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The Amgen Scholars Program
2012 Amgen Faculty
Below is a final list of participating faculty in the 2012 University of Washington Amgen Scholars Summer Program.
Click on the names below to learn more.
William (Bill) M. Atkins - Medicinal Chemistry
Description: Multiple exciting projects are available. The first involves preparation and characterization of lipid nanodiscs, which are a new type of nanoparticle that is revolutionizing the study of membrane proteins. These nanoparticles hold great promise as drug delivery vehicles and as models for LDL particles that are enzymatically transformed into HDL particles that transport cholesterol. This process is important for understanding heart disease and the formation of cardiovascular plaques. The second project is a drug design project that aims to design inhibitors of cytochrome P450s for use in engineering drug interactions for safer use of existing drugs. Both projects will require biophysical and chemical methods.
Requirements: Introductory chemistry course with lab.
Andrew (AJ) Boydston - Organic Chemistry
Description: When one considers an energy source for driving a chemical reaction, the first thoughts are usually thermal, photo, or electrical impetus. Much less common is the application of mechanical forces to provide energy to overcome activation barriers along a reaction coordinate. This practice, known as mechanochemistry, involves the use of mechanical energy to influence chemical phenomena, including bond making and breaking events. In this regard a mechanophore may be viewed as a moiety that is sensitive to applied stress, which can be applied either in the solid-state (e.g., via shearing) or in solution (e.g., via ultrasound). Our group focuses on the design and synthesis of specialty mechanophores that can be incorporated into macromolecular architectures and applied as stimulus-responsive materials. From these materials, we target applications in areas ranging from stress-sensors to drug delivery.
Requirements: Completion of all introductory organic chemistry courses (237-239, or honors track) and any associated laboratory courses.
Champak Chatterjee - Chemistry
Description: The Chatterjee lab is interested in understanding how chemical changes to proteins can influence their functions inside cells. We are particularly interested in reversible changes to histone proteins that are associated with the regulation of gene activity. The specific histone modification that we are studying is by a small protein called SUMO (small ubiquitin-like modifier). We are employing the tools of protein chemistry and molecular biology to make synthetic SUMO-modified histones that will be subjected to biophysical and biochemical assays in order to study the effects of SUMO on chromatin function. Specific details of the project will be decided after considering the students background and interest but will be focused on (i) applying synthetic organic chemistry to make modified histone proteins and, (ii) performing biochemical or biophysical assays with synthetically modified histones. Results from these studies will uncover new mechanisms by which histone modifications can regulate gene function. This is important for understanding how cells develop normally and also how diseases such as cancer arise from the incorrect timing of histone modifications.
Requirements: Completion of an introductory organic chemistry course along with associated laboratory courses. A background in biochemistry is helpful but not essential.
Horacio de la Iglesia - Biology
Description: Research in our laboratory is guided to understand the neural basis of behavior. Specifically, we are interested in biological timing, which can be studied at different levels of organization, using different approaches and throughout the phylogenetic tree.
Virtually all living species have biological clocks that generate and control the daily cyclic variations in physiology and behavior, such us rhythms in locomotor activity, temperature and hormonal secretion. In mammals, the master control of these so-called circadian rhythms is exerted by a biological clock located within the suprachiasmatic nucleus (SCN) of the brain. We use behavioral, physiological and molecular techniques in order to understand how the SCN generates and orchestrates this array of circadian rhythms.
Stan Fields - Genome Sciences and Medicine
Description: Ubiquitin is a 76 amino acid protein that is an essential signaling molecule in nearly every pathway in eukaryotic cells. Ubiquitin attachment to a protein often targets that protein to the proteasome for its degradation. The regulation of proteolysis is critical to maintain cellular function, and failure to appropriately degrade certain proteins underlies many human diseases. To understand regulated proteolysis, we have to be able to measure protein stability, which has traditionally used biochemical approaches that do not scale well. We have developed a new method that combines yeast genetics with high throughput DNA sequencing to measure the stability of up to hundreds of thousands of proteins in parallel. This method is being applied to the complete set of proteins produced by yeast. We are interested in using this method to address the question of how ubiquitin-tagged proteins are transferred from the ubiquitination machinery to the proteasome. The student will use the high throughput measurement of protein stability in yeast strains deleted for components of the ubiquitin proteasome system to characterize this transfer process.
Requirements: Some basic biology coursework.
Gwenn Garden - Neurology
Description: Inflammation has an important influence on the outcome of disease and injury in the CNS. Our laboratory studies the molecular regulation of inflammatory behaviors in the context of CNS diseases including Alzheimer's Disease, Stroke, Huntington's Disease and HIV associated neurocognitive disorders. We employ engineered mouse models of human disease as well as autopsy tissue from affected patients in these studies.
