This research explores the underrepresentation of students of color in the STEM fields, focusing on the University of Washington as a case study and examining retention, representation and inclusion. In recent years, there has been a push to graduate and increase the number of students joining the STEM work fields in the U.S. The completion rates of STEM students, especially students of color, has increased concern. A study found that only 37% of students studying a STEM major completed their degree. That percentage is much smaller when students of color are taken into account. When education prior to college comes into play, studies have noticed that many of these students may not have the chance to consider STEM because of the lack of resources and opportunities in their middle schools, high schools and even as early as elementary school. This is a problem because pre-college achievement and participation in STEM go hand in hand. I have examined change over a 10 year period at the UW and compared my findings to the change on a national level. To understand the trend of underrepresentation of students of color at our school, I have collected quantitative and qualitative data in various forms including data from the UW president and offices. It's believed that students of color simply are not interested in STEM or college but this is not the case. My research explores the access of STEM for students of color, representation and exposure and specifically takes a look at retention, representation and inclusion within the UW system.

lncRNAs play a wide range of cellular functions, and the roles they play in cell maintenance are of increasing importance. An unusually conserved lncRNA, OIP5-AS1 (known as Cyrano), plays a crucial role in stem cell differentiation and development. It has also been shown to interact with the miRNA miR-7 and the protein HuR. Although there is growing information about interactions of Cyrano, truly understanding this lncRNA’s function is hindered by the lack of structural information. To gather information on the structure of the evolutionary conserved region of Cyrano, the secondary structure was elucidated using SHAPE and RNA prediction software. A 4-way junction was observed when assessing these data. The 2D predictions were used as constraints to generate 3D models of the 4-way junction. Overall, three separate prediction software generated topologically similar 3D models of Cyrano (RMSD range of 13.362 Å). These models produce a 4-way junction with 2 coaxial stacked helices (H1H2, H3H4). These modeled structures suggest a Family cH 4 way junction, where H1 and H3 interact forming an A-minor interaction between junction J(1,2) and Helix H3. This model is important as it aids in directing future experimental approaches for studying Cyrano, and also hint at a potentially important structural motif for Cyrano function.

This research project is part of the Puget Sound Foraminifera Research Project at the Burke Museum, which uses benthic Foraminifera to measure and assess anthropogenic impacts and mitigation efforts in Puget Sound. Benthic Foraminifera, shelled marine protists, are readily preserved in sediments and can be very sensitive to their environment, allowing us to use them as a proxy for changes in marine ecosystems. My project looks at mismatches between Foraminifera that were living and dead at the time of collection to determine whether these discordances can be used to measure anthropogenic ecological change in Puget Sound. In addition, it attempts to validate the use of assemblages containing only dead Foraminifera which were used in the past. Anthropogenic ecological change is a widespread problem and is difficult to measure both the rate of changes and the success of efforts to mitigate problems. We look at Foraminiferal assemblages to establish the health of benthic ecosystems. Sediment samples used in this project are collected by the Washington State Department of Ecology in their annual sampling program. For this particular project, 12 samples from Sinclair Inlet and Bellingham Bay, were collected in Spring of 2015, 2016 and 2017. The Foraminifera were stained with Rose Bengal to identify those individuals that were living at the time of collection and identified to species. The species assemblage from each was then assessed to establish ratios of living to dead individuals and see if the dead population is representative of that of the live population. Results to date indicate that all samples from Sinclair inlet have a smaller ratio of living to dead Foraminifera than other bays. Because the ratios were radically different it may be possible to establish an index to classify embayment health based on live-dead ratios of Foraminifera individuals to use in future assessments.

This project aims to create a comprehensive park master plan for the transformation of the City of Westport, WA’s Pacific Ave property into a functional public park by utilizing principles of ecological restoration and community-based restoration. The City of Westport recently finalized its Comprehensive Park and Recreation Plan. Within the plan, the Pacific Ave property is zoned as a park, but is not currently used as a public park and has no intention of redevelopment by the city in the near future. The underutilized site has served many important uses throughout its history, and is located on the shore of the Elk River with a beautiful panoramic view of the bay and the mountains. The master plan is focused on research regarding site restoration with an assessment of the needs of both the community and the City of Westport. The information gathered through research and community engagement meetings will be synthesized into a master park plan for the Pacific Ave Property that will be presented to the Westport City Council in order to pursuade them to pursue funding for the project. This parcel holds historic and aesthetic value, and with restoration, it can be turned into a unique and valuable asset for both the city and the community.

This research explores the questions: How is identity shaped by our built environment? Can storytelling along with physical movement alleviate place attachment? This research also seeks to preserve the historic identity of Seattle's central district neighborhood through the memories of its residents. It is my hope that by understanding the relationship between the built environment and human consciousness, I will learn how to design spaces that nourish the human soul while honoring it physical history. To examine these questions, I conducted an extensive literature review on theories about place and identity, and the human experience of place. I also published an online survey and conducted ten oral interviews of central district residents. A composite walking tour was then created from the physical places in their stories to highlight the overlap in their experiences, values, and identities. Through storytelling, archival research, observation, field research, map making and physical movement in these spaces, I have demonstrated a connection between memory, history, and place. My final product, a narrated walking tour, serves as a mechanism to bring people together, to educate the public about the central district and to highlight the interplay between spatial geography and social identity. The tour conjures lost places and memories into the physical world and diminishes feelings of place attachment. The tour also serves as an urban planning tool to heal displaced communities. As Seattle continues to grow and change, experiences such as this walking tour provide a living, breathing example of our shared history to anchor old residents while inspiring new citizens to honor our natural and built environment.

Clayoquot Sound is an estuary on the west coast of Vancouver Island, BC, Canada composed of a series of fjords. Given the complex topography and bathymetry of this region, many of the inlets are susceptible to periodic hypoxia/anoxia, as well as dramatic spatial and temporal fluctuations in oceanographic properties which influence local primary productivity. University of Washington Tacoma has been collecting water property data, phytoplankton, sediment and plastics samples in Barkley and Clayoquot Sounds since 2001. In the fall of 2014, Pacific Northwest estuaries experienced an anomalous warm water intrusion (“the blob”) from the upper eastern Pacific Ocean. For this presentation, annual pre- and post “blob” time series of autumnal phytoplankton assemblages for Tofino Inlet within Clayoquot Sound will be compared for 2013, 2014, and 2016. A seasonal comparison of the fall 2016 phytoplankton community with spring 2017 phytoplankton data from Tofino Inlet will also be presented. Further comparison of the temporal inshore phytoplankton dominance and abundance data from Clayoquot Sound will be made with summer offshore Vancouver Island shelf data collected via ships of opportunity in 2017. Primary productivity due to the diversity and distribution of phytoplankton, including harmful algal species, impact local aquaculture which is an important economic industry in the region.

If you're tiling a circular room with square tiles, how many do you need? What if your tiles are parallelograms? As the circle gets larger, is there a pattern? Mathematically, this can be framed as counting integer points in a large circle. We're interested in how this count changes as you change the shape of the tiles, and to understand this better, we started by counting the number of integer vector pairs within a ball of radius R so that the parallelogram they make has a fixed area (determinant). We created a Python program that would generate all of the primitive points out to radius R, which we then extended to count the number of vector pairs with a certain determinant k. We were able to compute the limiting density of this count, extending known results for the case of determinant 1. We are now studying other discrete sets, such as ones generated by objects from hyperbolic geometry, known as Hecke triangle groups. In the future, we plan to use our research for counting pairs of vectors in different spaces and generalize it for counts of k-tuple vectors. Come for floor tilings, stay for beautiful pictures!

The majority of urinary tract infections are caused by E. coli bacteria. E. coli infections are strengthened due to E. coli’s ability to bind to mannosylated cells. A receptor protein on E. coli, FimH, has two domains: a regulatory pillin domain and a lectin domain (LD). In the presence of a force, the pillin domain detaches from the LD allowing the LD to go from its low to high affinity state. The naturally occuring mannose sugars on Horseradish Peroxidase (HRP) are known to bind the LD of FimH. The mannose binding pocket is suspected to open transiently, even when bound to mannose sugars. Based on the interaction of HRP with FimH, HRP may not regularly dissociate during these episodes, but we suspect that free mannose can induce the dissociation of HRP from FimH in these moments. To determine if mannose can improve HRP dissociation from LD, we are using an assay similar to a competitive Enzyme Linked Immunosorbent Assay. We expect to see a decrease in HRP bound to LD in the presence of free mannose compared to the absence. Ultimately this experiment provides an explanation of mannose monomers as an inhibitor for longer chains of mannose binding and a premise for a larger study on alternatives to E. coli antibodies that can competitively inhibit FimH from binding mannosylated cells.

APOBEC3G (A3G) is a host protein that acts as a cytidine deaminase to inhibit HIV replication as part of the innate immune system. A3G has been shown to cause Guanine to Adenosine hypermutation. This host protein cannot deaminate the proviral HIV DNA because of the HIV accessory protein Vif. The Vif protein interrupts the antiviral activity of A3G by inducing ubiquitination and degradation via the host proteasome. In this project, we investigated the deamination ability of A3G and deamination inhibition ability of Vif in vivo. While much of the published work on A3G has involved the investigation of Vif-induced A3G degradation, bacterial models have also revealed a degradation-independent mechanism of A3G inactivation by Vif. We looked for direct inhibition of A3G deamination ability by Vif in vivo. We found that the deamination of the proviral genome was correlated with the concentration of A3G in both NL4-3 and NL4-3 (vif-) strains. Unexpectedly, we observed deamination in the viral genome, in NL4-3 at higher concentration. In comparison, packaging of A3G into NL4-3(vif-) virions caused much larger amount of deamination than in Vif-expressing NL4-3 virions. In the case of wild-type NL4-3, the virus remained infectious despite significant levels of deamination. This represents a novel phenomenon that suggests that the Vif protein has an additional function within the viral replication cycle. Our results, although preliminary, set the stage for a more extensive analysis that may provide novel insights into the biological function of Vif. By studying A3G and Vif interactions in vivo, we are getting closer to understanding the viral replication cycle as it occurs in the human body. By understanding the complete range of function of Vif, new antiviral therapies could be developed to target Vif.

The Jasmonic Acid (JA) sensitive system is an important stress and pathogen resilience pathway in plants. Understanding the kinetics of the components of this system allows for a more rational approach to improving crop resilience than traditional breeding.  MYC transcription factors upregulate the expression of particular defense or stress response genes, and these are inhibited by JASMONATE-ZIM-DOMAIN (JAZ) proteins, which are in turn degraded in the presence of JA-Ile, the bioactive form of JA. This leads to a system whereby MYC transcription factors are only active when JA-Ile is present. The variable defenses plants are capable of mounting may be regulated by differential interactions between some of the 12 JAZ proteins and 3 relevant MYC proteins in Arabidopsis thaliana. We have used a fluorescent yeast model to characterize the differences in those interactions in order to predict changes in plant responses when particular JAZ proteins are up or down regulated. Although we have been unable to replicate the canonical direct repression of MYC transcription factors by JAZ proteins, repression was observed when the JAZ protein was fused with an Mxi1 repression domain. This allows us to determine the relative effect of each JAZ protein on MYC transcription factors. A rough model involving related Hill functions is built using this information which can be used to predict the effect on the downstream response based on the abundance of the different JAZ proteins. The model can then be verified in planta using a dCas9 transcription factor with an appropriate gRNA, and a MYC-responsive GUS gene in a transient transformation.

It is not fully known what controls signal preference in branched signal transduction pathways. One hypothesis is that the configuration and orientation of receptors determines signal preference. We are investigating this hypothesis in the context of the Tie2 receptor pathway which has downstream signaling involved in cell survival via Akt, migration via Dok-R, and sprouting via FAK, among other branches. We are using computer designed protein tools, short-armed claw trimers and nanocages, conjugated to F domains of the canonical Tie2 ligand angiopoietin 1 in our investigation. We have shown that short-armed claw trimers with three conjugated F domains do not yield increased phosphorylation of Akt, suggesting that more than three receptors must cluster together for signal activation. The nanocages are multivalent, for they have multiple F domains conjugated to them. We have different valency nanocages with different percentages of F domain conjugation. We are using these different valency nanocages to investigate which valency is optimal for receptor activation. We have shown that higher valency nanocages yield increased phosphorylation of Akt. We predict that higher valency nanocages cluster more Tie2 receptors together in a specific conformation. Thus, we show a positive correlation between Tie2 clustering and the phosphorylation of Akt due to Tie2 activation. Now we will investigate combination conjugations of F domain and integrin binders to the nanocages as well as other branches of the Tie2 pathway: Dok-R corresponding to wound healing ability and FAK corresponding to tube formation ability. This work has potential to help generate therapeutic compounds for wound healing.

The development of tubes is a conserved process observed in a wide variety of species; tubes contribute to structures such as neural tubes, digestive systems, and vascular systems. For a tube to form correctly, individual cells within a sheet of cells (epithelium) must move and change shape in very specific ways. My goal is to understand what controls this movement. Polarity proteins help to establish the directional identity of cells and tissues. This identity is important to ensure that cells coordinate their behaviors. I hypothesize that the proteins that help establish polarity also play key roles in the development of tubes, including in proper closing of the tubes and correct directional elongation. To study the involvement of polarity proteins during tube formation, I am using the dorsal appendages (DAs) on Drosophila melanogaster egg shells. Because the appendages form as a direct readout of morphology, I can see how tissues developed earlier on. These appendages, which provide the developing laid egg with oxygen, are formed from an epithelium that wraps and elongates into a tube, then fills with eggshell protein; the initial epithelium sloughs off, leaving the appendages as a visualization of the earlier tube formation. To test my hypothesis, I am using RNA interference (RNAi) to knock down the expression impact of various proteins and evaluate the impact on DA formation. The RNAi system induces transcript loss, eventually revealing the impact of protein loss. I am using RNAi in epithelial follicle cells to test 20 candidate polarity genes. This analysis will help me identify a few genes to then characterize further. These results will inform future studies and add to the knowledge of the role of polarity proteins in the patterning and subsequent growth of epithelial tubes across many species.

In the traditional sense, preservation of architecture has been around for centuries. With changes in warfare, increased human rights abuse, and impending climate change, many architects and theorists are being confronted with a need for new perspectives on preservation. This project aims to expand the idea of preservation within the field of architecture by examining three contemporary case studies, all prompted by violence or the threat of destruction. The first case study introduces the work of Andrew Herscher in the context of the Kosovo conflict. Herscher, a self-proclaimed preservationist, is an advocate for the protection of heritage sites. His work examines the evolving definition of “heritage,” particularly through cultural preservation. Another contemporary group, Forensic Architecture, a University of London architectural research agency, examines areas of conflict and reconstructs structures through computer modeling with the intent of legal prosecution of war crimes and increased public awareness. The theories of its founder, Eyal Weizman introduces and lays the groundwork for their 2016 examination of Saydnaya, a Syrian military prison. This case highlights the importance of witness testimony in reconstructing architectural models which preserve the memories of survivors and act on their behalf as material witnesses. The final example highlights the exhibition from the 2016 Venice Biennale, A World of Fragile Parts. This show examines the role of replication in preserving structures threatened by violence as well as climate change. Within this, the work of architect Sam Jacobs is integral, particularly his concrete caste reconstruction of a typical refugee shelter. The implications of this example on the field of preservation serves as the final point of study. A new sense of urgency, in the wake of violence as well as climate change, is challenging architects to question what moments in history should be preserved, honored or forgotten.

Gene expression constitutes the foundation of all cellular processes. The general transcription factor (TF) complex, TFIID, is essential for the proper execution of gene expression, as it binds to the promoter region of genes and initiates the recruitment of RNA Polymerase II to begin transcription. The TAF1 protein is the largest subunit of the TFIID complex and possesses histone acetylation activities. Our lab and others have shown that TAF1’s ability to bind to acetylated histones is critical for regulating key steps in gene transcription and cell cycle progression. Whole genome and exome sequencing of individuals diagnosed with intellectual disability has revealed mutations in the TAF1 gene. This project is interested in introducing a disease associated missense mutation (S1600G) into TAF1 to investigate its functional consequences using biophysical approaches. We used polymerase chain reaction to amplify the domain of TAF1 containing the missense mutation. The produced product was inserted into an expression vector with an N-terminal histidine tag for purification and the resulting plasmid was transformed into competent bacterial BL21 cells for protein expression. The TAF1 protein was extracted and then purified from bacterial lysates. The purified wild type and mutant proteins will be compared using functional biophysical analysis. By using Bio-layer interferometry, an optical analytical technique for measuring binding between two molecules, we can measure the interaction between TAF1 and histones in real time as indicated by different shifts in interference patterns. Any change in the number of histone molecules bound to the TAF1 protein immobilized on the biosensor tip causes a shift in the interference pattern that can be measured as an indicator of how the missense mutations affect histone binding activity. Ultimately, significant deviance from normal histone binding activity will be an indicator of functional disruption due to these specific missense mutations possibly causal for the disease phenotype.

Reactive oxygen species (ROS) are byproducts of photosynthesis that can damage plastid DNA (ptDNA), and 8-oxoguanine (8-oxoG) is the most common DNA lesion. Our lab previously showed that maize ptDNA damage, in general, increases during the development of non-green proplastids to green, photosynthetic chloroplasts. The objective here is to determine the amount of 8-oxoG in ptDNA during plastid development under light and dark growth conditions. DNA damage will be assessed using a semi-long qPCR procedure and the enzyme formamidopyrimidine DNA glycosylase (Fpg) which selectively removes 8-oxoG lesions. Testing of the semi-long qPCR method was performed with control DNA treated with damage-inducing UV light. After UV treatment, PCR amplification decreased, as expected for Taq DNA polymerase inhibition by bulky lesions. PCR amplification of ptDNA also decreased after UV light treatment of light-grown, dark-grown, and dark-to-light transferred seedlings. When ptDNA was extracted from plants grown in these three conditions, treatment with Fpg affected the PCR amplification, indicating removal of 8-oxoG lesions. 8-oxoG will now be assessed along the developmental gradient from proplastid to mature chloroplast. We may find more 8-oxoG lesions in mature chloroplast due to high ROS from photosynthesis than in the undeveloped proplastids, as well as more 8-oxoG in light than dark growth conditions.

Misinformation has flourished in the wake of the internet boom. Due to the increased velocity and volume of the information being generated, accurate and efficient identification of misinformation is a high priority for fact-checking organizations. Snopes.com, “the oldest and largest fact-checking site on the internet”, crowd-sources reports from their large user base to inform their journalists about which topics to cover. In this study, we analyze methods for increasing both the quantity and quality of user submissions. We decrease the cognitive load imposed by the Snopes reporting system through a simplified user interface. We also utilize clustering and labeling techniques to aggregate user reports and make them more actionable. To collect initial data for our study, we enhance the user experience and metadata collection of a web-based content reporting system used by Snopes. We develop an analytics framework to clean and aggregate the reports, with the goal of decreasing the lag between initial rumor creation and the response from Snopes. We develop metrics based on article metadata to quantify rumor virality and corresponding Snopes rebuttals. The results of this study show improvements to the process of collecting data that informs fact-checking organizations. Our methods reduce the manual curation required by fact-checking journalists, which enable them to reallocate their resources to debunking rumors.

Lateral flow tests are assays conducted on porous media, commonly referred to as paper, that can detect and quantify analytes in a sample. They have the potential to return results within minutes and can be used in low-resource or non-medical settings. Protein adsorption is critical in these tests because protein interaction with a media can affect the delivery of reagents or choice of blocking agents to prevent nonspecific binding. A computational model of the fluid and adsorption physics may improve the development of paper-based assays. Yet-to-be-published data from the Yager group evaluates protein adsorption based on the deposition and analysis of protein spots on paper. The computational model used is derived from Darcy’s law, commonly used to model fluid flow in porous media and to calculate volumetric flow rates. This model makes two main assumptions: the porous media is fully saturated, and there is zero outflow on the boundaries of the media. These assumptions are not applicable because the protein spot dries as a result of evaporation, creating a non-zero outflow at the surface of the paper. The saturation level in the paper will also vary therefore Darcy’s law is not an adequate representation of the paper. My project aims to develop a more accurate computational model of fluid and protein absorption dynamic by modeling protein spots on paper. I incorporated an evaporation component that will allow the use of Richards equation to model fluid flow, which applies to unsaturated conditions. This is coupled with a protein transport and adsorption component to achieve a complete model. Although literature on evaporation from sand or soil is abundant, these results cannot be directly applied to evaporation from paper. This model will aid the diagnostic community in better understanding their assays and ultimately help improve the sensitivity and specificity of their assays.

Many membranes spontaneously demix into coexisting liquid phases. These include membranes that are as simple as three-component lipid vesicles and as complex as protein-rich vacuole membranes within living yeast cells. The resulting membrane phases are enriched in particular lipids and proteins. Membrane phase separation is one of several mechanisms proposed to explain the observation of heterogenous distributions of lipids and proteins in cell membranes ("rafts"), which are thought to be important in cell signaling, apoptosis, and protein regulation. The overwhelming majority of experiments that probe phase separation in membranes uses only one type of lipid (namely phosphatidylcholine). However, it is known that biological membranes also contain significant fractions of other kinds of lipids (e.g. phosphatidylethanolamine, or PE-lipids). An experimental challenge is that membranes composed of high fractions of PE-lipids are unstable – the lipids assemble in tubes instead of lying in sheets. In my project, I am [1] determining the maximum amount of saturated and unsaturated PE-lipids that can be incorporated into stable membranes, [2] measuring the temperature at which the membranes demix into coexisting phases, and [3] imaging the vesicles by fluorescence microscopy. Results from Aim 1 inform future researchers which lipid ratios they can use to produce stable membranes. Results from Aim 2 provide data against which the scientific community can calibrate molecular dynamics simulations. Results from Aim 3 provide a direct test of a recent prediction that PE-lipids should be anti-registered across fluctuating membranes.

UW Solar is an interdisciplinary student-led organization committed to developing solar infrastructure projects at the University of Washington. Solar arrays on campus not only produces clean renewable energy, but also helps the UW meet its carbon neutrality goals of its Climate Action Plan while providing a sustainable return on investment. UW Solar is working with UW Sustainability to maximize solar capacity on campus in support of the first UW Sustainability Plan to achieve the goals of the UW Climate Action Plan. Therefore, UW Solar is proposing a multi-phase plan for solar development at UW Seattle which aims to maximize solar capacity while providing a positive return on investment for Capital projects. UW Solar assessed all buildings on campus, and has identified the top 30 projects to be developed over the next 30 years to meet the UW’s 2050 Carbon Neutrality Goals. UW Solar’s scope of work for the Campus Plan includes the evaluation of all buildings on campus for potential solar installations and ranking them based on a suite of criteria that takes into consideration the following: energy generated, financial value of energy generated, cost of installation, return on investment, identifying funding options, working with campus stakeholders to develop the solar plan and timeline, assisting with schematic design, selection of contractor, oversight of installations, monitoring of energy generated for research and education. The total solar capacity for the Seattle campus could reach 8,000,000 kWh/year, with an annual energy value savings of $600,000. UW Solar will continue evaluating buildings on campus and working with all stakeholders to decide the priority of solar installations over the next 30 years.

For many rising metropolitan cities across the United States, the implementation of a major mass-transit system is a potential means of combating unemployment by connecting citizens to jobs that might be otherwise inaccessible. However, relatively little is known about how the effects of mass-transit systems scale with population density, which may deter many cities that stand to gain from investing in such a project. This study examines the effect of population density on the impact of Commuter Rail, Light Rail, and Street-Car transit systems on unemployment rate across every metropolitan city in the United States, in order to enable more informed policy and investment decisions. In applying a difference-in-difference regression model to panel data that spans 192 cities from 1990 to 2016, it is revealed that the introduction of a mass-transit system results in a 19% average decrease in unemployment rate. In addition, it is shown that the existence of a mass-transit system reduces the effect of each percent increase of population density in driving up unemployment by 64%. This study’s findings underscore the viability and effectiveness of mass-transit infrastructure as a means of combating rising unemployment rates by providing citizens with a cheap and consistent method of connecting with a wider selection of job opportunities.

Effective communication between critical care nurses, physicians, and other team members responsible for Neurocrital Care is essential for maintaining the quality of patient care. The volume of and importance of communications between team members creates opportunities to optimize currently utilized communication systems. Analyzing approximately 40,000 unique records of recent communications data enabled the project to develop with a better understanding of current usage patterns of existing communications systems. Input on communications preferences and current limitations were obtained anonymously from critical care clinicians and proved instrumental in the design of new proposed communications expectations. These will be implemented alongside measures to boost adoption and consistency of new procedures.

Necroptosis is a lytic and immunogenic form of programmed cell death (PCD), characterized by pro-inflammatory cytokine production and the release of intracellular molecules, including cell-associated antigens. This form of death occurs after RIPK3, Receptor-Interacting Protein Kinase 3, activation. RIPK3 is a cell death regulator that promotes necroptosis. Previous studies have shown that necroptotic cells can promote maturation of antigen presenting cells (APCs) and are capable of priming antigen-specific CD8+ T cell responses. Understanding the downstream immunogenic effects of necroptosis allows for implicative applications within the field of tumor immunology. Previous work has shown that necroptotic NIH-3T3 fibroblasts produce inflammatory cytokines and chemokines, contributing to their immunogenicity. To recapitulate the immunogenic nature of 3T3s, we evaluated inflammatory chemokine and cytokine production via ELISA (enzyme-linked immunosorbent assay), quantifying these productions through antibodies and color-change, from necroptotic tumor cell line supernatants, including B16.F10 melanoma and LL/2 adenocarcinoma cells. Surprisingly, our results did not show significant chemokine or cytokine production from necroptotic tumor cells, suggesting that anti-tumor effects are not from signals derived from the tumor micro-environment (TME). This suggests that other forms of signaling downstream of RIPK3 activation, such as upregulation of non-chemokine transcriptional programs, could be the source of inflammatory signal production by necroptotic tumor cells. Further actions include RNA sequencing of necroptotic cancer cell lines to differentiate global changes between apoptotic and necroptotic forms of cell death, to provide unbiased analysis of transcriptional changes. With evidence of T cell-mediated immunity and the immunogenic nature of necroptosis, induction of this form of cell death within the TME will activate anti-tumor immune responses, potentially controlling tumor growth and contributing to the field of immunotherapy.

