Patients with Type 2 diabetes have insulin resistance, which continues to manifest as hyperglycemia and results in the cells failure to absorb insulin. Insulin resistance in the brain affects cognitive abilities such as learning, memory and also alters synaptic plasticity. The purpose of this study is to investigate cognitive impairments in rodent models of T2 diabetes. Minimal doses of streptozotocin (STZ), which is toxic to insulin producing beta cells, were given for 9-10 weeks. Once glucose levels reached above 250mg/dl which is considered indicative of a hyperglycemic state similar to Type 2 diabetes injections would stop. Weights were takes consistently for appropriate injection volume. We utilized a spatial working memory task known as delayed alternation to test cognitive impairments. We found a significance between control and experimental rats in working memory accuracy using a one-way ANOVA p=.05. Similar to diabetic patients, we saw weight fluctuations in experimental rats, but weights were stable for the control group. This type of task requires strong working memory demands on subjects, which may be compromised by a hyperglycemic state. Additionally, previous research shows that elevated glucose levels and chronic neuroinflammation are also found in Alzheimer's disease (AD) patients. Neuroinflammation might be a pathological similarity in the progressions of Type 2 diabetes and AD.

Graphene is a ground-breaking material with over twenty thousand patents involving its applications and modifications. It is the strongest, yet thinnest material known with semi-conducting properties. Extensive research has been performed on graphene to improve characteristics such as its conductivity, formation of holes and chemically manipulating its structure. Specifically, graphene is a two-dimensional, single atomic layer of graphite; which is an allotrope of carbon made up of tightly bonded carbon atoms organized into a hexagonal lattice. What makes graphene of interest is its sp2 hybridization and nanoscopic atomic thickness (of 0.345nm). An alternative structure comparative to graphene involves utilizing a self-assembly condensation between amine containing compounds and carbonyl groups, which form a graphene-like nitrogenated derivative. These materials have ordered pores with high crystallinity. The synthesis of such compounds is well established and have been characterized as Covalent Organic Frameworks (COFs). This amine/carbonyl condensation reaction can produce significant control of the lattice structures desired in the final 2-D material. This material can then be fabricated into membranes for applications in separations, batteries and more. The goal of my work utilizes this condensation method to chemically synthesize a framework with two chemically distinct pores in the lattice. The two pores are capable of chemical manipulation, which would potentially be superior to graphene. This gives rise to a variety of applications of the material and its derivatives, which we hope to improve on by using these nitrogenated frameworks.

The Possession Sound’s Snohomish River Estuary (PSSRE) provides a prime habitat for a large nesting population of North American osprey (Pandion haliaetus) in the Puget Sound region. The ospreys that nest in the Possession Sound are migratory, arriving between mid-March and mid-April to nest and leaving between late-August and late-September to winter in Southeastern Texas, Mexico, and Central America. Male and female ospreys migrate separately, with males returning first to prepare the nest and females leaving first to travel farther south. Juvenile ospreys do not make the return migration from their southern winter location until their second spring. As of 2016, osprey attendance reached 24 nesting pairs in the PSSRE. As apex predators whose diets are comprised primarily of fish, ospreys are considered sentinel species for studying contaminant levels in marine environments. Therefore, monitoring behavior, breeding success, and contaminant levels of ospreys can provide a census for the health of the local marine ecosystem. This study will take place on the return of the ospreys to the PSSRE in 2018 and will entail visually surveying the estuary to determine the nesting locations, return rates for both males and females, and dietary habits of ospreys. Past nest locations and populations will be compared to 2018 data. Additional research will utilize a remote camera with pan/tilt/zoom capabilities to observe and record three nest sites near the Port of Everett for nesting behaviors, fecundity, and identification of prey targets for potential heavy metal analysis.

Inpatient hypoglycemic events less than 50 mg/dL are prevalent among hospitalized patients and can lead to poor health outcomes, including increased mortality. Some studies indicate that among hospitalized patients, older individuals, patients with co-morbidities, and those who are admitted to intensive care units are the most common inpatient populations to suffer from hypoglycemic events. Studies also suggest that inpatient hypoglycemic events are more often medication attributable in contrast to physiologic causes. The aims of this quantitative study are to: 1) determine the root causes that lead to hypoglycemic events in the hospital setting, 2) describe patterns in chart documentation related to hypoglycemic events, and 3) identify measures to attain effective prevention of hypoglycemia. Specifically, this study examines the time range between the hypoglycemic event measurement and the blood glucose measurement prior to the event to determine if tighter glycemic control results in improved patient outcomes, the use and documentation of rescue medications after a hypoglycemic event, and the presence of dietary intake charting in the medical record prior to the hypoglycemic event. We collaborated with the glycemic team at a local medical center to collect data drawn from patient medical records. Patient medical records were selected if they had experienced a hypoglycemic event less than 50 mg/dL between March 2017 and June 2017. Analysis used descriptive measures to identify patterns and inconsistencies in the data derived from the medical charts related to potential root causes of hypoglycemia. Using a systematic approach to identify the root cause of inpatient hypoglycemia informs future development of tools and policies to reduce the incidence of inpatient hypoglycemia in the future and improve patient outcomes. The expected results of this study attributes the hypoglyemic events to infrequent and inaccurate diet intake documentation, and longer time intervals between blood glucose monitoring. 

Increasing world energy consumption is accompanied by rising concerns over non-renewable fossil fuel usage and its detrimental environmental impacts. Even if we were to try to meet future energy demands exclusively with fossil fuels, we would fall woefully short of our projected global needs. Consequently, there are compelling economic and environmental reasons that support a dramatic shift in future energy utilization to renewable technologies. The development of solar-driven technologies to generate renewable, transportable, and storable fuel sources is desirable since these energy-dense fuels can be used in the future regardless of the time of day, season, or geographic location. My research explores the utilization of nanomaterials for solar energy-catalyzed biomass decomposition into fuels and valuable, small molecules with diverse industrial applications. Specifically, this work shows the potential of using nanomaterials of a variety of structures to convert lignin (which composes 20-30% of biomass) into more useful small molecule components. To do this, we strive to understand how to make a nanomaterial that both efficiently absorbs light and subsequently uses that absorbed energy to power lignin degradation. The ability of a nanomaterial to absorb light and catalyze this reaction depends on its electronic properties, which is dependent on both its elemental composition and morphology. Our work explores the various catalytic efficiencies of nanomaterial systems of different shapes and sizes.

Eelgrass, Zostera marina, is a critical nursery for numerous marine organisms in Puget Sound. A variety of fish species benefit from eelgrass ecosystems, using the blades of sea grass as anchor points to ensure the safety for eggs through larval fish stages. This study compared larval fish densities in eelgrass beds versus offshore from the eelgrass sites. Higher numbers of larval fish are expected to be found in samples collected within eelgrass beds rather than those collected further offshore. A variety of local fish species are expected to be found both within and outside of the eelgrass beds, including forage fish and rockfish. Samples were at three sites of eelgrass beds located in the Possession Sound in Puget Sounds’ Whidbey Basin. The samples were collected once a month from December to March with a 500-micron net deployed for three minutes at speed of 1 knot at a depth of 2 to 3 meters below the surface directly over the eelgrass bed and repeated offshore from the site. After collection, the larval fish were extracted and sent to the Shoreline Community College Laboratory for DNA barcoding to allow for species identification. Preliminary data indicates that higher numbers of larval fish were present within eelgrass beds as opposed to the offshore areas. A greater understanding of the important role that these eelgrass ecosystems play as nurseries for larval fish is necessary to provide context and further reason for conservation efforts and general awareness of human impact on these lively nearshore environments. Identification of the larval fish species that inhabit eelgrass beds provides a greater understanding of these species’ preferred laying conditions.

Infants with predominantly female primary caregiver experience show a visual preference for female faces and process female faces with relative ease in comparison to male faces. Yet, little is known about infants with male primary caregivers. The proposed study will examine how predominant male caregiver experience in infancy influences the development of implicit gender associations in early and middle childhood. Additionally, parents will complete a week-long survey of experience and behavior scales examining the caregiver-child relationship. We predict that children with predominantly male primary caregiver experience will show fewer implicit associations towards females and warmth and males and power. The primary caregiver-child relationship might also modulate the development of implicit biases related to biological sex. This study will be the first to investigate the development of implicit association related to biological sex in children with a male primary caregiver.

Research has shown that drinking motives (or reasons for consuming alcohol) are strong predictors of alcohol use; moreover, enhancement and social motives are among the strongest predictors of alcohol use. Given limited research to date, the purpose of the current study is to examine how drinking motives relate to drinking alone and also to drinking with friends. College student drinkers 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 on alcohol use, drinking motives, and drinking context were used for the current analyses (N = 292 to date; 52% female, 71% Caucasian, mean age = 20.17 years). Participants were asked to report how often they drank alone and with friends on a scale from “never” to “daily or almost daily.” In addition, they were asked to report motives for drinking on each of five subscales using response options from “almost never/never” to “almost always/always." The current study will use regression analyses to test associations with four of the subscales: coping-anxiety, coping-depression, enhancement, and social motives. We hypothesize that higher coping motives will be associated with being more likely to report drinking alone and with friends. Additionally, we hypothesize that higher social and enhancement motives will be associated with being less likely to report drinking alone and more likely to report drinking with friends. Results from this study will provide a better understanding of why people decide to drink and in which different social contexts, thus providing valuable information to guide interventions on how to better incorporate drinking motives and social context.

Childhood asthma accounts for 571,000 ER visits, 136,000 hospitalizations, and $10 billion in healthcare costs annually in the United States. Fewer than 50% of children with asthma are adherent to their treatment regimen, leading to worse health outcomes. The purpose of this study is to develop and test the usability and acceptability of the symptom monitoring and response module of the Child Asthma Management Program (CHAMP), a new web-based, tailored asthma shared management health application for 7 to 11-year-old children with persistent asthma and their parents. A user-friendly and visually engaging module was developed with content focused on asthma symptom identification, monitoring, and response. Using a human-centered design framework, dyads of children and parents were recruited to participate in two rounds of design and usability sessions with prototypes of the module. Additionally, dyads completed the Asthma Responsibility Questionnaire, CHAMP acceptability questionnaire, and a semi-structured interview following the sessions. Thematic analysis using an investigator-developed coding frame was used to code all interview data using ATLAS.ti software and quantitative data from the acceptability survey was transferred to SPSS 24 for analysis. Results from both design and usability sessions will inform final revisions to the module. The final version of this module will guide dyads in improving their asthma shared management. This module meets a considerable need for effective asthma management interventions and represents a step towards better tools for improved chronic disease management for pediatric patients.

In the Pacific Northwest the Endangered Species Act (ESA) protects wild salmonids from commercial fishing. The current commercial fishing gear, including gill nets but not limited to, disrupts the recovery of these species because fishermen can not selectively harvest the hatchery fisheries without wild salmonids as bycatch, which have high mortality rates. Once ESA quotas are met this can effectively shut down commercial fisheries. The exploration of alternative fishing tools that can select for certain species will lower bycatch mortality rates of ESA species, and in turn allow commercial fisheries to operate longer. On August 26th through September 29th of 2017 Wild Fish Conservancy conducted follow up research, to a 2016 pilot study of Pound nets, in the Lower Columbia River Sub-Basin. Post release survival rates were evaluated in a modified stock selective pound-net. Using Mark Recapture methodology, with a Passive Integrated Transponder (PIT) tags, and genetic clippings for later analysis. Survival rates of control specimen to treatment specimen were captured as they traveled past dams upstream. Data analyzed were total catch, catch per unit effort and covariates of recapture probabilities. The preliminary results show that fishing with stock selective nets can effectively target hatchery fisheries while successfully releasing ESA listed species, reducing mortality rates. In 33 days WFC and a local fisherman captured and released 7,129 salmonids with a post release survival for steelhead and trout ( Oncorhynchus Mykiss) of 94.0%, and 96.6% for Chinook salmon (Oncorhynchus Tshawytscha) listed as ESA species. Hatchery fisheries of these species along with coho salmon (Oncorhynchus kisutch) were effectively selected with viable commercial quantities. Future subset data of genetic clips and a Jolly-Seber analysis will give more precise information of these post-release survival estimates.

Heat exposure is associated with several potential adverse heat health effects, including heat-related illness and kidney injury, for example in outdoor workers who labor in the heat. In order to best study and prevent these heat effects, accurate assessment of personal ambient heat exposure is needed. An iButton® is a small coin-shaped data-logging thermometer that can measure and log ambient temperature and humidity. The iButton® has been adapted for use in environmental human health research as an easy to use and affordable data logger for personal ambient temperature measurements. The degree to which personal iButton® measurements are influenced by heat generated by the human body, for example during physical exertion, or solar radiation (iButtons® are contained in stainless steel cases), has not been systematically described. The goal of this study is to quantify the radiated body heat from subjects exercising in both direct sunlight and shaded settings. We recruited a sample of 15 adults, who participated in sessions that were roughly two hours long, with half of the time in a shaded area followed by the same activities in direct sun. Ambient temperature was recorded using iButtons® attached to participants as well as two, five, and ten feet away. Data collected will be analyzed using R 3.4.2 data analysis software. Preliminary results suggest that monitors attached to the participant capture the release of some body heat but that this dissipates by two feet away from the participant. Preliminary results also suggest that, while monitors positioned facing the sun capture some of the effects of solar radiation, monitors in the shade or facing away from the sun do not. This information is expected to contribute to the interpretation of personal ambient temperature measurements used in future studies that examine the relationship between heat exposure and health effects.

