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Rogers Science Research

2010 Abstracts for Rogers and HHMI Programs

April 02, 2010

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), and some Psychology projects.
  • HHMI and Rogers: some projects are eligible for both programs.

Prerequisites must be completed by the end of spring semester 2010.


Kellar Autumn: Biology and Physics of Gecko Adhesion

This project is eligible only for Rogers applicants.

Gecko toe pads are sticky because they bear millions of adhesive setae (foot hairs) that function as a smart adhesive. Prior research in the Autumn lab has revealed that gecko adhesion is due primarily to van der Waals forces, and that gecko setae are self-cleaning. However, recent results show an effect of humidity on gecko adhesion and some researchers propose that capillary adhesion occurs. We will measure the effects of humidity on keratin stiffness, and adhesion on hydrophobic and hydrophilic substrates. We will also study the effects of electrostatic charge on self-cleaning of gecko setae.

Prerequisites: We seek one biology-focused student, and one physics-focused student

Preferred courses for biology-focused student: Physics 151 or 141, strong math skills, experience or interest in handling geckos

Preferred courses for physics-focused student: Physics 151/152, interests or coursework in E&M

Greta Binford 1: Are species definitions in Loxosceles spiders valid?

This project is eligible only for Rogers applicants.

Delineating species boundaries is a considerable challenge for many types of organisms including Loxosceles spiders (brown recluse and kin). Species delimitations in spiders historically rely on genitalic differences, but Loxosceles have simple genitalia without many distinguishing characters. In these species, patterns of genetic divergence and phylogenetic relationships are helpful for making decisions about species delineations. This project will focus on a group of spiders in the Desert Southwest of the United States that have historically posed a species problem. We will collect Loxosceles in Texas, sequence genetic markers, and do phylogenetic analyses to test species boundaries in this group.

Prerequisites: Biology 141, 151, 200 required, 390 will be helpful.

Greta Binford 2: What genes are expressed in venom glands of spiders related to the brown recluse (Loxosceles)?

This project is eligible only for Rogers applicants.

Spider venoms are complex chemical mixtures. Although brown spiders (Loxosceles) venoms cause dermonecrotic lesions in humans, outside of the dermonecrotic toxin sphingomyelinase D, little is known about chemical components in venom. We are doing transcriptome analyses to characterize genes expressed in venom glands of the Arizona brown spider, Loxosceles arizonica. The student working on this project will help with construction and analysis of libraries that contain genes that encode all proteins expressed in the venoms of select species in this genus. The work will involve cloning, sequencing and bioinformatics analyses of venom genes in this lineage.

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

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

This project is eligible for HHMI and Rogers applicants.

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 discovering and analyzing the function of genes controlling the assembly and morphology of lysosomes in the model organism, Caenorhabditis elegans.

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

Peter Kennedy: Investigating ecological patterns in Alnus ectomycorrhizal assemblages

This project is eligible only for Rogers applicants.

Research in our lab 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 assemblages associated with Alnus (alder) trees. We will sample ectomycorrhizal root tips in different Alnus forests and use molecular techniques (PCR and sequencing) to identify the sampled fungi. Using a range of statistical analyses, we will look at patterns of co-occurrence as well as spatial autocorrelation. Students with a strong background in field ecology, molecular biology, and statistics are encouraged to apply.

Prerequisites: Biology 141, Biology 200, Biology 343

Gary Reiness: Mechanism of Unconventional Secretion of a Cell-Cell Signaling Protein

This project is eligible for HHMI and Rogers applicants.

We study “unconventional” protein secretion of ciliary neurotrophic factor (CNTF). Most secreted proteins move sequentially through the endoplasmic reticulum, Golgi apparatus, and secretory vesicles, but some, including CNTF, use other, unknown pathways to exit cells. Because CNTF acts in cell-to -cell communication during nervous system development, investigating its secretory pathway will increase understanding of intercellular communication and neural development. Several projects in cell and molecular biology are available, including microscopic identification of the cellular structures involved in CNTF secretion, analysis of mutant CNTFs to identify the secretory signal, and inhibiting caspase-1, a protein thought to be involved in unconventional secretion.

Prerequisites:. Students who have taken Biology 311/312, 361, and/or Chemistry 330/335/336 will be given preference.


James Duncan: CASPT2//CASSCF Molecular Orbital Study of the Allenyl Cope Rearrangement of the Cycloocta-1,2,5-triene System

This project is eligible only for Rogers applicants.