Standard medical practice does not consider a lateral leaning uterus to be medically relevant. However, many indigenous cultures globally have used uterine abdominal massage to correct a “displaced” uterus to enhance fertility. A leaning uterus could theoretically interfere with ovarian function. Additionally, Research indicates that the circulatory functions, the autonomic innervations of the uterus, and pelvic vein incompetence may negatively affect ovarian function, and fertilization. This study examines a population of 30 U.S. fertility patients undergoing ovarian stimulation for an In Vitro Fertilization (IVF) procedure (an assisted reproductive medical technique used to assist with the conception of a child). We will identify differences in the quantity, and size of follicles that are produced by the ovaries of patients with a leaning uterus. At the beginning of a patient’s IVF cycle, researchers will palpate the lower abdomen to determine the position of the uterus. After the patient completes their series of gonadotropins, prescribed hormones used to stimulate follicular growth in the ovaries, physicians will record the number, size, and location of each follicle observed. We predict that a laterally leaning uterus reduces follicle number and size. If our results identify a correlation between uterine displacement and follicle development, then additional research should explore potential causes. A positive correlation would also suggest that complementary treatment options for a laterally leaning uterus should be investigated.

This presentation reports polymer-based apparatus with embedded flexible thin-film electrodes to monitor electrocardiogram (ECG) of zebrafish under mild or zero anesthesia. The apparatus were made of polydimethylsiloxane (PDMS) using the molding technique with molds formed by 3D printing. The system is capable of acquiring intrinsic ECG from multiple fish simultaneously, thus introducing a novel method to phenotypically assess the hearts’ functionalities, supporting heart regeneration studies, drug screening and other related bio- investigations using the zebrafish model. Smart algorithms were developed to facilitate data processing and analyses. The recorded ECG was compared with that of the same fish under full sedation and a proof-of- concept 4-chamber system was demonstrated. The process does not require a cleanroom, therefore being cost effective and holding promise to accelerate numerous studies in various disciplines using the zebrafish model.

The removal of contaminants from aqueous media is a challenge faced in many engineering systems. In particular, fermentation processes during biofuel production is hampered by a variety of toxic compounds present in hemicellulosic hydrolysates. Adsorption is an efficient and economic method of reduction in the amounts of phenolic compounds, acetic acid, aromatic compounds, furfural and hydroxymethylfurfural normally found in hemicellulosic hydrolysates. Activated carbon is currently the most widely used adsorbent. However, its poor reusability and its limited capacity to uptake larger molecules due to size exclusion effects necessitate the investigation into alternative materials. Carbon nanomaterials exhibit high specific surface area and open pore structure, making them very compelling for hydrolysate detoxification. To overcome the tendency of carbon nanomaterials to aggregate, which greatly reduces the number of sites available for adsorption, we developed mesoporous, nitrogen-doped, reduced graphene oxide aerogels with an open three-dimensional network. Graphene oxide was first prepared from renewable carbon sources and reduced by hydrothermal treatment to form hydrogels, which were then freeze-dried in tert-butanol to form aerogel sorbents. By adjusting the different synthesis parameters (i.e. temperature, pH, chemical dosages…), we were able to finely control the pore structure and chemical composition of the nitrogen-doped graphene aerogels, as measured by nitrogen physisorption and elemental analysis. Results revealed superior adsorption properties than activated carbon for the hydrolysate detoxification, which improved fermentation yields.

Autism spectrum disorder (ASD) is a developmental disorder in which children have difficulty with intercommunication, repetitive and restrictive behaviors, and atypical sensory processing. The CDC reports ASD is about 4.5 times more prevalent in males than in females. Less is known of gender differences in diagnosis and symptoms like atypical sensory processing. In a study of sensory behaviors in adults with ASD, females scored significantly higher in “unusual sensory response”. In past studies higher sensory processing sensitivities in ASD have been connected to more externalizing behaviors. This study’s aims are to: (1) compare sensory processing of typically developed (TD) children with children diagnosed with ASD, (2) determine if there is a difference in sensory sensitivity between females and males with ASD, (3) examine the relationship between sensory sensitivity and externalizing behaviors in adolescents with ASD, and (4) explore gender differences in the correlation between the two. 102 children with ASD (45 females, 57 males) and 105 TD children (57 males, 48 females) aged 11 to 17 completed the self-report adolescent Dunn Sensory Profile which asks about sensory related behaviors. Participants’ parents completed the Child Behavior Checklist, which provided scores of externalizing behaviors. We predict the children with ASD will have significantly greater sensory sensitivity than TD children, females with ASD will show more sensory sensitivity than males with ASD, and greater sensory sensitivity will relate to more externalizing behaviors. We will explore potential gender differences in correlation of externalizing behaviors and sensory sensitivity. Through this study, differences in the way males and females with ASD process sensory information and its relation to behavior may be found, furthering our understanding of gender differences and behaviors in ASD.

To appreciate where blockchains fit into the history of the internet, we must consider the three different generations of the Internet. Initially, the Internet of the late 20th century is a period of decentralization with very little integrated security. Conversely, beginning in the 21st century, we entered a period characterized by large, centralized repositories of information. Given the cyclical nature of this system, blockchain is anticipated to spur the next era of the Internet called Web 3.0, as a decentralized ledger providing provenance of data through foundational cryptography.This project constitutes an exploration into the uncharted territory of designing and implementing economic contracts on a blockchain, a new form of infrastructure serving as a framework to build applications. We employ game theory to design these systems in the Ethereum blockchain ensuring that economic incentives lead to efficient interactions, with the blockchain as an unalterable proof. The goal is to establish the usefulness of this public blockchain, in a financial process traditionally carried out by an intermediary called an escrow, implemented in the programming language called Solidity with accessible code and replicable results. Careful induction of blockchain technology will serve to complement existing technology allowing professionalsto focus on higher-order tasks while also increasing business decorum through improved transparency.

Prior research has shown that virtual reality (VR) has great promise as a science and engineering teaching tool at the primary and secondary school levels. Unfortunately there is little VR educational content for schools since the education marketplace is poorly funded. Our objective is to solve this problem by teaching middle school students how to build their own immersive 3D virtual worlds that can used as teaching aids for other students and schools. To investigate this approach we are working with Robert Eagle Staff Middle School in an after-school engineering club teaching world building tools and processes to 6th graders. We have organized the students into four teams to create VR games that teach STEM concepts including scale, gravity, light, and momentum. University of Washington engineering students are assigned to mentor these teams while serving as role models to the middle school students.The middle school students not only learn world building techniques but also understanding of these STEM concepts well enough to teach others. To create the VR games, we are instructing the students how to use Unity3D as a game engine. The virtual worlds will operate in real time on the HTC Vive VR headsets with high-end Intel-powered computers. In addition to the world building efforts student learn how to set up, configure and operate the technology within the VR workspace at the school. Our final product will be both the educational content designed by the students but also a prototype of the way to do it. We are documenting our findings in scholarly reports and a documentary film that can be used to inform schools across the nation of how to use virtual reality as a teaching tool and to build a repository of virtual worlds that can be exchanged across schools.

Parasite burden can vary over time due to a variety of factors, including environmental change, competition, and niche differentiation. Clavinema mariae is a parasitic “blood worm” nematode that affects several species of commercially important fishes in Puget Sound, living below their skin and feeding on their blood. C. mariae burden increased dramatically in English sole, Parophrys vetulus, from 1930 to 2016, but it is unclear whether this same pattern affected other host species, including the southern rock sole, Lepidopsetta bilineata. I used rock sole specimens from the Burke Museum’s Ichthyology Collection to determine whether the burden of C. mariae changed over time in this host species. I examined preserved specimens that were collected from various locations in Puget Sound in the period of 1930 to 2016, taking note of the abundance of C. mariae in each individual. Creating a timeline of the parasite’s abundance helps us to narrow in on the various factors, such as fishing pressure, climate change, and nutrient pollution, that may influence C. mariae abundance. Parasite burden can negatively impact commercial fisheries and the overall health of the environment, making this study important for both economic and conservation purposes.

Non Hodgkin Lymphoma (NHL) affects over 70,000 people in the United States each year. Inappropriate activation of B-cell receptor signaling is associated with NHL, and therapies that target this pathway are showing promising results in the clinic. One example is ibrutinib, a small molecule inhibitor of Bruton’s Tyrosine Kinase (BTK). While ibrutinib has improved the prognosis for the majority of NHL patients, many patients eventually develop resistance to ibrutinib due to mutations in BTK and its downstream target Phospholipase C gamma 2 (PLCG2). Thus, it is important to understand how these mutations affect cell signaling, with the ultimate goal of designing new strategies to mitigate ibrutinib resistance. Previous studies in the James Lab suggest that long-term treatment of cultured cell lines with ibrutinib leads to increased cellular reactive oxygen species (ROS). However, it is unclear if ROS contribute to ibrutinib resistance or if they are a byproduct of other mechanisms that drive resistance. I hypothesize that cells with mutations commonly seen in ibrutinib-resistant patients may also exhibit increased ROS, and these cells may be sensitive to small molecules that regulate ROS. In order to test this hypothesis, I used CRISPR/cas9 gene editing with homology-directed repair to generate lymphoma cell lines that express a leucine-to-phenylalanine mutation in PLCG2. This is a well-described mutation in ibrutinib-resistant patients. Preliminary analysis shows that these mutant cells are resistant to ibrutinib. I measured ROS in these cells by ROS-Glo luminescence. Then, I cultured the cells with ROS-regulating compounds including SOD-1 and NADPH oxidase inhibitors to assess how ROS affect their viability. My goal is to clarify the role of ROS in the acquisition of ibrutinib resistance. These studies may provide justification for further pre-clinical evaluation of small molecule regulators of ROS in lymphoma, especially among subjects with acquired ibrutinib resistance.

In the US, someone needs blood every two seconds, making blood transfusion a frequently performed procedure in hospitals. Transfusion of incompatible blood due to clerical error in clinical blood typing procedures can induce a multitude of life-threatening immune responses in the recipient’s body. The most prevalent typing procedures are based on the overly simplified characterization of surface antigens on an individual’s red blood cells (RBCs) into the commonly known ABO blood type system. However, studies have shown that the antigens embedded in the RBC membrane, comprising of glycolipids and glycoproteins, are structural determinants of variations in the blood type outside of the ABO system, elucidating the limitations of current typing methods. This project follows the hypothesis that gas-phase hydrogen/deuterium exchange (HDX) and ion mobility mass spectrometry (MS) techniques can be employed to characterize and further elaborate the structure of these RBC antigen constituents. To test this hypothesis, genotypically defined donor blood samples undergo an osmotic lysis procedure to obtain RBCs ghosts, which are RBC membranes without the cellular components. Glycoprotein and lipid fractionation, and digestion is employed to isolate carbohydrate components in preparation for MS analysis which provides insight into structural composition of the carbohydrate antigens. Preliminary analysis on the donor samples has suggested the presence of clinically relevant carbohydrate antigens.This knowledge will be crucial in further developing glycobiological sensors that can be functionalized onto silicon chips used by Ratner Lab, facilitating novel blood typing techniques. Through this study, we expect to develop a deeper understanding of the heterogeneity encoded into the carbohydrate RBC antigens which play a critical role in transfusion medicine.

The electrochemical growth of single-crystalline germanium (Ge) nanowires has been previously demonstrated in an aqueous solution for use in complementary metal oxide semiconductor (CMOS) technologies. The motivation for growing these nanowires using electrodeposition is to improve the purity of germanium nanowires relative to traditional synthetic methods. However, nanomaterial growth has been shown to be highly sensitive to both oxygen and water and can lead to impurities, surface layers or morphology changes. . We have grown germanium nanowires in anhydrous organic solution in a nitrogen blanketed electrochemical cell. We have then compared the morphology and material properties of the wires grown in aqueous solution to the wires grown in organic solution to determine the effects of water and oxygen on the wire growth. Improving nanomaterial growth will help in having more efficient computers and cell phones by improving semiconductors.

G Protein-Coupled Receptors (GPCRs) are seven-transmembrane proteins present throughout the body that can be activated upon binding of drugs, hormones, or neurotransmitters. Acting like an inbox for messages, these multi-protein complexes play a significant role in the body by regulating cell expression and signaling, making them attractive targets for drug development. One class of GPCRs, known as the adrenergic receptors (ARs) are critical in modulating the function of numerous targets, including cardiac muscle, vascular smooth muscle, and bronchial smooth muscle. There are nine AR subtypes: three α1s, three α2s, and three βs. In my research, I focus on deciphering the interactions of proteins with the α1D-AR due to a recent publication of the Hague Lab, which discovered that α1D-AR forms a multi-PDZ protein complex. To determine the participants of this complex and identify the presence of associated proteins, I first purified the proteins that potentially bind to α1D-AR. In my purification process, I first conducted Polymerase Chain Reactions (PCRs), transformed my bacteria, grew my bacteria, and finally purified my proteins of interest. With this information, my lab and I intend to identify the complexes using mass spectrometry and Octet. Determining how α1D-ARs are organized can create a deeper understanding of how drugs work in the body and assist in new drug development.

On October 5, 2017, the New York Times revealed sexual harassment allegations against American film producer, Harvey Weinstein. The allegations opened up a floodgate on social media. Actress Alyssa Milano tweeted, “If all the women who have been sexually harassed or assaulted wrote ‘Me too’ as a status, we might give people a sense of the magnitude of the problem.” When networked publics joined in, creating a hashtag, adding their voices, they demonstrated the staggering number of people who have experienced or had something to say about sexual harassment or assault (according to their own definitions). This study examines the cultural and institutional changes created from the hashtag movement. Tweet and retweets with the hashtag #Metoo were collected and analyzed using RiteKit, the social media toolkit. A qualitative analysis was done through tracking the terms “sexual assault,” “sexual misconduct,” “sexual harassment,” or “me too” during the past four months using TheSkimm, an American media company that provides a subscription-only newsletter. The two-part study looked at the use of #MeToo, which created a cultural change as people began to publicly acknowledge sexual harassment and assault as issues and sought to understand how #MeToo lead to substantial and concrete changes, implementations, progress, and/or actions.

The majority of adults have acquired cytomegalovirus (CMV), a human herpes virus transmitted by close personal contact, during life. Primary infection is usually asymptomatic in otherwise healthy persons, and is followed by life-long latent infection. Immunosuppression (from conditions such as HIV or transplant) predisposes to severe and symptomatic disease resulting either from primary infection or reactivation of latent infection, and CMV infection is a major cause of morbidity and mortality in organ transplant recipients. Antiviral agents are commonly used for prevention/suppression of CMV in transplant patients, but their use is limited by toxicities and emergence of resistance. Despite the use of antiviral agents as prophylaxis, CMV disease continues to occur, either as breakthrough infection in patients receiving prophylaxis, or after prophylaxis has been discontinued. The incidence, timing, clinical characteristics, and risk factors for CMV disease in heart transplant patients receiving antiviral prophylaxis has not been well-characterized. The goals of the present study are to retrospectively characterize the incidence, timing, clinical characteristics, and risk factors for CMV disease in a large cohort of heart transplant recipients at the University of Washington Transplant Program. We will use descriptive analyses for incidence and timing of CMV disease and multivariate logistic regression and Cox-proportional hazard models to assess risk factors. The cohort consists of 333 consecutive orthotopic heart transplant recipients between 1 July 2005 through 30 September 2016, with at least 1 year of follow-up. Overall incidence of Cytomegalovirus disease as well as by Donor+/Recipient- and Recipient+ serologies is respectively 10.5%, 27.9%, and 5.2% at a median of 10 months post transplant. 68.6% of patients who acquired disease had D+/R- serology, and the most common manifestations were Syndrome, Colitis, Pneumonia and Gastritis. Analysis of optimum prophylactic course length and associations between Cytomegalovirus and Cardiac Allograft Vasculopathy are in progress.

The innate immune system employs various tactics to protect our bodies against foreign pathogens. For example, during a viral infection, virus particles selfishly enter a host cell to propagate and make copies to infect neighboring cells. But during this infection, the host’s innate immune system recognizes certain pathogen-associated molecular motifs which signals for the production of proteins, known as restriction factors. These restriction factors can then block the viral pathogen by inhibiting various steps in the viral life cycle. One class of restriction factors active against influenza virus, are Mx proteins. Previous research indicates that these proteins may exert their antiviral activity by inhibiting the processivity of the viral RNA-dependent RNA polymerase during transcription and synthesis of influenza viral RNA (vRNA). Based on these findings, we hypothesized that the production of longer vRNA segments will be blocked in the presence of Mx proteins, with minimal effect on the production of shorter vRNA segments. To test this hypothesis, I designed fluorescent reporter constructs that mimicked the sizes of both short and long influenza genome segments and measured the ratio of short to long vRNA segments in the presence or absence of Mx using flow cytometry. Preliminary results indicate that Mx localized to the cell nucleus restricts the production of long vRNA segments, supporting our hypothesis. In contrast, Mx that is cytoplasmically-localized does not seem to have any effect on the production of long vRNA segments. Overall, this research will elucidate the previously unknown mechanism of viral restriction by Mx proteins, while also giving us insights into mechanisms of pathogen recognition by the innate immune system.

Accurate thermodynamic properties of aqueous solutions are typically described using arbitrary and custom combinations of global basis functions (GBFs) that are designed to fit specific data sets. This approach is revision-intolerant, since each set of GBFs is fixed to a particular data set, and an entirely new set of basis functions may be required when data sets are expanded. Reusable thermodynamic representations that can accommodate new data for an ever-widening range of conditions can be achieved using multivariate tensor B-splines, a series of smoothly-connecting local basis functions (LBFs) that each represents an arbitrarily narrow regime. However, the current implementation of LBFs for thermodynamic representations requires proprietary software, and widespread acceptance of this new paradigm may be contingent on the availability of easy-to-use, platform-agnostic tools that simplify the dissemination and utilization of such information. I am developing Jupyter notebooks that accept previously developed LBF-based equations of state covering a defined range of pressures, temperatures, and concentrations, and, within the specified regime, return graphical or numerical representations of thermodynamic properties including Gibbs energy and its derivatives including density, specific heat, isothermal and adiabatic bulk moduli, thermal expansivity, and chemical potential. These tools will eventually accommodate both those seeking a simple prediction of state variables and those who seek to expand, reproduce, or refine an existing LBF equation of state. Use by the latter group has the potential to strengthen a model over time by providing straightforward and open-source opportunities for collaborative evolution of thermodynamic representations, whereas the conventional methodology requires highly specialized skills that inhibit such improvement.

Antibiotic resistance is an enormous public health problem and causes death for 23,000 Americans each year due to ineffective treatments. Many strategies to target resistance have emerged, the majority of which target resistance machinery directly. In Escherichia coli, the TEM-1 gene encodes for the β-lactamase enzyme which can degrade penicillins, a subclass of β-lactam antibiotics. Alleles of this gene can either improve or weaken the ability of β-lactamase to degrade other subclasses of β-lactam drugs. One strategy that can potentially slow the evolution of bacteria and select against antibiotic resistance is exploiting collateral sensitivity – mutations that confer resistance to one drug and confer sensitivity to another. Utilizing a technology called Deep Mutational Scanning, we are screening every amino acid variant of the TEM-1 gene, and examining growth patterns in twelve different β-lactam antibiotics. This will allow us to quantitatively measure the effect of every single protein variant on the fitness of the organism in hopes of identifying patterns of collateral sensitivity. This is done by first optimizing growth parameters and next sequencing the DNA of each amino acid variant before and after exposure to drug. The large data set produced allows us to uncover common evolutionary trends. This foundational knowledge will potentially allow us to predict drug pairings that exploit collateral sensitivity, leading to more successful treatments.

In the context of the cell, molecular crowding can be described as the summation of molecular forces acting on polypeptides at the high protein concentrations that exist naturally in membrane-bound structures. This phenomenon of molecular crowding can affect protein conformations and interactions, particularly for proteins that require high flexibility to recognize and bind a large number of interactors like the chaperone Hsp90. To observe changes in protein conformations and interactions, we cross-link proteins with lysine-reactive linker molecules, then identify and quantify cross-linked sites using mass spectrometry. The linkage sites provide physical distance constraints useful for structural predictions, and the observed changes in cross-link abundance levels is informative of conformation and interaction changes. In this project, we apply chemical cross-linking to proteins under conditions that exert different levels of molecular crowding. These conditions include in vivo cross-linking of in-tact cells where high protein density causes high levels of crowding, and cross-linking of cellular lysates where protein density and molecular crowding effects are reduced. This presentation will highlight cross-linked peptides in Hsp90 and how these are being used to improve our understanding of the effects of molecular crowding on the function of this important chaperone.

Enteric diseases, or diseases of the Gastrointestinal (GI) tract, remain one of the most prevalent killers of children in sub-Saharan Africa. The most practical way to prevent such diseases is through vaccination, but antigens for enteric diseases need to be delivered directly to the GI tract to be most efficient, making vaccination difficult. Recent studies by the von Adrian group at Harvard University have found that both T and B cells are reprogrammed to home to the GI tract when they encounter retinoic acid, a metabolite of vitamin A. The King Lab at the University of Washington is working to develop a novel vaccine candidate using recently developed self-assembling protein nanoparticles, that can simultaneously package all-trans retinoic acid (ATRA) and multivalently display enteric antigens. Recent data indicate that preliminary versions of these nanoparticles can successfully elicit a mucosal immune response when delivered with free ovalbumin, an avian egg protein that is frequently used as a model antigen. We expect to elicit more potent immune responses when the antigen is multivalently displayed at high density on the nanoparticle. To accomplish this, I created a library of plasmid constructs combining ovalbumin and several nanoparticle subunits using a variety of different linkers. I expressed, purified, and evaluated these nanoparticles for their expression of the antigen using enzyme-linked immunosorbent assays, or ELISAs.

Fluid mixing is big business, both its application and research. Many manufacturers must be able to reliably mix fluids to a satisfiable level of homogeneity. Fluids taking longer to mix are fluids not being used for their intended purpose. This research explores two specific uses of random processes in an attempt to increase the speed and/or quality of the mixing process. While most mixing processes are in practice deterministic, the ansatz of this inquiry is that fluid mixing may be better applied through randomness. In this research, two different models for fluid mixing are explored, implemented and statistical measurements are taken. The first is the Gather and Spread model proposed by Diaconis and Pal in 2017, the second is the Toroidal Lattice Mixing model proposed by Pierrehumbert in 2000. We calculate Kendall’s τ (tau), and show evidence for a linear relationship between the number of points in the Gather and Spread model, and the number of trials. We show evidence against Gather and Spread distributing its points in Poisson manner. We calculate the standard deviation and relative entropy in the Toroidal Lattice Mixing model. We find strong evidence for the TLM having an exponential mixing rate, and strong evidence suggesting that advection diffusion mixing methods are always faster than diffusion alone.

At the 2017 Undergraduate Research Symposium, I presented a low-cost, automated device for influenza detection that was being developed in the Yager lab. After creating, testing, and optimizing this device, we were left with many questions. While certain components of fluid flow in paper are understood, there is much more to learn. In this device alone, three different types of paper were used to run the two-dimensional assay. Current unanswered questions include the following: how do additives affect protein deposition, rehydration, and capture? How much of a dried protein on paper can be rehydrated by a passing solution, and which paper and solution properties affect this value? How do the viscosity and complexity of our patient samples affect the quality of our results? Our overall goal is to determine how to optimize our test line and generate a better understanding for optimization of future diagnostic devices. To make progress towards this goal, my project centers on the development and characterization of a laboratory technique to quantitatively study the effects of these parameters on protein interactions with membrane surfaces and other proteins bound to those membrane surfaces. Improving our understanding of these interactions in membranes will enable better diagnostic device optimization and enable illness detection with lower amounts of infected sample – allowing for earlier detection and better disease treatment. Through the development of this testing apparatus, I have begun to address these questions.

The North Creek Wetlands Restoration on the University of Washington Bothell campus is home to a large nocturnal American crow (Corvus brachyrhynchos) roost. Each day from Autumn to Spring, crows form pre- and post-roost aggregations, which consist of between tens and hundreds of crows. Crows on these aggregations are often highly vocal, but the functions of their vocalizations are not well understood. Identifying any context-dependent patterns in these vocalizations is critical to fully understand communication in this highly social and intelligent species. Previous studies have shown the presence of human observers near large groups of crows may disrupt natural vocal and non-vocal behavior. In this study, the potential confound of these observer effects are eliminated by recording crow vocalizations using a remotely activated, time-synched microphone array. Simulations are undertaken to study the performance of the Time Difference of Arrival (TDOA) method to localize individual callers. A parametric study is used to analyze the effects of number of receivers, signal frequency and duration, and crow location on the performance of TDOA. In addition to the simulation, different types of previously recorded crow vocalizations are used to design robust playback experiments in order to fine-tune our localization technique for use in actual crow aggregations in future.

Large data centers, such as those built by Google, Amazon, and other information technology leaders consume about 1.3% of the world’s energy, of which about 40% is used on electronics cooling [1, 2]. This amounts to 245 TWh per year, which, with the average US price of 12 cents per kWh, amounts to about $29.4 billion dollars spent per year on cooling high heat semiconductors [3, 4]. The work presented here proposes an innovative way to improve this cooling process. The proposed concept features a levitating inner rotor using fluid bearings that result in no physical contact between solid parts, eliminating friction. For the first time, precision-manufactured plastic parts are utilized to achieve both a low cost and a high reliability. The micropump is expected to last in operation for over one million hours Mean Time to Failure. This work emphasizes model-based design verification and optimization to ensure adequate performance for different form factors – so that a drop-in replacement of an air fan passive heat sink can be quickly developed for every microelectronics product. Twenty-four designs and prototypes were used in evaluation of two key criteria in order to optimize the pump’s design. Three separate herringbone geometries, square, beveled-step, and circular, of herringbone grooves were prototyped based on experimentation of optimum groove parameters. These findings helped determine the optimal layer height of 100 micron for use in the micropump design. Finally, the application of a sensorless, brushless DC motor reduces overall cost of the pump and increases efficiency due to the removal of friction.

Seismic reflection surveys use acoustic energy to image the structure beneath the seafloor by broadcasting broadband impulsive sound signals (called airguns) that reflect off the sea floor and are recorded through long arrays of hydrophones (called seismic streamers). During these surveys it is important to have a model to predict how much noise will be added to the ocean environment. The complexity of local geology, seafloor topography, and uncertainty in water properties makes it difficult to mathematically model acoustic propagation in ocean. However, ocean data like many other branches of science is experiencing an explosion in the amount of data collected and available for analysis. The goal of this research is to use previously recorded ocean data to (1) calculate the sound power levels generated by airguns during seismic reflection surveys and (2) use machine learning to create a predictive model of airgun noise considering various variables such as ocean depth and distance from the airgun. Several regression methods in Python were used and the method that resulted in the most accurate regressor was chosen. The data used in this experiment spanned a wide range of water depths from the continental shelf (∼40 m) to deep water (∼2600 m). In this presentation, the performance of a machine learning algorithm trained by the sound power levels calculated through one track line of this cruise is investigated.

