menu
  • expo
  • expo
  • login Sign in
Office of Undergraduate Research Home » 2020 Undergraduate Research Symposium Schedules

Found 19 projects

Oral Presentation 1

11:00 AM to 12:30 PM
A Cross Platform Study to Treat Duchenne Muscular Dystrophy
Presenter
  • Aniruddh Saxena, Senior, Bioengineering Mary Gates Scholar, UW Honors Program
Mentors
  • David Mack, Bioengineering, Rehabilitation Medicine, Institute for Stem Cell and Regenerative Medicine
  • Shawn Luttrell, Rehabilitation Medicine
Session
    Session O-1F: Health Sensing and Modeling
  • 11:00 AM to 12:30 PM

A Cross Platform Study to Treat Duchenne Muscular Dystrophyclose

The dystrophin protein protects cardiac and skeletal muscle from damage during normal contraction and relaxation by acting as a shock absorber in the cell. Mutations in the dystrophin gene lead to Duchenne muscular dystrophy (DMD), an X-linked recessive disease. Boys suffering from the disease become ventilator dependent at a young age and usually succumb to cardiac failure in their thirties. Other symptoms of DMD include muscle wasting, cardiomyopathy and respiratory failure. Currently there is no cure for DMD and while gene therapy has shown great promise, it still needs to be complemented with additional therapeutic interventions in order to fully address the symptoms of DMD. Previous work by our lab identified several drugs that blocked a certain type of calcium channel in cardiac muscle and protected the cells from damage following injury by correcting calcium movement into and out of the cell during muscle contraction. In this study, the leading drugs will be tested further using a cross-platform approach. The drugs will initially be tested in cardiac and skeletal muscle differentiated from healthy and DMD patient-derived induced pluripotent stem cells (iPSCs). The top three drugs that restore normal contraction and relaxation kinetics in vitro will then be tested in the DMDmdx rat. This novel, small animal model has a similar progression of DMD symptoms to human patients. The rats will be fed the drugs in their chow. Skeletal and cardiac muscle performance will be evaluated to determine whether correcting muscle contraction kinetics ameliorates the symptoms of DMD. Furthermore, we will show whether the same drug is equally effective in treating both cardiac and skeletal muscle. The cross-platform approach may help to better predict drug efficacy, leading to a reduced rate of failure in clinical trials. Moreover, this approach may serve as a benchmark for drug discovery in other neuromuscular diseases.


Poster Presentation 1

9:00 AM to 9:55 AM
Investigating the Role of Notch in Cardiomyocyte Cell Cycle Regulation
Presenter
  • Akshita Khanna, Senior, Biochemistry
Mentors
  • Charles Murry, Bioengineering, Medicine, Pathology
  • Silvia Marchiano, Pathology
Session
    Session T-1E: Medicine: Critical Care, Pathology, Urology
  • 9:00 AM to 9:55 AM

  • Other Pathology mentored projects (31)
  • Other students mentored by Charles Murry (1)
Investigating the Role of Notch in Cardiomyocyte Cell Cycle Regulationclose

Heart disease is a major health pandemic, and the myocardial infarction (MI), also known as a heart attack, is the leading cause of death. This is because adult cardiomyocytes (CMs) present in the heart cannot divide and proliferate, preventing the heart from regenerating itself and repairing tissue damage. From developmental studies in rodents, we know the Notch signaling pathway is crucial in mediating expansion and proliferation of CMs during development, as impairments in Notch lead to cardiac defects. Notch is inactive in adult CMs, which suggests it plays a role in CM renewal; however, this mechanism is still unknown. Thus, our goal is to investigate the role of Notch in CM proliferation and cell cycle regulation. For the purpose of this study, we are using CMs differentiated from a human embryonic stem cell line, RUES2. Differentiation was completed over a 17-day period by culturing the cells as a monolayer. On Day 0, Chiron 99021 is added to activate Wnt signaling, promoting mesoderm formation. Wnt-C59 is added at Day 2 to inhibit Wnt signaling and differentiate the cells into progenitors, and B27 supplement at Day 6 promotes full differentiation into CMs. This adherent protocol recapitulates every step of natural heart development in vitro. Purity of the cell populations, as assessed by flow cytometry staining for cardiac troponin T (cTnT), was 97.1 ± 0.9% cTnT+. We then determined the proliferative capabilities of CMs in the presence of a Notch inhibitor, DAPT. DAPT inhibits gamma-secretase, a transmembrane protein that normally proteolytically cleaves Notch during signaling, thus inactivating the Notch pathway. Treatment with DAPT significantly decreased cell proliferation by about 50%, confirming that Notch directly affects CM proliferation. The results of this study increase our knowledge of CM physiology and the mechanisms behind cell cycle withdrawal, and provide new insights into improving CM renewal.


