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Opportunities in Science at Lewis & Clark

2012 Project Descriptions for Rogers and HHMI Programs

February 03, 2012

Each project indicates which program it is eligible for. There are three possibilities:

  • Rogers only: most of the projects.
  • HHMI only: All OHSU projects (end of this list).
  • HHMI and Rogers: some projects are eligible for both programs.

Prerequisites must be completed by the end of spring semester 2012.



Greta J. Binford (Project 1):  How has evolution created the arsenal of toxins in brown recluse venoms?
This project is eligible only for Rogers applicants.

Spider venoms are complex chemical mixtures. Venoms of brown recluse spiders cause dermonecrotic lesions in humans. Their venoms have a dermonecrotic toxin sphingomyelinase D and a suite of other enzymes and neurotoxins. We are characterizing “venomes” of relatives of brown recluse to answer questions about evolutionary dynamics of venom toxins in this lineage. Students working on this project will do transcriptomic and protomic analyses to discover venom-expressed toxins in relatives of the brown recluse. They will compare these transcriptome data with similar data from a phylogenetic spread of other species. The work will involve cloning, sequencing, protein analyses and bioinformatics.

Prerequisites:  Bio 151 required; Bio 200, Bio 311/312, Bio 390 and Bio 408 helpful but not required.


Greta J. Binford (Project 2):  The creation of a biodiversity hotspot: comparative biogeography of Caribbean arachnids
This project is eligible only for Rogers applicants.

The Caribbean is a designated global biodiversity hotspot, yet historical influences of high levels of endemism in the region and not well understood. An international collaborative group of arachnologists is undergoing a large-scale inventory of arachnids on the Caribbean. We are targeting multiple independent lineages of arachnids and comparing their biogeographic histories to uncover shared patterns of divergence in space and time. We will infer the relative influence of geographic isolation and dispersal on patterns of colonization and divergence. We will undertake an expedition to Hispaniola, and use molecular tools to analyze diversity of spiders previously collected on the islands.

Prerequisites:  Bio 151 required; Bio 200, Bio 311/312, Bio 390 and Bio 408 helpful but not required.


Greg J. Hermann:  Investigating the biogenesis of lysosomes in a multi-cellular animal
This project is eligible only for Rogers applicants.

Lysosome related organelles are membrane bound compartments that carry out specialized functions within a diverse array of organisms. While much is known regarding the biochemical activities of these organelles, the processes involved in their assembly and maintenance remain poorly understood. An understanding of these processes is important since the abnormal formation of these compartments underlie a number of human genetic diseases. We are discovering and analyzing the function of genes controlling the assembly of lysosome related organelles in the model organism, Caenorhabditis elegans.

Prerequisites:  Bio 151 or AP equivalent; Bio 200 and Bio 311/312 or Bio 361 suggested but not required.


Peter Kennedy:  Investigating the ecology of plant-microbe symbioses
This project is eligible for HHMI and Rogers applicants.

Our lab’s research focuses on microbial ecology and the factors that determine the structure and diversity of microbial communities. This summer we will be conducting research on the ectomycorrhizal fungal assemblages associated with alder and a range of conifer trees. Part of that work will involve sampling ectomycorrhizal root tips from different forests and growth chamber experiments and using molecular techniques (PCR and sequencing) to identify the fungi present. A second component will be conducting a culture experiment to examine the effects of nitrogen and pH on ectomycorrhizal fungal growth. Students with a background in field ecology, molecular biology, and microbiology are encouraged to apply.

Prerequisites:  Bio 141, Bio 151, Bio 200


Deborah E. Lycan:  Ribosome biogenesis and export
This project is eligible only for Rogers applicants.

