2011 Abstracts for Rogers and HHMI Programs

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

Prerequisites must be completed by the end of spring semester 2011.

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Biology

Greta 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 construct and analyze libraries of genes that encode 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 408 helpful but not required.

Greta Binford:  (Project 2)  Biogeography of Caribbean spiders
This project is eligible only for Rogers applicants.

The Caribbean is an International Biodiversity Hotspot with a complex geological history. With a international team of collaborators we are analyzing biogeographic patterns of multiple arachnid lineages in the Caribbean that differ in dispersal ability. These analyses will help to infer historical processes that have generated the high levels of biodiversity in this region. The student working on this project will participate in a spider collecting expedition to Puerto Rico. They will also collect molecular sequence data from those specimens and others in collection and use these data to infer phylogenetic relationships among species in the Caribbean.
Prerequisites:  Bio 151 required.  Bio 200, Bio 311/312. Bio 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).

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Chemistry

Anne Bentley: Manipulation of Nanoparticle Surface Chemistry and Formation of Nanoparticle/Thin Film Composite Materials
This project is eligible only for Rogers applicants.

The nature of the capping molecules surrounding nanoparticles is key to determining their stability in a wide variety of solution conditions (ie, ionic strength, pH, temperature).  This project will explore the ability to control nanoparticle surface chemistry and the incorporation of nanoparticles into thin films.  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:  Completion of Chem 210 and 220

James Duncan: A CASSCF Computational Study of the Mechanism of the Key Cyclization Step in the Synthesis of Isoindazole Heterocycles from Diazines and Triazines: Are the Transition State Orbital Topologies Coarctate or Pseudocoarctate?
This project is eligible only for Rogers applicants.

Our group studies complex and controversial mechanisms of concerted organic chemical reactions by performing high-level (CASSCF) quantum mechanical calculations on computers. We seek an understanding at the most fundamental level through close examination of transition state (TS) molecular orbitals (MOs). Here we propose to use CASSCF to fully differentiate between two proposed TS MO topologies deemed coarctate (meaning constricted) and pseudocoarctate. A coarctate MO topology consists of at least one atom at which two bonds are broken and made simultaneously (the “coarctations”), while a pseudocoarctate one also contains one or more orbital disconnections. In particular, we propose a comparative study of the rearrangement of diazine 1 to carbene 2, purported to be coarctate (coartate atoms marked with a “C”), and the rearrangement of the similar triazine 3 to carbene 4, purported to be pseudocoartate (orbital disconnection on middle N). Increased mechanistic understanding of such reactions should allow fuller advantage to be taken of them in organic synthesis.

 

 

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

Janis Lochner & Greta Glover: Synaptic Secretion of Neuromodulatory Proteins from Dense-Core Granules
This project is eligible for both HHMI and 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 Biochemistry (Chem 330), Molecular Biology (Bio 311, 312) and Neurochemistry (Chem 421).

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Mathematical Science

Paul Allen: Reaction-diffusion equations with applications in chemistry
This project is eligible only for Rogers applicants.

Reaction-diffusion equations appear in a variety of contexts in both pure mathematics and applications. The goal of this project is to develop a general method for the numerical simulations of reaction-diffusion equations, while simultaneously obtaining specific results concerning a particularly interesting reaction from chemistry.

We will first perform a theoretical analysis of the Belousov-Zhabotinskii chemical reaction. We then will develop a PDE model and construct a numerical simulation, describing both qualitative and quantitative properties. Once the numerical simulation is operational, we will be able to apply our code to other systems (of the student’s choosing).
Prerequisites: Students interested in this project should have a mathematics background which includes Calculus 3 and Differential Equations. Linear algebra is not strictly required, but would be helpful. Students should also have background in chemistry which includes stoichiometry, reaction-oxidation analysis, reaction analysis and other general chemistry. Experience in organic chemistry is highly desirable. Experience with computer programming would be advantageous.

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, with written reports generated using the LaTeX typesetting environment.

Naiomi Cameron: Combinatorial Interpretations of Commutative Ideals
This project is eligible only for Rogers applicants.

Combinatorics is a subfield of mathematics sometimes described as the study of counting. The Catalan number sequence is one of the most ubiquitous sequences in all of combinatorics.  Like the famous Fibonacci numbers, the Catalan numbers appear as the answer to many problems which ask questions like “…under these conditions, how many of these objects will exist after n iterations…?”  Since the first known description of the Catalan numbers by Leonhard Euler in the 18th century, there have been at least 180 documented combinatorial interpretations of the Catalan numbers.  One example is the number of ideals in the ring of square upper triangular matrices.  It has been shown that, among these ideals, the number of those which are considered commutative is a power of two.  This project seeks to use combinatorial methods to precisely describe the combinatorial objects which correspond to these commutative ideals in the context of some of the most important of the 180 known Catalan interpretations.
Prerequisites:  Discrete Math (required), Linear Algebra (preferred).

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.

Jens Mache: Parallel Computing and Security
This project is eligible only for Rogers applicants.

The continuing growth of network connectivity, multi-core processors and embedded devices presents both challenges and opportunities for computer scientists. This summer, we will conduct research on parallel computing, performance and security. This internship includes studying existing systems, writing software and experimentation with various designs and algorithms.
Prerequisites:  Computer Networks CS 393,  Security CS 495 and Algorithms CS 383

Liz Stanhope: From orbifolds to orbigraphs
This project is eligible only for HHMI applicants.

