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Opportunities in Science at Lewis & Clark

2016 Project Descriptions for Rogers and CELS Programs

February 09, 2016

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

  • Rogers only: most of the projects.
  • CELS only: some projects and all OHSU projects.
  • CELS and Rogers: some projects are eligible for both programs.

Prerequisites must be completed by the end of spring semester 2015. 

Please review application instructions and forms here.


1. Investigating Forest Recovery After Removal of Invasive Plant Species

Principal Investigator: Paulette Bierzychudek
Program: Rogers only
How do forests recover after invasive species removal? We will continue a monitoring study on the Lewis & Clark campus, begun in 2012, to examine ecological changes following removal of invasive ivy, laurel, and holly. Intern will sample the plant species composition of study plots to compare community composition after invasives were removed to conditions before removal. Results will help develop effective strategies for conservation and restoration of urban forests. Intern will develop skills in plant identification, geographic information systems (GIS), and data analysis.

Note: This internship is 5 weeks long, in the first half of the summer.

Prerequisites: Student must have taken Bio 141. Bio 335 (Ecology) and/or Bio 223 (Plant Biology) are desirable but not required. Student must develop accurate plant identification skills. Experience with GIS and/or R is desirable but not required. Eagerness to learn new skills is essential.

2. The evolution of venom-expressed gene families in Haplogyne spiders

Principal Investigator: Greta J. Binford
Program: Rogers only
Venoms are complex mixtures of peptides and proteins that include products of multiple gene families. The histories of the gene families in venoms typically include duplication of a gene that codes for a protein that does not have venomous function, the evolution of differences in functional specificity, and change in expression patterns. We are analyzing the histories of proteins in venoms of brown recluse spiders and their relatives. This work applies bioinformatics and molecular tools to analyze expression of members of gene families in venom glands and other tissues, and to infer the evolutionary histories of venom proteins. 

Prerequisites: Bio 151 required; Biol 200, Biol 390 and Biol 408 helpful but not required.

3. The creation of a biodiversity hotspot: comparative biogeography of Caribbean arachnids

Principal Investigator: Greta J. Binford
Program: Rogers only
The Caribbean is a global biodiversity hotspot, yet historical influences on taxonomic diversity in the region are not well understood. An international group of arachnologists is undergoing a large-scale inventory of arachnids on the Caribbean. We are collecting multiple lineages and comparing their biogeographic histories to uncover shared patterns of divergence in space and time. This summer will involve lab work on a lineage the genus Loxosceles including molecular phylogenetics and morphological analyses of specimens collected across the Caribbean Region.

Prerequisites: Bio 151 required; Biol 200, Biol 390 and Biol 408 helpful but not required.

4. Construction and movement of cellular compartments during embryonic development.

Principal Investigator: Greg J. Hermann
Program: CELS and Rogers
Lysosome related organelles (LROs) are compartments that carry out specialized functions within particular cells of an organism. While much is known regarding the functions of LROs (for example pigment formation in melanosomes), the processes involved in their assembly and positioning remain poorly understood. Defects in these processes underlie a number of human genetic diseases.  We are discovering and analyzing the function of genes controlling the formation and motility of LROs in the model organism, Caenorhabditis elegans, whose homologues function similarly in humans.  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)

5. Seedling dynamics and the role of oomycete pathogens in maintaining diversity in an old growth forest

Principal Investigator: Margaret Metz
Program: Rogers only
This project examines the potentially beneficial ecological roles played by oomycetes, or water molds, in the maintenance of biodiversity in an old growth forest near Portland. These are highly destructive fungus-like plant pathogens, best known for causing the Irish potato famine in the 1850’s or for widespread mortality when introduced to forests. Native oomycetes are abundant in forested systems, and yet we know very little about their role in driving the dynamics or diversity of forests. This summer we will establish seedling monitoring plots in the Wind River Experimental Forest to assess the interactions between native trees and their pathogens.


  • BIO 141 or equivalent. BIO 223 or 335 preferred.

  • Wilderness First Aid certification or willingness to obtain (wilderness first responder certification preferred)

  • Fieldwork will entail long days, strenuous hiking, and the ability to lift and hike with heavy backpacks on uneven terrain. Experience working in rugged field conditions, and/or orienting in the back country will be very useful, as will a positive attitude, enthusiasm for learning, the ability to work as part of a team, and the interpersonal skills needed to work and live closely with other team members.

