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Undergraduate Research Program

2007-08 WRF Fellows

Joan Bleecker - Chemistry

Joan Bleecker working in fume hoodJoan now hails from Gig Harbor, WA, but has lived all over the United States. She has wanted to attend the University of Washington since she was 10 years old.

The summer of her freshman year, Joan was given an opportunity to perform research in the Dovichi Lab working with breast cancer cells, and has been researching ever since. She cannot say enough for the importance of research for any would-be-chemist. After all, knowledge is nothing without practical application.

Research has also given Joan the chance to present her work all over the country. She enjoys these trips immensely, even though she has a tendency to get incredibly nervous before speaking in front of others.

Joan’s chemistry career began with an amazing high school chemistry teacher. She believes it is important that young students get a good introduction to chemistry. Joan tutors at the University of Washington’s CLUE center and for the Youth Tutoring Program (YTP) in Jackson Park. After getting her degree in chemistry, she hopes to teach chemistry for a few years before attending graduate school and getting her Ph.D.

Mentor: Norman Dovichi, Chemistry

Project Title: Cell cycle-dependent characterization of single MCF-7 breast cancer cells by two-dimensional capillary electrophoresis

Abstract: Breast cancer is leading cause of cancer mortality for women in the United States. Prognostic indicators like progesterone receptor and Her2/neu proteins guide treatment and predict outcomes. Their expression levels directly affect patient survivability. Even with these indicators, there is a need for more detailed information to guide therapy. By generating protein fingerprints, which show the expression levels of multiple proteins at one time, our lab hopes to provide a valuable prognostic tool for cancer patients. MCF-7 is an established breast cancer cell line. By dosing MCF-7 with the chemotherapeutic agent mitomycin C (MMC), we hope to isolate survivor populations for protein studies. Cell viability will be determined by hemocytometry with Trypan blue staining and flow cytometry. Proteins in the survivor cell lines will be analyzed using 2D SDS PAGE/LC-MS and capillary electrophoresis with laser-induced fluorescence detection.

Sam Burden - Electrical Engineering

Sam Burden working in the labWhen I started high school, I had no plans to attend college after graduation. I found high school rather droll, and reasoned that college wouldn’t be much better. It wasn’t until I participated in a math camp at UW during the summer after my junior year of high school that my perspective changed. At the camp, I was part of a vibrant intellectual community, surrounded by passionate people working collaboratively to master difficult material. When I came to UW, I wanted to immerse myself in a similarly challenging community, and thought participating in research might fulfill that desire. Through the NASA Space Grant program, I started working for Professor Eric Klavins in Electrical Engineering during the summer before my freshman year. I found the lab environment exciting and intellectually stimulating, so I stuck around; I’ll finish my fourth year with the group this Spring. I’ve enjoyed participating in research so much that I want to extend the experience as long as possible. Consequently, I’ll be continuing my education next year in a Ph.D. program studying legged robots.

Mentor: Professor Eric Klavins, Electrical Engineering

Project Title: Immunology for Self-Organizing Robots

Abstract: Self-organization drives assembly in nature. Crystallization, protein synthesis, and cell specialization all occur in a distributed manner between a large number of relatively simple components. Understanding how to engineer such processes should enable us to construct computational devices and novel materials at small scales. Current efforts to design self-assembled structures do not scale well. As assembly size increases, errors introduced by thermodynamic noise compromise the integrity of the structures. Therefore to develop scalable methods for engineering self-organizing systems, we must either design fault-tolerant assembly schemes or develop methods to perform error identification and recovery on self-assembled structures. Drawing on inspiration from immunological systems observed in nature, we aim to develop methods to perform error identification and recovery in assemblies formed by a collection of self-organizing robots. By studying self-assembly at the macro-scale, we intend to uncover design principles that can be applied to self-organization at all scales.

Gargi Chakraborty - Neurobiology and Biochemistry

Gargi Chakraborty sitting in front of computer screensMy interest in studying Neurobiology stems from a qualitative research study on Alzheimer’s disease that I undertook in high school. At the University of Washington, I had the opportunity to conduct quantitative research by applying mathematical modeling to brain physiology. In Dr. Swanson’s Neuropathology lab, my primary investigation focuses on assessing glioma (brain tumor) growth in vivo through multimodal clinical imaging. In the two and a half years I have worked in this lab, Dr. Swanson has served not only as my research mentor, but also as a personal guide who has exposed me to various avenues of investigative learning. This learning serves as a pillar in my pursuit of a medical profession. As a future physician and biomedical researcher, I hope to apply the insights I have gained from my research work to study human disorders by combining non-invasive clinical techniques and mathematical modeling.

