Biochemistry and Molecular Biology Track
EBS 512 /EBS 612 Biochemistry I: Proteins and Enzymes
Primary, secondary and tertiary structure of proteins; enzyme mechanisms; enzyme kinetics.
EBS 513 /EBS 613 Biochemistry II: Introduction to Molecular Biology
DNA replication, RNA synthesis and protein synthesis; genetic code; gene regulation.
EBS 514 /EBS 614 Biochemistry III: Metabolism and Bioenergetics4 credits
Metabolism of carbohydrates, lipids and amino acids; bioenergetics; photosynthesis; oxidative phosphorylation.
EBS 515 /EBS 615 Environmental and Biomolecular History of the Earth
This course will explore the origin and evolution of the environment, including physical, chemical and biological contributions and interactions. Topics will be taught along a timeline from the origin of the earth to present day, and will include the biological and chemical evolution of Earth; an introduction to metabolism and microbial energetics; effect of the environment on microbial growth, activity and processes; microbial interactions and evolution of higher organisms.
EBS 516 /EBS 616 Metals in Environmental & Human Health
This course covers bioinorganic chemistry in environmental systems. Topics will include oxidation-reduction cycles, metal speciation, receptors and uptake systems, micronutrient requirements and utilization, enzymology and distribution of enzymes in the environment.
EBS 517 /EBS 617 Environmental Systems and Human Health4 credits&n
This course addresses perturbations of Earth’s biogeochemical cycles by human activities, and the impacts of resulting environmental hazards on human health and natural ecosystems. Lecture materials provide assessment of molecular to global scale processes in covering the tangible relationships between environmental degradation and human health. Student assignments confront current problems related to nitrogen pollution, climate change, and disease pressures.
EBS 510 /EBS 610 Aquatic Chemistry4 credits
General acid/base concepts (mono- and polyprotic systems); pH; making activity corrections; numerical calculations; titration concepts as applied to natural systems; buffer intensity; dissolved CO2 chemistry; acidity and alkalinity in open CO2 systems; minerals and their role in controlling natural water chemistry; solubility characteristics of oxide and hydroxides; introduction to redox chemistry in natural systems; pe-pH diagrams.
EBS 535 /EBS 635 Chemistry of Organic Contaminants4 credits
This course provides an overview of the processes that determine the fate of organic substances in the environment and impact on human health. It covers pathways, mechanisms, and kinetics of volatilization, sorption, hydrolysis, oxidation, reduction, elimination, and conjugation; and the application of all these topics to understanding the environmental fate and remediation of organic chemicals. Media represented include reactor fluids, groundwater, surface water, rain, and fog. Both chemical (abiotic) and microbially-mediated (biotic) processes are included.
Term Offered Winter
EBS 575 /EBS 675 Chemical Transport Processes in Environmental Health4 credits
The aim of this class is to introduce mass transport to graduate students. The basic processes of chemical mass transport will be studied and the students will be introduced to the equations governing mass transport. Some familiarity with multivariate calculus and differential equations will be helpful, but not required.
EBS 565 /EBS 665 Estuary and Ocean Systems I
First of two-course sequence. This fast-paced two-course sequence provides an advanced introduction to marine systems. The sequence covers multiple scales, from cells to ocean basins. It is structured in three discipline-centric segments (cross-scale circulation processes, marine biogeochemistry, and marine organisms). Estuaries and Ocean Systems I covers marine biogeochemistry and climate-scale ocean circulation, while Estuaries and Ocean Systems II (offered Winter quarter) covers marine organisms and estuary-plume-scale circulation.
EBS 566 Estuary & Ocean Systems II4 credits
Second of two-course sequence. This fast-paced two-course sequence provides an advanced introduction to marine systems. The sequence covers multiple scales, from cells to ocean basins. It is structured in three discipline-centric segments (cross-scale circulation processes, marine biogeochemistry, and marine organisms). This course covers marine organisms and estuary-plume-scale circulation.
EBS 517 /EBS 617 Environmental Systems and Human Health4 credits
This course will cover environmental hazards and their impact on human health and on natural ecosystems. It will include the assessment of molecular to global scale processes of 2 or 3 general topics (e.g., metal contaminants, organic contaminants, and infectious agents). Each year, the specific topics will be chosen corresponding to their societal significance and impacts on natural ecosystems and human health. Students will apply what they learn in class to a final project on a related topic of their choice.
EBS 511 /EBS 611 Advanced Aquatic Chemistry4 credits
Role of complexing ligands in solution chemistry; redox chemistry in natural systems; pe-pH diagram construction and use; solid/solution interfacial considerations; the electrical double layer; and selected advanced topics. Prerequisite: EBS 510/610.
EBS 518 /EBS 618 Metals in Biochemistry4 credits
Comprehensive study of the chemistry and biochemistry of metal ions in biological molecules and living systems. Topics include metalloprotein structure, metal ion specificity, biological oxidation mechanisms, metal ion catalysis in enzymes, metal ion transport and gene regulation.
EBS 520 /EBS 620 Coordination Chemistry
Structures and stabilities of transition metal coordination compounds with mono- and multi-dentate ligands; coordination compounds as models for biological metal centers; strategies for synthesis of transition metal complexes.
EBS 525 /EBS 625 Bioenergetics and Membrane Transport
Critical evaluation of the chemiosmotic theory with specific reference to oxidative phosphorylation, photophosphorylation and metabolite transport. Biochemical mechanisms of energy transduction common to bacterial and mitochondrial respiration, and bacterial and plant photosynthesis are reviewed.
EBS 528 /EBS 628 Enzyme Structure, Function and Mechanisms4 credits
Provides an in-depth analysis of the structural origins of protein interactions and catalysis that are the basis for biological function. The course develops the basic principles of structural biology through an overview of X-ray crystal structures and folding processes, acquainting the students with computational resources for protein structure analysis. The structural foundation is expanded into a detailed investigation of enzyme active sites, including the application of kinetic approaches to understanding enzymatic reaction mechanisms.
EBS 537 /EBS 637 Chemical Degradation and Remediation
A thorough introduction to the transformation reactions that contribute to the fate of organic substances in the environment. The course covers pathways, mechanisms and kinetics of hydrolysis, oxidation, reduction, elimination, conjugation, etc. Treatment is balanced to reflect the importance of these processes in all types of environmental waters ranging from engineered systems to groundwater, surface water, rain and fog. Recommended preparation: EBS 510/610, 511/611 and/or 535/635.
EBS 540 /EBS 640 Instrumental Methods in Biophysics I
Theory and application of physical techniques to problems in biochemistry. Optical, fluorescence, circular dichroism, infrared and Raman spectroscopy of chromophoric groups. Magnetic susceptibility and nuclear magnetic resonance of metalloproteins.
EBS 541 /EBS 641 Instrumental Methods in Biophysics II
Investigation of physical techniques particularly useful for studying metalloproteins. Electron paramagnetic resonance, electron spin echo, magnetic circular dichroism and X-ray absorption spectroscopy. The course has significant “hands-on” exposure to both instrumentation and computer simulation techniques.
EBS 547 /EBS 647 Uncertainty Analysis
A survey of basic probability concepts followed by introductions to several statistical advanced techniques that play an important role in environmental data analysis. Topics may include distribution functions, propagation of error, hypothesis testing, analysis of variance, experimental design, sampling theory, regression analysis, time-series analysis and spatial statistics techniques. The course provides a balance of theory and application using environmental data sets.
EBS 550 /EBS 650 Environmental Systems Analysis
Introduction to techniques of systems analysis applied to environmental quality management. Emphasis is on development and application of mathematical models with computer simulation and optimization. Analysis includes efficient computational algorithms and search techniques. Linear and separable programming applied to evaluate management alternatives. Applications to air, water, solid and hazardous waste management. Prerequisites: Computer programming and calculus.
