Biology

Courses

Biology 101 - Topics in Biology I - Website

Full course for one semester, taught by several staff members. The course furnishes an understanding of biological principles and the properties of life. Among topics considered are structure and function of plants and animals, relations of organisms to each other and to their environment, energy relations of organisms, integrative and coordinating mechanisms of organisms, cell biology principles, genetics, molecular biology, reproduction, development and growth, and the evidence for organic evolution. The laboratory deals with the descriptive and experimental aspects of the topics covered in the lectures. Lecture-laboratory.

Biology 102 - Topics in Biology II - Website

Full course for one semester, taught by several staff members. The course furnishes an understanding of biological principles and the properties of life. Among topics considered are structure and function of plants and animals, relations of organisms to each other and to their environment, energy relations of organisms, integrative and coordinating mechanisms of organisms, cell biology principles, genetics, molecular biology, reproduction, development and growth, and the evidence for organic evolution. The laboratory deals with the descriptive and experimental aspects of the topics covered in the lectures. Prerequisite: Biology 101 or consent of the instructor. Lecture-laboratory.

Biology 131 - Introduction to Computational Biology

Full course for one semester. This course provides an integrated survey of fundamental questions in molecular biology and the computational tools that are used to solve them. Elements of molecular biology and computer programming are presented in parallel throughout the semester. Topics include molecular sequence analysis (identifying repeats, regulatory/binding motifs, and genetic variation) using pattern-matching operations on text strings. Assignments will include writing Python programs to analyze human DNA, RNA, and protein sequences. Prerequisite: Biology 101 or consent of the instructor. Lecture-laboratory.

Biology 211 - Introduction to Scientific Literature and Discourse

One-half course for one semester. In parallel with the biology department seminar series, this course explores current topics in biology through reading and discussion of primary literature. The course is designed to deepen understanding of the many forms of biological inquiry; students will learn to evaluate biology scholarship, pose questions, and participate in scientific discourse. Prerequisite: Biology 101 and 102 and sophomore standing, or consent of the instructor. Credit/no credit only. Conference.

Biology 251 - Plant Communities of the Pacific Northwest

One-half course for one semester. An exploration of the principles underlying the distribution and abundance of plants in the Pacific Northwest. Topics include the structure and basic ecological features of communities, adaptation of organisms to their abiotic and biotic environments, symbiotic relationships, success, endemism, and biogeography. These concepts will be developed to address current environmental problems such as resource extraction, climate change, invasive species, pollution, and loss of biodiversity. The course will include field trips. Suitable for nonmajors. Prerequisite: Biology 101/102 or equivalent. Lecture-conference.

Not offered 2017–18.

Biology 256 - Human Genetics - Website

One-half course for one semester. The nature and function of genes and genomes, using human case studies. Readings will include classic and modern examples from the primary literature to illustrate fundamental molecular genetic approaches and concepts. Consent of instructor is required for students who have completed Biology 356 or 363. Prerequisite: Biology 101/102. Lecture-conference.

Not offered 2017–18.

Biology 301 - Ecology

Full course for one semester. This course examines fundamental concepts in ecology such as limits to distribution, behavioral ecology, population ecology, species interactions, community ecology, and ecosystem ecology, and will examine the relevance of such topics for addressing contemporary applied issues of global change, human health, and sustainability. Central objectives of this course are to 1) evaluate the evidence that supports major theories in ecology and 2) actively participate in the process by which theories are tested, falsified, and refined. Weekly laboratories will help facilitate the latter objective. Lectures and laboratories will emphasize how ecologists gain inference from experiments, observations, and ecological models. Prerequisite: Biology 101 and 102, or consent of the instructor. Lecture-laboratory.

Biology 322 - Plant Physiology - Website

Full course for one semester. An analysis of cell biology, biochemistry, metabolism, ecophysiology, and development of plants. Lecture topics include water relations, respiration, photosynthesis, nitrogen fixation, mineral nutrition, plant hormones, plant molecular biology, genetic engineering, the role of environmental signals in plant development, and the environmental physiology of Pacific Northwest forests. Lectures will be supplemented with readings in research journals. Laboratory exercises are designed to demonstrate basic research techniques as well as the principles covered in lectures. Students are required to conduct an advanced, independent project. Prerequisites: Biology 101/102 and Chemistry 101/102. Chemistry 201/202 is recommended. Lecture-laboratory.

Biology 331 - Computational Systems Biology

Full course for one semester. A survey of network models used to gain a systems-level understanding of biological processes. Topics include computational models of gene regulation, signal transduction pathways, protein-protein interactions, and metabolic pathways. Laboratory exercises will involve building a collection of biological networks from public data, implementing a graph library and foundational algorithms, and interpreting computational results. A programming-based independent project will answer biological questions by applying graph algorithms to experimental data. Prerequisite: Biology 101 and 102, and either Biology 131 or Computer Science 121 or consent of the instructor. Lecture-laboratory.

