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Rogers Science Research

2008 Abstracts for Rogers Science Program

April 02, 2008

Faculty Abstacts


Paulette Bierzychudek: Restoring violets and butterflies to Cascade Head preserve

Cascade Head (CH) supports one of the last populations of the Oregon silverspot butterfly (OSB). Its larvae feed only on leaves of Viola adunca. We hypothesize that OSB numbers have declined because violet densities are too low for successful hostplant-finding by larvae, and plan to supplement violet numbers at CH. This summer we will: a) quantify the foraging behavior of larvae in different violet densities (how densely must violets be planted?), b) determine how to prepare sites for restoration (which methods produce the highest violet survival?), and c) discover whether violets from different populations differ in their success.

Prerequisites: Students should be patient, conscientious, have good manual dexterity, and some experience gardening/growing plants. Physical fitness (hike several miles, carrying loads), ability to focus while cold and wet are essential. Some experience performing statistical analyses/graphing data highly desirable.

Greta Binford – 1: Molecular evolution of the toxic enzyme sphingomyelinase D in venoms of brown spiders (Loxosceles)

Brown spider (Loxosceles) bites cause dermonecrotic lesions in human tissues. An enzyme in these venoms, sphingomyelinase D (SMD), is central to lesion formation. The genus Loxosceles has 100 species from the Americas, Africa and Mediterranean Europe. One student on this project will use DNA sequences to estimate phylogenetic relationships among species of brown spiders and their relatives. Another student will express SMD genes from a range of species related to the brown recluse and analyze the enzymatic activity. Results will elucidate the evolutionary processes that have led to the current distribution of SMD, and improve treatment and diagnosis of bites.

Prerequisites: Bio 200 required, Biol 311/312, Biol 390 and 408 preferred but not required.

Greta Binford – 2: Evolutionary patterns of neurotoxin expression in spider venoms

Venoms of spiders in the genus Loxosceles and Sicarius (Sicariidae) are notorious for causing dermonecrotic lesions in mammals. While the causal agent for dermonecrosis is well known, these venoms also include a complex of proteins and peptides with unknown bioactivity. The specific objectives for this summer’s work are to: (1) use DNA-based approaches to isolate and express uncharacterized peptide toxins from sicariid venoms; (2) assay purified expression products for insecticidal activity; (3) preliminarily characterize the specific mechanism of neurotoxic activity of insecticidal toxins. This work will be done in collaboration with Dr. Janis Lochner and Dr. Nikolaus Loening.

Prerequisites: Biol 200 required; 311/312, 390 and 408 preferred but not required.

Greg Hermann: Investigating the biogenesis of lysosomes in a multi-cellular animal.

Lysosomes are membrane bound organelles that function as major degradative sites within cells. While much is known regarding the biochemical activities of lysosomes, the processes involved in their assembly and maintenance remain poorly understood. An understanding of these processes is important since the abnormal release of lysosomal contents is associated with a variety of human diseases including, Alzheimers, arthritis, and cancer. We are characterizing the function of genes necessary for the assembly and stability of lysosomes in the model organism, Caenorhabditis elegans. Our work will focus on investigating the cellular pathways controlled by these genes.

Prerequisites: BIO151, BIO 200, & BIO 311/312 or BIO 361

Peter Kennedy - 1: Examining patterns of Frankia diversity in canopy and ground roots of Alnus rubra in the Olympic National Rainforest.

This project will investigate patterns of diversity of a microbial symbiont of the tree Alnus rubra (Alder) in Olympic National Park. Specifically, the research will compare the strain diversity of an actinomycete bacterium in the canopy and belowground roots of alders. Students will participate in bacterial nodule collection, which will involve a week of tree climbing and camping in the ONP in the second week of May. The samples will then be processed at Lewis and Clark using molecular techniques to quantify bacterial diversity in each location. A student comfortable working outdoors and having some familiarity with molecular analyses is preferred.

Prerequisites: Bio 141, Bio 151

Peter Kennedy – 2: Exploring the structure of ectomycorrhizal fungal communities in alder and Doug fir forests in the Tillamook State Forest.

