Botany and Plant Pathology
Undergraduate Studies
Botany and plant pathology are concerned with the study of plants at all levels of biological organization, from molecular and cellular processes to the global ecosystem. This breadth of field reflects the wide range of issues and problems that confront plant biologists. In addition to addressing fundamental questions in plant biology, plant scientists in the 21st century will be called upon to provide information useful for producing food, fiber, and medicine for an increasing population, and for increasing our understanding of the diversity of plant and ecological systems and their interactions with humans. Students studying botany and plant pathology at OSU receive the basic science background necessary for such contributions, and may choose to focus in a particular area within plant science.
The undergraduate program in the Department of Botany and Plant Pathology is designed for students who wish to receive a BS in Botany degree and for students pursuing degrees in other fields that require a knowledge of plant biology. For example, students who have an undergraduate major in biology or environmental sciences may wish to emphasize botany courses in their upper-division course work.
Completion of the undergraduate curriculum in botany can qualify students for graduate work in various areas of plant biology and plant pathology, and for positions in state and federal agencies, and industries concerned with plants and their products.
Prospective botany majors should obtain a strong background in the biological and physical sciences at the high school level. Specifically recommended are a minimum of three years of high school mathematics, including algebra, geometry, and some exposure to trigonometry, one year of chemistry, one year of biology, one year of physics, and courses designed to develop computer and writing skills. Students without an adequate background in mathematics and science may make up these deficiencies early in their college careers.
Graduate Studies
The Department of Botany and Plant Pathology offers graduate programs in the following areas of concentration: ecology, genetics, genomics and computational biology, molecular and cellular biology, mycology, plant pathology, plant physiology, and systematics.
Students with majors in any one area may incorporate into their programs minors in other areas within the department or in other departments and colleges. Integrated minors, and interdisciplinary programs in plant physiology, molecular and cellular biology, genetics, and environmental sciences are also available.
The MS and PhD degrees offered by the Department of Botany and Plant Pathology require, in addition to course work, research resulting in presentation and defense of a thesis. A nonthesis MS degree also is available. PhD candidates must pass a written and oral preliminary examination upon completion of their course work. In addition, PhD students are required to be a teaching assistant for two quarters.
Inquiries concerning graduate studies can be forwarded to the chairperson of the department's Graduate Studies Committee (Andrew.Jones@oregonstate.edu) and additional details are available online.
Undergraduate Programs
Major
- Biological Data Sciences
Options: - Botany
Options:
Minor
Graduate Programs
Major
Minor
Joseph Spatafora, Department Head
2082 Cordley Hall
Oregon State University
Corvallis, OR 97331-2902
Phone: 541-737-3451
Email: bpp-off@science.oregonstate.edu
Website: http://bpp.oregonstate.edu/
Faculty
Professors Behrenfeld, Ciuffetti, Dolja, Fowler, Ingham, Johnson, Liston, McCune, Mundt, Pscheidt, Spatafora, Stone, Tyler, Wolpert
Associate Professors Chang, Goyer, Jaiswal, Jones, Megraw, Milligan, Ocamb, Parke, Santamaria
Assistant Professors Anderson, Busby, Dung, Frost, Graff, Hagerty, Hardison, KC, LeBoldus, Luh, Naithani, Westberry
Senior Instructor Putnam
Instructors Curtis, Link-Perez, Smyth
Courtesy Faculty
Professors Gent, Grunwald, Loper, Martin, Rothwell, Stockey
Associate Professors Hansen, Kentula, Mahaffee, Pyke, Stockwell, Zasada
Assistant Professors Cronn, Grevstad, Kaye, Meinke, Reichman, Weiland
Adjunct Faculty
Professor Freitag
Biological Data Sciences (BDS)
BDS 211, USE AND ABUSE OF DATA: CRITICAL THINKING IN SCIENCE, 3 Credits
Critically examine how data analysis can support legitimate conclusions from biological datasets and also how deceptive visualizations, misleading comparisons, and spurious reasoning can lead to false conclusions. Analyze data to break down the logical flow of an argument and identify key assumptions, even when they are not stated explicitly.
Prerequisite: (MTH 251 (may be taken concurrently) with C- or better or MTH 251H (may be taken concurrently) with C- or better) or MTH 227 with C- or better or MTH 241 with C- or better or MTH 245 with C- or better
BDS 311, COMPUTATIONAL APPROACHES FOR BIOLOGICAL DATA, 3 Credits
The theory and practice underlying widely used computational methods for biological data analysis. Focuses on the analysis and visualization of large data sets using Python, with broad applications to genomics, ecology, and other disciplines. Topics may include image processing, time series analysis, dimensionality reduction, and resampling methods. Develops student expertise in designing and implementing algorithms in the Python programming language.
Prerequisite: (BI 223 with C- or better or BI 223H with C- or better) and (MTH 252 [C-] or MTH 252H [C-] or MTH 228 [C-]) and (CS 161 [C-] or BDS 470 [C-] or BOT 470 [C-] or BOT 476 [C-])
BDS 406, SPECIAL PROJECTS, 1-99 Credits
This course is repeatable for 99 credits.
BDS 411, ^ANALYSIS OF BIOLOGICAL DATA: CASE STUDIES, 3 Credits
Case studies; synthesize previously acquired knowledge and skills in biology, mathematics, statistics, and computer science to implement, in writing, an analysis strategy. (Writing Intensive Course)
Attributes: CWIC – Core, Skills, WIC
Prerequisite: ((BI 311 with C- or better or BI 311H with C- or better) or (BB 314 with C- or better or BB 314H with C- or better) or MB 310 with C- or better) and ((MTH 252 with C- or better or MTH 252H with C- or better) or MTH 228 with C- or better) and CS 261 [C-] and (ST 352 [C-] or ST 412 [C-])
BDS 446, NETWORKS IN COMPUTATIONAL BIOLOGY, 3 Credits
Emphasizes computational and applied mathematical methods for modeling and analyzing biological networks. Covers various network centralities, topological measures, clustering algorithms, probabilistic annotation models and inference methods. Introduces those concepts in the context of protein interaction, gene regulatory, and metabolic networks. Uses graph frameworks, data frames (and related data structures for data science), and programming in Python or R. CROSSLISTED as BDS 446/CS 446 and CS 546.