Biochar is used as a soil amendment and is created from plant biomass through pyrolysis. Biochar is thought to help plants grow by increasing the fertility of soil as well as impacting water retention in soils. This led to the question: Does biochar increase the water retention of soils found in the Lower Yakima Valley, allowing for a reduction in the amount of water that is needed to grow bell pepper plants in this water-stressed region? This research delves into the effectiveness of biochar by testing water level usage in real world plants grown in two concentrations of biochar (0.5% and 1%) applied to soils trial plots located in the Heritage University Research Farm. A random generator was used to create a split-plot design with three concentrations of biochar (0% or control, 0.5%, 1%) each with three replicates. The spilt-plot contained two different watering schemes. A total of 576 greenhouse grown Capsicum annum plants were transplanted to 18 plots, each plot containing 32 plants. To test the efficiency of biochar in soil water retention, soil moisture data, plant height, dry weight of the plants, and yield abundance were measured. Results indicate that the presence of biochar in soil can lead to increases in biomass of up to 100% in certain conditions. However, there were irrigation engineering complications that led the inability to reliably control the irrigation rates in the two split plots (originally planned for 100% in section 1, 80% reduced flow in section 2). The soil moisture data were inconsistent and highly variable reflecting potential instrument calibration issues, multiple instances of damage to the drip tape leading to water leaks, and persistent problems with the timing mechanisms for watering lines. This experiment led to significant improvement our methods for the following bell pepper research for the following year.

Previous research has shown that biochar is a supplement in fertile soil productivity. Biochar functions as a water and nutrient retention tool. Biochar helps prevent and decrease local eutrophication in local streams and water ecosystems by reducing the amount of fertilizers applied. Moreover, it’s essential in reducing the amount of water used, thus critical with projected looming drought conditions. In order to test the validity of the impacts of biochar in crops growth, we compared the diameter measurements of approximately 270 Capsicum annuum bell pepper plants. We selected bell peppers as our experimental crop for their practicality as an economical, simple crop and their pertinence of larger diameters which was correlated to the soil. According to preliminary results, we recommend the use of biochar as an enhancement product in pepper farming. Future research could explore the impacts of biochar on crop size on the different crops in the region. This research will provide beneficial information about enhancements to current agricultural practices regarding water and nutrient efficiency in crop growth.

Family size matters. As a family grows, parents dedicate less time as well as financial and emotional support to each child. Siblings often have to compete for parental resources whereas only children receive full support from parents throughout their lives. Previous research has found that competition leads people to adopt performance goals (i.e., motivation to perform better than others). In big families, competitive environments may signal that being more successful than others is important, making performance goals more salient than in a family where one is the only child, where mastery goals (i.e., motivation to master new skills) may be more salient. In an exploratory study, we examined whether family size shapes people’s motivations for learning. We predicted that students with siblings would be more motivated to learn by competing with others (performance orientation) while only children would be more motivated by honing their skills (mastery orientation). To test this hypothesis, we recruited 328 participants (166 only children and 162 with siblings) for an online study in which they completed the Achievement Goal Questionnaire and provided information about their race and number of siblings. As predicted, only children more strongly endorsed mastery orientation (M=3.93, SD=.58) compared to students with siblings (M=3.80, SD=.62, t(326)=1.99, p=0.5). Students with siblings endorsed performance orientation (M=4.05, SD=.78) marginally more than only children (M=3.90, SD=.73, t(326)=1.90, p=.06). While further research is needed to understand why these differences emerge (e.g., due to competition or other differences in family environments), our study lends insight into how people’s family experiences shape their academic motivation. These findings many help educators learn how to best motivate students from different types of families.

Chaos refers to dynamical systems that are exponentially sensitive to their initial conditions. While the sensitivity of the initial conditions of a chaotic system results in unpredictable long-term behavior, the global nature of a chaotic system often plays an important role for predicting its subsequent behavior. Using the logistic map (one of the simplest chaotic systems) and its Lyapunov exponents (a measure of the degree of chaos), I explore the pattern and stability of the high-order periods—one of the distinct global characteristic features of the logistic map—using Matlab. In this study, the simulations show a new pattern of repeating odd-cycle periods stemming from the 3-period cycle: a symmetric doubling cascade of odd-number periods in the chaotic phase of the map which are independent of their initial conditions. From further exploration of the even-cycle periods, a more complex ordered pattern of the whole number period cycles was found and it was found that the stability of higher periods in the chaotic region is highly dependent on their initial conditions. The closer the initial condition is to 0.5, which is the superstable fixed point of the logistic map, the more the stable high-periods are formed within the limited set of iterations. The discovery of the new ordered pattern and the stability of the whole-number periods in the chaotic phase of the logistic map can be used to predict the stable states of growth of a population model in its chaotic phase, and can be used for population studies in which the initial conditions are known only approximately. This has ramifications for mathematics, population biology, chemistry, physics, and the social sciences.

Foliar (leaf) diseases and epiphytes are a major hindrance to photosynthesis throughout the wet tropics. The research sought to determine whether there is a correlation between foliar epiphyte and disease coverage in a relatively small elevational gradient with a hypothesis that a decrease in elevation increases humidity levels which then correlates with greater coverage by foliar diseases and epiphytes on Geonoma oxycarpa. The study took place in three wet pre-montane secondary forest sites in southern Costa Rica, ranging in elevation from 1130.8 – 1188.7 m, and focused on G. oxycarpa due to its accessibility and observable patterns of foliar epiphytes coverage and disease. Three specimens of G. oxycarpa were chosen at each site, and initial estimates of the percentage of foliar epiphytes and diseases were done visually. Photos were then taken for analysis using ImageJ and a metric scale ruler was used to determine the total area of a leaf sample and the healthy portions of the leaf. Weather meters were used to determine the average relative humidity at each of the three sites. All the data was used in linear regression exploratory analysis using the open source software ‘R’. It was determined through clear, though not statistically significant, trends in the data that increased coverage of foliar diseases and epiphytes was related to a decrease in elevation and a corresponding increase in humidity, confirming our hypothesis. These findings indicate that native plants that can tolerate or better defend themselves against the onslaught of foliar epiphytes and diseases should be chosen for the more humid, lower microclimates. Because of this implication, this study is particularly important regarding the preservation of forest microclimates for indigenous cultures that depend upon native tropical plant life for a wide variety of ethnobotanical uses and crucial to the success of native plant restoration and preservation efforts.

Chronic stress induces the release of hormones and neuropeptides including dynorphin, which activates Kappa Opioid Receptors (KOR) to encode the anxiogenic components of the stress response. Previous studies have identified the specific dynorphin-KOR neurochemical signaling responses in the regions of the brain known for regulation of reward systems, and thus may be potential therapeutic targets for stress-related conditions such as depression, anxiety, and substance use disorders. Formally, cells containing dynorphin-KOR have been difficult to study due to technical limitations of the available reagents. However, the generation of new tools including mice expressing promotor-driven cre-recombinase (e.g. KOR-Cre and prodynorphin-Cre) have allowed cell-specific gene expression using Cre-dependent viral expression of fluorophores combined with in-situ staining. In this study, the reliability of a phospho-KOR antibody was tested. The specificity of the immunostaining was verified by administering a KOR agonist, U50,488, in wild-type animals or transgenic animals lacking the G protein-coupled receptor kinase 3 (GRK3), which phosphorylates the KOR. Additionally, wild-type mice with a pre-treatment of norBNI, a KOR antagonist, followed by U50 were also tested. Immunohistochemistry of animal brain tissue showed that the norBNI pre-treated, wild-type animals and GRK3 knock-out animals had lower KORp-IR fluorescence compared to their wild-type counterparts treated with U50,488, verifying that the KORp antibody was reliable. After verification, this KORp antibody was utilized to characterize the dynorphin-KOR circuitry in the mouse brain. To do so, an excitatory opsin was injected into the DR of pDyn-Cre mice with an optic fiber implant. The DR region was then optically stimulated with blue light and dynorphin-releasing projections into the ventral tegmental area were verified by measuring KORp fluorescence. This experiment details one specific dynorphin-KOR pathway in the mouse brain that was not previously studied, and future experiments will utilize this approach to map the extent of dynorphin/KOR localization within the reward circuitry.

The President’s Council of Advisors on Science and Technology estimates that the United States will need to increase its number of science, technology, engineering, and mathematics (STEM) professionals by 34% over the next decade. This guidance seems contrary to the rising trend of STEM majors becoming increasingly selective of the students they admit. Competitive degrees with additional requirements for entry (ARE) are a universally accepted phenomenon here at UW. However, there are no studies characterizing their prevalence in higher education or investigating their impact on students. We are conducting an exploratory study to characterize the number of STEM degrees across the U.S. with ARE and the factors departments use to admit students. First, we compiled institutional data for the research universities (R1) and Master’s-granting institutions with the highest number of undergraduates in each state. Next, we determined whether or not they offered STEM degrees with ARE. Programs were identified through a combination of data-mining institutional websites and contacting individuals at each institution. Finally, we administered an online survey to each department to gain deeper insight into the factors used in their admission decisions. We hypothesized that variables such as high school GPA, university GPA, and SAT score will commonly be used in the decisions to admit students. SAT scores and GPA often have significant socioeconomic and demographic biases. Consequently, if we confirm our hypothesis, this could raise questions about the equity of the admission processes for selective degrees. Preliminary results revealed over 250 degrees with ARE. Most of those degrees are offered in biology, health science, or engineering departments at R1 institutions. Ultimately, our results will inform a future study that will take a closer look at the impacts of degrees with ARE on STEM retention and diversity from a representative sample of institutions.

Synaptogenesis is the developmental process in which neurons form connections with their appropriate partners. However, the mechanistic bases for synaptic partner matching are largely unknown. To help address this gap in our knowledge about neural circuit formation, we are attempting to identify factors that drive specificity in synapse formation between nociceptive sensory neurons, known as Class IV dendritic arborization neurons (C4da), and their synaptic partners, A08n interneurons in Drosophila melanogaster. We hypothesize that C4da neurons express cell adhesion molecules that serve as specificity factors. Expressing such specificity factors in sensory neurons that do not normally synapse with A08n, for example C3da neurons, should drive spurious synapse formation with A08n. To test this, I used the split Gal4 system to develop transgenic tools for targeting gene expression specifically in C3da neurons. In this system the Gal4 transcription factor is split into its DNA binding domain (DBD) and activation domain (AD) which are independently expressed in overlapping cell populations and assemble to yield functional Gal4 only in cells that co-express both pieces. The complete Gal4 protein can then interact with UAS (upstream activating sequences) elements to drive gene expression. To develop a C3da-specific Gal4 driver I first engineered transgenes containing the Gal4-DBD fused to promoters predicted to be expressed in C3da neurons and other non-da neurons. I generated transgenic fly lines harboring these transgenes via direct injection of DNA into the fly germline. I then crossed these transgenic lines to a fly line that expresses the Gal4-AD element in C1-C4da sensory neurons. I expect to see functional Gal4 only in C3da neurons, which I can test by monitoring Gal4-dependent Green Fluorescent Protein expression. The resulting C3da neuron-specific driver will allow us to test whether ectopic expression of candidate specificity factors in C3da neurons is sufficient to drive synapse formation with A08n interneurons.

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

Reports have shown the importance of student engagement and student-centered pedagogies in biology classes. A sense of community in a classroom can help students be less isolated from their peers and increase their willingness to answer questions, as well as their willingness to ask for help. This classroom sense of community can enhance students’ perception of learning and can be achieved online. Furthermore, a sense of community among underrepresented groups (URG), which have the highest attrition rates in STEM, can be a powerful tool for increasing student retention.  We hypothesize that blogging enhances a sense of community and connectivity among students. Our study analyzed 82 students’ interactions during a semester-long writing assignment in a biology class for non-biology majors at Emory University. Half of the students submitted their assignments as blog posts, the other half through a traditional educational content management system. Both groups had equivalent distributions of diverse ethnicities. Student connectivity was incentivized and monitored by having students turn in editor-sheets, reporting whose assignment they edited, and how. This student connectivity was subsequently analyzed via a Network Analysis.  Student surveys showed trends of higher perceived sense of community among bloggers relative to traditional writers. The network analysis revealed double the average connectivity among bloggers, with 2-folds higher average connections per student in the blogging group. Students also showed more evenly distributed connections among bloggers relative to traditional writers.  We conclude that the use of blogging among non-biology majors can facilitate student-student interactions and has the potential to create a sense of community, which has positive implications in the retention of under-represented groups in STEM fields.

Diverticulitis is a common gastrointestinal condition in both the United States and Europe. Approximately 200,000 people are hospitalized for cases of diverticulitis in the United States alone on a yearly basis. When small pouches called diverticula develop along the sigmoid colon, the lower part of the colon, this initial condition is known as diverticulosis. Diverticulosis turns into diverticulitis when these diverticula, located in the left lower quadrant (LLQ) of the abdomen, become inflamed usually due to a bacterial infection. A common symptom of diverticulitis is when patients generally have LLQ pain sustained over a period of time. We, the Surgical Outcomes Research Center (SORCE), are conducting the Diverticulitis Evaluation of Patient Burden, Utilization, and Trajectory (DEBUT) study to investigate the impact of diverticulitis treatment options on patients and to improve the understanding about how physicians and patients decide to have elective surgery for diverticulitis. Currently, the optimal timing for elective (non-emergency) colectomy surgery to treat diverticulitis is unclear, and diverticulitis affects individuals in many different ways. Through our patient-centered research approach in DEBUT, we hope to determine the impact of treatment decisions on a patient's quality of life, work, and clinical symptoms. These patient-reported outcomes are measured over time among patients who do and do not undergo elective colectomy surgery to treat diverticulitis. Our goals are to better understand how physicians and patients decide to undergo elective colectomy surgery to treat diverticulitis as well as provide higher quality evidence that can help patients and their physicians to make better-informed decisions about the timing of surgery for diverticulitis. Results gained from this study may eventually help inform current medical recommendations for diverticulitis treatment and give current healthcare professionals the tools necessary to develop more effective guidelines for treating patients with diverticulitis.

