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Biochemistry [clear]

Title	Offering	Standing	Credits	Credits	When	F	W	S	Description	Preparatory	Faculty	Days	Multiple Standings	Start Quarters	Open Quarters
Biogeochemistry: Microbes, Rocks, and Soils Andrew Brabban and Abir Biswas biochemistry biology chemistry environmental studies field studies geology	Program	SO–SRSophomore–Senior	16	16	Day			S 16Spring	This upper-division science program will examine the interplay between the biological and chemical processes of the Earth's hydrosphere and lithosphere. Many environmental processes occur as a result of specific microbial processes that are intrinsically controlled by the substrate (geology) and the geochemical parameters (redox, pH), making these studies inherently interdisciplinary.Over the quarter, we will investigate biotic and abiotic controls on the cycling of important elements (specifically key biological and chemical elements of carbon, nitrogen, iron, etc., and elements we often consider toxic such as arsenic and heavy metals) in both "pristine" and polluted systems, and in aerobic to anaerobic systems. Students will cover topics in environmental microbiology examining the roles microorganisms play in the environment, their metabolism, and the broad diversity of the ecosystems they occupy. Likewise, students will cover topics in geochemistry and geobiology examining the role of microbes in element cycling at the Earth's surface. Laboratory work will focus on both classical microbiological methods, as well as newer biochemical and molecular procedures to determine the biodiversity of soil and water samples and the activity of specific organisms within an ecosystem. In addition, students will learn field sampling techniques, collect soil and/or water samples in the field during day trips, and conduct relevant geochemical analyses in the laboratory to elucidate element cycles. Weekly seminars and student presentations discussing recent research from the primary literature will be important components of the program.		Andrew Brabban Abir Biswas	Mon Mon Tue Wed Wed Thu	Sophomore SO Junior JR Senior SR	Spring	Spring
Molecule to Organism Paula Schofield and James Neitzel biochemistry biology chemistry Signature Required: Fall Winter Spring	Program	SO–SRSophomore–Senior	16	16	Day	F 15 Fall	W 16Winter	S 16Spring	This program develops and interrelates concepts in experimental (laboratory) biology, organic chemistry, and biochemistry, thus providing a foundation for students who plan to continue studies in chemistry, laboratory biology, field biology, and medicine. Students will carry out upper-division work in organic chemistry, biochemistry, cellular and molecular biology, and genetics in a yearlong sequence. The program integrates two themes, one at the cell level and the other at the molecule level. In the cell theme, we start with the cell and microbiology and proceed to the whole organism with the examination of structure/function relationships at all levels. In the molecular theme, we will examine organic chemistry, the nature of organic compounds and reactions, and carry this theme into biochemistry and the fundamental chemical reactions of living systems. As the year progresses, the two themes continually merge through studies of cellular and molecular processes in biological systems.Each aspect of the program will contain a significant laboratory component. On a weekly basis, students will write papers and maintain laboratory notebooks. All laboratory work and approximately half of the non-lecture time will be spent working in collaborative problem-solving groups. Spring quarter student-designed research projects are a culmination of all major concepts learned throughout the year.This is an intensive program. The subjects are complex, and the sophisticated understanding we expect to develop will require devoted attention and many hours of scheduled lab work each week.		Paula Schofield James Neitzel		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring
The Science of Sensory Perception Neil Switz and Michael Paros biochemistry biology physics physiology	Program	SO–SRSophomore–Senior	16	16	Day	F 15 Fall			Students in this lower-division physics/optics and upper-division biology program will gain exposure to how the sensory organs and systems for touch, taste, smell, hearing, and vision work on a basic scientific level. Students will learn the fundamental steps in sensory perception, starting with the transmission of a given physical phenomenon from the outside world to a molecular cell receptor and ending with neurophysiologic interpretation by the brain.The physics component of the program will focus primarily on the wave behavior and optics underlying the detection of sound and light. In the biology component, the somatosensory, olfactory, gustatory, auditory, and visual systems will be used as focused topics to study more general concepts in molecular cell biology and neuroscience.Weekly assignments will consist of textbook readings with assigned problem sets as well as primary scientific and review papers. Electrophysiology, cell signaling, synaptic function, neuroanatomy, psychophysics, and neural integration will be emphasized for each sensory system studied, with special emphasis on physics of the auditory and visual systems (wave propagation, interference, and ray optics). Laboratory sessions will reinforce the physics and biology concepts learned in lecture and provide students with opportunities to learn fundamental optical, cell, and molecular biology techniques.This program is appropriate for students interested in pursuing further work in biophysics, biological research, neurobiology, and the biomedical sciences. Students who successfully complete this program will attain upper-division credit in cell biology, molecular biology, and neuroscience, and lower-division credit in both introductory physics (equivalent to one quarter of algebra-based physics) and biophysics.		Neil Switz Michael Paros		Sophomore SO Junior JR Senior SR	Fall	Fall
