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Undergraduate Research Program

2014-15 WRF Fellows

Andy Chan - Bioengineering

Chan, Andy

Andy (Ho Wing) Chan is a Senior in the Department of Bioengineering. It has been his dream to improve the current state of cancer treatment since childhood. He came from Hong Kong to the US to pursue a degree in bioengineering and for the opportunity to do hands-on cancer research. He joined Professor Narendra Pal Singh’s laboratory in the Department of Bioengineering during his freshman year. For the first two years, he contributed to the development of a small-molecule cancer drug, called artemisinin. In his junior year, he started working on a project to develop a surgically implantable radiofrequency radiation emitting device for cancer treatment. He has been very grateful for the support from his peers, Professor Singh and other mentors, especially Professor Henry C. Lai who has been a collaborator and great teacher to him. Andy is also very thankful for the generous support from Washington Research Foundation as it further motivates him to pursue his passion. He is interested in pursuing a career that involves both clinical medicine and cancer research. Outside of school, Andy likes volunteering, photography, reading science fiction, ball games, swimming and sailing.

Mentor: Narendra Singh, Bioengineering

Project Title: Development of an Implantable Electromagnetic Field-Emitting Device for Cancer Treatment

Abstract: Malignant solid tumors cause millions of deaths per year worldwide. Low-intensity non-thermal non-ionizing electromagnetic fields (EMF) in the ranges of extremely-low (<100Hz) to low-frequency (30-300 kHz) have been shown to have the potential to be a low cost, effective, and target-specific cancer treatment modality. In application, EMF cancer treatment requires a technical solution to the problem of focusing sufficient EMF energy in the tumor site. In this project, a microchip system that can concentrate EMF in a tumor will be investigated in vitro on cancer cells. Contributions of EMF frequency and emission pulse rate will be studied in order to optimize the system for cancer treatment. We also hypothesize that EMF generates free radicals via the Fenton Reaction to kill cancer cells. To test the hypothesis, the effects of a spin-trap compound (free radical scavenger) and an iron chelating agent on the toxicity of the proposed microchip system toward different cancer cell lines will be investigated. This can provide insight into the anticancer mechanism of action of EMF. The optimized method of EMF concentration and knowledge about the anticancer mechanism of EMF generated by this project could improve cancer treatment.

Natasha Christman - Oceanography

Christman, Natasha

Having harbored an interest in the marine sciences for many years, Natasha Christman was introduced to field research by Dr. Jude Apple where she subsequently found a passion investigating the dynamics of marine microbes. In the Apple lab, Natasha has been able to investigate her curiosity of the effect of climate change and anthropogenic stressors on coastal plankton communities. While continuing work with Dr. Apple, she was introduced to Dr. Jan Newton who has since helped to broaden the scope of research to include the implications of ocean acidification on such systems. Natasha’s current research focuses on the relationship of climate change and acidification on bacterioplankton metabolism and function in near-shore environments. Upon completion of her degree in biological oceanography, she plans on pursuing a doctorate in the field so she can continue to conduct such research for a career. Natasha would like to express her sincere gratitude to the Washington Research Foundation for supporting her research project.

Mentor: Jan Newton, Applied Physics Laboratory, Schools of Oceanography and Marine Affairs

Project Title: Metabolic Responses of Heterotrophic Bacterioplankton to Climate Change and Acidification in Coastal Oceans

Abstract: Heterotrophic bacterioplankton play a significant role in the ocean’s carbon cycle as consumers of organic matter produced by phytoplankton through aerobic pathways. As atmospheric CO2 conditions are expected to increase in the coming decades due to anthropogenic carbon emissions, the global ocean is poised to undergo major chemical and physical changes such as decreased pH and elevated temperature. Coastal systems are particularly vulnerable due to proximity to high density human populations and further potential environmental stressors such as eutrophication and nutrient loading. These changing dynamics of ocean chemistry pose to alter the stoichiometry and quality of organic matter in addition to exposing microbial communities to CO2-rich conditions. However, despite the known importance of heterotrophic bacterioplankton communities to marine organic carbon dynamics and the potential for these communities to serve as carbon sinks, the response of these communities to these climate-driven changes is largely unknown and absent from literature. The proposed study aims to explore the effect of altered carbon stoichiometry of consumed phytoplankton by heterotrophic bacterioplankton communities as well as the metabolic response of these communities to acidified conditions in manipulative experiments. The project additionally seeks to investigate the contribution and significance of heterotrophic respiration to carbon cycling dynamics in two economically and ecologically significant coastal systems, the Strait of Juan de Fuca and Bellingham Bay in Washington State.