Homelessness among youth in Seattle’s University District has become a crisis that has been overlooked and neglected by our community. The lack of accessible resources and poor educational opportunities, have made it difficult for this population to have their basic needs met. A major resource homeless youth lack is a solid support system. This research project is part of a larger community project that is looking at the barriers that are inhibiting homeless youth from meeting their needs and escaping homelessness. The purpose of this study is to describe, from the youth’s perspective, the resources and support that are needed to help them achieve overall health. The larger study will design and implement a sustainable community café for homeless youth and youth at risk for homelessness in the University District that provides services and support. For this study, we applied a digital storytelling methodology, which is used as a community based participatory approach, to gain better understanding of youth homelessness and their needs in their own words. Digital storytelling is typically a short video 3-5 minutes long. The interviews were guided by questions as well as open conversation for the participant’s to share their story of homelessness. We conducted three interviews and created three digital stories. This study did not contain random sampling and was conducted strictly by a volunteer basis. After the interviews were conducted we used digital images with voice-over narrative to create the digital story. The aim was to analyze these videos to shed light on the specific needs the youth have. It also served to give researchers more information on the particular barriers homeless youth are currently facing and guided activities within the community café. These will also help suggest legal and policy reform in the homeless youth community as well as bring greater awareness to the community.

Hydrological models make predictions by either simulating physical processes or by using statistical techniques. When we evaluate the accuracy of model outputs and predictions, we often observe that statistical models perform better than physically-based process models. Investigating why this happens can give us insight into how to improve the process-based models. This research evaluates how information given to different statistical and process-based land surface models at 20 sites around the world affect their performance. For this project, we use the Structure for Unifying Multiple Modeling Alternatives (SUMMA) framework, a modeling framework that allows users to decide what representations of various hydrologic processes to use during simulations. Using SUMMA and statistical measures, we estimate the effects of decisions made at each modeling step. We can also determine which model processes have the greatest effect on the results. We will compare the results from our SUMMA implementations with results from statistical models that were developed and published as part of a previous experiment. The results of this analysis will provide insight into which model components best represent observed hydrological processes and how model components can be improved and refined. Our goal is that we can produce process-based model simulations that perform better than the statistical models we previously compared them to.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by difficulties in social communication and having repetitive behaviors or interests. Sensory processing disorder (SPD) is a term used to describe a collection of symptoms stemming from atypical neural integration of sensory information. Evidence from animal models suggests a significant role of GABAergic signaling in the amygdala in regulating behaviors related to anxiety. Previous research suggests that an imbalance in inhibitory and excitatory signaling in neural connections is present in ASD, a neurodevelopmental disorder that is associated with high rates of co-morbid anxiety (up to 40%). This current study investigated the relationship between anxiety and neurochemical profiles in high-functioning children between 8 and 12 years of age with ASD and a clinical comparison group, children with SPD. Our hypothesis is that there are underlying biological differences in amygdalar functioning between children with ASD and those with SPD, despite these two groups sharing similarities in sensory sensitivity and comorbid anxiety. To explore this hypothesis, a composite of anxiety symptoms was created (α = 0.790) using questions from the Child Sensory Profile-2, Vineland Adaptive Behavior Scales, and the DSM-5 Cross-Cutting Symptom Measure. Presence of anxiety was also investigated using the Kiddie Schedule for Affective Disorders and Schizophrenia (KSADS). Using a 3T MR system, brain metabolite concentrations (i.e., γ-Amino Butyric Acid (GABA) levels) in the left amygdala-hippocampal region were measured using single-voxel proton magnetic resonance imaging (1H-MRS). We ran a regression analysis looking at the interaction between anxiety symptoms and amygdalar GABA levels in the ASD and SPD groups while controlling for autism symptoms.

The ability to quantify rat and mice ultrasonic vocalizations (USVs) can provide ethological validity to animal models of affective disorders. Vocalization frequencies are key indicators of a rodent’s subjective state and are closely tied to their behavior. For example, 50-kHz calls in rats are emitted during positive events such as sucrose drinking, and are attributed to a positive affective state. In contrast, 22-kHz calls are ascribed to a negative affective state, and are emitted during negative events such as shock. Current methods for manually scoring vocalizations are slow and labor intensive, while automated programs lack the accuracy to produce satisfactory scoring under non-ideal recording conditions. In order to create a more precise program for detecting these USVs, we applied deep learning, which has revolutionized the field of bioacoustics through image detection and recognition of audio files. By converting soundwaves produced by mice and rats into spectrograms, we can train convolutional neural networks to distinguish between vocalizations and noise. Using these methods, we created the software DeepSqueak©, a Deep Learning Based System for Quantifying USVs and Extended Analysis Kit, which outperforms current state-of-the-art, commercially available software. Hundreds of rat calls from the 18-75kHz were manually isolated from spectrograms and used as training data for our neural network, allowing it to differentiate calls from noise. As a result, USV detections using DeepSqueak are far more rapid and accurate in comparison to existing software. The detected calls produced from the software were then reviewed and re-entered into the neural network as another training set to consolidate its precision and efficiency. With the speed and reliability of DeepSqueak, quantification of USVs can become more widespread and lead to a wealth of new knowledge relating to affective disorders.

As more technology that utilizes personal electronic devices (PEDs) are being integrated in classrooms, the possibility of cell phone distraction is a real concern amongst many educators. Because of this, we became interested in cell phone use patterns in highly interactive biology classrooms at UW, and what factors influence their use. To answer this, we investigated the impact of in-class polling using PEDs or using clickers (older, standalone devices). We compared cell phone use in two different quarters (same course, same instructor) that either used PEDs or clickers for in-class polling. We also compared the cell phone use in the beginning of quarter vs. the end. In addition, we looked at whether classroom seat location correlates with cell phone use. To assess cell phone use, we directly observed active learning introductory biology lectures. Three to four researchers observed each seat in a designated section of the lecture hall and noted if a cell phone was visible (used as a proxy for use), three to five times during a class session. We used logistic regression and model selection to find a best fit model to determine if polling technology type, seat location or time of quarter (beg. vs end.) can predict cell phone visibility. To our surprise, the results indicated that neither Poll Everywhere nor time of quarter increased the already low cell phone visibility. However, our results also indicated that students that are sitting away from professor (back of classrooms) are more likely to use their cell phone than their peers regardless of polling technology. Taken together, we suggest instructors with highly interactive classrooms should not worry about integrating newer polling technologies. Further, instructors may look into having more TAs or peer facilitators roam around the classroom, especially in the case of large lecture halls to avoid cell phone misuse.

According to the Center for Disease Control, more than one third of the U.S population is obese. Preliminary data in our laboratory has shown that obesity reduces the number of T cells in the intestines of mice. This reduction of T cells leads to impaired tissue repair in dextran sulfate sodium (DSS)-induced colitis models and compromises the protective barrier against pathogens and exposure from the outside environment. Thus, our goal was to identify how to restore the number of T cells to improve intestinal homeostasis. We investigated whether T cell numbers in the intestine can be fully restored through diet-induced weight loss. Briefly, 6 week old male mice were placed in one out of three cohorts: one cohort was placed on a normal chow diet for 14 weeks, the second cohort was placed on a high fat diet for 14 weeks, and the third cohort was placed a high fat diet for 7 weeks and switched to a normal chow diet for the remaining 7 weeks. While mice placed on a high fat diet exhibited a significant reduction in T cell number, mice that underwent diet-induced weight loss exhibited a full restoration of T cell number in the small intestine. In addition, the dieted mice also showed improved survival when challenged with DSS-induced colitis. These studies are now being followed up with RNA-sequencing experiments to investigate how gene expression is changing within the intestine and better understand the mechanisms of T cell loss in obesity.

Listeners perceive foreign speech as faster than native speech, even when both are the same speed. This phenomenon is called the ‘Gabbling Foreigner Illusion.’ This illusion may occur because language-specific experience is necessary to temporally parse speech into intelligible units as it unfolds over time. Similarly, one study reported that people tap faster to music that is culturally unfamiliar than to music that is culturally familiar. Like the gabbling foreigner illusion, lack of cultural expertise with music might interfere with listeners’ capacity to find temporal units (the beat), leading them to perceive the tempo of the music as faster. We directly addressed the question of whether listeners are less accurate at perceiving the beat and tempo of culturally unfamiliar music as compared to culturally familiar music by asking them to rate the tempo of music from various cultures (West African, American, Indian, Turkish, and Latin). Musical excerpts were presented in pairs and listeners chose which of the two was faster. We also asked listeners to tap along to the music and examined if their tapping speed corresponds to their perceptual judgments of tempo. We hypothesize that listeners systematically rate culturally unfamiliar music as faster than familiar music, suggesting that listeners experience a “gabbling foreigner illusion” for music. In summary, this research is a first step towards investigating how our culture-specific experiences influence our temporal perception of music.

Current global population growth has led to higher demands for food production, increasing our reliance on synthetic fertilizers. These are formed via the Haber Process, where nitrogen from air and hydrogen (currently obtained from natural gas combustion) is used to produce the needed ammonia. More sustainable ways of generating hydrogen gas that don’t involve burning fossil fuels are necessary. One possible replacement is nanoscale cobalt phosphide, a known, effective electrocatalyst for the hydrogen evolution reaction (HER), defined as transforming two protons and two electrons into hydrogen gas. However, this electrocatalytic system requires energy input to achieve the transformation. This project investigates the design of a synthesis to produce an indium phosphide/cobalt phosphide (InP/CoP) core/shell structure that can generate H₂ photocatalytically. The InP quantum dot will be used to generate a photoexcited electron using visible light, and then this photoexcited electron will be transferred to the CoP catalyst to perform the desired proton reduction step. Regeneration of the quantum dot ground state will be mediated through the use of a sacrificial electron donor. Here we present our findings evaluating several approaches to the colloidal synthesis of the desired core-shell heterostructure using an aminophosphine precursor and the corresponding metal halides. Success of the various syntheses was determined by examining data from multiple characterization techniques including UV-Vis spectroscopy, X-ray diffraction, electron microscopy, and elemental analysis. We expect these methods to be generalizable to a suite of electrocatalytically active transition metal phosphide shell materials. This work will ultimately contribute new methods to the sustainable production of hydrogen for industrial scale applications.

Stress is highly correlated with negative physical health impacts and an estimated 75 to 90% of primary care visits are attributed to stress related conditions. Currently available treatments for anxiety are not always effective and very limited, therefore identifying new targets for the development of medication is important. Recently, neuropeptides have drawn interest as potential targets for drug therapies. Pituitary adenylate cyclase-activating polypeptide, or PACAP, is a neuropeptide that has been linked to stress responses in a variety of brain regions. For example, the amygdala is a crucial brain region for mediating chronic stress, acute stress and fear and contains numerous PACAP-expressing neurons. My research focuses on the amygdala and the expression of PACAP following an acute stress. In my experiment, I quanitfied PACAP levels both with and without acute stress. After stressing rats using a forced swim protocol, I measured PACAP and mRNA expression in the amygdala using RNAscope in situ hybridization. Brain slices were imaged using fluorescence microscopy to quantify the RNA scope signal. To analyze these images quantitatively, I have developed a CellProfiler code to accurately and rapidly analyze the proportion of neurons expressing PACAP mRNA as well as the intensity of expression within the neurons. I hypothesize that PACAP mRNA expression will be increased in the rats subjected to the acute stressor, indicating that PACAP is an important mediator for the neural stress response. By determining this relationship between neuropeptide expression and stress response, PACAP antagonists could be potentially used in drug therapies to help patients experiencing stress related health conditions.

Anthropogenic nitrogen (N) emissions have caused an increase in global N deposition, and the northeastern United States is a N deposition hotspot. Nitrogen deposition could impact soil microbial abundance because most soil biota evolved under low N conditions. Soil microbes are key to many ecosystem processes such as organic matter decomposition, which makes nutrients available for plant growth. Therefore, understanding the factors controlling microbial abundance is critical for being able to predict ecosystem processes. We hypothesized that fungal and bacterial abundance and the fungi:bacteria ratio in soil would decrease along a natural N deposition gradient in the northeastern US, and be further reduced by fertilizer application. To address our hypothesis, we collected soil from eight different sites, six of which had experimental plots where N fertilizer had been added. At each site, we collected soil from four ambient or control plots and, if available, four fertilized plots (48 total plots). We measured microbial abundance using phospholipid fatty acid analysis (PLFA). We compared microbial abundance in fertilized to control plots using t-tests, and we analyzed changes in microbial abundance along the natural N gradient using regression analysis. We found that ambient N reduced bacterial abundance (p = 0.03, R² = 0.08), but it did not affect fungal abundance (p = 0.17, R² = 0.02). Fertilizer had no overall effect on fungal (p = 0.72, t = 0.36) or bacterial abundance (p = 0.91, t = -0.12). However, fertilizer did reduce bacterial (p = 0.02, F = 5.6) and fungal (p = 0.02, F = 5.8) abundance at high levels of ambient N deposition. In conclusion, our study showed that soil microbial responses to fertilizer in the northeastern US depend on the background levels of atmospheric N deposition. 

Post 9/11 Veterans are more equipped to be successful than any other veteran generation. After three years of honorable enlistment, service members can use the G.I. bill to receive 36 months of tuition and living expenses for education at state and private institutions. Despite increased access to education, there is a decrease in veteran entrepreneurs compared to post WWII veterans. The present demographics in the military consist of individuals from a wide range of cultures and backgrounds with more female and non-white ethnicities represented. Additionally, the current military service is largely non-combatant and voluntary, which contrasts to the conflicts in the last century such as a draft in the Vietnam Era and WWII. The diversity and skill sets of the current veteran population align more with the growing diverse general population. Yet, Bunker Labs has found primarily a specific demographic of the veteran population, white male officers, pursue entrepreneurship disproportionately. Bunker Labs and other similarly focused organizations look to continue positive leadership experiences that the military establishes, that are hard to find after service. This research looks to compare the barriers and assets veterans specific to Bunker Labs and the local veteran populace face as entrepreneurs, and how the not for profits such as Bunker Labs and institutions such as the University of Washington, business, and local governments can work to create a successful startup ecosystem. This paper reflects the differences between different types of backgrounds, rankings, and specializations that veterans bring into business to understand the kind of needs that our nation's heroes require to make their dreams come true.