Temperate Rainforests: Genetics and Biogeochemistry Dylan Fischer and Clarissa Dirks biochemistry biology ecology environmental studies	Program	JR–SRJunior–Senior	16	16	Day	F 15 Fall			Forested ecosystems are complex biogeochemical systems represented by a genetically diverse array of species. Forests are some of the largest carbon sinks on Earth, while hosting a complex array of ecological interactions linked to ecosystem processes. Further, genetic variation is poorly understood in these systems for both macro- and microorganisms. By focusing on genetic variation, evolutionary history, and biogeochemistry in these forests, we will learn about the interplay between biotic and abiotic phenomena. We will examine techniques for assessing genetic diversity, ways of understanding patterns in population genetics, and the potential for linkages between genetic variation in forest organisms and ecological processes in forests.Our lectures, laboratory work, and field labs will focus on forests across a range of elevations, latitudes, and climates. We will also have a multi-day overnight trip at the beginning of the quarter to see patterns in forest ecosystems and large-scale experiments firsthand. Laboratory work will allow students to learn about new methods and applications in molecular biology and ecological genetics. Students will also acquire experience with various sampling techniques that are used to measure nitrogen, water, and carbon in forested ecosystems. Weekly seminars will focus on understanding scientific articles from the primary literature. Students will develop scientific research projects throughout the quarter that require the development of research and quantitative skills. We will emphasize fundamental concepts in ecology and genetics, techniques in molecular biology and biogeochemistry, scientific writing, and communication skills.		Dylan Fischer Clarissa Dirks	Tue Wed Thu Fri	Junior JR Senior SR	Fall	Fall
Undergraduate Research in Scientific Inquiry Paula Schofield, Richard Weiss, Andrew Brabban, Neil Switz, Brian Walter, Abir Biswas, Michael Paros, Dharshi Bopegedera, Rebecca Sunderman, EJ Zita, Donald Morisato, Clarissa Dirks, James Neitzel, Sheryl Shulman, Neal Nelson and Lydia McKinstry biochemistry biology chemistry computer science mathematics physics Signature Required: Fall Winter Spring	Program	SO–SRSophomore–Senior	V	V	Day	F 15 Fall	W 16Winter	S 16Spring	Rigorous quantitative and qualitative research is an important component of academic learning in Scientific Inquiry. Research opportunities allow science students to work on specific projects associated with faculty members’ expertise. Students typically begin by working in an apprenticeship model with faculty or laboratory staff and gradually take on more independent projects within the context of the specific research program as they gain experience. Students can develop vital skills in research design, data acquisition and interpretation, modeling and theoretical analysis, written and oral communication, collaboration and critical thinking. These are valuable skills for students pursuing a graduate degree or entering the job market. Faculty offering undergraduate research opportunities are listed below. Contact them directly if you are interested. (geology, earth science) studies nutrient and toxic trace-metal cycles in terrestrial and coastal ecosystems. Potential projects could include studies of mineral weathering, wildfires, and mercury cycling in ecosystems. Students could pursue these interests at the laboratory scale or through field-scale biogeochemistry studies, taking advantage of the Evergreen Ecological Observation Network (EEON), a long-term ecological study area. Students with backgrounds in a combination of geology, biology, or chemistry can gain skills in soil, vegetation, and water collection and learn methods of sample preparation and analysis for major and trace elements. (biotechnology) studies the physiology and biochemistry of prokaryotes of industrial and agricultural importance. Students who commit at least a full year to a research project, enrolling for 4 to 16 credits each quarter, will learn a broad range of microbiology (both aerobic and anaerobic techniques), molecular (DNA analysis and cloning), and biochemical techniques (chemical and pathway analysis, protein isolation). Students will also have opportunities for internships at the USDA and elsewhere, and to present data at national and international