This project will examine the community structure of fungi associated with the roots of alder (Alnus rubra) and Douglas fir (Pseudotsugua menziesii) in the Tillamook State Forest. Specifically, the research will involve a molecular characterization of the hyphal communities of fungi present in each forest type. Students research will include DNA extraction, PCR, cloning, sequencing, and phylogenetic analysis. The student will also be involved in the set-up and harvesting of a greenhouse bioassay from the soils of each forest type. A strong background with molecular techniques and familiarity with basic statistical principles is greatly preferred.

Prerequisites: Bio 141, Bio 200, Bio 311

Deborah Lycan: Nuclear export: How are ribosomal subunits exported through nuclear pores?

The eukaryotic ribosome is the largest and most complex RNA:protein machine assembled in higher cells. It is composed of some 80 ribosomal proteins and 3 ribosomal RNAs. Assembly of the ribosome has been analyzed most extensively in the unicellular eukaryote, S. cerevisiae. Ribosome assembly is a highly complex and coordinated process that occurs mostly in the nucleus from pre-made protein components that are imported from the cytoplasm. The two subunits are assembled independently and exported through nuclear pores at rates that can exceed 40 subunits/sec in exponentially growing cells. More than150 accessory proteins are required for the proper assembly and export of ribosomes in yeast. Many of these proteins have been implicated in rRNA modification and cleavage, but recently proteins with other roles in assembly and in export have been identified. Nonetheless, it is fair to say that we are largely ignorant of the details surrounding eukaryotic ribosome assembly and export. For example, we do not know the order of protein addition or how this is controlled, which steps are under regulatory control (ribosome biogenesis is linked to the growth state of the cell), how subunits are exported and whether export is subject to quality control to ensure that only fully functional subunits leave the nucleus for the cytoplasm.

In my lab we are studying three proteins with roles in the assembly of the small 40S subunit; RpS3, Yar1 and Ltv1. RpS3 is a structural component of the mature 40S subunit, and it interacts with both Yar1 and Ltv1. Cells lacking either Yar1 or Ltv1 produce only half the normal number of 40S subunits. These cells are also defective in rRNA processing, which could be the cause or the consequence of other defects in ribosome assembly or export. Students in my lab have shown that Ltv1 shuttles between the nucleus and cytoplasm via the exportin protein, Xpo1, and that RpS3 export is reduced in cells lacking Ltv1. Our working model is that Ltv1 may be an export adapter for 40S subunit, linking the pre40S subunit to the XpoI exportin. Work this summer will be directed towards exploring this hypothesis. Experiments in my lab involve genetic, biochemical, molecular and cell biological techniques.

Prerequisites: Biology 200. Molecular Biology 311/312 or Cell Biology 360 preferred but not required

Gary Reiness: Characterization of a “non-classical” protein secretion pathway. This project has been withdrawn.

We study protein secretion. Most secreted proteins exit cells through the �classical� pathway, moving sequentially through the endoplasmic reticulum, Golgi apparatus, and secretory vesicles before being released. Some secreted proteins, including ciliary neurotrophic factor (CNTF), which we study, use some other, unknown, pathway(s). CNTF acts in cell-to -cell communication during formation of the nervous system. Thus investigating �nonclassical� secretory pathways will aid understanding of intercellular communication and nervous system development. Several projects in cell and molecular biology are available, including microscopic analysis of the cellular structures involved in CNTF secretion and manipulation of CNTF to identify its secretory signal.

Prerequisites: Students must have completed Biology 200. I prefer students who have taken Cell Biology (Bio 361), Molecular Biology (Bio 311/312), or Biochemistry plus lab (Chem 335/336). Familiarity with fluorescence microscopy and molecular biological techniques is highly desirable.


Anne Bentley: Formation of Nanoparticle / Solid State Thin Film Composite Materials via Electrochemical Co-Deposition

This project will explore a new approach to solid-state materials synthesis: the incorporation of nanoparticles into thin films formed on electrodes by reducing metal ions at an electrode surface. Tuning the chemistry of the nanoparticle and electrode surfaces will provide control over the formation of the composite. Nanoparticles that emit visible light under UV illumination will be embedded in transparent metal oxide films, and their luminescence properties are expected to improve. Students will gain experience in nanoparticle synthesis, altering surface coatings, and electrodeposition. Characterization tools will include IR spectroscopy, fluorescence spectroscopy, powder X-ray diffraction, and electron microscopy.