Prerequisite: CS 161 with C or better or BDS 470 with C or better or BOT 470 with C or better or BOT 476 with C or better
Equivalent to: CS 446
Recommended: Completion or concurrent enrollment in CS 325
BDS 470, INTRODUCTION TO COMPUTING IN THE LIFE SCIENCES, 3 Credits
Covers the basics of writing a well-organized computer program to perform tasks that are commonly needed for effective data analysis in the life sciences. Incorporates reading data from a variety of file formats, parsing relevant information from data which comes in as text, putting this information into storage structures that make sense for the task at hand, applying basic mathematical functions to the data, and writing results to an output file. Provides students with the foundation to rapidly expand their knowledge of Python and other programming languages as needed in the future. CROSSLISTED as BDS 470/BOT 470 and BDS 570.
Equivalent to: BOT 470, BOT 476
Recommended: CS 161 or exposure to programming logic
BDS 472X, ADVANCED COMPUTING FOR BIOLOGICAL DATA ANALYSIS, 3 Credits
Provides a broad overview of machine learning or “pattern recognition” approaches to problems in biological data analysis. Focuses on understanding the basic concepts necessary to effectively apply several popular ‘supervised learning’ techniques. Develops skills in biological applications that center on recognizing useful patterns in genome-scale datasets, with emphasis on carefully considered scientific interpretation of machine learning model outcomes. Covers use of Python Scikit-Learn libraries for implementation of model-based analyses. CROSSLISTED as BDS 472X/BOT 472X and BDS 572X/BOT 572X.
Prerequisite: BOT 476 with C- or better or BOT 470 with C- or better or CS 162 with C- or better
Equivalent to: BOT 472X
Recommended: BDS 311 and BDS 474/BOT 474
BDS 474X, INTRODUCTION TO GENOME BIOLOGY, 3 Credits
Explores how genomes underlie and influence biological phenomena, across the diversity of life, from prokaryotic microbes to eukaryotic multicellular organisms. Covers genome organization: the structure of chromosomes and chromatin; genes and gene families; and mechanisms that remodel genomes, such as mutation, recombination and transposable elements in the first part of the course. Focuses on genome expression and regulation: gene expression, cellular functions and biochemical pathways; transcriptional and post-transcriptional regulatory mechanisms; and genotype-to-phenotype relationships in the second part of the course. Emphasizes the use of recent technological advances and genome-wide assays that enable investigation of these topics.
Prerequisite: BI 311 (may be taken concurrently) with C- or better or BB 314 (may be taken concurrently) with C- or better
Equivalent to: BOT 474X
BDS 475, COMPARATIVE GENOMICS, 4 Credits
Explores principles of comparative genomics. Examines methods for genome assembly and annotation. Discusses genomic approaches for the study of structural change, whole genome duplication, gene family evolution, gene networks, gene regulation and epigenetics. Lab topics include the analysis of next generation sequencing data and conducting comparative genomic analyses. CROSSLISTED as BDS 475/BOT 475 and BDS 575/BOT 575/MCB 575.
Prerequisite: (BB 314 with D- or better or BB 314H with D- or better) and (BI 311 [D-] or BI 311H [D-] or PBG 430 [D-])
Equivalent to: BOT 475
Recommended: Basic working knowledge of cell and molecular biology and genetics
BDS 477X, POPULATION GENOMICS, 3 Credits
Enables translation of fundamental knowledge in genetics and genomics to the study of evolution and gene function in populations. Applies skills in computational biology to process, analyze, and draw conclusions from genomic datasets at the population and ecosystem level. CROSSLISTED as BDS 477X/BOT 477X and BDS 577X/BOT 577X.
Prerequisite: (BI 311 with C- or better or BI 311H with C- or better or PBG 430 with C- or better) and (BDS 474 [C-] or BOT 474 [C-] or BOT 474X [C-] or BDS 474X [C-] or BB 314 [C-]) and (BDS 470 [C-] or BOT 470 [C-] or BOT 476 [C-] or CS 161 [C-])
Equivalent to: BOT 477X
BDS 478, FUNCTIONAL GENOMICS, 3 Credits
Introduces conceptual approaches and associated laboratory techniques that rely on genome-scale datasets to investigate the function of, and interactions between, genes as well as their RNA/protein products. Examples include: predicting protein function based on nucleotide and amino acid sequence analysis; large-scale genetic approaches to identifying novel genotype-phenotype associations; and analysis of transcriptomic, proteomic and metabolomic datasets, which measure changes in RNA transcripts, proteins and metabolites, respectively, to explore gene function and cellular/organismal networks. Provides a conceptual framework for understanding how the wide range of available large-scale technologies can be applied to solve biological problems. CROSSLISTED as BDS 478/BOT 478 and BDS 578/BOT 578.
Prerequisite: BB 314 with C- or better or BB 314H with C- or better
BDS 491, CAPSTONE PROJECTS IN BIOLOGICAL DATA SCIENCE I, 3 Credits
Quantitative skills and biological thinking will be used to analyze and draw conclusions from real-world biological datasets. Projects will be completed in the context of small groups. Draws on skills in mathematics, statistics, computer science, and biology.
Prerequisite: (ST 352 with C- or better or ST 412 with C- or better) and (CS 162 [C-] or BDS 470 [C-] or BOT 470 [C-] or BOT 476 [C-] or BB 485 [C-] or MTH 427 [C-])
BDS 492, CAPSTONE PROJECTS IN BIOLOGICAL DATA SCIENCE II, 3 Credits
Quantitative skills and biological thinking will be used to analyze and draw conclusions from biological datasets retrieved in BDS 412. This is a synthesis course that draws skills in mathematics, statistics, computer science, and biology, in which the students will process their curated datasets and draw conclusions.