This research investigated how User-Centered Design methodology, a multi-stage problem-solving design process, can be applied to improve the novice audience's experience in watching a modern dance concert. Modern dance, in which each generation of choreographers rejects the aesthetic values of the generation that preceded them, can be difficult to access for novice audience members. User-Centered Design was utilized to develop solutions by involving the human perspective in all steps of this problem-solving process. My hypothesis was that designing the experience holistically surrounding the concert could be an alternative to years of dance training to provide a framework for novice audience members to become more engaged in watching modern dance. The research started with field observation, which incorporated contextual inquiries with multiple focus groups. Interviews were conducted with both experienced and inexperienced audience members, and surveys were sent out to a broader sample of audience members. I will present preliminary design solutions that address one of my key findings: the need for more personal communication among audience members.

Through my own experience of attending therapy sessions that evolve mostly through verbal communication, I often find myself caught up in words, not able to fully verbalize how I feel. Being a dancer, I experience how movement plays a role in extending my emotions and expression in ways that cannot be described by words. I imagine how using the embodied knowledge I have learned as a dancer could bridge the expression of feeling and thinking towards my intended career as a psychotherapist. What would it look like for me to acknowledge movement to be a huge part of communication in therapy, to provide my patients with a larger vocabulary to really express what they feel? By conducting oral interviews in conjunction with movement prompt explorations, I have attempted to distinguish and contrast what my participants “think” from what my participants “feel.” The interviews, which were conducted with individuals from the Seattle community ranging in age from 18 to 70, centered on the concept of confidence. I asked each participant to define “confidence,” to move in a way that was “not confident” and “with confidence,” and to reflect on how they felt about the concept of confidence after moving. I will share preliminary findings from this study, contrasting the kind of knowledge people access when they respond verbally (more closely aligned with thinking) with the knowledge discovered through movement (more closely aligned with feelings).

Contact improvisation (CI) is a duet dance form based on the “dialogue of weight, balance, reflex, and impulse between two moving bodies that are in physical contact.” The inter-dependent disposition of the partnership in this non-choreographed dance duet constitutes CI as significantly reliant on the physical communication with another person. My own experience of vigorously practicing contact improvisation last year led me to begin journaling about my experiences with different partners and scores. I gradually developed a curiosity about whether (and, if so, why) observation and analysis of one’s own patterns of improvisational dance decision-making affect the dancer’s awareness of behavior patterns in other aspects of one’s life. I grew eager to answer the following questions. How does the process of observing one’s own patterns of behavior affect the improviser? How do the brain-body transmitters operate, archive and evaluate or filter our life history? And how does our history (including our cultural make-up, personality type, family history and gender) influence the ways we improvise? To answer these research questions, I assigned prompts to an enrolled group of four volunteers (three males and one female) who agreed to dedicate 2-3 months of their time to reflect regularly on their CI experiences and meet with me for a follow-up interview to discuss their findings. My primary goal of those designated “pathways” was to stimulate my subjects to draw conclusions about how their improvisations impact their identity and why correlations between their movement tendencies and personal lives might be developing.

8-methoxypsoralen is a photoactivated DNA-intercalating agent which, after receiving two high energy UVA photons, covalently binds pyrimidine bases on both strands of DNA, forming an Interstrand Crosslink (ICL). These lesions represent a complete block to replication and transcription, and ICL-inducing agents have been used widely in chemotherapies, yet the mechanism by which these lesions are processed in the cell remains poorly understood. In 1985, Ahmed and Holland reported an Escherichia coli mutant that was hyper-resistant to ICL agents. The mutation was mapped to 57.2 minutes on the chromosome and potentially encoded a 55-kDa protein that was induced during stress as part of the SOS response. Although these genes were never identified, hscA and hscB genes map to this location, have a similar size, and are SOS-inducible. To determine if these genes are responsible for ICL resistance, two strains of E. coli were constructed. In the first strain, the genes of interest were deleted and replaced by genetic recombination with chloramphenicol resistance. In the second construct, a wild-type strain was stably transformed with an arabinose-inducible plasmid containing hscA and hscB, which allows them to be overexpressed when the sugar arabinose is added to media. Here I report the resistance of both of these constructs and discuss the likelihood that these are involved in the cellular response to ICLs. In a second approach to identify ICL-resistance genes, a screen was established in which wild type cultures were grown and exposed to UVA light and 8-methoxypsoralen. Surviving colonies were then recovered and subsequently re-exposed to the ICL-inducing agents over several iterations. The accumulated resistance of this strain will be documented, with genome sequencing of any hyper-resistant mutants being performed to identify alterations contributing to ICL-resistance.

Understanding the population structure and biogeography of avian fauna is an important tool for gaining insight into the historical and evolutionary processes leading to the diversification of North American birds. Research into the extensive adaptive radiation by the New World Setophaga warblers of the Parulidae family has been especially useful in illustrating these processes. Through phylogenetic analyses, we investigated the population structure of black-throated gray warblers (Setophaga nigrescens) in the Western United States. Previous analysis describes two distinct groups; a northwestern clade, known as S. n. nigrescens, and a southwestern clade, known as S. n. halseii. To elaborate on this study, we analyzed a larger number of Setophaga nigrescens samples that encompass a wider distribution across the Western US. Using mitochondrial sequences of the ND2 gene, we constructed several phylogenies using 48 S. nigrescens samples and 1 S. graciae sample as the outgroup. Our results support subpopulation structure as indicated by two haplotypes. One haplotype is regularly found in populations west of the Cascades and Sierra Nevada, while the second haplotype is common in the Southwestern US. Admixture appears to be occurring over a wide geographic range extending throughout Northern Arizona, Utah and Nevada, and possibly spanning farther north based on both haplotypes occurring in Washington State East of the Cascades. With a sequence divergence of about 0.8%, a Pleistocene origin seems likely; numerous glaciation cycles during this period may have facilitated this genetic divergence. However, additional samples will be needed to better illustrate the extent of their structure. This will have important implications for the diverse relationships found within the Setophaga genus of the Parulidae family and may benefit future studies involving the evolutionary processes that have led to the diversification of this group and North American birds in general.

High Mass X-ray Binaries (HMXBs) are some of the most physically extreme sources in the universe. They comprise of a compact object such as a black hole or a neutron star, and a high mass companion star. The compact object accretes matter from the companion star and forms an accretion disk of material that has temperatures in excess of ten million degrees Kelvin. This accretion disk then radiates out in the X-ray energy band and allows us to ascertain physical properties for the source. However, the very nature of an HMXB constrains the age of the source to a very high degree--this is because the source needs to be old enough for the compact object to form yet it needs to be young enough for the high mass companion star to still have fusion fuel in its core. In this project, we have created star formation histories at the locations of unknown X-ray emitting objects using optical observations from Hubble Space Telescope. These star formation histories determine if there are stars that have an age consistent with HMXBs present. The age of these unknown sources may be associated with these stars, which means they could be HMXBs. We then looked for star formation histories that have constrained ages consistent with an HMXB to try and give more evidence for an unknown object being an HMXB.

Across animals, embryos can hatch in response to environmental cues. Early hatching can improve embryo survival when eggs are in danger, but may come at a cost to the larval life-stage. Thus, understanding the adaptive value of hatching plasticity requires evaluating the costs and benefits that characterize selective trade-offs. Several species of glassfrogs (Centrolenidae) can hatch as early as 7 days in response to predators, dehydration, and parental abandonment, or delay hatching to 20 days under good conditions. We measured two fitness correlates, for survival and growth, to test the adaptive value of delayed hatching in five species: Cochranella granulosa, Hyalinobatrachium fleischmanni, Hyalinobatrachium colymbiphyllum, Teratohyla pulverata, and Teratohyla spinosa. Hatchlings fall from arboreal eggs into streams and must dive to the bottom to escape predatory fish. We measured diving performance for early and late hatchlings to infer predation risk. As tadpoles cannot benefit from external food resources until they reach feeding competence, we quantified the onset of feeding and compared gut-coil development in siblings of different hatching ages. Older hatchlings dove faster and began feeding sooner after hatching than did younger individuals, suggesting that delayed hatching is advantageous for escaping predators and reducing lag-time in exotrophic-based growth of larva. This study provides insight on the selective trade-offs that favor hatching plasticity in glassfrogs.

Pseudomonas fluorescens strain L5.1-96 has been known to help combat the wheat take-all fungal pathogen, Gaeumannomyces graminis var. tritici (Ggt). Strain L5.1-96 is maintained in the soil longer than others, so it is known as a supercolonizer, which contributes to the phenomenon referred to as Take-All Decline (TAD). The strain L5.1-96 is a non-pathogenic bacterium which grows in the rhizosphere of plants and produces an antifungal agent known as 2.4-diacetylphloroglucinol (DAPG) causing TAD. The DNA fragment we amplified, sequenced, and analyzed was a perfect match to P. brassicacearum strain BS3663. Through bioinformatics, we also found our fragment matched the genetic code for pyridoxal 5'-phosphate (PLP)-dependent aminotransferase, a co-enzyme which catalyzes the transamination of amino acids to alpha-keto acids. We did not identify new proteins that are responsible for the advantages that this bacterium holds against wheat take-all; although, we did find the best phylogenetic fit for this strain. These findings contribute information to the broader study at Washington State University to investigate whether strain L5.1-96 can be used as a biocontrol agent against wheat take-all.​

Wheat Take-All Disease (TAD) is caused by the effect of the soil-based fungus Gaeumannomyces graminis var. tritici on wheat crops. We as Pierce College Biology students in conjunction with other local institutions sequenced part of a strain of Pseudomonas fluorescens, L5.1-96 (P.f. L5.1-96), because of its known trait to supercolonize soil. Sequencing was initially achieved at Pierce College by linear sequencing reaction before being completed by Sanger Sequencing at Washington State University. Resulting data was then interpreted using FinchTV, and the NIH BLAST and tBLAST programs. P.f. L5.1-96 produces 2,4-diacetylphloroglucinol (DAPG) which is a key component in Take-All Decline, the natural suppression of the fungus after several generations, in soils. Using Escherichia coli bacteria to clone 1.7kb long plasmids of the P.f. L5.1-96 strain, the plasmids were amplified and purified in order to discover genes relevant to the empirical objective to better understand this bacteria. Our DNA insert, the portion of data analyzed from FinchTV by cross reference with BLAST, aligned with several important enzymes related to antibiotic resistance and toxin metabolism, both of which could be key to supercolonization of soil. In addition, a phylogenetic relationship has been established using BLAST between P. brassicacearum, P. chlororaphis, and our strain of Pseudomonas fluorescens L5.1-96. The findings of the research could provide greater insight into what constitutes an effective biological control agent against TAD in Washington, and possibly other affected areas of the world.

Pseudomonas fluorescens is a bacterium recognized for producing an antifungal against the debilitating wheat take-all disease. In this study I am investigating the Pseudomonas fluorescens L5.1-96 strain to identify the genes making it a supercolonizer of take-all disease resistant soil and how it fits phylogenetically with other bacteria. This project will contribute to the understanding of how biological agents may be used to combat wheat take-all disease. To investigate this, a plasmid of DNA from strain L5.1-96 was inserted into Escherichia coli to make a bacterial library. I separated the plasmid from the E. coli and amplified it by linear sequencing then sent the DNA to Bellevue College for Sanger sequencing. I used bioinformatics to analyze my unique insert which I found did not match unknown genes, rather it coded for proteins regarding nitrogen fixation. The sequences matched those of Pseudomonas brassicacearum. This provides evidence to renaming the bacterial strain. A match to an anaerobic enzyme in nitrogen fixation might provide insight to its supercolonizer abilities. As we are sequencing a minor portion of the strain L5.1-96 genome, there is need for further gene sequencing in order to complete its genome.

In this study, we focused on identifying specific genes that make Pseudomonas fluorescens L5.1-96 a potential biocontrol agent to combat wheat take-all disease. This strain is a supercolonizer meaning it suppresses fungal pathogens in the soil and colonizes the rhizosphere of plants. This strain has not yet been fully sequenced; therefore, analyzing genomic data will contribute to its classification. Our first step was increasing the amount of L5.1-96 DNA through culturing E. coli that contained an insert of L5.1-96 DNA. Next we extracted L5.1-96 DNA using the Qiagen miniprep kit, amplified the DNA insert using linear sequencing, and sent our cleaned DNA samples to Bellevue College for Sanger sequencing. We ran bioinformatics software (NCBI BLAST) to compare our DNA insert with previously sequenced genomic data. We found our DNA sample resulted in a 98% match with genes from Pseudomonas brassicacearum strain BS3663; therefore this indicates a phylogenetic relationship between the two Pseudomonas species. While we did not discover any new genes or novel proteins, our sample coded for tRNA preQ1(34)S-adenosylmethionine ribosyltransferase-isomerase QueA which is a nutrient protein found in both eukaryotes and bacteria. We have contributed to the genomic analysis of strain L5.1-96 and with this information it is possible one day all of the data together will lead researchers to fully evaluate strain L5.1-96 and its ability to suppress wheat take-all disease.

One of the most inflammatory topics in animal welfare and wildlife conservation is the issue of feral domestic cats. Wild bird advocates favor lethal eradication programs to protect wildlife from cats, and feral cat advocates support reducing their populations non-lethally through trap-neuter-return programs. Little research has been done regarding the motivations and beliefs of the humans behind this conflict, a gap that this study has sought to remedy. Feral cat and wild bird advocates are as worthy of investigation for potential commonalities as they are for their history of strife. Both groups express a connection to animals which they cannot share much, if any, contact. Most human-animal bond research focuses on traditional pets, and questionnaires routinely use physical closeness as a metric of one's bond to an animal. An online survey was conducted of 3859 adult Americans who identify as advocates for either feral cats or wild birds. Questions included demographics, motivations, political engagement, how the animals make them feel, and what they enjoy or admire about feral cats or wild birds. The groups had statistically significant differences in more areas than they had commonalities. Areas of difference include number of pets, level of emotional attachment, and why they like their focal species. The groups did not have significant differences in subjects such as household size, enjoying feral cat/wild bird activities because they are challenging, and reporting that being a "feral cat person" or "wild bird person" is an important part of their identity. This is the largest study that has been conducted on a human-animal bond topic, as well as the most comprehensive study examining the people behind an important area of policy debate. These results could be useful in deescalating future policy battles and trying to pave a path forward to compromises that both stakeholder groups could accept.

