2012-13 Levinson Scholar
Hunter Bennett is a junior in the Department of Bioengineering. Upon arriving at UW in Fall 2010, he was amazed at the work being done across campus to create novel systems for disease treatment and prevention and sought to get involved as a way to apply what he had learned in high school and to make a positive change in the medical field. This interest in research led him to the lab of Dr. Kim Woodrow in the Department of Bioengineering where it grew into a passion. In the Woodrow Lab, Hunter investigates the potential of cell-seeded hydrogel systems to induce mucosal and systemic immunity to HIV. He is also involved in a project investigating the chemokines responsible for dendritic cell recruitment during acute HIV-1 infection at the vaginal mucosa. Over last summer, Hunter participated in the Amgen Scholars Program at UCLA where he worked on social signaling in African Trypanosomes under Dr. Kent Hill in the Department of Microbiology, Immunology and Molecular genetics. After graduation Hunter plans to follow his passion for research by pursuing a PhD. Outside of lab, Hunter enjoys running, playing basketball and reading.
Mentor: Kim Woodrow, Bioengineering
Project Title: Encapsulation of Cell Based Therapeutics for the Prevention of HIV Infection
Abstract: The Human Immunodeficiency Virus (HIV) is a cause of widespread global suffering infects 2.7 million new patients each year. No cure exists for HIV and many experts believe that the disease will only be eradicated through the development of an effective vaccine. Virus-like particle (VLP) based vaccines capable of lowering the rates of HIV infection are promising but have been limited in application by their short half life in vivo and requirement of significant medical infrastructure. The implantation of cell lines producing HIV VLPs into patients represents a potentially cost-effective strategy for providing long-term protection from the HIV virus. Different alginate-based microcapsules will be made using electrostatic droplet generation. Particles will be examined for stability in conditions modeling that of common implantation sites, with promising microcapsules proceeding to cell viability studies. Results from cell viability studies will be used to select microcapsule formulations capable of sustaining healthy cell populations for long periods of time in vivo. 293T cells transfected with either the HIV gag gene or the HIV env gene will then be seeded in the microcapsules and assessed for its ability to elicit an anti-HIV antibody response and lower rates of infection in both cell and animal models. The goal of this research is to produce a cell-seeded alginate based microcapsule system capable of lowering rates of HIV transmission over extended periods of time.
Now immersed in my fourth year as a senior in the Bioengineering department, with a capstone design project underway, I am able to reflect on my research experiences. Coming into college, I had never anticipated reaching the level of research involvement I have been able to obtain during my undergraduate years. In addition to my capstone work, I have been fortunate enough to have taken part in a diverse set of research experiences through summer programs at the Wake Forest Institute for Regenerative Medicine and the Johns Hopkins Institute for NanoBioTechnology (NSF REU). Nevertheless, I developed an interest in actively engaging in research with applications toward global health and medicine, which allowed me to find footing with the Woodrow Lab for my senior capstone project. Since junior year, I have been working to develop nanoparticles to achieve combination delivery of antiretroviral drugs with different mechanisms of action. My project aims to gain insight in identifying unique drug-drug interactions for HIV prevention. Altogether, I have come to appreciate not only my interdisciplinary research background but also its gradual impact in shaping me into the student I am today. I am extremely thankful for the generous support provided by the Levinson Emerging Scholars program as it will further motivate me to focus on my research and pursue my interest in medicine and biomedical research.
Mentor: Kim Woodrow, Bioengineering
Project Title: Developing nanoparticle-based antiretroviral topical microbicides for HIV prevention
Abstract: According to the UNAIDS 2010 Global Report, roughly 33.4 million people were living with HIV in 2008, with two thirds of them being in Sub-Saharan Africa. Females are disproportionately affected by the HIV epidemic and women-initiated prevention methods are lacking. To address this, we propose nanoparticle-based combination antiretroviral microbicides as an effective topical strategy for the prevention of HIV infection. Currently, most candidate-microbicides consist mostly of gels, which have demonstrated poor efficacy in clinical trials. Studies have supported the successful impact of highly active antiretroviral therapy (HAART) as a standard of care for HIV/AIDS affected individuals, which has motivated the investigation of the topical delivery of combination antiretroviral drugs. The proposed work has the potential to address the delivery challenges brought upon by the diverse classes of ARV drugs. The primary appeal for this approach lies in the combination delivery of drugs with different properties and mechanisms of actions to minimize chances of resistance and improve efficacy. In Phase 1, design of the nanoparticles as well as drug encapsulation and release kinetics will be assessed. In Phase 2, bioactivity and combination studies (Chou and Talalay method) will be performed to identify synergistic drug combinations and favorable drug-drug interactions. In Phase 3, tissue biodistribution and penetration of the nanoparticle microbicides will be performed. The research plan is designed to develop and evaluate nanoparticle microbicides as drug delivery systems for HIV prevention. Successful outcomes of this endeavor could have profound implications on microbicide research and a potentially viable female-controlled prevention method for HIV.
