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Opportunities in Science at Lewis & Clark

2013 Project Descriptions for Rogers and CRT Programs

February 12, 2013

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

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

Prerequisites must be completed by the end of spring semester 2013.



Paulette Bierzychudek & Peter Kennedy
Investigating Forest Recovery in River View Natural Area After Removal of Invasive Plant Species

This project is eligible only for Rogers applicants.

How do forests recover after invasive species removal? We propose to continue a long-term monitoring study in the River View Natural Area, begun in summer 2012, to examine ecological changes following the removal of invasive ivy, laurel, and holly. Students will survey plant species composition and abundance within two areas: a) where ivy and other invasive non-native plants were treated with herbicide and/or manually removed by the City of Portland, and b) in control areas where no removal efforts have taken place. These data will be used to better understand the effects of species invasions and of invasive removal.

Note: This internship is 5 weeks long and will occur in the first half of the summer.

Prerequisites: Students should have taken Bio 141. Bio 335 (Ecology) and/or Bio 223 (Plant Biology) are desirable but not required. Students will be expected to develop accurate plant identification skills. Experience with GIS is desirable.

Greta J. Binford
The creation of a biodiversity hotspot: comparative biogeography of Caribbean arachnids

This project is eligible only for Rogers applicants.

The Caribbean is a global biodiversity hotspot, yet historical influences on high levels of endemism in the region are not well understood. An international group of arachnologists is undergoing a large-scale inventory of arachnids in the Caribbean. We are collecting multiple lineages and comparing their biogeographic histories to uncover shared patterns of divergence in space and time. We will infer relative influences of geographic isolation and dispersal on patterns of colonization and divergence. This summer students will work at the University of Vermont. They will analyze arachnids collected in the Lesser Antilles, and participate in a collecting expedition to Florida.

Prerequisites: Bio 151 required; Bio 200 and Bio 390 helpful but not required.

Greg J. Hermann
Constructing cellular compartments during embryonic development

This project is eligible for CRT and Rogers applicants.

Lysosome related organelles are membrane bound compartments that carry out specialized functions within particular cells of an organism. While much is known regarding the biochemical activities of these organelles (for example pigment formation in melanosomes), the processes involved in their assembly remain poorly understood. An understanding of these processes is important since defects in the 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. Our studies are focused on the initial formation of these compartments, which occurs during embryonic development.

Prerequisites: BIO151 or AP equivalent (BIO 200 or BIO 311/312 or BIO 361 suggested but not required)

Deborah E. Lycan
Ribosome biogenesis and export

This project is eligible for CRT and Rogers applicants.

The long-term goal of this project is to understand how cells make ribosomes. Ribosome biogenesis is critical for cancer cells as they ramp up their metabolic rate and their rate of cell division. Understanding how eukaryotic cells assemble and export ribosomes will provide new therapeutic targets for the specific inhibition of cancer cell growth without affecting normal cells. 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 compared to the dimensions of the nuclear pore. Second, export must be coupled to proper assembly to prevent the premature export of incomplete subunits. 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 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 will use embryonic microinjection techniques, 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; Neuroscience background and/or interest. (Additional background in cellular or molecular biology is ideal but not essential.)



Anne K. Bentley
Controlled Growth of Metal /Metal Oxide Thin Film Composite Electrodes for Energy Storage and Generation

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). The use of surfactant molecules to control the shapes formed by deposits will be explored. 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, Professor of Chemistry
Fundamental Mechanistic Investigations of (Pseudo)pericyclic and (Pseudo)coarctate Reactions via CASSCF, CASPT2, and DFT Computational

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.

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

Janis E. Lochner
Synaptic Secretion of Neuromodulatory Proteins from Dense-Core Granules

This project is eligible only for Rogers applicants.

The regulated release of proteins from dense-core granules (DCGs) is critical to fundamental processes such as neuronal survival and synaptic transmission. Many of the underlying molecular events that drive the synaptic secretion of proteins from DCGs have not been elucidated. We propose to evaluate the relevance of a recently identified postsynaptic domain to DCG exocytosis and assess if this domain functions as a general activity-triggered plasticity module that facilitates exocytosis of secreted neuromodulatory proteins. Findings derived from these studies are relevant not only to physiological processes in the nervous system such as learning and memory but also to neuropathological processes.

Prerequisites: Prefer students who have completed Structural Biochemistry (Chem 330), Molecular Biology (Bio 311, 312) and/or some neuroscience course work.

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


• Biochemistry lab experience preferred…particularly experience with generating and working with protein samples (such as Bio 312 and Chem 336)

• Coursework in biochemistry/molecular biology preferred (such as Bio 200, Chem 330, and Bio 310)


Mathematical and Computer Science

Yung-Pin Chen
The Game of Go: Statistical Approach to Artificial Intelligence

This project is eligible only for CRT applicants.

A main goal of this project is to improve the performance of computer in playing the game Go through Monte Carlo methods. The central idea of this statistical/machine learning approach is to use a large number of random play-outs (possibly crafted with domain-specific knowledge) to quantify the quality of a move from a given board state. Through the Monte Carlo simulation, we will explore and employ various statistical computational methods and machine learning algorithms for search trees.

Prerequisites: Desired skills include programming experience (especially in Java), basic knowledge in statistics, and basic understanding of the rules of the game Go.

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 Goremains 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.

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. Coursework in statistics is also helpful, but not required.

Jens Mache (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, four or six-core chips 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-277 Computer Architecture, CS-363 Operating Systems and CS-383 Algorithms.