Prerequisite: BDS 491 with C- or better
BDS 570, INTRODUCTION TO COMPUTING IN THE LIFE SCIENCES, 3 Credits
Covers the basics of writing a well-organized computer program to perform tasks that are commonly needed for effective data analysis in the life sciences. Incorporates reading data from a variety of file formats, parsing relevant information from data which comes in as text, putting this information into storage structures that make sense for the task at hand, applying basic mathematical functions to the data, and writing results to an output file. Provides students with the foundation to rapidly expand their knowledge of Python and other programming languages as needed in the future. CROSSLISTED as BDS 470/BOT 470 and BDS 570.
BDS 572X, ADVANCED COMPUTING FOR BIOLOGICAL DATA ANALYSIS, 3 Credits
Provides a broad overview of machine learning or “pattern recognition” approaches to problems in biological data analysis. Focuses on understanding the basic concepts necessary to effectively apply several popular ‘supervised learning’ techniques. Develops skills in biological applications that center on recognizing useful patterns in genome-scale datasets, with emphasis on carefully considered scientific interpretation of machine learning model outcomes. Covers use of Python Scikit-Learn libraries for implementation of model-based analyses. CROSSLISTED as BDS 472X/BOT 472X and BDS 572X/BOT 572X.
Equivalent to: BOT 572X
BDS 574X, INTRODUCTION TO GENOME BIOLOGY, 3 Credits
Explores how genomes underlie and influence biological phenomena, across the diversity of life, from prokaryotic microbes to eukaryotic multicellular organisms. Covers genome organization: the structure of chromosomes and chromatin; genes and gene families; and mechanisms that remodel genomes, such as mutation, recombination and transposable elements in the first part of the course. Focuses on genome expression and regulation: gene expression, cellular functions and biochemical pathways; transcriptional and post-transcriptional regulatory mechanisms; and genotype-to-phenotype relationships in the second part of the course. Emphasizes the use of recent technological advances and genome-wide assays that enable investigation of these topics.
Equivalent to: BOT 574X
BDS 575, COMPARATIVE GENOMICS, 4 Credits
Explores principles of comparative genomics. Examines methods for genome assembly and annotation. Discusses genomic approaches for the study of structural change, whole genome duplication, gene family evolution, gene networks, gene regulation and epigenetics. Lab topics include the analysis of next generation sequencing data and conducting comparative genomic analyses. CROSSLISTED as BDS 475/BOT 475 and BDS 575/BOT 575/MCB 575.
Equivalent to: BOT 575, MCB 575
Recommended: BB 314 and (BI 311 or PBG 430) and basic working knowledge of cell and molecular biology and genetics
BDS 577X, POPULATION GENOMICS, 3 Credits
Enables translation of fundamental knowledge in genetics and genomics to the study of evolution and gene function in populations. Applies skills in computational biology to process, analyze, and draw conclusions from genomic datasets at the population and ecosystem level. CROSSLISTED as BDS 477X/BOT 477X and BDS 577X/BOT 577X.
Equivalent to: BOT 577X
BDS 578, FUNCTIONAL GENOMICS, 3 Credits
Introduces conceptual approaches and associated laboratory techniques that rely on genome-scale datasets to investigate the function of, and interactions between, genes as well as their RNA/protein products. Examples include: predicting protein function based on nucleotide and amino acid sequence analysis; large-scale genetic approaches to identifying novel genotype-phenotype associations; and analysis of transcriptomic, proteomic and metabolomic datasets, which measure changes in RNA transcripts, proteins and metabolites, respectively, to explore gene function and cellular/organismal networks. Provides a conceptual framework for understanding how the wide range of available large-scale technologies can be applied to solve biological problems. CROSSLISTED as BDS 478/BOT 478 and BDS 578/BOT 578.
Equivalent to: BOT 560, BOT 578
BDS 599, SPECIAL TOPICS, 1-4 Credits
This course is repeatable for 99 credits.
Botany and Plant Pathology (BOT)
BOT 003, UNDERGRADUATE RESEARCH, 0 Credits
Engage in research activities appropriate to the discipline; and through the research experience, acquire skills, techniques, and knowledge relevant to the field of study. In consultation with a faculty mentor, engage in research activity, and make and execute a plan for a project.
BOT 004, INTERNSHIP, 0 Credits
Provides basic personal and professional skills that can be used within and outside of a work setting. Through practice, this experience guides students in building and maintaining positive professional relationships, networking/mentoring relationships, and enhances students’ understanding of the connection between theory and practice in their respective disciplines.
BOT 101, *BOTANY: A HUMAN CONCERN, 4 Credits
Introductory botany for non-majors, emphasizing the role of plants in the environment, agriculture and society. Includes molecular approaches to the study of plant function and genetic engineering. Lec/lab. (Bacc Core Course)
Attributes: CPBS – Core, Pers, Biological Science
BOT 220, *INTRODUCTION TO PLANT BIOLOGY, 4 Credits
Introduction to plant biology including an overview of major groups of plants, plant cells and cell types, plant anatomy and architecture, physiology and function, and ecology and the roles of plants in the environment. Laboratory exercises build on lecture themes and provide hands-on learning experiences including field trips. Lec/lab. (Bacc Core Course)
Attributes: CPBS – Core, Pers, Biological Science
Available via Ecampus
BOT 313, PLANT STRUCTURE, 4 Credits
The structural components of vascular plants and how plant structure relates to function, development, environment, evolution, and human use of plants.