6. How seedling functional traits interact with environmental conditions to maintain forest diversity in an Amazonian rainforest

Principal Investigator: Margaret Metz
Program: Rogers only

My research examines the ecological mechanisms that drive tropical forest dynamics, particularly processes hypothesized to maintain forest diversity in the Amazon. Many hypotheses invoke processes that occur very early in a plant’s life, at the seed and seedling stage, such that the dynamics of regeneration create the template for future diversity of the forest canopy. As part of a long-term study of seedling dynamics, a student will visit Ecuador to collect seedling functional trait data, quantify light availability, and participate in an annual seedling census, with data analysis upon return to Lewis & Clark.


  • Course prerequisites: BIO 141 or equivalent. BIO 223 or 335 preferred.

  • Spanish proficiency (fluency, preferred), esp. for taking data in Spanish and conversing with Spanish-speaking collaborators. Valid passport and availability to travel in May immediately following the end of the semester.

  • Willingness to work under humid, muddy, buggy conditions with long days of strenuous hiking in a remote location. Ability to remain focused on high quality, detail-oriented data throughout. Experience working in rugged field conditions or traveling in remote locations will be very useful, as will a positive attitude, enthusiasm for learning, the ability to work as part of a team, and the interpersonal skills needed to work and live closely with other team members while far from home.

7. Discovering the mechanisms underlying the effects of nicotine on development and drug-induced behaviors in Drosophila melanogaster

Principal Investigator: Norma A. Velazquez Ulloa
Program: CELS and Rogers
Nicotine is the chemical in tobacco associated to addiction, yet little is known about the changes nicotine causes that produce addiction. My lab uses Drosophila, the common fruit fly, to discover the mechanisms for nicotine’s effects. Students working in this project will expose flies to nicotine, dissect brains, stain them, and use fluorescence and confocal microscopy to characterize nicotine’s effects on brain morphology. To find novel genes involved in nicotine’s effects, students will test mutant fly lines on nicotine to identify lines that respond to nicotine differently from control, then use molecular biology to identify and characterize these genes.


  • Required course pre-requisites: BIO 151or AP Biology score high equivalent to BIO151 AND previous experience working with fruit flies; BIO 200 by summer 2016.

  • Having taken any of the following courses would be useful, but not necessary: Intro to Neuroscience or Basic Neuroscience course; Animal Behavior, Cellular Biology, and Molecular Biology, Biochemistry, Physics, Intro Statistics.

  • Good communication and organization skills preferred.

8. Evaluation of the effects of resveratrol on the genotoxicity of nicotine on the wing SMART test in Drosophila melanogaster.

Principal Investigator: Norma A. Velazquez Ulloa
Program: Rogers only
Resveratrol is a chemical found in wine and is considered an antioxidant. Nicotine is the chemical in tobacco associated to addiction. In humans, nicotine has been found to be genotoxic and to affect expression of CYP2A6, which is involved in the metabolism of foreign substances in the body. I am interested in testing if the genotoxic effects of nicotine can be ameliorated by resveratrol. Gentoxicity will be assessed on the wing SMART assay in Drosophila melanogaster. This assay relies on tracking known markers that become expressed when there are mutations induced by toxins.

Note: This internship is 5 weeks long, in the first half of the summer.


  • Required course pre-requisites: BIO 151or AP Biology score high equivalent to BIO151 AND previous experience working with fruit flies.

  • Having taken any of the following courses would be useful, but not necessary: BIO200, Intro to Neuroscience or Basic Neuroscience course; Animal Behavior, Cellular Biology, and Molecular Biology, Biochemistry, Physics, Intro Statistics.

  • Good communication and organization skills preferred.

9. Mapping neuronal development using multicolor imaging in Brainbow zebrafish

Principal Investigator: Tamily Weissman-Unni
Program: Rogers only
Mapping neuronal development using multicolor imaging in Brainbow zebrafish Brain function relies upon the precise organization of neural circuits. The majority of neurons are born during early brain development, but there are many questions regarding how neuronal production is regulated. Our lab uses a 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 dividing cells in vivo (in living fish). Our investigations will focus on mechanisms that regulate the dividing cells that generate neurons during brain development.

Prerequisites: Bio 151 or equivalent; Neuroscience background and/or interest. (Bio 200 and/or additional background in cellular or molecular biology is ideal.)