Prerequisites: Chemistry 110 and 120

James Duncan: CASSCF Computational Investigation of the Mechanisms of [3,3]Sigmatropic Rearrangements

Our group studies mechanisms of organic reactions by performing high-level quantum mechanical calculations on computers, most commonly employing a so-called Complete Active Space (CAS) method. We seek to further understand the fundamental nature of reacting molecules through close examination of the molecular orbitals thought to be most involved (CAS ones) in a particular reaction. This summer we expect to complete a promising study, begun last summer, of so-called allenyl Cope rearrangements that appear to be highly stereoselective in an interesting way. Then we hope to expand our study to include other similar rearrangements, defined as [3,3]sigmatropic, with particular emphasis on determining whether they are “pericyclic” (changes in bonding relationships take place on a closed curve of interacting orbitals) or “pseudopericyclic (bonding changes involve at least one orbital disconnection). Students will routinely use what are arguably the two most sophisticated suites of computational software currently available—Gaussian and MOLCAS—and be introduced to the latest advances in computational chemistry.

Prerequisites: Successful Completion of Chemistry 210 and 220 (Organic Chemistry I and II) or equivalent.

Louis Kuo – 1: Isolation and Purification of Diterpenoid Metabolites Used in Herbivory Deterrence from marine Algae. This work will be done in collaboration with Dr. Ken Clifton

Organic molecules that deter herbivore activity have applications towards pest control and anti-cancer studies. On coral reefs, where herbivore activity by fish play a significant ecological role, several classes of compounds have been isolated from marine algae, including a class of metabolites that contain carbon double bonds. These diterpenoids deter herbivory and concentrations appear to vary during the reproductive ecology of algae in the genus Halimeda. The first portion of the project entails isolation of these diterpenoids from marine algae to the point where they can be quantified in ecological studies and chemically labeled for cellular investigations in algae.

Prerequisites: Chem 220 (Full year of Organic chemistry), Chem 366 and Chem 365 Preferred (Inorganic Physical chemistry laboratory), Bio 141, 151 and 200 (Biology core courses)

Louis Kuo -2: Hydrolysis of phosphate triester neurotoxins with Organometallic Complexes

This project explores using a class of organometallic complexes called metallocenes (metal = molybdenum) to carry out the degradation of a class of phosphate neurotoxins. Phosphino-thioates are the functional core of neurotoxins, some of which have been used as pesticides. Besides inert and strong P-alkyl and P=O bonds, the core consists of P-S and P-O linkages wherein the preferably mode of degradation involves cleavage of the P-S bond; scission of the P-O bond yields a complex just as toxic as the parent neurotoxin. We have recently found that molybdenum metallocenes yields this preferable bond scission on a model phosphinothioate in aqueous solution. This project will synthesize new molybdenum complexes with the objective of determining structure-activity relationships on how metallocenes affect the degradation/hydrolysis of phosphinothioates.

Prerequisites: Chem 220 (Full year of Organic chemistry), Chem 366 preferred (Inorganic chemistry laboratory)

Janis Lochner: Synaptic secretion of neuromodulators implicated in long-term memory formation

Long-term memory formation occurs in the hippocampus and is accompanied by enduring changes in synaptic organization. The structural and functional changes that underlie these changes in synaptic efficacy are triggered by the release of neuromodulators. To better understand the molecular determinants of synaptic plasticity, we will characterize the properties and cellular mechanisms of secretion of neuromodulators from cultured hippocampal neurons. The proposed studies rely on the use of molecular cloning techniques to create fluorescent chimeras of neuromodulatory proteins and multi-wavelength, time-lapse fluorescence imaging to follow release of these chimeras from synaptic sites.