Oral Presentation 2

1:00 PM to 2:30 PM
Evolution of a Self-Assembling Synthetic Nucleocapsid with Enhanced mRNA Packaging
Presenter
  • June Kim, Senior, Bioengineering Levinson Emerging Scholar, Mary Gates Scholar
Mentors
  • David Baker , Bioengineering
  • Issa Yousif, Bioengineering
Session
    Session O-2E: Protein Biochemistry
  • 1:00 PM to 2:30 PM

  • Other Biochemistry mentored projects (21)
  • Other students mentored by (1)
Evolution of a Self-Assembling Synthetic Nucleocapsid with Enhanced mRNA Packagingclose

RNA-based therapeutics have attracted significant interest as a promising alternative to traditional cancer therapy methods. Coupled with other technologies such as the application of nanocarriers, RNA-based treatments have shown the potential to regulate gene expression in tumor cells with high efficacy and reduced safety risks. Despite these advantages, delivering sufficient amounts of therapeutic cargo while escaping from the proteolytic environment of the endosome has remained a long-standing challenge. This project focuses on addressing this issue by evolving the I53-50-v4 (V4), a self-assembling synthetic protein nanoparticle engineered to encapsulate its own mRNA, to increase RNA packaging and prevent degradation upon endocytosis. With previous data suggesting a decrease in mRNA encapsulation with an increase in mRNA length, additional designs were generated to further validate this finding. Furthermore, different variations of de novo pH-responsive trimers for endosomal escape were fused to the exterior of the V4 and tested for RNA packaging. Using computational tools, algorithms were also developed to model the porosity of the nanoparticle and to label residues for cationic mutations. Protein nanoparticles were expressed and purified via Immobilized Metal Affinity Chromatography (IMAC) and SEC (Size Exclusion Chromatography). Constructs were then analyzed in their mRNA encapsulation levels through RT-qPCR. Success of this project would demonstrate an increase in encapsulation levels with a decrease in mRNA length. As the phenotype of each nanoparticle design is spatially linked to its genotype, the top performing designs can also be selected and further evolved using both experimental and computational approaches. This will allow the development of a novel assay for screening desired proteins and narrow the gap towards achieving an efficacious RNA-delivery system.


Oral Presentation 3

2:45 PM to 4:15 PM
Interactions Between Dopamine and Kappa Opioid Receptors in the Nucleus Accumbens Using Fluorescent Biosensors
Presenter
  • Mingkang Zhou, Senior, Neuroscience, Psychology Mary Gates Scholar, Innovations in Pain Research Scholar, UW Honors Program
Mentor
  • Michael Bruchas, Anesthesiology, Bioengineering, Pharmacology, Departments of Anesthesiology and Pharmacology
Session
    Session O-3E: Neurosciences: Behavior, Injury, and Neuroengineering
  • 2:45 PM to 4:15 PM

  • Other students mentored by Michael Bruchas (2)
Interactions Between Dopamine and Kappa Opioid Receptors in the Nucleus Accumbens Using Fluorescent Biosensorsclose

People suffering from stressful events are likely to experience negative affective states. Previous studies have shown that stress induces the release of neuropeptides including dynorphin, which acts presynaptically on kappa opioid receptors (KOR) and may act to inhibit neurotransmitter release in the limbic brain areas. In this project, we investigated the interaction between KOR and dopaminergic systems in the ventral shell of the Nucleus Accumbens (NAc) to determine how dopamine release is altered during in vivo dynorphin activation of KORs. To monitor and manipulate dopamine and KOR dynamics, we injected genetically encoded fluorescent indicators of dopamine (dLight) and KOR (kLight) respectively and implanted optical fibers in the NAc ventral shell in transgenic mice brains. In collaboration with Lin Tian at UC Davis, we also characterized the in vivo fidelity and accuracy of a newly developed kLight—version 1.2a. To light-stimulate dynorphin neurons in vivo, we injected a red-shifted channelrhodopsin, Chrimson that acts as a light-gated ion channel to depolarize dynorphin neurons. We recorded dopamine/KOR activities during behavioral experiments including Pavlovian conditioning using sucrose pellets. We hypothesized that upon dynorphin neuron activation, there will be a decrease in the amount of dopamine release in the NAc, an increase in KOR light activity and fewer motivated behaviors observed in mice to obtain sucrose pellets. Here we will present our findings measuring dopamine and kappa opioid function in the NAc. These results could have implications for neuropsychiatric diseases including depression and addiction.


Poster Presentation 3

10:55 AM to 11:40 AM
Investigating Key Transcription Factors Involved in Drug Resistant Subpopulations of Melanoma
Presenter
  • Daniel G Chen, Sophomore, Center for Study of Capable Youth Mary Gates Scholar
Mentor
  • James Heath, Bioengineering, Institute for Systems Biology
Session
    Session T-3F: Global Health, Environmental & Occupational Health Sciences
  • 10:55 AM to 11:40 AM

Investigating Key Transcription Factors Involved in Drug Resistant Subpopulations of Melanomaclose