Nile Graddis is currently a senior majoring in Psychology. He became involved in research as a sophomore working in Dr. Mizumori’s lab. Nile is interested in examining the neurobiology of learning and memory because of the critical contributions that learning makes to human as well as animal behavior. He hopes that by elucidating some of the basic mechanisms of learning, we might be better able to help those with learning disabilities or addictions. In Dr. Mizumori’s lab Nile has used electrophysiological and behavioral methods to explore the role of burst dopamine release on hippocampal place cell activity and local field potentials. His current research focuses on the influence of striatal projection neurons to modulation of learning rate. He seeks to use pharmacological, behavioral, and electrophysiological techniques to better understand the contributions that the neurons of distinct striatal projection pathways make to the activity of midbrain dopamine neurons and to learning. In his spare time, Nile enjoys reading and spending time with his friends.
Mentor: Sheri Mizumori, Psychology
Project Title: Understanding the roles of striatal projection neurons in modulating prediction error signaling
Abstract: How do we learn from our mistakes? One interesting possibility is that dopamine neurons in the midbrain compute a prediction error signal, which reflects the difference between expected and received rewards. This signal, which has been observed at the level of individual neurons, can then inform learning and future behavior. Despite the potential importance of this signal, the brain systems that modulate it are not well understood. Neurons of the ventral striatum project reciprocally to midbrain dopamine neurons, and may thus be involved in modulating the prediction error signal. These neurons project along two pathways, the direct striatonigral pathway and the indirect striatopallidal pathway, which have historically been difficult to manipulate separately. Recent advances in optogenetics and pharmacogenetics have made study of the pathways possible, leading to findings that these two populations of neurons antagonistically modulate learning. I propose to extend these behavioral findings by using electrophysiological and pharmacogenetic techniques in concert to investigate the roles that these distinct pathways play in modulating prediction error signaling. I will assess reward prediction signaling in midbrain dopamine neurons as rats learn on a two-choice operant maze task. I will use designer receptors exclusively activated by designer drugs to selectively inactivate neurons of the two striatal populations as rats perform this task. This will allow me to assess the roles played by neurons of these populations in modulating prediction error signaling. I hypothesize that inactivating one population of striatial neurons (striatonigral) will inhibit learning and impede the development of prediction error signaling while inactivating the other (striatopallidal) will have opposite effects. This work will provide valuable insight into the neural processes through which we learn from our mistakes. Such knowledge may allow us to provide better help to people suffering from addictive or compulsive behavioral disorders.
Danee Hidano is currently a senior majoring in Bioengineering. She originally discovered her passion for research during her senior year of high school while interning at ZymoGenetics. As a freshman at UW, she joined Professor Dan Ratner’s lab. The Ratner lab specifically focuses on the role of carbohydrates in the body and how they can be utilized to develop new drug delivery mechanisms. She was particularly drawn to biomedical research for its direct clinical relevance. In the lab, Danee synthesizes sugar-based polymers that are designed to carry toxic drugs into specific cells via active-targeting. Danee also works at PhaseRx, a pharmaceutical company in Seattle, as a chemistry lab assistant. After graduation, Danee intends to pursue a career in medicine with a continued emphasis in biomedical research. In her spare time, Danee enjoys playing soccer, drinking coffee, and hanging out with friends.
Mentor: Daniel Ratner, Bioengineering
Project Title: Using Carbohydrate-Targeting Copolymers for Drug Delivery
Abstract: Carbohydrate complexes, such as glycolipids and glycoproteins, serve as cellular markers and receptors universally found on the outer membranes of mammalian cells. These glycoconjugates distinguish different types of cells from one another and enable cellular recognition and adhesion. Both the immune system and foreign pathogens rely on these glycoconjugates to bind and enter host cells. For viruses and bacteria, adhesion to receptors is the first step in infection. Carbohydrates are highly diverse and are each able to bind to unique receptors. By mimicking nature, chemists use carbohydrates to bind and enter specific cells for drug delivery.
Active drug targeting is highly advantageous because the ability to deliver drugs exclusively to specific cells or organs reduces increases efficacy of the drug and decreases toxicity. In my current research, I am designing a drug carrier that takes advantage of these specific carbohydrate-receptor interactions to deliver small molecules into cells. Currently, I have successfully synthesized and characterized the carbohydrate monomers responsible for targeting. Next, I will synthesize the glycopolymer to function as the drug carrier. The glycopolymer is composed of three main components: (1) carbohydrate, (2) pyridal-disulfide methacrylamide (PDSMA), and (3) hydroxyl-ethyl methacryamide (HPMA).
Firstly, the carbohydrate monomers enable specific binding interactions that are leveraged to exclusively deliver therapeutics to intended cells. Secondly, the PDSMA monomers allow for versatile conjugation of any thiolated small molecule – including Doxorubicin (for chemotherapy treatment), peptides (for vaccines), or genetic material (for gene therapy) – through a disulfide exchange. Lastly, HPMA gives the copolymer biocompatible characteristics, such that it is more soluble and less immunogenic in vivo. Overall, due to the natural complexity and diversity of carbohydrates, the carbohydrate-based copolymer construct has promising potential as an active targeting drug carrier to both reduce toxicity and increase in drug efficacy.
Ben is currently a senior and will graduate in the spring with degrees in Chemistry (BS, ACS certified), Biochemistry (BA), and Mathematics (minor) as well as College Honors and Departmental Honors in Chemistry and Biochemistry. He got his first research experience the summer after his freshman year in the lab of Professor Sarah Keller fabricating and analyzing model cellular membranes. With the Keller group he presented work at the Undergraduate Research Symposium, the Northwest ACS Undergraduate Symposium, and the 2012 National Biophysical Society Meeting. The time he spent in the Keller Lab propelled him to take the next step in his research career by joining the group of Professor James Mayer in studying inorganic chemistry, specifically reduction/oxidation and biomimetic inorganic chemistry, and nanoparticles. When Ben first joined the Mayer group, he undertook a project himself without a graduate student or postdoctoral mentor to study a specific type of reduction/oxidation mechanism called a Multiple-Site Concerted Proton Electron Transfer reaction in which a carbon hydrogen bond is cleaved by transferring the proton to a base and the electron to an oxidant. Now he is collaborating on a new project that combines TiO2 nanoparticles and Concerted Proton Electron Transfer to complete a non-trivial two electron, two proton transfer under relatively mild conditions.
When not in the lab, Ben enjoys TAing in the Chemistry department, running, hiking, sports, and music, playing snare drum in the University of Washington Drumline and singing bass in an a cappella choir on campus.
Mentor: James Mayer & Sarah Keller, Chemistry
Project Title: Model System for Multiple Site Concerted Proton Electron Transfer
Abstract: Reduction/oxidation reactions are crucial for energy transfer in a wide variety of applications such as water oxidation, water remediation, and biological processes. Proton Couple Electron Transfer (PCET) reactions are increasingly recognized as an important class of this type of reaction. As hinted by their name, these reactions involve the transfer of a proton and an electron from a substrate to other molecules. However, PCET reactions can be delineated further into Single Site PCET reactions, where a single reagent acts as both the electron and proton acceptor, and Multiple Site PCET reactions, where different molecules accept either the proton or the electron. This investigation focuses on these specific Multiple Site PCET reactions (MS-PCET) which are generally not well understood, specifically the breaking of a C-H bond. Using a model system consisting of an oxidant (FeIII(bpy)3-), a base (2,2′-bipyridine) and a substrate (9,10-dihydroanthracene), MS-PCET reactivity will be monitored in an attempt to understand the kinetics of the reaction. Different techniques are used to elucidate the progression of the reaction including UV/Visible and 1H NMR spectroscopy, and stopped-flow injection. The rate of reaction is dependent on each of the reaction components, as well as solvent, temperature, and the surrounding atmosphere. Kinetic analysis of the reaction will eliminate other proton electron transfer reactions and show that the Multiple Site PCET is the singular, plausible mechanism. These reactions will help to establish an understanding of MS-PCET reactions which are crucial to so many biological systems and new technologies such as fuel cells and solar energy.
Emily Hsieh was first exposed to the field of evolutionary biology the summer before entering the University of Washington and since then has been interested in utilizing the intricacies and wonders of Drosophila genetics to better understand one of Darwin’s “mysteries of mysteries” – the formation of new species. Under the direction of her mentors Drs. Harmit Malik and Nitin Phadnis, she has been involved in various projects exploring her research interests of genetic conflict and speciation in the context of Drosophila. With the generous support of the Levinson Emerging Scholars Program, Emily hopes to continue her research in understanding the genetic basis of speciation in Drosophila and contribute to the understanding of the origin of species. The culmination of Emily’s undergraduate experience as a MCD biology and biochemistry student and as a Malik lab undergraduate researcher has strengthened her desire to pursue a PhD in biology. Emily enjoys spending her spare time mentoring students through the UW Dream Project and would also like to integrate educational outreach and science into her future career.
Mentors: Harmit Malik & Nitin Phadnis, Fred Hutchinson Cancer Research Center
Project Title: Disentangling the Role of Dosage Compensation in F1 Hybrid Incompatibility
Abstract: The process for how species form in nature remains a complex and fascinating puzzle. One approach to solving this mystery is by identifying genes involved in F1 hybrid incompatibilities, characteristics that typify an F1 hybrid offspring. Of particular interest is the dosage compensation complex, also known as the male-specific lethal (MSL) complex in Drosophila, since it contains MSL proteins that show strong signatures of rapid evolution, but not in all closely related species. Much controversy surrounds the idea of the MSL complex playing a role in F1 hybrid incompatibility, and here, I use a three part analysis to approach this question. Drosophila melanogaster and simulans are fitting models to study F1 hybrid incompatibilities as they are recently diverged species that produce inviable F1 hybrid males. The first experiment will test to see if the MSL complex is functional in F1 hybrid males through the usage of a male-killing bacterium Spiroplasma poulsonii, a detector of functional MSL complexes. The second assay will examine if the MSL complex is aberrantly turned on in attached X F1 hybrid females as a proxy to study MSL complex function in F1 hybrid males. Finally, the third experiment determines the functional divergence of D. melanogaster and D. simulans MSL complex proteins. Within the MSL complex, either MSL1 or MSL2 are necessary for male viability, so by creating transgenic flies with different combinations of D. melanogaster and D. simulans msl1 and msl2, I will be able to use an interspecies complementation test to identify if divergence of these two genes has led to F1 hybrid incompatibility. This inclusive set of experiments offer multiple approaches to uncover a possible role of dosage compensation in the mechanism of speciation in Drosophila.
Growing up in the forests of Battle Ground, WA, Joanne frequently encountered flora and fauna of diverse phenotypes as she explored the woody backyard, which was what first inspired her passion for the biological sciences. Her interest in exploring biological processes and function on level of proteins inspired her to conduct proteomics research with Dr. Judit Villen in the Department of Genome Sciences, where she studies the evolution of phosphoregulation across yeast species using proteomic techniques and mass spectrometry. The goal of this project is study the conservation of phosphorylation sites across representative yeast species from different phylogenetic lineages, to identify specific orthologs that regulate key cellular functions and also better understand the evolution of phenotypic diversity.
Joanne is very grateful for the support from the Levinson scholarship on her research.
