Course Descriptions

BE/RNR 613 - Applied Biostatistics
Typically offered: Fall; 4 units

Online:
No online sections
BIOC 565 - Proteins and Enzymes
Typically offered: Fall; 3 units
Advanced consideration of enzyme structure and function.

Online:
No online sections
BIOC 585 - Biological Structure I
Typically offered: Spring; 4 units
Introduction to the current understanding and methods used for study of the structure, thermodynamics, and dynamics of proteins, nucleic acids, and membranes.

Online:
No online sections
ECOL 518 - Spatio-Temporal Ecology
Typically offered: Fall; 2 units
Population growth and species interactions in spatially and temporally varying environments. Meta populations and communities. The scale transition, the storage effect, nonlinear competitive variance, fitness-density covariance, disturbance, competition-colonization tradeoffs. Graduate-level requirements include the additional challenge of including less assistive text, as these students are expected to possess a broader knowledge base.

Online:
No online sections
ECOL 526 - Population Genetics
Typically offered: Spring; 3 units
General introductory course on empirical and theoretical population genetics. It will involve two weekly lectures, weekly problem sets, and regular readings from the primary literature. A major goal of this course is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. As much as any field of biology, population genetics has been divided into a theoretical and an empirical branch. However, these two bodies of knowledge are intimately related and this course will cover both in roughly equal amounts. We will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision), methods of measuring genetic variation in nature, and experimental tests of important ideas in population genetics. The course will also cover a few more specialized topics such as transposable elements, the evolution of multigene families, and molecular clocks. Graduate-level requirements include additional exam questions, additional readings from the literature, and presentation of a 15 minute overview and synthesis of a specialized topic in population genetics.

Online:
No online sections
ECOL 553 - Functional and Evolutionary Genomics
Typically offered: Fall; 4 units
Computational, functional, and evolutionary approaches to genomics, including bioinformatics and laboratory methods relevant to many modern research approaches in biology. Graduate-level requirements include students completing independently designed lab exercises and relate these to the primary literature in a paper. Undergraduate students will only complete defined lab exercises.

Online:
No online sections
ECOL 565 - Phylogenetic Biology
Typically offered: Spring; 3 units
Concepts in phylogenetic biology, focusing on the phylogenetic (evolutionary) tree of species. The form of the tree, character evolution, speciation, and gene trees. Graduate-level requirements include a more in-depth term paper.

Online:
No online sections
ECOL 572 - Systematic Botany
Typically offered: Spring; 4 units
Evolutionary relationships and characteristics of seed plants: systems of classification; acquisition of skills to identify members of almost 50 families, collection and identification of local flora. Graduate-level requirements include study of additional plant families and increased depth regarding class project.

Online:
No online sections
ECOL 575 - Freshwater and Marine Algae
Typically offered: Spring; 4 units
Systematics, ecology, and evolution of planktonic and benthic species; field techniques and lab culture. Graduate-level requirements include a special topic report on an aspect of freshwater algae.

Online:
No online sections
ECOL 579 - Art of Scientific Discovery
Typically offered: Fall; 3 units
Techniques of posing questions and solving puzzles encountered in scientific research, with emphasis on life sciences and mathematics. Graduate-level requirements include use of all techniques in a semester-long research project and final paper.

Online:
No online sections
ECOL 600A - Fundamentals of Evolution
Typically offered: Spring; 3 units
The fundamentals of modern Evolutionary Biology, including molecular evolution, phylogenetics, macroevolution, and population/quantitative genetics.

Online:
No online sections
EVNS 502 - Nutrient Dynamics in Soil
Typically offered: Spring; 3 units

Online:
No online sections
EVNS 520 - Environmental Physics
Typically offered: Fall; 3 units

Online:
No online sections
MCB 546 - Genetic and Molecular Networks
Typically offered: Spring; 4 units
This course will explore the logic of genetics by discussion of primary literature papers focusing on model systems.