Melanoma is the most aggressive type of skin cancer. It can quickly metastasize and usually develops drug resistance to standard treatments. Our lab is working on investigating the transcription factors (TF) responsible for drug resistance in melanoma to help create more effective drug treatments. Single cell RNA-seq and ATAC-seq (assay for transposase accessible chromatin) was used, with single-cell level resolution, to ascertain transcriptome and epigenome information, respectively. This data was analyzed using bioinformatic toolkits to predict the transcription factors that control drug resistance. These predictions were validated using CRISPR knockout cell lines and melanoma cells with a specific transcription factor removed. Analysis of single cell RNA-seq data of melanoma cells after 24 days of drug treatment, when the cells typically become drug resistant, reveal the co-existence of four distinct subpopulations. These four subpopulations can be categorized into two groups, drug sensitive (melanocytic and neural crest) and drug resistant (mesenchymal and novel). We also gathered single cell RNA-seq and ATAC-seq on a timeline with days 0, 3, 6, 13, 17, and 24 to monitor the trajectories cells undertake to obtain the drug-resistant state. Analysis of the timeline single cell RNA-seq mapped out this trajectory from drug sensitivity to drug resistance and associated changes in cellular phenotypes. We expect analysis of the timeline single cell ATAC-seq data will show similar results and through an integration of the two layers of information, more solid predictions can be made for the TFs driving the transition towards drug resistance. We expect the cells with these TFs knocked out to be unable to form drug resistant subpopulations, as they can no longer activate drug resistance. Discovery of such TFs would suggest additional or more effective treatments that could halt drug resistance and mitigate the effects of melanoma.


Quantitative Characterization of Controlled Drug Release From Polymeric Prodrugs
Presenter
  • Neona Lowe, Senior, Bioengineering Mary Gates Scholar
Mentor
  • Daniel Ratner, Bioengineering
Session
    Session T-3H: Medicine & Bioengineering
  • 10:55 AM to 11:40 AM

  • Other Bioengineering mentored projects (24)
Quantitative Characterization of Controlled Drug Release From Polymeric Prodrugsclose

Each year, nearly 6 million deaths worldwide are caused by lower respiratory tract infections, diarrhoeal diseases, and tuberculosis. These infectious diseases are leading causes of death worldwide. Currently, the pharmacological treatment of infection is encumbered by the presence of inaccessible intracellular pathogen reservoirs, and the need for prolonged treatment regimes. Drug delivery systems can be engineered to overcome these biological barriers for effective treatment by facilitating intracellular delivery and tailored release. Extended release of drugs alleviates the need for exhaustive treatment regimes and increases patient compliance. Furthermore, this can decrease treatment duration, reduce the cost of treatment, and improve access for disadvantaged populations. Our research utilizes modular polymeric prodrugs composed of molecular targeting agents, cleavable linkers, and antimicrobial drugs. This platform permits facile alteration of functional modalities, enabling custom tailored treatments for each disease setting. By utilizing tunable linkers, we can control the precise delivery mechanism and therefore direct the localized release of drugs. To characterize the controlled release of antimicrobial drugs from our polymeric prodrugs, we are designing high performance liquid chromatography (HPLC) and liquid chromatography mass spectrometry (LC-MS) assays. The developed assay will evaluate the release mechanism with stability and release studies. Furthermore, the robust methodology will enable the determination of the pharmacokinetics of the polymeric prodrug delivery system. The assay and results from this study will ultimately support the development of improved therapies.


Poster Presentation 4

11:45 AM to 12:30 PM
A Biopsy Tissue Processing Microfluidic Device for Triple Negative Breast Cancer Biomarker Detection
Presenters
  • Samuel Chen, Junior, Engineering Undeclared
  • Garrett Michael (Garrett) Foster, Senior, Biochemistry, Environmental Health
  • Wyatt Douglas Miller, Senior, Biochemistry
Mentor
  • James Lai, Bioengineering
Session
    Session T-4B: Bioengineering & Laboratory Medicine
  • 11:45 AM to 12:30 PM

  • Other Bioengineering mentored projects (24)
A Biopsy Tissue Processing Microfluidic Device for Triple Negative Breast Cancer Biomarker Detectionclose

Triple-negative breast cancer (TNBC), the most aggressive form of breast cancer that accounts for 15% of all breast cancers, tests negative for the three common breast cancer oncogene proteins– estrogen receptor, progesterone receptor and HER2. Without specific biomarkers to be targeted for treatment, TNBC treatments are limited to combinations of immunotherapy, chemotherapy, lumpectomy and radiation therapy. Alternative biomarkers such as the PD-L1, PD-L2 and CD-86 are utilized to explore more specific treatment options with minimal side effects. Detecting biomarkers in the tumor tissue typically utilizes immunohistochemistry (IHC), which exhibits limited quantitative precision, sensitivity and multiplex capability. To address the challenge, multiple reaction monitoring mass spectrometry (MRM-MS) has been developed for quantitating multiple tumor biomarkers simultaneously. Accurate detection of targeted biomarkers on the MRM-MS requires samples with high purity. However, the current microbead immunoprecipitation process results in a noticeable level of background impurity. To compensate for this impurity, the assay requires higher peptide yield by using at least 5 mg of tissue (around 100 µg of protein), which may not be available or can only be obtained with more invasive procedures. Additionally, the current biomarker extraction protocol is a 16 manual-step workflow that takes 38 hours. To speed up the biomarker purification process while using less tissue sample, our group has developed a biopsy tissue processing microfluidic device. Instead of magnetic microbeads, the device utilizes smart polymer reagents with higher capture efficiency to improve the peptide purification process and reduce the required sample size down to less than 5 mg of tissue. The device contains pre-loaded reagents, which streamlines the processes of deparaffinization, cell digestion, protein digestion and peptide purification to only 8 hours with 4 manual steps. The new device with the smart polymer reagents can potentially enable comprehensive tumor microenvironment characterization using MRM-MS with needle biopsy tissue.


