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Undergraduate Research Program

2013-14 Levinson Scholars

Trung Phan in lab

Trung Phan
2013-14 Levinson Scholar

Levinson 10-year Quote 3










Derek Britain - Biochemistry, Bioengineering

Derek Britain in lab
Derek Britain is a senior in the Departments of Bioengineering and Biochemistry. He got his first exposure to research his freshman year when he joined Dr. Deok-Ho Kim’s lab in Bioengineering. While there, Derek worked on creating a novel cell culture device that combined a nano-patterned substrate with a microfluidic gradient system for the organization of stem cells into cardiac tissue grafts. While testing his device, he became fascinated with how the stem cells were able to sense and respond to the substrate and chemotaxic gradient. Derek continued to pursue his interest, and at the start of his junior year join Dr. Roger Brent’s lab at Fred Hutchinson Cancer Research Center. Using budding yeast as a model organism, Derek now researches how cells gather information from their environment, how this information is processed by the cell, and how a cell makes a decision based on the results. Currently, he is investigating the role microtubule end binding proteins play in signal transmission and fidelity. Derek is also investigating mutant forms of these proteins found in the human population, and if these mutations result in poor signal handling that could result in poor cell decisions. After completing his undergraduate degrees Derek plans to further pursue his research in a Systems Biology PhD program.

Mentor: Roger Brent, FHCRC

Project Title: The effects of human variants of yeast Bim1 on signaling in the yeast pheromone response pathway

Abstract: The three mammalian MAPRE proteins (EB1, RP1, and EBF3) play important roles in the stability and localization of microtubules, and facilitate the binding of other proteins to microtubule plus ends. The 1000 Genomes Project and The Exome Sequencing Project have elucidated non-conservative coding sequence allelic variants of the MAPRE proteins in the human population. Disruption of MAPRE protein function could decreases signal fidelity and microtubule function, leading to poor cell decision making and mitotic chromosome separation. The MAPRE proteins are related by descent from a common ancestor to the Bim1 protein in budding yeast. By designing and building mutated versions of Bim1 that contain mutations corresponding known MAPRE allelic variants and expressing them in yeast, we hope to elucidate the effects of the MAPRE polymorphisms. In particular, we will observe changes in signaling fidelity in the yeast pheromone response pathway. Budding yeast will be exposed to a linear gradient of mating pheromone, and various florescent reporters will be monitored through live-cell epi-fluorescent and FRET microscopy. Florescent signals will be quantitatively analyzed to determine protein abundance, indicating the degree to which signal fidelity has been affected. Adverse effects on signal fidelity can result in poor decision making and environmental response, potentially leading to the generation of disease. By better understanding the effects of allelic variants in the human population, we will be able to develop individualized health plans and therapies.

Cara Comfort - Bioengineering, Neurobiology

Cara Comfort in labCara Comfort is a senior double majoring in Bioengineering and Neurobiology. Since her first year at UW, she has been actively immersed in research. As she was interested to find a way to integrate her two majors, she joined Bill Moody’s cortical development lab the summer after her sophomore year. There she enjoys the combination of creative stimulation inherent in experimental design as well as the mathematical challenges demanded by MatLab and scientific analysis. Through her senior capstone project, Cara plans to synthesize the skills developed in both her majors to help elucidate the complex mechanisms behind cortical development, an area she has grown very passionate about. After graduating UW, she intends to pursue a Ph.D. in neural engineering, preferably continuing her research in the field of neurodevelopment. Cara is extremely grateful for the support by Dr. and Mrs. Arthur D. Levinson on her current interdisciplinary research project.

Mentor: William Moody, Biology

Project Title: A computational model of GABAergic cells to elucidate initiation of SSA in developing mouse cortex

Abstract: It is poorly understood how cortical connections are established in the brain during development. In the past decade, it was established that waves of synchronous spontaneous activity (SSA) are essential for developing the proper circuitry in the neonatal mouse cortex. These waves of electrical activity, involving a vast number of neurons firing bursts of action potentials simultaneously, produce transient increases in intracellular calcium concentration, which can be imaged with calcium-sensitive fluorescent dyes. The Moody lab recently determined that during early developmental stages, waves of SSA originate from the ventral piriform cortex and are dependent on GABAergic transmission. Since developmental problems may arise when these wave fail to initiate at the proper time, it is crucial to determine exactly how SSA is initiated. My research project aims to 1) identity the exact subpopulation of GABAergic cells that generate SSA and 2) determine what combination of intrinsic physiological properties and synaptic connectivity defines the pacemaker population. In particular, I will estimate key system and cellular parameters that define GABAergic networks using past experimental data. Then, I will build a computational model of GABA pacemaker cells in MATLAB that simulates wave initiation and propagation, implementing the previously estimated parameters in the model. By matching the simulated wave propagation frequency and speed to those determined by experimental data, I will gain insight into the parameter spaces of cell connectivity and integration time, which are difficult to estimate given the current data. Finally, I will attempt to validate the model by first estimating more realistic values of these parameters via patch clamp experiments, and then comparing these obtained values to the parameter spaces calculated by the model.