conferences. (chemistry) would like to engage students in two projects: (1) There is concern that toxic metals are found in unsafe quantities in children’s toys and cosmetics. She would like to engage a student in the quantitative determination of these metals, using the AA and the ICP-MS. Students who are interested in learning to use these instruments and quantitative analysis techniques will find this project interesting. (2) Science and education. With Dharshi, students will work with local teachers to develop lab activities that enhance the science curriculum in local schools. Students with an interest in teaching science who have completed general chemistry with laboratory would be ideal for this project. (3) Dharshi is also interested in looking at chemicals present in e-cigarettes. A student interested in this project could work on the organic or inorganic chemicals. (biology) conducts research in many areas of microbiology and ecology. Her recent work in microbiology has focused on the biodiversity and distribution of tardigrades in different ecosystems. She also aims to better understand the evolutionary principles that underlie the emergence, spread, and containment of infectious disease by studying the co-evolution of retroviruses and their hosts. Lastly, she is conducting snail surveys in Washington state to better characterize the species in the state, something that hasn’t been done in many decades. Depending on the project, students will gain experience in molecular biology technique, microbiology, field ecology, genetics, bioinformatics, and tissue culture. (organic chemistry) is interested in organic synthesis research, including asymmetric synthesis methodology, chemical reaction dynamics, and small molecule synthesis. One specific study involves the design and synthesis of enzyme inhibitor molecules to be used as effective laboratory tools with which to study the mechanistic steps of programmed cell death (e.g., in cancer cells). Students with a background in organic chemistry and biology will gain experience with the laboratory techniques of organic synthesis,as well as the techniques of spectroscopy. (biology) is interested in the developmental biology of the embryo, a model system for analyzing how patterning occurs. Maternally encoded signaling pathways establish the anterior-posterior and dorsal-ventral axes. Individual student projects will use a combination of genetic, molecular biological, and biochemical approaches to investigate the spatial regulation of this complex process. (biochemistry) uses methods from organic and analytical chemistry to study biologically interesting molecules. A major focus of his current work is on fatty acids; in particular, finding spectroscopic and chromatographic methods to identify fatty acids in complex mixtures and to detect changes that occur in fats during processing or storage. This has relevance both for foods and in biodiesel production. The other major area of interest is in plant natural products, such as salicylates. Work is in process screening local plants for the presence of these molecules, which are important plant defense signals. Work is also supported in determining the nutritional value of indigenous plants. Students with a background and interest in organic or analytical biochemistry will contribute to this work. (computer science) is interested in working with advanced computer topics and current problems in the application of computing to the sciences. His areas of interest include simulations of advanced architectures for distributed computing, advanced programming languages and compilers, and programming languages for concurrent and parallel computing. (physiology, microbiology, veterinary medicine) is interested in animal health, diseases that affect the animal agriculture industry, and basic ecology of bacteriophage in physiologic systems. Currently funded research includes the development of bacteriophage therapy for dairy cattle mastitis. A number of hands-on laboratory projects are available to students interested in pursuing careers in science, with a particular emphasis on microbiology. (organic, polymer, materials chemistry) is interested in the interdisciplinary fields of biodegradable plastics and biomedical polymers. Research in the field of biodegradable plastics is becoming increasingly important to replace current petroleum-derived materials and to reduce the environmental impact of plastic wastes. Modification of starch through copolymerization and use of bacterial polyesters show promise in this endeavor. Specific projects within biomedical polymers involve the synthesis of poly (lactic acid) copolymers that have potential for use in tissue engineering. Students with a background in chemistry and biology will gain experience in the synthesis and characterization of these novel polymer materials. Students will present their work at American Chemical Society (ACS) conferences. (computer science) is interested in working with advanced computer topics and current problems in the application of computing to the sciences. Her areas of interest include advanced programming languages and compilers, programming language design, programming languages for concurrent and parallel computing, and logic