10. Zebrafish to study cellular mechanisms of Parkinson’s Disease

Principal Investigator: Tamily Weissman-Unni
Program: Rogers only
Parkinson’s Disease involves the abnormal aggregation of a protein called alpha-synuclein. Zebrafish is a useful model system for studying Parkinson’s Disease for two major reasons: 1) First, human forms of alpha-synuclein are readily expressed in zebrafish, including forms that recapitulate human mutations in Parkinson’s Disease; 2) The developing zebrafish is optically transparent, allowing for clear visualization of expressed proteins. Students will use embryonic microinjection techniques, express fluorescent proteins in zebrafish larvae, and use fluorescence microscopy to visualize neurons and their connections in vivo. Our investigations will focus on the role of alpha-synuclein aggregation in disease.

Prerequisites: Bio 151 or equivalent; Neuroscience background and/or interest. (Bio 200 and/or additional background in cellular or molecular biology is ideal.)



11. Porous Ceramic Nanoparticle Scaffolds for Electrochemical Growth of Manganese Oxide Supercapacitors

Principal Investigator: Anne Bentley
Program: Rogers only
Manganese dioxide (MnO2) is a low cost and non-toxic supercapacitor that can store and release electrical charge more quickly than a battery. This project will focus on improving the electrochemical capacitance of MnO2 thin films by forming hybrid supercapacitor materials featuring TiO2, SiO2, AlOOH, and ZnO nanoparticle scaffolds supporting MnO2 thin films. Students will synthesize the ceramic oxide nanoparticles using sol gel methods and will coat them with polymeric ionic liquid (PIL) capping agents to enhance the charge transfer properties. 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, cyclic voltammetry, powder X-ray diffraction, and electron microscopy. 

Prerequisites: General Chemistry (Chem 110 and Chem 120) or previous chemistry research experience required

12. Surface Chemistry of Gold Nanoparticles in Natural Environments

Principal Investigator: Anne Bentley
Program: Rogers only
Gold nanoparticles (AuNPs) have the potential to be used in disease diagnosis, imaging, and treatment. They are favored for these applications because they are relatively chemically inert and their surfaces can be easily modified to affect their stability and/or transport desired medicines. As AuNPs advance from research lab to manufacture and use in applications, it is expected that they will be released to the environment, either intentionally or inadvertently. However, little is known about how the AuNPs will interact with the molecules found in natural environments. This project will examine the stability of AuNPs under a variety of environmental conditions using UV-vis spectroscopy, dynamic light scattering, and transmission electron microscopy techniques.

Prerequisites: General Chemistry (Chem 110 and Chem 120) or previous chemistry research experience required

13. Computational investigation of organophosphate hydrolysis by molybdenum oxide catalyst

Principal Investigator: Louis Kuo
Program: Rogers only
We recently discovered a simple molybdenum oxide compound that catalyzes the hydrolytic degradation of an organophosphate neurotoxin under mild aqueous conditions (40 oC, pH 7). The organophosphate neurotoxin mimics a chemical warfare agent and the metal complex is the compound MoO4-.  Various mechanisms have been proposed for this useful transformation and this project seeks to use computational methods in conjunction with experimental data (i.e. thermodynamic parameters) to arrive at a possible mechanistic route. The project is a joint effort with a PSU collaborator and it paves the way for developing better metal oxides to accomplish the hydrolytic degradation of organophosphate neurotoxins.

Prerequisites: Chem 210/220 required; Chem 366 preferred; Computer science classes preferred

14. Application of molybdenum peroxo compounds for degrading organophosphate neurotoxins

Principal Investigator: Louis Kuo
Program: Rogers only
Molybdenum(VI) peroxo compounds of the form Mo(O-O)n have been applied as oxidation catalysts for a variety of industrial transformations.  A series of these compounds have been found by our group that effectively degrade organophosphate pesticides and neurotoxins. This project seeks to examine the mechanistic chemistry of one class of molybdenum peroxo complexes, and it entails a battery of spectroscopic (i.e. NMR) and computational tools.  In addition, inorganic synthetic manipulations will be required to make several derivatives of the molybdenum peroxo compounds to test hypothetical mechanistic proposals.

Prerequisites: Chem 210/220 required; Chem 366 preferred

15. Structural Studies and Functional Characterization of Neurotoxic Venom Peptides from Sicariidae Spiders

Principal Investigator: Nikolaus Loening
Program: Rogers only
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.