Jennifer Gile - Neurobiology

Jennifer Gile in labJennifer Gile is a senior majoring in Neurobiology. She transferred from the Johns Hopkins University after her freshman year. She works in the de la Iglesia laboratory, which focuses on the pathways by which the central nervous system controls the timing of behavior and physiology. Her area of research is in circadian biology, with a current research focus on the circadian modulation of neuromotor control. The goal of this research project is to understand how the circadian system regulates the primary motor cortex programs. This will be essential for the design of BCI (brain computer interface). Jennifer is a Gates Millennium Scholar who makes several trips back to her old high school in Idaho to educate diverse populations of students about the scholarship and inspire them to realize the value of a college education. Jennifer would like to thank her wonderful mentors Dr. De la Iglesia, Dr. Smarr, Dr. Chizeck, and Oliver Johnson. She would also like to thank the Levinson Scholarship for the support. All of this would not be possible without their support. She is planning on pursuing an M.D./Ph.D. upon graduation in Winter 2015.

Mentor: Horacio de la Iglesia, Biology

Project Title: Circadian Modulation of Neuromotor Control

Abstract: The circadian system controls daily rhythms of behavior and physiology, including locomotor activity and motor-task performance. The master regulation of these rhythms is achieved by a circadian clock located in the suprachiasmatic nucleus of the hypothalamus; however, it is not clear how motor tasks are programmed by the motor cortex at different times of the day. Our hypothesis is that similar motor tasks executed at different times of the day may require different motor programs to account for the daily variance introduced by the circadian system. How and where in the brain this variance in motor control manifests has not been established. We propose to identify specific primary motor cortex activity patterns associated with specific motor outputs across the 24-hour day. We implant electrocorticographic (ECoG) electrodes onto the motor cortex of mice and record brain wave activity during wheel running and rest. We first test whether the motor cortex may show a brain-wave signature for wheel running, and second whether this signature may change predictably across the 24-hour day. Initial results indicate a broad-spectrum power increase in brain-wave output from the motor cortex associated with wheel running. Furthermore, there appears to be a circadian modulation of the power of specific ECoG frequencies. The decoding of motor cortex signals is at the core of the design of brain-machine interfaces (BMIs). These devices decode signals from the conscious brain to drive the execution of specific tasks by a machine, such as an artificial limb. Our work will directly contribute to our understanding of how the motor cortex decodes circadian time. This knowledge is essential to create BMIs that can operate effectively throughout the 24-hour day to execute tasks by brain-operated artificial devices.

Nicolette McCary - Biology, Oceanography

Nicolette McCary in labBiology and the Ocean have inspired Nicolette from a very young age, as she was raised spending most summer and weekend days on the beaches of Puget Sound. She was always fascinated by the barely perceptible organisms in tide pools, wondering what they were. After being invited to join Dr. Gabrielle Rocap’s Environmental Genomics Lab in the department of Oceanography her sophomore year, she was able to spend two years researching marine viruses and phytoplankton. She hopes to contribute to the limited knowledge of diatom virus seasonality, and identify Pseudo-nitzschia hosts that can be used to effectively isolate viruses in the future. After graduating with a degree in Oceanography (BS), she plans to remain engaged in research through the realm of scientific outreach. Her dream is to work with the younger generation, involving them in exciting scientific opportunities. In her spare time she loves to swim and volunteer with children at her church.

Mentor: Gabrielle Rocap, Oceanography

Project Title: Exploring host permissivity and the seasonality of viruses that infect the diatom Pseudo-nitzschia