Quantum Dots (nanoparticles with semiconductor properties) are currently produced from potentially toxic materials, and are expensive to prepare. Developing a less toxic, more renewable quantum dot has the potential for utilization in biosensors and bioimaging without the high cost or environmental pollution associated with current metal-based quantum dots. Methods for developing graphene quantum dots are being investigated by utilizing a sustainable carbon source. Specifically, the use of hydrogen peroxide as an oxidant in a hydrothermal reaction is being optimized in terms of reaction time, temperature, carbon:oxidant ratio, and oxidant concentration. Carbon sourced from research being conducted on campus allows for reduced cost and waste treatment while providing an alternative to metal-based quantum dots. Further work on the subject will include incorporating the quantum dots into handsheets (paper samples) to test fluorescence, which ultimately will be used as optical and photoelectric sensing materials due to their high stability and distinct long-term fluorescent properties. Additionally, there is potential to explore other oxidants and carbon sources that have minimal environmental impact.

Bone histology, the study of bone tissue, has become a critical tool in the field of paleobiology as a proxy for life-history information, such as growth rates, that is otherwise inaccessible from fossils. However, the bulk of bone histological research has focused on birds, crocodilians, and large-bodied mammals, leaving the extent to which bone microstructure acts as an indicator of growth rates among small mammals largely unknown. Therefore, we generated thin sections from the limb bones (e.g., tibiae, humeri, and femora) of a taxonomically diverse sample of 12 extant, small-bodied (<1 kg) mammals in an attempt to build a framework upon which we may make inferences about the evolution of mammalian growth dynamics. In general, vascularity is low or absent in our samples, and the degree of vascularity appears to decrease with decreasing body mass. All specimens exhibit two types of bone matrix: well-organized parallel-fibered bone and disorganized woven bone. Often, this parallel-fibered tissue lines the interior and exterior of the bone cortex, bordering an intermediate band of woven tissue. This middle band likely represents a period of rapid bone deposition, possibly corresponding with rapid growth in early ontogeny, while the parallel-fibered bone represents deposition after growth had slowed. We hypothesize that the structurally competent parallel-fibered bone bordering the cortex may act to buffer the intermediate, structurally weak, woven bone against mechanical strain during locomotion. To test these hypotheses, we will compile existing life-history data and quantify the histological features of our sample using NIS Elements photo documentation software, and apply multiple linear regression models to test for relationships of significance. By investigating the impact of life-history characteristics upon small mammal bone microstructure, we hope to make important inferences about the lives of extinct small mammals, and thus create a more comprehensive understanding of mammalian growth dynamics. 

Consumers are drawn to things with nostalgic elements, like old cars and childhood toys, which unconsciously have an effect on consumption patterns. Our current research is focused on nostalgia, both personal and vicarious, evoked by the television series "Stranger Things". We are using this specific show because of its success in utilizing nostalgia as a powerful marketing tool. We will be conducting an in-depth content analysis on the show for (1) unpaid product placements, (2) nostalgic elements, and (3) the effect it has on consumers and companies. To give some background: Personal nostalgia is a complex feeling produced by a reflection on things (ideas, people, and objects) associated with one’s past, and vicarious, or historic, nostalgia is a romanticized longing for a time before one was born. Stranger Things, a Netflix original, is an intersection between a-coming-of-age story, a paranormal horror, and a nostalgic love letter to 1980s cinema. Stranger Things uses products in the show to accurately portray the 1980s small town culture, including Eggo waffles, Dungeons and Dragons, and Chevrolet. Companies such as Eggo have capitalized on the unpaid and unintentional product placement that the retro series features by creating advertisements directly targeting Stranger Things fans. Some of the nostalgic elements in Stranger Things are childhood innocence, eerie supernatural mystery solving, the pre-digital era, and young love. Stranger Things has a positive effect on consumers because so many people can relate to the 1980’s, namely Generation X and Millennials, making the show one of Netflix’s top earners, demonstrating that nostalgia marketing is an effective technique. Through this content analysis, we aim to advance the knowledge of the powerful impact that nostalgia marketing can have through the popular show Stranger Things.

Chronic pain affects millions of people worldwide, and current treatments and ineffective and come with unwanted side effects. Modern research focuses on studying the mechanisms of pain sensation in the nervous system, with the goal of using our improved knowledge to develop more efficient analgesics. Our research focuses on neurons located in the trigeminal and dorsal ganglia, as they are known to play an important role in the sensation of touch and pain; we also study the genes that regulate the development and function of these neurons. Recent advances in gene editing methods, particularly the CRISPR/Cas9 system, allow us to mutate specific genes of interest in a living animal and monitor the effect of such mutations within a matter of days. To this end, we have developed a behavioral assay which determines the effect of CRISPR induced mutations on pain sensation in zebrafish larvae. CRISPR injected larvae are exposed to noxious stimuli such as AITC (mustard oil) and extreme temperatures. The CRISPR treated larvae’s response to the painful stimuli is compared to wild type larvae’s response to determine the impact that the gene we targeted had on their nociception. Through this assay we have identified a gene, zbtb7b, as potentially important to the sensation of noxious stimuli. Further experiments are now required to determine the precise mechanisms through which this genes plays a role in the sensation of pain, including other behavioral assays, RNA hybridizations, and imaging techniques. Several improvements can also be made to this assay to increase the efficiency of future runs.

Rhabdomyosarcoma (RMS) is a rare pediatric cancer characterized by abnormal muscle development. In order to provide insight into muscle development and the pathogenesis of rhabdomyosarcoma, I developed a muscle cell lineage-specific CRISPR/Cas9 gene targeting system in zebrafish that will enable the study of gene function specifically in muscle cells. To create the zebrafish muscle tissue-specific CRISPR/Cas9 gene-editing model without disrupting endogenous gene function, I inserted the Cas9 gene at the end of the zebrafish myf5 gene locus. Myf5 is a gene expressed in developing skeletal muscle tissue and muscle stem cells. By inserting Cas9 downstream of the myf5 gene, Cas9 expression will be induced by the myf5 promoter resulting in gene targeting specifically in muscle tissue. I accomplished this by microinjecting zebrafish embryos with DNA containing the Cas9 gene flanked by short myf5 sequences matching the genome. Cas9 will be inserted at the myf5 locus through a homology independent CRISPR/Cas9-mediated gene knock-in approach which uses a cut and paste mechanism to insert genes into specific locations in the genome. All injected zebrafish embryos were screened for correct integration using polymerase chain reaction (PCR). Founder zebrafish (those with correct integration) were bred to create a stable line of myf5-Cas9 zebrafish. The myf5-Cas9 expressing zebrafish line will be used to target genes specifically in muscle cells and in our zebrafish model of rhabdomyosarcoma (RMS) to identify genes essential for growth of RMS cancer cells. Identification of genes essential for RMS growth will enable the development of new targeted therapies to improve survival of cancer patients.

Although crystalline two-dimensional (2D) protein arrays are often found on the surface of archaea and bacteria where they form a protective S-layer, their potential in bionanotechnology applications remains unfulfilled. Progress in computation has recently allowed the (re)design of proteins for self-assembly into arbitrary structures. We are working with a rationally modified protein from S. typhimurium that can self-assemble into large (> 100 µm) and thin (~ 5 nm) hexagonal 2D arrays pierced by ~ 3 nm pores upon addition of divalent cations (e.g., Ca²⁺). The goal of our research is to test the ability of these arrays to organize gold nanoparticles (AuNPs) with desirable plasmonic characteristics. To this end, we stain protein arrays with the lipophilic fluorescent dye Nile Red, and analyze fluorescence microscopy images to quantify how the decoration of arrays with various concentrations of AuNPs affects the rate of photobleaching of the Nile Red fluorophore. Understanding how AuNPs bind to protein arrays could lead to further applications, such as templated growth of inorganic materials or co-assembly of enzymes and inorganic catalysts.

Excessive and unchecked deforestation can create a cascade of extinctions. A field-deployable DNA screening tool that can be used by non-scientists will prevent illicit timber shipments from reaching a commercial market by flagging products sourced from endangered species. The DNA screening tool transports reagents and samples using the anisotropic ratchet conveyor (ARC), a portable digital microfluidic system. The screening tool recognizes the DNA barcode using species specific primers and DNA amplification indicates the identification of a species. Isothermal amplification methods are easier to integrate into the portable DNA screening tool and there is currently no isothermal amplification method for timber DNA. The loop-mediated isothermal amplification (LAMP) method was designed for integration in a portable identification system since this method has the ability to perform rapid amplification and is robust to inhibitors. The species for which amplification was performed were eastern white pine (Pinus strobus), Spanish cedar (Cedrela odorata), and white oak (Quercus alba). The first step was to identify the genetic target for amplification and design LAMP primers for this sequence. The genes selected were rbcL and matK since these chloroplast genes diverge between species and are conserved within tree species. LAMP uses six primers: the backward inner primer(BIP), forward inner primer(FIP), the forward loop primer(FL), backward loop primer(BL), forward primer(FP), and backward primer(BP). Species specific LAMP primers were designed. The primers were validated on synthetic oligos. Extraction of DNA is challenging because the DNA is trapped in between thick cell walls. Timber DNA amplification is challenging because inhibitors, include polysaccharides and phenols, bind or degrade DNA polymerase, and prevent amplification. Extraction and purification methods were investigated to provide amplifiable DNA. Isothermal amplification was performed on the ARCs. The portable DNA identification system will identify timber species for conservation biology.

Sometimes speech sounds (phonemes) can be ambiguous, and people have a tendency to interpret the ambiguous phoneme differently in different contexts so that they perceive a real word, as opposed to a non-word. This effect is called "lexical bias." For example, when there is ambiguity between whether /m/ or /n/ is heard, /m/ is more likely to be perceived if it is followed by "uch," because "much" is a word, but "nuch" is not (and vice versa if the context is "udge"). We hypothesized that for people who have hearing loss or use a cochlear implant, there will be additional ambiguity in hearing speech, and that the lexical bias effect would be stronger. We simulated degraded hearing using vocoded speech played to listeners with normal hearing. Participants heard speech continua that gradually morphed from /m/ to /n/ in the "uch" and "udge" contexts, and either had a clear spectral quality or a degraded spectral quality. Results suggest that the lexical bias is stronger when the speech signal quality is less clear, which is consistent with the hypothesis because of the increased phonemic ambiguity in these conditions. By understanding how signal degradation impacts the perception of phonemes, audiological tests for speech reception can be improved to separately acknowledge the effects of hearing from the adjustments that the listener makes to maintain lexical biases in speech perception.

Cancer is one of the deadliest ailments in the United States, killing hundreds of thousands of people per year. One group of proteins that have been implicated in human cancers are the Phosphatase of Regenerating Livers, or PRLs. PRL-1 has been shown to have differing effects on cancer. Some research has found this protein to be an oncogene while others have found it to be a tumor suppressor. In our lab, past research has shown that for dPRL-1 to function as a tumor suppressor, it must localize to the adherens junction. The adherens junction helps glue epithelial cells together; malfunctioning adherens junctions, found in some cancers, no longer glue cells together thereby allowing them to metastasize. To better understand how dPRL-1 can function as a tumor suppressor, I performed a co-immunoprecipitation on the homolog, dPRL-1 in Drosophila melanogaster to discover the proteins that dPRL-1 interacts with in vivo at the adherens junction. To do this, I overexpressed dPRL-1 in the developing wing epithelium of the organisms and used an antibody to dPRL-1 for co-immunoprecipitation. This approach is an unbiased way to identify proteins that dPRL-1 interacts with while functioning as a tumor suppressor. My initial attempts at co-immunoprecipitation revealed one unknown protein of possible significance, but I have been unable to identify it yet. I am also testing my protocol to see if E-cadherin, a protein component of the adherens junction that contributes to cell adhesion, and dPRL-1 co-immunoprecipitate. We expect this interaction since our lab found that the two proteins colocalize via fluorescence microscopy. The proteins that dPRL-1 interacts with when functioning as a tumor suppressor could be mutated or missing in cancer cells thereby preventing dPRL-1 from functioning as a tumor suppressor. Hopefully, this knowledge will help clinicians make more effective chemotherapies to target cancers affected by PRLs.

Synthetic biology allows us to use an organism’s metabolic pathways to produce new, useful metabolites cost-effectively. Growing organisms in a culture allows the production of these metabolites on a commercially-viable scale. However, management of these cultures is time-consuming and labor-intensive, such as HPLC. Our project aims to provide a low-cost, automated system that analyzes the culture in real time at low cost. Our device, a turbidostat bioreactor called the Chromastat, uses images and other optical data to measure the current state of a culture. If these measurements show metabolite production outside specifications, the system modifies the culture’s metabolic expression by adding inducers. To make this system cost effective, we focused on using affordable materials, an open-source controller and analysis system, and visible color outputs instead of the traditional fluorescence. To test our system, we used the violacein metabolic pathway in yeast. By regulating gene expression with inducible promoters, this pathway yields up to four visually distinct pigments. In a production environment, these pigments could provide a proxy measurement to produce useful substances which are costlier to detect. Pigment production is measured by the popular low-cost and open-source Raspberry Pi computer running a program displayed in Java Swing. Optical sensors collect color and opacity information about the culture. Our software, installed on the Raspberry Pi, analyzes the color, and in response, the hardware introduces inducers to stabilize the culture’s production. Data recorded by the Pi over time reveals the relationship between gene expression and metabolite production rates. By combining biological, software, and hardware systems, our unique design can generate previously unavailable visual data in certain biosynthesis processes, such as those involved in antibiotic production or fermentation.

Regenerative medicine that utilizes pluripotent stem cells (PSCs) has the potential to transform the treatment of the many debilitating conditions that face modern society. Although research regarding the control and use of PSCs is prevalent, there has been little translation of this research to the clinic. Critically, there remain significant knowledge gaps regarding peri-gastrulation cell fate decisions — the decisions at an early phase in development during which pluripotent stem cells first begin to differentiate toward specific cell fates. Currently, the widely used systems for understanding cell fate decisions rely on differentiating populations of PSCs toward a single target cell lineage in a well plate via uniformly applied morphogen signals. Such uniform stimulation lacks the ability to reproduce the same spatial cell fate decisions as is observed during embryogenesis. We have developed a technology that establishes in vitro morphogen gradients to better recapitulate peri-gastrulation cell fate decisions. This research focuses on precision cell colony patterning using CNC milled and stereolithography 3D printed constructs to better characterize the effect of in vitro morphogen gradients on single populations of PSCs. This was done by patterning PSC colonies and subsequently forming morphogen gradients of Activin A and BMP-4/CHIR99021 to establish subpopulations of ectodermal, mesodermal, and endodermal lineages. The growth factors Activin A and BMP-4 and CHIR99021 (a small molecule agonist of Wnt signaling) are biochemical factors that influence signaling pathways which control early cell fate decisions. The cells were then fixed and stained for markers of ectoderm (CDX-2), mesoderm (Brachyury), and endoderm (Sox2) to quantify the induced subpopulations. The ability to control cell fate decisions of PSCs is an integral step in developing functional and effective regenerative medicine technologies. Ultimately, this technology has the potential to develop more effective induced differentiation techniques for creating therapeutic, mature cell populations.

In vitro aptamer ribosensors use small molecule binding kinetics to sensitively discriminate between concentrations of a target ligand. Ribosensor devices have been used to quantify metabolite production for metabolic engineering but are also potentially useful for fields such as point-of-care diagnostics. To be useful in this field, further understanding of the parameter space in which these devices work is required. Two big unknowns within the parameter space are how different media conditions and how the use of lyophilized T7 RNA polymerase affect ribosensor function. To evaluate the potential of ribosensors in point-of-care applications, we measured RNA aptamer ribosensors with in vitro fluorescence assays of the ribosensors in both synthetic urine and its control media. Lyophilizing the T7 polymerase allows for easier transport of heat-sensitive proteins; enabling the use of ribosensors as shelf-stable molecular diagnostics even in low resource clinical care settings. We demonstrate the effects of different factors during lyophilization on the function of aptamer ribosensor devices and optimized lyophilization conditions for optimal function from the reconstituted enzymes. These optimized conditions utilize cryoprotectants to ensure that the T7 polymerase maintains its stability during and after the lyophilization process. Cryoprotectants that have been found to best stabilize T7 polymerase are the addition of sucrose solution and liquid nitrogen flash freezing. This project clarifies the conditions that are essential in transitioning the ribosensor devices from the laboratory to point-of-care diagnostics. We show how these new conditions affect the ability of the ribosensor devices to make accurate measurements. Future work will aim to modify the design for the RNA aptamer ribosensors to function more optimally within the point-of-care parameter space.

A greater understanding of snow accumulation patterns in our mountains has proven critical in predicting water supply, preventing floods, forecasting avalanches, and generating hydropower. One way to improve this understanding is through study of the melting layer, or the layer within a cloud where falling snow and ice begin to melt into liquid during a precipitation event. The upper bound of the melting layer is the 0°C temperature level, and the lower bound the altitude at which snow has fully melted into rain. This project aims to improve understanding of the melting layer and its variation in thickness and elevation on the windward (southwest) versus leeward (northeast) side of the Olympic Mountain Range. Hypotheses are explored through the analysis of radar imagery on opposing sides of the mountain range, weather balloon profiles of temperature, wind and humidity, and ground observation data - including hourly temperature values from sites throughout the mountains. Results of these data are compared to snow and weather models and reanalysis products such as WRF (Weather Research and Forecasting Model), NARR (North American Regional Reanalysis) and ERA-Interim, to explore the predictability of melting layer behavior for use in hydrologic forecasting. Through analysis of preliminary results, the occurrence of a lower leeward melting level has been captured through vertical temperature profiles that reanalysis products failed to account for. One hypothesized process contributing to this melting layer variability could include the trapping of cold air at lower elevations from continental sources on the lee-side thus lowering the melting layer, and further altering the thickness of the melting layer as this trapped air mixes with the air modified over the windward slopes originating from the Pacific Ocean.

The trio of crops that are responsible for the bulk of human nutrition are pollinated by wind. Wind pollination has evolved repeatedly from insect pollination in angiosperms, however the mechanism for these shifts, such as the specific morphological traits and genes involved, has not been explored. Thalictrum (in the buttercup family Ranunculaceae) is a genus of herbaceous perennials with considerable floral diversity and multiple transitions to wind pollination in closely related species, making it an ideal system to study pollination syndrome shifts. Insect-pollinated species have larger, showier flowers with pigmented organs, while wind-pollinated species have green floral organs, exserted carpels and pendulous stamens. Here, I set out to characterize and quantify floral traits in wind and insect-pollinated species in Thalictrum to: 1) Test whether there is a suite of floral traits associated with wind pollination syndrome; 2) Prioritize the traits that contribute the most to pollination syndrome; and 3) Find the genetic basis of these traits. Flower scans from live plants, in addition to specimen from the University of Washington Herbarium, were used to measure floral traits using imageJ in 17 species across the Thalictrum phylogeny. Multivariate analysis of floral traits using Principal Component Analysis, showed that species cluster by pollination syndrome. Correcting for phylogenetic relatedness resulted in most of the variance being explained by the first principal component, clustering species by pollination syndrome even when they are distantly related. This evidence suggests that a specific combination of traits has been independently selected via convergent evolution in the transition from insect to wind pollination in this group. Next, I plan to conduct reconstruction of ancestral character states to track trait evolution and identify those that most closely correlate with shifts in pollination mode, followed by expression analysis of candidate genes.

Helicobacter pylori is a gastric bacterial pathogen that infects about 50% of the world’s population. Chronic infection with H. pylori causes inflammation and increases the risk for developing gastric cancer. H. pylori colonizes the human stomach where it uses a type IV secretion system to deliver bacterial factors to the gastric epithelial cells. Once infected, gastric epithelial cells initiate different immune responses, one of which is the release of a protein; lipocalin 2 (LCN2). Like nearly all pathogenic bacteria, H. pylori must acquire iron, which is important for colonization, persistence, and virulence. LCN2 behaves like a competitor for iron and limits bacterial growth by depleting intracellular iron stores. LCN2 is highly upregulated in gastric tissue during H. pylori infection, however it is still unclear if LCN2 plays a beneficial role for the host by controlling H. pylori growth. My project tests the hypothesis that if host LCN2 is sequestering iron, then H. pylori survival rates will be decreased. My first aim characterizes the kinetics of LCN2 expression determining when this gene is most highly expressed during H. pylori infection. My second aim uses novel and innovative CRISPR/Cas9 genome editing techniques to engineer LCN2 knockout gastric cells. If my hypothesis is correct, I expect that H. pylori survival rates will increase when co-cultured with LCN2 knockout cells since there will be no sequestering of iron by LCN2. Understanding how the host tries to defend itself through proteins such as LCN2 will provide better insight into the host immune response and may inform vaccine design and novel treatment strategies for populations with a higher predisposition for developing gastric cancer as a result of H. pylori infection.

This project focuses on fifteen potentially unpublished species of molluscan fossils—specifically gastropods and oysters—originating from the Sinop-Boyabat sedimentary basin in north-central Turkey. The intent is to identify each fossil in order to date the surrounding rocks, as paleontologists have discovered an unusual mammalian fossil fauna in close proximity. Marine sedimentary rocks from this region accumulated in a small rift basin connected to the Black Sea, and span from the early Cretaceous to the late Paleogene periods (140 to 30 million years ago). The invertebrate fossils were unearthed in the uppermost part of the sedimentary section consisting of shallow water coastal and reef limestones, and calcareous mudstones. Investigations in the Sinop-Boyabat have provided detailed rock descriptions, but additional clues gleaned from the invertebrate identifications will help determine a more temporally restricted age. The fossils must be identified to the generic level and, ideally, to the species level as well. Identification occurred in four stages. First, I separated each fossil in to the taxonomic classes, Bivalvia and Gastropoda. Then I separated them based on shell characteristics and markings such as whorl length, aperture shape and size, and the presence or absence of axial ridges, sutures, or an apex. Next, I took photos of the most intact specimens. The final step has been reading through the literature and attempting to find a fossil description that matches each group. This is the most challenging stage as we cannot find publications that describe any of our specimens. Thus, we are using texts focusing on European and East Asian fossil faunas, none of which include matching identifications. Throughout the search for applicable literature, it became clear that the Sinop-Boyabat invertebrate specimens have not been studied before and many are new species.

Watching entertainment media is a popular activity for children’s learning and leisure, playing a central role in children’s everyday lives. However, Child Development research shows that extensive video consumption is linked to unhealthy development, including disrupted sleep patterns, increased likelihood of obesity, and reduced imaginative play. In this study, we explore how video-viewing platform design features contribute to children’s media use. We introduce CoCo’s Videos: a video-viewing platform for preschoolers with features that encourage children to self-manage media consumption, enabling children to play a role in setting and sticking to their own limits on the amount of video consumption. We deployed three different versions of CoCo’s Videos to 24 different families for three weeks in a counterbalanced within-subjects study design. Preschoolers experienced three different versions of CoCo’s Videos: one version is neutral to the limits they set, another version enforces limits they set (“lock-out”), and the last version challenges the limit by automatically playing more content after their set limit (“post-play”). Our results show that the post-play feature significantly decreased children’s autonomy and self-regulation, indicated by extended video-viewing time beyond the set limit, leading to increased parent intervention. Our results show that the lock-out feature did not reduce viewing time or parent intervention. Ultimately, our research advises others to avoid platforms that undermine children’s autonomy and intention, which will likely be more effective than parental controls in developing healthy media habits.

Cancer stem cells are thought to play a role in relapses and metastasis in numerous cancers. The inability of traditional cancer therapies, such as chemotherapy, to eradicate these cancer stem cells prompted a search for small molecules that induced apoptosis in cancer stem cells. Drosophila germline stem cells can be used as a model system to emulate cancer stem cells. Upon irradiation, Drosophila germline stem cells are able to survive apoptosis through a molecular signal released by the apoptotic daughter cells via the TIE receptor. We have conducted an in vivo drug screen of 512 compounds in Drosophila melanogaster to find drugs that would disrupt this protective mechanism and induce apoptosis. In particular, Camptothecin, NSC 125197, and NSC 127458 were effective in killing germline stem cells. To test the effect of the small molecules we fed female flies the compound for 3 days, dissected and fixed the ovaries and stained for an apoptosis marker, activated caspase, and the GSC marker, adducin. We quantified the effect of the drug by analyzing the number of germline stem cells and caspase signaling on a confocal microscope. Through this system we aim to find potentially new, and more powerful anti-cancer drugs that can affect cancer stem cells. Future directions include attempting to understand the mechanism of action of these apoptotic compounds in hopes that they might be useful in the fight against cancer stem cells.

Diophantine equations are polynomial equations with integer coefficients. In 1970, Matiyasevich proved that an algorithm to decide whether a given Diophantine equation has a solution does not exist. We investigated some such equations including Pell and Thue equations, that have an infinite and finite number of solutions, respectively. Geometrically the solution set of Diophantine equations in 2 variables corresponds to plane curves, e.g. elliptic or hyperelliptic curves, and the number of rational solutions is related to the genus of the corresponding curve. We gathered statistics on the size of the solution sets in an attempt to address an important unsolved problem in arithmetic geometry, known as Uniformity Conjecture of Caporaso, Harris and Mazur. Our project involved an analysis of Python and C code, specifically through the CoCalc development platform, utilizing data from the L-functions and Modular Forms Database (LMFDB). Currently our results agree with the current known data on the sizes of solution sets, and we hope to extend our results to gather data on curves not currently in the LMFDB. This will serve as a testing ground for the Uniformity Conjecture.

Hybridization is an event that occurs when different species or populations reproduce to create offspring, and represents a possible way to fast track adaptation by introducing an abundance of genetic variation all at once. Investigating the adaptive potential of hybrids is especially relevant under our current conditions where stresses from climate change and global warming are increasing the frequency of hybridization, and putting increased pressure on species to rapidly adapt to new conditions. We have used yeast as a model organism to look at how hybrids adapt to new environments. We used Saccharomyces cerevisiae, a strain that prefers warm temperatures, and Saccharomyces uvarum, a strain that prefers cold temperatures, and evolved their hybrid offspring in both warm and cold temperatures. Using whole genome sequencing, we discovered mutations which may be important in temperature and nutrient adaptation, including a mutation involving the gene PHO84 that has differential allele selection depending on temperature. I then tested the fitness effects of these mutations by measuring a strain’s competitive growth over time compared to a common ancestor in both cold and warm temperatures. I expect to find other specific genes that are involved in temperature sensitivity, and possibly reveal ways these and other species have adapted to withstand divergent temperatures.