John Cisney - Chemical Engineering

Cisney, John

John Cisney joined the Jiang group in November of 2012 through a program called Building Bridges to Bioengineering (B3) while finishing his prerequisites at Seattle Central Community College. John began working on formulating and applying special non-fouling coatings, which are composed of zwitterionic polymers, to substrates for testing in marine environments. The intent for this research is to apply these coatings to sea vessels in an effort to eliminate the accumulation of biomass on the exterior of the vessel. If utilized in the shipping industry, these coatings will reduce transportation and maintenance costs by improving fuel efficiency and by reducing the amount of time spent removing this biomass.

Shortly after being accepted into the chemical engineering department, John began working on independent projects within the Jiang group. With the demand for fresh drinking water increasing worldwide, John proposed the use of these non-fouling coatings in the ocean water desalination industry. The goal of this research project is to eliminate the bio-fouling of the membranes used to filter out the harmful impurities in sea water, and ultimately to find a viable solution to the growing drought issues around the world.

John returned to college with the intent of making a lasting positive impact on society, and undergraduate research has provided him with this opportunity where he can directly apply his growing chemical engineering knowledge. Following his graduation, John plans to pursue a PhD in chemical engineering and continue on with a career in scientific research.

Mentor: Shaoyi Jiang, Chemical Engineering

Project Title: Fabricating Zwitterionic Polymer Coatings to Eliminate Bio-fouling of Reverse Osmosis Desalination Membranes

Abstract: Droughts of devastating proportions are becoming more frequent and widespread. Many areas of the world are unequipped to deal with the economic and agricultural impacts. Almost half of the world’s population resides in and around coastal regions. Thus, resorting to the oceans for clean drinking water is an obvious solution. Zwitterions are environmentally friendly molecules that maintain a positive and negative charge simultaneously. Research has shown that these types of molecules possess non-fouling or fouling release capabilities in a variety of marine applications due to their hydrophilic properties. Therefore, using zwitterionic polymer coatings in an effort to eliminate the membrane fouling issue that plagues ocean water desalination plants is encouraging. Currently, harmful chemicals are added to the inlet water to reduce membrane fouling, but this approach merely suppresses the issue while potentially resulting in unforeseen environmental ramifications. Membrane fouling has prevented ocean water desalination from emerging as a viable source of fresh water due to the high maintenance and operation costs. Most commercially available desalination membranes are comprised of polymers that are susceptible to fouling. A zwitterionic polymer, poly(sulfobetaine methacrylate) (DOPA-PSB), was synthesized and grafted to the surface of a polysulfone-polyamide membrane. Enzyme-linked immunosorbent assays (ELISA) were used to determine the adhesion of the coating to the membrane. The result of the ELISA indicates the successful adhesion of the polymer coating to the membrane and a substantial decrease in biofouling of the membranes. Next, fluorescently tagged proteins will be used to further quantify the biofouling by measuring the intensity of light emitted from the adsorbed proteins. The designed water flow characteristics of the membrane will be measured with a flow chamber in an effort to preserve these characteristics. Utilizing the zwitterionic coatings to eliminate the fouling issues experienced by desalination plants will reduce the monetary and environmental costs.

Max Ferrin - Biology (Molecular, Cellular & Developmental)

Before starting my undergraduate education at UW, I was already bitten by the research bug. Upon studying Charles Darwin’s quest for an explanation behind the diversity of life in high school biology, I was struck by its representation of the immense power in methodical observation and hypothesis-testing toward elucidating the world’s greatest mysteries. My curiosity became more focused as I learned about molecular biology, amazed at how tiny collections of complex chemicals interact to produce the emergent properties of life.

Wanting to get involved in active science as soon as possible, I joined Dr. Joseph Mougous’s lab in the Microbiology department during my freshman year at UW. With attentive mentorship from him and postdoctoral fellow Dr. Seemay Chou I quickly began contributing to the lab’s goal of characterizing the bacterial type VI secretion system (T6SS). The T6SS is a molecular export pathway that allows bacterial cells that possess it to interact with a wide variety of neighboring cells by injecting them with effector molecules. My current project aims to exploit what we have learned so far about the system’s antibacterial properties for engineering an alternative strategy to traditional antibiotic drugs.