Requirements: One year of biology and chemistry coursework. Experience with commonly used equipment in molecular and cellular biology laboratories.
Jens Gundlach - Physics
Description: We are working on a new and direct technique for sequencing DNA. In this technique, single-stranded DNA molecules are driven through a biological pore where they produce a measurable obstruction of an ionic current that also flows through the pore. In collaboration with a microbiologist we are mutating a naturally occurring pore protein to make it suitable for this sequencing technology.
Matt Kaeberlein - Genetics, Biochemistry, Molecular Biology
Description: The Kaeberlein lab is interested in understanding the basic biology of aging. Projects in the lab have a common theme centered on defining the genetic and environmental factors that influence longevity and healthspan. We use three different model organisms for our research: the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and mice. Depending on interest and experience, an Amgen Scholar summer student would have the opportunity to work on an aging-related project in yeast or C. elegans (or possibly both). Currently available projects include (1) mechanistic studies aimed at defining why specific yeast mutants respond differentially to dietary restriction, (2) characterizing the relationship between mRNA translation and aging, with specific emphasis on the interplay between mitochondrial and cytoplasmic translation, and (3) defining the mechanisms by which the hypoxic response influences aging and healthspan in C. elegans. Opportunities to contribute to our SAGEWEB project (http://www.sageweb.org) are also available for students interested in aging-related bioinformatic/computational studies and/or software development.
Requirements: Enthusiasm and interest in the biology of aging.
Xiaosong Li - Computational Science, Chemistry and Materials Science
Description: Research in the Li group focuses on developing and applying computational methods and theories for studying properties and reactions that take place in large systems, such as polymers, biomolecules, and clusters. Students will have a unique opportunity to participate in interdisciplinary research subjects.
Requirements: Interest and motivation in computational research.
Dustin Maly - Chemistry
Description: Cells are able to integrate an enormous array of environmental information and convert these signals into complex behaviors such as growth, differentiation, and motility. This relay of extracellular stimuli into a phenotypic response involves the transfer of information through complex signal transduction networks that are precisely regulated, both spatially and temporally. Determining how these signal transduction networks are able to turn simple inputs into complex behavior is one of the greatest challenges in modern biology and will provide valuable insight into the cause and treatment of many diseases such as cancer, diabetes, and inflammation. Our group studies how cells sense and respond to their environment, by developing new biochemical and chemical tools that allow a greater quantitative understanding of cellular signaling than is possible with currently available methods. Using the tools of organic synthesis and protein biochemistry we are generating cell permeable small molecules that allow the activation or inactivation of specific signaling enzymes in living cells. While we are interested in studying the function of a number of protein families that are involved in signaling, our initial efforts are focused on enzymes that mediate intracellular phosphorylation (the protein kinases and phosphatases). These studies focus on three main areas: 1) The location-specific function of kinases and phosphatases. 2) The quantitative characterization of specific intracellular phosphorylation events. 3) The conformational plasticity of signaling enzymes.
The specific project within these areas will depend on your interests and prior research experience.
Requirements: Completion of an introductory organic chemistry course (and any associated laboratory courses).
Danilo C. Pozzo - Chemical Engineering
Description: In this project, selected students will be directly involved in the development of new technologies for photo-thermal therapeutic agents and ultrasound imaging contrast agents based on nanoparticle assemblies that effectively absorb near-infrared (NIR) light. This form of electromagnetic radiation effectively penetrates through many biological tissues and can induce localized heating for applications in targeted thermal cancer therapy and in medical imaging. The proposed new technologies are enabled by recent developments in the Pozzo laboratory related to the synthesis of nanoparticle-surfactants and their controlled assembly into multi-particle structures with adjustable optical properties (plasmon resonance). Selected students will learn and apply a variety of synthesis and structural characterization techniques including, but not limited to, small angle x-ray scattering and electron microscopy. They will also benefit from numerous opportunities to collaborate in an interdisciplinary environment of scientists from medical and engineering research departments at the University of Washington.
Requirements: Interested students must have completed all of the basic Chemistry courses as well as Organic Chemistry and Physics. Basic laboratory experience is also essential. Students from Chemical Engineering Departments are especially encouraged to participate.
Suzie Pun - Bioengineering
Description: The Pun Lab develops nanoparticles for delivery of genes, siRNA, and molecular imaging agents. Applications for these delivery vehicles include siRNA to the central nervous system, cancer therapy, and tissue engineering. Researchers in our lab learn techniques related to mammalian cell culture, nanoparticle formulation and characterization, and gene transfection assays.