Active nests at the world’s largest Magellanic penguin (Spheniscus magellanicus) colony at Punta Tombo, Argentina have declined 40% since 1987. Climate change has increased rainfall and intense storms resulting in high chick mortality. Although these large-scale weather changes are known to factor into the decline, the effect of weather patterns on the scale of individual days is uncertain. To gain insight into penguins’ daily foraging patterns throughout the annual breeding season, automatic tread scales were placed on a penguin “highway” so when a penguin crossed we could document their time and direction of crossing, weight, and RFID tag. We sought to redesign the scales to improve energy efficiency by switching to solar power and increase accuracy and durability by changing the protective covers on the devices. Most importantly, the modified scales were required to be waterproof to protect internal components from heavy rain and flooding. The batteries used to power the scales had to last 7 days before needing to be replaced. Lastly, the materials used had to withstand temperature fluctuations and be animal-proof. The new design implements solar panels to charge batteries for the scales and cable glands to prevent water ingress through sides of the scales. The updated scales are made of wood and fiberglass then encased in heat-sealable fabric and sealant for waterproofing. Prototypes were firstly tested in the lab to see if they resisted flood-like conditions. Next, we tested whether the scales performed well after being exposed to large temperature changes using temperature controlled rooms. Additional tests were performed in the field to determine whether the design modifications decreased the amount of water ingress and increased battery life. Long-term tests in the field will be important to see how the materials weather over time when faced with temperature fluctuations, flooding, and animal usage. 

Carnivorous plants live in low nutrient environments and consume insects for heterotrophic nutrients. While previous research has typically focused on how pitcher plants capture prey, there is a lack of research concerning how pitcher plants attract pollinators. Scent is an important component of insect attraction, and this study explored whether pollinated and unpollinated plants produce different scents. This information will help us better understand the mechanism of pollination in carnivorous plants. We hypothesized that unpollinated plants will give off a different scent than the pollinated plants in order to attract more pollinators. The plants used for this experiment are the Sarracenia flava (yellow pitcher plant) which is endemic to the southeastern United States. We created two treatment groups consisting of pollinated and unpollinated plants inside a climate-controlled growth chamber at 25°C. Plants were watered from the base with unfertilized water. Scents were collected for 24 hours using Porapak Q adsorbent matrix and analyzed using a Gas Chromatograph Mass Spectrometer to identify the compounds. We anticipate that our results will further our understanding of how plants and insects interact. Future studies and analyses will focus on insect behavioral responses to plant scents, and on how insect antennae respond to each scent component.

Stable isotope geochemistry is a powerful tool used to track changes in elemental composition of rocks to understand geologic history. A few of the more popular elements analyzed by geologists include magnesium and iron. Potassium analysis is a relatively new technique offering opportunities to delve into questions of continental erosion. My research project will aid in the development of potassium as a useful isotope tracer. I am determining the potassium isotopic compositions of 40 seawater samples with column chemistry methods and multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) to investigate the homogeneity of potassium isotopes in seawater and the subsequent mixing potential of the Earth’s oceans. I chose my samples with the goal of providing a wide distribution of data both spatially and vertically within the water column, including seawater from the Gulf of Mexico, southern Hawaii coast, and the greater Pacific and Atlantic Oceans. Potassium composition of the oceans is controlled by river and groundwater input of crustal material. Considering that potassium has a residence time (~12 Ma) orders of magnitude larger than the hypothesized mixing time of the oceans (~10 ka), the data should show a homogeneous potassium composition of seawater consistent with globally circulating ocean currents and a steady-state marine potassium budget. Presently, there is no global seawater potassium isotope literature value; previous studies have limited investigations to variability of potassium compositions in crustal, igneous or biological samples. Seawater is a useful geostandard for isotopic analysis because it is a readily available and vast resource that can be easily sampled and processed. The primary goal of this project is to provide a global seawater literature standard for future potassium isotopic analysis, given that my data will indicate homogeneous, well-mixed oceans representing an all-inclusive average of global potassium composition with a natural range of variation.

Multiple factors interact to determine the lifespan of an organism. The Promislow lab uses the fruit fly Drosophila melanogaster to study the interaction between the metabolome (the profile of all small molecules within an organism), and the lifespan of a fly under stress. In a study of metabolome and lifespan data for many genotypes of Drosophila, our lab found that fly strains with relatively long lifespans when exposed to oxidative stress (peroxide food), had high levels of maltose, a disaccharide of glucose. We hypothesized that maltose was beneficial to flies on peroxide food, and tested this by supplementing the diet with maltose to see if this would extend lifespan. Flies fed supplemental maltose prior to exposure to peroxide food lived longer than flies fed unsupplemented food, supporting our hypothesis. Maltose could extend lifespan by providing energy to the fly via metabolism into glucose, or through another function as a disaccharide. To distinguish between these possibilities, we tested lactose, a disaccharide, to determine if any disaccharide could extend lifespan. Lactose did not extend lifespan, suggesting that disaccharides in general do not extend lifespan under stress. We found that glucose extended lifespan, supporting the hypothesis that maltose extends lifespan via conversion to glucose. Maltose can be stored as glycogen, a polysaccharide, and glucose is derived from glycogen by glycogen phosphorylase, encoded by the gene GlyP. To test the role of glycogen metabolism on lifespan under stress, we manipulated the expression of GlyP. Several transgenes were used to reduce the expression of GlyP by RNA interference (RNAi). RNAi of GlyP decreased lifespan, which supports our hypothesis that glucose derived from glycogen promotes survival. Our work suggests that glucose derived from glycogen or maltose is an important determinant of lifespan under stress, furthering our understanding of links between metabolism and complex phenotypes, like lifespan.

Plants recycle resources from dying organs to feed the development of new ones. For example, chloroplast degradation in senescing leaves is a major source of nitrogen for seeds. Darkness or shade can induce leaf senescence and chloroplast degradation, but if light returns soon enough, new chloroplasts are made and the leaf remains photosynthetically active. Phytochrome B (PHYB) is a protein that serves a key role in resource allocation throughout the plant. phyB null mutants of the model crop species Brassica rapa (Br) exhibit low chloroplast count, poor seed production, and a reduced increased growth response to high CO2, as compared to wild type. We will investigate the underlying cause of these phenotypes by comparing the transcriptomic response of chloroplast-biogenesis and nitrogen-assimilation-related genes in wild-type and BrphyB null mutants before and during dark-induced senescence, as well as after recovery. Establishing a deeper understanding of the scope of PHYB's role in resource recycling will help us isolate appropriate targets for engineering more drought-resistant and nutrient efficient crops.

Paper fluidic devices expanded diagnostic medicine to applications beyond lab testing. A key example is the common pregnancy test, which relies on an antibody capture line and detection antibodies conjugated to a colorimetric label to provide a diagnostic readout. This detection method requires high concentrations of target proteins. However, by incorporating isothermal strand displacement amplification (iSDA) and antibody capture of proteins tagged with nucleic acids (rather than colorimetric labels) much smaller protein concentrations can be detected. The Yager Lab has shown that this method increases sensitivity by 10⁴ in comparison with conventional lateral flow methods. Incorporating iSDA into a multistep fluidic device poses the challenge of transporting, delivering, and holding solutions with accurate concentrations of iSDA reagents in an amplification region for thirty minutes. A specific difficulty is delivering the flow of rehydrated iSDA reagents and subsequently stopping fluid movement over the protein capture region. My initial work has been focused on designing and optimizing a device with stopped flow to create ideal amplification conditions evaluated with fluidic dye testing. By using fluorescein and ImageJ analysis to iterate device and membrane design, correct concentrations were delivered to the amplification region. To further the device automation, timers were incorporated so the only user step would be inputting the sample. The device then isolated the target protein, amplified the signal, and provided a diagnostic analysis for the user using a fluorescent probe. Such an advancement can further the reach of higher sensitivity protein diagnostic technologies to low resource settings and for in home testing.

Prolonged wakefulness is the root cause of significant incidents and accidents across numerous shift-working industries. Laboratory research has indicated that exposure to short-wavelength (visibly blue) light enhances alertness and performance, and shifts circadian phase. The strategic use of short-wavelength light may be a suitable fatigue countermeasure to decrease the risk of accidents in demanding occupations. Despite many laboratory studies demonstrating the efficacy of blue light, little work has been done to investigate the translation of such strategies in an occupational setting, where workers are more likely to experience confounding factors that could dampen the effectiveness of lighting countermeasures. One area where lighting countermeasures could be useful is among pilots who must awaken early to begin flying in the early morning hours. Our research aims to investigate the efficacies of integrating fatigue countermeasures in time-sensitive operations to bolster work safety and performance. We conducted a randomized, cross-over study to determine whether blue-enriched lighting could be used to shift circadian phase and sleep, and improve performance among airline pilots working early shifts using 6-sulfatoxymelatonin (aMT6s) concentrations as a default for circadian cycle. Volunteer participants working for a short-haul airline completed a fixed-pattern design (FPD) roster schedule and aMT6s collection protocol outlined in the methods section. The aMT6s data were subjected to a best-fit cosinor analysis to determine the acrophase. Analyses are underway to determine whether circadian phase shifts occurred following the blue-enriched lighting condition.

Microglia are the innate immune cells of the central nervous system that exhibit a sustained pro-inflammatory response in the Alzheimer’s disease (AD) brain. Regulation of inflammatory gene expression in microglia by microRNA miR-155 modulates transition between distinct phases of the inflammatory response. Though altered expression profiles of miR-155 is seen in other neurodegenerative disorders, the precise role of this microRNA in modulating inflammation and downstream behavioral deficits in mouse models of AD remains unknown. We hypothesize that microglia specific deletion of miR-155 will alter neuroinflammation and behavioral phenotypes in transgenic mice expressing human mutant amyloid precursor protein and presenilin 1 (APP/PS1), an AD model that exhibits Aβ pathology and memory impairments. We generated trigenic (Cx3cr1-Cre^+/-/Floxed-miR155^+/+/APP/PS1^+/-) to acutely induce microglia specific Cx3cr1 driven Cre-mediated deletion of floxed miR-155 alleles in the APP/PS1 mouse AD model. Changes in inflammatory gene and microRNA expression in microglia 6 and 9 months post miR-155 deletion were assessed by qPCR. We expect that conditional deletion of miR-155 leads to anti-inflammatory gene expression and thus improve cognitive performance. To measure anxiety, spatial memory, and spatial learning, we employ open field chambers with and without novel object recognition and T-maze assessments. Preliminary results support the hypothesis that conditional miR-155 deletion specifically in microglia alters innate immune gene expression and behavioral phenotypes in the APP/PS1 mouse model of AD, further elucidating the impact of the molecular regulators in neuroinflammation in AD.

Mental health services are infrequently used by Arabs and Arab-Americans despite experiences of hardship and emotional distress, which have only become more frequent and intense due to recent state conflicts, population displacements, and patterns of racial/ religious discrimination. In mental health literatures, this "underutilization" of mental health services is often explained in terms of "culture" and "stigma" associated with mental illness. To better understand these issues for Arab populations, we reviewed multiple literatures related to culture, stigma, and mental illness and distilled important lessons for clinical practitioners, researchers, and policy makers. Key findings highlight the diversity of Arab peoples, suggesting important but complex cultural differences that do not easily lend themselves to generic or formulaic clinical responses. Instead, attention to common factors in psychotherapy (e.g., developing shared understandings of the illness experience) and the (mis)alignment of assumptions about the origins of distress (intra-psychic vs inter-personal) and forms of personhood (referential vs indexical) between client and service provider is encouraged. Such considerations in clinical treatment and research can enable more effective psychotherapy for Arab clients and offer important insights into Arab culture and social reticence toward mental illness and its treatment. Structural issues, like limited resources and support for mental health care, were also relevant as they can reinforce stigma by offering ineffective mental health services that fail to ameliorate suffering. Thus, increased resources in terms of funding, training, and infrastructure is essential to creating a more effective mental health system that appeals to Arab populations.

Credible threats of nuclear war have not been as profound as they are in the society of today, since the Cold War. The nuclear tension between North Korea and the United States has been escalating at an alarming rate. As a resident of Seattle, I am living in the target area of a potential strike. As a United States Marine, I am one of the first to go when our Nation calls. But what is the likelihood of us actually engaging in nuclear war? Is Kim Jong-un really an insane dictator— lost in his own version of reality, or is he an intelligent and calculating leader attempting to influence the world around him? By using something from the social sciences called game theory, we can break away from the speculation in the media and systematically begin to understand the problem. We can analyze the people involved, their preferences and expectations, and what available actions they can take to achieve these goals. By attaching a theoretical payoff to every action a nation may take, such as North Korea or the United States, we can compare the possible outcomes and accurately predict the course of action by relying on two fundamental theories— first that people are rational. And secondly, that people are always looking to rationally maximize their utility. Through my research, I have found that when you analyze a leader like Kim Jong-un, you realize that his actions, however brash or combative they may be perceived, are actually rational choices. Furthermore, his decision to progress his nuclear program is also rational. Despite that, the crux of my research is that nuclear war with North Korea is currently very unlikely. Using the models from game theory, I can change this assertion from one that typically comes from speculation, to one of calculation.

Research has examined the association between marijuana use and delay discounting (i.e., relative preference for immediate versus future rewards). However, limited research has compared those who use marijuana and those who do not on future self-consideration. The purpose of this study is to examine the association between marijuana use and consideration of consequences. College students ages 18-24 were recruited for an ongoing study. To be eligible, participants had to report alcohol use two or more days a week and one or more occasions of heavy episodic drinking in the last two weeks. Baseline data were used for the current analyses (N = 292 to date; 52% female, 71% Caucasian, mean age = 20.17 years). Participants were asked to report on current marijuana use, number of hours high from marijuana in a typical week, and number of marijuana-related consequences experienced in the last three months. To assess participants’ consideration of immediate rewards and future consequences, participants answered questions on the Zimbardo Time Perspective Inventory (ZTPI) and the Consideration of Future Consequences (CFC) scales, respectively. Independent samples t-tests will compare current marijuana users (57%) to nonusers (43%) on CFC and ZTPI scores. We hypothesize that students who report current marijuana use will report significantly lower scores on the CFC scale (i.e., less consideration of future consequences) and significantly higher scores on the present hedonistic ZTPI subscale (i.e., greater consideration of immediate rewards) compared to those who do not use marijuana. Among marijuana users, regression analyses will examine associations between the CFC and ZTPI with levels of marijuana use and consequences. We hypothesize that people who score lower on the CFC and higher on the ZTPI will report higher marijuana use in a typical week and more marijuana-related consequence. Results will inform how future-self consideration may be addressed in interventions.

The spread of disease can occur through bacterial colonization of shared contact points within a community. Potential platforms for bacterial colonization and subsequent spread have been introduced with the bike share applications across the city of Seattle. The bike handles serve as a shared contact point for each rider with the extent of bacterial colonization of those handles unknown. Using swabs to collect bacteria samples from bikes, we are able to assess the number of colony forming units present on each handle. Our ongoing research is examining the levels of bacteria found on the bikes in different parts of the city at different times. This analysis will show the extent of bacterial colonization, whether there is a time or location dependence, and provide a basis for further study into the risk this new shared contact point may pose.

Spinal cord injuries affect over 276,000 people in the U.S. alone. After the initial injury, a secondary injury occurs which results in further neuronal cell death as a result of the inflammatory response and microglial activation in the damaged tissue. Anti-inflammatory drugs have proven effective in reducing the secondary response, however side effects prevent their full-scale clinical use. A localized, controlled system is needed to target the secondary response and reduce the further cell death. To solve this, we have designed a controlled, localized drug release hydrogel-based system that can be placed on the spinal cord injury. The localized system allows for a lower steroid dose, thus side effects should be reduced, and the controlled release should improve the efficacy of the drug. With the continued damage reduced, patients should see increased mobility.

Ultrasonic transducers are key components in the probes of ultrasound devices used for medical imaging. The probe consists of 4 different materials; a piezoelectric element, backing material, an acoustic matching layer and an acoustic lens. The properties of these materials will directly impact the performance of the transducer and the quality of the images produced, making them a high priority for future development. Currently, researchers at Siemens Healthineers are looking to develop new materials for our ultrasound probes to help increase device performance and make better ultrasound devices. This senior capstone project looks to develop the Acoustical Properties Measurement System (APMS), a characterization testing system, to aid in the production of the new transducer materials. Development of new MATLAB and LabView code has been carried out to provide a smoother operating experience and enhanced design simulation. Data storage has been revised to provide a single location for users to access all collected data and a new naming system has been implemented for easier sample tracking. A standard operating procedure has also been established to help aid new users in operation of the system and a new method for measuring high attenuation materials has been developed. These improvements to the APMS system will further benefit the research and development of Siemens Healthineers ultrasound devices, providing customers and their patients with provide accurate diagnoses and help them to make the best decisions for their care.

Mechanistic Target of Rapamycin (mTOR) is a highly conserved serine/threonine kinase originally discovered in yeast as a central regulator of cellular growth and proliferation in response to adequate nutrients and energy levels. mTOR is activated in a complex with an essential co-activator called Raptor. Our lab recently discovered that mTOR holds an essential role in early murine B-cell development; B-cell specific disruption of Raptor inhibited mTOR activity and resulted in a complete block in B cell development at the precursor-B (pre-B) cell stage. We hypothesize that B-cell specific disruption of Raptor will inhibit B-cell transformation induced by the Myc oncogene, and/or will inhibit the survival of B-cell lymphoma cells, by inhibiting cell growth induced by mTOR. We conditionally disrupted Raptor using gene targeting strategies in a mouse model of Burkitts Lymphoma whereby the c-Myc oncogene is expressed under control of the immunoglobulin heavy chain enhancer. We found that Raptor deficient mice took significantly longer to develop B-cell tumors when bred to c-Myc transgenic mice; our Kaplan-Meier Survival curve revealed that disruption of Raptor improved survival rates significantly, such that Raptor knockouts rarely showed growth of tumors. To better understand cellular mechanisms by which Raptor may inhibit B-cell lymphoma formation, we utilized flow cytometry to measure cell proliferation and survival of B cell lymphoma cells in the presence or absence of Raptor. Our results revealed a distinct reduction in both cellular proliferation and survival in the absence of Raptor, which suggests Myc driven B-cell proliferation and survival is highly dependent on Raptor and mTOR activity. In the next part of our studies, we will inducibly disrupt Raptor in already established primary Myc-induced B-cell lymphomas to determine whether Raptor and mTOR activity are essential for lymphoma cell survival. Through these results we will be able to determine whether inhibition of Raptor could be utilized as a strategy to inhibit cancer cell proliferation and/or survival.

Flatfishes of Puget Sound commonly host Clavinema mariae nematode “blood worms”, which reside in the subcutaneous tissue of the host, rendering them unmarketable. Recently, we observed C. mariae in blackbelly eelpout, Lycodes pacificus, which has never before been reported to carry this parasite. Because blackbelly eelpouts have no economic importance, there may have been little incentive for reporting this infection in the past; whether our recent observations of eelpout infection represent a new development or a long-standing host–parasite relationship is therefore unclear. To estimate C. mariae burden in eelpouts from Puget Sound, I am counting subcutaneous parasites in preserved specimens collected between 1911 and 2014, from the University of Washington Ichthyology Collection. If C. mariae appear only in eelpout collected recently, this may indicate a host switch from flatfishes to eelpouts. In the future, DNA sequence analysis will be conducted to determine if C. mariae from flatfishes and eelpouts are indeed the same species. Our work will reveal whether the recent appearance of C. mariae in eelpout is due to host-switching, parasite spillover, or improved observation and reporting.

Organic electronics have generated wide interest and excitement because they are relatively inexpensive to produce and are created from abundant resources, unlike their inorganic counterparts. Many organic materials also possess the unique potential of being stretchable in electronic applications including solar cells, OLEDs, and transistors. These materials can be made into wearable electronic devices and have the potential to power other advanced technology. Organic electronics are often made using semiconducting polymers. However, these polymers are semi-crystalline and brittle in solid state. To enhance their stretchability, our approach is to incorporate stretchable rubber into the semiconducting material by chemically linking the two polymers to combine their properties. This research investigates the crosslinking the well-known semiconducting polymer P3HT, poly(3-hexylthiophene), with polybutadiene (PB), a common rubber, to create a stretchable semiconducting material. To make crosslinking possible, we synthesize P3HT that includes a functional bromine to produce P3HBrT, poly(3-(6-bromohexyl)thiophene). Once the P3HBrT is synthesized, it can then be crosslinked with PB at different ratios to optimize for conductivity and stretchability. The crosslinked P3HBrT/PB can then be made into a thin film transistor and characterized for the desired properties. Ultimately, future research in this area will lead to a new generation of electronic devices with improved material properties.

Glioblastoma (GBM WHO grade IV) is the most dangerous brain tumor in adults and comes in two types, primary and secondary. Primary GBMs form de novo and are more common and more aggressive than secondary GBMs, which develop from grade 2 and grade 3 gliomas. Despite primary and secondary GBMs displaying identical tissue, there are significant differences in the genes expressed that affect the GBMs responsiveness to alkylating treatment. Our research focuses on secondary GBMs and why they have an association with higher progression free survival (PFS) than primary GBMs, in hopes to aid the personalization of treatment plans. Our hypothesis that O6-methylguanine-DNA methyltransferase (MGMT) activity is inversely related to PFS. Our method of experimentation includes taking the MGMT content of the extract, which is supernatant liquid that lies above a precipitate of whole tissue lysates. We then use the radioactivity transfer from a DNA substrate containing O6-methylguanine-DNA to protein as a quantitative measure. In secondary GBMs, there are sometimes mutations in the Isocitrate Dehydrogenase 1 (IDH1) gene. These mutations reduce substrate affinity, decreasing the enzymatic activity. Furthermore, the enzyme develops the ability to produce an oncometabolite, D-2-hydroxyglutarate (2-HG). 2-HG synthesis leads to genome wide hypermethylation of CpG islands potentially causing the MGMT gene to be silenced. The MGMT protein repairs DNA and prevents it from breaking. By silencing the MGMT protein activity, DNA gets repaired less and usually results in double strand breaks. The higher PFS associated with secondary GBMs could be affected by the IDH1 mutation, which can reduce MGMT protein activity and lead the tumor DNA to break, making treatment more effective. Establishing this association could lead to personalized treatment because patients with IDH1 mutations respond better to alkylating agents, such as TMZ.

X-ray spectroscopic techniques utilize selective x-ray absorption or fluorescence to interrogate the element-specific properties of atoms in a sample of interest, such as oxidation state, ligand identities, and bond lengths. Until recently, x-ray spectroscopic techniques have been primarily limited to large-scale synchrotron facilities employing expensive commercial crystal analyzers. This leads to high barriers to access because of high competition for synchrotron beamtime and the large cost of acquiring optics not presently possessed by the facility. Over the past several years, the Seidler lab has pioneered solutions to both these problems. First, the development of lab-scale x-ray absorption and emission spectroscopy apparatus has enabled a wide range of studies without need for the synchrotron, and second, by designing an inexpensive method for manufacturing the necessary crystal analyzers. I focus here on the second issue, improving the availability and decreasing the cost of the crystal analyzers. Crystal analyzers are at the heart of high energy resolution x-ray spectrometers. They serve the same role as a prism or grating in visible-light spectrometers, that is, they disperse x-rays into their component energies. Our work using temporary vacuum forming of silicon wafers reduces the cost of such optics from $5000 - $10,000 to only a few hundred dollars. Furthermore, the use of vacuum together with modern computer-assisted machining gives the freedom to use either the traditional spherical shape or a superior customized toroidal form, specific to each study. These advances in instrumentation will dramatically speed up analysis of materials and permit feedback on synthesis procedures, battery performance, detection of hazardous chemicals, and catalyst activity.

The main control of ocean acidity is the concentration of dissolved CO₂, which depends on the concentration of CO₂ in the atmosphere. CO₂ is a greenhouse gas that plays a vital role in climate change. Boron isotopes in marine carbonates can be used as a paleo-pH proxy for the oceans, and therefore can shed new light in paleo-climate reconstruction. A method that accurately and precisely analyzes boron isotopic compositions must be developed before analyzing any natural samples. This study aims to establish an optimized boron extraction procedure that is done by column chemistry using boron specific resin (Amberlite IRA-743). This resin has a high affinity to boron at pH > 5 and will be bound to the resin. Lowering the pH will decrease the resin's affinity for boron and release it from the resin. In this calibration we tested three mirco-columns (made in house) of our standard (NIST- SRM951a) in a slightly basic solution (pH ~8) and then elute them with H₂O and HNO₃ through the columns. Each column is eluted with 100μl of 1N HNO₃ 10 times and collected. Inductively-Coupled Plasma Mass Spectrometry (ICP-MS) is then used to determine the total recovery rate and how many times the column must be eluted to get 100% yield. This column calibration procedure is an important step towards quantitative analysis on boron in natural carbonate samples.

Irreversible damage to organs due to various illnesses that impacts millions of people daily are derived from a common problem: a lack of oxygen. This includes myocardial infarctions that reduce oxygen to the heart and lead to extensive tissue damage. Stem cell-derived cardiomyocytes have been used for direct injection into the heart after an infarct to increase muscle regeneration, but the survival rate and engraftment of these cells are found to be only five to ten percent due to the ischemic conditions. This project aims to increase cardiac regeneration after myocardial infarction through the development of photosynthetic stromal cells that can be injected alongside the stem cell-derived cardiomyocytes. Our initial research has been focused on combining mammalian cells with chloroplasts. We isolated chloroplasts from spinach and measured their oxygen output to demonstrate that chloroplasts produce oxygen. We have then successfully inserted the chloroplasts into mouse fibroblast by incubating them together in the presence of Epidermal Growth Factor as a proof of concept. Once the chloroplasts are successfully uptaken by stromal cells, their ability to produce oxygen upon light exposure will allow surrounding stem cell-derived cardiomyocytes to survive in ischemic conditions. Application of these cells would not be limited to cardiac regeneration, as they could be injected with other cell types into damaged tissues from ischemic conditions to increase oxygen and facilitate regeneration.

Adaptive learning technologies are regarded as an innovative approach to personalize student learning in large college classrooms where interaction with instructors is limited. Such software allows students to learn at their own pace, and to concentrate their efforts on topics which need improvement. However, studies on adaptive learning systems across disciplines have yielded mixed results as to whether they have an impact on improving course mastery. Our research focused on testing how use of adaptive learning reading quizzes in the final quarter of an introductory biology series impacted student exam performance. Students (n=576) enrolled in this course were distributed across 25 lab sections. Students were randomly assigned by lab section to either static or adaptive learning pre-lecture reading quizzes. Both types of quizzes were provided to students through Macmillan’s LaunchPad portal, and points were awarded on a completion/ no completion basis. We used multiple linear regression with model selection to compare student performance between the two treatments, controlling for student characteristics (e.g., GPA, gender). When student performance on in-class reading quizzes and course exams was compared, no statistically significant differences were found between treatments. Similarly, through the administration of three surveys throughout the quarter, we were able to measure students’ attitudes toward different course components. Our findings show that there was no statistically significant difference as a result of adaptive learning reading quizzes on how prepared students felt for class, how much they enjoyed the course, how much they valued reading quizzes, or if they preferred the reading quiz format in this course to those in previous courses. Our findings suggest that given the additional financial cost of adaptive learning technologies to students, instructors should first verify that adaptive learning significantly impacts mastery of course material prior to fully integrating it into their course structure.

