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Rogers Science Research

2009 Abstracts for Rogers and HHMI Programs

March 31, 2009

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

  • Rogers only: most of the projects.
  • HHMI only: 3 projects based at OHSU (listed at the bottom of this webpage).
  • HHMI and Rogers: some projects are eligible for both programs.

Prerequisites must be completed by the end of spring semester 2009.


Greta Binford 1: Molecular evolution of the toxic enzyme sphingomyelinase D in venoms of brown spiders (Loxosceles)

This project is eligible only for Rogers applicants.

Spider venoms are diverse and evolve rapidly making them excellent models for studying how proteins evolve. We study the evolution of venom toxins in brown recluse and their relatives (Loxosceles). A venom enzyme in these spiders, sphingomyelinase D (SMaseD), damages human skin. We have isolated genes related to this toxin from 21 species of Loxosceles and relatives including species whose venoms have no SMase D activity. The goal of this project is to use comparative analyses to identify characteristics that confer SMase D- specific function in these genes and to identify other related functions. We will analyze the enzymatic activity, and paralytic activity on crickets of expressed proteins of SMase D homologs.

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

Greta Binford 2: Evolutionary patterns of diversification of North American spiders in genus (Loxosceles)

This project is eligible for HHMI and Rogers applicants.

There are over 100 Loxosceles species worldwide and 50 in North America. Previous work indicates that the earliest species in this genus originated before Africa and South America separated (>95 million years ago) and colonized North America from South America before the modern Isthmus of Panama was in place. The research goal this summer is to finish ongoing analyses of the timing of colonization and patterns of dispersal and speciation of North American (Loxosceles). This will involve collecting DNA sequence data, confirming species identities, inferring patterns of relationships using bioinformatic analyses and learning about North American geological history.

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

Ken Clifton: Investigating the effects of elevated atmospheric CO2 upon the structure and function of calcium carbonate accretion in tropical green algae of the genus Halimeda

This project is eligible only for Rogers applicants.

A variety of marine organisms sequester calcium carbonate for structural or defensive purposes. This ability to build calcified skeletal material may decline as rising levels of atmospheric carbon dioxide permeate into ocean waters, causing acidification. Such a decline has recently been confirmed experimentally for a variety of reef-building corals; however, the impact of elevated carbon dioxide levels on other calcified members of shallow tropical marine habitats has not been investigated. I propose to experimentally examine this relationship for an ecologically important group of calcified green seaweeds that occur in abundance within shallow tropical marine habitats world-wide.

Prerequisites: Bio 141, 151; Chem 110, 120.

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 characterizing the function of genes necessary for the assembly and stability of lysosomes in the model organism, Caenorhabditis elegans. Our work will focus on investigating the cellular pathways controlled by these genes

Prerequisites: BIO 151, BIO 200, (BIO 311/312 or BIO 361 suggested but not required).

Peter Kennedy: Exploring the factors controlling microbial community structure: competition and host specificity

This project is eligible only for Rogers applicants.

Research in our lab focuses on microbial ecology and the ecological factors that structure microbial communities. Specifically, we study two kinds of plant-associated microbes, ectomycorrhizal fungi and nitrogen-fixing bacteria (see lab website for additional details: In the summer of 2009, we will be conducting research in three areas. Two projects will examine the dynamics of competition among ectomycorrhizal fungi. One of the competition projects will focus on spore density and the other on soil water availability. Both will use fungal species in the genus Rhizopogon. The third project will examine how the composition of Frankia nitrogen-fixing bacterial assemblages are influenced by host plant species. Projects will involve research in both field and laboratory settings. Techniques will include microscopy, culturing, and molecular identification analyses. Students familiar with PCR and other molecular techniques, sterile laboratory practices, and basic statistical principles will be preferred.

Prerequisites: Bio 141, Bio 151 and Bio 200.

Deborah Lycan: Ribosome biogenesis and export

This project is eligible only for Rogers applicants.