Our group studies mechanisms of organic reactions by performing high-level quantum mechanical calculations on computers, most commonly employing a so-called Complete Active Space Self Consistent Field (CASSCF) method. We seek to further understand the fundamental nature of reacting molecules through close examination of the molecular orbitals thought to be most involved (CAS ones) in a particular reaction. This summer we intend to study the known 1 to 5 + 6 and 3 to 7 + 8 rearrangements shown in the scheme below. We seek to understand why the unconventional, and relatively less stable, compounds 6 and 8, are formed in much higher yield than compounds 5 and 7 in these formal allenyl Cope rearrangements. We hope our study will also contribute to improvements in the synthesis of stable molecules containing eight-membered rings which have been called “recalcitrant and elusive,” though they occur naturally in many compounds with significant biological activity (e.g., the cancer drug Taxol).

from Professor James Duncan


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

Louis Kuo: Investigation of Molybdenum Metallocene and Nanoparticles for Degrading Neurotoxin Analogues

This project is eligible only for Rogers applicants.

This project explores a class of metal complexes called metallocenes (metal = molybdenum) to carry out the degradation of a class of phosphate neurotoxins. Phosphinothioates are the functional core of organophosphate neurotoxins. This core of consists of P-S and P-O linkages wherein the preferable mode of degradation is P-S bond cleavage; scission of the P-O bond yields a complex just as toxic as the parent neurotoxin. We recently found molybdenum metallocenes yield this preferable bond scission in aqueous solution. This project will use these complexes with the objective of promoting turnover in the hydrolysis of phosphinothioates with nanoparticles.

Prerequisites: Chem 220 and Chem 366 preferred.

Mathematical Science

Paul Allen: The Dirichlet Problem for Curve Shortening Flow

This project is eligible only for Rogers applicants.

Geometric heat flows are a modern tool for addressing questions in geometry and topology. One example is the curve shortening flow, which evolves curves in such a way that their total curvature decreases. The Dirichlet problem is the study of this flow with the endpoints fixed. This project seeks to understand the flow by a combination of rigorous mathematical methods, used to prove certain properties of the flow, and numerical simulations, used to visualize and develop heuristics concerning the flow. Students interested in either the mathematical or the numerical aspects of the problem are encouraged to apply.

Prerequisites: Students interested in studying mathematical aspects of the curve shortening flow should have a working knowledge of differential equations (Math 235) and multivariable calculus (Math 233). Linear algebra (Math 225) is highly recommended. It would be advantageous, though not strictly necessary, that students have experience with one or more of geometry (Math 355), topology (Math 358), or advanced calculus (Math 441).

Students interested in studying the numerical aspects of curve shortening flow should have a working knowledge of calculus (Math 131-132). Experience in multivariable calculus (Math 233) or differential equations (Math 235) would be helpful. In addition, such students should be familiar with writing code using C, C++, Java, or some other appropriate computational language. It is possible that this project will involve learning to program in the MATLAB environment, so willingness and ability to adapt to new coding situations is important. It is also possible that the computational mathematics course (CS 230) would be useful.

In addition to the technical background described above, students should be willing and able to work hard on difficult problems for extended periods of time with minimal supervision. Students should also be prepared to create written and oral reports on their work, possibly using the LaTeX typesetting environment.

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.

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

Iva Stavrov: Finding examples of general-relativistic initial data with non-constant mean curvature

This project is eligible only for Rogers applicants.

In general relativity our “universe” is modeled as a 3-dimensional curved geometry which evolves in “time” according to a set of second order differential equations. General-relativistic initial data refers to both the initial geometry (e.g. how we measure distances) and the (infinitesimal) “direction” in which the geometry is to evolve; this includes the information about the initial rate of change of volume (e.g. mean curvature). Data with spatially constant mean curvature (CMC) have been studied extensively, but the non-CMC setting is largely unexplored due to its mathematical complexity. This project examines potential examples of non-CMC data with (near) spherical symmetry.

Prerequisites: Fluency in differential equations and multivariable calculus are absolutely required. Familiarity with advanced calculus / real analysis, linear algebra and computer programming may be extremely helpful.


Bethe 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 Alzheimer’s disease.

Prerequisites: None

Stephen Tufte: Observational Investigations of Short-Period Eclipsing Binary Stars

This project is eligible for HHMI and Rogers applicants.