Stuttering is a speech disorder that prevents people from communicating effectively. Stuttering is characterized by disfluencies that disrupt normal speech such as repetitions or prolongations of sounds or syllables. While approximately seventy million people suffer from stuttering worldwide, the cause of stuttering remains unknown. However, researchers have found a neurological difference between people who stutter when compared to people who do not stutter. Our lab has recently discovered that people who stutter do not exhibit a phenomenon called pre-speech auditory modulation. This phenomenon, observed in typical speakers, refers to the differential response of the auditory cortex to probe tones that are presented immediately before speaking as compared with the control condition of probe tones presented with no speaking. We hypothesize that pre-speech auditory modulation reflects adjustments in auditory processing in preparation for monitoring auditory feedback during speech production. Disruptions in this feedback monitoring process may play a role in causing the speech disfluencies observed in the speech of people who stutter. To test this hypothesis, we are investigating the presence or absence of pre-speech auditory modulation in children. Children will perform speech tasks while probe tones are administered through earphones. Non-speech control tasks will also be performed for comparison. The response of the auditory cortex to these sounds during the two test conditions will be recorded using electroencephalography (EEG). A difference in response would indicate pre-speech auditory modulation is occurring. During early speech development, children rely on auditory feedback more than adults whose speech motor system is fully developed. Hence, if pre-speech auditory modulation reflects preparation for monitoring auditory feedback during speech production, then the phenomenon should also be observable in the speech of young children. Results will advance our understanding of typical speech development and provide control data for future studies involving stuttering children.

Periodontal disease (PDL) results from a serious infection in the gingival tissue (gum) that can eventually lead to tooth loss and jawbone damage. The disease is common with more than 3 million cases in the US per annum. Bacteria build up in plaque lead to gingivitis and periodontitis under improper oral hygiene. If left untreated, the supporting tissues of the teeth e.g., cementum and periodontal ligaments will be lost, therefore making the teeth and supporting tissues vulnerable to bacterial attack, leading to serious infections and, even, to death. Current approaches in regenerating periodontal ligaments include the use of bioactive molecules and barrier membranes for guided tissue regeneration using human stem cells. Although the utilization of such materials enhances the cell proliferation and differentiation to a degree, the absence of cementum-like tissue prevents the complete regeneration of periodontal ligaments on the tooth surface. The aim of this project is to develop a biomimetic strategy to restore cementum tissue and regenerate the periodontal ligaments using human periodontal ligament (hPDL) cells in vitro. Using peptide-guided remineralization, we created a new cementum-like mineral layer on exposed dentin. The hPDL cells are then cultured and seeded on the novel cemento-mimetic layer and induced to differentiate. The proliferation and differentiation of the hPDL cells are monitored in detail using 3-(4,5-Dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) and alkaline phosphatase (ALP) assays, respectively. Our results show that the newly formed cemento-mimetic mineral layer facilitates the hPDL growth and differentiation. The method described herein offers a unique biomimetic solution to regenerate periodontal ligaments and thereby ultimately prevent tooth loss and eliminate periodontal disease. This work is supported by WA-State Life Sciences Discovery Funds, UW-School of Dentistry Spencer Funds, and Amazon-UW/CoMotion Catalyst Program.

American Indian / Alaskan Native communities are asserting their rights as sovereign nations to integrate culturally relevant practices and community-wide protections into research that is conducted within their Nations. Institutional Review Boards are entities responsible for overseeing all research that involves human subjects and ensuring that ethical standards are met. This work seeks to examine the similarities and differences between Tribal Institutional Review Board (IRB) and Non-Tribal IRB application processes.  We compared six Tribal IRB applications created by three different tribal communities, one tribal college, one tribal health organization, and an Indian Health Service Area Office. The major contributions of this work include a dataset of all federally registered tribal IRBs, a systematic analysis of the difference in online presence and format for application requirements, and a better understanding for the unique place-based requirements central to tribes. Preliminary results include a new dataset of 33 active and 17 deactivated federally registered Tribal IRBs. Our comparison of six of these active Tribal IRBs has revealed notable areas in which they are similar to each other and different from Non-Tribal IRBs.  These areas include community involvement in the research process, ensuring research meets communities' needs, awareness and implementation of culturally respectful methodologies, meaningful reporting of results to the researched communities, and tribal ownership of research data.

The upper campus of UW Bothell contains 570 trees, the most prominent species including Douglas-fir (287), western redcedar (153), and big leaf maple (83). All trees (outside of the campus floodplain restoration project) greater than 6 inches in diameter (DBH) were measured for parameters of size (stem diameter, canopy height and widths, and overall height) and function / health (proportion of missing canopy, total area exposed to direct sunlight, proportion of canopy in healthy condition) as well as GPS. These measurements were then processed by the US Forest Service i-Tree Eco modelling program to estimate individual tree carbon sequestration and storage, stormwater interception and runoff reduction, air pollutant removal, and oxygen production. The GPS data in ArcGIS was merged with the i-Tree model in order to produce maps of tree stands and individual trees, along with their respective ecological values. This map allows for the ecological impacts of the construction of new buildings to be estimated, as well as the magnitude of potential savings in ecological function that can be made with detailed adjustments in building orientations. It has been determined that the stand of trees to be removed for the construction of UW4 stores up to 24.7 tons of carbon within tree tissue, which translates to 90.5 tons of CO2, which is roughly the equivalent of CO2 released if all 16 UW Seattle Biology lecturers flew round-trip in their own separate airplanes from Seattle to Miami, then each drove their own buses from Seattle to Miami and back again 4.6 times. As campus growth proceeds, it’s essential to lay the groundwork for quantifying and understanding the spatial pattern of potential losses in ecological function so we might be able to make better choices about development options.

Biomaterials are frequently utilized in today’s society for a variety of applications from joint replacements to pacemakers to synthetic skin. Biomaterials often serve to replace missing or damaged tissue in the body. Alginate is a commonly used carbohydrate polymer that is derived from seaweed and the base for many tissue engineering applications. This research is working with an alginate-polypyrrole composite that can form a hydrogel. Polypyrrole an intrinsically conducting polymer, which allows the entire hydrogel to have a low conductivity for signal transfer. Composites similar to this are used in bionics as well as nerve regeneration research. It is also inexpensive and biocompatible. This project aims to utilize a 3D bioprinter to optimize the printing alginate-polypyrrole bioinks at varying viscosities. This biomaterial serves as a foundation for the potential creation of 3D printed conducting scaffolds that could be used in applications such as peripheral nerve damage (e.g. arm or leg partially severed in IED detonation). By using the spreading ratio formula (printed needle diameter / needle diameter) we will first need to determine which gauge needle and viscosity of alginate-polypyrrole gives us the closest value to 1. A spreading ratio of 1 tells us that the material coming out of the needle and being laid on the print bed is equal to the needle diameter selected; in other words, no “blobs” are occurring and the material is being properly crosslinked and will serve its function. We predict that using a smaller gauge needle (22, 23) after approximately 30 minutes of crosslinking will give us optimal results.

Recent advances in RNA sequencing and molecular biology has allowed them to be at the forefront of diagnostic care. Although sequencing costs have decreased, existing methods for detecting gene expression levels are not feasible in a clinical setting. Creation of a simpler molecular diagnostic based on measuring gene expression levels in blood could provide an alternative as a reliable, fast and easy to perform diagnostic. Multiple genes can have various expression levels across patients and patterns of this differential gene expression is key in studying multiple diseases including cancer or autoimmune disorders. Before testing the platform with clinical samples a smaller classifying circuit that fluorescently differentiates between a series of different cancer cell lines was created. Directly, my work has been developing fluorescent reporter probes that will be able to categorize weighted genes in our classifiers neural network. Positive and negative gene weights can be used to differentiate between cancer cells lines as cells express certain genes in varying amounts between populations. When running samples in our qPCR protocol, addition of the fluorescent probes, allows each gene to be sorted into distinct fluorescent channels. After testing the probes using RNA extracted from our cancer cells (HEK, HEPG2, MCF7) results were similar to the known gene expression data when measuring a series of 5 genes across these cell lines. Additional, experiments are currently underway to establish a gradient for fluorescence so that not only the type of cancer cell can be determined, but the proportional amount with high specificity and low variability. After development the fluorescent probe system will be incorporated into a clinical sample protocol and the platform will undergo further optimization for clinical applications. For patients a novel diagnostic platform allows for a more thorough disease screening, longer treatment time and hopefully a more positive prognosis outcome.

This project is a discourse analysis of biomedical studies on Asian American mental health within the past twenty years, examining the extent to which trends are interpreted as due to cultural difference rather than sociopolitical factors. When researchers ascribe health outcomes to false and overgeneralized perceptions of Asian American culture, stereotypes are replicated as biomedical fact at the expense of Asian American wellbeing. For instance, many studies in Asian American mental health literature emphasize low help seeking. While some researchers cite preconceived monolithic notions of ‘Asian’ values surrounding shame and stigma, other research has revealed more compelling correlations such as lack of insurance, gender, and nativity status. Approaching from an American Ethnic Studies lens, I examine the extent to which research design and terms used in data analyses integrate understandings of Asian American history and politics. Examples include use of data disaggregation, to understand trends of individual Asian American ethnic groups, as well as references to landmark legislation.

Imidacloprid (IMI), a neonicotinoid, is being sought as an alternative to the carbamate pesticide, carbaryl to control burrowing shrimp (ghost shrimp, Neotropea californiensis) in Willapa Bay and Grays Harbor, Washington. The shrimp destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster (Crassostrea gigas). Previous laboratory tests indicate juvenile and adult ghost shrimp are overtly affected (immobilized) when exposed to IMI in artificial seawater (SW) at concentrations expected during control operations, but not killed and subsequently recover. Our objective was to determine if emamectin benzoate (EB) is an alternative to IMI. EB, the active ingredient (a.i.) in Slice®, is currently registered for use in marine waters for the control of sea lice on farmed salmon. We targeted juvenile shrimp because they are likely more sensitive than adults and reside within the upper 10-15 cm of the sediment facilitating control. In an initial test to determine the effective range, we exposed juvenile ghost shrimp (mean carapace length = 2.3 mm) to static concentrations of EB (as the insecticide Proclaim®) ranging from 0.01 to 100 ppb a.i. within artificial SW for 96 h. All shrimp within the 100 ppb treatment died within 48 h and 27% exposed to 10 ppb succumbed by 96 h. In a subsequent 96-h test (static 48-h renewal), we exposed juveniles (mean carapace length = 2.1 mm) to concentrations of EB ranging from 10 to 100 ppb to determine the median lethal concentration (LC50). All shrimp exposed to 100 ppb died within 24 h. The 96-h LC50 was 18.8 ppb compared to >12,000 ppb for IMI. EB may provide more effective control than IMI because it targets the primary neurophysiology of the shrimp. Further tests are required to determine effective concentrations within sediment, assess potential non-target effects, and evaluate environmental fate.

Traumatic spinal cord injuries may lead to devastating loss of neurological function and there are currently no effective clinical methods to regenerate damaged nerve tissues. Besides, the inflammatory response can cause secondary injuries and inhibit regeneration. Novel treatments like cell therapy and localized drug delivery have shown greater efficacy when delivered by hydrogel scaffolds. However, effective scaffolds that can both culture neuronal cells and deliver therapeutic drugs are rare. Therefore, there is a need for an effective treatment of spinal cord injury that can locally deliver therapies with anti inflammatory properties to the spinal cord, as well as provide a support material for neural stem cell therapy. Here, we report a hydrogel composed of peptides that can self-assemble into a hydrogel in physiological conditions. The self-assembling peptide is conjugated to a polymer that enables drug loading and bioactive properties. Self-assembling peptides and a drug loading polymer were synthesized and characterized, loaded with bivalirudin, a model anti-inflammatory peptide drug, and assembled into a hydrogel formulation. The hydrogel was used to encapsulate neural stem cells to assay its efficacy as a support material. The gel was also assayed for its ability to release the anti-inflammatory drug when exposed to enzymes upregulated during inflammation. We anticipate seeing effective ligation of the polymer with the self-assembling peptide, successful hydrogel formulation, and neural stem cell viability when encapsulated in the hydrogel. A successful self-assembling formulation will ultimately work to provide effective cell therapy and anti-inflammatory drug delivery to the spinal cord, with potential for broader drug loading applications in the future.

With the recent legalization of recreational marijuana use in states spanning the country, rates of marijuana use among college students are climbing. Marijuana is one of the most heavily used drugs among young adults and the literature on sex differences in consequences of marijuana use is sparse. This study examined sex differences in marijuana-related negative consequences among college students. Data were collected from students across 9 campuses who indicated past year non-medical use of prescription stimulant medication as part of a larger web-based study. Participants (n=341) reported past year frequency of marijuana use and related consequences using the Rutgers Marijuana Problem Index. Results revealed a main effect of sex on "feeling down about yourself" as a consequence of marijuana use, indicating that men were more likely to endorse this consequence than women. Results also revealed a main effect for marijuana use frequency; indicating heavier users were more likely to report feeling down about themselves, trouble managing their time, and making decisions they later regretted. Two-way interactions between marijuana use frequency and sex were also explored. A marginally significant interaction revealed that male, but not female, frequent users reported feeling down about themselves because of their marijuana use more than less frequent users. We also found a marginally significant interaction among lower frequency users, where men report having trouble managing their time more than women, but this was reversed when looking at higher frequency marijuana users, with women indicating greater endorsement. Lastly, we found that among women, marijuana use frequency was unrelated to making decisions they later regretted. Conversely, among men, more frequent marijuana users reported this consequence more than all other groups, whereas less frequent male marijuana users reported this consequence the least. Differences in consequences associated with marijuana use have implications for intervention efforts for male and female students. 

Telehealth is being widely adopted in medicine, but is still novel in the field of dentistry, especially in therapy. Dentists rely on in-clinic visits and application of therapies rather than prescribing drug treatments outside the clinic. In this paper, we have developed and introduced an app that dentists can use to establish and maintain trust for fluoride treatments to be conducted correctly at home. Pediatric patients and their caregivers can access the client app on their phone to guide them remotely and record progress. A unique aspect of this app is rapid and accurate display of the child’s own emerging teeth and the sites for fluoride therapy. In our study, we surveyed 16 dentists that were equally divided into two groups, half being exposed to a demonstration of the tool before taking the survey, and the other half taking the survey without any exposure. Although the randomly selected group which saw the app received their dental degrees on average 8 years earlier, four times the number of these dentists would allow off-label at-home use of the highest level of fluoride varnish for the youngest ages of patients. The tools present in this pilot study appear to influence pediatric dentists' management plans and attitudes towards home treatments, demonstrating the potential of expanding teledentistry to incorporate at-home care and treatment in addition to self-monitoring and tracking.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder involving impairments in social communication and repetitive and restrictive behaviors. Children with ASD are oftentimes diagnosed with cognitive impairment, specifically below average intelligence scores and atypical brain function in relation to early developmental regression. In order to analyze neural activity, Electroencephalogram (EEG) is used to monitor brain activation during certain tasks. EEG is a non-invasive tool that uses scalp electrodes to record neural activity frequency. EEG is divided into frequency bands, including the Alpha band frequency (neural activity between 6 and 12 Hz), which is present during the relaxed awake state of individuals and thought to be related to functional inhibition. Previous EEG studies consistently detected abnormalities in resting state alpha among individuals with ASD when compared to neurotypical counterparts. Findings suggested that reduced resting state alpha power was exhibited in brain regions involved in sensorimotor skills and higher-order cognitive functioning. Although many studies compare the difference between ASD group and neurotypical group, more research is needed to study the alpha power patterns within the ASD group. This study aims to compare EEG peak alpha power and average alpha power between high functioning (NVIQ>100) and low functioning children with ASD. 100 participants (50 males and 50 females) aged 6-18 participated in the study. All participants met criteria for autism diagnosis on a clinician administered standard interaction, and completed the DAS-II, which measures verbal and non-verbal cognitive abilities. Participants watched calm screensaver like videos while high density EEG was collected. We hypothesize that the children with ASD and lower functioning will have reduced average alpha power and reduced peak alpha frequency when compared to higher functioning children with ASD. The results of this study will provide insight into of differences within children with ASD.

New techniques in mapping genome structure have revealed a high level of spatial organization in the nucleus. The 3D location of a gene within this high order structure is thought to impact its transcriptional state. Long-range DNA loops could link distal regulatory elements to their gene targets. To test this hypothesis we plan to develop a programmable system that allows us to loop DNA loci together, bringing them in spatial proximity. We hope to explore whether we can create or disrupt interactions between genes and regulatory elements by engineering new DNA loops. We will use programmable CRISPR-Cas DNA binding domains to target specific sites in the genome. The CRISPR-Cas complex will be tethered to an interaction domain (ID) that can dimerize with another ID at a distant DNA locus. A main challenge faced when building DNA loops is free IDs are likely to outcompete looping interactions between complexes bound to DNA. To favor interactions between complexes bound to DNA, we will use protein switches designed in the Baker lab to sense whether the CRISPR-Cas complex has engaged its DNA target. I am currently testing prototype protein switch designs and measuring their ability to activate when assembled on DNA. Initial results have shown that our switch designs can activate upon DNA binding, but that our system still needs optimization. After our switch design is optimized, we can move on to the full-fledged looping system and begin to assess the regulatory consequences that spatial repositioning has on gene regulation.

Autism spectrum disorder (ASD) is one of the fastest growing childhood disorders, becoming a major public health concern. Studies have shown that children with ASD are more likely to be exposed to perinatal complications than typically developing (TD) children. Sex differences have also been shown to affect ASD diagnoses. However, variables that affect severity of ASD are still understudied. Understanding factors that impact ASD severity may assist in establishing methods to identify ASD outcomes, and target children at high risk for worse outcomes with treatment. The study aims to investigate IQ differences in children with ASD on variables including birth weight, gestational age, sex, and birth order. 150 children (75 males and 75 females) aged 6 to 18 years with a confirmed diagnosis of Autism participated in the study. Autism diagnoses of the participants were confirmed via ADOS-2, a clinician-child measure that scores on child’s social, repetitive behaviors and communication skills. Parents completed a self-reported demographic questionnaire about family demographics, and the Autism Center of Excellence subject medical history form, a medical interview with information on pregnancy complications and child medical history. All subjects completed the DAS-II evaluation tool that measures the cognitive abilities (IQ) of children on verbal and non-verbal domains. We hypothesize that children with lower IQ levels (full scale IQ<80) will have lower average birth weight, average smaller gestational ages and a higher number of pregnancy related complications. We also expect that given the higher rate of ASD incidence in boys, within the ASD group, there will be a main effect of sex with more males (n=75) having higher rate of pregnancy complications than females (n=75). Results will help establish a better understanding of other prenatal variables that may be correlated to later severities of ASD, and provide support for treatment targeted at prenatal risk.

This abstract is no longer available. Please contact urp@uw.edu if you have any questions.

With the growth of the internet, social networking sites have become an important part of relationships. A preliminary literature review has found post-dissolution distress is positively associated with online surveillance. Limited research has been done in understanding if breakup distress can predict post-dissolution online surveillance on other platforms. Therefore, systematically investigating the relationship between post-dissolution online surveillance and distress among young individuals will fix this gap in knowledge. As there has been a contradiction of gender as a predictor of breakup initiation, this study will also look at gender difference and breakup initiation as predictors of post-dissolution distress. There are three hypotheses in this study. H1: There is a positive relationship between post-dissolution online surveillance and post-dissolution distress. H2: There will be a statistically significant difference in distress between male and female. Female will experience more post-dissolution distress. H3: There will be a statistically significant difference in post-dissolution distress between those who attribute the breakup to their partner and those who initiate the breakup. Those who attribute breakup to their partners will experience more post-dissolution distress. This study will go under IRB review shortly and data collection and analysis will be conducted in April. The long-term goal of the research is to provide positive insights to human use of social networking sites and emotional health. Results of this project will ultimately help young individuals further their personal well-being.

Kilauea Iki Lava Lake, a lava lake in Hawaii Island, was formed during the summit eruption of Kilauea Iki caldera from late 1959 to early 1960. It has been a closed system since the event since no material was added after its formation, and it then became an excellent place to study magma differentiation. During cooling, different minerals cool at different temperature due to their difference in composition, and magma gradually differentiate along with temperature decrease. Thus, by knowing the primary composition of the magma, the differentiation pattern can be indicated. In order to observe differentiation process, the changes in oxide content in the remaining liquid were compared with MgO, the temperature-related oxide. In this project, MELTS, a software package designed by Mark.S.Ghiorso is used for my analysis. By utilizing MELTS, weight percentage of oxides vs MgO models can be calculated with known primary composition and assumed temperature, pressure and volatile content. After adjusting the model by comparing with real sample data of cooled lava, reliable models of content of oxides can be generated to be a strong indicator of differentiation process, and can be used in future studies of Kilauea Iki Lava Lake.

The midbrain is a critical region of the brainstem that houses the cranial nuclei necessary for coordinating eye movements. It has been observed that neurons in the midbrain express T-box Brain 2 (Eomes/Tbr2), a transcription factor generally associated with development of glutamatergic neurons. Because it has such a diverse role throughout the development of multiple neural structures (i.e. cerebral cortex, olfactory bulb, retina, and cerebellum), Tbr2 is thought to be implicated in the development of certain forms of autism. The purpose of our experiments was thus two-fold: first, we investigated the neurotransmitter phenotype of Tbr2+ neurons in the midbrain. Second, we wanted to identify the function of Tbr2+ neurons in the brain by studying these populations in relation to known, molecular markers of specific, anatomical features. In order to accomplish these aims, we collected tissues at various ages from transgenic mice. We utilized endogenous reporters such as VGlut2-Cre^Ai14 and Tbr2mTnG alongside immunohistochemical staining with the following antibodies: urocortin-1 (UCN-1; which marks the centrally-projecting Edinger-Westphal nucleus, EWcp, in the postnatal brain); cocaine- and amphetamine-regulated transcript (CART, which marks EWcp in the embryonic and postnatal brain); and 2H3 (which marks neurofilaments). We then used a confocal microscope to visualize fluorescence and collect images. We found that Tbr2+ neurons in the midbrain were glutamatergic but not cholinergic. We also found that Tbr2 neurons were not Edinger-Westphal cells, leaving their ultimate anatomical identity unknown. Understanding the identity of Tbr2 cells is a prerequisite for beginning to understand the constellation of features that make up autistic spectral disorder, thereby guiding future clinical and scientific research.

Microglia are the resident immune cells of the CNS and are hypothesized to influence aging in the brain. Like somatic cells, microglia can be replaced by self-renewal. Recently, some studies have suggested that new microglia derive from asymmetric cell division of a progenitor population. Microglia progenitor cells have been difficult to study due to a lack of specific molecular markers of this population. However, the Garden lab has recently identified novel candidate markers. We hypothesize that in neurodegenerative disorders associated with advanced age, microglia progenitor senescence may contribute to disease pathology. To efficiently study the senescence of microglia progenitors, we turned to neonatal mixed glia cultures, in which the presence of microglia progenitors has long been inferred. In these cultures, microglia are harvested from cells floating above a monolayer culture of mixed neonatal glial cells. The size of each microglia harvest generally decreases with successive harvests. This suggests that microglia progenitors in the attached monolayer may become senescent after multiple rounds of the cell cycle, leading to stagnation in the generation of new floating microglia. We evaluated microglia progenitor senescence in neonatal mixed-glia cultures by labeling with BrdU, a thymidine analog taken up by proliferating cells and remaining in their daughters. Microglia harvested from these cultures weekly were assessed for BrdU incorporation using flow cytometry and immunofluorescent microscopy. We co-labeled floating microglia and dissociated monolayer mixed glia cultures with antibodies directed against a progenitor marker (CD133), a microglia marker (Iba1), and BrdU. The attached mixed-glia cell layer was also labeled for SA-ß-Gal, an indicator of cellular senescence. Progenitor senescence will be detected by a decrease in CD133/BrdU-positive cells and an increase in CD133/ SA-ß-Gal positive cells.

One issue in many medical applications is detecting the presence of forced exhalations or breaths through audio data. For example, analysing sleep disorder breathing or analysing a person's lung function from audio of their exhalation first requires localization of a breath event in an audio file. Past work has focused on extensive feature extraction from sound and machine learning methods to detect these events. However, these black box methods require significant feature engineering dependent on the type of exhalation and environment the audio data is recorded to find the start and end of an exhalation event. We present a novel method for detecting the start and end of forced exhalations for spirometry, a medical test of lung function, in audio files. The algorithm requires an initial set of audio files containing exhalations to be manually labelled for locations where exhalations can be heard. Then, we build an envelope which encapsulates the shape of our exhalation signal. We take the cross-correlation of this initial envelope with vast amounts of unlabelled audio data containing exhalations, and use the estimated locations of exhalation events to recalculate the envelope. We repeat this process with the new envelopes until convergence. The converged envelope is then used to autocorrelate an audio signal to detect the start and end of exhalation. While preliminary results show that this method only achieves comparable performance to ad-hoc approaches currently used compared to human labels, it has the benefit of being simpler and more interpretable, enabling easier improvements and runtime of the algorithm.

Roughly 20% of young adults in the United States experience some sort of mental health disorder. The majority of this research has focused on young adults in general or 4-year college students, however less is known about the mental health and coping strategies of young adults not currently attending school. The purpose of this study was to compare mental health, the use of alcohol and/or other substances as a coping mechanism for stress, and alcohol and marijuana use among young adults who attend 4-year colleges and those not attending school. A subsample (N=552; 56% female, 59.5% White, M age=20.58, SD=1.7) of young adults using baseline data from a larger longitudinal study on health behaviors was used for the current analyses. The subsample included 355 students currently attending 4-year college and 197 young adults not attending school (highest education status of these individuals included less than a high school diploma (1.5%), high school diploma (19.3%), some college (15.2%), 2-year degree (10.1%), 4-year college degree (52.8%), and graduate degree (1%). Findings indicated that young adults not in school reported significantly higher rates of depression, anxiety, and perceived stress in the past month than students in 4-year colleges. Similarly, findings indicated that non-students reported being high from marijuana for more hours, higher rates of alcohol use and coping with stress through alcohol and/or substance use in the past month than 4-year college students. Further research is needed, which focuses on young adults who are not currently attending 4-year colleges as they may face different life stressors and cope differently than 4-year college students.