Mentor: Dr. Kristin R. Swanson, Department of Pathology

Project Title: Spatio-temporal modeling of hypoxia and glucose metabolism in human gliomas

Abstract: Mathematical modeling presents a new tool to understand time and space dependent functions in biology. Modeling the growth of gliomas, which are primary brain tumors, involves quantifying their diffuse and proliferative capacity. These properties can be assessed in vivo through non-invasive imaging techniques, which include Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET). The current mathematical model developed by Dr. Kristin Swanson is based upon the Fisher equation and utilizes MRI scans from two time points to determine velocity of tumor growth. The purpose of this study is to enhance the Swanson model by incorporating metabolism within and outside the clinically defined tumor region. Two characteristic metabolic activities exhibited by gliomas include up-regulation of glycolysis and hypoxia (state of low oxygenation). These functional activities can be quantified via PET imaging using [18F]-Fluorodeoxyglucose (FDG) to monitor glucose uptake and [18F]-Fluoromisonidazole (FMISO) to monitor hypoxia. Using combinatorial imaging for in vivo studies, we have spatially localized regions of excessive glycolysis and oxygen depletion. Currently, we are developing a model to characterize spatial and temporal changes in peak metabolic activity driving tumor growth. This model incorporates heterogeneity of grey and white matter within the brain and the microenvironment of the tumor. Our goal is to develop simulations that mimic future FDG and FMISO PET scans based on original PET imaging conducted at the time of diagnosis. This mathematical model will allow early assessment of tumor behavior and prediction of its spatio-temporal spread enabling patient-directed treatment of gliomas.

Alevtina Gall - Cell and Molecular Biology & International Studies

Alevtina Gall working in the lab wearing a haz-mat suitTina first got involved in research in 2004 when she worked on the Jury and Democracy project with Dr. John Gastil in the Department of Communication. After having a very positive first research experience she decided to follow her interests and seek out research opportunities in the biological sciences. Tina discovered her passion for immunology and infectious diseases while working under the supervision of Dr. Martin Holland at the Medical Research Council in The Gambia, West Africa. She spent five months in The Gambia studying the immune responses of patients who had previously been infected with the ocular strain of Chlamydia trachomatis. Once she returned to Seattle, she joined Dr. Kevin Urdahl’s team and began working on a project looking at the role of a specific subset of immune cells in infection with Mycobacterium tuberculosis. Tina attributes her undergraduate research success to having the opportunity to work with incredibly inspiring and encouraging mentors, all of whom pushed her to become a better critical thinker and scientist. In the future, Tina hopes to combine her passion for immunology research and international health by pursuing an MD/PhD degree and apply her skills toward serving neglected communities in the United States and abroad.

Mentor: Dr. Kevin Urdahl, Pediatrics

Project Title: The role of regulatory T cells in Mycobacterium Tuberculosis infection

Abstract: Tuberculosis is a disease that annually kills two million people, predominantly those living in developing countries. Bacillus Calmette-Guerin (BCG), the currently used vaccine against tuberculosis, is not effective in geographical areas with the highest disease burden. The ability of Mycobacterium tuberculosis (Mtb) to establish a persistent infection may depend on a mechanism used by the pathogen to circumvent the natural immune response of the host. Regulatory T cells (Tregs), a subset of Foxp3-expressing CD4 + T cells, provide a “self-check” mechanism to prevent autoimmunity and play an important role in moderating the anti-microbial response of the host. We hypothesize that pathogen-specific regulatory T cells are activated during M. tuberculosis infection and suppress the proinflammatory response of the host that may otherwise be sufficient to clear the infection. My project focuses on designing an in vitro model to test our hypothesis that Mtb-specific regulatory T cells are induced during tuberculosis. Currently we are using bone-marrow derived dendritic cells (BMDCs) infected with Mtb to compare the proliferative capacity of regulatory T cells isolated from Mtb-infected and uninfected mice. We hypothesize that regulatory T cells from mice with tuberculosis will show high levels of proliferation in response to Mtb antigens presented by infected BMDCs. Using a complementary strategy, we will test whether Tregs from Mtb-infected mice are specific for an immunodominant Mtb-derived antigen using MHC class II tetramers. Understanding the role of Mtb-specific T regs in regulating immunity in tuberculosis has the potential to inform new strategies for designing an effective vaccine, and novel therapies for treating multi-drug resistant tuberculosis.