According to a January 2017 Point-in-Time count, there were over 11,000 individuals experiencing homelessness in the Seattle/King County region, with approximately 30% of those individuals under the age of 25. The University District of Seattle has been designated as an area needing special attention and increased funding to support homeless youth and young adults. Our proposal is to create an urban community café (The Doorway Café) to bridge the strengths of the University District with the social, legal, and health care needs of local homeless and food insecure youth in one centralized location. We predict that the creation of a navigation center/café will allow for an improved system of integrated services, ultimately leading to housing security and improved health outcomes. We conducted a qualitative study consisting of twenty in-depth, semi-structured interviews with homeless youth in the University District. Interviews were recorded, transcribed, and thematically analyzed to highlight data pertaining to personal lived experiences of homelessness, basic needs, and services to integrate into The Doorway Café. Preliminary thematic analysis suggests that having stable housing is a necessary prerequisite for youth and young adults to care for their other basic needs, such as health care. Interviewees expressed that the most successful café would feel safe and the resources offered would be low-barrier. The results of our research inform the services The Doorway Café should offer based on the responses of local homeless youth. Future research should explore the role that The Doorway Café has in continuity of services and in increasing housing stability among youth in the University District.

DREADD receptors (Designer Receptor Exclusively Activated by Designer Drugs) are engineered G-protein receptors which are exclusively activated by the inert-molecule CNO (clozapine-N-oxide) and to a lesser degree clozapine. DREADD receptors are often used, to identify the circuitry and cellular signals that specify behavior, perceptions, emotions, motivation, and motor functions in species ranging from flies to nonhuman primates. Heterologous overexpression of non-native genes in biological systems, is often confounded by varying degrees of overexpression and result in non-specific effects. Thus, our purpose is to determine effects on cell signaling pathways following varying levels of DREADD receptor expression. Our hypothesis is that, increased levels of DREADD receptor expression increase non-canonical cellular signaling pathway activation. We used human embryonic kidney cells (HEK cells), as our model system, then expressed various levels of DREADD receptors using Lipofectamine transfection and DNA-plasmids expressing Gs- and Gi-coupled DREADD receptors (Canonically, Gs-increases cAMP and Gi-decreases cAMP). After transfection, we treated transfected cells with 1µM of CNO or VEH (a control) for 5-30min and then lysed the cells with RIPA Buffer, and prepared samples for western blotting to detect activation of proteins of interest in the GPCR non-canonical signaling pathways (example: kinases and transcription factors). We used anti-HA antibodies to ensure dosage of receptor expression, and used a panel of antibodies to detect activated proteins in well-established non-canonical GPCR signaling pathways. Western blot results were measured using Odyssey scanner and the Image studio software suite. We expect to see an increase in non-canonical signaling with increased expression of both Gi- and Gs- coupled, specifically in the MEK/ERK and CREB signaling pathways. In summary, our findings will highlight additional considerations regarding the level of receptor expression when using DREADD receptors in vitro and in vivo experiments, and specifically measure the off-target “non-canonical” signaling pathways induced by DREADD receptor overexpression.

State-Owned Enterprises (SOE) are legal entities either partially or fully owned by the government that undertake commercial activities on behalf of the state. Their legal status, purpose of establishment and missions vary across countries with some becoming tools for countries to better position themselves in the competitive global economy and some to provide public services and ensure distribution of social welfare. In Malaysia, these SOEs are called Government-Linked Companies (GLCs) where the government owns 20% or more of issued or paid-up capital. GLCs not only account for 54% of market capitalization of the Kuala Lumpur Composite Index but also remain as main service providers to the nation in key strategic utilities and services. In 2004, the government of Malaysia introduced the Government-Linked Transformation Program (GLCTP) in response to observing the poor performance of GLCs relative to the broader market on all key financial indicators. It is a 10-year program consisting of 10 Initiatives, most of which aim to elicit better and effective governance through imposition of guidelines and standards supervised and enforced by the Putrajaya Committee on Government-Linked Companies, PCG. With GLCs presence being so abundant and influential, we question the effectiveness of the program which concerns the future of GLCs and non-GLCs in Malaysia. Thus, this paper aims to measure the impact of GLCTP on the financial performance of GLCs (and non-GLCs) by panel data estimation technique. In particular, this project examines the difference in the financial performances of GLCs relative to non-GLCs pre- and post the program after controlling for other confounding variables. Improvements in performances of GLCs compared to that of non-GLCs is expected. If results show statistically significant, the next interesting discussion would then be corporatization over privatization or divestment.

In developed economies, medium sized firms make up roughly half of all economic growth and employment. Among poor economies however, these firms are virtually absent, as is financing for the creation of them, despite the rise of innovative microfinance institutions. This phenomenon is termed the “missing middle”. My paper sought to understand how firms of this size were established in the developed world, by juxtaposing the financial ecosystem of Industrial Revolution era Scotland to those of developing countries today. I choose Scotland because of its’ rapid development during the 18th and 19th centuries, despite relative poverty and lack of infrastructure compared to contemporary western European countries. I studied primary sources such as accounting documents, and letters between firm owners and managers to develop a picture of the business strategies and financial products used by these firms. These historical strategies were compared to those employed by modern microfinance institutions such as Grameen, based on their published financial statements. Similarities abounded: schemes where individuals pool their savings to create loanable capital, easy loan terms, co-signing, and other practices. The differences however, are stark. Scottish banks lent small and medium sized debts, and rarely had more than a few hundred, local accounts. Modern microfinance institutions service millions of tiny borrowers. Additionally, Scottish banks were universally general-partnerships, a form mostly extinct today. I conclude by suggesting that these differences were key in allowing Scottish banks to finance the Industrial Revolution in Scotland, and that they could assist in financing the “missing middle” in the developing world today.

Digital media and mobile applications used for leisure have become increasingly interwoven into people’s daily lives. Although playful mobile applications and their effects on society have been studied from a psychological, business, and computer science perspective, they have not been heavily engaged in the field of geography. Using Pokémon GO as a case study, this work aims to explore the ties between the corporate history and digital data of Niantic (the company that made Pokémon GO) and the effect it imposes on the “real world”. It aims to conduct a spatial analysis of pokéstops and pokégyms in King County, Washington. In order to do this, a discourse analysis of online documents from Niantic, newspapers, social media, and fan websites recounting the company's history with previous applications and press interviews was conducted. In addition, a hotspot spatial analysis of Pokémon GO (pokéstops and pokégyms) overlaid on American Community Survey data was created. The purpose of this analysis is to see potential spatial inequalities that the application may have created. The findings show Niantic’s lack of ethical consideration by how it deals with users data and privacy and as a result shows how the users have responded to issues in the past. The results also illustrate the skewing of data toward urban tech centers and the relative sparsity in rural areas, rendering use of the app pointless for certain users. Pokémon GO is the first location-based augmented reality mobile application to garner worldwide attention, and many application developers will likely use it as a point of reference when creating their own applications. It is imperative that developers and researchers learn from this application’s successes as well as its failures.

The focus of my research is to clarify the population structure of sockeye salmon, and in particular kokanee salmon, in the Lake Washington and Lake Sammamish watershed. There is a poorly understood population of kokanee, a form of sockeye that does not migrate to the ocean, that often migrates from Lake Washington into the Sammamish river, and does not appear to be a part of the main sockeye population in our lakes. This population is understudied but is particularly intriguing because a native population of kokanee was once abundant in the lake. It is possible that this population is a remnant of these native kokanee and represents the only remaining native salmon genes in the lake. It is also possible that this population is a newly evolved freshwater form of introduced sockeye. Either result would be of great interest in terms of conservation and evolutionary biology. Native genes in Lake Washington would represent an important focus for conservation efforts (as are currently underway in Lake Sammamish), and finding a population that has evolved in Lake Washington within the last century would be an exciting demonstration of the adaptability of salmon. Physical examination of specimen scales, gill rakers and otoliths can reveal evidence of the populations life history and feeding habits. Furthermore, genetic analysis and comparison to known sockeye populations can also provide evidence to suggest the identity of this particular population. Using these morphological and genetic observations I hope to illuminate the mysterious origins of this population and contribute to their conservation and restoration. People living along the rivers in the Lake Washington drainage have benefitted from the kokanee salmon for hundreds of years. The little red fish continues to be a cultural icon and important natural resource in Washington state.

Sea otters (Enhydra lutris), members of the mustelid family, are distributed in the near-shore marine environment along the west coast of North America from southern California to Alaska. Sea otters are unique among marine mammals, in that they bring all captured prey to the surface to handle and consume. This behavior allows scientists to directly observe their foraging and estimate energy intake rates based on time spent at the surface processing and consuming prey (handling time), prey type and size, and dive time. The foraging behavior of sea otters is observed using standardized methods throughout the sea otter’s North American range. One assumption made when calculating sea otter energy intake rates is that the same prey type of a given size is equivalent across regions. However, an anomaly in the handling time of kelp crabs (Pugettia spp.) has been discovered, where Washington sea otters (Enydra lutris kenyoni) handle kelp crabs 1.5-2 times faster than sea otters in California (Enhydra lutris nereies). One hypothesis to explain this difference is that Washington kelp crabs have a lower edible biomass than kelp crabs in California, allowing for faster handling times by sea otters. To explore this hypothesis, I collected kelp crabs at two sites on the Washington coast. I measured and compared kelp crab maximum width and edible biomass to test whether kelp crabs in Washington are an equivalent sea otter prey item to kelp crabs in California. Kelp crabs comprise 20% of the overall diet of Washington sea otters, so accurately measuring the edible biomass of kelp crabs enhances the precision of estimating sea otter energy intake rates. Estimating the energy intake rate of sea otters provides additional information on their population health.

In the population of bottlenose dolphins (Tursiops aduncus) in Shark Bay, Australia, groups of two or three adult males form long-term alliances that sequester, harass, and intimidate adult females, presumably to increase their chances of mating success. Costs that males inflict on females include physical injury, changes in home range and habitat use, reduced foraging, and changes in calf care. Although altered female behavior is evident during association with males, the direct impact males have on female behavior is not entirely clear. That is, male behavior and female responses to such behavior during consortships have not been explicitly documented. A long-term study has collected detailed behavioral data on the Shark Bay population since 1988. Using this dataset, this project will quantify the rate of male aggression directed at females and how female activity budgets and foraging tactics change in response. Preliminary work indicated that rates of received aggression were higher for cycling females than non-cycling females, and higher when females were in the presence of more than one male, potentially confirming that males use aggression to coerce reproductively viable females. Females also spent less time foraging when in the presence of more than one male, hinting at potential costs to the female owing to loss of food. Because females have highly specialized foraging tactics, changes in foraging behavior and home range during prolonged or repeated consortships could impact female condition.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi’s Sarcoma (KS), a highly vascularized tumor made up of cells of endothelial origin. KSHV establishes a predominantly latent infection in endothelial cells in culture and in the KS tumor. A previous study has shown that KSHV induction of the Warburg effect is required for the survival of latently infected endothelial cells. The Warburg effect, a common metabolic alteration in cancer cells, refers to an increase in glycolysis and a decrease in oxidative phosphorylation. The mechanism of Warburg induction by KSHV is currently unknown. I proposed to evaluate the role of endothelial cell specific hypoxia-induced factors (HIFs) on KSHV Warburg induction since HIFs have been implicated in Warburg induction in other types of cancer. I hypothesized that HIF2α mediates KSHV Warburg induction through expression of glycolytic genes. To test this, I constructed HIF2α knock-out cells using CRISPR/Cas9 gene editing. I then used RT-qPCR to measure glycolytic gene expression during KSHV infection of wild-type and HIF2α knock-out cells. I found that the transcript levels of certain glycolytic genes remained constant in KSHV-infected HIF2α knock-out cells as compared to KSHV-infected wild-type cells, showing that HIF2α is not responsible for glycolytic gene expression during KSHV infection. I am following up on the role of the KSHV latent gene KapA on the induction of glycolytic gene expression. KapA was previously found to interact with components of the Ras pathway. As the Ras pathway activates glycolytic genes through HIF1α, I hypothesize that exogenous expression of KapA will lead to increased glycolytic gene expression through increased expression of HIF1α. I will construct an endothelial cell line that overexpresses KapA using CRISPR/Cas9 system and then use RT-qPCR to evaluate glycolytic gene expression. These results will aid in the future efforts to develop antiviral drugs by targeting cellular metabolism.

Epigenetic modifications regulate chromatin structure and function, playing important roles in altering DNA transcription levels and subsequently cell fate decisions. Various next-generation sequencing (NGS) methods have been developed to detect these epigenetic changes in the genome, such as chromatin immunoprecipitation followed by sequencing (ChIP-seq). Even though ChIP-seq is extensively used to analyze DNA and histone modification levels, this method is limited to one histone marker at a time and requires significant amount of input cells, which masks the profiles of cell-to-cell variation and the complex interaction between the epigenome and gene expression. To overcome these limitations in current next-generation sequencing methods, we have been developing a multiplexed assay that could detect multiple epigenetic modifications in single cells. So far, I have developed a NGS data analysis pipeline to identify potential gene candidates that are highly differentially modified by histone markers. In the future, we hope to use these gene candidates as templates to design DNA-fluorescent in situ hybridization (DNA-FISH) probes and perform Expansion Microscopy and DNA-FISH with these probes to link histone modifications to specific gene loci at high resolution. After the assay is fully developed and validated, we plan to utilize the assay to take the epigenetic profiles of hematopoietic stem cells and study cell fate decisions in hematopoiesis.