programming. (inorganic/materials chemistry, physical chemistry) is interested in the synthesis and property characterization of new bismuth-containing materials. These compounds have been characterized as electronic conductors, attractive activators for luminescent materials, second harmonic generators, and oxidation catalysts for several organic compounds. Traditional solid-state synthesis methods will be utilized to prepare new complex bismuth oxides. Once synthesized, powder x-ray diffraction patterns will be obtained and material properties such as conductivity, melting point, biocidal tendency, coherent light production, and magnetic behavior will be examined when appropriate. (physics) develops optical instruments for use in biophysical and biomedical applications, including low-cost diagnostics. Projects in the lab are suitable for motivated students with quantitative backgrounds in physics, biology, chemistry, mathematics, or computer science. (mathematics) is interested in problems relating to graphs, combinatorial games, and especially, combinatorial games played on graphs. He would like to work with students who have a strong background in mathematics and/or computer science and are interested in applying their skills to open-ended problems relating to graphs and/or games. (computer science, mathematics) has several ongoing projects in computer vision, robotics, and security. There are some opportunities for students to develop cybersecurity games for teaching network security concepts and skills. In robotics, he is looking for students to develop laboratory exercises for several different mobile robotic platforms, including Scribbler, LEGO NXT and iRobot Create. This would also involve writing tools for image processing and computer vision using sequences of still images, videos treams and 2.5-D images from the Kinect. In addition, he is open to working with students who have their own ideas for projects in these and related areas, such as machine learning, artificial intelligence, and analysis of processor performance. (marine science) studies the developmental physiology and ecology of marine invertebrates. She is interested in the biochemistry of the seawater-organism interface, developmental nutritional biochemistry and metabolic depression, invasive species, carbonate chemistry (ocean acidification), and cultural relationships with foods from the sea. Students have the opportunity to collaboratively develop lines of inquiry for lab and/or field studies in ecology, developmental biology, physiology, marine carbonate chemistry and mariculture. (physics), who has expertise in energy physics, modeling, and organic farming, is researching sustainability and climate change. Many students have done fine projects on sustainable energy and food production in her academic programs. Zita is working with Judy Cushing and Scott Morgan to establish a new research program at Evergreen. She and Cushing will model land use impacts on climate change; she and Morgan will plan and facilitate sustainability projects on campus. More information on Zita's research is available at .		Paula Schofield Richard Weiss Andrew Brabban Neil Switz Brian Walter Abir Biswas Michael Paros Dharshi Bopegedera Rebecca Sunderman EJ Zita Donald Morisato Clarissa Dirks James Neitzel Sheryl Shulman Neal Nelson Lydia McKinstry		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring
Undergraduate Research in Scientific Inquiry with J. Neitzel James Neitzel biochemistry Signature Required: Fall Winter Spring	Research	SO–SRSophomore–Senior	V	V	Day	F 15 Fall	W 16Winter	S 16Spring	Rigorous quantitative and qualitative research is an important component of academic learning in Scientific Inquiry. Research opportunities allow science students to work on specific projects associated with faculty members’ expertise. Students typically begin by working in an apprenticeship model with faculty or laboratory staff and gradually take on more independent projects within the context of the specific research program as they gain experience. Students can develop vital skills in research design, data acquisition and interpretation, modeling and theoretical analysis, written and oral communication, collaboration and critical thinking. These are valuable skills for students pursuing a graduate degree or entering the job market. (biochemistry) uses methods from organic and analytical chemistry to study biologically interesting molecules. A major focus of his current work is on fatty acids; in particular, finding spectroscopic and chromatographic methods to identify fatty acids in complex mixtures and to detect changes that occur in fats during processing or storage. This has relevance both for foods and in biodiesel production. The other major area of interest is in plant natural products, such as salicylates. Work is in process screening local plants for the presence of these molecules, which are important plant defense signals. Work is also supported in determining the nutritional value of indigenous plants. Students with a background and interest in organic, analytical or biochemistry could contribute to this work.	biochemistry, alternative energy, health sciences.	James Neitzel		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring