Faculty in the Department of Environmental and Biomolecular Systems at the OGI School of Science & Engineering are committed to stimulating students' research interests at all academic levels. We seek motivated upper-level undergraduate students who are interested in hands-on research in preparation for graduate school in a related field of science or engineering. Students will have opportunities to interact with faculty, post-doctoral, doctoral and masters students while learning new skills and contributing to scientific research.
The availability of research opportunities differs with each faculty mentor. Some opportunities may be available only in the summer, while others will be able to accommodate students throughout the academic year. To apply for any of the research positions listed below, please contact the faculty mentor directly.
The OGI School of Science & Engineering is one of the four schools of Oregon Health & Science University, an equal opportunity, affirmative action institution. We particularly welcome applications from women, minorities, and individuals with disabilities.
This project focuses on the characterization of environmental stressors in complex natural systems. We selected the Columbia River estuary where research is being actively used to address controversial management and sustainability issues (Bottom et al. 2001; USACE 2001) with the support of an advanced coastal observatory (Baptista 2002; Baptista 2004). Specific focus will be in characterizing the spatial and temporal variability of salinity, temperature and oxygen concentrations. The student will be introduced to state-of-the-art understanding of the estuary and its climate context, will be trained in the use of CORIE modeling tools (Baptista et al. 2004; Zhang et al. 2004 (Accepted)) and field instruments and procedures, and will design and conduct two model-assisted estuarine cruises to map the physical dynamics of specific estuarine environments: in principle, an estuarine turbidity maxima and a tidal flat. Physical data collected in the cruises will be integrated with multi-year databases of observations and simulations of water levels, velocities, salinity and temperature to provide specific physical context, in time and space, to biological and chemical samples simultaneously collected by other students during the cruises. [back]
Metal ions such as Fe, Cu, Zn, Mn, and Mo are essential to life. In general they form the active centers of a wide variety of enzymes with activities ranging from electron transfer to biosynthesis and biodegradation. However, these metals are also extremely toxic at higher concentrations, and cells have evolved complex mechanisms that ensure that metal ion concentrations are maintained at safe levels within the cell, without compromising the ability to selectively metallate important enzymes and pathways. These systems involve a critical balance between import, internal transport and export functions, and utilize novel transporters and chaperone proteins that maintain homeostasis. In addition to handling essential metal ion nutrients, cells must also be able to sequester and detoxify metal ion contaminants such as Cd, Hg, As, and Se. In this project we will investigate metal ion distributions across the Columbia River estuary (Blasco et al. 1999; Mierzykowski and Carr 2000). Of particular interest will be the levels of the essential metals Fe, Cu and Zn, and whether these nutrients are limiting. We will also investigate levels of the heavy metal contaminants Cd, As, Se, and Tl. To assess the effects of these contaminants on estuarine populations we will analyze the hemolymph of crayfish for the presence of these metals. This has a number of advantages: (a) protein components can be separated by chromatography and correlated with metal ion concentration (b) the proteins present in these fractions can be analyzed by mass spectrometry and their identity (metallothioneins, chaperones, transporters) determined by comparison with known or consensus sequences (c) crayfish from coastal rivers such as the Nehalem can be used as controls (d) exposure of the crayfish to elevated levels of metal ions under laboratory conditions can be used to calibrate dose-response data. The project will give undergraduate students training in techniques of metal analysis by ICP optical emission spectrometry, chromatographic separation and characterization of proteins by mass spectrometry, and other state-of-the-art methods. [back]
Iron porphyrins (hemes) are utilized as enzyme cofactors throughout biology to activate molecular oxygen and catalyzed reactions such as monooxygenases essential to life. For example, cytochromes P450 (CYPs) enzymes are involved in the biosynthesis of a wide variety of lipophilic endogenous compounds such as steroids and prostaglandin, and they participate in the detoxication response to exposure to xenobiotic chemicals (e.g., drugs and environmental contaminants). Their catalytic function can metabolize these exogenous molecules, produce carcinogenic molecules, and as a by-product of these processes produce reactive oxygen species detrimental to the cell. While the number of CYP families and subfamilies identified via basic molecular techniques continues to expand, characterization at the molecular level of specific P450 enzymes remains very limited. Focused structural information can be obtained from the rich spectroscopic signatures of heme cofactors. Electronic absorption, Fourier-transform IR absorption, electron spin resonance, and resonance Raman spectroscopies are tools we will employ to study hemoproteins (Koo et al. 2000; Auclair et al. 2001; de Vries et al. 2003). The student will be exposed to protein purification, spectroscopic data acquisition, data handling, and data analysis. The student will also learn basic techniques relating to the control of the samples’ anaerobicity, oxygenation, and redox cycles. [back]
Project Title: Control of gene expression in a saprophytic fungus
Matthew Sachs
(msachs@ebs.ogi.edu)
![[Summer Student]](http://www.ebs.ogi.edu/images/SummerStudent2.jpg)
An undergraduate in the Sachs lab will involve molecular genetic analyses of gene expression in the model saprophytic fungus Neurospora crassa. N. crassa is different from the model yeast Saccharomyces cerevisiae and is a filamentous fungus that inhabits soil and aquatic environments. N. crassa more closely resembles higher eukaryotes than yeasts in features such as how gene expression is controlled by DNA methylation or by the circadian clock. Dr. Sachs was a co-PI on the NSF-sponsored project to sequence the N. crassa genome (Galagan et al. 2003). Because of this organism’s known genome sequence and its rich history as the subject for genetic, biochemical and cellular studies, the NIH subsequently funded a program project grant to systematically analyze the phenotypes of gene knockout strains; Dr. Sachs is a co-PI on this project. The student's work will focus on using selected knockout strains (a collection of which will be available prior to the onset of the work) to evaluate the consequences of specific mutations on the control of gene expression. Gene expression studies will involve analyses of the knockout's effects on post-transcriptional control (Fang et al. 2004) of gene expression or on the expression of genes located near the N. crassa telomeres. The choice of knockout strains to be used for the research project, and which area(s) will be examined, will be determined by assisting the REU students in formulating testable hypotheses as to why these strains would be predicted to have consequences in one or the other of these areas. For example, strains deficient in nonsense mediated mRNA decay because of a knockout of a gene essential for NMD would be hypothesized to be affected in both areas, because that is what is observed in yeast. These two areas are currently subjects of investigation in Dr. Sachs’ laboratory. Because the student may not have extensive experience with microbiological procedures, in addition to analyses at the molecular level (e.g., immunoblotting) in the Sachs lab, training in classical procedures (e.g., setting up and scoring genetic crosses, measuring growth rates) will be integral components of their research experience. [back]
Project Title: Distribution of archaea across the oxic/anoxic interface of Columbia River estuarine sediments
Holly Simon
(simonh@ebs.ogi.edu)
Microorganisms can, in theory, be useful as indicators of ecosystem health due to their rapid response times to changes in the environment. The low-temperature crenarchaeota represent a ubiquitous, and often abundant, but because of their recalcitrance toward growth in culture, largely unknown group of microorganisms (in terms of their physiology and ecological functions,). Diverse members of this group are known to be present in estuarine sediments, but nothing is known about their niches there (Abreu et al. 2001). The student working on this project will apply cultivation-independent methods (Simon et al. 2000), such as DNA extraction, Polymerase Chain Reaction-Single-Strand Conformation Polymorphism (PCR-SSCP) and real-time PCR to determine the population structure and abundance of members of the low-temperature crenarchaeota in Columbia River estuarine sediments with relation to oxygen availability at the sediment-water surface and in sub-surface layers. These data will be analyzed by the student to determine whether oxygen concentrations are a determining factor in the distribution of crenarchaeota in estuarine sediment layers. This project will expose the student to state-of-the-art cultivation-independent techniques used in environmental microbiology (Delong and Pace 2001), and results from the project will contribute to our understanding of estuarine microbial communities. [back]
![[Summer Student]](http://www.ebs.ogi.edu/images/SummerStudent1.jpg)
One important area of environmental science is the chemistry of organic pollutant degradation. Organic pollutants that are studied in the Tratnyek lab include pesticides, chlorinated solvents, explosives, and phenols. In all cases, the research will be concerned primarily with the kinetics and mechanisms of oxidation-reduction reactions that can degrade these compounds. This research helps to provide the basis for explaining and predicting the fate of organic pollutants in the environment. The understanding such research provides can lead to improved technologies for controlling pollutant contamination and can make regulatory decision-making a more scientific process. For the most part, the work involves experimentation in the laboratory at OGI, although some field sampling is possible. Analysis of pollutant concentrations will be done by gas chromatography and/or liquid chromatography with computer data acquisition. Details on Dr. Tratnyek's research can be found at http://www.ebs.ogi.edu/tratnyek/. [back]