  • Biochemistry/molecular biology lab experience preferred…particularly experience with generating and working with single-celled organisms and protein samples (such as Bio 312 and Chem 336)

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


Environmental Studies

16. Cloud motion vectors: image processing meets meteorology

Principal Investigator: Jessica Kleiss
Program: Rogers only
I’m looking for students interested in Earth Science with a proclivity towards Math and Computer Science. In the late 1990’s weather stations replaced manual observations of cloud cover with point-observations of clouds taken by ceilometers. Although they can estimate cloud coverage, the information about cloud type (cirrus, cumulus, etc.) was lost. My research project aims to use image processing techniques to determine cloud type from digital images of the sky dome. We will use cloud motion vectors to inform the cloud classification, particularly focusing on cumulus humilis clouds, which are very important to earth’s radiative balance.

Prerequisites: None.
Preferred: a GEOL course, CS171, Math 233.

17. Shaping an “Earthquake Culture” Through Informal Learning

Principal Investigator: Liz Safran (ENVS), in collaboration with Erik Nilsen (PSY)
Program: Rogers and CELS
The Pacific Northwest is ill-prepared for the impending subduction zone earthquake because the last one struck before Euro-American settlement.  Traditional messaging promoting disaster preparation, typically simple and repetitive, neglects strong circumstance dependency of appropriate actions.  Narrative-based messaging can help deliver nuanced messages to diverse audiences, overcome resistance to conventional advertising, and make salient what we’ve never experienced.  Building on studies of framing, source-trust, and entertainment-education, we will first map out a multi-media campaign whose imaginary but information-rich narrative arc spans the future Cascadia event and then begin to develop and test the psychological efficacy of some pilot media pieces.  

Prerequisites: PSY 300: Psychology Methodology OR ENVS 220: Environmental Analysis.


Mathematical and Computer Science

18. Geometric Flows of Polygons

Principal Investigator: Paul T. Allen
Program: Rogers only
Geometric flows provide efficient ways to “improve” a shape or object. We study a natural, but nonlinear, geometric flows for polygons. The goal is understanding, and proving, their long-time behavior. This project includes both theoretical and computational aspects.

Prerequisites: Prospective researchers are required to have completed Math 225 Linear Algebra and Math 233 Calculus 3. Completion of Math 235 Differential Equations and CS 171 Introduction to Computer Science is highly desirable. 

19. Capture-the-Flag Challenges that Enhance Cybersecurity Analysis Skills

Principal Investigator: Jens Mache
Program: Rogers only
Cybersecurity analysis skills are of growing importance due to our increasing reliance on computers and networks 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 documentation that explains security implications. Scenarios may include capture the flag, web applications, malware analysis, data science, firewalls, buffer overflows, recover the network and intrusion detection.

Prerequisites: Ideally, students took CS-495 Adv. Security, CS-393 Computer Networks, CS-298 Data Science and CS-277 Computer Architecture.

20. Mathematics of relativistic point particles

Principal Investigator: Iva Stavrov
Program: Rogers only
It is somewhat common to treat a physical body as a cumulative effect of a big number of de-facto point particles. It might sound very surprising that such a line of reasoning is not commonly applied in the relativistic context. The reason for this is that the very idea of point particle is problematic in general relativity! Very roughly speaking, one cannot stuff a blob of mass into too tiny of a space without forming a black hole. This project will contribute to an ongoing effort of finding mathematical mechanisms for dealing with point particle limits in different physical contexts.

Prerequisites: Students participating in the project will need to have some familiarity with the following material before the beginning of the project:

• MATH 490: Curvature of Space and Time

• MATH 341: Real Analysis I or MATH 305: Calculus IV.

• MATH 215: Discrete Mathematics.

Preference will be given to students who have taken several physics courses. 

21. The Local Topology of Schubert Varieties at Singularities

Principal Investigator: Sweta Suryanarayan
Program: Rogers only
Schubert varieties are one the most important and best studied examples of algebraic varieties, which are the main objects of study in Algebraic Geometry. The study of singularities of Schubert varieties involves an interesting interplay between the fields of Algebraic Geometry, Lie Theory, Combinatorics and Toplogy. This project aims to provide students an introduction to these fields with the goal that they:

• Learn how these fields interact in the study of Schubert varieties.

• Explore major results from current research that deals with the important question: When is a Schubert variety non-singular and what is its singular locus?