Duchenne muscular dystrophy (DMD) is an X-linked recessive genetic disorder, marked by progressive muscle degeneration due to the absence or impairment of the dystrophin protein. Our laboratory has been developing methods for gene therapy of DMD. The dystrophin gene is the largest known gene, which complicates gene therapy. We have shown that gene delivery vectors based on adeno-associated virus (AAV) can be used to deliver new genes body wide. However, AAV has a ~5 kb carrying capacity, so we have been developing miniaturized dystrophins. These smaller, highly functional dystrophins, which we named micro-dystrophin (µdys) were tested in a transgenic mdx^4cv  mouse model for DMD. Furthermore, we sought to develop a non-invasive method to evaluate treatment efficiency of µdys. In this project, the gait of mdx^4cv, wild type (WT) and transgenic mice were observed to deduce potential benefits of the µdys transgene. We hypothesized that µdys treatment will enable the gait of the transgenic mice to resemble that of WT animals as opposed to mdx^4cv. To test this, gait was assessed at three time points: 1.5, 3 and 6 months of age using the video-based Noldus CatWalk XT. Our results show that the length of a single stride of the transgenic mice hind paws increased over time compared to mdx^4cv. The normal walking pattern of mice consists of placing diagonal paws on the surface, one front and one hind from opposite sides. In the case of mdx^4cv, more paws were placed down for majority of the walk, as a compensatory mechanism for muscle weakness. The transgenic mice were found to walk with a diagonal pattern more frequently, like WT mice. Similarities in the gait of transgenic and WT mice help us conclude the µdys treatment was successfully able to mitigate the effects of DMD as seen by the gait analysis.

Kidneys are responsible for regulating blood glucose levels in the body through the reabsorption of sugars in the proximal tubule of the nephron. Issues with glucose absorption can lead to diabetic nephropathies where too much glucose is excreted. To study kidney glucose absorption, the lab made kidney organoids, which are miniature stem cell-derived in vitro organs that mimic the structure and function of kidneys. We used induced pluripotent stem cells (iPSCs), a type of stem cell that can be generated directly from one’s own adult stem cells. In a previous experiment, the lab found glucose absorption was present through the Sodium Glucose Co-Transporter 2 (SGLT2). The lab wanted to see if this was the only channel responsible for glucose absorption. Using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system, we knocked out SGLT1 and SGLT2 separately and also knocked out Glucose Transporters (GLUT1 and GLUT2) separately in the WTC11 kidney stem cell line.  We selected a guide RNA corresponding with each glucose transporter in the cell membrane of kidney organoids.  Then RNA-guided Cas9 created the mutation by breaking the sequence for each glucose transporter in a specific site of the genome.  We verified our mutations were done correctly by sending our results to a DNA sequencing company.  We expect to find mutant lines will have less glucose absorption than our control and hope to learn which transporters are more active.  We are further using this method to create double and quadruple knockout lines with multiple glucose transporters knocked out at once.  We hope to learn which transporters are most responsible for glucose absorption, and in the future, can assess when certain transporters are used over others, which will open the doors for disease models for diabetes not only in kidneys but also in other organs.

With advances in sequencing technology it has become feasible to sequence a patient’s genome in a clinical setting, but our ability to interpret the effect of genetic variants on health and disease remains a large challenge. Genome-wide association studies (GWAS) have helped to interpret DNA variants by correlating thousands of variants in the genome with disease. However, many of these variants fall in noncoding DNA (making it hard to predict their effects) and are often in tight linkage with neighboring single nucleotide polymorphisms (SNPs) (meaning these neighboring SNPs may also be responsible for driving the correlation with disease). Consequently, most disease-associated variants still need functional validation. There is mounting evidence that a large number of these variants may be effecting gene regulation (when, where, and to what degree a gene is expressed), and several groups have tried testing whether these SNPs effect regulatory activity with traditional reporter assays. In this study, we aimed to validate GWAS candidates linked to osteoarthritis, a joint disorder with several SNPs previously associated. We compiled a list of these variants as well as all SNPs in linkage disequilibrium, for a total of 1,605 variants. To screen this list for functional candidates, we leveraged “self-transcribing active regulatory region sequencing” (STARR-seq), a reporter assay that can test thousands of sequences for regulatory activity in a single experiment. Our screen identified two variants with statistically significant differences between the major and minor alleles. To validate these findings in the genome, we introduced the minor allele of one variant into cell lines via CRISPR/Cas9. We found a similar difference in transcription between the major and minor allele in the genome as our initial episomal screen. We are currently working with our collaborators to further validate these findings in patient samples.

Treatment options for kidney disease are limited to dialysis and transplantation, which are of limited efficacy and availability. Human pluripotent stem cells (hPSCs) can be used to generate immunocompatible kidney organoids, which contain the major proximal structures of the nephron, including podocytes, proximal tubules, distal tubules, and endothelial cells. They can be made on-demand to study kidney disease and regeneration. Unfortunately, these organoids lack a collecting duct system, a crucial component of the kidney. To address this need, we have developed a protocol to differentiate hPSCs into ureteric bud (UB) cells, which are the precursors of collecting duct cells. First, we identified markers for the collecting duct lineage in developing kidneys. Immunofluorescence analysis of human kidney tissue revealed co-expression of cytokeratin 8 and Dolichos biflorus agglutinin (DBA) in the collecting ducts. These markers were not expressed in the proximal tubules. Next, we investigated the ability of hPSCs to express these markers. Undifferentiated hPSCs were treated with a concentration gradient of small molecules known to induce kidney lineage differentiation, including CHIR99021 and glial cell line-derived neurotropic factor (GDNF); their effects were jointly and individually examined. Immunofluorescence was used to characterize the resulting cells, which were initially stained with DBA and Lotus tetragonolobus lectin (LTL), a proximal tubule marker. We found that CHIR99021 alone was sufficient to produce DBA positive and LTL negative cells in vitro. Notably, the DBA levels in these cells were lower than observed in kidney tissue, indicating that the structures we obtained were not yet fully mature. These studies provide the first evidence that collecting duct cells can be generated from hPSCs. Optimization of this differentiation protocol will yield kidney organoid structures that include the collecting duct system, which will make them ideal for kidney disease modeling and regenerative medicine approaches to reduce the need for kidney transplants.

Approximately 14% of the United States population is currently living with chronic kidney disease (CKD), demonstrating the importance of developing effective treatments. Presently, the mechanisms and driving forces of the many diseases that comprise the spectrum of CKD are not well understood. Current methods for acquiring kidney cells for research purposes require an invasive biopsy taken directly from the kidney. We theorized that patient kidney cells can be acquired from a significantly less invasive urine sample, be expanded, and subsequently differentiated into new kidney tissues. We developed a method for accomplishing this, which enabled the collection of cells from the urine samples of over 40 different patients located across the globe with various subtypes of CKD. Reverse transcription polymerase chain reactions (RT-PCRs) probing for the expression of XIST, a RNA gene exclusively expressed in females, were conducted on urinary cells from patients who have had kidney transplants with donors of the opposite gender. Using this assay, we show that these urinary cells originated in the donor kidney. By introducing a set of transcription factors expressed in embryonic stem cells, urinary cells were further reprogrammed to induced pluripotent stem cells (iPSCs), an undifferentiated, stem cell-like state. Subsequently, the iPSCs were differentiated into patient-specific kidney organoids, marking the first time that new kidney-like structures have been generated from a urine sample. Hollow tubules, which better mimic the architecture of the kidney, were created by incorporating these urinary cells or iPSC-derived kidney organoid cells into three-dimensional microfluidic devices wherein normal cell viability and morphology was maintained up to twenty days. Immunohistological stainings indicate similar protein expression between the cell types, which will be further investigated in the upcoming months. These studies improve our ability to regenerate kidney tissue and disease processes from patients’ own bodies, starting with a simple urine sample.

Primary cilia are antenna-like structures on the surface of diverse cell types. Cilia are important for signal transduction and processes such as cell division and development, but their precise role in the cell remains poorly understood. Defects in cilia result in a wide spectrum of genetic disorders called ciliopathies, which commonly involve polycystic kidney disease (PKD), the formation of fluid-filled sacs in the kidney which eventually result in kidney failure. To understand the role of cilia in these diseases, we generated human pluripotent stem cells (hPSCs) with defects in cilia formation for the first time. We used the CRISPR-Cas9 genome editing system to introduce mutations in two different genes that are required for cilia formation, kinesin family member 3A (KIF3A) and kinesin family member 3B (KIF3B). We isolated four independent cells lines with indel mutations in exon 3 of the KIF3A gene and two in exon 2 of KIF3B. The introduced mutations led to frameshifts and protein truncations. Immunoblot analysis confirmed that no full-length protein was produced in these mutant cells. The cells were stained with acetylated alpha-tubulin, a marker of cilia. No cilia were detected in the mutant hPSCs, while an average of 48% cilia were detected in controls of identical genetic background. Surprisingly, the absence of cilia did not alter hPSC pluripotency, self-renewal, amniotic cavity formation, or growth. Further, we differentiated these cell lines into kidney organoids. The cilia deficient kidney organoids formed cysts reminiscent of PKD, while the isogenic controls did not. In conclusion, we have generated human cells and organoids lacking an entire organelle, the primary cilium, and used these to conclusively link cilia to PKD. These cilia deficient hPSC lines can be used to study cilia function, to model various ciliopathies, and to screen for drugs that can ameliorate the disease phenotypes associated with them.

Abnormalities in TGF-ß signaling are thought to cause aortic aneurysms and dissection in people with inherited syndromic illnesses such as Marfan's and Loeys-Dietz Syndrome. However, the mechanisms linking changes in TGF-ß signaling to aortic disease evolution are poorly understood. We developed a mouse model in which the type II TGF-ß receptor was deleted to characterize and study the effects of this perturbation in TGF-ß signaling. My research focused specifically on characterizing any histologic changes in the aorta in 7-8 week old mice, 1 week after deleting the TGF-ß receptor. To quantify changes in aortic architecture, we employed methods such as H&E staining and fluorescence microscopy. Our results showed that the ascending aortas of the mice with the TGF-ß receptor knockout had significantly larger medial thickness and medial area, with p-values of 0.0001 and less than 0.0001, respectively. However, we did not find a significant difference in elastic breaks between the two experimental groups, although previous research has shown increased elastic breaks in aortas of mice with the TGF-ß receptor deletion when measured at a later point (14 weeks post-deletion). Together, these results suggest that there are subtle but significant aortic changes as early as one week following receptor deletion. This suggests that losing TGF-ß signaling causes early and immediate changes in the aortic smooth muscle cells and matrix proteins that are quantifiable by histology. More research is needed to understand the precise mechanisms behind why these changes occur and how they might be related to the development of aneurysms.

Understanding the sexual regulation of sorority women, and their role in it, is important in fully understanding the function and impact of sororities as a whole in modern collegiate experiences. Through my study of the Greek system at the University of Washington (UW) I worked to investigate the question: Do sorority women submit to sexual regulation in order to maintain or raise the house’s position in the sorority hierarchy? I surveyed 48 sorority women at the UW using vignette based questions to gauge sorority norms surrounding sexuality and its regulation in the Greek system. Within my research I am working under the assumption that sororities are reinventive institutions; institutions where women voluntarily join for empowerment and willingly submit to the regulation of all aspects of their identity. Through this perspective in the study I was able to gain insight into the underlying social mechanisms that maintain the social norms governing the sexuality of sorority members and how this is related to chapter status on campus, while recognizing the importance of the role individual members play within this process.

Previous studies investigating the perception of sexual misconduct by individuals in a university setting have not examined the effects of socioeconomic status on attitudes towards sexual misconduct. While these effects were considered in a university setting, understanding male perceptions of sexual misconduct more broadly is becoming increasingly relevant as allegations against high status individuals of varying political backgrounds continue to emerge. This paper paves the way for future research as to the effects of socioeconomic status on these perceptions at a more universal level. Using a survey composed of different hypothetical scenarios, this paper examines the relationship between the socioeconomic status of a male perpetrator and the attitudes of male college respondents regarding sexual misconduct toward women. Male undergraduates at the University of Washington were recruited from different residence halls and classrooms on campus to ensure sociodemographic variation in the sample. The data supported an analysis of how perpetrator’s socioeconomic status and respondent’s socioeconomic status may separately or jointly shape perceptions of hypothetical misconduct, and whether a respondent’s beliefs about feminism influence these associations. This study expects to observe a significant impact from both the socioeconomic status of the perpatrator and the socioeconomic status of the respondent both jointly and when considered separately.

Increased racial tensions in America should be considered in evaluating current psychotherapeutic and social structures. Functional Analytic Psychotherapy (FAP) argues that divulging vulnerable information about oneself is essential for emotional intimacy. When vulnerability is responded to with attempts to build safety, vulnerable behavior is reinforced (strengthened). This reciprocal process of vulnerability and building safety aids in the development of intimate relationships across social and psychotherapeutic settings. The interaction model of FAP has never been examined through an interracial lens. In interracial interactions, people may be less comfortable being vulnerable, which may contribute to increased social anxiety. These communication differences may partially explain lower rates of efficacy in cross-cultural psychotherapy. Our study analyzed the effect of race on vulnerability and anxiety as important elements in the well-established model of intimate relationship development. During same-race and interracial mock therapeutic interactions, undergraduate participants (representing clients) were asked questions intended to elicit vulnerability by research assistants. Heart rate (HR) data were recorded from participants as a physiological measure of anxiety throughout the interaction. Participant vulnerability was assessed through self-report and behavioral coding by blind, independent research assistants. We hypothesize that participants in the interracial interactions will show higher levels of anxiety, as measured by HR data, and lower levels of vulnerability, as measured by self report and behavioral coding, compared to participants in same-race interactions. This project may reveal that developing organic interracial connections is more difficult than developing same-race connections. This would indicate a need to modify current social and psychotherapeutic structures to facilitate the creation of effective and meaningful interracial relationships.