Mentor: Judit Villen, Genome Sciences
Project Title: Elucidating the Conservation of Phosphorylation Patterns Across Yeast Species with Phosphoproteomics
Abstract: The reversible phosphorylation of proteins mediates a wide range of biological processes that range from signal transduction cascades to regulation of protein abundance. However, little is known about the mechanisms and evolution of phosphorylation networks. Despite the extraordinary advances in genome sequencing of many yeast species, evolutionary studies on the phosphoproteome of yeast species have been limited to the experimental analysis of phosphorylation in one species and computational analysis of the conservation of phosphor-acceptor residues with other species. To properly study evolutionary conservation across yeast proteomes, we are utilizing mass spectrometry to study and compare the phosphoproteome of over 15 species of yeast, including species representative from each clade on the yeast phylogeny. Most of these species have not been studied before by proteomics. This high-throughput phosphoproteomic study on the yeast species will contribute to the construction of phosphoproteome datasets, which can be exploited for comparative analysis of phosphorylation between yeast species. In this phosphoproteomic study, I will first analyze the reproducibility of the sample preparation techniques and data acquisition methodologies, which are key factors in the ability to distinguish true differences between samples. After developing an optimally reproducible methodology, I will construct growth curves for all the yeast species, in order to standardize an optimal optical density for the yeast cultures. Next, I will analyze the phosphoproteome of the yeast species using the optimized phosphoproteomic methodology, in order to construct the phosphoproteome datasets. To supplement the datasets, I will also analyze the protein abundances in each of the species. The relative overlap between the phosphoproteome datasets and the comparison of protein abundances between the yeast species will shine light on the evolutionary and functional relevance of phosphorylation in regulating protein concentration and mediating cellular signaling pathways.
Initially pre-med focused, Tinny Liang joined the joint lab of Professors Paul Yager and Elain Fu during her freshman year; joining the lab has since opened the doors to biomedical research as a career. Currently a senior In the Department of Bioengineering, Tinny was drawn to technology’s ability to expand access to health care. Her interest and motivation to pursue research on paper-diagnostics for low resource settings is motivated by the fact that while there are cures for many infectious diseases (e.g. malaria, dengue) millions of people in developing countries still die from them. Millions of lives can be saved, and quality of life can be improved if given the tools for accurate diagnosis. With her mentor Professor Elain Fu, she has designed a novel paper-based malarial diagnostic test with improved sensitivity for the detection of infectious diseases in low resource settings. Tinny is currently working on incorporating a new paper-based tool to control reagent transport through this novel test for further improved sensitivity and improved test usability. She plans to continue her passion for biomedical research by pursuing an MD/PhD. Outside of the lab, Tinny is an active Biomedical Engineering Society Officer, volunteers at the Anatomic Pathology department at the University of Washington Medical Center, and leads several Bioengineering outreach events for high school students. She also enjoys playing badminton and cooking with friends.
Mentor: Elain Fu, Bioengineering
Project Title: Development of a Prototype Paper-based Malarial Diagnostic Device
Abstract: Millions of people in developing countries die from infectious diseases (e.g. malaria and dengue), yet many of these deaths can be prevented if giving the tools for accurate diagnosis. However, current diagnostic capabilities with the required clinical sensitivity are confined to laboratory settings due to cost, electrical, and personnel requirements. The current method for diagnosis of infectious diseases in low resource settings is lateral flow tests (LFTs), which have the appropriate usability but confined to single chemical step lack the required sensitivity. Thus there is a medical need for diagnostic tools with the required level of clinical sensitivity and usability for use in low resource settings. I will design a novel device capable of controlling fluid steps within a two dimensional paper networks (2DPN), which enables more sophisticated chemical processes for diagnosis in low resource settings for improved sensitivity and usability. The novel device will utilize commercial enhancement solutions for signal amplification via a metal catalytic reaction to increase sensitivity. I will determine the optimal set of reagents and reagent volumes that yields the highest sensitivity. A new 2DPN assay device will be designed to accommodate the reagent set and volumes, where sequential delivery of reagents is achieved through manipulation of paper geometry. I will then incorporate a fluidic on-switch into the paper network to improve usability (i.e. by reducing the size of the device and the time to read out).