Precision-engineered Porous Gelatin Toward Reducing Foreign Body Response and Promoting Vascularization
Presenter
  • Louis Chen, Senior, Biology (Ecology, Evolution & Conservation)
Mentors
  • Buddy Ratner, Bioengineering
  • Le Zhen, Chemical Engineering
Session
    Session T-4B: Bioengineering & Laboratory Medicine
  • 11:45 AM to 12:30 PM

  • Other Bioengineering mentored projects (24)
  • Other students mentored by Buddy Ratner (3)
Precision-engineered Porous Gelatin Toward Reducing Foreign Body Response and Promoting Vascularizationclose

In the Ratner Lab, our research focuses on engineered biomaterials and surface coatings for improving biocompatibility of implantable medical devices and tissue engineering. Currently, the long-term performance of implantable medical devices is limited by the body’s foreign body reaction (FBR). The body reacts to foreign materials in an inflammatory manner and ultimately encapsulate the device with a dense, avascular scar layer. The Ratner Lab has developed multiple strategies to reduce scarring and improve vascularization, including precision-engineered porous materials. The lab has discovered that materials with uniform 40 μm pores seamlessly heal within the body in a vascularized fashion. Previous research has mostly focused on biostable synthetic materials which remain stable in the body over the duration of implantation. My research will explore the potential of gelatin, a biodegradable, bioderived material, as a precision-engineered porous scaffold to promote healing. IL-4 is a cytokine that directs the inflammatory response towards a healing response. My research will also incorporate IL-4 into the biodegradable porous material to further enhance healing. Our long-term scientific goal is to enable complete regeneration of tissue by first promoting healthy blood vessels growth throughout the porous structure, then allowing the material to completely disappear (biodegrade) to make room for rest of the tissue to heal.


Hybrid Nanocarriers for Lymphatic CD4+ T Cell Activation and HIV-1 Latency Reversal
Presenter
  • Sarah Danielle Slack, Senior, Bioengineering Mary Gates Scholar
Mentors
  • Kim A. Woodrow, Bioengineering
  • Jamie Hernandez, Bioengineering
Session
    Session T-4B: Bioengineering & Laboratory Medicine
  • 11:45 AM to 12:30 PM

  • Other Bioengineering mentored projects (24)
  • Other students mentored by Kim A. Woodrow (1)
Hybrid Nanocarriers for Lymphatic CD4+ T Cell Activation and HIV-1 Latency Reversalclose

Antiretroviral therapy (ART) cannot eliminate latently infected human immunodeficiency virus (HIV) reservoirs, the barrier to HIV cure. A “shock and kill” strategy has been proposed to cure HIV by using latency-reversing agents (LRAs) to reactive latent proviruses and allow for reservoir elimination. Due to the low potency and high toxicity of LRAs, none have yet been effective in reducing reservoir size in vivo. Here, we hypothesize that delivery of LRAs using nanocarriers (NCs) will improve drug solubility and safety, provide sustained drug release, and simultaneously deliver multiple drugs to reservoir tissues and cells. We developed hybrid nanocarriers to incorporate physicochemically diverse LRAs and target reservoirs in lymphatic CD4+ T cells. LRAs were formulated by physical encapsulation or covalent conjugation to the biodegradable polymer (PLGA) core. Drug combinations were evaluated in vitro using a J-Lat reporter cells and validated in CD4+ T cells from virologically suppressed patients. CD4+ T cell targeting specificity was tested ex vivo in non-human primate (NHP) peripheral blood mononuclear cells (PBMCs). Targeting and toxicity were also evaluated in vivo in mice following size optimization for increased passive drainage to lymph nodes. Optimized nanocarriers were used for identification of an LRA combination displaying synergistic latency reversal and low toxicity in vitro in model and patient cells. Long-term and specific activation of CD4+ T cells in NHP PMBCs ex vivo and in mouse lymph nodes in vivo was observed, with significant reduction in toxicity compared to free LRA delivery. This nanocarrier platform targets CD4+ T cells, successfully inducing latency reactivation in HIV reservoirs. The platform additionally enables new solutions for HIV cure with the potential to deliver anti-HIV agents, vaccines, immunomodulating agents, and gene-modifying oligonucleotide drugs.