When not in lab or class, I spend my time pursuing my secondary loves: snowsports and music. I am proud to serve as this season’s snowboard training director for the student-run nonprofit ski school Husky Winter Sports. I also play drums for local folk rock and metal bands in Seattle.

After I graduate from UW this spring, I intend to remain on the cutting edge of molecular biology research for a career. I aspire to earn a PhD and eventually become the principal investigator of my own lab. I am incredibly thankful for the Washington Research Foundation’s assistance toward meeting my academic and professional goals.

Mentor: Joseph Mougous, Microbiology

Project Title: Exploiting the Antimicrobial Properties of Type VI Secretion in Pseudomonas aeruginosa

Abstract: The type VI secretion system (T6SS) is a molecular export pathway that is
 widely found in Gram-negative bacteria. The T6SS mediates interbacterial
 competition by translocating antibacterial effector proteins from the donor cell 
to a neighboring cell. Included in the T6-secreted arsenal of the opportunistic 
pathogen Pseudomonas aeruginosa is Tse1, a lytic hydrolase effector that
 degrades the recipient cell wall by cleaving amide bonds in the peptidoglycan
 (PG) layer. P. aeruginosa also expresses a cognate immunity protein (Tsi1)
 that prevents intraspecies toxicity by binding and inhibiting Tse1 in the 
periplasm of sister cells. In light of the antibacterial capacity of the T6SS in 
polymicrobial settings, I hypothesize that this pathway can be exploited as 
an alternative strategy to conventional antimicrobial therapeutic approaches.
 Our group will engineer a P. aeruginosa strain that harbors a novel Tse1/Tsi1 pair
 (Tse1*/Tsi1*) that can escape recognition by native immunity. I predict that 
this strain will be able to outcompete its wild-type counterpart through the T6
 pathway. Towards this end, we previously screened a tse1 mutant
 library for variants that escape Tsi1 inhibition in E. coli cells. Here, I report my
 efforts to experimentally validate Tse1* variants identified by this screen.

Philip Lindstedt - Biochemistry

Lindstedt, Philip

I initially began my career in research as a sophomore in Dr. Folch’s lab in the Bioengineering department using newly developed user-friendly microfluidics to study neuromuscular junction formation. I had a great time working under the tutelage of one of the grad students in the lab, Jonathan Cheng, but when I took the last course of the honors organic chemistry sequence, taught by my current mentor Dr. Maly, I knew I wanted to pursue research in biochemistry. I am currently working in the Maly lab developing small molecule controlled split protein switches for highly selective enzymatic inhibition, which could be applied to study intracellular signaling pathways implicated in disease and cellular differentiation. We hope that this technology will provide a low cost, reliable, and rapidly expandable system for validating potential drug targets, a very arduous process at the moment. I really am thankful for the time that my mentor and colleagues in the lab, especially Dan Cunningham-Bryant, have invested in me. They’ve truly enhanced my education, cultivated my scientific interests, and helped me find my career path. Upon my graduation this spring I intend to pursue a Ph.D. in biochemistry or biophysics after a quick travelling stint to get some sun after four years of Seattle’s grey skies. Outside of the lab I enjoying climbing year round and in the winter I’m usually only found in the lab or on the ski slopes of the mountain with the most snow. With the generous support of this WRF fellowship I hope to apply myself in the lab as much as possible during my senior year and further guide the development of our split protein switches.

Mentor: Dustin Maly, Chemistry

Project Title: Small Molecule Controlled Split Protein Switches for Selective Enzymatic Inhibition