It was during his time at a high school internship at Seattle Biomedical Research Institute that Kien-Thiet Nguyen first became exposed to research culture. Since his first ELISA, he has eagerly pursued research opportunities. As an undergraduate intern in the lab of Theodore White, he researched the import and transcriptional effects of certain classes of antifungals. During his sophomore year, he joined Gwenn Garden’s lab researching the neurodegenerative disease, spinocerebellar ataxia type 7 (SCA7). His earlier research has shown in SCA7 there are changes in climbing fiber inputs to Purkinje cells, a vulnerable neuronal cell type in the cerebellum. His current research involves analysis of microRNA expression in microdissected Purkinje cells in SCA7 and nontransgenic mice. By utilizing basic bioinformatics techniques, Kien-Thiet hopes to identify and validate microRNA and their mRNA targets that are most differentially affected in SCA7. Kien-Thiet plans on pursuing a Ph.D. in neuroscience, with the goal of a career in translational research focusing on neurodegenerative diseases.
Mentor: Gwenn Garden, Neurology
Project Title: Analysis of Altered miRNA Expression in a Transgenic Mouse Model of SCA7
Abstract: Spinocerebellar ataxia type 7 (SCA7) belongs to a family of neurodegenerative diseases. It is characterized by degeneration of the cerebellum and brainstem. The disease is caused by an expanded polyglutamine tract in ataxin 7. This type of polyglutamine mutation is a common feature in many neurodegenerative diseases. Other neurodegenerative disease including those involving polyglutamine expansions demonstrate altered microRNA (miRNA) expression. Given the supporting evidence that miRNA are differentially expressed in other polyglutamine diseases, I seek to determine the role of miRNAs in SCA7. My proposed research will analyze altered miRNA expression in Purkinje cell neurons, a selectively vulnerable neuronal population that degenerate in SCA7. I will first identify miRNAs that are upregulated or downregulated in Purkinje neurons from SCA7 mice. Next using predictive databases I will identify their potential mRNA targets. I will then test identified miRNAs in cell culture to see if they will inhibit expression of their predicted target. If expression is inhibited, I will then measure the level of mRNA and protein of the predicted target in transgenic mouse tissue. By identifying miRNAs that are differentially expressed in SCA7 mice and confirming their activity, we can build our understanding of the mechanisms of disease progression in SCA7.
Jacqueline was forced to end her gymnastics career early due to a rare degenerative bone disease in her right elbow. However, investigations into the disease and lack of treatment inspired her to pursue bioengineering. Her passion lies in novel ways to treat disease. She joined Dr. Regnier’s Heart and Muscle Mechanics laboratory sophomore year, inspired by the ongoing work to address the loss of function post heart attack. The rich and supportive environment has helped her develop greatly as a scientist. Senior year she is collaborating with Dr. Marcinek’s Translational Center for Metabolic Imaging to investigate a novel gene therapy to treat loss of function in skeletal muscle. She plans to attend graduate school and earn her PhD in bioengineering. Following graduate school, she hopes to gain a faculty position at a top research institution and continue in meaningful research, as well as teach to help train the next generation of bioengineers.
Mentor: Michael Regnier, Bioengineering
Project Title: Performance characterization of cardiac and skeletal muscle with increased 2-deoxy-ATP
Abstract: Cardiovascular disease and skeletal muscle disease that result in loss of contractile function affect people around the world. Current heart disease therapies aid in slowing the progression of heart failure, but there are no treatments that restore healthy cardiac function short of transplant. Dr. Regnier’s laboratory is pursuing a novel treatment for heart disease that will prevent the progression of heart failure by restoring cardiac function to healthy levels. The laboratory has discovered that a nucleotide analog of ATP, 2-deoxy-ATP (dATP), which is produced in cardiomyocytes, greatly improves cardiac performance. The Regnier laboratory has studied the effect of increased dATP concentration in cardiomyocytes in both transgenic animals that overexpress the enzyme that catalyzes dATP formation, ribonucleotide reductase (R1R2), and in cells virally modified to have R1R2 overexpression. In both models, the therapeutic effect of increased dATP concentration was observed: cells with increased dATP concentration have an increased rate and magnitude of contraction, and an increased rate of relaxation. To further the study, I will be initiating collaboration with Dr. David Marcinek’s laboratory to explore the effects of dATP in skeletal muscle in transgenic mice. Twitch, tetanus, and fatigue protocols will be conducted on both in vivo and in vitro skeletal muscle from wild type and transgenic mice that overexpress R1R2. The combined findings from both laboratories will help complete the characterization of how increased dATP concentration affects muscle and whether upregulation of this nucleotide might be beneficial in treating skeletal muscle disease as well as cardiac disease.