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Opportunities in Science at Lewis & Clark

2014 Project Descriptions for Rogers and CELS Programs

February 13, 2014

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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 2014. 

Please review application instructions and forms here.

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Biology

 

Paulette Bierzychudek
Removal of Invasive Plant Species

This project is eligible only for Rogers applicants.
How do forests recover after invasive species removal? We will continue a monitoring study in the River View Natural Area, begun in 2012, to examine ecological changes following removal of invasive ivy, laurel, and holly. Research interns will compare plant species composition and abundance in areas where invasives were removed and in untreated control areas. The results will help land managers to develop effective strategies for conservation and restoration of urban forests and will develop skills in plant identification, geographic information systems (GIS), and statistical analysis.

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

Prerequisites: Students must have taken Bio 141. Bio 335 (Ecology) and/or Bio 223 (Plant Biology) are desirable but not required. Students are 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 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. We will infer influences of geographic isolation and dispersal on patterns of colonization and divergence. This summer students will work either at Lewis & Clark, or at the University of Vermont. They will do molecular and morphological analyses of arachnids

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

Greta J. Binford
The evolution of venom-expressed gene families in Haplogyne spiders

This project is eligible only for Rogers applicants.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, Bio 200 and Bio 390 helpful but not required.

Greg J. Hermann
Constructing cellular compartments during embryonic development

This project is eligible for CELS 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 only for Rogers applicants.
The long-term goal of this project is to understand how cells make ribosomes. One of the ways in which cancer cells differ from normal cells is their huge rate of ribosome biogenesis, and thus understanding how cells assemble and export ribosomes may provide new therapeutic targets for the specific inhibition of cancer cell growth. 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: Molecular Biology 311 or Cell Biology 361

Norma A. Velazquez Ulloa
Discovering the mechanisms underlying the effects of nicotine on development and drug-induced behaviors in Drosophila melanogaster.

This project is eligible for CELS and Rogers applicants.
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.

Prerequisites: : BIO 151, and BIO 200, or similar background from courses taken at other institutions. 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.

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. (Bio 200/additional background in cellular or molecular biology is ideal.)

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Chemistry

 

James A. Duncan
Fundamental Mechanistic Investigations of (Pseudo)pericyclic and (Pseudo)coarctate Reactions via CASSCF, CASPT2, and DFT Computational Studies

This project is eligible only for Rogers applicants.
Several related fundamental mechanistic studies, involving primarily CASSCF and CASPT2 computational methods, will be carried out simultaneously with attentive comparison of results. These studies will build on an original technique our group has recently developed 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

Casey Jones
Can red wine keep your arteries open?

This project is eligible only for Rogers applicants.
This organic chemistry project seeks to attach resveratrol, a compound found in red wine, to metal cardiovascular stents. Stents are used in patients with coronary artery disease, but often fail from improper healing. Resveratrol has been shown to have the potential to improve cardiovascular healing. Our hypothesis is that a stent releasing resveratrol or analogues will improve healing, leading to device success with less risk to patients. To accomplish this goal, we will (1) synthesize a library of resveratrol analogues, (2) optimize the attachment of these molecules to metal surfaces, and (3) characterize the release of molecules from the surface.

Prerequisites: Organic Chemistry 210 & 220

Louis Kuo
Development of Synthetic Teaching Labs for Crystallographic Analysis

This project is eligible only for Rogers applicants.
The recent arrival of a single crystal X-ray diffractometer (SC-XRD) means L&C is the first PUI in the Pacific Northwest to acquire this instrument for molecular structural elucidation. This acquisition was made possible through a NSF-TUES award, and the instrument will be used for teaching purposes in the first, second and third year chemistry labs. This summer project seeks to develop synthetic labs that lead to single crystals to be characterized by X-ray techniques. There will be a curricular approach that seeks to disseminate some of the information to other neighboring PUI’s who share this SC-XRD.

Prerequisites: Chem 220; Chem 366 strongly preferred

Louis Kuo
Application of molybdenum oxides for degrading sulfur-containing organophosphate toxins

This project is eligible only for Rogers applicants.
Sulfur-containing organophosphates (OP) are used as pesticides because of their neurotoxic properties. Hydrolysis is a common route for degrading these neurotoxins as it uses readily available reagents (i.e. water). One complication with sulfur-containing OP is that P-O hydrolysis yields a toxic byproduct. Therefore, it is desirable to have hydrolytic processes that yield only P-S scission. This proposal uses readily available molybdenum oxides to accelerate hydrolytic degradation of OP. The molybdenum oxide MoO4 is chosen because it promotes specific P-S scission with turnover under aerobic conditions. The specific goal is to find protocols that yield more rapid rates of OP hydrolysis.