Since the Apollo era, the question has remained where lunar swirls (high albedo regions coincident with regions of surface magnetization) originated from. Different ideas have been proposed for their origin. Our study focuses on one of these ideas that the reason lunar swirls have a higher albedo relative to the surrounding regions is because it deflects incoming solar wind particles. This can result in darkened or weathered lunar surfaces. We have used spectro-imaging to observe the thermal properties of lunar regolith (fine grained material on the surface of the moon) in a high temperature environment via nichrome wire to simulate this occurrence. With the spectro-images we are able to observe to great magnification the physical properties of the regolith of two particular grain sizes. The nichrome wire is woven into a shape that can cover an area of lunar regolith. A current is run through the wire allowing it heat up quickly. The study thus far shows evidence of the lunar regolith possessing an amount of water, raising its heat capacitance, giving a more resistive property. The regolith itself is able to retain a considerable amount of heat after heating with nichrome wire and remains widely on the surface layer of the regolith. These properties are necessary to quantify prior to the alteration of the regolith simulant by a directed plasma beam. This study will provide a baseline to qualitatively assess the alteration relative to our study.

Previous research has revealed that as new neural progenitor cells divide and migrate from the ventricular zone to the cortical plate in cerebellar mice tissue, they express a distinct sequence of transcription factors, including Tbr2, during phases of their migration. These proteins are presumed to be linked to vital events that occur during neurogenesis, and therefore can be used as markers to map both the birth, and trajectory of new neurons in mice. Tbr2 in particular, has been found to be a marker for Unipolar Brush Cells (UBCs) - a unique type of glutamatergic interneuron that is prominent in the cerebellar area of the brain. Work done previously in the Hevner lab has since shown that an ablation of Tbr2 in mice correlates with a marked decrease in UBC production. Therefore, we have hypothesized that first, Tbr2 is expressed in both mice and human cerebella, and may play similar roles in development. Second, Tbr2 is necessary for UBC development in mice cerebella. To test the first claim, slices of human cerebellar tissue ranging from 18 weeks of age (gestational), to 2 months of age (postnatal) were examined using immunohistochemical techniques. High magnification images were then collected using AxioVision software. From the collected data, we have concluded that humans also express Tbr2 in the cerebellum during neurogenesis. In order to test our second claim, we are using the Cre-Lox recombination system to develop a Tbr2 conditional knock-out mouse. We anticipate that this mouse tissue will demonstrate the dependence of UBC production and development on Tbr2 protein. Continuing to decipher the characteristics of these cells and the various developmental patterns that occur in the cerebellum, are the fundamental first steps in developing practical applications of neurological research.

Zika virus has become a major epidemic around the world due to the serious birth defects that it can cause; this has led to an increase in research regarding Zika and how to diagnose the disease. Diagnostic tests require a specific sample type to be tested for the presence of a virus, and because it has been shown that Zika viral levels are more consistent and reliable in whole blood compared to plasma or serum, whole blood is the more efficient sample type. Current strategies for diagnosing Zika fall short because there is limited data on how the virus presents itself in the body, and many of these strategies utilize expensive and time-consuming methods that are not feasible in low-resource settings where Zika is more prevalent. Therefore, there is a need for a low-cost and instrument-free process that can effectively purify Zika virus RNA from whole blood in order to allow for detection of the viral RNA. This project dealt with optimization of an existing lab protocol that required laboratory equipment and resulted in low efficiency. The aim was to develop a robust, high-efficiency, instrument-free RNA purification protocol for whole blood samples. The method of RNA purification consisted of a lysis and binding buffer, followed by RNA purification using silica beads embedded in paper to extract pure RNA from the sample. qRT-PCR was then used to quantify the resulting RNA. So far, the paper-based extraction method recovers approximately 20% of the initial target RNA; however, there are still some techniques that will be employed in the future to help improve this recovery rate. The goal of this project is to increase RNA purification efficiency and to provide an alternative mechanism to purify nucleic acids that can be used in a Zika virus diagnostic test.

In this economics thesis, I addressed one of the effects that the Affordable Care Act has had on US Health Care since its full implementation in 2014: supply side effects. Specifically, I answered the following question: what is the effect of the implementation of the Affordable Care Act on patient wait times in primary care offices? In order to narrow the field of research, I focused on the tier of the ACA that called for increased Medicaid expansion. Since Medicaid has not been expanded evenly in all states, it has created a robust control group for causal studies such as this. I used a difference-in-difference model and a multivariable regression to establish causality between Medicaid expansion and increased patient wait times. I used data gathered from the Current Population Surveys from 2004, 2009, 2014, and 2016, in 15 different cities around the US (some faced increased Medicaid expansion, and others did not). The dependent variable data (new patient wait times) were extracted from a 2017 Merritt Hawkins Survey which found the wait times for new patient appointments in different medical services across the 15 different cities for the four different years. The different services are as follows: cardiology, dermatology, obstetrics-gynecology, and orthodpedic surgery, and family medicine (where wait times were only measured in 2009, 2014, 2017). This thesis has been fully developed over a yearlong process of data collection and analysis. My findings highlight areas of the ACA that can be improved to accommodate the proven increased demand for health care, especially given that the supply of health care services responds slower than demand for health care, leading to longer patient wait times.

This research focuses on obtaining a better understanding of people’s knowledge regarding the US Civics Test or more commonly known as the Citizenship Exam. The US Citizenship Exam is taken by individuals who are in the process of becoming US citizens, meaning naturalized citizens. The purpose of this research is to survey individuals of different documentation status about their knowledge regarding the US Citizen Exam in order to obtain a better understanding of people’s interpretations of citizenship and Americanness, and to observe the correlation between key demographics and participants' beliefs. This research was conducted through an interview of 15 participants. The survey used to interview participants comprised of three parts: 1) demographic information about participants’ backgrounds, 2) five questions from the US Citizenship Exam, and 3) five conceptual questions about citizenship. This meant observing if participants knew the correct answers to questions from the Citizenship Exam, or were knowledgeable about the process to become a US citizen. Through the responses to the conceptual questions about citizenship, we obtained a better understanding of participants’ interpretations of citizenship and Americanness. With this data, we observed correlations between the demographics (identities) and the results (knowledge and beliefs). As a result, we find that the US Citizenship Exam neither efficiently nor accurately captures the meaning of citizenship. In addition, we also find that citizenship is not synonymous with feelings of being American. One may have legal status but may not feel American, while one may feel American and not have legal status. Overall, the findings complicate the concept of citizenship, and question about what it means to be American.

Icelandic wetlands have ecological, climatological, and historical significance. The Millennium Ecosystem Assessment defines ecosystem services as the benefits humans receive from nature. Many of these benefits are not included in the economic market which leaves them out of cost-benefit analysis in decision making. Although the Kyoto Protocol approved wetland restoration as an official climate mitigation activity, wetland restoration activities in Iceland have yet to catch up. Valuing the ecosystem service of carbon sequestration can help clarify for Icelandic policy-makers that the benefits outweigh the costs of restoration. This study conducts an economic valuation of the carbon sequestration service in Úlfarsárdalur to provide the city of Reykjavik with new information to include in a cost-benefit analysis of restoration. Three methods are used to quantify the monetary benefit provided by potential carbon sequestration in Úlfarsárdalur – direct market pricing, damage avoidance cost, and replacement cost. The results relied on physical data provided by the Verkís report of restoration potential in Úlfarsárdalur as well as data collected by Hlynur Óskarsson, a wetland ecology expert. In accordance with claims from the Millennium Ecosystem Assessment, all three methods reflected that the economic benefits of carbon sequestration exceed the costs of restoration by a significant amount. The direct market pricing and replacement cost methods yielded similar values, while the damage avoidance cost came out much lower. These findings suggest that wetland restoration to promote carbon sequestration could serve as a cost-effective climate mitigation measure. Researchers must continue to investigate the accuracy of such valuation techniques as well as their transferability and scalability to larger ecosystems.

There is low economic incentive to pursue treatment and cure research and development for rare diseases; this leaves millions of patients living with rare diseases understudied and undertreated. With the inception of groups such as the Undiagnosed Diseases Network (UDN) there is now a wealth of rare disease patient data. One way to increase the number of diagnoses, and hopefully treatments, would be to use the data already available to identify disease causing genes and potentially treatments as well. It has been shown that the integration of network-interaction and genetic data can further our understanding of disease pathways and genes. We investigate how to unify rare disease patient data from sources like UDN and Protein-Protein Interaction (PPI) data to identify potential novel gene candidates on the individual patient level. We developed a pipeline integrating patient genetic data and PPI that shows promise in identifying novel disease genes. For one of our patients, our pipeline predicted a very compelling disease gene and their clinician was notified of our finding. In other cases, no disease genes were identified. These findings suggest that our pipeline shows promise but further optimization and validation are necessary. As more data becomes available and sequencing technologies become more inexpensive, we hope that our pipeline will be more accessible and find use to undiagnosed patients and their clinicians around the world.

Color blindness is defined as a perspective understanding one’s racial identity is irrelevant and it is best to ignore the importance of race and skin color. This ideology is embraced by whites who deny their prejudice through this modern form of racism by diminishing other’s race and culture and claiming to view all people as equal. Although white people may believe their intentions behind color blindness are good by not judging people by the color of their skin, but rather by the content of their character, alternately the true motivation behind the color blindness ideology may be white people’s discomfort around black people, which causes them to avoid color all together. We believe that color blindness is a modern form of racism in which individuals suppress their discomfort among blacks. Therefore, we predict higher levels of color-blindness will correlate with lower levels of allophilia, which represents positive attitudes, feelings, and demeanor towards minorities. We tested this prediction in a survey study in which UW undergraduate students completed measures of color-blindness and allophilia towards Black people. The current study also seeks to investigate how social desirability influences this relationship between color blindness and allophilia. Social desirability is a biased response in which the respondent answers the survey question in a way that would be generally accepted and favored by society rather than being truthful. We hypothesize that if we account for social desirability, the correlation between color blindness and allophilia will be stronger because we predict that social desirability masks the real relationship between the two variables. Thus, people with higher social desirability will be more untruthful, resulting in a higher score of allophilia, when in reality their allophilia score should be lower. Our study explores the relationship between color blindness and allophilia and the role in which social desirability plays.

Inferior olive (IO) is part of the brain stem that projects their climbing fibers in the cerebellum's Purkinje cells and receives input from the deep cerebellar nuclei DCN to regulate the strength of electrical coupling in the IO. The structure of the IO contains a high density of gap junctions that are responsible for weak spontaneous subthreshold oscillation (STO). The weak electric potential STO can depolarize the neuron and open the N-methyl-D-aspartate receptor (NMDA) channel that is located close to the gap junction by removing its Mg ion. The activation of the NMDA receptor can play a role in strengthening the STO, increasing its synchrony, and inducing a new STO. Increase the synchrony in IO may contribute to the precision learning of the motor skills. Therefore, our study was done on mice in vivo, and extracellular recording technique was used to record from IO before and after the addition of NMDA. It was found that adding NMDA changed the firing of the neuron relative to itself. Second, NMDA decreased the power spectra density's raw power in both groups 2 Hz and 3-6 Hz, however, there was some increasing in the PSD at 5 Hz in the group of neurons that fire with 2 Hz. Third, the coherence value between the neuron and the local field potential (LFP) decreased after the addition of NMDA. There was an exaption in which the coherence value increased at specific frequences. Finally, we found that a neuron showed phase locking its firing activity with the LFP, which was in the negative firing phase. In conclusion, NMDA receptor plays a role in increasing the synchrony of neuronal electrical synapses in IO, involves in the IO rhythmogenesis, and may add temporal precision to coordinate the muscle activity.

Cas9 has long been used as an effective genome-editing tool for its ability to knock out genes with high efficiency; only in recent years has it been used to activate genes as well. Our current research aims to develop Cas9 as a gene activating tool in zebrafish, and to use that tool to target genes associated with rhabdomyosarcoma, a devastating pediatric cancer, in order to better understand the genetic factors and interactions leading to tumor growth and progression. When a dead form of Cas9 is used (dCas9), it will bind to the specified site without cutting/knocking out the gene. We have developed a gene-activating system using dead Cas9 fused with a transcriptional activator (dCas9-VPR), and are currently optimizing its use with Csy4 in order to activate multiple genes in a pathway or genetic network. We have seen low efficiency success so far by injecting zebrafish with DNA coding for Csy4, dCas9-VPR, and guide RNAs downstream of the ubiquitin promoter. Once the system is optimized, we hope to use it to test interactions between multiple genes simultaneously, which would allow us to determine how interactions between genes impact cell behavior.
This will allow us to gain a more wholistic understanding of how a genetic pathway works.

Modes and forms of communication have evolved drastically over the last several decades, with the emergence of large social media platforms and an increased accessibility to information over the Internet. Traditionally, journalists played the role of both providing and curating information to the general public, but with these new forms of communication, the role of journalists is evolving too. We examine how this role is changing in the crisis context. Specifically, we look at the interactions between journalists, citizens and government information workers after the Oso Landslide that occurred on March 22 of 2014. We analyzed the tweets from this event to see the interaction between these groups at specific points in time as the crisis unfolded. From a collection of ~1 million tweets, we conducted a micro-analysis of two important time periods: 1) all tweets about the Slide in the first two hours after it occurred and 2) all tweets over the first three weeks that included the hashtag created by the lead response agency (530slide.) We combine ethnographic analyses, descriptive statistics, and network analyses to better understand how contemporary crisis information is shared among these groups as presented on Twitter. Preliminary results show that there were common content themes that each represent a specific ‘information need’: situational awareness, public safety, aid, and commentary. 

Headaches are debilitating conditions that can impose a severe drop in quality of life and productivity. Local anesthetic blocks of the greater occipital nerve (GON) have been shown to reduce pain in various forms of headaches that are resistant to conservative treatment. We are performing a quality improvement project on GON blocks in different forms of headache. One aspect of the project is to evaluate whether the block affects the area of referred pain. We analyzed 12 patients undergoing a GON block at the Center for Pain Relief of the University of Washington Medical Center. Bupivacaine 0.25% was injected under ultrasound guidance. Before and 30 minutes after the injection, patients drew their pain localization on a high-resolution 3D body schema on a computer tablet. Pain area was quantified in terms of number of pixels. 30 minutes after the injection, the patient’s global impression of change was recorded. The data were analyzed by paired t-test. The median pain area (interquartile ranges) prior to and 30 minutes after the procedure was 622,271 pixels (158,216-795,912) and 104,961pixels (27,466-448,391), respectively (p=0.0277). Analysis of global impression of change in pain showed 2 of the patients experiencing very good improvement, 3 good improvement, 2 minimal improvement, 2 who had no change in perceived pain, and 3 whose pain minimally worsened. GON blocks reduce the referred pain area of patients, pointing to potentially significant benefits of the procedure for patients suffering from headaches. However, the qualitative marker of patient impression of change shows that GON block efficacy may vary significantly on a case-by-case basis.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that impairs an individual's social, communicational, and behavioral skills. Males are 4.5 times more likely to be diagnosed with ASD compared to females. One possible reason for the difference in diagnostic rates is that females may be better able to mask their symptoms and therefore go undiagnosed more often than males. If females with autism are better at masking, then it is possible that standard diagnostic tools underestimate their impairment due to the clinician not seeing the full extent of individual's symptoms. The goal of this study is to understand the potential for sex bias in two measures of ASD by examining measurement consistency between parent and clinician report of ASD symptoms. 140 children (70 males, 70 females) aged 8-17 years with a confirmed diagnosis of autism participated in this study. Participants' diagnoses were confirmed via the ADOS-2, a clinician-child interaction measure that scores the child's communication, social skills, and restricted or repetitive behaviors. Parents completed the Social Responsiveness Scale (SRS-2), a survey about their child's social and autism-related impairments. To look at potential bias, we first compared males and females with ASD on both the ADOS and SRS to examine sex differences in autism severity. Second, we examined the relation between parent and clinician report for differences in consistency of ASD symptoms by sex. If females are better at masking their autistic traits, we expect a lower correlation between ADOS and SRS scores in females compared to males, indicating lower parent-clinician agreement. Third, we explore these analyses in children who had clinical diagnoses but who did not meet research criteria for ASD (n = 20). Understanding the relationship between sex and measurement tools should help inform whether traditional diagnostic measures are as effective in diagnosing both males and females.

ImageJ allows users to create plugins that work with other imported packages and the ImageJ libraries. Using the ImageJ API (application program interface) and the macros recorder built into ImageJ, each image analysis performed within the Lee laboratory at the Department of Radiology was programmed into individual plugins by both Vineeth Narajala and Selina Liu, to be used by research scientists. Before writing each data analysis plugin, the standard operating procedure (SOP) of image analysis created by the Lee lab was practiced manually by both the programmers so we understood the process researchers perform on each data set. After understanding the SOP, we commented a simple outline in Java to start writing the plugin code. After the code was outlined with comments, Selina wrote algorithms for portions of the analysis that required numeric patterns and searched through the ImageJ API to manipulate the image using built-in commands. Methods were created to perform calculations, scale the images, and close extra images that were generated during the analysis. These methods helped generate the final image map used for measurements by the researchers. Plugins were tested for usage and updated when a researcher required other procedures that were not specified in the SOP. We also created a python program in Python 2.7 to automate the data analysis of the dataset. The program can also plot rudimentary graphs of the analyzed results. The python program used pandas to analyze the data and matplotlibs to create the graphs. Overall, each plugin and the automation program save researchers hours of time from importing, calculating, and archiving the images when following a single SOP. The research scientists typically used Microsoft Excel to analyze the data after the images were created and regions of interest were identified. This method was very time consuming and could not be scaled to different input sizes.

Diet, lifestyle, and environment can influence an individual’s behavior and brain function through epigenetic mechanisms. The Lattemann lab is investigating the effect that one factor, high fat diets, has on epigenetic regulation in hippocampus a key area for learning, memory and cognition. Previously, the lab determined that rats fed high fat diets exhibited increased sucrose motivation, and this behavioral effect was later linked to stearic and palmitic fatty acids explicitly. It was also shown that high fat, high sugar diets are associated with impaired place memory in rats. Most recently, the lab has analyzed hippocampal chromatin from rats fed high stearic and palmitic acid diets and is in the process of determining the effect of these diets on histone modifications. Histones regulate gene expression by binding to DNA: modifications to these histones influence how readily the DNA is transcribed, and how the gene expressed. These modifications are being screened for using Western blot analysis. In addition to screening for modifications in histones, the Lattemann lab also directly analyzed DNA for the expression of target genes. This screening procedure included measuring expression of candidate histone-target genes using PCR, and ChIP-Seq (Chromatin Immunoprecipitation and unbiased gene screening) assays. By locating histone modifications and quantitating the expression of hippocampal candidate genes, the lab has provided an epigenetic explanation for the behavioral effect of the diets, and a possible molecular mechanism by which the diets can induce this effect.

Recent attention has been given to the high cost of medical care, to which hospital costs are a main contributor. The ability to predict how long a given patient would remain in the hospital once admitted would be useful to hospital administrators for planning purposes. The purpose of my research is to examine the role of pre- and post- hospitalization factors in determining hospital stay in patients with Acute Myeloid Leukemia (AML). We examine the relationship between treatment-related mortality (TRM) score - which is collected prior to hospitalization and defined as the probability of death within 28 days of treatment initiation to length of hospital stay after admission for reasons other than receipt of chemotherapy. A common reason for admission is fever, so we also examine the relationship between cause of fever and length of hospitalization. All data on TRM score and infection status is abstracted from a large AML database (2973 entries), which contains entries on all AML patients admitted to the University of Washington Medical Center from 2008-present. After examining pre-admission factors as predictors of hospital stay, we examine the effect of length of current hospital stay on probability of subsequent hospital stay (i.e. is a patient who spends one week in hospital more likely to spend the next week in hospital than a patient who has already spent two weeks in hospital?) To account for patients who die before it is known whether they would have been discharged, we use the Kaplan-Meier method, with hospital discharge as the event of interest. The results of this study may help hospital administrators use the TRM score, infection status, and current length of stay to emphasize cost-reduction measures in AML patients, and inform the development of similar models for other diseases.

Mutations in the Presenilin 2 gene, (PSEN2), cause early onset familial Alzheimer’s disease (FAD). PSEN2 encodes the presenilin 2 protein which forms the catalytic subunit of the gamma-secretase complex, responsible for cleaving amyloid precursor protein into fragments. One of the resulting fragments is Aβ_1-42, a major component of brain amyloid plaques and a clinical hallmark of Alzheimer’s disease. Microglia are the resident innate immune cells in the brain clearing the brain of Aß plaque and debris through phagocytosis. Without presenilin 2 protein present, levels of secreted cytokines increase implying a higher immune response, and recent data suggest that hyper-activation of an inflammation state can contribute to development of Alzheimer's disease. We hypothesized that FAD mutations can impair normal presenilin 2 protein function and therefore promote AD through dysregulation of immune function. We have developed a mouse model to study the impact of the most common FAD PSEN2 mutation, the PSEN2N141I, also known as the “Volga German” mutation. Previous experiments in the lab have shown that the absence of wild type PSEN2KO disrupts normal microglial phagocytosis of neuronal debris. My work involves measuring phagocytosis of apoptotic bodies by mouse primary neonatal microglia expressing the FAD PSEN2 mutation to determine if AD associated mutations contribute to AD through altering microglia phagocytosis behavior. Microglia from wild type mice, mice with presenilin 2 knocked out, and mice heterozygous for the human N141I mutation are collected and co-cultured with apoptotic cell bodies. Microglia and apoptotic cell bodies are membrane-labeled and FACS analysis is used to measure percent phagocytosis. My studies will further our understanding of how familial AD mutations alter the normal cellular behavior of brain immune cells and may highlight new areas in pathways appropriate for therapeutic targeting.

Study of the thermodynamic properties of pure water and aqueous salt solutions of NaCl and Na2SO4 were undertaken to determine the equations of state for ices VI and VII at pressures from 1 to 4 GPa and temperatures from room temperature to approximately 300 ℃. The analysis was performed on data along the melting curves of pure water and aqueous solutions of up to 4 mol/kg of Na2SO4 and NaCl as measured within the pressure chamber of a Diamond Anvil Cell (DAC) utilizing ruby fluorescence spectra as a pressure gauge. The data were fit using a local basis function representation, allowing the comparison of the melting surfaces for the two salt solutions over a range of concentrations. Equations estimating evolution of the liquid-ice VI-ice VII triple point with increasing salt concentration, and prediction of the eutectic were enabled from the fit, providing better constraints on structural and geodynamic modelling of icy worlds. Melting point depression with increasing concentration of salt and incorporation of the salt ions into the crystal lattice, and density inversion between the high-pressure ices and saline solutions suggest the possibility of deep oceans of alternating layers of water and ice. Quantification of the effects of aqueous salts on these ices will allow the development of realistic modelling of the hydrosphere of icy worlds and exoplanets. Such modelling can be used to test the possible existence of chemical composition and water/rock dynamics favorable to the existence of habitable zones in these extreme environments.

Astrophysical measurements indicate that the universe has three main constituents: the ordinary matter, dark matter, and dark energy. Ordinary matter is the matter that we see in our daily lives and only contributes a small percentage of the total matter of the universe, while the dark matter takes up 84.5% of the total mass of the universe. There are several candidates for what dark matter could possibly be, one of which is a particle called the axion. The axion may be detected using a device called "axion haloscope", in which axion dark matter resonantly converts to a microwave photon when interacting with the magnetic field. These resulting photons can be detected with low noise electronics. The Electric Tiger is an "axion haloscope", an experiment made up of a waveguide. The waveguide is a rectangular box which contains dielectrics positioned at equal distances within the cavity, with the distance between the dielectrics retracting or extending. Changing the distances between the dielectrics makes the device sensitive to the detection of the axion signal in the magnetic field for a range of possible axion signals. The preliminary results of this experiment will detect or exclude axion dark matter in the previously unexplored range of masses for the axion particle.

Osteocalcin is a protein implicated in bone growth and bone reconstruction in several vertebrates, including humans. In this project, we analyzed the decarboxylated form of osteocalcin’s first alpha helix (hOC-a1) using circular dichroism and isotherms. Circular dichroism spectroscopy uses polarized light to determine whether the peptide fragment forms alpha helices or beta sheets. Using adsorption isotherm experiments will determine the protein’s ability to bind onto hydroxyapatite, silica, and titania mineral surfaces. Osteocalcin is known to change conformation and form a helical structure in the presence of calcium ions and adsorb onto HAP. Previous studies attributed these characteristics to the gamma-carboxyglutamic acid (Gla) residues at positions 17, 21, and 24, which lie within its first of three alpha helices. However, a mutant form of osteocalcin which has its Gla residues reduced to glutamic acid has also been shown to adsorb onto HAP. It is unknown why the protein containing glutamic acid in place of Gla can adsorb onto the mineral surface. Using circular dichroism, the experiment showed that the decarboxylated hOC-a1 peptide fragment was a random coil and unable to form a helical structure with or without the presence of calcium ions. Isotherms determined the peptide fragment’s ability to non-cooperatively bind onto HAP, as well as silica and titania. This project determined that the decarboxylated peptide fragment could adsorb onto the mineral surfaces as a random coil, suggesting there are alternative mechanisms of adsorption in comparison to the native protein. The Drobny Group intends to continue studies of the peptide fragment by labeling residues and performing experiments using solid-state nuclear magnetic resonance spectroscopy (ssNMR).

Spinal cord injury (SCI) is a debilitating disease with few treatment options available for recovering motor function. Based on past studies using electrical stimulation of the spinal cord, we believe that long-term optogenetic spinal stimulation (OSS) may improve motor function after an SCI. We are investigating this therapeutic potential using a rat model of SCI with an implantable LED to deliver optogenetic stimulation in vivo. However, activation of the LED produces heat that could damage the surrounding tissue. I have modified these LED implants by incorporating a thermistor that tracks temperature changes during optical stimulation. Using this device, I determined how the modulation of stimulation parameters affects heat production at the site of the implant and have identified several safe parameter sets. These results will inform the parameter choices used in future studies on OSS. An optimized OSS methodology has the potential to improve the lives of those with an SCI by enhancing their capability for volitional movement.

The goal of this project is to explore how Brain-Computer Interface (BCI) devices are depicted in the media, especially news media. BCI technology is not new, but it is still very much in its infancy, with few feasible embodiments usable for practical, non-medical applications. Additionally, a majority of BCIs that are (only somewhat) feasible require dangerous invasive surgical procedures. Yet in the last year, the technology has received a higher-than-average level of press coverage. Media coverage of upcoming medical technology is not a trivial issue. Substantial research has shown that positive portrayals of novel medical technology in the media can indirectly affect patient consent to undergo treatment. Consequently, we argue that it is essential that the media reports and discusses the ethical impacts of BCIs. We aim to discover whether media coverage depicts the technology realistically, discussing its shortcomings, risks associated with its use, and ethical issues related to neural implantation. We use a research software called FACTIVA to survey and analyze the depiction of BCI technology inn English-speaking media such as news publications, radio transcripts, press releases, etc. This content analysis allows us to understand mass media values and narratives in three general ways: 1) it generates evidence to demonstrate whether there is any positively-biased and over-enthusiastic depiction of BCI in mass media; 2) it sheds light on whether there is an absence of discussion of risks and ethics associated with BCI technology; and 3) it exposes unrealistic discourse, such as wide-reaching claims of the panacean nature of BCIs (i.e. transhumanist arguments, the race against artificial intelligence, etc.). In brief, this study allows us to explore whether media misrepresentations of BCI could influence the narrative about the technology in ways that may increase the risk of harms for prospective patients and their families.