Peter Rabinovitch - Experimental Pathology
Description: Aging is single greatest risk factor for many human diseases; however, the biological process of aging is often overlooked as a causative mechanism of disease. The Rabinovitch laboratory has focused on two disease processes in which to study the contribution of aging mechanisms. Studies of cardiac aging, hypertrophy and failure primarily utilize mouse models, while studies of ulcerative colitis utilize human biopsies and resection specimens. In either of these areas, the Amgen Scholar would learn of the mechanisms of aging that contribute to disease and the use of cutting-edge molecular and genomic research technologies.
Cardiac aging. We use mouse models to examine the effects of cell signaling and reactive oxygen species (ROS) on cardiac aging. Transgenic mice that overexpress catalase have been found to be protected against multiple health challenges, including cardiac aging. A mitochondrial antioxidant drug, SS-31, appears to provide similar protection. The interrelationships of mitochondrial ROS and mitochondrial damage with cell signaling pathways that mediate improved healthspan, including resistance to cardiac hypertrophy and failure, are studied. As the mTOR pathway is a strong candidate in this linkage, we are using transgenic mice with altered mTOR signaling to explore this relationship. Global proteomic and genomic approaches are also used to study the effects of ROS and mTOR on protein translation and turnover.
Aging and Genomic Instability in Ulcerative colitis. Aging, telomeres and mitochondrial function appear to interact with genomic instability as mechanisms behind the increased cancer risk in ulcerative colitis. Confocal microscopy and immunohistochemistry are used to study these processes in UC colon biopsies and resection specimens.
Requirements: Should have completed some biology coursework and lab experience.
Dan Ratner - Bioengineering
Description: The exciting new field of silicon photonics is revolutionizing our ability to manipulate light on the chip-scale, with broad implications to biomedical science, lab-on-a-chip technologies, distributed diagnostics and low-cost medical sensors. For instance, the silicon microring resonator is a highly sensitive and label-free biosensing technology that is based on nanometer-scale silicon waveguides (wires) that allow us to use light to rapidly detect proteins, viruses and even whole cells from complex biological samples. The goal of this Amgen summer project is to design a biocompatible interface on a silicon photonics biochip capable of performing real-time diagnostics in human blood and plasma.
Requirements: To ensure a successful research experience, applicants should have a basic familiarity with general/organic chemistry and introductory biology (protein structure, basic cell biology).
Michael Regnier - Bioengineering; Physiology & Biophysics
Description: The goal of our research is to understand the molecular and cellular mechanisms that regulate cardiac and skeletal muscle contraction, and how these mechanisms are disrupted in diseases. We use the knowledge gained from these experiments to design protein and gene based therapies to improve the performance of diseased muscle and to develop tissue engineered muscle constructs as cell-replacement therapy for myocardial infarct (heart attack) and skeletal muscle injuries. Many research projects are done in collaboration with other laboratories at the University of Washington, at other institutions across the US, and in Italy.
Requirements: Basic Biology and Chemistry courses are essential. Coursework in Biochemistry, Cell Biology and Physiology would help.
Hannele Ruohola-Baker - Biochemistry, Institute for Stem Cells and Regenerative Medicine
Description: My laboratory works on stem cell biology utilizing two systems, Drosophila germ line stem cells and human embryonic stem cells. In both cases we have shown that microRNAs play an important role in stemness. Our goals now include defining the key microRNA targets and their function in stem cells and their differentiating progeny. Further, we seek to understand the regulation and importance of the stem cell specific hypoxic metabolism. The goal is to understand whether the key stemness character observed in normal stem cells is also observed in pathological stem cells, so called cancer stem cells.
Lynn Schnapp - Pulmonary and Critical Care Medicine
Description: Mechanisms of Acute Lung Injury and Repair
Our lab is focused on the processes that govern acute lung injury and its resolution. In particular, we are interested in why lung injury resolves under certain circumstances (i.e. Adult Respiratory Distress Syndrome) and progresses to end-stage fibrosis in other circumstances (i.e. Idiopathic Pulmonary Fibrosis). To answer these questions, we use different models of lung injury in transgenic mice to examine select pathways in injury and fibrosis. To complement these studies, we are analyzing samples from patients with acute lung injury and other lung diseases using cutting-edge methodologies in proteomics to identify new pathways in lung injury.
Eric Shea-Brown - Applied Mathematics
Description: COMPUTATIONAL DYNAMICS OF BRAIN FUNCTION
We work on the dynamics of neurons, structured neural networks, and large neural populations. The goal is to help uncover mechanisms that enable these systems to encode, propagate, and make decisions about sensory inputs. I enjoy the highly collaborative work with cognitive neuroscientists, with electrophysiologists, and with psychiatrists and neurologists that this requires. Achieving this goal also requires generalizing mechanisms uncovered in these and other studies to develop the mathematical theory of spiking neural networks. The shared aim is a theoretical framework which describes and connects the neural dynamics occurring on different spatial and temporal scales, ranging from single neurons and small circuits to populations.