Prerequisite: ((BI 212 with D- or better or BI 212H with D- or better) and ((BI 211 with D- or better or BI 211H with D- or better) or (BI 213 with D- or better or BI 213H with D- or better)) ) or ((BI 221 with D- or better or BI 221H with D- or better) and (BI 222 [D-] or BI 222H [D-])) or (BI 205 [D-] and BI 206 [D-])
Recommended: BI 213 or BI 213H or BI 223 or BI 223H
Available via Ecampus
BOT 321, PLANT SYSTEMATICS, 4 Credits
Vascular plant classification, diversity, and evolutionary relationships. Lab emphasizes the collection and identification of ferns, gymnosperms, and flowering plants in Oregon. Field trips. Lec/lab.
Recommended: BI 213 or BI 213H or BI 223 or BI 223H
Available via Ecampus
BOT 322, ECONOMIC AND ETHNOBOTANY: ROLE OF PLANTS IN HUMAN CULTURE, 3 Credits
Economic and cultural (ethnobotanical) uses of plants and fungi by humans, including domesticated cultivated plants as well as wild-growing plants, and uses of plants and fungi by indigenous cultures. Ecampus course only.
BOT 323, ^FLOWERING PLANTS OF THE WORLD, 3 Credits
Global perspective of plant biodiversity with a focus on evolutionary origins, classification, and evolutionary relationships of the major groups of plants. Development and application of scientific writing and utilization of online information resources in plant evolutionary biology. (Writing Intensive Course)
Attributes: CWIC – Core, Skills, WIC
Recommended: (BI 211, BI 212, BI 213) or (BI 221, BI 222, BI 223) or (BI 204, BI 205, BI 206)
Available via Ecampus
BOT 324, *FUNGI IN SOCIETY, 3 Credits
Explores the diverse roles played by fungi in relation to human civilization and the natural environment. (Bacc Core Course)
Attributes: CSST – Core, Synthesis, Science/Technology/Society
Recommended: One course in biological sciences.
Available via Ecampus
BOT 325, *INTERSECTIONS BETWEEN PLANTS AND HUMANITY, 3 Credits
The unique attributes of plants--including aspects of their biochemistry, growth, structure, and physiology--have influenced all aspects of life on earth, from biogeochemical cycles to the rise and expansion of human civilizations. Plants are sources of medicines, stimulants, hallucinogens, fibers and woods, resins and latex, oils and waxes; plants have inspired technological innovation, exploration, and exploitation of people and the environment. This course critically examines the intersections of plants with society and technology by exploring the roles plants have played in both historical and modern contexts. (Bacc Core Course)
Attributes: CSST – Core, Synthesis, Science/Technology/Society
Recommended: One course in biological sciences and junior standing.
BOT 331, PLANT PHYSIOLOGY, 4 Credits
Survey of physiological processes in plants, including photosynthesis and plant metabolism, mineral nutrition and ion uptake processes, plant cell/water relations, regulation of plant growth and development, and transpiration and translocation. Lec/rec.
Prerequisite: ((BI 212 with D- or better or BI 212H with D- or better) and (BI 213 [D-] or BI 213H [D-])) or ((BI 221 [D-] or BI 221H [D-]) and (BI 222 [D-] or BI 222H [D-])) or (BI 205 [D-] and BI 206 [D-]) and (CH 123 [D-] or (CH 233 [D-] and CH 263 [D-]))
Recommended: (BI 213 or BI 213H or BI 223 or BI 223H) and (CH 123 or (CH 233 and CH 263))
Available via Ecampus
BOT 332, LABORATORY TECHNIQUES IN PLANT BIOLOGY, 3 Credits
Laboratory experiences in the manipulation and observation of physiological processes in plant systems. Analysis and interpretation of physiological data generated in experimentation with plant systems. Training in basic laboratory skills, including the principles and procedures involved in the use of common items of laboratory instrumentation. Lab.
Recommended: BOT 331 or BI 314 or BB 314
Available via Ecampus
BOT 341, PLANT ECOLOGY, 4 Credits
Study of higher plants in relation to their environment. The relationship of plant physiology and reproduction to environmental factors; competition and other species interactions; the structure, dynamics and analysis of vegetation. Field trips. Lec/lab.
Recommended: BOT 321 and ((BI 213 or BI 213H) or (BI 223 or BI 223H))
Available via Ecampus
BOT 350, INTRODUCTORY PLANT PATHOLOGY, 4 Credits
Symptoms, causal agents, diagnosis, and prevention of plant diseases, with emphasis on fungi, bacteria, nematode, and virus pathogens. Lec/lab.
Prerequisite: ((BI 211 with D- or better or BI 211H with D- or better) and (BI 212 [D-] or BI 212H [D-]) and (BI 213 [D-] or BI 213H [D-])) or ((BI 221 [D-] or BI 221H [D-]) and (BI 222 [D-] or BI 222H [D-]) and (BI 223 [D-] or BI 223H [D-])) or (BI 204 [D-] and BI 205 [D-] and BI 206 [D-])
Available via Ecampus
BOT 401, RESEARCH, 1-16 Credits
This course is repeatable for 16 credits.
Available via Ecampus
BOT 403, THESIS, 1-16 Credits
This course is repeatable for 16 credits.
BOT 405, READING AND CONFERENCE, 1-16 Credits
This course is repeatable for 16 credits.
BOT 406, PROJECTS: CURATORIAL ASSISTANT, 1-6 Credits
Students assist with curatorial projects in the OSU Herbarium. Admission is by application to the Department of Botany & Plant Pathology.
This course is repeatable for 6 credits.
Available via Ecampus
BOT 407, SEMINAR, 1 Credit
Section 1: Departmental seminar. Section 2: Lichens and Bryophytes Research (1). Weekly one-hour meetings for reporting and discussion of active research projects, discussion of proposal research, review and discussion of recent literature, and mini-workshops on particular problems.
Equivalent to: BI 407H, BOT 407H
This course is repeatable for 16 credits.
Available via Ecampus
BOT 407H, SEMINAR, 1 Credit
Section 1: Departmental seminar. Section 2: Lichens and Bryophytes Research (1). Weekly one-hour meetings for reporting and discussion of active research projects, discussion of proposal research, review and discussion of recent literature, and mini-workshops on particular problems.