The long-term goal of this project is to understand the nuclear export of the eukaryotic small (40S) ribosomal subunit. Ribosomes are among the largest and most complex ribonuclear-protein machines assembled in eukaryotes, and their export, from the nucleus where they are assembled, to the cytoplasm where they function, presents some unusual challenges for cells. First, ribosomes are huge and very hydrophilic compared to the dimensions and hydrophobicity of the nuclear pore. Second, like processed pre-mRNAs, export must be coupled to final assembly to prevent the premature export of incomplete subunits. Export receptors may be key to solving/regulating both these issues. Recently, significant progress has been made towards identifying the export receptors for the large (60S) ribosomal subunit, but the factor(s) necessary to export the small (40S) subunit remain largely undefined. In my lab we use a combination of genetics, biochemistry and microscopy in the yeast S. cerevisae, to understand the role of specific genes in this evolutionarily conserved process.

Prerequisites:  Students should have completed Biology 200. Students who have taken either Cell or Molecular biology will find this background useful.


Tamily Weissman-Unni:  Mapping neuronal circuitry using Brainbow zebrafish
This project is eligible only for Rogers applicants.

Brain function relies upon the precise organization of neural circuits. Relatively little is known about how complex neural circuits form in the nervous system. Our lab uses a new multicolor fluorescence labeling approach (“Brainbow”) to label neuronal populations in many different colors within the living, developing zebrafish brain. Students working on this project will express fluorescent proteins in zebrafish larvae and use fluorescence microscopy to visualize neurons and their connections in vivo. Students will also use 3-D digital reconstruction methods to analyze their data. Our investigations will focus on the mechanisms that underlie neural circuit development and function.

Prerequisites:  Bio 151 or equivalent; additional background in cellular or molecular biology is helpful but not required.



Anne K. Bentley:  Electrodeposition of Transition Metal Oxide Thin Films for Energy Generation and Storage
This project is eligible only for Rogers applicants.

Transition metal oxide thin films are a promising class of materials for use in generating energy from solar sources and storing energy for later use. This project will explore routes to improve thin film electrochemical behavior by the incorporation of metallic and ceramic nanoparticles. Students will gain experience in nanoparticle synthesis, exchanging surface capping agents, and electrodeposition (applying an electrical potential to form a material on an electrode). Characterization tools will include dynamic light scattering, zeta potential measurements, fluorescence spectroscopy, cyclic voltammetry, powder X-ray diffraction, and electron microscopy.

Prerequisites:  Chem 110/120 required.


James A. Duncan:  Fundamental Mechanistic Investigations of (Pseudo)pericyclic and (Pseudo)coarctate Reactions via CASSCF, CASPT2, and DFT Computational Studies
This project is eligible only for Rogers applicants.

Several related fundamental mechanistic studies, involving primarily CASSCF and CASPT2 computational methods, will be carried out simultaneously, with attentive comparison of results. They will build on an original technique we have recently used to differentiate between pericyclic and pseudopericyclic reaction mechanisms. It will do so through the study of additional examples of such reactions whose mechanisms are still controversial, as well as used to differentiate between so-called coactate (meaning constricted) and pseudocoarctate mechanisms. In addition, certain DFT calculations will be carried out for comparison purposes. Finally, the potential energy surfaces mapped at the CASSCF level will be compared to those that will be mapped at the CASPT2 level that includes dynamic electron correlation for all electrons.

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


Louis Kuo:  Degradation of Phosphonothioate Neurotoxins
This project is eligible only for Rogers applicants.

Organophosphates are neurotoxins, and this project looks at the chemistry of organophosphate degradation with water and alcohols. It also seeks to use metal complexes as a catalyst to accomplish this useful transformation in a benign fashion (i.e. neutral pH and room temperature). Sulfur containing phosphates, specifically phosphonothioates, are the targets for this degradation study as these neurotoxins are used in a variety of venues including chemical warfare agents. The work entails organic syntheses of various phosphonothioates to find structure-activity relationships for phosphonothioate degradation (with water or alcohol); NMR spectroscopy is the main tool for monitoring the phosphonothioate hydrolysis or alcoholysis.