EBS 555 /EBS 655 Computational Fluid Dynamics
This course describes advanced topics in computational fluid dynamics, including specialized discrete methods (e.g., for advection-dominated problems), formal analysis of stability and accuracy, and selected simulations of complex environmental and biological systems. Prerequisites: Advanced calculus and EBS 545/645.
EBS 560 /EBS 660 Introduction to Environmental Observation and Forecasting Systems4 credits
This course introduces environmental observation and forecasting systems and their application toward the enhanced understanding and management of natural resources. Emphasis is on estuaries and coasts. Students are exposed to a novel, cross disciplinary culture for understanding and interacting with environmental systems. This culture relies heavily on "real-time" generation of modeling and observational data, which are integrated and distributed through information networks designed to bring the right environmental information at the right time to the right user. Prerequisite: Instructor permission.
EBS 570 /EBS 670 Groundwater and Watershed Hydrology
Hydrologic cycle, principles of unsaturated and saturated flow in the subsurface; characterization of groundwater/surface interactions, water balance, modeling of watershed-scale processes.
EBS 571 /EBS 671 Groundwater Modeling
Applied groundwater modeling using the finite difference method. Introduction to numerical methods for solving the partial differential equations for saturated and unsaturated subsurface flow. Model execution and calibration. Prerequisite: EBS 570/670.
EBS 572 /EBS 672 Contaminant Hydrology
Processes controlling subsurface contaminant movement in porous and fractured media, including groundwater flow, dispersion, diffusion, sorption, and degradation. Parameter estimation, mathematical and laboratory modeling of aquifers is also covered.
EBS 573 /EBS 673 Modeling in Contaminant Hydrogeology4 credits
This course is designed to be taken concurrently with EBS 572/672. It emphasizes the hands-on use of common mathematical models for groundwater flow and transport (e.g., MODFLOW/MODPATH/ MT3D/RT3D) to examine real groundwater contamination problems. Prerequisite: EBS 572/672.
EBS 585 /EBS 685 Advanced Molecular Biology
An in-depth study of the molecular mechanisms governing the replication, recombination, transcription, and translation of genetic material. Emphasis is placed on experimental approaches that have led to our understanding of these fundamental processes.
EBS 586 /EBS 686 Molecular Genetics of Development
A focused study of selected topics examining the regulation of gene expression during cellular differentiation. Emphasis is placed on the molecular nature of cell-cell interactions and the genetic control of complex cellular responses to developmental and environmental stimuli.
EBS 590 /EBS 690 Environmental Microbiology
Introduction to environmental microbiology, with emphasis on the role of microbes in the environment and in remediation processes. Microbes and their interaction and activities in soil and aquatic environments will be discussed, as well as elemental cycling as influenced by microbes. Microbially mediated transformation of organic pollutants, transformation kinetics and remediation technologies will be considered. In 2003-2004, may be offered in combination with EBS 593/563.
EBS 593 /EBS 693 Biodegradation and Bioremediation4 credits
A process-oriented survey of microbially mediated transformations of organic pollutants. Transformations occurring in the natural environment as well as in remediation technologies are considered. Emphasis is on the pollutant properties, microbiological factors, and medium properties that determine the pathways and kinetics of biodegradation. Recommended preparation: EBS 590/690.
EBS 502 M.S. Independent Study1 to 12 credits
Typically involves a scholarly and critical review of an advanced scientific topic by one or more students together with one or more faculty members. Requirements of the student typically include a written review paper and/or a seminar to be given as part of EBS 507A/607A - EBS 507B/607B - EBS 507C/607C. Selection of this course for credit and the topic to be investigated must be approved by the SPC. For letter grade only.
EBS 505A /EBS 605A Reading Group: Environmental and Biomolecular Systems
Presentation and discussion of journal articles from the recent literature in environmental and biomolecular systems.
EBS 505C /EBS 605C Reading Group: Molecular Biology and Biochemistry
Presentation and discussion of journal articles from the recent literature in molecular biology, genetics and biochemistry.
EBS 505D /EBS 605D Reading Group: Environmental Science and Engineering
Presentation and discussion of journal articles from the recent literature in environmental science and engineering.