Attributes: HNRS – Honors Course Designator
Equivalent to: BI 407H, BOT 407
This course is repeatable for 16 credits.
BOT 408, WORKSHOP, 1-16 Credits
This course is repeatable for 16 credits.
BOT 410, INTERNSHIP, 1-16 Credits
This course is repeatable for 16 credits.
Available via Ecampus
BOT 413, FOREST PATHOLOGY, 3 Credits
Effects of diseases on forest ecosystems. Recognition of important groups, prediction of pathogen responses to environmental changes, and management strategies for protection of forest resources. Field trips. Lec/lab. CROSSLISTED as BOT 413/FOR 413.
Prerequisite: BI 204 with C or better or BI 212 with C or better or BI 212H with C or better or BI 213 with C or better or BI 213H with C or better or BI 221 with C or better or BI 221H with C or better
Equivalent to: FOR 413
BOT 416, AQUATIC BOTANY, 4 Credits
Taxonomy and ecology of aquatic vegetation, emphasizing freshwater and marine algae and the submergent vascular plants. Morphology, physiology, and classification of the algae; morphological and physiological adaptations of aquatic vascular plants; and primary production in aquatic ecosystems. Laboratory practice in the identification of local taxa. Field trips. Lec/lab.
BOT 417, PHYCOLOGY, 4 Credits
Introduces micro- and macro-algal biology, reproduction and evolution. Emphasizes how the endosymbiosis theory ties algae together as a functional group. Explores algal diversity through lectures and experiential learning activities (e.g., laboratory, field trips). Develops skills in laboratory methods for isolation, culturing and maintenance of algae for aquaculture and research.
Equivalent to: BOT 417X
Recommended: One year of college-level biology
BOT 417X, PHYCOLOGY, 4 Credits
A field and laboratory based introduction to micro- and macro-algal biology, reproduction and evolution. Emphasis is placed on how the endosymbiosis theory ties algae together as a functional group. Algal diversity will be explored through lectures, laboratory and field trips. The laboratory experience will include methods for isolation, culturing and maintenance of algae for aquaculture and research.
Recommended: One year of biology
BOT 425, FLORA OF THE PACIFIC NORTHWEST, 3 Credits
Vascular plant identification, terminology, and diagnostic characteristics of plant families. Lab emphasizes the use of keys for identification to the species level and ability to recognize by sight those plant families found in the Pacific Northwest. Field trips. Lec/lab.
Recommended: BOT 321
BOT 440, FIELD METHODS IN PLANT ECOLOGY, 4 Credits
Concepts and tools for describing, monitoring, and experimenting on vegetation. Combines Web-based material, field experience at the student's location, and student projects.
Recommended: Course in ecology and a course in statistics.
Available via Ecampus
BOT 442, PLANT POPULATION ECOLOGY, 3 Credits
Ecological aspects of plant form and reproduction; demography and population modeling; species interactions, including competition, mutualism, and herbivory. Lec/lab.
Recommended: BOT 341
BOT 460, FUNCTIONAL GENOMICS, 3 Credits
Functional genomics describes a set of conceptual approaches and associated laboratory techniques that rely on large-scale DNA sequence datasets to investigate the function of, and interactions between, genes as well as their RNA/protein products. This course will provide an overview of these techniques, including a) approaches to predicting protein function based on sequence analysis, b) large-scale genetic approaches to identifying novel genotype-phenotype associations, and c) transcriptomic, proteomic and metabolomic approaches that reveal gene functions by measuring changes in abundance/modification of associated RNA transcripts, proteins and metabolites.
Prerequisite: (BI 311 with C- or better or BI 311H with C- or better) and (BI 314 [C-] or BI 314H [C-] or BB 314 [C-] or BB 314H [C-])
BOT 461, MYCOLOGY, 4 Credits
Broad taxonomic survey of the fungi and their biology. Examines fungal life histories, systematics, ecology, and genetics, as well as ethnomycology. Introduces approaches to mycology in the field, including collection and preparation of specimens.
Prerequisite: ((BI 211 with C- or better or BI 211H with C- or better) and (BI 212 [C-] or BI 212H [C-]) and (BI 213 [C-] or BI 213H [C-])) or (BI 204 [C-] and BI 205 [C-] and BI 206 [C-]) or ((BI 221 [C-] or BI 221H [C-]) and (BI 222 [C-] or BI 222H [C-]) and (BI 223 [C-] or BI 223H [C-]))
BOT 465, LICHENOLOGY, 4 Credits
Biology of lichens; includes structure, life histories, classification, and ecology. Field trip fee. Lec/lab. Offered alternate years.
Recommended: ((BI 213 or BI 213H) or (BI 223 or BI 223H)) and two botany courses
Available via Ecampus
BOT 466, BRYOLOGY, 4 Credits
Biology of bryophytes; includes structure, life histories, classification, and ecology. Field trip fee. Lec/lab. Offered alternate years.
Recommended: ((BI 213 or BI 213H) or (BI 223 or BI 223H)) and two botany courses
BOT 470, INTRODUCTION TO COMPUTING IN THE LIFE SCIENCES, 3 Credits
Covers the basics of writing a well-organized computer program to perform tasks that are commonly needed for effective data analysis in the life sciences. Incorporates reading data from a variety of file formats, parsing relevant information from data which comes in as text, putting this information into storage structures that make sense for the task at hand, applying basic mathematical functions to the data, and writing results to an output file. Provides students with the foundation to rapidly expand their knowledge of Python and other programming languages as needed in the future. CROSSLISTED as BDS 470/BOT 470 and BDS 570.