• Analyze a new question: What is the local topology of Schubert varieties at  singularities?

Prerequisites: A strong background in linear algebra (Math 225) and abstract algebra (Math 422) is required. Knowledge in Combinatorics (Math 325) and basic topology would be helpful. Computer skills (Mathematica or Python) are a plus.



22. Coherence-Derived Light Fluctuations for Atomic Magnetometry

Principal Investigator: Shannon O’Leary
Program: Rogers only
This project proposes a new platform for atomic magnetometry that utilizes a low-cost, “realistic” laser system. We will study and use an interaction between laser light and an atomic vapor that is highly sensitive to small changes in the ambient magnetic field, specifically laser intensity fluctuations (noise) derived from atomic coherence. Results from this project have the potential to impact a broad range of medical and scientific fields, such as monitoring biomagnetic responses of the human heart.

Prerequisites: PHYS 151 & PHYS 152

23. Musical Acoustics: Coupled Oscillators, Mandolin Bridges, and Holographic Interferometry

Principal Investigator: Stephen Tufte
Program: Rogers only
The project proposed herein is a broad-based experimental study of the acoustics of the mandolin. We will carry out a detailed study of the coupling of the doubled strings using high-speed video and the musical implications of these interactions will be elucidated. Measurements of the sound spectrum and bridge impedance combine to characterize the transfer of mechanical energy from string motions through the bridge to the motions of the instrument body that ultimately produce sound. Experiments to understand in detail the connection between the mechanical properties of the bridge and the resulting sound spectrum aim to identify potential improvements in bridge design. Details of the resulting body motions, the modes of vibration, will be studied using holographic interferometry.

Prerequisites: Preference for students equipped with skills learned in Physics 201: Experimental Methods in the Physical Sciences.

Other useful experience: computer skills, optics, differential equations, Physics 451.




Principal Investigator: Jennifer LaBounty

25. How Do We Feel About It? The role of emotional self-stereotyping in responses to sexism

Principal Investigator: Diana J. Leonard
Program: CELS and Rogers
What makes people take action in response to discrimination? Past research has shown that anger about injustice is a key ingredient in responding proactively (e.g., protesting). Our lab has shown that women who think women are an angry group will be more likely to see an ambiguously derogatory comment as sexist and want to do something about it. On the other hand, women who saw their group as low in anger were less inclined to do so. Our upcoming project will use experimental procedures to explore the role of anger norms in reactions to another type of discrimination: structural disadvantage. 

Prerequisites: For LC undergraduates, Psy 200 and 300 are strongly recommended; Psy 260 is preferred.

26. Walking the Oregon Trail to Fitness: Is it the trailmates or map that matters most?

Principal Investigator: Erik Nilsen
Program: CELS and Rogers
We have developed a web-based app that uses fitbit activity trackers and a google map-based competition to motivate people to maintain a healthy level of physical activity.  Teams of LC faculty, staff and students travel the Oregon Trail using fitbit activity trackers! Last summer we found that using the app increased activity by 12%.  The study this summer explores the relative impact of map-based performance feedback and social referencing used in the app. A second project will extend our research on the use of tangible technology to enhance shape recognition and creativity in young children.  An ipad app (Osmo) that incorporates physical tangram shapes will be evaluated for it’s effectiveness in teaching 4 – 6 year olds to arrange geometric shapes in both convergent and creative divergent problem solving.

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

27. Exploring the Relationship Between “Intuitive” Eating and the Neurocognitive Correlates of Food-Cue Processing in Adults and Young Children.

Principal Investigator: Todd D. Watson
Program: CELS and Rogers
We will examine the relationship between an adaptive, healthy habit/style of eating (“intuitive eating”) and behavioral and cognitive responses to food-related cues in two populations. We will use event-related potentials (a noninvasive measure of brain activity) to examine neural responses to distracting food-images in young adults with different levels of intuitive eating. Separately, we will examine if preschool-aged children’s eating habits and performance on food-related cognitive control tasks relate to their parent’s intuitive eating levels. In all, we hope to determine if intuitive eating is associated with increased cognitive control over distracting food related cues and improved neuropsychological functioning.

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 ≈ 3-6 years). There are no requirements for high school students other than enthusiasm, a strong work ethic, a willingness to work with both adults and children, and interest in neuroscience and/or psychology.