Microtubules are critical for cellular and developmental functions, including neurite outgrowth and maintaining stable wiring of the nervous system. Tau, an intrinsically disordered protein, plays important roles in microtubule assembly and stabilization. However, it dissociates from microtubules and forms amyloid fibrils in a set of neurodegenerative diseases termed tauopathies, which includes Alzheimer’s disease, and frontotemporal dementia. Mutations in the sequence of tau cause the disease FTDP-17T (frontotemporal dementia with parkinsonism linked to chromosome 17 and specially characterized by tau pathology), providing evidence that alterations in tau alone can cause tauopathies. Most mutations occur in or near the microtubule-binding domain of tau, which suggests that mutant protein may be deficient in its capacity to stabilize neuronal microtubules, yet efficient at speeding up the process of aggregation. In particular, disease-associated mutations such as ΔK280 and P301L appear to enhance tau’s propensity to aggregate into fibers, and alter its pathological activity. Molecular chaperone proteins are responsible for maintaining protein solubility, promoting proper folding, and preventing atypical aggregation. HspB1, a member of the small heat shock proteins (sHSPs), has been shown to delay wild-type tau fibril formation by weakly interacting with early species in the aggregation process. Hsc70 is a constitutively expressed chaperone that inhibits tau fibrils formation substoichiometrically. Both chaperones are able to recognize aggregation-prone motifs within the microtubule binding repeat region of wild-type tau. Therefore, our interest is to test the affinity and activity of HspB1 and Hsc70 against tau constructs containing the ΔK280 and P301L mutations, to see whether these mutations alter interaction with these chaperones. We will use various biophysical methods, including fluorescence spectroscopy and electron microscopy to analyze these interactions. This will extend our understanding of the characteristics and behaviors of disease-associated mutations of tau and the ways in which chaperones target aggregation-prone tau species.

Every non-negative integer can be written using what is known as the factorial base representation. We define this notion and explore certain combinatorial structures arising from the arithmetic of these representations. In particular, we investigate the sum-of-digits function, carry sequences, and a partial order referred to as digital dominance. Finally, we describe an analog of a classical theorem due to Kummer that relates the combinatorial objects of interest by constructing a variety of new integer sequences. Many of the combinatorial objects we describe are of interest in their own right and provide interesting avenues for future discoveries. For instance, the carry sequences we describe correspond to a new family of integer partitions that are analogous to hyper-binary partitions, which have been extensively studied. Moreover, the digital dominance order most likely contains interesting combinatorial information about the integers as represented in the factorial base. Finally, our analog of Kummer's theorem has helped to explain how the classical version of Kummer's theorem can be altered to fit with almost any positional numeration system.

In 2016, the global median favorability of the United States stood at 64%; in 2017, median favorability dropped to 39%. Causes for anti-American attitudes have been difficult to pinpoint, but research suggests the reach of the United States military-approximately 800 foreign military installments in 70 countries-could have a part in America's negative image. Past research has considered the impact of military presence on anti-Americanism versus the lack thereof. But, whether a greater military presence (i.e. more troops, funding, and base cost) accounts for higher levels of anti-American attitudes has not been considered. My research studies whether greater levels of military presence, measured by Plant Replacement Value (PRV), acreage, and personnel, contribute to unfavorable attitudes towards the United States. I predict that greater military presence significantly increases anti-Americanism because an overt outside military presence attributes to a perception of the United States as intrusive, politically motivated, and imperialistic. I use attitudinal data from the Pew Global Attitudes Project and data pertaining to military presence from the Department of Defense's annual Base Structure Report. This relationship, if substantiated, could have important consequences on the future of American trust, power, and foreign policy.

Speed of sound measurements in four geologically important aqueous solutions (sodium chloride, sodium sulfate, magnesium chloride, and magnesium sulfate) as a function of pressure (0.1 to 700 MPa), temperature (250 K to 360 K), and concentration allow determination of Gibbs Energy. Sound speeds, based on ultrasonic time-of-flight measurements in a temperature-controlled pressure vessel, are integrated as a function of pressure to get densities and heat capacities. Both of these are derivatives of Gibbs Energy, which can be used to find all thermodynamic properties of the solution at a given pressure and temperature. Aside from spending vast amounts of time in-lab to acquire ultrasonic data, my data processing programs have been helpful in assuring our data precision and accuracy throughout the research process. Since icy (ocean) worlds in our solar system (including Europa, Titan, and Enceladus) are believed to contain liquid water within the current range of measurements, this work is useful in constructing geochemical models for planetary evolution and guides astrobiology questions of whether habitable environments exist on these planets.

Solar energy has unmatched potential as the energy source of the future and semiconducting polymers offer a unique set of properties that can address many of the current barriers that hold solar technology back. Little work has been done investigating bulk film microstructure formation, but the ability to control and engineer defects opens the door to new applications that employ tunable energy levels and adjustable open circuit voltage and short circuit density. Semiconducting polymers are exciting because they have untapped potential for improvements in efficiency, they offer a cheap, energy efficient alternative to silicon, and can be easily mass produced via roll-to-roll printing. Solution processing via roll-to-roll printing is transformative as it allows for low energy, high throughput manufacturing of flexible devices. This research focuses on generalizing structure-property relationships for semiconducting polymers and investigating the locations and causes of crystalline defects. The goal is to extrapolate measurements made at a nanometer scale on self-assembled poly(3-hexylthiophene) (P3HT) nanowires to larger production of bulk films. Current understanding of polymer crystallization is built on two competing models, both of which were developed for non-conjugated, therefore non-semiconducting polymers. The Luscombe group has previously demonstrated that the crystalline defects, such as unfavorable monomer arrangement (regioregularity), bulky end groups, the range of polymer lengths (dispersity) and the specific polymer length (degree of polymerization (DP)) do not affect nanowire width, meaning defects are not excluded to the perimeter of the nanowires. This research isolates the variable of polymer length and controls other defects. Using X-ray diffraction and differential scanning calorimetry, nanowires synthesized from polymer lengths ranging 50 to 150 DP have been tested for melting temperature, level of crystallinity and dimensions to determine where the defects reside. Once this is understood, we can confirm which model for conjugated polymer defects is correct.

Advances in remote sensing of snowpack in complex terrain have made it possible to accurately determine snow depth at a high spatial resolution. In order to utilize these measurements for water resource management, snow density is needed at a comparable accuracy and spatial resolution. Current efforts to obtain accurate, fine scale maps of snow density focus on modeling it over broad areas that vary in land surface type. In order to validate these snow density models, measurements of mountain snowpack are needed. Snow density varies significantly depending on the local environment of the snowpack, so measurements are needed at a variety of sites. However, many prior field campaigns to measure snow density have a bias towards open sites since they offer many practical advantages to the surveyor. This results in uncertainty in snow density models in forested areas due to a lack of quality measurements for validation. This project improves our knowledge of differences in snow density between forested and open sites through a field campaign at Snoqualmie Pass. Each week throughout the winter, snow density and changes in snowpack depth were recorded. These measurements are then analyzed over the course of the season to look for significant differences between the two sites. Observations of settlement and densification rates are used to inform an empirical model of snowpack density as well. Detailed notes of the field campaign are also taken to document the practices of the study and suggest improvements in methodology related to snowpack measurements at forested sites.

According to the World Health Organization, Malaria is a disease that affected nearly 216 million people worldwide and caused 445,000 deaths in 2016. The disease is a Global Health concern that mainly affects young children and pregnant women in the subtropical and tropical poor regions, such as Africa and South America. My internship at the Center for Infectious Disease Research gave me an opportunity to learn more about the Plasmodium parasites that cause malaria and the research behind developing a cure. I learned to evaluate Plasmodium blood stages with light microscopy and to evaluate the morphological difference between the sexual and asexual stages of the parasite life cycle as well as to put this in context with the disease transmission and symptoms. I also evaluated morphological differences between rodent and human parasites. The female Anopheles mosquito is the vector that transmits Plasmodium Sporozoites into the host's bloodstream, where the parasite starts a journey to the liver. After reaching the liver, the Sporozoite starts a process of transformation into liver stage forms which eventually matures into a Schizont and releases Merozoites that will return to the host's bloodstream. In the bloodstream, the parasite invades red blood cells through asexual replication, the Merozoites amplify and continue to invade erythrocytes which result in the illness symptoms of malaria. Some of these parasites get a switching signal and become gametocytes, the transmission stages of the parasite. The mosquito is able to acquire the gametocytes during a blood meal. On this project, we will look into the transcript levels of a few genes at the stage of gametocyte by qPCR analysis.

Religious rhetoric has been a common tool in politics for the majority of American history, from Thomas Jefferson being “unfit to lead a Christian Nation” to Ronald Reagan’s “City Upon a Hill”. Although the Constitution declares the government to be secular, members of Congress, to varying degrees, regularly invoke religious imagery and rhetoric in the public communications. This study seeks to understand why. I examine congressional religious rhetoric using a unique data source of congressional webpages from the massive .GOV collection of the Internet Archive Project. I hypothesize that members' personal beliefs and electoral strategies help to explain differences in website content. I measure the personal religiosity of members using a carefully constructed scale of involvement in their religious communities. I measure district religiosity using information about district-level church attendance and prayer frequency from the Cooperative Congressional Election Survey. Finally, I draw from established religion lexicons to measure religious emphasis in congressional website content. I find positive, statistically significant support for both hypotheses. This work sheds light on politicians in particular members of congress are actively seeking to brand themselves through the internet for political purposes.

This research focuses on the mathematics of gerrymandering. Gerrymandering refers to how political parties draw district boundaries to give them better odds at receiving a majority during congressional elections. Every 10 years district boundaries in the United States are redrawn for congressional elections by the current majority party. With such change in political cartography, redrawing district boundaries not only affects who wins but also the people who live within them. Given the loosely defined criteria for redistricting, we seek to quantify the process of redrawing district lines to determine when this partisan process becomes an act of manipulation and exclusion. We will be use The Metropolis Hastings (M.H.) Algorithm to produce a random walk that has a stationary distribution that will be the probability distribution of all possible districting plans for a given U.S state. By collecting congressional maps and election results, we implemented the M.H. algorithm in python to produce sample spaces for Washington State and Iowa. We will simulate local and federal redistricting requirements using self-defined parameters which measure: compactness of districts, population division, division of counties, and minority voter populations. We simulated election results with respect to our sample districts and compared the simulated outcomes with actual district maps and their election results. This study helps to determine if current redrawn maps legitimately reflect the people they purport to represent or if they are manipulations and subversions of our democratic process.

Geographers generally define sense of place as the meaning an individual ascribes to a particular location. Collectively, sense of place creates the identity and character of a region and is represented through culinary, literary, visual, and many other forms of art unique to the local culture. Technological advancements in communication have changed sense of place by affecting how these cultural differences are maintained, but also offer new ways of capturing and sharing sense of place. What elements and by which means individuals choose to capture personal representations of an environment shape the way communities as a whole perceive, ascribe meaning to, and amass their own descriptions and representations of that place. My project explores this iterative relationship between visual representation and written description of place. I have selected a collection of crowd-sourced pictures of the local landscape using an app that pulls up publicly posted Instagram images that have been geotagged near the location of the user. I consider these pictures to be modern forms of landscape folk art and conducted visual content analysis to code the images with descriptive terms. I have also created an in-person, crowd-sourced cartography installation consisting of three simplified maps of Seattle that was placed in a gallery where patrons were asked to write, directly on the maps, descriptions of their own sense of place associated with the locations. I then compared the language from the installation to that from the analysis of the Instagram images. Strong similarities between the two suggest the possibility of using crowd-sourced visual representations of place from social media to offer a greater understanding of how natural and built environments evolve and what they mean to the people who inhabit them.

Active student reasoning during peer discussion reinforces students’ conceptual understanding of lecture material and provides students with the opportunity to practice articulating the logical explanations required for exam questions. The quality of student reasoning during in-class discussion, and hence their usefulness in improving exam performance, may be affected by the questions instructors choose to ask. To determine which question properties prompt higher reasoning quality, we recorded and transcribed instructor questions asked and eight volunteer student group discussions to those questions over seven days in an active learning introductory biology classroom. We coded the in-class discussions for reasoning quality. We characterized questions in four ways: 1) Bloom’s taxonomy level (i.e., higher or lower order cognition questions), 2) question format (i.e., clicker question using peer instruction, think-pair-share, in-class Canvas questions where students must upload a picture of their work to Canvas), 3) number of dimensions of science learning using the 3-D Learning Assessment Protocol, and 4) if the question included a general model of physiology. Our results indicate that, in general, higher Bloom level questions encourage higher quality of reasoning. However, clicker questions using peer instruction prompt higher reasoning quality regardless of Bloom level. Additionally, the highest level of reasoning quality was seen during in-class Canvas questions. Both questions types that are incentivized by course credit (i.e., clicker and in-class Canvas) prompted higher reasoning quality than non-credited questions (i.e., Think-pair-share). We suggest that instructors should incorporate credited and higher Bloom level questions to increase the amount of high level reasoning during student discussions in their classrooms.

Atherosclerosis is a disease in which cholesterol accumulates in the walls of arteries, limits blood flow, and causes heart attacks and strokes. Atherosclerosis could be prevented or reversed by expressing therapeutic genes in the artery wall. Gene therapy for atherosclerosis will require high-level therapeutic gene expression for two reasons: 1) to increase efficacy; and 2) to allow use of lower vector doses, thereby minimizing vector-related toxicity. Our goal is to increase expression of an apolipoprotein A-I (apoA-I) transgene, which both prevents and reverses atherosclerosis in rabbits. We used an in silico bioinformatics approach to identify endothelial cell-specific cis-regulatory modules (CRMs). CRMs are short enhancer regions of DNA that are expected – when introduced into endothelial cells – to increase transcriptional activity of a nearby gene. We identified 11 CRMs in the CDH5, EFEMP1, THBS1, and VWF genes. We hypothesize that insertion of these CRMs into a helper-dependent adenoviral vector encoding apoA-I will increase apoA-I expression in endothelial cells. We also hypothesize that the genomic regions surrounding these CRMs contain sequences that, along with the CRMs, could increase transgene expression above levels obtained with the CRMs alone. Our adenoviral vectors have a larger capacity for the insertion of DNA sequences than other gene-therapy vectors. This large capacity allows us to evaluate CRMs in their native genomic context (i.e., with several kilobases of neighboring DNA included). We cloned large CRM-containing regions of the 4 genes listed above and we are inserting the apoA-I gene into the translational start sites of these genes. We will test vectors containing individual CRMs and vectors containing the larger CRM-containing regions in cultured endothelial cells (in vitro) and in rabbit carotid arteries (in vivo) to identify CRM-containing constructs that express the highest apoA-I levels. This project may provide higher-expressing vectors for use in gene therapy for atherosclerosis.

The goal of this research is to improve breast cancer treatment by identifying novel imaging markers of tumor immune response. New immunotherapy treatment approaches are emerging that harness the body’s own immune system to fight cancer. These exciting advances increase the need for new tools to quantify response and assess treatment effectiveness in vivo.  We are investigating the potential role of magnetic resonance imaging (MRI) in monitoring chemotherapy-induced immune response in breast tumors. HER2 (human epidermal growth factor receptor 2) is a protein overexpressed in up to 30% of breast cancers that can increase cell proliferation and result in more aggressive cancers with worse outcomes. Trastuzumab is a drug that has been shown to not only amplify, but also induce immune response in HER2+ tumors. This induced immune response contributes to the effectiveness of trastuzumab in fighting HER2+ breast tumors and improving overall survival.  We hypothesize that functional MRI measures can identify changes associated with tumors’ immune responses. We are testing this hypothesis preoperatively in a group of patients with HER2+ breast cancer. Each patient has an MRI image taken and a tissue sampling of their tumor before and after a dose of trastuzumab. Quantitative MRI metrics we are measuring include contrast enhancement kinetics reflecting vascular permeability and diffusion coefficients reflecting tumor cellularity. Changes reflected on MRI are being compared with changes in histologic measures of immune response (including tumor infiltrating lymphocytes, TILs, and inflammation). Objectives are to identify quantitative MRI markers that are best suited to track breast tumor’s responses to trastuzumab. These findings are contributing to developing a novel method of observing immune response in tumors treated with a variety of emerging therapies.

Antiretroviral therapy (ART) is the standard of care for treating human immunodeficiency virus (HIV) infection and suppresses virus levels but cannot eliminate latent HIV reservoirs. Latently infected cells are a barrier to HIV cure. “Shock and kill” is a strategy that uses latency-reversing agents (LRAs) to reactivate latently infected cells under suppressive ART, making the cells vulnerable for removal by host immune responses or other strategies. However, “shock and kill” fails in clinical studies due to the low potency and high toxicity of LRAs. Here we have developed a lipid-polymer nanoparticle platform that addresses “shock and kill” limitations by incorporating multiple LRAs to increase potency and to reduce toxicity by targeting HIV reservoirs in lymphatic tissues. We have shown that ~200nm nanoparticles sustain LRA release and induce latency reversal in a human T-cell line in vitro. To target lymph nodes, we have synthesized nanoparticles smaller than 100nm in diameter, which literature shows enhances lymph node targeting following subcutaneous injection. By adjusting the polymer and lipid concentrations as well as the organic to aqueous solvent ratio during formulation, we obtained an ultrasmall particle of ~100nm. Ex vivo organ imaging from mice subcutaneously administered these ultrasmall particles shows successful targeting to draining lymph nodes as well as other HIV reservoir locations, including the spleen and the gut-associated lymphatic tissue. The ultrasmall nanoparticles also show similar drug release and latency reversal properties as our previous formulations. The nanoparticle platform demonstrated here is able to target latent HIV reservoirs in multiple areas of the body, which is crucial for eliminating latent HIV reservoirs and achieving a cure.

Organic materials show promise as alternative materials for many modern-day electronics applications, such as transistors, LEDs, and photovoltaics. They hold many advantages over their inorganic counterparts, such as being lighter weight, lower cost, and flexible. Self-healing polymers are a specific form of organic polymer that are particularly promising because of their potential use in flexible devices. Self-healing materials have the capacity to spontaneously reform damaged bonds, thereby returning the material to its original state and recovering its initial properties. Imine bonds are a type of self-healing bond. Imines have a highly dynamic nature, allowing for the reshuffling of bonds required to recover material properties. Much research has been done on the use of imine bonds in self-healing polymers; however, no work has been done utilizing imine bonds for self-healing in semiconducting polymers. To incorporate self-healing behavior into a semiconducting polymer, we have investigated the synthesis of a poly(azomethine), a semiconducting polymer with an imine bond along the backbone. Initially, as a proof-of-concept for the dynamic exchange of bonds in our specific system, we reacted aniline with 2-thiophenealdehyde to form an imine. Then, to determine if bond exchange occurred, the imine produced was reacted with another amine. The reaction showed that a significant amount of imine exchanged, so we moved on to a polymer system. We synthesized 4,4'-dinitrotriphenylamine, which we then reduced to produce a diamine species. This diamine was then polymerized with a dialdehyde species, resulting in a fully conjugated polymer with multiple imine bonds along the backbone. The polymer will be made into thin films for testing. Mechanical properties will be investigated to determine initial film properties. Additionally, transistors will be produced to see if electrical properties can be recovered after the film has been damaged.

The purpose of this research is to investigate novel techniques for worst-case analysis of electronic circuits. Worst-case analysis is used to ensure circuits work reliably and meet performance specifications. Circuit components have assigned tolerances based on operating temperature, manufacturing processes, expected lifetime, radiation, and various other effects. Worst-case analysis can help detect potential circuit failures that may cause a loss of data and as a result, incur financial loss. The proposed research uses optimization to perform the worst-case analysis. Optimization involves minimizing or maximizing an objective function (such as an expression for an output voltage of a circuit) subject to constraints (which is often an allowed set of circuit parameters). The research applies worst-case analysis to different circuits using the nonlinear optimization function fmincon() of MATLAB. Preliminary results show that optimization under proper constraints is more efficient than conventional methods which rely on statistical methods. The worst-case analysis results from MATLAB using optimization are compared against the results of conventional methods using Multisim, a circuit simulation software tool. The research aims to apply different methods of worst-case analysis to circuits with increasing complexity to determine whether or not one approach is more efficient/accurate than others.

The purpose of the project is to use benthic foraminifera to investigate the condition of the ecosystem of Possession Sound, Everett, WA, part of Puget Sound. Puget Sound is a polluted water system due to the ports, oil refineries, paper mills, agricultural runoff, and previously, a smelter. Possession Sound itself is home to private properties, a naval station, ports, marinas, and an asphalt plant on the waterfront. Foraminifera are marine protists with calcareous or agglutinated shells (tests) that are readily preserved in sediments. Because they are sensitive to environmental conditions such as bottom water pH, organic and metal pollutants, and change in temperature, they can be indicators of environmental conditions at the sediment/water interface. Calcareous foraminifera exposed to water with decreasing pH have increasing levels of test dissolution, however, agglutinated species don’t dissolve. For this study, sediment samples were collected by the Washington State Department of Ecology; and sub-samples were sent to the Burke Museum. Thirty samples were processed; each was washed through a 63 screen, floated in trichloroethylene to remove the heavier sediment, then picked for around 300 foraminifera/sample. Foraminifera were identified for analysis of their assemblages, condition, and signs of dissolution. These signs are chalkiness, pitting, holes in the shells, and removal of shell layers. The hypotheses are as follows. Dissolution will have increased over time as Puget Sound water quality has decreased in recent years. Worse water quality will result in fewer calcareous species. Foraminifera will be fewer in number since 1997, with a higher proportion being agglutinated species. Results of this investigation will deliver insight into benthic conditions of Puget Sound, specifically Possession Sound, but could also provide useful information for people who rely on Puget Sound’s benthic conditions, such as the oyster and crab industry.

90% of drugs fail in clinical trials. As a result, a successful FDA-approved drug costs an average of $2.6 billion to develop and takes a decade to reach the market. Pharmaceutical companies are unable to comprehensively evaluate drug toxicity before clinical trials because no methods exist to screen the thousands of protein-protein interactions (PPI) that a drug could unintentionally disrupt in the human body. The ability to disqualify drug candidates with off-target effects before clinical trials would greatly increase the speed at which useful drugs are introduced to the market and reduce the expense of developing new therapeutics for those who need them. Here, we demonstrate a novel synthetic biology-based method, SynAg, that enables thorough drug characterization by linking PPI binding strength to the cellular agglutination of engineered S. cerevisiae cells. SynAg is a library-on-library approach that conserves the accuracy of pairwise PPI toxicity screening in a high-throughput, one-pot format. Specifically, we construct a SynAg library to characterize a 20-by-20 protein interaction network involved in cellular apoptosis to demonstrate the accurate profiling of a complex and highly interconnected family of proteins. Finally, we use the SynAg library to characterize the on- and off-target effects of small-molecule cancer therapeutics, which are shown to be consistent with previous studies. 

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by marked impairments in social skills, communication, and behavioral aspects of typical development. Research has shown that individuals with ASD often present with psychiatric comorbidities such as Depression, Anxiety, Obsessive Compulsive Disorder, Attention Deficit Hyperactivity Disorder and Bipolar Disorder. Comorbidities can have a broad and significant impact on a child’s health and wellbeing and such conditions are significantly more prevalent in those with autism than in the general population. This study aims to explore the relationship between psychiatric comorbidities and autism severity in children with ASD. 100 children (males=50, females=50) aged 6-18 participated in the study. All participants met the Autism diagnostic criteria on the ADOS-2, a child-clinician interaction measure that measures child’s social, repetitive behaviors and communication skills. Parents completed the Autism Center of Excellence subject medical history form, with information on child medical history. Problem behaviors and low IQ scores in children with ASD may be the symptom of underlying psychiatric comorbidities instead of the autism itself. Due to this, treatment of comorbid medical conditions may result in dramatic improvements in the quality of life of both children with autism and their caregivers. In this study, we expect that children with a higher rate of psychiatric comorbidities will score higher ADOS calibrated severity scores with a higher rate of autism symptoms and will score lower on IQ measures. Results will help establish a better recognition of comorbid medical conditions as critically important issues to address in treatment approaches.
 

As demand for accurate evaluation of chemicals and their potential to cause effects on humans increases, we have designed in vitro methods to facilitate such assessments. However, models of in vitro cell cultures are limited in their approach typically using a monoculture of limited cell types. Using a 3 dimensional organotypic approach to culture multiple cell types more reflective of a functioning organ can provide a framework for evaluating systematic interactions minimizing the need for in vivo assessment. We utilized a novel organotypic, in vitro model of testicular development that mirrors the development shown by in vivo studies. Our baseline study isolated testes that were harvested from C57BL/6 male mice on post-natal day 9. Testicular co-cultures were maintained for up to 16 days in 24 well plates with data collections occurring at days in vitro (DIV) 3, 7, and 16. Plates were stained with antibodies providing markers that correspond to morphological features of specific cell type markers. Five different primary antibodies were used as markers to visualize the change in cell populations. Markers for Sertoli cells corresponded to Vimentin, Leydig cells with 3b-HSD, Germ cells to DAZL and c-kit, and proliferation with PCNA. For each well, we used an immunofluorescence dual staining technique with Scanning Laser Image Cytometery (iCys) to observe the percentage of cell types and to determine change in phenotypic distribution of the cell population. From our preliminary observations, we were able to observe changes in Sertoli cells, Leydig cells and Germ cells throughout testicular development. Future studies would further develop and confirm the population and morphological changes observed with the testicular cell cultures. With a baseline model created, this in vitro model can be used to test the lethality of chemicals without the need of in vivo alternatives.

