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Rogers Science Research

2006 Rogers Science Program Abstracts

April 02, 2006

Faculty Abstacts


Paulette Bierzychudek: Pilot experiments for restoring habitat for endangered butterflies

One of the last populations of Oregon silverspot butterflies (OSB) occupies a grassland on the Oregon Coast. We hypothesize that OSB numbers remain low, despite previous attempts at intervention, because densities of its foodplant, Viola adunca, are too sparse for successful hostplant-finding by larval butterflies. We propose a pilot study to determine approaches to test this hypothesis. The pilot study will plant experimental arenas with varying violet densities and observe foraging behavior and survival of OSB larvae, as well as rates of survival and spread of violets. Techniques developed this summer will shape the design of future studies.

Prerequisites: No coursework skills are required; I seek students who are self-directed and enjoy tinkering.

Greta Binford: 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. We will use molecular markers to estimate relationships among species of brown spiders and their relatives. We will also sequence cDNAs of SMD from a range of species related to the brown recluse and reconstruct patterns of molecular evolution of these proteins. Results will help direct research toward understanding the molecular evolution of the unique enzyme SMD and improving treatment and diagnosis of bites.

Prerequisites: Biology 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: BIO 151 or BIO 200. Prefer if have also taken BIO 311/312, BIO 361, or BIO412.

Deborah Lycan: Nuclear export: How do enormous particles like the ribosomal subunits get 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 premade protein components that must be imported from the cytoplasm. The two subunits are assembled independently and exported through nuclear pores at rates that can exceed 40 subunits/sec. Based on the composition of several ribosome precursor complexes, more than170 proteins are predicted to participate in ribosome biogenesis. So far, the majority of the characterized factors have been implicated in rRNA modification and maturation, but recent work has identified some factors with other roles; in assembly or export. Nonetheless, it would be 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 and to environmental stress conditions and several oncogene proteins are apparently anchored in the nucleolus), 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, Yor1 and Lov1. RpS3 is a structural component of the mature 40S subunit, and it interacts with both Yor1 and Lov1. Cells lacking either Yor1 or Lov1 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 Lov1 shuttles between the nucleus and cytoplasm via the exporting protein, Xpo1, and that RpS3 export is reduced in cells lacking Lov1. Our working model is that Lov1 may be the long sought adapter for the export of 40S subunits from the nucleus. Work this summer will be directed towards testing this model. Experiments in my lab involve genetic, biochemical, molecular and cell biological techniques.

Prerequisites: Bio 200. Molecular Biology or Cell Biology preferred.

Gary Reiness: CNTF Secretion: Cellular and Molecular Mechanisms

We are interested in the mechanisms of protein secretion. Most secreted proteins use a “classical” pathway to exit from cells; they move sequentially through compartments called the endoplasmic reticulum, Golgi apparatus, and secretory vesicles before being released. A few secreted proteins, including the one we study, ciliary neurotrophic factor (CNTF), do not use this classical pathway. CNTF is required for proper formation for the nervous system and, like other secreted proteins, acts in cell to cell communication. Thus understanding intercellular communication requires better characterization of “nonclassical” pathways. A variety of projects are available, depending on student interests and skills.

Prerequisites: Preference given to students who have taken Biology 311/312 and/or Biology 361. Preference given to students with experience with molecular biological techniques and/or fluorescence microscopy.


Barbara Balko: Investigation of the Enhanced Reactivity of Smectite Clays in Contact with Iron Metal

Reductants are often used to remediate organic contaminants in groundwater. The interaction of clay and iron metal creates a reductant, presumably sorbed Fe(II), that is stronger than either the iron metal or the clay. The primary goal of our research is to characterize these sites in terms of location, regeneration time, and reactivity. Our secondary goal is to explore the unique capabilities of the iron-clay system. Specifically, we will investigate how manipulation of the clay environment changes the reactivity of the system. We will use iron electrodes coated with a clay film in our proposed experiments to allow us to electrochemically control the interaction between the clay and iron metal.

Prerequisites: Preference will be given to students who have completed Chem310 (Physical Chemistry: Thermodynamics and Kinetics).

James Duncan: Investigation of Pseudopericyclic Pathways in Electrocyclic and Other Rearrangements Using CASSCF Ab Initio Molecular Orbital Calculations

We have recently studied the Cope rearrangement (usually a six-electron process) of 1 to 2. Through an active-space molecular orbital method, enabled by performing high-level CASSCF computations, we provided evidence that the rearrangement was pseudopericyclic involving eight-electrons, i.e., that the terminal p-bond on the allene group played a significant role in the rearrangement. We propose to extend this orbital method to both uncover and demonstrate other pseudopericyclic rearrangements. For example, the electrocyclic rearrangement of 3 to 4 would be pseudopericyclic if both the terminal p-bond and the lone pair on the nitrogen in 3 played significant roles in the rearrangement.

from Professor James Duncan

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

Janis Lochner: RNA Interference Studies Targeted at Identifying the Calcium Sensor that Triggers the Postsynaptic Release of tPA

Long-term memory formation involves the establishment of enduring changes in synaptic connections. A burgeoning body of data implicates the serine protease, tissue plasminogen activator (tPA), in modulating the plasticity of neural connections during learning and memory formation. Recent work from our laboratory indicates that tPA is localized at postsynaptic sites and is released in response to membrane depolarization. This summer, we propose to use a RNA silencing approach to identity proteins that elicit the calcium-dependent release of tPA from postsynaptic sites in hippocampal neurons:

Prerequisites: Students with a background in biochemistry or cell and molecular biology are preferred.