Prerequisites: Bio 200 and Chemistry 220 required

Niko Loening -1: Identification of the Autofluorescent and Optically Active Material Present Within Caenorhabditis elegans Intestinal Lysosomes

Soil nematodes, including C. elegans, have been known for over a century to contain autofluorescent and optically active intestinal material. Based on these characteristics, past researchers have suggested that the material is composed of tryptophan catabolites, retinol, or lipofuscin/“age pigment”. Although the characteristics of this material indicate the presence of chiral molecules and of delocalized electron bonds, nothing else is known about the specific chemical composition. We will work in collaboration with Dr. Greg Hermann’s group to continue the isolation of this material, and then use a variety of chromatographic and spectroscopic techniques to identify the chemical composition of the material.

Prerequisites: Instrumental chemistry skills such as those gained in Chem 220 (Organic II), Chem 365 (Physical Chemistry Lab), and/or Chem 355/Physic 201 (Experimental Methods in the Physical Sciences), Experience handling biological samples. Coursework in biology/biochemistry/molecular biology.

Niko Loening – 2: The Development and Characterization of Chemical Shift Thermometers for Nuclear Magnetic Resonance Spectroscopy

The goal of the proposed research is to design improved chemical-shift thermometers (CSTs) for use in solution-state nuclear magnetic resonance (NMR) spectroscopy. Our plan is to use paramagnetic molecules as CSTs, and then to encapsulate them within dendrimers or micelles so that they do not adversely affect the NMR spectrum. The proposed development of better CSTs will allow more accurate quantification of physical parameters by NMR spectroscopy and help solve problems of sample stability.

Prerequisites: Synthetic chemistry skills (Chem 220 at a minimum, additional advanced courses preferred). Some background in quantum mechanics and spectroscopy is useful, but not necessary.

Niko Loening – 3: Structural Studies and Characterization of Neurotoxic Venom Peptides from Sicariidae Spiders

Spider venoms contain hundreds of components, including neurotoxic peptides and proteins. These venom components are of interest for their potential use as therapeutic drugs and as tools for neurophysiology research, as many of them specifically inhibit or activate ion channels and receptors in nerve cells. The aim of this research is to discover interesting peptides and proteins from the venom of the brown recluse spider and its relatives (the Sicariidae spiders), and then to characterize their structure and function. We will recombinantly-express spider venom peptides and then use NMR spectroscopy to study the structures of venom peptides. This work will be done in collaboration with Dr. Greta Binford and Dr. Janis Lochner.

Prerequisites: Biochemistry lab experience…particularly with generating and working with protein samples. Coursework in biochemistry/molecular biology (preferably structural biochemistry and/or Chem 464)


Dr. Liz Safran: Impact of Extrafluvial Events on River Valley Evolution

Dr. Liz Safran is recruiting students to conduct geologic research with her on the impacts of large landslides and lava flows on river channel incision in central and eastern Oregon. These large, infrequent events have the potential to alter a river’s behavior for tens of thousands to millions of years. Dr. Safran and a team of collaborators from Central Washington University; University of Nevada, Reno; U.S. Geological Service; and U. S. Forest Service are doing some geologic detective work to determine the conditions under which the river’s business of chopping down through bedrock is either slowed or accelerated by “invasions” by landslides or lava flows. The research will involve a combination of: 1) spatial analyses using Geographic Information Systems (GIS) software; 2) several multi-day field excursions to sites of interest in central and eastern Oregon; 3) analysis of topographic patterns using tools available in Matlab, a high-level programming language.

Prerequisites: Geology 150 *OR* basic computer programming skills

Mathematical Sciences

Jens Mache: Wireless Sensor Networks

Wireless sensor networks can create what Scientific American deemed “macroscopes,” systems of small devices that can collaboratively detect events in the physical world, such as temperature, sound, vibration, motion or pollutants. Named to MIT Technology Review’s list of “10 Emerging Technologies that Will Change the World,” sensor networks combine potentially hundreds of low-powered, remotely-deployed mini-computers, embedded in the physical world. New applications as well as security issues are rising. In order to achieve performance, scalability and robustness, many system problems have to be solved. This project includes studying existing systems, writing software and experimentation with various designs and algorithms.