Prerequisites: Chem 220; Chem 366 strongly preferred

Janis E. Lochner
Interaction of SNARE- Neuromodulatory Proteins from Dense-Core Granules

This project is eligible only for Rogers applicants.
The regulated release of neuromodulatory proteins from dense-core granules (DCGs) in hippocampal neurons is critical to long-term memory formation. However, limited insight exists regarding the molecular machinery that mediates release of these proteins from the synaptic sites of hippocampal neurons. We are evaluating several distinct soluble N-ethymaleimide sensitive factor attachment protein receptor (SNARE) proteins in an attempt to identify the key proteins that are required for mediating synaptic secretion of neuromodulators from DCGs. 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), Neuroscience course work ( Bio252 or Bio 422) and also have previous research experience.

Nikolaus Loening
Structural Studies and Functional Characterization of Neurotoxic Venom Peptides from Sicariidae Spiders

This project is eligible only for Rogers applicants.
Spider venoms contain hundreds of components, including neurotoxic peptides and proteins. These venom components are of interest for their potential use as therapeutic drugs and as tools for neurophysiology research, as many of them specifically inhibit or activate ion channels and receptors in nerve cells. The aim of this research is to discover interesting peptides and proteins from the venom of the brown recluse spider and its relatives (the Sicariidae spiders), and then to characterize their structure and function. We will recombinantly-express spider venom peptides and study them using NMR spectroscopy and other techniques. This work will be done in collaboration with Dr. Greta Binford

Prerequisites: 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)

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Mathematical and Computer Science

 

Yung-Pin Chen
Studying Convergence Rates of Markov Chains

This project is eligible for CELS and Rogers applicants.
Imagine you have a deck of N cards, and the N cards are initially arranged in numerical order from 1 to N. You like to randomize the deck by shuffling. One shuffling scheme is to select a card at random from the deck and place it on the top of the deck. You may also bridge shuffle the deck like people normally do in a poker game. Which shuffling scheme randomizes the deck faster? Under each shuffling scheme, we can model the states and the shuffles of a deck by a stochastic process called Markov chain. We will study how fast a Markov chain settles down to its equilibrium distribution. In addition to understanding the theoretical foundation, a primary aim of this project is to investigate the applications of Markov chain convergence rate in the scientific computation.

Prerequisites: Students should have some working knowledge of probability, statistics, and matrix algebra. Computer skills (experiences in Java, C, Mathematica, or R) are a plus.

Peter Drake
Orego: 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 courses using the Java programming language. Students must know the rules of Go; any skill at playing the game is a bonus.

Jens Mache
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.

Jens Mache
Parallel computing with higher-level languages and compelling examples

This project is eligible only for Rogers applicants.
Computer hardware is undergoing a major shift. Four or six-core chips are now standard, and future processor generations are expected to further increase core counts. 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-495 Parallelism, CS-277 Computer Architecture, CS-363 Operating Systems and CS-383 Algorithms.

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Physics

 

Shannon O’Leary
Understanding Laser Noise in an Atomic Vapor for Magnetometry

This project is eligible only for Rogers applicants.
Advancements in magnetometry have profound impacts on many scientific fields and medical applications. This experimental optics project seeks to develop a new magnetometer using an interaction between light and matter that is highly sensitive to magnetic fields, laser noise derived from quantum interference in an atomic vapor. We use a quantum interference process called Electromagnetically Induced Transparency (EIT), which causes an otherwise opaque material to become transparent over a narrow 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.

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Psychology

 

Jennifer LaBounty
Development of Individual Differences in Social Cognition in Young Children

This project is eligible for CELS applicants only.
My research focuses on “social cognitive” development in infants and young children. Social cognition refers to children’s understanding of other people’s thoughts and feelings. Previous research has demonstrated a link between advanced social cognition in early childhood and many important social and academic outcomes later in life. Our research is concerned with discovering the factors or experiences in a child’s early life that may be contributing to improved social cognition, including the quality and content of parent-child interactions as well as the effects of a child’s own personality on their understanding of other people.