Daniel Kim - Neurobiology, Biology

Daniel Kim writing on a whiteboardI actually didn’t ever believe that in college I would be doing research. Originally, I planned to get a degree in engineering, get a job at Boeing, start a family, and settle into the IKEA life. However, my life plans were turned upside down when one day my best friend told me that she had been diagnosed with a terminal brain tumor. For us and our friendship, there was nothing that I could do but watch over the next few months as her health, cognition, and life faded away.

Armed with the memory of my friend, I feel that I now realize my purpose in life. I live and breathe to further scientific thought, to push the boundaries of research and to discover novel ways to treat human diseases.

In a perfect world, no one would ever have to watch a loved one slowly wither away. Today, we do not live in a perfect world. But it is my will to continue innovating, thinking and researching until we do.

Mentor: Xiaohu Gao, Bioengineering

Project Title: Enhanced chemotherapy tumor targeting utilizing the DV3 ligand and a gold nanoparticle complex

Abstract: Modern chemotherapy is a double edged sword: while it does effectively inhibit the mitotic division of cancerous cells, it also prevents the normal division of healthy cells. This leads to side-effects such as nausea, hair loss, and in some cases, death of the patient. Therefore, the goal of our project is to create a gold nanoparticle (AuNP) that enhances the targeting and delivery of chemotherapy agents to cancerous cells only. We hypothesize that through bioconjugation with the DV3 ligand, which binds preferentially to a tumorous chemokine receptor (CXR4), we can accomplish our goal of enhanced targeting. Once the DV3 ligand and CXR4 receptor have bound, the disulfide bond connecting the DV3 ligand to the AuNP will be cleaved by an extracellular enzyme, freeing the AuNP to enter the cell via endocytosis. The AuNP now inside the cell will be free to release its cargo of chemotherapy drugs, resulting in autolysis and automated cell death. Overall, this project is just a small slice of what the broad field of nanotechnology offers in the exciting and promising future of the treatment of human disease and health care to alleviate the suffering of people worldwide.

Katherine Liu - Biochemistry, Neurobiology

Katherine Lu in a farm fieldI came to the University of Washington only knowing I wanted to earn a degree in something-biology. I had no idea what either what academic research was or how it might involve me. The summer after my freshmen year I participated in the NASA Space Grant’s Summer Undergraduate Research Program, recommended to me by friends who had completed the experience the summer before. SURP matched me with a mentor in the department of Electrical Engineering. Although the experience didn’t cause me to pursue that particular field, it did open my eyes to the benefits and opportunities inherent in conducting undergraduate research.

In total, I have participated in five research projects ranging from basic neuroanatomy research at Woods Hole Marine Biological Laboratory to the development of a MATLAB based program for analyzing radar data from the West Antarctic Ice Sheet. Research has given me contacts and allowed me to explore potential career interests in a way I never would have accomplished in the classroom. Perhaps most importantly, as a person hoping to pursue a career in medicine, undergraduate research in the biological sciences has introduced me to the process of discovering and developing medical therapies.

Planning to study abroad for the year with the UW-Sichuan Exchange program, this current project is the result of taking a topic I love, neurobiology, and finding a way to apply it to the field. Many thanks to Professor Elizabeth Van Volkenburgh and Professor Stevan Harrell, who have helped me develop and bring into reality this project. For the 2007-2008 academic year I plan to be in Chengdu, Sichuan Province, China, studying Mandarin and conducting research.

