental Genetics 1.5 Unit

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

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

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

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

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 Systems Biology 1.5 Unit

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.

PLANTBI 201 Faculty Research Review 2 Units

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

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

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

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

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

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

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

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

The students will be provided with both the basic framework and current topics of microbial physiology.

PLANTBI 220F Microbial Ecology 1.5 Unit

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

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

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

Special Topics and Advanced Seminars in Plant Pathology. Seminar/discussion by graduate students of current research in the field of plant pathogenic bacteria.

PLANTBI C244 Introduction to Protein Informatics 4 Units

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.

PLANTBI C244L Protein Informatics Laboratory 3 Units

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.

PLANTBI 290 Seminar 1 - 2 Units

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 296 Graduate Supervised Independent Study 1 - 12 Units

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

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

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

Graduate student research.

PLANTBI 375 Workshop on Teaching 2 Units

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 - 8 Units

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.

PLANTBI S602 Individual Study for Graduate Students 1 - 6 Units

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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