New Courses for Spring 2013
From the Secret Life of Plants to Fungi, History and Society, classes in the department are varied and interesting, and taught by world experts in their fields.
Plant and Microbial Biology offers a full slate of undergraduate and graduate courses each semester, packed with information that reflects the ongoing and fast-changing world of plants of all kinds and the fascinating field of microbial biology.
Our courses emphasize hands-on learning and integrate current topics. Our faculty is consistently rated top-notch when it comes to teaching.
We encourage and include the latest applications in bioinformatics and computational biology, and are continually creating new courses that keep pace with the latest scientific developments, and current news and information.
New Courses in Plant & Microbial Biology:
PMB 11 - Fungi, History and Society
|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. No prerequisites.|
PMB 101L - Experimental Plant Biology Lab
The goal of the course is to involve students in ongoing scientific research, providing them the opportunity to apply their theoretical knowledge gained in the Plant Biology curriculum to a current scientific question in plant biology. Under the guidance of the Professor and Graduate Student Instructor, students will work in teams of four. Students will be involved in every aspect of their experimental work including documentation for possible publication. They will also troubleshoot and repeat most experiments to ensure the accuracy and reproducibility of results. Students will learn the theory behind each technique employed and be exposed to alternative approaches. Data analysis and interpretation will be emphasized and there will be progressive instruction on how to present research findings in both oral and written formats.
PMB 142 - Plant Genomics and Bioinformatics
|This course is designed as a companion course to Plantbiology 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.|
PMB 165 - Plant-Microbe Interactions
This upper division course will cover topics in 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.
Spring 2013 Courses:
For more information about PMB undergraduate majors, visit pmb.berkeley.edu/academics/undergraduate-program.
|PMB 13 - Genetic Revolutions||Freeling, Mike||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.|
|PMB 24 - Freshman Seminar||Varies||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 freshman.|
|PMB 40 - The (Secret) Life of Plants||Zambryski, Patricia||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.|
|PMB 98 - Directed Group Study||Varies||Lectures and small group discussions focusing on topics of interest, varying from semester to semester.|
|PMB 99 - Supervised Independent Study and Research||Varies||Lower division independent study and research intended for the academically superior student. Enrollment only with prior approval of faculty advisor directing the research.|
|PMB C103 - Bacterial Pathogenesis||Portnoy, Dan||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. Also listed as Public Health C102 and Molecular and Cell Biology C103.|
|PMB C112L - General Microbiology Laboratory||N/A||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. Also listed as Molecular and Cell Biology C112L.|
|PMB C114 - Introduction to Comparative Virology||Glaunsinger, Britt||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. Also listed as Environ Sci, Policy, and Management C138 and Molecular and Cell Biology C114.|
|PMB 122 - Bioenergy||Melis, Anastasios||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.|
|PMB C134 - Chromosome Biology / Cytogenetics||Cande, W. Zacheus||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. Also listed as Molecular and Cell Biology C134.|
|PMB C144 - Introduction to Protein Informatics||Sjolander, Kimmen||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. Also listed as Bioengineering C144.|
|PMB C144L - Protein Informatics Laboratory||Sjolander, Kimmen||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. Also listed as Bioengineering C144L.|
|PMB C148 - Microbial Genomics and Genetics||Barsky, Daniel||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. Also listed as Molecular and Cell Biology C148.|
|PMB 160 - Plant Molecular Genetics||Fischer, Robert||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.|
|PMB 165 - Plant-Microbe Interactions||Somerville, Shauna||This course will cover topics in plant-microbe interactions reanging from how microbes cause disease to how plants defend themselves.|
|PMB 180 - Environmental Plant Biology||Terry, Norman||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.|
|PMB H196 - Honors Research - Plant and Microbial Biology||Varies||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.|
|PMB 198 - Directed Group Studies in Plant Biology||N/A||Group studies of selected topics.|
|PMB 199 - Supervised Independent Study||N/A||Enrollment restrictions apply; see the Introduction to Courses and Curricula section of this catalog.|
For more information about PMB graduate programs, visit pmb.berkeley.edu/academics/graduate-program. To view a list of the PMB graduate core classes / requirements, visit micro.berkeley.edu/current-students/requirements.
|PMB 200B - Genomics and Computational Biology||Brenner, Steven||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.|
|PMB 200D - Plant Cell Biology||Luan, Sheng||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.|
|PMB 200E - Plant Biochemistry||Scheller, Henrik||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.|
|PMB 210 - Scientific Reasoning and Logic||McCormick, Sheila||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.|
|PMB 220A - Microbial Genetics||N/A||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.|
|PMB 220B - Genomics and Computational Biology||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.|
|PMB 220D - Cell Structure and Function||Komeili, Arash||The students will be provided with both the basic framework and current topics of cell structure and function.|
|PMB 222 - Biochemistry of Biofuels: Concepts and Foundations||Melis, Anastasios||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.|
|PMB 238 - Readings in Environmental Microbiology||Lindow, Steve||Special Topics and Advanced Seminars in Plant Pathology. Seminar/discussion by graduate students of current research in the field of plant pathogenic bacteria.|
|PMB C244 - Introduction to Protein Informatics||Sjolander, Kimmen||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. Also listed as Bioengineering C244.|
|PMB C244L - Protein Informatics Laboratory||Sjolander, Kimmen||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. Also listed as Bioengineering C244L.|
|PMB 290 - Seminar||Somerville, Shauna||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.|
|PMB 298 - Plant Biology Group Studies||Fischer, Robert||Advanced study of research topics which will vary semester to semester. Enrollment in more than one section permitted.|
|PMB 299 - Graduate Research||N/A||Graduate student research.|
|PMB 602 - Individual Study for Graduate Students||N/A||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.|