Equivalent to: BDS 470, BOT 476
Recommended: CS 161 or exposure to programming logic
BOT 472X, ADVANCED COMPUTING FOR BIOLOGICAL DATA ANALYSIS, 3 Credits
Provides a broad overview of machine learning or “pattern recognition” approaches to problems in biological data analysis. Focuses on understanding the basic concepts necessary to effectively apply several popular ‘supervised learning’ techniques. Develops skills in biological applications that center on recognizing useful patterns in genome-scale datasets, with emphasis on carefully considered scientific interpretation of machine learning model outcomes. Covers use of Python Scikit-Learn libraries for implementation of model-based analyses. CROSSLISTED as BDS 472X/BOT 472X and BDS 572X/BOT 572X.
Prerequisite: BOT 476 with C- or better or BOT 470 with C- or better or CS 162 with C- or better
Equivalent to: BDS 472X
Recommended: BDS 311 and BDS 474/BOT 474
BOT 474X, INTRODUCTION TO GENOME BIOLOGY, 3 Credits
Explores how genomes underlie and influence biological phenomena, across the diversity of life, from prokaryotic microbes to eukaryotic multicellular organisms. Covers genome organization: the structure of chromosomes and chromatin; genes and gene families; and mechanisms that remodel genomes, such as mutation, recombination and transposable elements in the first part of the course. Focuses on genome expression and regulation: gene expression, cellular functions and biochemical pathways; transcriptional and post-transcriptional regulatory mechanisms; and genotype-to-phenotype relationships in the second part of the course. Emphasizes the use of recent technological advances and genome-wide assays that enable investigation of these topics.
Prerequisite: BI 311 (may be taken concurrently) with C- or better or BB 314 (may be taken concurrently) with C- or better
Equivalent to: BDS 474X
BOT 475, COMPARATIVE GENOMICS, 4 Credits
Explores principles of comparative genomics. Examines methods for genome assembly and annotation. Discusses genomic approaches for the study of structural change, whole genome duplication, gene family evolution, gene networks, gene regulation and epigenetics. Lab topics include the analysis of next generation sequencing data and conducting comparative genomic analyses. CROSSLISTED as BDS 475/BOT 475 and BDS 575/BOT 575/MCB 575.
Prerequisite: (BB 314 with D- or better or BB 314H with D- or better) and (BI 311 [D-] or BI 311H [D-] or PBG 430 [D-])
Equivalent to: BDS 475
Recommended: Basic working knowledge of cell and molecular biology and genetics
BOT 476, INTRODUCTION TO COMPUTING IN THE LIFE SCIENCES, 3 Credits
Introduction to management of large datasets (e.g., nucleic acids, protein), computer programming languages, application of basic mathematical functions, and assembly of computational pipelines pertinent to life sciences.
Recommended: Cell and molecular biology or genetics. Familiarity with text editing software and unix/linux operating system is advantageous
BOT 477X, POPULATION GENOMICS, 3 Credits
Enables translation of fundamental knowledge in genetics and genomics to the study of evolution and gene function in populations. Applies skills in computational biology to process, analyze, and draw conclusions from genomic datasets at the population and ecosystem level. CROSSLISTED as BDS 477X/BOT 477X and BDS 577X/BOT 577X.
Prerequisite: (BI 311 with C- or better or BI 311H with C- or better or PBG 430 with C- or better) and (BDS 474 [C-] or BOT 474 [C-] or BOT 474X [C-] or BDS 474X [C-] or BB 314 [C-]) and (BDS 470 [C-] or BOT 470 [C-] or BOT 476 [C-] or CS 161 [C-])
Equivalent to: BDS 477X
BOT 478, FUNCTIONAL GENOMICS, 3 Credits
Introduces conceptual approaches and associated laboratory techniques that rely on genome-scale datasets to investigate the function of, and interactions between, genes as well as their RNA/protein products. Examples include: predicting protein function based on nucleotide and amino acid sequence analysis; large-scale genetic approaches to identifying novel genotype-phenotype associations; and analysis of transcriptomic, proteomic and metabolomic datasets, which measure changes in RNA transcripts, proteins and metabolites, respectively, to explore gene function and cellular/organismal networks. Provides a conceptual framework for understanding how the wide range of available large-scale technologies can be applied to solve biological problems. CROSSLISTED as BDS 478/BOT 478 and BDS 578/BOT 578.
Prerequisite: BB 314 with C- or better or BB 314H with C- or better
BOT 480, PHOTOSYNTHESIS AND PHOTOBIOLOGY, 3 Credits
Explores the diverse use of light in biological systems, with particular emphasis on photosynthesis. Lectures will discuss the nature of light, light in the natural environment, light absorption in biological systems, use of light energy for photosynthesis, communication, defense, motility, and vision, as well as deleterious effects of light and its use for global monitoring satellite systems.
Recommended: One course in plant physiology or ecology
BOT 483X, PRIMARY PRODUCTION IN AQUATIC ECOSYSTEMS, 3 Credits
Covers major primary producers in aquatic ecosystems. Explores both the bottom-up (light and nutrients) and top-down (grazing and mortality) controls on primary production. Addresses the ecosystem services provided by aquatic primary producers in supporting food webs and fisheries.
Prerequisite: (BI 211 with C- or better and BI 212 [C-]) or (BI 211H [C-] and BI 212H [C-]) or (BI 211 [C-] and BI 213 [C-]) or (BI 211H [C-] and BI 213H [C-]) or (BI 212 [C-] and BI 213 [C-]) or (BI 212H [C-] and BI 213H [C-]) or (BI 204 [C-] and BI 205 [C-]) or (BI 204 [C-] and BI 206 [C-]) or (BI 205 [C-] and BI 206 [C-]) or (BI 221 [C-] and BI 222 [C-]) or (BI 221H [C-] and BI 222H [C-]) or (BI 221 [C-] and BI 223 [C-]) or (BI 221H [C-] and BI 223H [C-]) or (BI 222 [C-] and BI 223 [C-]) or (BI 222H [C-] and BI 223H [C-])
BOT 488, ENVIRONMENTAL PHYSIOLOGY OF PLANTS, 3 Credits
Introduces students to mechanisms of plant responses to environmental change caused by humans, including atmospheric, nutrient, water, and global climate factors. Concepts are built around principles of plant environment relations. Lec/lab.