One beautiful aspect of mathematics is that results in one subfield
can inspire startlingly similar results in another seemingly
unrelated area.  One example of this is the link between spectral
geometry and spectral graph theory.  Spectral geometry examines the
vibrational resonances of curved spaces such as spheres, tori and
possibly our own universe as it bends around large gravitational
bodies.  Spectral graph theory focuses on the eigenvalues of matrices
associated to graphs formed of nodes and edges.  The aim of this
project is to develop a graph theoretic analog of the geometric
objects that are the heart of my research program:  Riemannian
orbifolds.  Hints on how to do this were left in a paper called
Non-Sunada graphs by  mathematician Robert Brooks.  By following
these hints and considering Riemannian orbifolds, I hope that my
research group will add another connection between the fields of
geometry and graph theory.
Prerequisites: Technical Prerequisites:  Math 215 and Math 225 are required
prerequisites for this project.  In addition students who have taken
all or some of the following courses will be given preference: Math
325, Math 385 and Math 421.   Work Prerequisites:  Candidates with a
record of enthusiasm and experience in teaching or mentoring others
will be given preference.
Final note:  Students should be willing and able to work hard on
difficult problems for extended periods of time with minimal
supervision.

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Psychology

Erik Nilsen: Serious Games to Change Attitudes and Advance Science
This project is eligible for only HHMI.

“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 and conducting formative research for the development of a serious game to be used for research projects.   The first empirical study will be a follow-up to last summer’s project focusing on human rights issues in the Palestine/Israel conflict.  The second empirical study will focus on the use of a serious game incorporating crowd-sourcing techniques that involves people playing games online that aids in scientific discovery.
Prerequisites: Statistics (Psych. or Math Stats). 

Todd Watson: Event-Related Potential and Psychological Correlates of Risk Taking and Risky Patterns of Alcohol Use in College-Aged Adults
This project is eligible only for HHMI applicants.

Our lab is interested in the relationship between brain function and behavior. We record event-related potentials (ERPs), a safe and noninvasive measure of the electrical activity of the brain, while participants perform a variety of cognitive tasks. We will use these techniques to explore patterns of brain activity that may be related to constellations of disinhibited and potentially risky behaviors (e.g., binge drinking) in young adults. We will record ERPs while participants perform an attention task and determine if changes in brain function relate to patterns of alcohol use, risk taking behavior, and individual psychological and/or personality characteristics.
Prerequisites: For the undergraduate student, previous experience with electrophysiological techniques is highly preferred, but not necessary. No specific skills are required for the high school student other than enthusiasm.

Yueping Zhang: Hormonal Responses to Stress, Prefrontal Lobe Executive Functions and Drinking Behavior in College Students
This project is eligible only for HHMI applicants.

This study investigates how the Hypothalamic-Pituitary-Adrenocortical axis (HPA) reactivity, prefrontal lobe executive functions, and impulsivity are associated with different levels of drinking behavior in college students. Dysfunction of HPA responsivity to stress (measured by salivary cortisol change in response to psychological stress), PFC functions (measured by a neuropsychological test), and impulsivity (indicated by the ability to defer gratification in a behavior test) have all been implicated in different stages of alcoholism, and in non-drinkers with a family history of alcoholism. This project investigates how these variables are related with one another and with drinking behavior among college students.
Prerequisites: Courses in Statistics and Research Methods are highly desirable; courses offered by departments other than psychology are acceptable.

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OHSU Projects (HHMI only)

Research is conducted at Oregon Health & Science University

Claudio Mello: 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: Genetic 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.

Garet Lahvis: Social Motivation and Acoustic Communication
This project is eligible only for HHMI applicants.

Social interactions among humans and animal models can vary with respect to the environmental context of the social interaction and the emotional states of the participants.  The ability to regulate social interactions requires a capacity to express signals that communicate emotional information and to correctly modify one’s own behaviors in response to the signals of others. Deficits in these core abilities are featured in mental illnesses including addiction, depression, schizophrenia, and autism.  My laboratory studies the interactions between these aspects of social behavior and their anatomical and physiological substrates. We are particularly interested five social endophenotypes of juvenile mice; social interaction, social reward, fear learning in the context of a distressed conspecific, changes in the vocal expression in response to exposure to varied social situations, and changes in behavior in response to vocalizations of others.  We primarily study these aspects of sociality in BALB/cJ and C57BL/6J mice.  These strains express remarkable differences in social motivation and use a different vocal repertoire.  To compare mouse social abilities, we employ a variety of social behavioral tests, brain imaging techniques, such as radio-labeled glucose uptake, as well heart rate monitoring, administration of mu-opioid agonists and antagonists, and mouse genotyping.  We are particularly interested in how our measures of social ability in mice can be translated to clinical assessments of mental disability. 

My lab also has an ongoing interest in the expression of social abilities among feral animals that have not undergone extensive genetic selection through domestication.  In this regard, we have an ongoing interest in feral rodents, such as 13-lined ground squirrels (Spermophilus tridecemlineatus), and marine mammals, particularly California sea lions (Californianus zalophus). 

Armand Bankhead: Leveraging Pathway Knowledge for Cancer Treatment
This project is eligible for HHMI applicants only. 

The complexity of biological systems continues to hamper the treatment of disease such as cancers.  High throughput technologies make it possible to simultaneously measure thousands of gene activation events, but the interpretation of this data remains a challenge.  Our knowledge of how gene products interact in networks, called pathways, has improved over the past several decades.  Dr. Bankhead is interested in working with students on computational approaches to 1) investigate pathway understanding, 2) use pathways to interpret high throughput data and provide insight to cancer treatment.
Prerequisites: some coursework in biology and an interest in interpreting biology with computers.