Prerequisites:  Chem 220 (required); Chem 366 (preferred)


Nikolaus Loening:  Structural Studies and Functional Characterization of Neurotoxic Venom Peptides from Sicariidae Spiders
This project is eligible only for Rogers applicants.

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 study them using NMR spectroscopy and other techniques. This work will be done in collaboration with Dr. Greta Binford.

Prerequisites:  Bio 312 and/or Chem 336 is required. Chem 350 and/or Chem 464 preferred.


Environmental Science

Jessica Kleiss:  River currents acting as a wave guide in the Columbia River Gorge
This project is eligible only for Rogers applicants.

Waves breaking on the ocean surface play a key role in atmosphere and ocean dynamics. Bubbles are mixed into the water, sea spray is injected into the atmosphere, and wave energy is lost. Yet the effect of ocean currents on wave breaking is poorly understood. In this study, we will use the Columbia gorge as a research site to study wave-current interaction. Video and infrared digital cameras will observe wave breaking, accompanied by estimation of the river current, wind speed, and wave state. The results will inform wave studies in both ocean and river settings.

Prerequisites:  Math 131, 132 (or equivalent), AND Phys 141 & 142, OR  Phys 151 & 152


Elizabeth Safran:  Biting the Bedrock: How Rivers Cut Through Landscapes
This project is eligible only for Rogers applicants.

In many landscapes, the pace and pattern of landscape evolution is set by the rate at which rivers gnaw their way down through bedrock. The Finger Lakes region of central New York exhibits spectacular examples of two key processes of river incision through bedrock: abrasion and quarrying. The conditions that promote the dominance of one process over another are not well understood. We will explore this issue, beginning with a literature review and spatial analyses using geographic information systems (GIS) software and culminating with a brief stint of field work in the Finger Lakes.

Prerequisites:  Geology 150


Mathematical Science

Peter Drake:  Artificial Intelligence and the Game of Go
This project is eligible only for Rogers applicants.

Writing computer programs to play games is an important steppingstone to solving more difficult problems. Computers now outperform humans at almost every widely-played abstract strategy game, including Backgammon, Checkers, Othello, and Chess. The classical Asian game of Go remains unconquered despite recent breakthroughs involving Monte-Carlo simulation. This project seeks to expand and refine these techniques. We are particularly interested in the human ability to divide the board into semi-independent regions, each of which can be considered separately.  This project may end up being funded by the Willamette Valley REU-RET Consortium for Mathematics Research. Interested students should ALSO apply there:

Prerequisites:  Students should have taken at least one (and ideally two) computer science course using the Java programming language. Students must know the rules of Go; any skill at playing the game is a bonus.


Jens Mache (Project 1):  Parallel computing with higher-level languages and compelling examples
This project is eligible only for Rogers applicants.

Computer hardware is undergoing a major shift. Two and four-core machines are now standard, and future processor generations are expected to increase core counts exponentially. This revolution in hardware has dramatic implications for software. Only parallel applications will benefit from increasing core counts, meaning that soon every programmer will need to learn parallel computing. This project seeks to examine higher-level tools and languages for parallel programming that to date have limited adoption. In addition to evaluating languages, the team will explore compelling example applications. This project includes studying existing systems, writing software, and experimentation with various designs and algorithms.

Prerequisites:  Ideally, students took CS-373 Programming Languages, CS-393 Networking, CS-488 Software Development, CS-277 Computer Architecture and CS-383 Algorithms.


Jens Mache ( Project 2):  Cybersecurity Competition Platform to Enhance Security Analysis Skills
This project is eligible only for Rogers applicants.

The widespread use of electronic data processing and electronic business conducted through the Internet fuels the need for security analysis skills. Current security exercises typically lack interactive, experiential components and configuration flexibility. This project seeks to develop a series of configurable cybersecurity scenarios, the infrastructure necessary for running them, and concise documentation that explains security implications. Scenarios may include social networks, firewalls, buffer overflows, capture the flag, recover the network and intrusion detection.