Hong Shen - Chemical Engineering
Description: My laboratory has three research thrusts:
Thrust II: designing materials that can either engage or avoid the immune system
Thrust III: mathematical modeling of the interactions between materials and the immune system
The materials we designed are applied to vaccines, drug delivery systems, biosensors, and tissue implants.
Kristin Swanson - Pathology, Mathematics, Applied Mathematics, Neuro Pathology
Description: The Swanson research lab is located in the University Medical Center, and focuses on mathematical modeling and the analysis of quantifiable data obtained through medical imaging such as MRI, PET, and CT. With our convenient location in the UMC, we are in a unique position to compare model results and predictions with data obtained from real patients receiving care at the University. Student researchers necessarily learn aspects of neuro anatomy, tumor evolution and biology, medical imaging, computational and data processing methods. Individualized projects are chosen to best meet the student's interests and abilities, while at the same time serving the overarching goals of the lab.
The lab's current focus includes, but is not limited to, the modeling of brain tumor growth, evolution and response to therapy, and comparisons of information obtained from superficially disparate imaging modalities such as MR and PET. This modeling effort provides many interesting avenues for student research: from data acquisition and processing to investigation and development of new mathematical models of tumor processes.
Our lab is truly interdisciplinary: with over a dozen members with backgrounds ranging from biology to applied mathematics and computer programming, we are able to determine suitable research projects for just about anyone with a scientific background. A vast majority of our lab members are pre-med, providing a stimulating environment with many resources for information and opportunities.
Students are supervised daily by the lab manager, with at least once weekly lab meetings involving progress reports to Dr. Swanson.
Requirements: The student should have a strong interest and background in either mathematics or medical imaging, and be in good academic standing. Student should have intermediate to advanced computer experience and be comfortable spending extended periods of time at a computer. A strong candidate will have a background in mathematics, including a full calculus sequence, differential equations and linear algebra. Preference will be given to students with experience in any of the following computer programming languages: MATLAB, C++, FORTRAN, PHP, SQL.
Rheem A. Totah - Medicinal Chemistry
Description: Our lab is interested in investigating cytochrome P450 enzymes that are involved in drug metabolism and have a known endogenous function. Several research opportunities exist to study the biochemical role of these enzymes. One project focuses on CYP2J2 and its role in drug induced cardiac toxicity. Stem cell derived adult cardiomyocytes are treated with various drugs and the change in RNA and protein expression is measured. Also the effect of drugs on the activity of CYP2J2 is assessed using LC-MS. A second project investigates the pharmacogenetic nature of CYP2C8. This enzyme is polymorphically expressed in various ethnic groups which results in a variable pharmacological response to drugs metabolized by this enzyme. We are currently investigating the mechanism behind the variable activity of the main variants of this enzyme. We utilize molecular biology to engineer the different variants, UV spectroscopy and LC-MS to assess the changes in activity.
Requirements: Intro to Chemistry and intro to Biochemistry
Judit Villen - Genome Sciences
Description: My lab is interested in how signaling networks shape the cellular proteome and function, and how the structure and activity of these networks is altered upon disease onset and progression. To learn about these questions, we develop and apply mass spectrometry-based approaches that involve quantitative measurements on nearly complete proteomes. Our team is very interdisciplinary with a background ranging from chemistry and biology to engineering and computer sciences. Opportunities for summer students include experimental and computational options. Specific projects can be assigned based on background and interests.
Requirements: Previous research experience is preferable.
Paul Yager - Bioengineering
Description: We are developing microfluidics-based analytical techniques for molecules of biomedical interest. Ongoing projects focus on the use of novel and extremely low cost paper-based diagnostic tools for optical detection of proteins, nucleic acids, and small molecules. Projects are funded by NIH and DARPA.
Bo Zhang - Bioanalytical Chemistry, Electrochemistry
Description: Our group research is focused on developing new electrochemical methods to solve important challenges in electron transfer, neurochemistry, and electrocatalysis. We currently have two projects available for incoming Amgen students. The first project studies electron-transfer and electrocatalysis at single metal/semiconductor nanoparticles using nanoelectrodes. The second project develops and uses electrochemical arrays to image neuronal secretion from single cells and cells in a network. Students with strong motivation and interest in analytical chemistry and physical chemistry are welcome to participate in our research.
Requirements: A strong background and motivation in chemistry.