Every year there are at least one million new cases of sport-related concussion in children younger than 18 in the United States. Current diagnostic screening tools, such as CT and MRI, are insensitive to the subtle microstructural changes that occur following concussion, and in pediatric concussion, there is additional complexity of the still-developing brain and how concussion affects its long-term development. While these patients’ radiographic images often appear normal, they report an array of post-injury symptoms, which questions the true extent of brain injury after concussion. The aim of this research project is to utilize advanced neuroimaging and analysis tools, diffusion tensor imaging (DTI) and graph theory, to explore short-term and longitudinal changes in the brain following pediatric sports concussion and to obtain a more reliable and sensitive method to diagnose pediatric concussion. Children aged 10 – 14 with unresolved symptoms from a sports-related concussion and age-matched controls were included in this study. Each participant underwent MRI scans and clinical assessments 4-6 weeks post-injury and 6 months after the initial visit . We used DTI, which has been shown to be sensitive to microstructural changes related to concussion in adults. In addition, we analyzed the DTI data using graph theory, which is a mathematical tool that models information as a network. We investigated differences in network properties between concussed and non-concussed children and used random generated networks as a control. We confirmed that the network properties of children were distinct from random networks. We also observed a 9% reduction in global clustering and 16% increase in local connectivity in the concussed patients, suggesting overall network disconnect and stronger, but more segmented, local network groups. These preliminary results encourage further exploration of the methods employed and display clinical relevance in distinguishing between concussed and non-concussed youth. 

The Standard Model of elementary particle physics (SM) describes a connection between electromagnetic and radioactive decays known as the Conservation of Vector Current. One area of new physics research is in the formation of additional currents that are not in the SM called “Second Class Currents” (SCC). It is thought that these could possibly produce a breaking of the Conservation of Vector Current. An experiment performed previously at Lawrence Berkeley National Laboratory (LBNL) showed evidence for a large breaking of the expected connection between the beta and electromagnetic decay of 22Na. Although one possibility for explaining the discrepancy is to attribute it to the SCC’s mentioned above it is also possible to explain it without introducing new physics. The electromagnetic transition in 22Na, which has so far been assumed to be purely of magnetic character (M1), could actually have a (so-far unexpected) contribution of electric character (E2). We ran an experiment to determine the E2/M1 ratio, by measuring the angular distribution of gamma rays from oriented 22Na. The orientation is naturally obtained when producing the excited 22Na state via a 21Ne(p, γ) resonance at ~7.8 MeV, which is known to predominantly feed the analog 2+ state in 22Na. The decay goes from 21Ne with a certain momentum, p, to 22Na via emission of electromagnetic radiation (γ: gamma ray emission). The data will be collected with five Germanium detectors at different angles simultaneously.

Magellanic penguins (Spheniscus magellanicus) have highly variable reproductive success, and while most eggs successfully hatch, about 50% of the chicks survive to fledging. What determines which of the two chicks in a brood fledges? Typically the first chick hatches two days before its sibling, and has an early size advantage in terms of weight. We predict that larger chicks will occupy the preferred nest position, switching from the warmer position early in development to the optimal feeding position. We also expect that chicks more often found in the “better” position at these different stages will be more likely to fledge. To assess optimal nest positioning we collected weight, nest position, and fledging data on over 1,200 chicks during the 2017-18 Magellanic penguin breeding season at Punta Tombo, Argentina. We extracted data from our SQL Database using a number of SQL queries, and we will use R Studio to analyze our results. We expect to find larger chicks preferentially in the back (warmer) position of the nest early in growth for better thermoregulation, and in the front of the nest later in development since they would be closer to the adult’s head during feeding. Developmental priorities should change as the chicks begin to independently thermoregulate at around 15 days old, so we expect a transition in chick positions at this time. Chicks consistently in the preferred position should have a higher likelihood of weight gain and fledging. These findings will further our understanding of the key factors and challenges in fledging and reproductive success at our study colony at Punta Tombo, Argentina.

Alzheimer's disease (AD) is a neurodegenerative illness responsible for 60-80% of dementia cases in the United States. Studies have shown that the formation of two primary pathologies, amyloid plaques and tau tangles, are present prior to neuronal death that results in this loss of memory and worsened motor function. Our research focuses on understanding the role of tau in disease progression. Tau stabilizes microtubules in the cell, which function to maintain cell structure and assist in intracellular transport. To successfully regulate microtubules, tau is modulated by site-specific phosphorylation. Evidence points specifically to the hyperphosphorylation of tau by certain kinases in playing a key role in neurodegenerative dieases such as AD. One kinase that has been identified as a tau-phosphorylating agent is tau-tubulin kinase 2 (TTBK2). To understand the role of TTBK2 kinase activity in the context of tau, we created double transgenic C. elegans lines expressing both human tau and TTBK2. We assessed behavioral abnormalities in our subsequent populations using locomotor assays of the homozygous crosses. From the data that was generated, we observed a significant difference in the movement of the double transgenic tau/TTBK2 strains as compared to their controls. The crosses moved substantially less than the other strains, and exhibited a more uncoordinated phenotype. These results support the hypothesis that the abnormal phosphorylation of tau by TTBK2 results in worsened motor control and general health of affected individuals. Additional testing of protein levels within the double transgenic lines will enable us to determine the mechanisms underlying this effect, and could eventually lead to information that might inform treatments counteracting the activity of kinases such as TTBK2 involved in hyperphosphorylation of tau proteins. Furthermore, this research has the potential to aid in finding a cure for a currently incurable disease and providing a hopeful future for Alzheimer's-affected individuals.

My research investigates the role that two genes play in prostate cancer. Gene PENK is a potential signaling molecule involved in prostate epithelial stromal interaction that is missing in prostate tumors; AGR2 is a gene expressed by both normal and cancer cells, but only secreted by cancer cells. Both genes are involved in the development of prostate cancer - one that prevents it (PENK), and the other that activates it (AGR2). By introducing PENK into prostate cancer cells through transfecting PENK into normal and cancer cells, we can determine if there is a difference in its subcellular localization (intracellular vs. extracellular) as well as the effect on gene expression. PENK and AGR2 cDNA were cloned into mammalian expression plasmid vectors to be electroporated into recipient cells. Transfected cells are selected by drug resistance (G418). The resultant colonies are photographed under magnification. We used LNCap cancer cells and human embryonic kidney HEK239F fibroblasts as normal cells. Cells were analyzed to show expression of the transfected genes. The colony morphology of both LNCaP/PENK and LNCaP/AGR2 was altered. LNCaP/PENK showed a slower growth rate than parental LNCaP. AGR2 was detected in the media of both transfected cancer and normal cells. The transfected cells were prepared for DNA microarray analysis. These single genes appear to be able to alter the cellular phenotype, which results from gene expression changes. PENK could be used to prevent the cancer phenotype, since it is down-regulated in tumors. Further work is necessary to understand the difference in AGR2 secretion in cancer vs. normal cells. 

Rhabdomyosarcoma (RMS) is a rare and devastating pediatric soft tissue sarcoma, predominantly diagnosed in children and adolescents. Metastases and disease relapse rates continue to remain poor with a 5-year survival rate of less than 30%. Current therapeutic methods continue to remain inefficient in causing complete remission. Cancer stem cells (CSCs), a subpopulation of cells within tumors, are able to resist standard therapeutic treatments leading to disease relapse and metastases. Studies using human cells and a zebrafish model of RMS has shown that a population of CSCs exists within RMS. Thus, I am interested in characterizing potential genes that serve as a marker for CSCs in RMS. I am currently pursuing two candidate genes called PAX7 and CD82. Both PAX7 and CD82 have been demonstrated to play an essential role in regulating the function of skeletal muscle stems cells. The molecular signature of the CSCs in RMS is similar to that of skeletal muscle stem cells. Our preliminary data in the Chen lab also demonstrated increased expression of CD82 in a sphere assay, a surrogate in vitro assay to assess stem-like features in tumor cells. Based on these findings, my central hypothesis is that PAX7 and CD82 can potentially serve as specific markers of the CSCs in RMS. To test the hypothesis, I tagged PAX7 and CD82 with the aid of the CRISPR/Cas9 genome editing technology in order to isolate populations of RMS cells that either express PAX7 or CD82. I will perform cell-based assays in order to assess whether the stem-like qualities are enriched in isolated PAX7 and CD82-labeled RMS cell population. The identification of the CSCs in RMS will provide insight for a novel solution in overcoming drug-resistant RMS, tumor recurrence, and metastasis, through CSC-targeted drug therapy.

Stellar mass loss is enormously important for a wide range of astronomical subfields from galactic feedback to stellar evolution, and is particularly vital for understanding time-dependent and transient phenomena like supernovae, gamma-ray bursts, and neutron star and black hole mergers. Despite years of study, it remains poorly understood, and the physical mechanisms driving mass loss remain unclear - especially in the case of stellar binaries. The binary star system V367 Cyg's complex structure offers a unique testing ground for binary mass loss theories. The more evolved star in the system is losing mass that is accreting onto the secondary star, creating a thick disk around it. The thick disk and small separation between the stars prevents us from directly observing the mass transfer, but we can investigate the structure of the V367 Cyg system using polarimetry - the analysis of polarized light - to disentangle its complex spectrum originating from multiple sources. I will discuss the disk-stream geometry of V367 Cyg using new polarization light curves of the system which I extracted from 7 years of spectropolarimetric data taken with the University of Wisconsin’s Half-Wave Spectropolarimeter (HPOL).

Familial caregivers often serve as the primary coordinator of care for children with medical complexity (CMC). However, they currently lack a central tool to organize their child’s health information from multiple fragmented information sources and support their unique information needs. The primary objective of this study was to develop a user-centered, care organization tool by incorporating the information needs and preferences of CMC caregivers. Following a user-centered design methodology, we first conducted interviews with CMC caregivers between 3/16-11/16 to understand their information needs and elicit their preferences for a care organization tool. Next, we conducted design sessions with caregivers between 8/17-12/17, which involved content categorization activities, drawing exercises, and scenario-based prototype testing. Between design sessions, we applied content analysis to interview and design session transcripts, and incorporated findings into the ongoing development of a functional prototype. We conducted interviews with 17 caregivers and design sessions with 6 caregivers. We grouped findings into two categories: design and implementation. An overarching theme of both categories was the need for customizability, as the primary purpose of the tool differed based on the caregiver’s main information needs. In terms of design, caregivers voiced a desire for both mobile and web interfaces, with a customizable home screen, containing templates to track medications, symptoms and major events, and outline communication preferences based on their child’s developmental status. In terms of implementation, caregivers were agreeable to the idea of a cloud-based tool which would provide easy access to emergency information. However, they wanted control over customizable permission settings for others to view and/or edit other content within the tool. We developed a novel, user-centered, cloud-based care organization tool for CMC families by engaging caregivers in the design process. Next steps include examining prototype usability, effectiveness, and integration with provider health records.

The reduction of drug craving and subsequent relapse is central to the recovery process for individuals with substance use disorders. One of the goals of this project is to improve pharmacological treatment interventions for substance use disorders by better understanding how the neurotransmitter dopamine is involved in relapse. We investigated the relationship between drug craving and dopamine release in the nucleus accumbens core (NAC), an area of the brain that plays an integral role in reward-based learning and addiction, in male rats that have been trained to consume cocaine or alcohol. We tested the effects of L-DOPA, a chemical precursor to dopamine and a treatment that could reduce drug consumption, on craving and relapse-like behavior. Recent evidence from our lab suggests that decreased dopamine release in the NAC correlates with increased cocaine consumption in rats, and that L-DOPA administration attenuates drug intake. Preliminary data from our current project shows a similar effect of L-DOPA on alcohol or cocaine relapse. Our characterization of dopamine release in the NAC during both periods of drug abuse and withdrawal provides new insights for future studies and our use of innovative electrode implants for monitoring dopamine neurotransmission will pilot the technology for other drug self-administration studies. This will help to determine whether L-DOPA should be considered for treatment of cocaine and alcohol addiction in humans.

The Internet of Things (IoT), is used to describe a network that connects objects installed with autonomous components to other objects and to computers. This has made inroads into many aspects of our lives. The application of IoT has enhanced our workplace with such technologies as RFID sensors for tracking and replenishing resources. Yet, there is limited research about the way human processes, and in particular, team processes are changed by IoT objects. Herein, we focus on sociotechnical systems theory in order to connect IoT and team processes, where IoT objects are differentiated based on functionality. We draw on the team process framework to clarify the type of task-oriented activities team members engage in overtime as they collectively complete work projects. We connect different IoT objects to team processes and propose that the synergies may enhance team efficiencies and effectiveness. As well, we provide a real-world scenario about air conditioning service that illustrates how different IoT objects may be introduced to affect the team processes that apply. Using my business discipline perspective, my research provides a IoT framework that projects can adopt to improve team efficiency and effectiveness. This research demonstrates how “smart” automation engages with service, via the aid of Internet of Things, enhances team processes, and may improve the service customer experience. From other disciplines, this research encourages information technology and hardware advancement to explore more comprehensive and utilized networks to abridge convenience created by updated tech and skills with people’s desire and satisfaction, that can be applied to any aspect of contemporary human lives.

Patagonian Welsh is a dialect of the Welsh language spoken in the southern Argentinian province of Chubut, brought to Argentina in the mid-1800s by settlers seeking to establish an enclave of Welsh culture abroad in the face of British persecution. It is spoken today by a small community, and very little scholarship exists on the dialect. This project’s purpose is to take a first step towards cataloguing the phonology, grammar, and sociolinguistic status (the relationship between speakers of the language/dialect and social phenomena such as race, class, age, or gender) of Patagonian Welsh, and to answer the question “How, or to what degree, has Patagonian Welsh diverged from Standard Welsh?” Sociolinguistic studies are often conducted using a “man on the inside” from the community whose language is being studied, in order to avoid the researcher's presence altering social dynamics in data elicitation that may distort results. To that end, we have recruited volunteers from the Welsh-speaking community of Argentina to aid in interviewing fellow community members and record data. We have also prepared elicitation materials, including translation exercises, a collection of Welsh texts to be read and compared with Standard Welsh readings, and interviews in order to expose preferred grammatical formations, variation of the language between casual and formal diction, and phonology. Based on existing scholarship and observation, we anticipate that the language will show influence from Spanish phonology and vocabulary, and that it will display marked age-grading, with divergence from Standard Welsh varying with age. An observance of such behaviors may suggest that Spanish and Patagonian Welsh may be undergoing language mixing, which would mark the first observance of such a phenomenon in the case of a Celtic language. As such, this project will constitute a significant expansion of historic and linguistic knowledge concerning the Welsh diaspora and language.

The alpha-1D adrenergic receptor (A1DAR) is a G-protein coupled receptor (GPCR) and is known for its function as a regulator for cardiovascular, urinary, and central nervous system function. This unique GPCR has a PDZ ligand at the C-terminus of this receptor. A PDZ ligand is a region on a protein that can bind to a PDZ domain on another protein and is named based on the three proteins that it was observed in. Previously, it has been discovered that this ligand interacts with the syntrophin family of PDZ domain proteins. The hDLG1 protein is a human homologue of the Drosophila disc large (DLG1) tumor suppressor protein and contains three PDZ domains that have been implicated in interacting with A1DARs. By determining how/if the PDZ domains on the hDLG1 protein bind to the A1DAR, a more accurate depiction of this macromolecular complex can eventually be determined. Several methods were used in order to determine this. First, I cloned hDLG1 PDZ domains separately as well as varying combinations of the three domains. Next, I purified the protein constructs so I could determine the binding efficiency of the hDLG1 proteins to the A1DAR via Bio-Layer Interferometry (Octet). SNAP gel assays can also be used to determine the interaction with the A1DAR. Upon reviewing the results of these techniques, the nature of the interaction between the PDZ domains of the hDLG1 protein to the A1DAR can be determined. Understanding the architecture of this structure has many implications in pharmaceuticals as this protein can be specifically targeted by medications to treat a multitude of diseases. Side effects can be minimized by targeting specific parts of this large protein complex with medications than produce more specific responses thus limiting unwanted side effects. Medications that target the proteins involved in this complex can affect the function of the cardiovascular, urinary, and central nervous system.

The PTEN (phosphatase and tensin homolog) protein negatively regulates growth-promoting PI3K-Akt signaling in cells. Due to its function as a tumor suppressor, PTEN is often mutated in diverse cancers. Unfortunately, most PTEN variants have not been individually studied, making it difficult to ascertain their functionality within cells. Our lab recently demonstrated that thousands of PTEN missense variants exhibit decreased steady-state abundance when expressed in human cell lines and likely have reduced function. However, the mechanism behind their lower abundance is currently unknown. We hypothesized that many low-abundance PTEN variants are thermodynamically unstable and possess a reduced melting temperature. To test this, we fused EGFP, Enhanced Green Fluorescent Protein, to a panel of PTEN single amino acid variants, and these fusion proteins were expressed within human cell lines. Then, we cultured these cells at their standard growth temperature (37°C) and two lower temperatures (33°C and 30°C). We found that a subset of variants of intermediate abundance at 37°C exhibit WT-like abundance at decreased temperatures, while variants of extremely low-abundance remain unchanged. These results suggest that we can identify missense variants with reduced thermodynamic stability using this method. Next, we will repeat this experiment at high throughput to identify hundreds of temperature-dependent PTEN variants. We will determine biochemical properties shared by partially stable variants and compare them to computational predictors of protein folding. We will also identify variants of intermediate abundance that are not temperature-dependent, which may reveal other mechanisms by which variants lower a protein’s abundance. Our results demonstrate that we can characterize the thermodynamic stability of PTEN variants by measuring their abundances in cells grown at different temperatures. These results might be more physiologically relevant because the variants were studied in a cellular environment. Furthermore, our methods may be applied to other proteins that cannot be studied as purified protein.

Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder in which fluid-filled cysts form in the kidneys and other organs. Mutations in the PKD1 and PKD2 genes, encoding the polycystin-1 (PC1) and polycystin-2 (PC2) proteins respectively, result in ADPKD. The underlying mechanisms that connect these mutations to ADPKD pathogenesis are poorly understood. Therefore, there is a great need to understand the mechanism of this disease and find an effective treatment. Our laboratory has developed an ADPKD cellular model by differentiating human pluripotent stem cells (hPSC) with mutations in PKD1 or PKD2 into kidney organoids. We are using this model to screen drugs that potentially induce or inhibit cyst formation in a dish. The cyclic AMP signaling pathway is hypothesized to contribute to cystogenesis in PKD. To test this, PKD mutant hPSC lines and isogenic controls were differentiated into kidney organoids and treated with forskolin, a strong cAMP agonist. Images of live organoids in adherent cultures were acquired in intervals and quantified for cyst formation using the cell counter feature of ImageJ. Organoids were subsequently fixed, stained, and imaged with fluorescent microscopy. Forskolin, induced a rapid and dose-dependent swelling in kidney organoids derived from both PKD hPSCs and isogenic controls. After removal of the drug, the tubules returned to its original form. These studies show that chemical modifiers of cystogenesis can be successfully tested using this system. Surprisingly, cyclic AMP does not appear to have effects that are specific to PKD. We are currently testing other drugs and culture conditions for cyst-inducing or –inhibiting effects. Interestingly, PKD kidney organoids form cysts in suspension cultures at significant higher rates than adherent cultures, revealing a role for the microenvironment in cystogenesis. These findings help us gain insight into the disease pathophysiology, which will ultimately guide us to discoveries of better treatments for PKD.

Organic photovoltaic (OPV) cells are an emerging technology with the potential to become a major source of energy in our future. In addition to a lower environmental impact than common silicon-based solar cells, OPV cells are flexible, lightweight, and comparably inexpensive to fabricate. They are also quite customizable via molecular engineering providing the opportunity for much novel architecture. Our research team focuses on innovating a modular processing system for OPV cells in the form of multi-component fibers by continuously coating device layers onto wires. Using a small, user-friendly system allows us to focus on the most important factors that affect the morphology of the resulting OPV fiber. After characterizing the fibers we are able to consider what changes need to be made to the modular system, allowing us to better advise on the design of a larger-scale manufacturing process for organic photovoltaic fibers.

Autism Spectrum Disorder (ASD) is a collection of neurodevelopmental disorders characterized by social-communicative and behavioral impairments and affects approximately 1 in 68 children in the U.S. Children with ASD, on average, score lower on language measures than their typically developing peers and suffer from social impairments involving speech quality, social-communication, and interpersonal interaction. Children with ASD often report a desire for more peer social interaction, but have poor social support and more loneliness than their typically developing peers. In typical development, siblings can positively influence social skills and promote language, cognitive development, and understanding of emotions. This study (1) compared the social communication and language ability in children with ASD with siblings to those with ASD without siblings, (2) compared the severity level of autism spectrum-related symptoms between the two groups, and (3) investigated whether age differences of the siblings affect these measures. Participants included children with ASD with siblings (n=20) and children with ASD without siblings (n=50), between the ages of 8 and 17 years. Social communication was measured via clinical report using the Autism Diagnostic Observation Schedule (ADOS-2) and by parent report using the Social Responsiveness Scale (SRS-2). To assess language ability, participants completed the Differential Ability Scales, 2nd Edition (DAS-II) and the Clinical Evaluation of Language Fundamentals (CELF-4). To measure autism severity, we used ADOS-2. We predicted that (1) children with ASD with siblings would exhibit better social communication and higher language ability than those without siblings, (2) ASD children with siblings would experience less severe autism spectrum-related symptoms, and (3) ASD children who are closer in age with their siblings would show more benefit of having a sibling than those that are farther in age. The results of this study will provide insight into social and language benefits of siblings in children with ASD.

The Nanoscribe is a high-resolution (500nm) Nano 3D printer that is new to the Washington Nanofabrication Facility. It was acquired through a National Science Foundation (NSF) Major Research Instrumentation (MRI) grant. The tool uses a technology called two-photon polymerization. This involves the use of photoresist, which is a light sensitive material, and an infrared laser that directs brief pulses of light through a microscope objective in different patterns to create 3D objects. The highly focused laser beam allows for dimensions of less than 500 nanometers in X and Y directions to be achieved. One major limitation of the tool is that unlike most photolithography equipment, it is not programmed to do basic alignment. Most fabrication applications require at least two layers of materials to be aligned. For example, when making electronic circuits, there is a top and bottom layer at a minimum, and a vertical layer in between, thereby requiring at least two alignments to the first layer. Our research is focused on understanding and testing test code to add pattern recognition alignment capabilities to the Nanoscribe instrument. For our test application, we applied test aligning microneedles to pre-patterned electrodes fabricated using conventional photolithography. We then 3D printed microneedles that are subsequently used to release drug therapies in test wells via an applied electrical potential (voltage). The alignment process that we developed can be used as a basic construct and capability for other applications being developed on the tool.

This work seeks to address some problems faced by deaf and hard of hearing persons who work in confined or hazardous spaces. The issue they face that I am focusing on is the timely access of alerts and alarm, which are commonly provided solely through sound. Many approaches used in more general work conditions, such as flashing wall lights or another person notifying them, are heavily impeded by a confined work area. Additionally, a hazardous environment requires strict safety features regarding electronics. Any tool used must not have exposed electrical connections that could cause a spark or that it could break in such a way that could provide a source of ignition to flammable gases. Currently available bluetooth headsets and pagers do not meet these safety specifications and would be an additional piece of equipment for workers to carry. We have worked to develop a device that can clip onto existing safety equipment, conform to hazardous environment safety standards, and pair with the user’s current cell phone and radio to notify them through vibration and light patterns. We are working with people who would benefit from the device as the design improves to its signals are clear in an industrial environment and that it suits their need. Future developments include allowing the device to relay more complex messages from multiple sources.

Smartphones and mobile applications have enabled users to access a world of features and content in the palm of their hands. Many of these mobile applications are professionally designed to keep the user engaged, or what some consider "addictive." Our goal in this study is to understand what specific user interface features make it more or less likely a user will feel that an experience is addictive. We also hope to learn more about what specific features prompt users to self-interrupt to engage with an app. We are currently developing a mobile application that helps spark conversation about phone usage and helps users reflect on their behaviors and habits. We are also conducting interviews that include a phone demo and participant sketching, enabling us to co-design new interfaces with users. As phones become ever-present in all of our activities, we seek to understand people’s experiences with feelings of addiction, self-interruption, and checking in, and to identify what designers can do to help users engage in behaviors they feel good about. We have found that participants can identify negative feelings about their phone usage behaviors but those feelings are not strong enough for them to actively seek change

Cancer is the 2nd leading cause of death in the United States. Of these cases, 6-7% are pancreatic cancer (PC), yet this disease is ranked 1st in mortality because what causes PC and how it manifests is still relatively unknown. Early detection is difficult and in a majority of cases, patients are diagnosed after the cancer has progressed to final stages. For the last 7 years, the Human Photonics Laboratory (HPL) has been dedicated to early detection and diagnosis of PC through the next generation 3D pathology (and all aspects of its infrastructure: 3D microscopy, 3D reconstructions/supercomputing, millifluidic device development/whole tissue processing, clinical evalution/validation). For PC, cell and tissue specimens which have been imaged in 3D and reconstructed in an advanced 3D visualization software (Amira) require an appropriate gray scale and RGB color scheme to determine accurate cancer diagnoses. Ideal and non-ideal samples may then be passed onto collaborating pathologists for clinical evaluation and validation. This research project seeks to satisfy three primary aims: (1) properly match the color metrics/scheme of the raw optical 3D microscope datasets to 3D computer reconstructions and analyze (qualitatively/quantitatively) the gray scale/RGB color histogram between normal/cancerous (human) pancreatic samples, (2) compare/contrast the pathological metric known as the nuclear-to-cytoplasmic (N/C) ratio between a small sample of normal/cancerous specimens, (3) choose 5-10 ideally processed/matched specimens and submit to pathologists for clinical evalution. The outcome of this project is expected to accelerate the diagnosis of PC.

Blockchain is a technology as fascinating as fast-evolving. It is a data recording paradigm which allows encrypted transactions among the participating entities in the network. These transaction data are then recorded on a public ledger through a multi-party authentication process. The absence of central authority and the immutability of the recorded data make corruption or fraud less likely on Blockchain, which contributes to its increasing popularity today. Its most famous application is cryptocurrency, such as Bitcoin and Ethereum. Unbeknownst to the general public, however, is the flexibility of Blockchain that can be applied to many purposes other than cryptocurrency. For this research, I explore the potential usage of Blockchain for protection and promotion of human rights around the world. My hypothesis is the implication of blockchain for applications for human rights, both socio-economic and civil-political. I intend to focus on three human rights specifically: access to food and shelter, rights to political participation, and rights to healthcare. By the end of this research, I will have approached this through the case studies of countries that have started applying the technology in various usages. For instance, in Spain, Estonia, and South Korea, companies and organizations started developing and using voting systems based on Blockchain; in Jordan, the UN World Food Program provided Ethereum voucher to Syrian refugees to help their needs. I will also have explored its technical limitations by examining cybersecurity risks of various blockchain technologies. For instace, I will have looked into the blockchain technologies which cryptocurrency companies have used, such as the DAO, Mt. Gox, and Bitfinex, which experienced cyberattacks and lost hundreds of millions of dollars. For a successful application of Blockchain to human rights protection, such cybersecurity risks must be identified and prevented. I expect to find that despite its evident vulnerabilites, blockchain has indisputable benefits must be utilized for human rights protection.