Jens Mache (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: Ideally, students took CS-495 Security, CS-277 Computer Architecture and CS-363 Operating Systems.

Liz Stanhope
Computational models of hair bundles in the inner ear

This project is eligible for CRT and Rogers applicants.

How do our ears turn vibrations in the air into signals to our brain’s hearing centers? One small part of this complex process is the hair bundle on cells in the inner ear. By reading existing literature we will learn about current mathematical models of these hair bundles. We will implement one of these models computationally using Matlab. With insights gained from this process we will ask if the methods of differential geometry might offer ways to improve existing models.

Prerequisites: Motivation and willingness to learn new things are the primary prerequisites. In addition:

  • One student with interest in teaching, cell biology and/or biophysics
  • One student with interest in teaching, and skills in computer programming. Matlab experience a plus.



Shannon O’Leary (1)
Using Laser Noise to Build a Magnetometer

This project is eligible only for Rogers applicants.

Advancement in magnetometry will have profound impacts in diverse array of scientific fields and medical applications. This experimental quantum optics project investigates an interaction between light and matter that is highly sensitive to magnetic fields, specifically laser noise derived from quantum interference in an atomic vapor. The quantum interference process we 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.

Prerequisites: PHYS 152

Shannon O’Leary (2)
Using Holographic Optical Tweezers to Study Microbubble Dynamics

This project is eligible only for Rogers applicants.

Medical researchers are interested in developing a drug delivery system that uses directed ultrasound to rupture drug-filled microbubbles that have been injected into a patient’s bloodstream. Toward that end, this project seeks to study how microbubbles confined within a capillary respond to ultrasound. We will begin by designing and building an optical trap using holographic tweezers to hold microbubbles in place within a capillary. This research will be done in collaboration with Professor Azzdine Ammi’s group at OHSU, where the microbubbles are subjected to ultrasound and their dynamics are observed using one of the highest-speed video cameras in the world.

Prerequisites: None

Bethe A. Scalettar
Super-resolution microscopy studies of mechanisms underlying delivery of dense-core granules to synapses in hippocampal neurons

This project is eligible only for Rogers applicants.

Dense-core granules (DCGs) are organelles found in many types of neurons. In neurons of the hippocampus, DCGs house proteins that play a role in learning and that have implicated in Alzheimerʼs disease. In light of this, DCGs in hippocampal neurons are the subject of widespread interest.

My current research is directed at using cutting-edge, super-resolution microscopy techniques to elucidate mechanisms mediating the delivery of DCGs to sites of learning in hippocampal neurons. The goal is to obtain results that provide fundamental insight into physiological processes that underlie learning as well as insight into pathological processes that may underlie Alzheimerʼs disease.

Prerequisites: Preference will be given to students who are familiar with molecular biology and microscopy/imaging.



Erik Nilsen
Serious Games for Scaffolding Creative Problem Solving and Motivating Healthy Behaviors

This project is eligible for CRT 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 in preschoolers at OMSI using magnetic blocks. The second study will involve the development and evaluation of several technological approaches to support changing health related behaviors including social media, web-based activity tracking and various reward systems including collaboration and competition.

Prerequisites: Experience in either Behavioral Research and/or computer Programming. This can be met through coursework (Psy 300 or CS 171/172) or other experience.

Todd D. Watson
Investigations of Response Inhibition and Risky Behaviors in Young Adults and Preschool-aged Children

This project is eligible for CRT and Rogers applicants.

We will examine the relationship between cognitive control (response inhibition) and risky behaviors in two distinct populations. We will use event-related potentials (a noninvasive measure of brain function) to explore the neural correlates of response inhibition during an alcohol-cue processing task in healthy young adults with and without a history of binge drinking. In a separate study, we will explore the relationship between response inhibition, risk-taking, and externalizing behavior in preschool-aged children. In all, we hope to determine if the ability to inhibit inappropriate cognitive responses is related to lower levels of risky behaviors in the “real world”.

Prerequisites: It is highly preferred (but not required) that undergraduate students have previous experience with human electrophysiology and/or experience working with young children (aged ≈ 3-5 years). There are no requirements for high school students other than enthusiasm, a strong work ethic, and interest in neuroscience and psychology.


OHSU Projects (CRT only)

Claudio V. Mello and Christopher Olson
Research in the Vocal and Auditory Learning Laboratory

This project is eligible for CRT 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 CRT 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 Shinde
Design and analysis of bipartite inhibitors of proprotein convertases

This project is eligible for CRT 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 design and analyze bipartite peptide inhibitors that can block specific proprotein convertase paralogs. 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 Tanyi
Title To Be Announced

This project is eligible for CRT applicants only.

The use of stereotactic body radiotherapy (SBRT) is expanding rapidly to include many treatment sites throughout the human body, including the lung, liver, spine and prostate. SBRT requires very accurate patient localization and reliable immobilization to safely deliver ablative doses of radiation. The most commonly used method of localization for SBRT patients is conebeam CT (CBCT) because it allows volumetric visualization of patient anatomy. Immobilization techniques and devices used for SBRT include the Bodyfix system with/without abdominal compression. The primary purpose of this study was to analyze the setup differences as assessed by CBCT for patients localized and immobilized in a stereotactic body frame receiving SBRT to the lung and liver. The secondary goals are to compare the localization results for our patients to published studies in which different immobilization devices and techniques have been used and to calculate the margins needed to account for residual setup error after CBCT.