Abstract: Diatoms are unicellular photosynthetic algae, or phytoplankton, and account for approximately 20% of global primary production. The pennate diatom Pseudo-nitzschia can produce a neurotoxin called domoic acid (DA) that builds up in the tissues of shellfish when this diatom blooms. DA poisoning causes life-threatening conditions in mammals and humans when these shellfish are ingested. One mechanism of bloom regulation that we know little about is that of viral infection, despite viruses being the most abundant predator in the ocean. One Pseudo-nitzschia infecting virus, the PmDNAV, was isolated in 2009. I hypothesize that there are many different viruses that can infect diatoms of the genus Pseudo-nitzschia in addition to the PmDNAV. In order for future researchers to be successful in Pseudo-nitzschia virus isolation, I am studying the seasonality of Pseudo-nitzschia viruses and finding permissive hosts to isolate them with. A permissive host is more susceptible to viral attack, and thus is more effective to use when isolating viruses. There have only been two studies on diatom virus seasonality, neither of which addresses the Pacific Northwest or Pseudo-nitzschia. To get a systematic look at virus seasonality, I am sampling the viral community once a month at two locations: Gray’s Harbor off the Washington Coast, and Penn Cove in the Puget Sound. I started in April 2013, and will continue for the full year. At each location I take water samples for concentrating viral particles, and a net tow of the planktonic community for Pseudo-nitzschia isolation. I am using infection experiments to determine viral presence, while also determining host permissivity. No one else in the science community is studying Pseudo-nitzschia viruses, with very few studying diatom viruses at all. After my data is published, it will be much easier for researchers to isolate Pseudo-nitzschia viruses in the future.

Trung Phan - Molecular, Cellular, & Developmental Biology

Trung Phan in labTrung’s strong interest in reproductive biology and developmental genetics emerged during the summer of his freshman year when he began researching Drosophila fertilization under the guidance of Dr. Barbara Wakimoto. Confronted with an exciting and novel research question about the enigmatic proteins that regulate sperm activation, Trung was inspired to investigate the molecular events that facilitate sperm development and function. His current project focuses on the characterization of an interesting protein that plays a role in acrosome biogenesis in Drosophila and has a complex evolutionary origin. With the generous support of the Levinson Emerging Scholars Program, Trung hopes to take his project to completion and share his findings with the scientific community to contribute to our understanding of species reproduction. Trung’s involvement with undergraduate research has enriched his knowledge of biology and helped him develop habits of independent learning and critical thinking that will further his growth as a scientist. After graduating, Trung intends to pursue a career in medicine that will integrate his training as a cellular and molecular biologist.

Mentor: Dr. Barbara Wakimoto, Biology

Project Title: Analyzing the Critical Role of Pskl, a Sperm Membrane Protein, in Drosophila Fertilization

Abstract: The process of sexual reproduction in plants and animals is both a fascinating and mysterious property of life. During fertilization, the sperm delivers the paternal genetic material to the egg to begin formation of an embryo. However, the mechanisms that regulate sperm and egg interactions, such as gamete membrane fusion, are not well understood at the molecular level for any organism. The goals of this project are to identify and characterize the proteins that mediate sperm and egg interactions in Drosophila, an ideal model organism to study fertilization due to its rapid reproduction, short generation times, and genetic traits that are easy to observe. In Drosophila, an uncharacterized protein called Pop-sickle (Pskl) is of particular interest because pskl mutants are male sterile, despite having motile sperm. Additionally, Pskl has a structural region similar to GCS1, a sperm-specific protein required for sexual reproduction in flowering plants, malaria parasites, and alga. To better understand Pskl’s function in fertilization, we propose a two-fold approach to identify the protein’s site of action and its functional domains. The first experiment will subcellularly localize Pskl in developing spermatids by expressing a version of the protein marked with a fluorescent tag. In the second experiment, we will generate internal pskl deletions in the GCS1-like region and another region similar to a family of protist proteins. This will enable us to determine if these domains are necessary for normal Pskl function. Taken together, the results from this study will help clarify the molecular mechanisms required for sexual reproduction and ultimately contribute to the development of reproductive therapeutics that will treat male sterility. Furthermore, studying Pskl’s role in sperm-egg interactions might provide insight into mechanisms of fertilization that are evolutionarily conserved across diverse species.

Margaux Pinney - Biochemistry, Chemistry

Margaux Pinney in labMargaux is a senior in Biochemistry (BS), Chemistry (BS) and Mathematics (minor) with Departmental Honors in Chemistry and Biochemistry. After transferring to UW from Green River Community College, Margaux began doing research in the lab of Professor Jim Mayer. In the Mayer Group, she investigated the potential for proton-coupled electron transfer at synthetic iron-sulfer clusters, before moving on to her current, independent project. She now investigates the reversibility of Compound I formation in horseradish peroxidase. Compound I is also an intermediate in the catalytic cycle of cytochrome P450s. Since approximately 70% of xenobiotics, such as drugs or chemicals from the environment that enter the body, are oxidized by P450s, this research has pharmaceutical and toxicological implications. This research could also be applied to synthetic processes, due to the unique mechanism of oxidation. Based on her experience with undergraduate research at the University of Washington, Margaux will be pursuing her PhD. in biochemistry after graduation. Margaux is also involved with several groups on campus, such as the Tolo Chapter of Moratar Board, a senior honors society, as well as the Undergraduate Research Leaders, and is particularly interested in getting students, particularly women, involved in undergraduate research.