Joubert syndrome (JS) is a neurodevelopmental disorder characterized by developmental delay and a specific hindbrain malformation resulting in the “molar tooth sign” (MTS) as seen on MRI. Individuals with JS have variable intellectual disabilities, polydactyly, retinal dystrophy and cystic kidney disease. JS is classified as a ciliopathy—disorders with overlapping phenotypes affecting 1/1000 live births combined. Currently, 36 genes when mutated cause JS, and all their encoded products localize in and around the primary cilium—a cellular organelle important for signaling and human development. We recently identified the newest JS-associated gene ARMC9 and its function, like the molecular mechanism(s) underlying JS, is unknown. Our preliminary data suggest that ARMC9 is required for cilium stability by promoting post-translational modifications (PTM) of ciliary microtubules. In stably ciliated, fixed (non-living) cells, ARMC9 localizes to the ciliary base, but to understand ARMC9’s role in cilium stability, we must determine ARMC9 localization during ciliogenesis (ciliary growth). We hypothesize that ARMC9 redistributes to the ciliary tip to promote tubulin PTMs during ciliogenesis. To test this hypothesis, I am using GFP and BFP (green and blue fluorescent protein) tags to visualize ARMC9 and primary cilia respectively. I created 5HT₆-BFP, a DNA vector encoding a BFP-tagged serotonin receptor fragment called 5HT₆ which naturally localizes to cilia. Currently, I am optimizing the transfection of 5HT₆-BFP and ARMC9-GFP into control cells for live imaging. As suggested by our data, I expect to see ARMC9 at the ciliary tip during growth, then redistribution to the base once the organelle is built. Determining where ARMC9 localizes during ciliogenesis will give us additional insight into its mechanism of action and role in JS. Ultimately, this work will allow us to identify therapeutic targets to mitigate the progressive features of JS and improve the quality of life of affected individuals.

Impella devices provide temporary mechanical circulatory support (MCS) by means of a catheter consisting of a left ventricular (LV) inlet, a microaxial pump within the catheter, and an outflow port in the proximal aorta. The recommended position of the inlet is 4-4.5cm below the aortic valve annulus. Following initial placement, the device is prone to migration, potentially leading to ineffective support, hemolysis, ventricular arrhythmia, or mitral regurgitation. Positioning is typically monitored by echocardiography. However, the Impella device has a bend between the inflow and outflow ports, and traditional 2D-imaging may not be reliable in assessing the location of the device, as single plane 2D windows may not include both the inflow port and the aortic annulus, leading to foreshortening of the cannula and under-measurement of the distance. We hypothesized that 3D echocardiography provides more accurate characterization of the Impella cannula location. We analyzed 25 echocardiograms of patients with Impella devices placed in LV which had analyzable 2D and 3D images. Measurements of the distance from the aortic annulus to the inflow port were made according to recommendations from established measurement guidelines. Three sets of measurements were made at end systole and at end diastole. Full volume 3D datasets acquired from the parasternal window were acquired an analyzed using Qlab software to overcome possible foreshortening of the Impella cannula. In addition, the 3D dataset was used to measure the angle deviation of the cannula from the long axis of the left ventricular outflow tract. There was no recognizable benefit of 3D techniques in measuring aortic annulus to Impella inflow port distance. A larger sample size may be necessary to detect a significant difference. 3D imaging may have a benefit in observing other relationships, such as the mitral apparatus, and bears ongoing investigation.

Stroke is the leading cause of long-term disability in the USA. Ischemic preconditioning (IPC) is a neuroprotective phenomenon wherein a brief ischemic exposure induces robust neuroprotection against subsequent prolonged ischemia. The Weinstein laboratory has previously demonstrated: (i) a robust type 1 interferon response in cortical microglia following IPC, (ii) type I interferon signaling in microglia is required for IPC-mediated protection and (iii) IPC induces a robust increase in the number of microglia in preconditioned cortex. An initial component of my project was to validate this microglial response by first staining for Iba1 (a microglial marker) alone and then double staining for Iba1 and proliferation marker BrdU. We used immunofluorescent microscopy (IFM) following by quantitative stereology (QS). Our hypothesis was that type I interferon signaling is necessary for IPC-induced microglial proliferation. We carried out IPC on WT and type 1 interferon receptor deficient (IFNAR-/-) mice and quantified cortical microglial number and proliferation as above. Preliminary results were: (i) in naïve WT, 0.643 ± 0.038 (mean ± S.D), Iba1+ cells per position, (ii) in preconditioned WT, 1.113 ± 0.1385, (iii) in naïve IFNAR1-/-, 0.751 ± 0.058 and in preconditioned IFNAR1-/-, 0.903 ± 0.125. Two way ANOVA revealed a significant difference between naïve and IPC-induced cortical microglia numbers [F(1,14)=9.62, p=0.0078], but no significant effect of genotype [F(1,14)=0.258, p=0.619]. IPC induced increases in the number of cortical Iba1+/BrdU+ proliferating microglia in both IFNAR1-/- (0.451 ± 0.107) and WT (0.205 ± 0.069) mice. These results suggest a complex picture in which deficiency in type 1 IFN signaling may not influence IPC-induced microglial proliferation but does attenuate the overall number of cortical microglia. This raises the possibility that type 1 IFN signaling may be required for optimal microglial survival following IPC. More studies will be required to confirm the above findings and explore possible mechanisms.

RNA Polymerase (RNAP) is found in all cellular organisms and synthesizes RNA from DNA through a process known as transcription. Using a single-molecule tool, Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT), developed by Gundlach’s Nanopore Lab at the UW, we can track the motion of individual RNAP molecules along DNA at unprecedented spatial and temporal resolution. In this technique, a single nanopore, a biological transmembrane protein, is isolated in a phospholipid bilayer separating two wells both filled with salt solutions. An applied electric field drives ions through the pore, and the ion current is measured. Negatively charged DNA is also driven through the nanopore, partially blocking the ion current. The DNA is sequenced based on the changing ion current as each of the four DNA nucleotides sequentially pass through the pore and block the flow of ions. In SPRNT, the motion of a known sequence of DNA through the nanopore is controlled by a molecular motor (like RNAP), in order to understand how an enzyme moves along DNA. Using this technique, we can detect single base pair steps of RNAP along DNA as brief as 1 ms. In this work, we expand upon initial SPRNT experiments tracking RNAP and analyze the kinetics of RNAP during transcription in biological relevant conditions (1 mM NTPs, 37C) on a long DNA template (up to 6 kbp). We calculate the rate of NTP incorporation and stepping behavior (probabilities of different step types) at many different DNA template sequences using this technique. The results demonstrate how DNA sequences as well as applied force can affect the stepping behavior (probabilities of different step types) and stepping rate of RNAP. A complete understanding of RNAP and its transcriptional regulatory behaviors will enable scientific and medical communities to better understand a variety of genetic diseases associated with transcription.

Oral history projects documenting Japanese incarceration typically prioritize the stories of those that directly experienced the traumas of incarceration. Although trauma can be experienced by one generation, it can manifest and be passed down to subsequent generations through storytelling; trauma can also be experienced through silence, or the refusal to share stories surrounding a traumatic event, affecting individual and cultural identity. Very little scholarship has documented or closely examined the oral histories of those who did not experience Japanese incarceration themselves but have family members who did. The goal of this project is to examine the intergenerational communication of trauma and the cross-generational effects of Japanese incarceration on the Sansei generation (grandchildren of Japanese immigrants). Densho is an organization that documents and makes accessible through their online database the oral histories of Japanese incarceration experiences using digital video recordings and full written transcriptions of interviews conducted by them. I used digital video footage and interview transcriptions to qualitatively analyze for emerging themes or trends among the Sansei interviews surrounding how incarceration was communicated to them and its effects on them. I expect a common theme of emotional restraint and lack of communication of trauma among family members due to the impact of incarceration on identity and cultural practices. I also expect a trend among the Sansei interviews for seeking alternative means outside of family storytelling to learn about Japanese incarceration. Another result I expect is having their sense of cultural identity radicalized to seek justice for incarceration in varying ways. Placing significance on the generation of Japanese Americans who did not directly experience incarceration can further broaden the discourse of meaningful oral histories.

Some of the most widely used medications have unknown side effects on wildlife after disposal. One of these compounds is 17α-ethynylestradiol (EE2), a potent synthetic estrogen and endocrine disrupting compound. EE2 is an active ingredient in birth control pills and has been found in environmentally relevant concentrations in waterways due to the inability of wastewater treatment systems to completely remove it. Even at parts per-trillion, EE2 can cause male fish to develop female sex organs in a process known as intersex. EE2 mimics estradiol, the natural female sex hormone that causes feminization, and affects reproduction and development. Another role of estradiol is it binds to estrogen receptors on cells to modulate immune responses. Our group has observed increased mortality rates in fish exposed to EE2 prior to pathogen challenge. Additionally, we have shown that EE2 down regulates genes and pathways involved in innate immunity in fish, some of which are tied to phagocytosis, a process essential for ridding the body of pathogens and cell debris. Therefore, altered phagocytosis rates may be contributing to the increased mortality of fish when they are exposed to EE2 and challenged with pathogens. My hypothesis is that EE2 alters phagocytosis. To test this hypothesis, I’ve developed an in vitro phagocytosis assay using a rainbow trout macrophage cell line (RTS11). In this assay, RTS11 cells are cultured with fluorescently tagged bacteria that only fluoresce when eaten by phagocytic cells. Cells can be cultured in the presence or absence of endocrine disrupting compounds with potential changes in phagocytosis being measured using a flow cytometer and associated statistics to assess if a compound alters phagocytosis—a key component of innate immunity. This study will provide insight into the biological mechanisms that contribute to higher mortality rates in fish exposed to EE2 prior to being infected with pathogens.

Prevention of aquatic invasive species transmission by recreational fishing and boating is a fundamental management challenge. These activities can entrain non-native plants and animals via tangled lines, bait buckets, or hull encrustation, leading to introductions into new waterbodies. With hundreds of millions of people participating in fishing trips each year, understanding angler movement behavior can provide critical insight into the most effective locations and scales at which to apply preventative measures. Angler behavior is often inferred from infrequently and sparsely conducted surveys that provide limited spatial and temporal insight into this challenge. Here we capitalize on a big data opportunity provided by ReelSonar’s recently launched iBobber, a sonar-enabled bobber with over 3,000,000 records of fishing location, water depth, and environmental variables collected over three years. By quantifying geographic patterns of fishing activities and assessing how these patterns change seasonally, we explore angler behavior in terms of fishing frequency and distance traveled between sites, and characterize the attributes of fished ecosystems. Our study offers novel insight into spatiotemporal patterns of angler behavior and carries important implications for predicting and preventing future transmission of aquatic invasive species via recreational fishing.

Possession Sound is a salt-wedge estuary influenced by both sea water entering through the Puget Sound and fresh water entering from the Snohomish River. Regionally, upwelling off the Pacific Coast during spring and summer months brings acidic deep water into the Puget Sound. Locally in the Possession Sound, previous research has shown that seasonal cycles in both temperature and river discharge are the primary influencers of pH. These cycles are affected by the El Niño Southern Oscillation (ENSO) climate pattern, which alternates between a cooling phase (La Niña), a warming phase (El Niño), and a neutral period. The biological processes of many organisms are influenced by pH levels, and few studies have examined interannual pH variation in estuaries. This study seeks to identify the influence of ENSO on pH cycles in two different areas of Possession Sound, based on proximity to the Snohomish River. Surface pH and temperature data were analyzed at two sites, Buoy (closer to the river) and MBT (farther from the river) from January 2010 to September of 2017, using Yellow Springs Instruments and a Niskin Bottle. River discharge data was ascertained from United States Geological Survey data recorded near Monroe, Washington (2010-2017). The hypothesis of spatial variability in pH due to proximity to the river was not supported. Many of the trends at Buoy were the same or more pronounced at MBT, suggesting that the influence of the Snohomish River at Buoy did not make that site more sensitive to ENSO than MBT. Surface pH was more variable at MBT than at Buoy during the summer months, presumably due to eutrophication and subsequent decay during periods of intense biological productivity. Future studies are planned for seasonal variations of biological factors along with dissolved oxygen variation with depth to further analyze these pH trends.

From November 2015 through March 2016, the Olympic Mountains Experiment (OLYMPEX) field campaign was conducted on the Olympic Peninsula to study how wintertime precipitation is modified as it passes over coastal mountains and to validate satellite-derived precipitation measurements from the U.S.-Japan Global Precipitation Measurement (GPM) mission. This project uses OLYMPEX data to explore the topographic effect on these Pacific frontal systems by examining cloud and precipitation structure on the leeward side (usually northeast) of the Olympic Mountains, where there is typically a minimum in precipitation relative to the windward side. While most research has focused on the structure of the windward side, this study uniquely examines the leeward side of the mountains. A radar managed by Environment and Climate Change Canada on Vancouver Island provided measurements of the vertical structure of the frontal systems over the northern Olympic Mountains, including intensity inferred from radar reflectivity. Using environmental data from NCEP North American Regional Reanalysis on the windward side (usually southwest) of the mountains, this study classifies the leeward radar data based on upstream synoptic conditions. It then examines the cloud and precipitation structure on the leeward side of the mountains in various atmospheric environments. Preliminary findings of this study reveal, for example, that the intensity of cloud systems on the leeward side is dependent on upstream stability. Locally, these findings will inform studies of snowpack and water supply as many reservoirs depend on precipitation that occurs on the leeward side. Outside of the Pacific Northwest, these findings can be applied to other midlatitude coastal mountain ranges on the west side of continents around the world.

The Puget Sound is a complex estuarine system within the Salish Sea, fed by both high salinity water from the Pacific Ocean and freshwater from a number of rivers. The Snohomish River is the second largest input, transporting freshwater from the Skykomish and Snoqualmie rivers to Port Gardner Bay off the coast of Everett. At its mouth, the higher density salt water from the Puget Sound intrudes into the freshwater, forming a salt wedge that causes a highly stratified water column which rapidly changes with the tidal cycle. These mixing dynamics may be the primary driver of biological productivity in the estuarine system. To characterize the density profile relative to tidal patterns and season, current speed and velocity were recorded utilizing a Nortek ADCP. During normal outflow (3,500 f^3/s) of the Snohomish River, upward velocities were positive during flood tide and negative during ebb tide, following a typical salt-wedge trend. During a peak outflow event (56,000 f^3/s) on October 22nd, this tidal cycle dependence was disrupted and downwelling dominated in the form of negative vertical velocities throughout the water column. In addition, the magnitude of east/west velocities increased during peak outflow. This signaled a period of intense turbulence at the bottom of the water column. During the same time span, data concerning turbidity and chlorophyll levels were recorded utilizing a Seabird CTD. No clear trend was evident in chlorophyll levels at both normal and peak outflow timespans. Turbidity maintained high levels (35 NTU) following peak outflow, possibly reflecting the transportation of sediment from the river bed into the water column. This transportation would be caused by the turbulence reflected in the higher magnitude of the east/west velocity data.