Online:
No online sections
MCB 573 - Recombinant DNA Methods and Applications
Typically offered: Fall, Spring; 4 units
Relevant techniques for the isolation, purification, and cloning of genes in E. Coli hosts. Eukaryotic lambda genomic DNA clones will be characterized by restriction mapping, hybridization analysis, and sequence analysis. Graduate-level requirements include a one hour discussion section of classic and recent papers featuring major advances in molecular biology or their application to current issues or problems.

Online:
No online sections
MCB 580 - Introduction to Systems Biology
Typically offered: Fall; 3 units
The proteins in a cell are organized into networks and circuits that act to process information and control cell activity. In this course we will explore the structure and function of these circuits through discussion of the relevant literature and by building and testing mathematical models of simple/toy circuits. Emphasis will be placed on key concepts such as hysteresis, ultrasensitivity, adaptation, robustness and noise propagation. Graduate-level requirements include more complex independent projects and a formal presentation to the class.

Online:
No online sections
MCB 572A - Cell Systems
Typically offered: Fall; 4 units
Advanced treatment of regulation of basic cellular processes in both single-celled and multicellular eukaryotic organisms. Focus on experimental research aimed at understanding cellular networks and circuitry, as well as their evolution. An introduction to modeling cell systems will be embedded within the context of the course. This is primarily a discussion-based, student-led course.

Online:
No online sections
MCB 575 - Scientific Communication
Typically offered: Fall; 3 units

Online:
No online sections
MCB 577 - Principles of Cell Biology
Typically offered: Fall; 3 units

Online:
No online sections
MCB 579 - Art of Scientific Discovery
Typically offered: Fall; 3 units

Online:
No online sections
MCB 582 - Frontiers in Biological and Biomedical Research
Typically offered: Spring; 3 units

Online:
No online sections
PLP 546 - Insect Pathogens: Biocontrol Agents & Biological Models
Typically offered: Spring; 4 units
Ecology and biology of insect pathogens (viruses, bacteria, protozoa, nematodes). Diagnostics, safety testing of pathogens. Genomics and genetic engineering of entomopathogens. Insect pathogens as biological model organisms. Applications in medical and veterinary research and pharmaceutical bioprospecting. Graduate-level requirements include students to prepare and give one oral presentation of a specific topic that will be coordinated with the instructor at the beginning of the course. Topics considered in the oral presentations will be included in the final exam.

Online:
No online sections
PLP 550 - Principles of Plant Microbiology
Typically offered: Spring; 4 units
[Taught alternate years beginning Fall 2002] . This course deals with the mechanisms that plants and associated microorganisms use to establish detrimental or beneficial relationships from the molecular level to the population level. Classical and contemporary research are used extensively to evaluate contemporary and emerging theories.

Online:
Online section offered
PLP 575 - Advanced Mycology
Typically offered: Spring; 3 units
Biology of fungi, including morphology, physiology, systematics, genetics, ecological significance, and economic importance; emphasis on plant pathogens and environmentally essential fungi.

Online:
No online sections
PLP 527 - General Mycology
Typically offered: Fall; 3 units
An exploration of the diversity of fungi and fungus like organisms covering general biology and roles as pathogens (of humans and plants), saprobes and symbionts. Fungi as models for eukaryotic molecular research and their uses in industry will be covered. Graduate-level requirements include a term paper 10 pages in length to allow a more in depth exploration of a topic in fungal biology. Also required is a 30 minute oral presentation on a topic of choice for 100 points of grade.

Online:
Online section offered
PLP 528L - Microbial Genetics (Laboratory)
Typically offered: Spring; 2 units
Laboratory associated with lecture course on Prokaryotic gene structure and function; methods of gene transfer and mapping, DNA structure, replication, transcription, and translation. Hands-on computer analysis of DNA sequences and gene cloning strategies. Graduate-level requirements include the DNA sequence of an entire operon from any one of a variety of bacteria and additionally analyze one product from the operon using several GCG protein analysis programs. Also extra exam questions.