The eukaryotic ribosome is the largest and most complex RNA:protein machine assembled in higher cells. Ribosome biogenesis involves the coordinated processing and assembly of rRNAs and ribosomal proteins into 2 subunits in the nucleolus. These subunits are then exported to the cytoplasm where final maturation steps must take place. In my lab, we are focusing on small subunit export and maturation. We are currently investigating the role of post-translational modifications of ribosomal subunits in regulating export, and trying to identify proteins that serve as export adaptors. Students will be involved in experiments utilizing genetics, molecular cloning and biochemistry techniques, and microscopy.

Prerequisites: Biology 151 and Biology 200 by summer 2009. Students who have completed Molecular Biology 311/312 or Cell Biology 360 or Chem 335/336 will be especially well suited to my lab.

Gary Reiness: Mechanism of Export of Chicken Ciliary Neurotrophic Factor

This project is eligible only for Rogers applicants.

We study “unconventional” protein secretion of ciliary neurotrophic factor (CNTF). While most secreted proteins move sequentially through the endoplasmic reticulum, Golgi apparatus, and secretory vesicles before being released, some, including CNTF, use other, unknown pathways. Because CNTF acts in cell-to -cell communication during nervous system development, investigating its secretory pathway will aid 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 and analysis of mutant CNTFs to identify its secretory signal. Some of this work will be conducted at OHSU.

Prerequisites: I would prefer students who have completed either Biology 311/12, Biology 361, Chemistry 330, or Chemistry 335 and 336 but will consider all who have completed Bio 200 or equivalent. Some experience with fluorescence microscopy or tissue culture would be particularly useful.


Anne Bentley: Formation of Nanoparticle / Solid State Thin Film Composite Materials via Electrochemical Co-Deposition

This project is eligible only for Rogers applicants.

This project will explore the ability to control the incorporation of nanoparticles into thin metal oxide films used in lighting and Li+ ion battery applications. By altering the types of molecules adsorbed onto the nanoparticle and electrode surfaces, we hope to control how the composite is formed. Students will gain experience in nanoparticle synthesis, altering surface coatings, and electrodeposition (applying an electrical potential to reduce metal ions at an electrode). Characterization tools will include dynamic light scattering, zeta potential measurements, fluorescence spectroscopy, cyclic voltammetry, powder X-ray diffraction, and electron microscopy.

Prerequisites: Chemistry 110 and 120.

James Duncan: Dynamic Electron Correlation Effects Applied to the Computational Study of the Mechanisms of Targeted Pericyclic and Pseudopericyclic Reactions

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 reinvestigate some of our recent findings using the even higher CASPT2 level of theory that employs a second-order perturbational approach to account for dynamic electron correlation. Students will routinely use what are arguably the two most sophisticated suites of computational software currently available—Gaussian and MOLCAS—and be introduced to the latest advances in computational chemistry.

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

Louis Kuo: Investigation of Molybdenum Complexes for Degrading Neurotoxin Analogues

This project is eligible only for Rogers applicants.

This project explores a class of organometallic complexes called metallocenes (metal = molybdenum) to carry out the degradation of a class of phosphate neurotoxins. Phosphino-thioates are the functional core of neurotoxins, some of which have been used as pesticides. Besides having inert and strong P-alkyl and P=O bonds, the core of phosphinothioates consists of P-S and P-O linkages wherein the preferable mode of degradation involves cleavage of the P-S bond; scission of the P-O bond yields a complex just as toxic as the parent neurotoxin. We have recently found that molybdenum metallocenes yield this preferable bond scission on a model phosphinothioate in aqueous solution. This project will synthesize new molybdenum complexes with the objective of determining structure-activity relationships on how metallocenes affect the degradation/hydrolysis of phosphinothioates.

Prerequisites: Chem 220.

Janis Lochner (and Bethe Scalettar): Neuromodulators and Memory

This project is eligible only for Rogers applicants.