Mentor: Jim Mayer, Chemistry

Project Title: Reversibility of Compound I Formation by Horseradish Peroxidase

Abstract: Horseradish peroxidase (HRP) is part of a family of heme-containing metalloenzymes that reduce the O-O bond of peroxides while oxidizing a wide variety of substrates; in the case of HRP, hydrogen peroxide is reduced to water. In the presence of an oxidant and the absence of a substrate to oxidize, hydrogen peroxide coordinates to the iron cofactor of HRP, forming a ferric-hydroperoxide intermediate known as Compound 0, and subsequent O-O bond cleavage forms water and a very oxidizing ferryl-oxo porphyrin radical cation intermediate, known as Compound I. Compound I is of particular interest because it is also formed by cytochrome P450s, a family of enzymes that react with almost all foreign substances entering the body, including drugs and other chemicals in the environment. HRP is an excellent enzyme to test this reversibility because, unlike P450s, it is extremely robust and easy to work with. The goal of this project is to probe the potential reversibility of Compound I formation, a step traditionally thought to be irreversible. A key experiment will react HRP with excess unlabeled H2O2 in 18O-labeled water, and determine whether mixed-labeled H2O2 is created, which indicates that the step that forms Compound I is reversible. The enzyme will be removed by protein filtration and the existence of mixed-labeled H2O2 will be probed by adding a water soluble phosphine to the filtrate, which will readily react with excess H2O2 and be oxidized. 31P NMR spectroscopy will be used to determine whether the phosphine oxide is labeled because the NMR shifts of 16O-phosphine oxide and 18O-phosphine oxide are distinct. If this reaction proves to be reversible, this knowledge could then be used to describe cytochrome P450s. This research would be immensely important to pharmaceutical and toxicological research, as well as synthetic processes.

Denis Smirnov- Biochemistry, Neurobiology

Denis Smirnov in labDenis Smirnov is a senior at the University of Washington majoring in Biochemistry and Neurobiology. Having grown up in Russia, he has spent the last 10 years of his life in Seattle, attending Juanita High School in Kirkland before coming to UW. He is currently working in the laboratory of John Neumaier, MD., PhD. in the Department of Psychiatry and Behavioral Sciences, on a project aimed to understand the neural circuitry underlying addiction and relapse to drugs of abuse. He recently presented this research at the Society for Neuroscience conference in San Diego, and was an author of a recent publication in the Journal of Clinical Investigation, detailing a novel microPET imagine technique to map whole brain function in both anesthetized and awake, freely-moving animals in a highly sensitive manner. Involved in research for over 3 years across three different labs ranging to biochemistry, to chemistry, to neurobiology, Denis has worked extensively to prepare himself for a career in academic medicine. Upon graduating in the Spring of 2014, he plans to pursue an MD at a research oriented medical school, with the hope of one day becoming a neurologist or neurosurgeon.

Mentor: John Neumaier, Psychiatry

Project Title: The Role of the Lateral Habenula and the Rostromedial Tegmental Nucleus in Cocaine Addiction

Abstract: An important problem in the treatment of cocaine addiction is the vulnerability of previously addicted individuals to relapse to cocaine use months or even years after abstinence. The lateral habenula (LHb), part of the habenular complex in the dorsal diencephalon, and the rostromedial tegmental nucleus (RMTg), a recently identified nucleus in the reticular formation, are important regulators of the midbrain dopaminergic systems that are known to be involved in cocaine taking and relapse behaviors. However, very little is known about the precise role of these nuclei in cocaine reinforced behaviors. Here, I initially characterize the anatomical location of the RMTg using expression of the transcription factor cFos, as a marker of neuronal activation in response to cocaine. Next, we utilize the Designer Receptor Activated Exclusively by Designer Drug (DREADD) technology, to investigate the role of modulating the activity of the LHb on cocaine-self administration in rats. We demonstrate that DREADD-mediated transient silencing of the LHb through the activation of a Gi-coupled signaling pathway increases cocaine self-administration, while transient stimulation through the activation of the Gq-coupled signaling pathway decreases self-administration on a progressive ratio schedule, suggesting a reciprocal role between LHb and VTA activity. We further show that inactivation of the LHb to VTA projections has no effect on cocaine self-administration. Given this, we propose to investigate the indirect LHb projections to the VTA through the RMTg using our newly developed dual-virus strategy to specifically target the LHb to RMTg projection for DREADD-mediated modulation on self-administration and reinstatement.