Online:
No online sections
PLP 528R - Microbial Genetics (Lecture)
Typically offered: Spring; 3 units
Prokaryotic gene structure and function; methods of gene transfer and mapping, DNA structure, replication, transcription, and translation. Hands-on computer analysis of DNA sequences and gene cloning strategies. Principles of regulation of gene expression. Graduate-level requirements include a DNA sequence of an entire operon from any one of a variety of bacteria and additionally analyze one product from the operon using several GCG protein analysis programs plus an extensive exam.

Online:
Online section offered
PLP 611 - Comparative Virology
Typically offered: Fall; 3 units
A comprehensive course covering broad-ranging aspects of modern virology with an emphasis on comparisons between representative virus groups, taking into account different host, tissue, cell, and vector tropisms, and modes of transmission. The team of instructors will highlight representative types of viruses across different life forms to encourage and illuminate inter-group comparisons in discussion sessions lead by the graduate students.

Online:
No online sections
PLP/PLS 596A - School of Plant Sciences Seminar
Typically offered: Fall, Spring; 1 units

Online:
No online sections
PLS 539 - Methods in Cell Biology and Genomics
Typically offered: Fall; 3 units
In-depth, practical and theoretical analysis of novel, experimental methods that advance our understanding of modern biology.

Online:
No online sections
PLS 560 - Advanced Plant Biology
Typically offered: Fall; 4 units
This course will build on your fundamental knowledge in the fields of plant biology, genetics, molecular biology, and biochemistry to enable you to gain a better understanding of the processes regulating plant growth and development and how these processes change during plant interactions with the environment and with other organisms. Information will be presented through lectures, review of the primary literature, and classroom discussions. An equally important goal will be to foster development of the skills needed to critically evaluate the primary research literature and effectively communicate scientific concepts orally and in writing. Successful completion of the course will lead to a better understanding of the concepts that underlie modern research in the field of plant signaling and will prepare you for more advanced courses and for conducting graduate research.

Online:
No online sections
PLS 583 - Controlled Environment Systems
Typically offered: Fall; 3 units
An introduction to the technical aspects of greenhouse design, environmental control, hydroponic crop production, plant nutrient delivery systems, intensive field production systems, and post-harvest handling and storage of crops. Graduate-level requirements include submission of a comprehensive report related to a specific greenhouse design project.

Online:
No online sections
PLS 472/572 - Plant Systematics
Typically offered: Spring; 4 units
This course is designed to introduce graduate and advanced undergraduate students to the field of plant systematics. Central concepts in systematic biology will be covered, as will a more detailed survey of selected lineages, with emphasis on the flowering plants. Phylogenetic history will provide the organizing theme as we study plant diversity and the evolutionary origins of traits. Goals of the course are to learn and understand: • Systematics — fundamental concepts and techniques of systematic biology, especially as applied to plants, including phylogenetic systematics, botanical nomenclature, and the role of systematics in other fields of plant biology; • Evolution — major processes and events in the history of angiosperm evolution, including speciation, polyploidy, vicariance, and co-evolution; • Diversity — macro- and micro-morphological characteristics and diagnostic traits of major clades in the angiosperms, including floral, fruit, and vegetative features; • Identification — terminology and tools needed for identifying plants from the field, including the use of literature, keys, and online resources.

Online:
No online sections
PLS 524R - Plant Biotechnology
Typically offered: Spring; 3 units
This course is designed for graduate students who are interested in strengthening their knowledge of the techniques involved in developing superior food, feed and fiber crops.

Online:
No online sections
PLS 539 - Methods in Cell Biology and Genomics
Typically offered: Fall; 3 units
This course is designed to provide students with an in‐depth understanding of selected experimental methods that are currently employed in addressing questions in cell biology, genomics, and biotechnology. The course will be taught as formal lectures, accompanied by occasional visits to laboratories and core facilities. The course may also involve guest lectures.