Biology 332 - Vascular Plant Diversity - Website

Full course for one semester. A survey of vascular plants using evolutionary and ecological principles to interpret patterns of diversity in vascular plant form and function. Topics include plant species, methods of phylogenetic reconstruction, paleobotany, plant reproductive biology, and plant ecological interactions. Laboratory work will include a survey of flowering plant families with an emphasis on learning elements of the flora of the Pacific Northwest. Laboratory projects will demonstrate methods used for establishing evolutionary relationships, assessing genetic structure in natural populations, and identifying adaptive features of plant form and function, and will include independent research in the laboratory or field. Prerequisite: Biology 101/102. Lecture-laboratory.

Biology 342 - Animal Behavior

Full course for one semester. An integrated approach to the study of behavior—the phenotype through which an organism interacts with, and also modifies, its environment. We will study how behavioral phenotypes are shaped by the social and physical environment and analyze how they are implemented through development by neural physiology, gene networks, and individual genes. Conversely, we will study how behaviors modify the environment and thus impact the physiology and genetics of organisms as well as the evolution of species. Examples will be drawn from both laboratory and field studies using comparative molecular and behavioral approaches to identify patterns and recurring themes, which will be discussed in the context of existing theories about animal behavior. The laboratory will cover both bench skills and field techniques that will then be applied in independent student projects. Prerequisite: Biology 101/102. Lecture-laboratory.

Biology 351 - Developmental Biology - Website

Full course for one semester.  Analysis of one of the most remarkable events in biology—the formation of a complex, multicellular organism from a single cell. With an emphasis on principles common among many species, this course explores how cellular, molecular, and genetic events contribute to distinct stages of embryogenesis. How are body patterns generated? What are the morphogenetic processes that give rise to specific organ systems? How is cell fate decided? What are the processes that guide tissue growth, regeneration, and differentiation? We will address these and other fundamental questions, discussing primary literature, recreating classic experiments, and performing new investigations. Students will apply the techniques and skills gained during the first part of the course to carry out an independent laboratory project. Prerequisite: Biology 101/102 and Chemistry 101/102. A course in genetics or cell biology is strongly recommended. Lecture-laboratory.

Biology 356 - Gene Regulation - Website

Full course for one semester. The molecular biology of eukaryotes, particularly as it relates to the control of gene expression. Genome organization, packaging and perpetuation, and mechanisms of gene regulation will be treated in depth, with the focus on experimental approaches and what they reveal about the conversion of genotype to phenotype. The laboratory will emphasize molecular approaches to analysis of genomes and gene expression, which will then be used in independent projects. Prerequisites: Biology 101/102 and Chemistry 101/102. Chemistry 201/202 is recommended. Lecture-laboratory.

Not offered 2017–18.

Biology 358 - Microbiology - Website

Full course for one semester. The biology of microorganisms, including structure and function of the prokaryotic cell, metabolism, genetics interactions with host organisms, and cell-to-cell communication. Course will emphasize current areas of active research using the primary literature to illustrate key concepts discussed in lecture. Laboratory exercises emphasize interactions of bacteria with their environment and with host organisms, using classical and molecular genetic techniques to address biological problems. An advanced independent research project is required. Prerequisites: Biology 101/102, Chemistry 101/102. Lecture-laboratory.

Biology 363 - Genes, Genetics, and Genomes

Full course for one semester. Overview and exploration of fundamental concepts and processes in genetics including heredity, mitosis, meiosis, DNA replication, transcription, translation, segregation, linkage, recombination, epistasis, selection, migration, drift, and evolution. Topics will also include DNA and RNA structure, coding and noncoding DNA, chromosomes, genome architecture, mechanisms of mutation, horizontal transfer, and genomics. Laboratories will provide the opportunity to investigate genetic questions and concepts using molecular and bioinformatic tools. Prerequisites: Biology 101/102, and Chemistry 101/102. Lecture-laboratory.

Biology 372 - Cellular Biology

Full course for one semester. An in-depth study of the structure-function relationships within eukaryotic cells. The course emphasizes macromolecular organization and compartmentation of cellular activities. Lecture topics include evolution of cells, cellular reproduction, motility, signal transduction, cell-cell interactions, energy transduction, functional specialization, cell death, and cancer. Laboratories investigate models of cellular regulation and incorporate methods that integrate morphological and biochemical techniques. Prerequisites: Biology 101/102 and Chemistry 101/102. Chemistry 201/202 is recommended. Lecture-laboratory.

Biology 381 - Neurobiology and Physiology

Full course for one semester. An examination of the nervous and endocrine systems, especially as they relate to the unique physiological challenges faced by animals. The course begins with fundamental concepts and mechanisms of nervous system function, followed by an exploration of the role that endocrine systems play in integrating a range of interdependent physiological processes. Readings from the primary literature will be chosen to demonstrate the multidisciplinary approaches used by researchers to investigate neurobiological and physiological processes. The laboratory will provide hands-on training in neurophysiological techniques that students will use to investigate their own questions. Prerequisite: Biology 101 and 102 and Chemistry 101 and 102. Chemistry 201 and 202 are recommended. Lecture-laboratory.