EBS 506 /EBS 606 Special Topics
3 to 4 credits
Special topics courses are offered in areas of particular relevance to the research interests of faculty or in response to industry needs. Special Topic courses are subject to change and are offered intermittently
EBS 506 EDA/EBS 606 EDA Special Topics in Environmental Data Analysis
This course will be an interactive forum for discussing and analyzing data contributed by the students in the class. In the first two weeks, students will present the critical data analysis challenges they face in their research. Several of these challenges will be selected to be pursued as case studies; with the class developing the background and applying statistical data analysis software to solving each problem. Short lectures will be given to provide the theoretical background for different data analysis methods, computer lab assignments will be used to provide students with hands-on experience in analyzing data, and class discussions will be used to interpret and discuss results. Data analysis software that may be used includes MatLab, R, or SAS. Students are welcome to use their favorite software to work on class assignments.
EBS 506 ESH/EBS 606 ESH Topics in Environmental Systems and Human Health
This course will discuss the origin, transmission and impacts of environmental hazards - one chemical contaminant (mercury) and one infectious disease agent (cholera). The course will provide a cross-scale understanding of each environmental hazard, from the molecular basis of the problem to its global implications. Course instruction will be focused on lectures, modeling exercises, student seminars, and literature readings.
EBS 506 ETM/EBS 606 ETM Estuarine Turbidity Maximum
The course addresses, through a mix of lectures, literature reviews, and hands-on data analysis, a complex and important process in estuaries: the Estuarine Turbidity Maximum (ETM). The umbrella framework for the course is provided by a set of questions: What are ETMS? Where do ETMs occur? What causes ETMs? Why are ETMs important? How can ETMs be observed/modeled? How do ETMs vary in time? How do ETMs affect estuarine productivity and microbial communities? How are ETMs affected by climate and human activities? What do ETMs look like in the Columbia River estuary?
EBS 506 ITF/EBS 606 ITF Indian Tribes and the Federal Government
The unique governmental status of Indian Tribes and their relationship to other governments federal, state and local with an emphasis on natural resources. For people working within the natural resource management fields, it is important to learn basic facts about Tribes, treaty rights and the federal trust responsibility to protect Tribes and tribal resources. The course will explore mutual responsibilities of Tribes and the US, as well as delegated responsibilities of the federal government to states and local governments.
EBS 507A /EBS 607A Division Seminar
Weekly seminars by invited guests. Public visitors are welcome.
EBS 507B /EBS 607B Student Seminar and Presentation Class2 credits
The student presentation reading group provides a supportive, interdisciplinary scientific environment where students will improve their oral presentation skills through instruction and practice. Each week a platform and a poster presentation will be given by students, then a discussion of each presentation will follow, and anonymously written comments will be provided to each speaker.
Research and Internships
EBS 503 M.S. Thesis Research1 to 12 credits
Research toward the M.S. thesis degree.
EBS 501 M.S. Non-Thesis Research
1 to 12 credits Supervised research as a component of the M.S. non-thesis degree. The plan of research and final deliverables must be approved by the research advisor and the SPC. Deliverables include a written report and/or seminar given as part of EBS 507A. A maximum of 8 credits from EBS 501 may be applied to a degree.
EBS 504 /EBS 604 Professional Internship1 to 12 credits
Professional internship credits provide students an opportunity to earn credit for relevant work experience in industry. Students gain valuable industrial experience that allows them to both apply the knowledge gained in the classroom and prepare for careers following graduation. Students on F-1 or J- 1 visas must obtain prior written approval for internships from OHSU's Office of International Students and Scholars before enrolling. Enrollment requires a faculty advisor and is limited by the number of internship opportunities available.
EBS 601 Ph.D. Prequalifying Research
1 to 12 credits
Research toward the dissertation for the Ph.D. degree before completing the comprehensive examinations.
EBS 603 Ph.D. Dissertation Research
1 to 12 credits
Research toward the dissertation for the Ph.D. degree after completing the comprehensive examinations.