Prerequisites:  CS-495 Security



Shannon O’Leary:  Noise from Quantum Interference to Measure Magnetic Fields
This project is eligible only for Rogers applicants.

This is an experimental quantum optics project. We will investigate an interaction between light and matter that is highly sensitive to magnetic field, specifically laser noise derived from quantum interference in an atomic vapor. The quantum interference process we will use is Electromagnetically Induced Transparency (EIT), which causes an otherwise opaque material to become transparent over a small color range. Because of its sensitivity to magnetic field, laser noise from EIT is an ideal mechanism on which to base a new class of compact and simple atomic magnetometers. Advancement in magnetometry can have profound impacts in diverse array of scientific fields and medical applications.

Prerequisites:  PHYS 151 and 152 (required), PHYS 201 (preferred)


Bethe A. Scalettar:  Release and Retrieval of Dense-Core Granule Proteins in
Hippocampal Neurons
This project is eligible only for Rogers applicants.

Several proteins that have been implicated prominently in learning are housed in, and secreted from, dense-core granules (DCGs) in neurons of the hippocampus. We are conducting experiments directed at determining mechanisms underlying the release and retrieval of DCG cargo proteins in hippocampal neurons induced by a spectrum of stimulation paradigms, including those linked to learning. These results will provide fundamental insight into cellular processes that may underlie learning and will reveal behavior of a DCG protein that has been implicated in physiological and pathological functions in the nervous system, including learning, memory, and neurotoxicity associated with Alzheimerʼs disease.

Prerequisites:  Preference given to applicants who have taken at least a one-year college physics course and a one-semester course on microscopy/imaging, and who have some familiarity with biology.



Erik Nilsen:  Serious Games for Creative Problem Solving and Healthy Behaviors
This project is eligible for HHMI and Rogers applicants.

“Serious games” is a term used to describe games that engage the player, but also aim to achieve a defined purpose other than entertainment. The research this summer will involve conducting two empirical studies of serious games. The first empirical study will be a follow-up to last summer’s project focusing on creative problem solving fostered by a game called SuperScribbleNaut. The second empirical study will be the first evaluation of a new serious game research platform for changing health related behaviors developed in collaboration with LC computer science class in Spring 2012.

Prerequisites:  Statistics (Psych. or Math Stats).


Todd D. Watson:  Neural correlates of cognitive control of food-related stimuli in “external” and “restrained” eaters
This project is eligible for HHMI and Rogers applicants.

Our lab is interested in the relationship between brain function and potentially unhealthy, impulsive behaviors in otherwise healthy adults. To study these phenomena, we employ a variety of research techniques. These include recording Event-Related Potentials (a safe, noninvasive measure of brain activity), conducting computerized cognitive testing, and administering clinical questionnaires. This summer, we will explore the neural, cognitive, and psychological correlates of processing food-related environmental cues in young adults. We will determine if brain responses to food-related stimuli are different in people who may be predisposed to impulsively overeat in certain situations.

Prerequisites:  For the undergraduate students, previous experience with electrophysiological techniques is highly preferred, but not absolutely necessary. No specific skills are required for the high school student other than enthusiasm and interest in neuroscience and psychology.


OHSU Projects (HHMI only)

Research is conducted at Oregon Health & Science University


K. Matthew (Matt) Lattal:  Mechanisms of memory formation and elimination
This project is eligible for HHMI applicants only.

My research examines behavioral and molecular processes that underlie learning and memory. My lab is particularly interested in the ways in which medications can be used to strengthen and weaken drug-associated memories. When a subject experiences a drug of abuse (such as cocaine) in a particular location, re-exposure to that place elicits craving and results in drug seeking, which contributes to maintenance of drug addiction. However, if the drug that is expected in that place is not delivered, the organism eventually learns that the place is no longer a reliable predictor of the drug. As a result of this learning, drug seeking is eliminated. This elimination process is called behavioral extinction, which suppresses the original place-drug memory, but it does not erase that original memory. A challenge for clinical therapies that use extinction is that because the original memory remains intact, drug seeking often returns with time. A major goal of our research is to understand the molecular mechanisms of memory formation and elimination so that we can design pharmacological treatments that enhance the development of extinction, resulting in the persistent suppression of the original memory.