A Novel Device for the Delivery of Microneedle Systems to the Buccal Mucosa
Presenter
  • Mitchell Ekdahl, Senior, Bioengineering Mary Gates Scholar, UW Honors Program
Mentors
  • Kim A. Woodrow, Bioengineering
  • Rachel Creighton, Bioengineering
Session
    Session T-4B: Bioengineering & Laboratory Medicine
  • 11:45 AM to 12:30 PM

  • Other Bioengineering mentored projects (24)
  • Other students mentored by Kim A. Woodrow (1)
A Novel Device for the Delivery of Microneedle Systems to the Buccal Mucosaclose

Microneedles are an effective method for transdermal delivery of a variety of pharmaceutically active agents primarily because of their ability to puncture the stratum corneum. Tissue puncture using microneedles also has potential to improve drug delivery at mucosal sites such as the buccal mucosa, where topical dosing is limited by a thick epithelial layer and continuous salivary flow. However, the low tissue stiffness and wide variance in epithelial thickness present in the oral mucosa preclude direct translation of currently available transdermal microneedle application methods. Further studies of microneedle drug delivery in the oral mucosa require methods for complete and reproducible microneedle application. This project aims to address this need with a device that can apply microneedles to the buccal mucosa with reproducible penetration depth and force, metrics which are correlated with delivery efficiency. The device is designed to be tunable to accommodate microneedle arrays with various dimensions and mechanical properties. Physical parameters of the device are optimized in silico via finite element analysis simulation of tissue puncture with a microneedle array. A prototype of the device is then evaluated using a tissue phantom model to assess penetration depth and force. Performance of the lead candidate device is then validated in tissue explants. This project provides insights for future improvements to microneedle application in the oral mucosa.


A Fully Genetically Encodable System to Reversibly Pattern Proteins Into Hydrogels Using Light
Presenter
  • Sebastian Kurniawan, Senior, Chemical Engineering Mary Gates Scholar
Mentors
  • Cole DeForest, Bioengineering, Chemical Engineering, Molecular Engineering and Science
  • Emily Ruskowitz, Chemical Engineering
Session
    Session T-4D: Chemical Engineering
  • 11:45 AM to 12:30 PM

  • Other students mentored by Cole DeForest (2)
  • Other students mentored by Emily Ruskowitz (1)
A Fully Genetically Encodable System to Reversibly Pattern Proteins Into Hydrogels Using Lightclose

In trying to understand biology’s dynamic heterogeneity, scientists have sought to recapitulate the spatial complexity and temporal presentation in which proteins are naturally presented to cells. Currently, the most promising strategies in this regard exploit sequential ligation/cleavage reactions, each controlled in time and space using light so as to reversibly immobilize proteins within synthetic biomaterials. Though our lab has utilized these approaches to spatially control complex biological fates with micron-scale resolutions, previous methods suffer from complex syntheses, as well as requirements for specialized equipment and skillsets rarely available in bio-based laboratories. Improving upon these fundamental limitations, our group has developed a scalable system wherein proteins can be bound/released from hydrogels using light, without the need for such expertise/equipment, by being fully genetically encodable. In this approach, biology performs all the modifications necessary to photopattern protein binding to gels, as well as install the reactive species requisite for the protein’s photo-mediated release. We have accomplished this using a photoactivatable protein-peptide ligation reaction developed by our lab, wherein UV irradiation “activates” the protein to ligate specifically with the peptide tag. Additionally, we exploit co-translational chemoenzymatic modification strategies to install a functional handle for tethering the protein into polymeric hydrogels during protein expression. To the peptide tag, we append a photocleavable protein that cleaves when irradiated by visible light, fused to a protein of interest (POI) to be tethered to the hydrogel. Expressing these proteins in E. coli yields the first-ever fully genetically encodable system which can reversibly pattern proteins into hydrogels, by first shining UV light to tether POIs into biomaterials, then subsequently shining visible light to photocleave the protein and trigger POI release. Highlighting the system’s versatility, we demonstrate that the approach is compatible with fluorescent proteins and bioactive growth factors to direct 4D cell fate.


Photo-Mediated Stiffening of Genetically-Encoded Hydrogels
Presenter
  • Alder Colleen Strange, Senior, Biochemistry, Individualized Studies, Psychology Mary Gates Scholar, UW Honors Program
Mentors
  • Cole DeForest, Bioengineering, Chemical Engineering, Molecular Engineering and Science
  • Emily Ruskowitz, Chemical Engineering
Session
    Session T-4D: Chemical Engineering
  • 11:45 AM to 12:30 PM

  • Other students mentored by Cole DeForest (2)
  • Other students mentored by Emily Ruskowitz (1)
Photo-Mediated Stiffening of Genetically-Encoded Hydrogelsclose

Water-swollen polymeric networks (i.e., hydrogels) provide a structural platform for the manipulation of chemical and mechanical signals that mimics the complex heterogeneous environment experienced by cells in vivo. Photoresponsive chemistries have been of particular interest to this end, as they allow for precise spatiotemporal control of physiochemical properties and, thus, cell behavior. Here, we present a novel protein-based network that will allow for the photo-mediated stiffening of genetically-encoded hydrogels. In this system, we exploit a biochemical technology recently pioneered by our lab in which two pairs of proteins undergo irreversible, covalent heterodimerization after photoactivation. Through the incorporation of an inert, unstructured polypeptide backbone, we have exploited the aforementioned reaction to induce gelation in response to light through the formation of four-arm protein crosslinks. Unlike previous synthetic polymer-based hydrogel systems, this system is entirely genetically encoded, which provides significant advantages in terms of cost, time, and production simplicity. As we intend to demonstrate through photorheometry, this reaction proceeds in a dose-dependent manner, providing step-wise control of both where and when gel stiffening occurs. Such 4D control of a gel’s mechanical properties can be used to influence cell migration, growth, and differentiation, and, thus, could have applications in tissue engineering. Furthermore, we anticipate our system could be utilized to model the stiffening of the extracellular matrix, which is commonly associated with pathologies such as cancer, fibrosis, and cardiovascular disease.