Prerequisites: Computer Architecture CS 277 or Internet Security CS 495


Thomas Olsen -1: Observation, Measurement, and Control of Chaos in Modified Taylor-Couette Flow

Taylor-Couette Flow is the motion of a fluid layer between two concentric cylinders, at least one of which is moving. Our system of interest is modified in that the inner cylinder is hourglass shaped. For a certain rotation rate of the inner cylinder, vortices (doughnut shaped patterns of fluid flow) form. We are concerned with the time intervals between vortex formation and the spatial variation of the position of vortex formation. We pursue this study both in the laboratory and via computer models. We seek algorithms for perturbing the system so as to return it to periodic vortex formation.

Prerequisites: For numerical calculation, classes in computer programming, linear algebra, and differential equations would be valuable. For experimental studies, Physics 201 “Methods of Experimental Physics” would be useful.

Thomas Olsen -2: Observation and Modeling of Eclipsing Binary Star Systems

Most stars are members of groups of two or more stars. Some binary pairs, viewed along their orbital plane, are seen to eclipse each other. We have measured the period for a complete mutual orbit of pairs of stars. In one, we have determined the rate at which this orbit is slowing. There is also a repeating perturbation with a period on the order of 60 years. We will continue to monitor the evolution of this and other star systems. We will model the appropriate gravitational interactions numerically to determine if the perturbation might be due to a planet.

Prerequisites: For numerical calculation, experience with Mathematica™ would be valuable. For observational studies, Physics 201 “Methods of Experimental Physics” would be useful.

Stephen Tufte: Investigating Interstellar Matter in Face-on Spiral Galaxies using Integral Field Spectroscopy

The universe is organized into a vast number of galaxies, each one a gravitationally bound collection of stars and interstellar material. Stars form within interstellar clouds, and once formed they affect their interstellar environment through intense star light, stellar winds, and sometimes by generating giant explosions called supernovae. When stars expire, they return some of their material to the interstellar medium where it is eventually incorporated into the next generation of stars. Understanding galaxies and how they evolve requires an understanding of this complex cyclic process.

We will investigate face-on spiral galaxies with data from the WIYN 3.5m telescope on Kitt Peak in Arizona. A new observational technique was used that allows the simultaneous measurement of high-resolution spectra for each location on the galactic image. The research students will help analyze these spectra probing the heating, excitation, and motions of interstellar gas in the vicinity of star forming regions with the goal of better understanding the interplay of stars and interstellar material in galaxies.

Prerequisites: Computer skills are desirable. Astronomy knowledge a plus.


Erik Nilsen: Dispositional and Physiological Influences on Risky Decision Making in the Game of Dice Task.

Since 1994, the Iowa Gambling Task (IGT) has been used to support Damasio’s Somatic Marker Hypothesis (SMH) that states that effective decision-making is aided by existence of a emotion-related physiological signal that is impaired by damage to the prefrontal lobes. However, the IGT has recently been criticized on methodological and theoretical grounds. This study examines a new laboratory task designed to address these problems. Participants with varying levels of impulsivity will play two versions of the Game of Dice Task to assess both behavioral and neurophysiological measures to try to distinguish between the impact of ambiguity and risk on betting.

Prerequisites: Statistics (Psych. or Math Stats)

Yueping Zhang: Dimensions of risk-taking: personality traits, behavioral measures, prefrontal lobe functions, and autonomic arousal

This project investigates the underlying psychological and physiological mechanisms of risk-taking by examining the relations among self-report measures of relevant personality traits (sensation seeking and impulsivity), a neuropsychological measure of prefrontal functions, a behaviorally-based measure of risk-taking, and autonomic nervous system activity. By incorporating carefully selected measures from different dimensions in one experiment, the current study will allow us to examine how variables from these dimensions relate to one another and to risk-taking tendencies and behaviors. Such research has important practical applications in understanding and intervention of risky behaviors such as drug addiction, unprotected sex, reckless driving and gambling.

Prerequisites: Courses in Statistics and Research Methods, offered by department other than psychology department are acceptable.