Recommended: One course in plant physiology or one course in ecology.
BOT 499, SPECIAL TOPICS, 0-16 Credits
Equivalent to: BOT 499H
This course is repeatable for 16 credits.
Available via Ecampus
BOT 499H, SPECIAL TOPICS, 0-16 Credits
Attributes: HNRS – Honors Course Designator
Equivalent to: BOT 499
This course is repeatable for 16 credits.
BOT 501, RESEARCH, 1-16 Credits
This course is repeatable for 16 credits.
BOT 503, THESIS, 1-16 Credits
This course is repeatable for 999 credits.
BOT 505, READING AND CONFERENCE, 1-16 Credits
This course is repeatable for 16 credits.
BOT 507, SEMINAR, 1-16 Credits
Section 1: Departmental seminar (F, W, S). Section 2: Communication in Ecology (F). Section 3: Community and Habitat Analyses (W). Section 4: Lichens and Bryophytes Research (S). Weekly one-hour meetings for reporting and discussions of proposal research, review and discussion of recent literature, and mini-workshops on particular problems.
This course is repeatable for 16 credits.
BOT 508, WORKSHOP, 1-16 Credits
This course is repeatable for 16 credits.
BOT 510, INTERNSHIP, 1-16 Credits
This course is repeatable for 16 credits.
BOT 513, FOREST PATHOLOGY, 3 Credits
Effects of diseases on forest ecosystems. Recognition of important groups, prediction of pathogen responses to environmental changes, and management strategies for protection of forest resources. Field trips. Lec/lab. CROSSLISTED as BOT 513/FOR 513.
Equivalent to: FOR 513
Recommended: BI 204 or BI 212 or BI 212H or BI 213 or BI 213H
BOT 516, AQUATIC BOTANY, 4 Credits
Taxonomy and ecology of aquatic vegetation, emphasizing freshwater and marine algae and the submergent vascular plants. Morphology, physiology, and classification of the algae; morphological and physiological adaptations of aquatic vascular plants; and primary production in aquatic ecosystems. Laboratory practice in the identification of local taxa. Field trips. Lec/lab.
BOT 517, PHYCOLOGY, 4 Credits
Introduces micro- and macro-algal biology, reproduction and evolution. Emphasizes how the endosymbiosis theory ties algae together as a functional group. Explores algal diversity through lectures and experiential learning activities (e.g., laboratory, field trips). Develops skills in laboratory methods for isolation, culturing and maintenance of algae for aquaculture and research.
Equivalent to: BOT 517X
Recommended: One year of college-level biology
BOT 517X, PHYCOLOGY, 4 Credits
A field and laboratory based introduction to micro- and macro-algal biology, reproduction and evolution. Emphasis is placed on how the endosymbiosis theory ties algae together as a functional group. Algal diversity will be explored through lectures, laboratory and field trips. The laboratory experience will include methods for isolation, culturing and maintenance of algae for aquaculture and research.
Recommended: One year of biology
BOT 525, FLORA OF THE PACIFIC NORTHWEST, 3 Credits
Vascular plant identification, terminology, and diagnostic characteristics of plant families. Lab emphasizes the use of keys for identification to the species level and ability to recognize by sight those plant families found in the Pacific Northwest. Field trips. Lec/lab.
Recommended: BOT 321
BOT 540, FIELD METHODS IN PLANT ECOLOGY, 4 Credits
Concepts and tools for describing, monitoring, and experimenting on vegetation. Combines Web-based material, field experience at the student's location, and student projects.
Recommended: Course in ecology and a course in statistics.
Available via Ecampus
BOT 542, PLANT POPULATION ECOLOGY, 3 Credits
Ecological aspects of plant form and reproduction; demography and population modeling; species interactions, including competition, mutualism, and herbivory. Lec/lab.
Recommended: BOT 341
BOT 543, PLANT COMMUNITY ECOLOGY, 3 Credits
The structure, diversity, and successional dynamics of terrestrial plant communities; methods of analysis. Lec/lab.
Recommended: BOT 341 or equivalent.
BOT 550, PLANT PATHOLOGY, 5 Credits
Causal agents of plant disease, diagnosis, pathogenesis, epidemiology, and disease management principles and strategies. Field trip. Lec/lab/rec.
BOT 552, PLANT DISEASE MANAGEMENT, 4 Credits
Analysis of host, pathogen, and environmental factors influencing the increase and spread of plant disease. Epidemiological theory will be used as a basis for developing and evaluating principles and concepts of plant disease management. Lec/lab/rec. Offered alternate years.
BOT 553, PLANT DISEASE DIAGNOSIS, 3 Credits
Diagnosis of plant diseases and identification of causal agents. Laboratory practice in identification techniques. Observation of symptoms exhibited by diseased plants in greenhouse and field locations. Field trips. Lec/lab. Offered alternate years in summer term.
BOT 561, MYCOLOGY, 4 Credits
Broad taxonomic survey of the fungi and their biology. Examines fungal life histories, systematics, ecology, and genetics, as well as ethnomycology. Introduces approaches to mycology in the field, including collection and preparation of specimens.
BOT 565, LICHENOLOGY, 4 Credits
Biology of lichens; includes structure, life histories, classification, and ecology. Field trip fee. Lec/lab. Offered alternate years.
BOT 566, BRYOLOGY, 4 Credits
Biology of bryophytes; includes structure, life histories, classification, and ecology. Field trip fee. Lec/lab. Offered alternate years.
BOT 570, COMMUNITY STRUCTURE AND ANALYSIS, 4 Credits
Quantitative methods for the analysis of biotic communities, including community concepts, estimation of community composition parameters, theoretical aspects of multivariate methods of analyzing species-importance data, and overview of multivariate tools; hands-on computer analysis of data sets. Lec/lab.