Abstract: Elucidating intracellular signaling networks is one of the preeminent goals and greatest challenges of modern day cellular biology. Understanding these systems and the individual events that comprise the complex orchestra that is intracellular signaling is integral to advancing knowledge on human diseases such as cancer and diabetes. Many tools have been developed and implemented in research to make great strides in this endeavor but there has yet to be a silver bullet; much of the difficulty in studying these systems lies in the importance of spatial and temporal regulation of the individual components composing a signaling cascade. Small molecule pharmacological agents are desirable tools for studying these signaling systems because of their capability for fast dose-dependent control of proteins within the cell. Although, designing and producing small molecule agents with the desired specificity and potency is a daunting task. We are working to create a new tool that takes all the advantages of small molecule controlled systems but without the laborious development issues. By combining two existing technologies, chemical inducers of dimerization systems and antibody mimetic proteins, specifically designed ankyrin repeat proteins (DARPins), we are looking to create small molecule controlled split protein inhibitors that act as a switch for turning off the expression of desired targets with the rapidity and dose dependence that is intrinsic to small molecule controlled systems. In this system the DARPin is split into two parts and each is fused to a component of a dimerization platform, when the halves are separately expressed in the cell they will not retain any inhibitory activity, but when the small molecule chemical inducer of dimerization is added the fused domains will form a dimer and the DARPin halves will be in close enough proximity to refold and regain function.

Austin Miner - Chemical Engineering: Nanoscience & Molecular Engineering

Miner, Austin

Austin Miner is a senior studying Chemical Engineering with the Nanoscale Molecular Engineering option. Austin started his research with Professor Hillhouse in the Winter of 2013 as a sophomore. As part of the Hillhouse group he is working on improving the efficiency of Copper Zinc Tin Sulfide (CZTS) photovoltaics (PV), finding new fabrication techniques for existing PVs, and exploring the viability of new inorganic materials for use in PVs. One of his ongoing projects focused on developing a Laser Beam Induced Current (LBIC) setup. This setup can be used to quickly identify inhomogeneities in the PV device. This setup is being expanded to include analysis of current related effects at grain boundaries as well. With the support of the WRF Fellowship, Austin’s project focuses on exploring the viability of Thin-Film Vapor-Liquid-Solid growth techniques for growth of GaAs layers.

Mentor: Hugh Hillhouse, Chemical Engineering

Project Title: Vapor-Liquid Solid Growth for Gallium Arsenide Films

Abstract: III-V based photovoltaics have shown the highest single and multi-junction efficiencies. Gallium Arsenide has been the leader in this reaching over 30% and 45% efficiencies for single and multi-junction cells. Synthesis of the GaAs layer in photovoltaic devices, however, requires expensive epitaxial growth methods which limit GaAs’s ability to compete with Silicon-based photovoltaics. Recently the Javey group from Berkley showed promising results for the growth of 1-3 um Indium Phosphide, a III-V material very similar to GaAs, films using vapor-liquid-solid (VLS) growth. The potential to adapt this methodology to create high quality inexpensive GaAs films for use in photovoltaic device is the focus of my research.

Rachel Park - Biology (Molecular, Cellular & Developmental)

Park, Rachel

I know from personal experience that our understanding of science is both incredibly powerful and tragically inadequate: medical science saved my mother but killed my aunt. This knowledge drives my passion for research. I seek to both improve our understanding of biology and to apply that understanding toward the development of new medical therapeutics and diagnostics. To that end, I am pursuing a double major in Biochemistry and in Molecular, Cellular and Developmental Biology. I am participating in cutting-edge research under the guidance of Dr. Neil P. King and Professor David Baker on the design of new protein-based nanomaterials with the aim of therapeutic applications. I plan to attend graduate school either at Stanford or Berkeley, obtain a PhD in biochemistry and continue to work in the field of protein design.

Mentor: David Baker, Biochemistry

Project Title: Solubilizing Computationally Designed Protein Nanocages

Abstract: Computational methods have recently been developed for designing cage-like protein nanomaterials built through the self-assembly of multiple copies of two distinct protein subunits. One desired but as of yet unrealized feature of our current designs is the ability to produce each protein subunit independently of one another and then trigger assembly by mixing the purified subunits in vitro. Obtaining this level of control over the assembly process requires that the individual protein subunits are stable and soluble in the absence of their designed binding partner. This property is not explicitly considered in our current design protocol. Here I present work aimed at improving the solubility of several protein cages by implementing new steps into my computational design protocol to remove hydrophobic surface area and refine the interface between subunits. I use a two-fold approach. Consensus design targets the surface area of the subunits and redesigns them based upon probability scores generated from a database of native protein structures. The second approach uses a new Rosetta tool still in development to design hydrogen-bonding networks at the subunit interfaces. Automatically generated designs are manually inspected and refined. The information from manual inspection is used to refine my protocol. By reducing the hydrophobic surface area on the subunits and increasing their solubility, aggregation of identical subunits is disfavored and cage formation is favored.

