2013-14 Catalog

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2013-14 Undergraduate Index A-Z

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Biochemistry [clear]


Title   Offering Standing Credits Credits When F W S Su Description Preparatory Faculty Days Multiple Standings Start Quarters Open Quarters
Lydia McKinstry and Clarissa Dirks
Signature Required: Fall  Winter  Spring 
  Program SO–SRSophomore - Senior 16 16 Day F 13 Fall W 14Winter S 14Spring This program develops and interrelates concepts in experimental (laboratory and field) biology, organic chemistry and biochemistry, thus providing a foundation for students who plan to continue studies in chemistry, laboratory and field biology and medicine. Students will carry out upper-division work in biochemistry, microbiology, cellular and molecular biology, field biology and organic chemistry in a yearlong sequence. This program will also give students many of the prerequisites needed for the following health careers: medicine, dentistry, veterinary medicine, naturopathy, optometry and pharmacy.The program examines the subject matter through the central idea that structure defines function, integrating a scaled theme from the "cell" to the "molecule" and "ecosystem" levels. We will start with the cell and proceed to the whole organism and ecosystem with the examination of structure-function relationships at all levels. We will examine organic chemistry, the nature of organic compounds and reactions and carry this work into biochemistry and the fundamental chemical reactions of living systems. As the year progresses, the scaled theme will continue through studies of cellular and molecular processes in biological systems.Each aspect of the program will contain a significant laboratory component, some of which may be based on field experiments, involving extensive hands-on learning. On a weekly basis, students will be writing papers and maintaining laboratory notebooks. All laboratory work, and approximately one half of the non-lecture time will be spent working in collaborative problem solving groups. Group work will also include reading and discussion of topics of current or historical significance in science. This is an intensive program; the subjects are complex, and the sophisticated understanding we expect to develop will require students to work for many hours each week, both in and out of class. laboratory and field biology, chemistry, education, medicine and health science. Lydia McKinstry Clarissa Dirks Sophomore SO Junior JR Senior SR Fall Fall Winter Spring
Paula Schofield and Andrew Brabban
  Program FR ONLYFreshmen Only 16 16 Day F 13 Fall W 14Winter Are you curious about the world around you? Would you like to really understand "buzz terms" the media uses such as sustainability, green materials, climate change, the water crisis, the energy debate, genetic engineering, DNA fingerprinting and cloning? How can we believe what we are being told? What is the evidence? How is scientific data actually collected, and what analytical methods are being used? Are the correct conclusions being drawn? As responsible citizens we should know the answers to these questions.In this two-quarter program we will demystify the hype surrounding popular myths, critically examine the data, and use scientific reasoning and experimental design to come to our own conclusions. In fall, we will study "water" and "energy" as themes to examine our environment, considering local and global water issues. We will also examine current energy use and demand, critically assessing various sources of energy: fossil fuels, nuclear, hydropower, etc.We will begin the program on September 23 (Orientation Week), one week BEFORE the regularly scheduled fall quarter start, so that we are prepared for our field trip by beginning our study of energy, and establishing our learning community. The Eastern Washington field trip will be a unique opportunity for personalized tours of Hanford Reactor B (the world's first full-scale nuclear reactor which produced the plutonium for the "Fat Man" bomb dropped over Nagasaki in 1945), Grand Coulee Dam (the largest hydropower producer in the U.S.), and the Wild Horse Wind and Solar Energy facility (150 turbines across 10,000 acres serving more than 80,000 homes). On this trip, we will also learn key field science techniques: how to take measurements in the field, collect samples for laboratory analysis and precisely determine concentrations of nutrients and pollutants.In winter quarter, we will use "natural and synthetic materials" as a theme to study petrochemical plastics, biodegradable plastics and other sustainable materials, as well as key biological materials such as proteins and DNA. We will carefully examine the properties of these materials in the laboratory and study their role in the real world. "Forensics" will be our final theme, learning techniques such as DNA fingerprinting, blood spatter analysis, ballistics and other modern forensic procedures.In this field- and lab-based program, scientific analysis—rather than conjecture or gut-feeling—will be the foundation of our work. Other class activities will include small group problem-solving workshops, seminars, student researched presentations and lectures. Paula Schofield Andrew Brabban Freshmen FR Fall Fall Winter