The Effect of Mitochondrial Targeted Therapeutic SS-31 on a Model of Accelerated Sarcopenia
Presenter
  • Kevin Andrew Nguyen, Senior, Biology (Physiology) Mary Gates Scholar, UW Honors Program
Mentors
  • David Marcinek, Bioengineering, Pathology, Radiology
  • Matthew Campbell, Radiology
Session
    Session T-4F: Medicine, Neurosurgery, Pediatrics, Pathology
  • 11:45 AM to 12:30 PM

  • Other Radiology mentored projects (9)
The Effect of Mitochondrial Targeted Therapeutic SS-31 on a Model of Accelerated Sarcopeniaclose

Sarcopenia, the age-related of loss of muscle mass and function, is associated with a decline in quality of life in the elderly and has few effective treatment options. Sarcopenia is linked to mitochondrial dysfunction and elevated mitochondrial oxidant production. We are investigating the role of elevated mitochondrial oxidative stress in sarcopenia using a mitochondrial targeted therapeutic and a mouse model of accelerated sarcopenia. SS-31 is a mitochondrial targeted peptide that associates with cardiolipin, decreases oxidant production, and increases ATP production in vivo. Superoxide dismutase 1 knockout (Sod1KO) mice lack superoxide dismutase 1 (an enzyme that converts the oxidant superoxide into hydrogen peroxide and molecular oxygen) resulting in an accelerated sarcopenia phenotype. We hypothesize that improving mitochondrial function with SS-31 treatment will delay the decline in muscle function in the Sod1KO mice. To test this, we administered SS-31 to SOD1KO mice through surgically-inserted osmotic pumps for 8 weeks between 3 and 4 months of age, the published timeframe for the onset of skeletal muscle decline in SOD1KO mice. Muscle force generation and fatigue resistance was tested in vivo in the gastrocnemius before pump insertion and monthly after pump insertion for 4 months. At the end of the treatment we used histological and biochemical analyses of mouse tissue samples to determine skeletal muscle fiber type, metabolite and protein concentrations, and muscle fiber respiration and oxidant production. We expected SOD1KO mice with SS-31 to have a lower rate of decline in muscle force production and increased fatigue resistance over time, higher max ATP production, and decreased oxidative stress. The effect of SS-31 on muscle function, mitochondrial quality, and redox homeostasis has exciting potential as a translational therapeutic treatment for human sarcopenia.


Poster Presentation 5

1:00 PM to 1:45 PM
A Characterization of Tissue-Specific Gene Bias in Gene Set Collections Used for Pathway Enrichment Analysis
Presenter
  • Gina T. Huynh, Senior, Biochemistry
Mentors
  • Nathan Price, Bioengineering, Computer Science & Engineering, Institute for Systems Biology, Institute for Systems Biology
  • Alison Paquette, Institute for Systems Biology
Session
    Session T-5B: Genomics
  • 1:00 PM to 1:45 PM

A Characterization of Tissue-Specific Gene Bias in Gene Set Collections Used for Pathway Enrichment Analysisclose

Although transcriptomes are highly tissue and cell type specific, curated gene set collections are not constructed or analyzed with recognition of this bias despite much of transcriptomic analysis depending on curated gene set collections. Prior work has recognized the potential for gene bias due to the variable nature of manually curating gene set collections, but coverage has yet to be characterized across all tissues and in all commonly used gene set collections. The goal of this study was to perform a comprehensive analysis of curated gene set collections from the data repository Molecular Signatures Database (MSigDB) based upon tissue specific expression. We analyzed KEGG, REACTOME, BIOCARTA, and Gene Ontology (GO) including Biological Processes, Cellular Components and Molecular Function gene set collections available on MSigDB. We curated lists of enriched and elevated genes as defined by Human Protein Atlas for 36 tissues. Analyses, visualization, and statistical analyses were performed using the R statistical programming language. We revealed that the MSigDB gene set collections differ among themselves in the fraction of tissue genes covered. GO Biological Processes has the highest gene coverage. BIOCARTA has the lowest gene coverage. Additionally, each collection differs among tissues in the fraction of genes covered. We also showed differential gene coverage among tissues even when collections are combined. Within elevated tissues, the liver has the highest and the fallopian tube has the lowest gene coverage. Within enriched tissues, the lymphoid has the highest and the testis has the lowest gene coverage. We created a database describing the presence or absence of tissue specific genes for each tissue with which researchers can elect the most appropriate gene set collection to use for analysis of a specific tissue. This increases the utility of our findings and creates a direct resource for researchers in the field.