28. Bilingualism and executive functions: is there a bilingual advantage over monolingual on cognitive control?

Principal Investigator: Yueping Zhang
Program: Rogers only
Studies have shown that bilinguals constantly juggle two languages even when only one is in use. Some studies have suggested a bilingual advantage over monolinguals in executive functions, presumably as a result of their language control practice. But this claim has recently been called into question – many studies failed to replicate the earlier results, especially with young adult participants. The current study examines the influence of bilingualism on executive functions by comparing the performance of young adult bilinguals and monolinguals on a variety of executive-control tasks, and by relating participants’ language experience with their performance on those tasks.

Prerequisites: Statistics (Psych. or Math Stats). Research Methods course and/or experience in behavioral research, especially computerized assessment, are preferred.


OHSU Projects (CELS only)

29. Neuroimaging and Brain Development

Principal Investigator: Damien Fair
Program: CELS only
The Fair Neuroimaging Lab at OHSU uses MRI (Magnetic Resonance Imaging) to examine typical and atypical brain development. The lab uses various functional and structural MRI techniques to study developmental neuropsychiatric disorders such as ADHD and Autism Spectrum Disorder (ASD). Functional and structural neuroimaging allows researchers to get a better understanding of the mechanisms and principles that underlie typical and atypical brain development (such as in ADHD and ASD) in order to help guide future diagnostic, therapeutic, and genetic studies. We have multiple ongoing translational projects applying neuroimaging techniques to human subjects, as well as rodents and non-human primates. Previous projects in the Fair Lab have included creating efficient ways to process imaging data in order to analyze key features of the brain. The majority of research done in the Fair lab is computer based, and projects for summer students will likely include the use of computer programming (Python, MATLAB, pipelines). Programming skills not required for lab placement.

30. Research in the Vocal and Auditory Learning Laboratory

Principal Investigator: Claudio V. Mello M.D., Ph.D. and Dr. Peter Lovell
Program: CELS 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 the 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. We have been involved in the completion of the zebra finch genome as well as in the comparative effort that recently resulted in the sequencing of ~50 avian genomes, leading to numerous novel insights into avian biology and a fundamental reformulation of avian phylogeny. We are also participating in on-going efforts to develop transgenic tools to manipulate gene expression in the songbird brain. Recently we have been involved in applying comparative genomics, transcriptomics and bioinformatics to gain a better understanding of avian genome evolution and brain gene regulation in the context of vocal learning. Possible projects this summer include: a)  analysis of brain gene expression in vocal areas of vocal learning birds based on evaluation of microarrays and in situ hybridization data; and b) comparative analysis of avian genomes to gain a deeper understanding of the evolution of vocal learning systems. A strong emphasis will be on genomics, computational and bioinformatics approaches. We believe this research experience will be particularly rewarding for students interested in genomics, computational biology and bioinformatics, and the neural and genetic basis of vocal communication and complex learned behaviors.

Interested undergraduate candidates are encouraged to contact Peter Lovell ( with questions. 

31. Genetic and Environmental Impact on Learning and Memory and Anxiety

Principal Investigator: Jacob Raber
Program: CELS 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.

32. MicroRNAs in Viral Pathogenesis

Principal Investigators: Rebecca Skalsky, PhD
OHSU West Campus Beaverton
Program: CELS only
An estimated 15% of human cancers are associated with viral infection. Members of the gamma-herpesvirus family, such as EBV and KSHV, are linked to AIDS-associated non-Hodgkin’s lymphomas and other B cell malignancies. The molecular mechanisms driving tumorigenesis are not well defined, presenting a major challenge in treating these diseases.

A major focus of the lab is to explore the roles of microRNAs in viral pathogenesis. miRNAs are a class of small, non-coding RNAs that widely impact gene expression. Due to the nature of their regulatory influence, miRNAs represent attractive therapeutic targets. Encoded by all metazoans, miRNAs have also been identified in many herpesviruses. One goal of the lab is to identify miRNA targets and/or targeted pathways that are critical for viral replication and contribute to pathogenesis. We use combined high-throughput biochemical and bioinformatic approaches to interrogate miRNA regulated pathways during viral infection.

Projects will involve characterization of miRNA interactions using molecular cloning, reporter assays, and gene expression analysis tools (i.e. real-time PCR). Students will be involved in all steps of experimental set-up, data collection, and analysis. An interest in molecular biology, virology, and/or computer science is preferred.


For more information:

Amy Timmins
Administrative Coordinator