José Pineda - Neurobiology, Mathematics

Pineda, Jose

José was born in the Philippines and immigrated to the United States in 2010 at age 16. He is currently a senior working towards the completion of his degrees in Neurobiology and Mathematics, as well as completing the requirements for the UW Honors Program. His current research explores how cooperative interactions in nature may have evolved. Specifically, he uses a synthetic yeast cooperative system to study mechanisms that stabilize cooperation. José’s degrees as well as his work have exposed him to a highly interdisciplinary training. After graduation, he plans to enroll into a PhD program, in molecular and cellular biology, where he can apply his training in quantitative biology and evolutionary science.

José is also active in programs that increase diversity of underrepresented groups in STEM research. He has participated in outreach activities aimed towards minority high school students and incoming freshman to increase interest in STEM research, hosted by the Summer STEM Institute, The Northwest Association for Biomedical Research (NWABR), and the CURE Program. He has served as a research mentor for summer interns of the 2011 and 2012 UW Genomics Outreach for Minorities (UW GenOM) program, a 10-week program that provides research training and experience to incoming minority freshmen and academic preparation before they enter the university. All the interns José has trained have had abstracts accepted to national research conferences. For the GenOM Project, José also has been part of the admissions committee, as well as the Chemistry Teaching Assistant and the Mathematics (Calculus and Pre-Calculus) and Chemistry Tutor for the participants.

José is very thankful for the support received at UW. In addition to the WRF fellowship, he has received the Mary Gates Research Research Scholarship twice (2010-2011 and 2011-2012); an Undergraduate Research Conference Travel Award, which allowed him to present his work at the Emerging Researchers National Conference in STEM in Washington D.C.; the Undergraduate Diversity at Evolution Award, which allowed him to present at Evolution, an international research conference on evolutionary science; a UW-HHMI Integrative Research Internship; two Biology Departmental Scholarships (Casey Award and the Frye-Hotson-Rigg Award); the Bank of America Endowed Scholarship during EOP’s Celebration; and the EIP Presidential Scholarship.

Mentor: Wenjing Shou, Basic Sciences, Fred Hutch Cancer Research Center

Project Title: Multi-level Selection: The Evolution of a Synthetic Cooperative System

Abstract: Cooperation is a widespread phenomenon. A cooperator provides benefits to its partner at a cost to itself, but derives a greater net benefit when reciprocated. However, Darwinian selection favors cheaters that consume the benefit of cooperation without paying the cost of cooperation. Thus, in a population of cooperators and cheaters, the higher-fitness cheaters are expected to drive the lower-fitness cooperators to extinction. However, since benefits are derived from reciprocity, a population of cheaters becomes less fit than a population of cooperators, hence the paradox. We posit that the crux of this paradox lies in the divergence between individual and group interest. We hypothesize that individual-level and multi-level selection during the evolution of cooperation will yield polarized results. Specifically, individual-level selection which favors the fittest individual is expected to promote cheating. In contrast, multi-level selection which also favors the fittest group is expected to promote cooperation. I will use an engineered cooperative system termed CoSMO in order to test this hypothesis. CoSMO consists of two complementary cooperator strains that supply each other with the necessary metabolite for survival. I will perform parallel evolution experiments using CoSMO under these two selection regimes to test whether multi-level selection results in stabilized cooperation. Under individual-level selection, all replicate CoSMO cocultures will be propagated, selecting for fastest growing individuals. Under multi-level selection only the fastest growing cocultures will be propagated, selecting against exploitative cheaters. In both cases, genetic mechanisms that drive responses to these different levels of selection will be identified. Through this investigation, we will be able to quantitatively couple the two fates of cooperation with the two opposing levels of selection.

William Walker - Bioengineering: Nanoscience & Molecular Engineering

Walker, William

I have always been fascinated with nanotechnology and the wealth of potential applications that are just now entering their nascent stages of research and development. In nanotechnology, the smaller we go, the more control we have over biology and chemistry. Once we reach the atomic level, who can say what we can’t do?