Poster Presentation 6

1:50 PM to 2:35 PM
Zwitterionic polymer brush coating to improve the longevity of insulin catheters in diabetic patients 
Presenter
  • Shreya Rajgopal, Sophomore, Bioengineering
Mentors
  • Julia King, Bioengineering, Chemical Engineering
  • Buddy Ratner, Bioengineering
Session
    Session T-6C: Biomedical
  • 1:50 PM to 2:35 PM

  • Other Chemical Engineering mentored projects (16)
  • Other students mentored by Buddy Ratner (3)
Zwitterionic polymer brush coating to improve the longevity of insulin catheters in diabetic patients close

More than 442 million people worldwide have been diagnosed with diabetes, many of which regulate their glucose levels using the pump/catheter system. However, just 2-3 days after the catheter is inserted into the body, the tissue clogs due to the foreign body reaction (FBR), an immune reaction elicited by the body in response to any foreign material injected in the body. At this point, the patient must remove the catheter and insert a new device into fresh skin elsewhere, resulting in excess scar tissue. Our project focuses on preventing the FBR by reducing its triggering event--protein attachment--so that insulin catheters can last longer (2-3 weeks) and can reduce fibrotic accumulation in patients. To combat the frequency of delivery site changes, we have designed a nonfouling zwitterionic polymeric brush coating for the surface of the catheter to reduce protein attachment. For the coating, zwitterionic sulfobetaine methacrylate (SBMA) was surface-polymerized onto the catheter using atom transfer radical polymerization (ATRP). SBMA has been shown to resist protein adsorption down to less than 1ng/cm2. The ATRP initiator was plasma-deposited to robustly adhere to the unique geometry of the catheter. In this work, we used a full factorial design of experiment (DOE) to determine significant experimental factors to the polymerization protocol to maximize the amount of SBMA on the surface. The coating was characterized using x-ray photoelectron spectroscopy (XPS) to confirm the presence of SBMA and the radiolabeled protein adsorption assay to measure the amount of protein adsorbed to the coating. We plan to use the results of the DOE screening to further optimize the nonfouling coating and ultimately plan to test this coating on insulin-delivering catheters in a diabetic mouse model to observe sustained lowered blood sugar levels and histologically review the extent of the FBR through collagen accrual.


Effect of RUNX2 on Calcific Aortic Valve Disease Progression
Presenter
  • Jake Lally, Senior, Extended Pre-Major
Mentor
  • Subramanian Dharmarajan, Bioengineering
Session
    Session T-6C: Biomedical
  • 1:50 PM to 2:35 PM

  • Other Bioengineering mentored projects (24)
Effect of RUNX2 on Calcific Aortic Valve Disease Progressionclose

Calcific Aortic Valve Disease (CAVD) is progressive calcium deposition and collagen buildup on the aortic valve, causing stiffness which impairs normal function ultimately leading to death. CAVD is common in older adults, present in 20-30% of individuals aged over 65, and 48% of patients over 85 years. Our long-term goal is to develop a therapeutic target which can be treated non-invasively as an alternative to surgical valve replacement, the only treatment currently available. This project is part of a larger investigation into the role of Runx2 on aortic valve function in CAVD progression using a unique mouse model developed by the lab. The mouse line has been designed to be genetically predisposed to developing CAVD. The sub-project is comparing variation in aortic valve calcium and collagen deposits, between the diseased model and mice having a Runx2 deletion. Echocardiography imaging comparing the two mice groups showed an improvement in aortic valve function in mice with Runx2 deletion, indicated by improved flow, velocity and pressure. To assess the changes in valve morphology which could contribute to the improvement, we will be using histological staining techniques on sections of the diseased aortic valves. The stain Picrosirius Red will be used to visualize collagen accumulation, and OsteoSense stain for calcium deposits. Sections are imaged using brightfield and fluorescence microscopy respectively. Levels of collagen and calcium will be quantified from the images using image processing programs NIS Elements and ImageJ. Staining analysis has shown a reduction in calcification and collagen deposits in mice with the deletion compared to the control. In the next stages, we plan to quantify the levels of calcification, collagen, and osteocalcin, another bone-like cell marker of cell morphological change, which might contribute to valve impairment. We will also investigate longer term effects of Runx2 deletion.


Poster Presentation 7

2:40 PM to 3:25 PM
Wireless, Low Cost, Semi-Autonomous Cage-side Training Reward System for Nonhuman Primates  
Presenter
  • Kali Morgan (Kali) Coubrough, Senior, Bioengineering Mary Gates Scholar, UW Honors Program
Mentors
  • Azadeh Yazdan-Shahmorad, Bioengineering
  • Devon Griggs, Electrical Engineering, University of Washington, Seattle
Session
    Session T-7B: Biomedical
  • 2:40 PM to 3:25 PM

  • Other Bioengineering mentored projects (24)
  • Other students mentored by Azadeh Yazdan-Shahmorad (1)
  • Other students mentored by Devon Griggs (2)
Wireless, Low Cost, Semi-Autonomous Cage-side Training Reward System for Nonhuman Primates  close