Mentor: Elizabeth Van Volkenburgh, Biology

Project Title: Exploring the properties of mechanoreceptors in D.peltata in both the lab and in its natural environment in the southwestern regions of China’s Sichuan Province

Abstract: The carnivorous plant Drosera peltata is unique in its ability to respond to tactile stimuli with movement. This ability suggests the existence of mechanoreceptors – specialized ion channels that allow an organism to sense tension, pressure or movement in tissues of its periphery. The sessile life of plants is misleading. It suggests they are passive things, incapable of interacting with their environment. This, however, is simply not the case. Plants grow to avoid obstacles, react to changing soil moisture or seasons. Well known oddities, plants like Mimosa and the Venus Fly Trap are capable of producing quick, visible movement in response to tactile stimuli. And while they do not possess any specialized neuron-like cells, plants do exhibit many analogues to the animal nervous system. Many plants have recordable action potentials – transient intracellular depolarizations that propagate along the plant’s length. They have also been shown to express neurotransmitters typically found in animal nervous systems including serotonin, glycine, acetylcholine and glutamate. In addition to action potentials, plants exhibit slow-wave potentials that follow changes in hydraulic pressure. Lastly, the plant signaling molecule auxin exhibits localized and polarized delivery, and seems to be associated with some form of vesicle mediated transport. These are all common features of neurotransmitter delivery in animals. In my proposed studies, I plan to further explore the properties of the D. peltata mechanoreceptor, using better characterized animal and Venus Fly Trap mechanoreceptors as analogues. The neurobiology of plants is under researched, studies like this one are important in contributing to the understanding of basic mechanisms organisms use in interacting with their environments.

Ryan Maas - Physics and Astronomy

Ryan Maas sitting in labRyan began doing research soon after taking an introductory astronomy class from his future advisor, Professor Julianne Dalcanton. After completing a summer project involving N-body simulations, he became involved in several others in that field at the University of Washington. His interests include such topics as the formation and evolution of galaxies, as well as investigating the nature of dark matter and dark energy.

Through his two major research projects, Ryan hopes to publish results that can be applied to future studies of astronomical objects and to contribute to a more complete understanding of the universe.

Mentors: Julianne Dalcanton, Astronomy Department, University of Washington; Victor P. Debattista, Astronomy Department, University of Central Lancashire

Project Title: Exploring Dark Matter Collisions in Dwarf Galaxies

Abstract: Dwarf spheroidal galaxies are much smaller than the Milky Way and have surface brightness profiles that fall off exponentially as opposed to the power law dependence of disk galaxies. It is not well known how these galaxies can be heated as much as they are without having collided into a larger galaxy. One possibility may be related to another cosmological theory known as hierarchal merging. From simulations it is believed that the largest galaxies in the universe were formed from the collision of much smaller clumps of matter, and that the number distribution of objects in the universe tends heavily to the halos that are less massive than the dwarf spheroidals themselves. While we do not see the number of dwarf galaxies predicted by hierarchal merging, the presence of these small dark matter halos may have a substantial impact on the morphology of objects like dwarf spheroidals. I am testing this hypothesis by creating initial conditions for impact simulations of this sort and comparing the results with observed data on dwarf galaxies to determine an upper limit on the heating produced. As the dark matter halos colliding with the galaxy cannot be observed there are many parameters which need to be tested, such as the mass, incidence, and energy of the colliding objects. The results of this project would reveal whether hierarchal merging is indeed responsible for the state of these dwarf galaxies or if another explanation must be found.

Jessica Smith - Chemistry, Biochemistry

Jessica Smith sitting in labI’ve been lucky to have a lot of enlightening research experiences which have helped me refined my interests within my major, Chemistry. For the last five summers and most school years I’ve contributed to research projects in a few different labs, giving me a taste of everything from applications of bioluminescence to electrical circuits to interactions between proteins and metal nanoparticles. The Washington Research Foundation generously awarded my first Research Fellowship for Advanced Undergraduates in 2006 for work I’d been conducting with Prof. Beth Traxler in Microbiology concerning protein-protein interactions in membrane protein complexes. This award was particularly special to me, because the project I was on was under-funded. In order for me to keep working on it, I needed to find independent funding to pay my stipend. The people in the undergraduate research office were so helpful, particularly in allowing me to receive funding on a different schedule than the other awardees so that I wouldn’t need to put my research on hold to wait for funding. I received another RFAU for this school year to study gold and silver nanoparticles with potential applications to biosensing and solar cells. Getting the RFAU again allowed me to switch research projects and explore another aspect of a very broad field without having to juggle a part-time job along with classes and research.