My current research at UW is in protein engineering in the Daggett Lab. Specifically, I use computational protein engineering and molecular dynamics to simulate and explore the fold/function relationship of the most common protein folds. My current project has gone beyond simulations and involves the development of short peptides that are engineered to act as broad-spectrum therapeutics against amyloid diseases such as implant-derived bacterial infections and Alzheimer’s and Parkinson’s diseases. If successful, this project means the start of a new class of therapeutics that could benefit the hundreds of thousands currently inflicted with some form of amyloid disease in the United States alone. It is my career goal to develop novel, protein-based therapeutics to tackle diseases that are currently beyond the scope of modern medicine.

After my time as an undergraduate, I intend to head to industry to refine and tune my research focus then return to academia to receive a PhD and continue my research in protein engineering. Through my time as an undergraduate, I could not have reached this point without the help and support of my lab mentors, classmates, and of course, my family. I would like to extend my heartfelt thank you to the Washington Research Foundation for the support and generosity of this fellowship. This award will allow me to continue my academic and personal growth, and for that, I will be forever grateful.

Mentor: Valerie Daggett, Bioengineering

Project Title: Development of Amyloid-Inhibiting Peptides to Disrupt Amyloid-Based Bacterial Biofilms

Abstract: Spurred by recent advancements in modern medicine, the number of implanted medical devices is on the rise. Unfortunately, the rise in implants has promoted nosocomial, or hospital-acquired, bacterial infections to become the fourth leading cause of death in the United States. Implant-derived infections are deadly due to the formation of bacterial biofilms that physically shield and protect bacteria from the host immune system and conventional antibiotic therapies. Recent research has provided evidence that a fundamental structural component of these biofilms is an aggregated amyloid protein that forms via a similar mechanism as other mammalian amyloid diseases, such as Alzheimer’s and Parkinson’s disease. The aggregation and progression of amyloid diseases is thought to involve the self-aggregation of a unique secondary structure element, called an alpha sheet. Thus, there exists an opportunity to prevent the formation of these bacterial biofilms by developing a novel therapeutic that prevents aggregation by emulating the alpha sheet structure. The aims of my project are to (1) design and synthesize a novel class of alpha sheet peptides and (2) determine their ability to inhibit amyloid aggregation. I will use computational protein engineering and molecular dynamics simulations to design and score multiple amino acid sequences with a high propensity for the alpha sheet conformation. Next, I will use solid phase protein synthesis to produce the high scoring peptides and use amyloid dye-binding assays and dynamic light scattering to determine their efficacy in inhibiting amyloid aggregation. It is my goal to set precedence for a novel class of protein therapeutics that can reduce the 100,000 annual deaths associated with nosocomial bacterial infections. Furthermore, due to the similar aggregation mechanism amongst amyloid proteins, another prospective outcome is a broad spectrum therapeutic that is effective in treating all forms of amyloid disease, including Alzheimer’s, Parkinson’s, and Huntington’s.

Jessica Wang - Bioengineering, Biology (General)

Wang, Jessica Mentor:

Jessica Wang is a senior at the University of Washington majoring in Bioengineering. When she was a freshman, she happened to stumble upon an opportunity to volunteer and travel in Ecuador for a month in the summer, and the things she learned and saw while abroad helped shape the course of her education. While part of a team building houses for a rural town called Pallatanga, she learned some of the challenges people in low resource areas face, one of them being difficult access to medical care and medical technology. She thought it was bothersome that her new friends in Ecuador were at a much greater risk of developing serious medical complications from things that were easily treatable in larger cities. This realization was what prompted her to become a student in Department of Bioengineering and join Dr. Paul Yager in his lab’s efforts to create affordable and easy-to-use diagnostics for use in both non-clinical environments and low resource settings. What she really enjoys about her research project is that she has been able to take a problem that she is personally invested in and work towards creating a solution with the help of invaluable mentors and peers who support her in her work. After graduation, she would like to pursue a MD degree and volunteer her time as a physician to help underserved patients. She also has a strong interest in continuing to be a part of research and engineering efforts to continue improving and developing new medical technology. Jessica would like to thank the Washington Research Foundation for their generous support in helping her pursue her academic and personal interests. When Jessica is not in the lab, she enjoys swimming, reading, cooking, volunteering, and chatting with her friends in Ecuador over the Internet in rudimentary (but functional) Spanish.