Biology 431 - Seminar in Biology: Contemporary Topics

One-half course for one semester. An examination of current topics and areas in biology with an emphasis on primary literature. Participants will lead group discussions and/or make oral presentations. Prerequisites: Biology 101/102, two additional units of biology with laboratory, and junior or senior standing. Conference. Not all topics offered every year.

Bacterial Pathogenesis. An examination of how bacterial pathogens interact with host organisms in order to cause disease. Topics include adhesion, colonization, invasion, toxins, subversion of host cell signaling events, immune evasion, and bacteria-to-bacteria communication as they pertain to pathogenesis.

Behavioral Genomics. An exploration of current research that pairs genomic techniques and bioinformatics approaches with classic questions in animal behavior.

Chromosome Structure and Function. Investigation of elements needed for chromosome stability, using contemporary studies of telomere metabolism, regulation of telomere length, and the role telomeres play in cellular senescence and cancer. Prior coursework in genetics or cell biology is required.

Computational Cancer Biology. Investigation of computational methods to analyze high-throughput biological measurements collected from hundreds to thousands of cancer samples. Biological topics include tumor classification, tumor heterogeneity, and dysregulated signaling pathways. Computational topics include algorithms and models to synthesize, integrate, and manage large-scale cancer datasets.

Cytoskeletal Dynamics. An exploration of our current understanding of the cytoskeleton and its role in cell migration, morphogenesis, and disease. We will explore the primary literature and discuss how the cytoskeleton (actin, microtubules, and intermediate filaments) is regulated and how the molecular motors (kinesin, dynein, and myosin) contribute to cellular function.

Developmental Neurobiology. An exploration of our current understanding of how brains and eyes form, focusing on the visual system. Our investigations will focus on patterning, size determination, morphogenesis, neuronal connectivity, regeneration, stem cells, and cancer. Examples of developmental diseases will provide context. This course includes a collaborative writing component.

Ecology and Evolution of Plant-Human Interactions. Ecological and evolutionary contexts of interactions between plants and humans. Potential topics include agricultural ecology, grazing, plant-resource extraction, crop evolution and their diseases/pests, plant breeding, transgenic species, and invasive plants.

Evolutionary Genetics. The course will focus on reading, discussing, and presenting papers from the primary literature. Topics may include a variety of phenomena and ideas in genetics and evolution. For example, we can focus on papers related to mechanisms of non-Mendelian inheritance, genetic conflict, levels of selection, codon bias, vertical versus horizontal transmission genetics, gene drive, genetic engineering, the evolution of chromosome number/shape, organellar evolution, complex trait evolution, and/or the evolution of sex determination systems.

Global Change Ecology. In light of ongoing environmental change, how are the Earth’s ecological systems likely to respond? We will discuss and present primary literature related to advanced basic and applied concepts in ecology to 1) explore the theories and tools for understanding the ecological response to environmental change and 2) identify sources of uncertainty for accurately understanding such issues.

The Human Microbiome. Microbes comprise over 90% of the cells of the human body, and form distinctive communities in different regions of our bodies. The microbiome is a complex and dynamic community of microbes having major impact on human health. Using the primary literature, we will investigate how the microbiome intersects with organ development, the immune system, gut health and nutrient acquisition, acute and chronic disease, dysbiosis, and behavior.

Integrative Neuroethology. Neuroethology is an integrative approach to understanding the neural basis of behavior. While the discipline has historically been dominated by physiological approaches, neuroethologists today increasingly rely on genomic and bioinformatics tools to address their questions. We will explore modern research that integrates physiological and genomic approaches to understanding how evolution has shaped behaviors and the neural circuits that generate them.

Molecular Genetic Analysis of Plant Evolution. An exploration of issues of current controversy and active research in plant evolution, highlighting places where molecular techniques and data are providing new insights for classical problems in plant evolution.

Neuroethology. Exploration of modern and classic research aimed at understanding the neural basis of behavior. Neuroethologists investigate how the brains of diverse species generate natural behaviors, with the goal of elucidating fundamental principles of brain function. Topics may include animal communication, learning and memory, locomotion, prey capture, and escape behavior.

Plant Biotechnology. An exploration of emerging technologies, especially genetic engineering, that are revolutionizing agriculture and allowing for the production of plants with enhanced qualities. Emphasis will be placed on the molecular and physiological principles involved as well as the ecological risks and benefits.

Biology 463 - Immunology

One-half course for one semester. A discussion of the properties of innate and adaptive immunity, the cells of the immune system, antibody structure and function, antigen recognition, lymphocyte activation, and immunity to microbes. Topics also covered will include immunodeficiency and AIDS, and transplantation. An inquiry-based laboratory exercise will be required. Prerequisite: Biology 101, 102, and one of Biology 358 or 372. Lecture-laboratory-conference.

Not offered 2017–18.

Biology 470 - Thesis

Full course for one year.

Biology 481 - Special Topics

One-half course for one semester. Independent laboratory or library research on a topic chosen in consultation with the instructor. A final written report is required. Prerequisites: standing as a junior or senior biology major, and approval of instructor, department, and division.