Long-term memory formation occurs in the hippocampus and is accompanied by enduring changes in synaptic organization. Release of neuromodulatory proteins at synaptic sites triggers the structural and functional changes associated with the changes in synaptic organization. To better understand the molecular determinants of synaptic plasticity, we will characterize the properties and cellular mechanisms of presynaptic secretion of neuromodulators from cultured hippocampal neurons. These studies rely on the use of molecular cloning tools to create fluorescent chimeras of neuromodulatory proteins and multi-wavelength, time-lapse fluorescence imaging to follow release of the fluorescent chimeras from synaptic sites.

Prerequisites: Required course work – Chemistry 210-220. Recommended course work – Bio 200 or a course in biochemistry or cellular or molecular biology.

Niko Loening : Structural Studies and 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 then use NMR spectroscopy to study the structures of venom peptides. This work will be done in collaboration with Dr. Greta Binford.

Prerequisites: Biochemistry lab experience…particularly with generating and working with protein samples. Coursework in biochemistry/molecular biology (preferably structural biochemistry and/or Chem 464).


Liz Safran: Impact of large landslides on river valley evolution, Central and Eastern Oregon

This project is eligible only for Rogers applicants.

The rate at which rivers incise through bedrock sets the pattern and tempo of landscape evolution in geologically active settings. Many such regions are characterized by steep topography and seismic activity, conditions which also promote large landslides. These landslides locally disrupt river channels by changing channel width, slope, and bed character. It remains unknown, however, whether these disruptions have any significant effect on long term patterns of river evolution and downcutting. This project focuses on how the desert rivers of Central and Eastern Oregon deal with large landslide incursions, using a variety of GIS, Matlab modeling, and field techniques.

Prerequisites: Geology 150 *OR* basic computer programming skills.


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, 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: Cognitive Construal and Somatic Markers in Two Games of Risk

This project is eligible for HHMI and Rogers applicants.

Construal Level Theory (CLT) provides evidence that placing people in an abstract mindset leads to better decision making than instilling a concrete mindset. The Somatic Marker Hypothesis (SMH) states that effective decision-making is aided by the existence of an emotion-related physiological signal. The current study examines the relative influence of cognition and emotion in two games involving risky decision-making. The Game of Dice Task is a gambling task involving a series of bets based on a roll of a single die. The Peacemaker Game is a first-person computer simulation of the Israeli Palestinian crisis. By manipulating mindset and measuring skin conductance levels in these two games we will evaluate the explanatory and predictive power of these theories.

Prerequisites: Statistics (Psych. or Math Stats).

Yueping Zhang: Understanding college students drinking Prefrontal lobe functions, social influence, and personality traits

This project is eligible for HHMI and Rogers applicants.

Alcohol use and abuse are common among college students, and often lead to negative consequences. This project attempts to further our understanding of drinking behavior among college students from several perspectives: a social factor (social norm perception), a personality trait (impulsivity), and brain function (prefrontal functions). By examining multiple factors in one study, the proposed research will allow us to examine how variables from social, psychological, and neuropsychological dimensions relate to one another in mediating drinking behavior. Results from such research may also lead to better prevention and intervention strategies for reducing drinking-related problems.

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 at the Oregon National Primate Research Center/OHSU is undertaken to improve understanding of human health and disease. Animal models are essential in this pursuit, and students need to be aware that in certain cases invasive animal procedures are necessary. Ethical issues associated with research in humans and other animals can evoke strong controversy, yet animal research is presently our only means of answering certain critical questions that we hope will lead to improved therapies and/or cures for disease. Federal law mandates adherence to regulations that ensure our research procedures are both humane and justified in terms of their contribution to knowledge and medical practice. Students who apply for this internship should support the ethical conduct of animal research that is carried out in compliance with federal laws and regulations.

Kathy Grant, PhD: OHSU Project 1.

This project is eligible only for HHMI applicants.