Prerequisites:  Students should be comfortable working with mice.  Experiments may involve injecting substances into mice and histological examination of mouse brains.  Personnel in my lab would help with injections and HHMI students will not have to sacrifice animals, but will have to handle mice daily and conduct behavioral experiments.


Claudio V. Mello:  Research in the Vocal and Auditory Learning Laboratory
This project is eligible for HHMI applicants only.

The Mello Lab investigates vocal learning in songbirds, hummingbirds and parrots. These animals share with humans the ability to learn complex vocalizations, which is the basis for speech and language acquisition. Songbirds provide a unique model system to investigate the behavioral neurobiology of vocal learning and auditory perception. They possess a system of discrete brain nuclei that function in feedback loops during song learning. We use a number of molecular tools to understand the genes that are critically related to the song system and that regulate song production and perception. We make extensive use of in situ hybridization to detect and measure the expression of specific genes in the brain, and we are developing a comprehensive molecular atlas of the zebra finch brain. Specific projects will investigate the effects of ethanol on the juvenile song learning and the underlying development of the song system in the brain. Work will incorporate the use of the zebra finch genome, the second avian genome sequenced to date, which has made it possible for us to apply computational and comparative genomics to better understand brain gene regulation in the context of vocal learning. Students may also participate in efforts to apply transgenic tools to better understand development in the songbird brain.


Jacob Raber:  Genetic and Environmental Impact on Learning and Memory and Anxiety
This project is eligible for HHMI applicants only.

The principal research goal in the Raber laboratory is devoted to the characterization of the effects of genetic and environmental factors on learning and memory and the regulation of anxiety. This characterization is subsequently used to develop and evaluate novel treatments to improve learning and memory and reduce anxiety levels. Specific projects include the decline in learning and memory with age and following exposure to radiation. The research project(s) of the summer intern might involve detailed analyses of already acquired rough data and/or the generation of new data.


Ujwal Schinde: Mechanisms by which propeptides control protease activation and design new proteins
This project is eligible for HHMI applicants only.

Our lab’s research focuses on understanding structure, function, folding and evolution of proteins, using subtilases as our model. Subtilases are synthesized as multi-domain proteins. We discovered that N-terminal propeptides are important for folding and function as inhibitors that regulate activity in an organelle specific manner. This summer we will analyze the mechanisms by which propeptides control protease activation and design new proteins that can regulate organelle specific protease activity. Our research involves multidisciplinary approaches that cover the fields of biochemistry, biophysics, cell and computational biology. Students with a background in field chemistry, physics, biology, computer-science, or statistics are encouraged to apply.


James A. Tanyi:  Implication(s) of breathing motion on lung and liver cancer radiotherapy
This project is eligible for HHMI applicants only.

In the Department of Radiation Medicine at OHSU, treatment planning in stereotactic body radiation therapy (SBRT) is based on combined image information derived from both free-breathing and respiratory-correlated (4D) CT image data. The clinical target volume (CTV), represented by the motion envelope of a gross tumor volume (GTV) as reconstructed from the 4DCT simulation imaging study, is delineated and compared with tumor representation in the associated free-breathing CT scan. An isotropic margin, typically 5 mm, is added to the CTV to generate a planning target volume (PTV). The goal of this study is twofold: (1) to evaluate if there is a need for free-breathing CT acquisition, that is, if the motion overlap derived at the time of simulation sufficiently encompasses the range of target motion, (2) to evaluate if the motion overlap derived at the time of simulation encompasses the range of target motion observed prior to each treatment fraction, and if not, to evaluate the need for treatment adaptation. The research project(s) of the summer intern will involve detailed data extraction, data compilation and data analyses. The Intern will read existing literature and participate in manuscript drafting for a complete learning experience.