Equivalent to: BI 570
BOT 572X, ADVANCED COMPUTING FOR BIOLOGICAL DATA ANALYSIS, 3 Credits
Provides a broad overview of machine learning or “pattern recognition” approaches to problems in biological data analysis. Focuses on understanding the basic concepts necessary to effectively apply several popular ‘supervised learning’ techniques. Develops skills in biological applications that center on recognizing useful patterns in genome-scale datasets, with emphasis on carefully considered scientific interpretation of machine learning model outcomes. Covers use of Python Scikit-Learn libraries for implementation of model-based analyses. CROSSLISTED as BDS 472X/BOT 472X and BDS 572X/BOT 572X.
Equivalent to: BDS 572X
BOT 574X, INTRODUCTION TO GENOME BIOLOGY, 3 Credits
Explores how genomes underlie and influence biological phenomena, across the diversity of life, from prokaryotic microbes to eukaryotic multicellular organisms. Covers genome organization: the structure of chromosomes and chromatin; genes and gene families; and mechanisms that remodel genomes, such as mutation, recombination and transposable elements in the first part of the course. Focuses on genome expression and regulation: gene expression, cellular functions and biochemical pathways; transcriptional and post-transcriptional regulatory mechanisms; and genotype-to-phenotype relationships in the second part of the course. Emphasizes the use of recent technological advances and genome-wide assays that enable investigation of these topics.
Equivalent to: BDS 574X
BOT 575, COMPARATIVE GENOMICS, 4 Credits
Explores principles of comparative genomics. Examines methods for genome assembly and annotation. Discusses genomic approaches for the study of structural change, whole genome duplication, gene family evolution, gene networks, gene regulation and epigenetics. Lab topics include the analysis of next generation sequencing data and conducting comparative genomic analyses. CROSSLISTED as BDS 475/BOT 475 and BDS 575/BOT 575/MCB 575.
Equivalent to: BDS 575, MCB 575
Recommended: BB 314 and (BI 311 or PBG 430) and basic working knowledge of cell and molecular biology and genetics
BOT 577X, POPULATION GENOMICS, 3 Credits
Enables translation of fundamental knowledge in genetics and genomics to the study of evolution and gene function in populations. Applies skills in computational biology to process, analyze, and draw conclusions from genomic datasets at the population and ecosystem level. CROSSLISTED as BDS 477X/BOT 477X and BDS 577X/BOT 577X.
Equivalent to: BDS 577X
BOT 578, FUNCTIONAL GENOMICS, 3 Credits
Introduces conceptual approaches and associated laboratory techniques that rely on genome-scale datasets to investigate the function of, and interactions between, genes as well as their RNA/protein products. Examples include: predicting protein function based on nucleotide and amino acid sequence analysis; large-scale genetic approaches to identifying novel genotype-phenotype associations; and analysis of transcriptomic, proteomic and metabolomic datasets, which measure changes in RNA transcripts, proteins and metabolites, respectively, to explore gene function and cellular/organismal networks. Provides a conceptual framework for understanding how the wide range of available large-scale technologies can be applied to solve biological problems. CROSSLISTED as BDS 478/BOT 478 and BDS 578/BOT 578.
Equivalent to: BDS 578, BOT 560
BOT 580, PHOTOSYNTHESIS AND PHOTOBIOLOGY, 3 Credits
Explores the diverse use of light in biological systems, with particular emphasis on photosynthesis. Lectures will discuss the nature of light, light in the natural environment, light absorption in biological systems, use of light energy for photosynthesis, communication, defense, motility, and vision, as well as deleterious effects of light and its use for global monitoring satellite systems.
Recommended: One course in plant physiology or ecology
BOT 583X, PRIMARY PRODUCTION IN AQUATIC ECOSYSTEMS, 3 Credits
Covers major primary producers in aquatic ecosystems. Explores both the bottom-up (light and nutrients) and top-down (grazing and mortality) controls on primary production. Addresses the ecosystem services provided by aquatic primary producers in supporting food webs and fisheries.
BOT 588, ENVIRONMENTAL PHYSIOLOGY OF PLANTS, 3 Credits
Introduces students to mechanisms of plant responses to environmental change caused by humans, including atmospheric, nutrient, water, and global climate factors. Concepts are built around principles of plant environment relations. Lec/lab.
Recommended: One course in plant physiology or ecology
BOT 599, SPECIAL TOPICS, 0-16 Credits
This course is repeatable for 16 credits.
BOT 601, RESEARCH, 1-16 Credits
This course is repeatable for 16 credits.
BOT 603, THESIS, 1-16 Credits
This course is repeatable for 999 credits.
BOT 605, READING AND CONFERENCE, 1-16 Credits
This course is repeatable for 16 credits.
BOT 607, SEMINAR, 1 Credit
Section 1. Departmental seminar
This course is repeatable for 16 credits.
BOT 608, WORKSHOP, 1-16 Credits
This course is repeatable for 16 credits.
BOT 651, MOLECULAR BASIS OF PLANT PATHOGENESIS, 3 Credits
Analysis of current concepts in the physiology, biochemistry, and genetics of host-parasite interactions. Topics covered include specificity, recognition, penetration, toxin production, altered plant metabolism during disease, resistance mechanisms and regulatory aspects of gene expression during host-parasite interactions. Offered alternate years.
Equivalent to: MCB 651
Recommended: BOT 550
BOT 668, PLANT DISEASE DYNAMICS, 4 Credits
Evaluation of processes affecting the dynamics of plant disease and pathogen populations through analysis of current literature. Students will be expected to conduct extensive reading and analysis of literature and to meet with the instructor for small group discussions. Offered alternate years.
BOT 692, SELECTED TOPICS: PLANT PATHOLOGY, 1-3 Credits
Selected topics concerning plant pathogens and plant disease processes, emphasizing current literature and theory. Topics vary from year to year.
Equivalent to: MCB 692
This course is repeatable for 99 credits.
Recommended: BOT 550
BOT 699, SPECIAL TOPICS, 1-16 Credits
This course is repeatable for 16 credits.