Prerequisites: Students working in my lab are expected to work with very young children (ages 2.5-3.5 years old). Some previous experience working with children and/or families would be helpful.

Diana Leonard
Group-based emotions as antecedents and consequences of competitive victimhood claims

This project is eligible for CELS applicants only.
Competitive Victimhood (CV) occurs when individuals attempt to establish that their group has suffered more than an adversarial group. One motive for claiming victimhood may be to restore the moral image of the in-group during a destructive conflict. Despite this seemingly positive function, however, CV may be a barrier to reconciliation between groups. Our project uses experimental procedures with online samples to examine emotional responses to such victimization, such as the United States’ use of drone strikes in the war on terror. Our project seeks to examine the role of specific emotions as likely causes and consequences of intergroup conflict.

Prerequisites: Psy 200 and 300 are strongly recommended; Psy 260 is preferred.

Erik Nilsen
Motivating Healthy Behaviors with Quantified Self Technology.
Tangible Technology for Teaching Toddlers

This project is eligible for CELS and Rogers applicants.
Quantified Self involves the use of web and sensor based technology to improve health and motivate behavior change. We will be exploring three technologies spanning physical (Fitbit Activity Trackers), emotional (Wild Divine biofeedback devices) and cognitive health (Lumosity brain training games). The research team will be engaging in a self-experimentation project using each technology throughout the summer. A second study will recruit participants to use the Fitbit Trackers using field and lab-based research methods to explore various motivational strategies including the use of badges, achievement goals, and collaboration versus competition. A third project will extend research, conducted at OMSI, on using toys to enhance spatial reasoning and creativity in young children.

Prerequisites: Statistics (Psych. or Math Stats). Experience in either behavioral research and/or web development. This can be met through coursework (Psy 300 or CS 171/172) or other experience.

Todd D. Watson
Investigations of Inhibitory Cognitive Control Related to Images of High-Calorie Foods in Adults and Young Children

This project is eligible for CELS and Rogers applicants.
We will explore the correlates of cognitive control over food-related cues in two distinct populations. We will use event-related potentials (a noninvasive measure of brain function) to explore the neural correlates of cognitive control during a food-cue processing task in healthy young adults with different eating habits. In a separate study, we will explore the relationship between the cognitive correlates of viewing high and low-calorie food images with externalizing behavior and sensation seeking in preschool-aged children. In all, we hope to determine if inhibiting inappropriate behavioral responses to images of high-calorie foods is associated with higher demands on neurocognitive resources.

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.

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OHSU Projects (CELS only)

 

Damien Fair

Title to be announced 
This project is eligible for CELS applicants 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 in translational studies of developmental neuropsychiatric disorders like ADHD and autism. We have ongoing projects applying imaging techniques in human infants, children, and adults, as well as in non-human primates. Projects may include use of Microsoft Office Suite (Work, Excel, Outlook, and Publisher) and computer programming languages (C++, Python, and S).

Jacob Raber
Genetic and Environmental Impact on Learning and Memory and Anxiety

This project is eligible for CELS 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 CELS 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
Is intrafraction motion assessment necessary for cranial Stereotactic Radiosurgery? A dosimetric evaluation

This project is eligible for CELS applicants only.
Intracranial stereotactic radiosurgery (SRS) is characterized by accurate targeting and delivery of highly focal and large radiation doses with steep dose gradients to small discrete targets. For the past fifty years, invasive head fixation techniques have been the standard of care for intracranial stereotactic treatment. Recently, the necessity for rigid immobilization is being supplanted by the integration of advanced image-guidance technologies with standard linear accelerators (linacs). Today non-rigid (frameless) immobilization with relocateable thermoplastic mask combined with online imaging for alignment has become an established paradigm for cranial stereotactic treatments. Nevertheless, thermoplastic mask immobilization may have elastic tendencies with the potential for underlying patient motion. Currently, there are no guidelines on the frequency of verification and/or validation of immobilization integrity; while some institutions may monitor patients continuously, others only perform pre-positioning image-guidance. It thus begs the question of whether we can assume intrafraction motion as non-significant, particularly during stereotactic radiosurgical procedures where submillimeter accuracy is the norm. The primary goal of the current study is to evaluate the dosimetric consequences of intrafraction motion on both target volumes and adjacent critical structures of a homogenous subset of patients that had undergone intracranial SRS. The secondary goal is to define the optimal frequency of intrafraction motion interrogation in order to minimize the dosimetric consequences of patient motion during treatment.