Nikolaus Loening:

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

Project 2: The Development and Characterization of Chemical Shift Thermometers for Nuclear Magnetic Resonance Spectroscopy

Project 3: Pulse Sequence Development for Nuclear Magnetic Resonance Spectroscopy

Project 1:

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, and Coursework in biology/biochemistry/molecular biology.

Project 2:

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.

Project 3:

Nuclear magnetic resonance (NMR) spectroscopy is a fundamental instrumental technique that has seen application to a wide range of problems, including chemical analysis, screening drug targets, the determination of protein structures, understanding fluid dynamics, and medicine. In comparison to other spectroscopic techniques, NMR has drawbacks in that it is relatively insensitive and advanced experiments can take a long time to complete. This project will focus on the development of techniques that can be used to reduce the experiment time and increase the sensitivity of NMR spectroscopy, including the design of new experiments, physical modifications of the instrument, and the study of advanced processing techniques for analyzing NMR data.

Prerequisites: A solid background in quantum mechanics (chemistry 320, physics 321, or equivalent), Mathematics through Calc II, Experience with computer languages (preferably C/C++), and Basic chemistry laboratory skills

Environmental Studies

Liz Safran: Impact of extra-fluvial events on river valley evolution

This project will focus on documenting and understanding the impact of channel-invading lava flows and large, valley wall landslides on channel evolution in the semi-arid interior of the northwest. These high magnitude, low frequency events introduce coarse debris or new rock to channel beds, thereby potentially inhibiting downcutting locally. On the other hand, some of these events create temporary dams which, if catastrophically breached, can generate floods that dwarf floods of meteorologic origin. We will focus on defining the range of “extrafluvial” (originating outside the channel) events that promote vs. inhibit net channel incision.

Prerequisites: Geology 150, Geology 240

Math Science/Computer Science

Peter Drake: Small Board Computer Go

Writing programs to play the classical Asian game of Go is widely considered one of the grand challenges of artificial intelligence. While Chess programs are on a par with the best human players, Go programs still play at the amateur level. This summer’s work will address Go played on small boards (4x4 through 9x9). We have developed an architecture based on pattern recognition and minimax search. Research will involve expanding the database of patterns (both manually and via machine learning techniques such as genetic algorithms), enriching the pattern representation, and improving the search algorithms.

Prerequisites: Students must know how to play Go and have some experience programming in Java. CS 383 (Algorithm Design & Analysis) is a general prerequisite, but an exceptional student might be accepted with only CS 172 (Computer Science II).

Jens Mache: Network security and Internet research

The Internet, computer networks and distributed systems are fascinating topics. This summer, we will conduct research on grid computing (Globus Toolkit 4), web services and sensor networks. We will focus on security and performance issues. This internship includes studying existing systems, writing software and experimentation with various designs and algorithms.

Prerequisites: CS 172, Computer Architecture (CS 277) and preferably Algorithms (CS 383)

Iva Stavrov – Octonionic Projective Plane

Parallel lines, such as railroad tracks, often appear to us to be intersecting at a very distant point. Projective geometry is often described as a geometry in which every two lines intersect. This geometry can be studied with use of coordinate systems; the coordinates may be real or complex numbers, quaternions or even octonions. This project will rigorously examine octonionic projective plane.

Prerequisites: Required: Linear Algebra (Math 225 or equivalent) and Multivarible calculus (Math 233 or equivalent). Preferred: Geometry (Math 355).

Liz Stanhope: Music of the Sphere Quotients

Using mathematics we can study sphere-shaped drums made from an infinitely thin membrane with perfect spherical curvature. We can mathematically ‘strike’ one of these drums and record the infinite list of tones that the resonating sphere produces. Suppose I fold one of these spheres into a funny shape. Can you tell me what the folded sphere will sound like? If I ask you to close your eyes and listen as I strike the folded sphere, can you tell me how it was folded? We will examine these questions, which arise in the field of pure mathematics called spectral geometry.

Prerequisites: Math 233; and one of: Math 215 or Math 225


Thomas Olsen: Studies in the Characterization and Control of Chaos, with particular applications to One-Dimensional Fluid Flow systems

Systems subject to deterministic evolution in time may proceed in an aperiodic, unpredictable manner. This phenomenon is known as chaos. It requires a system to be extremely sensitive to its initial conditions. This sensitive may be used to return the system to periodic behavior by small perturbations of the initial conditions at the beginning of each cycle, the control of chaos. We will study various control algorithms and their stability. We are especially interested in applications of these algorithms to One-Dimensional Fluid Flow systems. We are actively engaged in modeling such pattern forming systems, to develop more successful control schemes.

Prerequisites: Mastery of mechanics at the level of Physics 151-2; Mastery of differential equations and linear algebra at the level of Math 235 & 225; Mastery of computing at the level of CS 171; knowledge of Mathematica™ and C.

Thomas Olsen: Measurement and Characterization of Eclipsing Binary Star Light Curves

The light from pairs of stars whose orbital plane includes the Earth is seen to vary as the stars eclipse each other. Graphs of these varying light intensities are known as light curves. We extend a 50-year study of nearby eclipsing pairs of stars, with orbital periods that last hours. We seek to observe how the periods of these systems vary over long time spans on the order of decades. In addition, we seek to learn the mechanisms of these changes in the evolution of the individual binary star system.

Prerequisites: Knowledge of astronomy at the level of Physics 105 or 205; Mastery of calculus at the level of Math 132; Mastery of computing at an elementary level.