Paul Yager, Bioengineering

Project Title: Developing an Automated Paper Platform to Run Influenza Diagnostic Tests

Abstract: The goal of my research in the Department of Bioengineering is to create a device that runs an assay for the detection of influenza (flu) A nucleoproteins in an automated and user-friendly format. This project develops aspects of a larger project in the Yager Lab to build a novel paper diagnostic for influenza using samples from a nasal swab. My specific contribution will be an application of the lab’s current paper technology to reduce the number of user steps necessary for a test that will receive samples from a swab, undergo viral lysis, deliver capture antibodies, and perform unamplified detection of nucleoprotein using gold nanoparticles. Development of this project will occur in three main phases: 1) development and testing (using colored fluids and simulants) of an automated paper network capable of performing our lab’s nucleoprotein assay, 2) integration of the paper network with the antibody and labeling components necessary to perform the nucleoprotein assay, and 3) testing and design of a swab interface in which a user would insert a nasal swab to initiate viral lysis and the automated flu detection sequence. Being able to automate assays within paper devices is important because simplifying the user process would make diagnostics more accessible to people with little laboratory training. In this way, future automated diagnostic technology has the potential to be implemented in the home by everyday users, in airports by customs personnel, and in low resource settings by health care providers who lack access to electricity and power. Although the scope of this project considers only influenza A, the blueprint produced from this work will have potential for integration with assays for other pathogens, thus providing a design that can be adapted to create rapid and affordable diagnostics in response to emerging diseases for the promotion of public health.

Wenxuan (Vince) Wu - Electrical Engineering

Wu, Wenxuan (Vince)

WenXuan (Vince) Wu is a senior student in the Electrical Engineering Department, whose major concentrations are medical instrumentation and sensor and analog circuit design.
Inspired by his parents, both of whom devote their lives in helping as medical professionals, Vince has a goal to innovate and advance medical technologies in an engineering aspect and ultimately improve access to healthcare. With the eagerness to explore and participate in hands-on research in state-of-the-art technology development, Vince transferred to the University of Washington from University of Macau (China) in 2012 and immediately started seeking out medical-related projects. Vince joined Prof. Daniel Ratner’s research group in the summer of 2013. For 15 months he has been studying and researching an area called Silicon Photonic Biosensing, which shows great promise to challenge and revolutionize the current medical diagnostic gold standard – the Enzyme-Linked Immune-Sorbent Assay (ELISA). His project aims at developing an efficient and affordable diagnostic platform for Silicon Photonic Biosensing applications and drive it toward Point-Of-Care settings. Vince intends to pursue a PhD degree after graduation where he can continue researching on translational technology and contributing in medical areas that could improve people’s lives. Vince wants to express his greatest gratitude to the Washington Research Foundation (WRF) for the generous financial support of his future education and research.

Mentor: Daniel Ratner, Bioengineering

Project Title: Development of Rapid and Affordable Silicon Photonic Biosensors Platform for Point-Of-Care Diagnostic Applications

Abstract: The current gold standard for clinical diagnostic, the Enzyme-Linked Immunosorbent Assay (ELISA), requires sophisticated and delicate laboratory work. While ELISA demonstrates good sensitivity and reliability, the method is limited by costly instrumentation and reagents, is time-consuming, and requires a multi-step labeling processes. These limitations make ELISA impractical for the Point-Of-Care (POC), self-administered, or low-cost setting. My research leverages emerging silicon photonic label-free biosensing technology and aims to develop a rapid and affordable medical diagnostic platform as a competitive alternative to ELISA for POC applications. During the last year’s development, I have built a prototype platform consisting of optical hardware and control software necessary to explore silicon photonic biosensing applications. However, the current requirement for trained manual operation and costly instrumentation prevents the platform from becoming a truly POC diagnostic application. My proposed research plan aims to mitigate these limitations by replacing costly and cumbersome external hardware with low-cost, and on-chip solutions. Specifically, I will integrate a low-cost laser diode, accompanied with Complementary Metal Oxide Semiconductor (CMOS) based on-chip current supply design, as an alternative to the external laser source. I will also design and integrate CMOS Trans-impedance Amplifier (TIA) array as on-chip detectors to replace the external inefficient detector. Additionally, I will utilize advanced image processing, spatial capacitance estimation, as well as mathematical modelling to fully automate the platform operation and result reporting. The success of these research activities will significantly reduce the overall cost and experimental time and improve the efficiency of the current diagnostic platform. This effort will not only dramatically further the state-of-the-art in biosensor sensitivity, speed, and cost, but also greatly advance the translation of this technology into POC and home care diagnostic application.