Paula Schofield, Neil Switz, David McAvity, Andrew Brabban, Brian Walter, Richard Weiss, Abir Biswas, Michael Paros, Clyde Barlow, Judith Cushing, Dharshi Bopegedera, Rebecca Sunderman, EJ Zita, Donald Morisato, Clarissa Dirks, James Neitzel, Sheryl Shulman, Neal Nelson and Lydia McKinstry
Signature Required: Fall  Winter  Spring 
  Program SO–SRSophomore - Senior V V Day F 13 Fall W 14Winter S 14Spring 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. (chemistry) works with biophysical applications of spectroscopy to study physiological processes at the organ level, with direct applications to health problems. Students with backgrounds in biology, chemistry, physics, mathematics or computer science can obtain practical experience in applying their backgrounds to biomedical research problems in an interdisciplinary laboratory environment.. (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 could 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) Quantitative determination of metals in the stalactites formed in aging concrete using ICP-MS. Students who are interested in learning about the ICP-MS technique and using it for quantitative analysis will find this project interesting. (2) Science and education. We will work with local teachers to develop lab activities that enhance the science curriculum in local schools. Students who have an interest in teaching science and who have completed general chemistry with laboratory would be ideal for this project. (computer science, ecology informatics) studies how scientists might better use information technology and visualization in their research, particularly in ecology and environmental studies. She would like to work with students who have a background in computer science or one of the sciences (e.g., ecology, biology, chemistry or physics), and who are motivated to explore how new computing paradigms can be harnessed to improve the individual and collaborative work of scientists. Such technologies include visualizations, plugins, object-oriented systems, new database technologies and "newer" languages that scientists themselves use such as python or R. (biology) aims to better understand the evolutionary principles that underlie the emergence, spread and containment of infectious disease by studying the coevolution of retroviruses and their primate hosts. Studying how host characteristics and ecological changes influence virus transmission in lemurs will enable us to address the complex spatial and temporal factors that impact emerging diseases. Students with a background in biology and chemistry will gain experience in molecular biology techniques, including tissue culture and the use of viral vectors. (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, analytical or biochemistry could contribute to this work. (computer science) and (computer science) are interested in working with advanced computer topics and current problems in the application of computing to the sciences. Their areas of interest include simulations of advanced architectures for distributed computing, advanced programming languages and compilers, programming languages for concurrent and parallel computing and hardware modeling languages. (biology, veterinary medicine) is interested in animal health and diseases that affect the animal agriculture industry. Currently funded research includes the development of bacteriophage therapy for dairy cattle uterine infections, calf salmonellosis and mastitis. A number of hands-on laboratory projects are available to students interested in pursuing careers in science. (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 simulations of advanced architectures for distributed computing, advanced programming languages and compilers, programming languages for concurrent and parallel computing, and hardware modeling languages. (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. (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 who 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, video streams 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. (physics) studies the Sun and the Earth. What are the mechanisms of global warming? What can we expect in the future? What can we do about it right now? How do solar changes affect Earth over decades (e.g., Solar Max) to millennia? Why does the Sun shine a bit more brightly when it is more magnetically active, even though sunspots are dark? Why does the Sun's magnetic field flip every 11 years? Why is the temperature of the Sun’s outer atmosphere millions of degrees higher than that of its surface? Students can do research related to global warming in Zita's academic programs and in contracts, and have investigated the Sun by analyzing data from solar observatories and using theory and computer modeling. Serious students are encouraged to form research contracts and may thereafter be invited to join our research team. Please go to the catalog view for specific information about each option. Paula Schofield Neil Switz David McAvity Andrew Brabban Brian Walter Richard Weiss Abir Biswas Michael Paros Clyde Barlow Judith Cushing 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
James Neitzel
Signature Required: Fall  Winter  Spring 
  Research SO–SRSophomore - Senior V V Day F 13 Fall W 14Winter S 14Spring 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