Course Offerings in Plant Biology at Stanford


BIO 161
Molecular Basis of Biological Communication
Across molecular, cellular, organismal and communal biological scales, communication among elements of a system is required for its function. The molecules and logic at the heart of communication at levels from the interactions between cells in a developing body to how organisms perceive and respond to their physical environment and the organisms around them; how these systems normally work and how failures in communication result in and from disease. Current research literature.
Prerequisites: BIO 41, 42.
Recommended: BIO 160A, 129A.
4 units, Spr (Bergmann), alternate years, next offered 2011
BIO 200
Advanced Molecular Biology (BIO 104) 
Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Satisfies Central Menu Area 1.
Prerequisite: Biology core.
5 units, Win (Frydman, Gozani)
BIO 203
Advanced Genetics (DBIO 203, GENE 203) 
For graduate students in Bioscience programs; may be appropriate for graduate students in other programs. The genetic toolbox. Examples of analytic methods, genetic manipulation, genome analysis, and human genetics. Emphasis is on use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. Faculty-led discussion sections with evaluation of papers. Students with minimal experience in genetics should prepare by working out problems in college level textbooks.
4 units, Aut (Kim, Sidow, Stearns)
BIO 207
Life and Death of Proteins 
How proteins are made and degraded in the cell. Discussion of primary literature. Case studies follow the evolution of scientific ideas, and evaluate how different experimental approaches contribute to our understanding of a biological problem. Emphasis on multidisciplinary approaches. Topics: protein folding and assembly, mechanisms of chaperone action, sorting into organelles, misfolding and disease, and the ubiquitin-proteasome pathway. Enrollment limited to 30.
3 units, Win (Frydman)
DBIO 210
Developmental Biology
Current areas of research in developmental biology. How organismic complexity is generated during embryonic and post-embryonic development. The roles of genetic networks, induction events, cell lineage, maternal inheritance, cell-cell communication, and hormonal control in developmental processes in well-studied organisms such as vertebrates, insects, and nematodes. Team-taught. Students meet with faculty to discuss current papers from the literature. Prerequisite: graduate standing, consent of instructor. Recommended: familiarity with basic techniques and experimental rationales of molecular biology, biochemistry, and genetics.
5 units, Spr (Nusse, Villeneuve)
GENE 211
Genome evolution, organization, and function; technical, computational, and experimental approaches; hands-on experience with representative computational tools used in genome science; and a beginning working knowledge of PERL.
3 units, Win (Cherry, Sherlock)
BIOC 218
Computational Molecular Biology (BIOMEDIN 231)
For molecular biologists and computer scientists. Representation and analysis of genomes, sequences, and proteins. Strengths and limitations of existing methods. Course work performed on web or using downloadable applications. See Prerequisites: introductory molecular biology course at level of BIOSCI 41 or consent of instructor. All offerings are via internet only.
3 units, Aut, Win, Spr (Brutlag)
GENE 218
Computational Analysis of Biological Images (PATH 218)
Physical and computational tools for acquisition, processing, interpretation, and archiving of biological images. Emphasis is on digital microscopy.
2 units, Spr (Fire)
BIO 224
Advanced Cell Biology (BIO 214, MCP 221) 
For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, compartmentalization, transport and trafficking, motility and adhesion, differentiation, and multicellularity. Current papers from the primary literature.
Prerequisite for advanced undergraduates: BIO 129A,B, and consent of instructor.
2-5 units, Win (Kopito, Nachury, Pfeffer, Straight, Theriot)
BIO 232
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIOPHYS 232, MCP 232)
Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, and optical trapping. Limited enrollment.
Recommended: basic physics, Biology core or equivalent, and consent of instructor.
4 units, Spr (Block, Smith, Stearns)
GENE 233
The Biology of Small Modulatory RNAs (MI 233, PATH 233)
Open to graduate and medical students. How recent discoveries of miRNA, RNA interference, and short interfering RNAs reveal potentially widespread gene regulatory mechanisms mediated by small modulatory RNAs during animal and plant development. Required paper proposing novel research.
2 units, Aut (Chen, Fire)
BIO 237
Plant Genetics and Genetics Laboratory (1 extra unit) (BIO 137)
Offered in alternate years for graduate students and advanced undergraduates. This course covers methods of genetic analysis of particular importance in maize and Arabidopsis, two model plant species, and current understanding of key processes in plants as elucidated through genetics.   The laboratory focuses on dahlia plants and the regulation of anthocyanin pigmentation in leaves, stems, and flowers as manipulated in genetic stocks and by environmental factors (light quantity and quality, temperature, metal ion availability).  Lecture and discussion topics include review of Mendelian genetics in elucidating regulatory gene structure and function, molecular mapping, role of gene duplications, impact of transposons on gene structure, chromosome translocation stocks, plastid and mitochondrial genetics, nuclear - cytoplasmic interaction, self-incompatibility, generation and analysis of transgenic plants, imprinting, paramutation, and transcriptional and post-transcriptional gene silencing. Case studies will include genetic analysis of meristem organization and function, epidermal specializations, leaf development, and root growth.
Prerequisite: Bio core or permission of the instructors.  No exams:  a midterm paper, final paper, problem sets, and discussion sections are graded. Graduate students enroll in Biology 237. 
3 units, Spr (Walbot)
BIOC 241
Biological Macromolecules (BIOPHYS 241, SBIO 241) 
The physical and chemical basis of macromolecular function. Forces that stabilize biopolymers with three-dimensional structures and their functional implications. Thermodynamics, molecular forces, structure and kinetics of enzymatic and diffusional processes, and relationship to their practical application in experimental design and interpretation. Biological function and the level of individual molecular interactions and at the level of complex processes. Case studies in lecture and discussion of classic and current literature. Enrollment limited to 40. Prerequisites: None; background in biochemistry and physical chemistry preferred but material available for those with deficiency; undergraduates with consent of instructor only.
3-5 units, Aut (Block, Ferrell, Garcia, Herschlag, Puglisi, Weis)
BIO 244
Fundamentals of Molecular Evolution (BIO 113) 
The inference of key molecular evolutionary processes from DNA and protein sequences. Topics include random genetic drift, coalescent models, effects and tests of natural selection, combined effects of linkage and natural selection, codon bias and genome evolution. Satisfies Central Menu Areas 1 or 4.
Prerequisites: Biology core or graduate standing in any department, and consent of instructor.
4 units, Spr (Petrov) 
MCP 256
How Cells Work: Energetics, Compartments, and Coupling in Cell Biology (MCP 156)
Open to graduate and medical students, and advanced undergraduates. Dynamic aspects of cell behavior and function, including cellular energetics, homeostasis, heterogeneity of membranes, structure and function of organelles, solute and water transport, signaling and motility. Emphasis is on the principles of how coupling of molecular processes gives rise to essential functions at the cellular level. Mathematical models of cell function. Student presentations.
4 units, Aut (Goodman, Maduke)
BIO 257
Biochemistry and Molecular Biology of Plants (BIO 157)
Biochemical and molecular basis of plant growth and adaptation. Topics include: hormone signal transduction; photoreceptor chemistry and signaling; metabolite sensing and transport; dynamics of photosynthesis; plant innate immunity and symbiosis. Lectures and readings will emphasize research methods. Prerequisite: Biology core or equivalent, or consent of instructor.
3-4 units, Spr (Mudgett), alternate years, next offered 2011 
BIO 277
Plant Microbe Interaction (BIO 177)
Molecular basis of plant symbiosis and pathogenesis. Topics include mechanisms of recognition and signaling between microbes and plant hosts, with examples such as the role of small molecules, secreted peptides, and signal transduction pathways in symbiotic or pathogenic interactions. Readings include landmark papers together with readings in the contemporary literature. Prerequisites: Biology core and two or more upper division courses in genetics, molecular biology, or biochemistry. Recommended: plant genetics or plant biochemistry.
3 units, Spr (Long, Mudgett), alternate years, next offered 2012
CSB 278
Systems Biology (BIOE 310, CS 278)
Experimental and computational approaches to the dissection of complex biologcal systems. Topics include network structure, non-linear dynamics, numerical modeling approaches, noise, and robustness. Topics are introduced in the context of recent papers from the primary literature.
4 units, Win (Ferrell)
BIO 301
Frontiers in Biology 
Limited to and required of first-year Ph.D. students in molecular, cellular, and developmental biology. Current research in molecular, cellular, and developmental biology emphasizing primary research literature. Held in conjunction with the department's Monday seminar series. Students and faculty meet weekly before the seminar for a student presentation and discussion of upcoming papers.
1-3 units, Aut, Win (Morrison, Skotheim)
Plant Biology Seminar
Hot topics in plant biology are presented in the Carnegie Institution weekly seminar, Fridays at 4 pm at 260 Panama Street.  Seminars are a mix of outside guests and local speakers.  Typical topics include photobiology, hormone signaling pathways, plant-pathogen interaction, development, plant genome structure and evolution, and systems biology.  Participation at 3 units requires writing a 10 page term paper.
1-3 units, Aut., Win. or Spr. (Walbot). 
BIO 459
Frontiers in Interdisciplinary Biosciences (BIOC 459, BIOE 459, CHEM 459, CHEMENG 459, PSYCH 459) 
Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See
Recommended: basic mathematics, biology, chemistry, and physics.
1 unit, Aut, Win, Spr (Robertson)