Training a nonhuman primate (NHP) for research experiments generally requires the NHP to spend large quantities of time learning experimental tasks outside their home environment, and this requires a human researcher to be present at all times during training sessions. The purpose of this project is to create a wireless, semi-autonomous, low cost, cage-side training reward system allowing NHPs to train on experimental tasks for extended periods of time without the presence of a human researcher. An ideal device would allow for wireless data collection and provide both real-time and post-training information on the NHP’s training progress. Exposing NHPs to tasks first in the low-stress environment of their home cage before exposing them to the same task in an experimental booth can potentially speed up training processes. This lets research laboratories maximize researcher time and efficiently use equipment. Our cage-side training reward system consists of an iPad displaying touchscreen tasks, a speaker supplying audial cues for the tasks, an automatic feeder administering treats to the NHP for correct performance, and a computer to control the touchscreen tasks and collect data with custom MATLAB code. The iPad and computer communicate via a Wi-Fi router and this router also communicates with a Wi-Fi receiver which runs the feeder and speaker. The connection methods give the ability for wireless communication through walls, allowing the researcher to run tasks semi-autonomously from a computer outside the animal room. Excluding the costs of the iPad, computer, and MATLAB license, the system is estimated to cost under $300. Two rhesus macaques have undergone cage-side training with this device and have subsequently transitioned smoothly to learning tasks in a traditional experimental booth. In conclusion, this device serves as a low-cost method to enhance the training process for non-human primates while saving time and resources of the research laboratory.
 


Engineering a Multilayered Perfusable Tissue Construct that Integrates Two Different Vascualrization Techniques.
Presenter
  • Jason Fox, Senior, Bioengineering
Mentors
  • Ying Zheng, Bioengineering
  • Nicole Zeinstra, Bioengineering
Session
    Session T-7B: Biomedical
  • 2:40 PM to 3:25 PM

  • Other Bioengineering mentored projects (24)
Engineering a Multilayered Perfusable Tissue Construct that Integrates Two Different Vascualrization Techniques.close

In a given year, a combined surplus of 20,000 transplants are performed in the US for patients requiring a new kidney, liver, or heart, and the need for these organs continues to increase rapidly with changes in societal and cultural outlooks on personal behavior. Recent regenerative medicine techniques have been implemented in attempts to create engineered tissues that support solutions to these problems, yet they are limited to thin or avascular tissues. In order to create thicker tissue constructs for implantation, vascular networks must be introduced to supply nutrients and oxygen to highly metabolic tissues. Yet, current methods can be expensive or require high-tech equiptment. To address this issue, this project aims to design a construct that integrates two vascularization techniques into a multilayered tissue. This new design of a thicker tissue will benefit from the advantages of both independent systems, endothelial cords and perfusable, patterened microvessels, advancing the tissue engineering field.


Poster Presentation 8

3:30 PM to 4:15 PM
The Impact of Wi-Fi Energy on EZ-Water Development
Presenter
  • Jay Lee, Senior, Bioengineering Mary Gates Scholar
Mentor
  • Gerald H. Pollack, Bioengineering
Session
    Session T-8E: Engineering
  • 3:30 PM to 4:15 PM

  • Other Bioengineering mentored projects (24)
The Impact of Wi-Fi Energy on EZ-Water Developmentclose

Water is the substance that exists everywhere in our lives ranging from drinking water to the blood in the body. It is well known that there are 3 phases of water: gas, liquid and solid. Yet, in Dr. Gerald Pollack’s lab, we conduct researches on the Exclusion Zone (EZ) water, which we term as the ‘Fourth Phase of Water.’ Dr. Pollack’s lab centers largely on the identification of EZ water and many applications in nature and technology. Among the natural applications, the lab emphasizes on the role of EZ water in human health, including cell biology since cells are filled with EZ water and cannot function without enough EZ water. Dr. Pollack’s lab conducts the research uncovering the nature’s hidden secret that has tremendous potentials to be applied to different bioengineering products. I am currently conducting a project on how Wi-Fi impacts EZ water as an external source of disturbances. Humans are exposed to Wi-Fi signals constantly in our everyday lives. As human body cells are filled with EZ water, we predict the Wi-Fi signals could alter our bodily functions through changes in EZ water properties such as amount of EZ water. EZ water develops around hydrophilic substances, and we uesed blood vessel-like tube to observe EZ water development. Then, we measured the amount of EZ water and analyzed the data. For this project, we compare the difference in the amount of EZ water built with and without presence of Wi-Fi. We currently have statistically significant results that Wi-Fi decreases amount of EZ water developed by ~18%. As a further step in the future, we are investigating on how different types of disturbances such as cell phone impact on EZ water for further health care.


filter_list Find Presenters

Use the search filters below to find presentations you’re interested in!













CLEAR FILTERS
filter_list Find Mentors

Search by mentor name or select a department to see all students with mentors in that department.





CLEAR FILTERS

Copyright © 2007–2026 University of Washington. Managed by the Center for Experiential Learning & Diversity, a unit of Undergraduate Academic Affairs.

The University of Washington is committed to providing access and reasonable accommodation in its services, programs, activities, education and employment for individuals with disabilities. For disability accommodations, please visit the Disability Services Office (DSO) website or contact dso@uw.edu.