The majority of stars exist in binary or other multiple systems, wherein the stars orbit their mutual center of mass. When the observer is in the plane of the orbit, the stars are seen to eclipse each other. In our long-standing program at Lewis & Clark College to observationally study short-period eclipsing binary stars, we have observed steady and oscillating changes in the orbital period of such stars indicating mass transfer and potentially an undiscovered hidden companion star. We plan to continue and expand the observational program, further refine our data gathering, analysis and reduction systems, further develop models to investigate the hidden companion hypothesis, and publish previous results.

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


Erik Nilsen: Physiological and Cognitive Correlates of Playing Serious Games for Peace.

This project is eligible for HHMI and Rogers applicants.

“Serious games” is a term used to describe video 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 designed around the topic of peace. “The Peacemaker Game” is a computer simulation where players make strategic decisions to reduce tension in the Israel/Palestine. The second study will examine another computer game designed to enhance inner peace. One program, entitled “Healing Rhythms”, combines breathing and meditation exercises with biofeedback. Another program, entitled “MindHabits”, based on social cognition research, claims raise self-esteem and reduce stress.

Prerequisites: Statistics (Psych. or Math Stats).

Todd Watson: ERP and Neuropsychological Correlates of Drinking Behavior in Healthy Young Adults

This project is eligible only for HHMI applicants.

Our lab is interested in the relationship between the brain and behavior. We record event-related potentials (ERPs), a safe measure of the electrical activity of the brain, while participants perform a variety of tasks. We are interested in using these techniques to explore possible differences in brain function that may be related to binge drinking in college-aged adults. We will record ERP activity while participants who binge drink and those who do not binge drink perform attention tasks, and determine if changes in brain function relate to broader changes in complex cognition and/or behavior.

Prerequisites: For the undergraduate student, previous experience with electrophysiological or functional neuroimaging experience would be helpful, but not necessary. No specific skills are required for the high school student.

Yueping Zhang: The role of Hypothalamic-Pituitary-Adrenocortical axis activity, frontal lobe function, impulsivity in drinking behavior.

This project is eligible only for Rogers applicants.

Alcohol abuse and addiction are related to loss of frontal lobe function and increased impulsivity. The Hypothalamic-Pituitary-Adrenocortical (HPA) axis is a neuroendocrine network that is critical for regulating functions such as digestion, immune response, mood, sexuality, and metabolism. Dysfunction of the HPA axis appears linked to alcohol use and alcoholism, but the exact relation and the underlying mechanisms are unclear. This study investigates the relations among HPA axis function as measured by salivary cortisol level, drinking behavior patterns, prefrontal executive functions, and impulsivity among college students.

Prerequisites: Courses in Statistics and Research Methods are highly desirable; courses offered by departments other than psychology are acceptable.

OHSU Projects (HHMI only)

Research that takes place on the main campus of the Oregon Health & Science University

SuEllen Pommier, PhD: OHSU Project 1. Genetic Defects Underlying Breast Cancer

This project is eligible only for HHMI applicants.

Recent research suggests that breast cancer begins from a normal breast stem cell that becomes damaged through DNA mutations. The cancers that develop contain defective stem cells. Dr. SuEllen Pommier, Ph.D and her team are attempting to identify the genetic damage that is responsible for initiating breast cancer. In her study, she will sample breast cancer tissue donated from women who are undergoing an operation to remove breast cancer. Normal breast tissue will be obtained from women undergoing an operation to reduce the size of their breasts. The tissues will be compared in the laboratory to examine genes in the stem cells that are known to be involved in normal cell behavior and in cancer. By compiling genetic profiles for normal and cancer breast stem cells, Dr. Pommier will collect data that will help identify cancer-causing agents.      http://www.ohsuwomenshealth. com/

Claudio V. Mello M.D., PhD: OHSU Project 2. Research in the Vocal and Auditory Learning Laboratory

This project is eligible only for HHMI applicants.

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. Specific projects investigate processes of neurogenesis, neuronal incorporation and synaptic plasticity within the avian brain as well as the effects of sex steroids on the auditory nuclei. Finally, we have been involved in the recent completion 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. We are also participating in on-going efforts to develop transgenic tools to manipulate gene expression in the songbird brain.

Jacob Raber, PhD: OHSU Project 3. Genetaic and Environmental Impact on Learning and Memory

This project is eligible only for HHMI applicants.

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 methamphetamine before birth due to drug taking of the mother in both humans as well as animal models. The research project(s) of the summer intern might involve detailed analyses of already acquired rough data and/or the generation of new data.

Matt Lattal, PhD: OHSU Project 4. Ways in Which Medication can be used to Strengthen and Weaken Drug-Associated Memories.

This project is eligible only for HHMI applicants.

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.