Online:
Online section offered
PLS 540 - Mechanisms in Plant Development
Typically offered: Fall; 3 units
Focuses on the molecular genetic mechanisms of plant development using primarily the current model systems. Graduate-level requirements include seven journal club discussions and presentations for graduate students and honors undergraduate students.

Online:
No online sections
PLS 548A - Plant Biochemistry and Metabolic Engineering
Typically offered: Fall; 3 units
This course covers biochemical processes specific to plants and is aimed to allow students to gain an understanding and appreciation of how biochemical components are synthesized and utilized by plants during growth and development and in their interactions with their environment, as well as how these processes can be manipulated. This course includes topics in photosynthesis, carbohydrate, nitrogen, and lipid metabolism, specialized metabolism, and plant metabolic engineering.

Online:
No online sections
PLS 556 - Topics in Biotechnology
Typically offered: Spring; 3 units
This course is designed to help you develop a deeper understanding of a variety of current topics in Biotechnology including GMOs, Stem Cells, Designer Babies, Synthetic Biology, Nanobiotechnology, Cancer Biology, Epigenetics, Vaccines, Antibiotics, Immunotherapy, Aging, Cloning and Gene Editing. Graduate-level requirements include leading discussions, organizing undergraduates, a paper on one of our subject areas and organizing tours of appropriate laboratories that do research on one of our subject areas.

Online:
No online sections
PLS 558 - Plant Molecular Biology
Typically offered: Fall; 3 units
A consideration of the molecular-genetic and cellular biology of growth and development in plants and their response to biotic and abiotic stresses, with a primary focus on processes unique to plants. Experimental approaches will be emphasized. Graduate level course grades will be based on three paper presentations in addition to undergraduate requirements.

Online:
No online sections
PLS 560 - Advanced Plant Biology
Typically offered: Fall; 4 units
Advanced, graduate-level treatment of current understanding of development, metabolism, response to environmental signals and stress, interactions with other organisms, and plant origins and crop domestication.

Online:
Online section offered
PLS 575A - Physiology of Plant Production under Controlled Environment
Typically offered: Spring; 3 units
Students will learn the major environmental factors affecting plant growth and development and will understand interactions between plants and their microenvironments, including light penetration and CO2/H2O diffusion. Students will learn energy and mass balance of leaves and canopy and correlate these phenomena with plant productivity and related plant physiological mechanisms. Lectures cover critical controlled environment issues and practices of plant production in greenhouse, plant production factory, tissue culture vessels and post-harvest storage, with an introduction to the current research status in these areas. This course will be offered in spring of even years. Graduate-level requirements include a research paper on a specific topic within plant physiology under controlled environment. The paper should be a critical review of the current literature on the topic chosen.

Online:
No online sections
PLS 579 - Applied Instrumentation for Controlled Environment Agriculture
Typically offered: Spring; 3 units
Students will learn principles, methods, and techniques related to the measurement and control of environmental factors affecting plant growth and plants¿ surrounding climate under controlled environments. Light intensity, light quality, temperature (air, plant), relative humidity, carbon dioxide, water, air current, and related factors are important variables in controlled environment plant production systems to measure and control since they affect and determine plant growth and development and processes such as heating, ventilating and air conditioning, fertigation etc. Therefore, students will learn application of sensors, instrumentation and designing of a simple system to measure and control environments for plant production systems. Graduate-level requirements include higher grading percentages for midterm, design project, and final exams.

Online:
No online sections
PLS 580 - Medicinal Plants
Typically offered: Fall; 3 units
Historical and cultural aspects of plants and medicine, therapeutic uses of plants, psychoactive and food plants, contribution of medicinal plants to modern medicine, future of medicinal plants. Graduate-level requirements include review of at least two leading papers in the field. Taught every other Fall semester (even years).

Online:
No online sections
PLS 695A - Plant Sciences Journal Club
Typically offered: Spring; 1 units

Online:
No online sections
STAT 571B - Design of Experiments
Typically offered: Spring; 3 units

Online:
No online sections