Dr. Grant uses neuroscience and pharmacology to learn about alcoholism. One project involves studying the brain receptor proteins that mediate the subjective effects of alcohol (e.g., intoxication, dizziness, decreased anxiety) using rats. Rats are trained to press a specific lever after alcohol is administered, and to press another lever after water is administered. When the rats press the correct lever, they receive sugar pellets. Once trained, rats can “tell” Dr. Grant (via their lever choices) whether test drugs have effects like alcohol or not. Hormones produced by the ovaries and adrenal glands get into the brain and produce alcohol-like effects. Since hormone levels fluctuate across the estrus cycle, Dr. Grant is interested in whether phase of the estrus cycle influences rats’ sensitivity to alcohol. The estrus cycle refers to physiologic changes induced by reproductive hormones that occur over a 4-day period in mature rats that regulate sexual behavior and fertility.

A student in the Grant Lab will be responsible for using a microscope to categorize cell types from rat vaginal smears in order to identify estrus cycle phase. The student will link estrus cycle data to behavioral data to find out whether rats’ sensitivity to alcohol depends on estrus cycle phase. The student will learn how the estrus cycle differs from the menstrual cycle and participate in discussions with lab scientists.

Student researcher qualities: This project requires a student that can seriously concentrate on a single task for several hours at a time over many days. The student should be enthusiastic, reliable, able to work independently, have superior attention to detail and ability to keep careful records. An eagerness to learn and inquisitive nature will be helpful traits.

Kevin Grove, PhD: OHSU Project 2.

This project is eligible only for HHMI applicants.

The Grove Laboratory examines the impact of maternal nutrition and obesity on the physiology, behavior and brains of offspring. A non-human primate model is used to compare offspring from obese mothers consuming a high fat diet and lean mothers consuming a low-fat diet. The impact of maternal obesity is being examined in a number of different parts of the body including the brain, cardiovascular system, liver and pancreas. The student will have the opportunity to participate in ongoing studies which examine the consequences of maternal obesity and high-fat diet consumption on the offspring’s body weight regulation, food preference and behavioral responses to novelty and stress. The student will assist in measuring the food intake, physical activity, food preference and behavior of juvenile monkeys. This will involve analysis of video recordings, and the analysis of data collected from activity monitors.

Student researcher qualities: This project requires a student that feels comfortable working with animals. Enthusiasm, reliability and time consciousness are also very important. The student must be able to focus for several hours at a time and be able to work independently. Being detail oriented with data collection and record keeping is also necessary.

Ilhem Messaoudi, PhD: OHSU Project 3.

This project is eligible only for HHMI applicants.

Aging is accompanied by an increase in susceptibility and severity of infectious diseases due to general decline in immunity. Since the proportion of aged individuals is rapidly increasing, understanding the defects in the immune systems of this vulnerable population will undoubtedly help us design interventions to improve immunity and increase the efficacy of vaccinations that could alleviate disease complications. The emphasis of the Messaoudi laboratory is to further our understanding of mechanisms underlying the decline in T cell immune function using nonhuman primate animal models. Our work is focused on two areas, the students will be able to choose one of the projects to participate in during the summer internship.

1) Elucidating immunological deficiencies that underlie varicella zoster virus (VZV) reactivation and the onset of shingles: We have developed an animal model whereby rhesus macaques (RM) are infected with simian varicella virus (SVV). We are identifying viral proteins that are frequently targeted by the T cell response. The identification of these proteins is a critical first step in the design of subunit vaccines to boost anti VZV immunity in the elderly.

2) Understanding how menopause affects immunity in aged women: We are studying the effect of menopause induced at different ages as well as hormone replacement regimens on the immune response to vaccination in female rhesus macaques. Furthermore, we are elucidating the mechanisms by which changes in these hormones might affect T and B cell function.

Student researcher qualities: Enthusiasm, persistence and reliability are very important, as is the ability to work independently. Students should be comfortable performing repetitive tasks. General curiosity and comfort with asking questions are also important.