Some spionid polychaetes can burrow into the shells of bivalves, creating unsightly mud blisters. Because they are unappealing to consumer and can burst, fouling oyster flesh, these blisters are an economic burden on affected oyster half-shell industries. Historical invasions by the spionid Polydora websteri have resulted in the collapse of aquaculture operations in Australia, New Zealand, and Hawaii, USA. Recent sightings of mud blisters on Pacific oysters (Crassostrea gigas) in Puget Sound, Washington, USA suggest that the area might be experiencing a spionid polychaete invasion. To determine whether P. websteri is the polychaete creating the mud blisters recently observed in Puget Sound, we obtained 170 Pacific oysters from six locations and examined for blisters and burrows. Polychaetes were extracted from the shells and vouchered for molecular analyses. We used mitochondrial (cytochrome c oxidase I [COI] and cytochrome b) and nuclear (18S rRNA) genes for species-level identification. Positive identification of P. websteri found in the mud blisters of Puget Sound Pacific oysters will be the first confirmed sighting in Washington, USA. This study is the foundation for advising the Washington shellfish industry on strategies for mitigating the economic impacts of this invasive polychaete.

The focus of this piece is the geographic area originally named “El Rincón Del Diablo” or “The Devil’s Corner”; now known as The City of Escondido, in California. (The Spanish word “escondido" means “hidden.”) This work proposes to “unhide” the true population of Escondido - hidden behind published numbers from accredited organizations and respected sources. By using the US Census data, the number of documented citizens in Escondido was accounted for as “visible numbers.” The undocumented residents estimated number was uncovered by this research and accounted for as “invisible numbers.” These human beings are community centered and contribute to the economy and to society. But according to the US Census, they are invisible, they are hidden in plain sight. Inspired by how John Cage adopted a consistent and relatively simple mathematical formula for composing his music, in this installation performance, I adopted the relative change calculation formula to find the ratio between the visible and invisible numbers, which turned out to be 20%. In conclusion, this ratio was used to develop the recipe for the bread made during the performance, as well as the displayed ingredients and all relative space vs surface area of the object made, and the piece of clothing used by the performer. The symbolism involving the choice of making bread evokes the thoughts of union and making peace among those sharing the bread, for in many different cultures those who share their bread make peace. All parts used to create the installation were acquired in salvage stores in Escondido, CA.

Post-secondary education is often seen as critical to the ultimate goal of progressing up the socio-economic ladder. However, social inequality can impact academic success. Social inequality can be expressed through classism, obstacles and interruptions in the academic journey of low-income college students, racial isolation in schools, residential segregation, negative academic experiences, and differences in child development. This type of inequality establishes divisions of privilege where obtaining the “American Dream” is easier for some and harder for others. So how can children from lower class families break out of the poverty cycle when society treats them unequally? This study examines social inequality in families, social institutions, and post-secondary education. This research focuses on racial/ethnic minorities in the United States within the age range of 21-25 years old and explores questions related to their family, childhood experiences, and future goals. This work aims to emphasize the great importance of breaking down the inequality barriers of classism.

Our research seeks to more accurately define how the Pacific Northwest regional climate will look in fifty to one hundred years. Our results help quantify the uncertainty in our climate predictions, a major shortcoming in climate research. Our research is interesting because it utilizes a high resolution numerical weather prediction model to examine regional climate change here in the Pacific Northwest. We are creating a large set (an ensemble) of predictions of climate change in the Pacific Northwest. The tool used in our research is the Weather Research and Forecast (WRF) model. WRF requires General Circulation Model (GCM, also known as Global Climate Model) data to feed it information on the larger-scale climate. A big part of our project is collecting GCM data from a variety of research centers worldwide, and preparing it to be used as input data for WRF. We expect to complete our model simulations by the end of Spring Quarter 2018. These results could be of direct use to a number of local agencies and policy makers so that they can shape their decisions around the future changes that our local climate may experience. We also expect our data to be of great use for further research in quantifying climate prediction uncertainty.

Current studies have shown that changing climate is responsible for methane releases from the seafloor, making it important to understand how methane plumes can impact the ocean. Methane plumes impact the stratification and circulation within the water column which can influence primary productivity and seawater chemistry and potentially atmospheric greenhouse gas levels if the methane from the plume undergoes exchange with the atmosphere. Along the Washington margin there has been over 1772 individual bubble plumes located and identified in depths ranging from 40 meters to 1988 meters water depth. Compilation of archived CTD (conductivity, temperature, depth) data at active methane plume sites including Southern Hydrate Ridge, Grays Harbor, and Vancouver Island, can provide estimates of the plume fluids temperature and salinity. Using these estimates, the point where buoyancy reaches zero determines the possible depth of horizontal plume fluid intrusion into the water column and the entrainment coefficient to quantify the fluid that’s entrained by the plume can be calculated., I can determine the plumes’ ability to penetrate through sea water density interfaces such as the thermocline by calculating the Richardson number for the plumes. Using pre-established bubble models, I will also quantify sea water entrainment by the plumes. Through these methods, I will be able to determine how methane plumes impact water column stratification on the Washington Margin.

Single electron devices (SEDs) are devices that can isolate individual electrons along a conducting path. SEDs have many proposed applications including their use in metrology, and quantum information science. However, there are many barriers that must be overcome before these applications are realized beyond the proof of concept experiments currently being performed in academic research labs. Our group’s work focuses on pathways to overcoming some of these barriers including the issues with material properties and device stability. My contribution focuses on data analysis of SED transport measurements. These analyses produce various metrics for both the SEDs under test as well as the measurement system probing them. They include determinations of charge offset drift, a metric for long term device stability, as well as electron temperature a limiting factor in magneto spectroscopy measurements.

How is star formation affected by its environment? How big is the effect of having differing metallicities during the star forming process? The goal of this research is to study star formation in low metallicity environments, which are well represented by dwarf galaxies. For this project, we used the Atacama Large Millimeter Array (ALMA) telescope, at an angular resolution of about 0.5 arcseconds (about 66 lys), to observe the 12CO (115 GHZ) distribution in the galaxy Henize 2-10 (He 2-10). He 2-10 is an irregular dwarf galaxy about 30 million lightyears (lys) away, about 1 kilolightyears (kly) across, and has a mass of about 10 billion solar masses. It has a high gas to dust ratio, is star forming, and has a low metallicity of about 12+log(O/H)~8.3. Additionally it contains a supermassive black hole candidate of about 1 billion solar masses, which could have significant dynamical interactions with the molecular gas. We created a zeroth moment map which we used to estimate several properties of the galaxy: including a molecular gas mass of about 38 million solar masses, an observable area of about 1850 square klys, and a molecular gas density of about 3.7x10^(-20) grams per cubic centimeter. We also created multiple channel maps which provide preliminary results that indicate the presence of at least 10 giant molecular clouds within He 2-10.  With what we have done so far, we will be able to compare our results to known giant molecular coulds in the Milky Way Galaxy, and begin to better understand the relationship, if any, between star formation and star forming environments. 

36.7 million people worldwide are living with HIV/AIDS, of which almost 15 million receive antiretroviral therapy (ART). These patients require regular HIV-1 viral load (VL) tests to monitor ART effectiveness and compliance. However, the majority of affected people live in low-resource settings where disease monitoring through medical laboratory-based systems, such as nucleic acid amplification tests (NAATs), are inaccessible. There is an increasing need for accurate, affordable HIV-1 VL tests at the point-of-care (POC). We previously demonstrated the ability to leverage an electrokinetic separation and preconcentration technique, isotachophoresis (ITP), and an isothermal nucleic acid amplification method to develop a proof-of-concept POC NAAT for extraction, amplification, and detection of nucleic acids from human serum. The limit of detection (LoD) of our paper-based test was hampered by the loss of nucleic acids during ITP across the paper membrane. This work is focused on lowering the LoD of our test by improving the isotachophoretic extraction of nucleic acids from human serum. We have addressed the adsorption of nucleic acids by screening membrane types and pre-treatment methods. We have observed significant nucleic acid entanglement of DNA greater than 50,000 base pairs in length, which we can mitigate using DNA shearing techniques. We have also developed specialized ITP chemsitries for increased extraction efficiency. The completion of this work will result in more effective separation and purification of nucleic acids from human serum, ultimately leading to a reduction of target loss and improved test sensitivity. Employing the ITP extraction techniques developed in this work will aid our lab's ongoing efforts to create a POC NAAT for monitoring HIV-1 viral load.

My paper focuses on the life of Rose McGrory to address broader shifts in identities across the Atlantic and throughout the United States. From a British colonial subject to an American colonial settler, Rose McGrory’s life illustrates how individuals refashioned their identities to confront and exploit the contradictions of race, gender, religion, and nation, revealing how they simultaneously challenged and conformed to societal norms in the process. Rose was born in 1884 in desolate Dunree, Ireland. Though Ireland and Britain were theoretically equals after their unionization in 1800, Rose lived in Ireland as a British colonial subject. For centuries, the British had represented the Irish as racially backwards to justify their colonization. In the decades after the Great Famine, females like Rose gained greater access to educational opportunities, but their socioeconomic prospects did not improve likewise. In this historical context, Rose immigrated to Boston in February 1905. Here, racial and gendered hierarchies confined Irish women like Rose to abject jobs like domestic servants. Although many Irish on the East Coast succeeded in their crusade to become perceived and treated as white, in part by distancing themselves from black people, Rose found Boston restrictive. Rose moved to Hood River, Oregon in 1910. In the west, the Irish had already associated their racial identity with whiteness by leading the racialization of the Chinese and Japanese as non-white. In this new racial landscape, Irish immigrants could transform themselves into “settlers”, an identity associated with whiteness and increased socioeconomic opportunity for Rose and her family. Rose’s life reveals the intricacies of her various identities and the complexities of the Irish-American immigrant experience. Integrating primary sources like censuses and newspapers with various scholarly literatures, my paper unveils Rose’s arduous journey and provocative story.

My research began with a discovery of manuscripts in the Royal BC Museum in Victoria, British Columbia. These manuscripts were written at Fort Nisqually during the 1840s. A series of journals and ledgers detailing the arrival of Americans into the Oregon Country in 1845 have been missing for over 150 years. They were taken to Victoria, BC in 1865 to provide evidence for the claims of the Hudson’s Bay Company and Puget Sound Agricultural Company in the joint commission hearings between Great Britain and the United States. Through letter books and other writings detailing events around the same time of the missing journals, I am piecing together some of this early 1840s history by working with the curators at the BC Archives. While the journals are yet to be found, my research at the Royal BC Museum has uncovered new leads to follow. The discovery of the journals will reveal farming practices employed by the fort and add detail to what is already known and would answer the unending questions regarding breeds of cattle and sheep arriving at Fort Nisqually, as well as specific cultivars of potatoes, grain, and other food stuffs grown at the fort. The discovery is not the last step in writing Fort Nisqually and the Puget Sound Agricultural Company history. After locating, transcribing and publishing the journals comes the true historiography. These journals hold the keys to a lifetime of research. By uncovering these stories, a box of knowledge will be opened which local historians will dig through for the rest of time. These manuscripts will be the keys to that box, and give future generations a chance to fully understand a history lost for 152 years.

A century of U.S. government-backed, anti-Asian discrimination culminated in the incarceration of Japanese Americans during World War II. Despite U.S. government insistence that anyone with up to 1/16th Japanese blood had to be incarcerated, the existence of white-looking children in concentration camps presented a segregation crisis. Race was segregation’s litmus test: if white was assumed loyal, Japanese was assumed disloyal. My paper uses original archival research to study attempts to reconcile this monoracial logic with the multiracial reality that exposed it - the U.S. government’s Mixed Marriage Policy (MMP). The MMP permitted some multiracial Japanese Americans to escape or avoid mass incarceration. My project argued that U.S. treatment of multiracial Japanese Americans rewarded the disavowal of Japanese identity with “integration” to project an image of liberal inclusion whilst allowing a reality of surveillance and segregation. When attempts to quantify racial mixtures became impossible, the MMP attempted to strip the trait of race from multiracial subjects in a policy of institutional “colorblindness” by evaluating loyalty on “objective” criteria alone. Individuals eligible for integration became symbols for the U.S. government to project an image of inclusive humanitarianism and racial tolerance in the post-war empire. However, these seemingly neutral criteria upheld U.S. imperial practices of racial segregation. The perceived disavowal of the racism behind incarceration sanitized the image of the U.S. government while quietly reproducing racial hierarchies through new domestic surveillance policies. Shifting segregation policies to subtler forms of institutional colorblindness strengthened the United States as an empire of white supremacy. Racism was at its most intractable and pervasive when acknowledging the existence of race became taboo. As the title “It Must be Odd to be a Minority” (Spanish translation) alludes, this research is significant to Asian American Studies because the current literature rarely address inter-sectional struggles with the greater community of color.

The Duino Elegies is a collection of ten elegiac poems written by Austrian-Bohemian poet Rainer Maria Rilke (1875-1926). At turns mournful and ecstatic, sardonic and visionary, the Elegies were composed from 1912-1922, a period marked by the so-called “language crisis” (Sprachkrise) in German-speaking modernist circles and the entirety of the First World War. The poems’ major themes include this crisis, the role of divinity in a secularizing society, and the ways in which the mass production of commodities threatens human relationships with things and with other humans. The latter point will be the focus of my presentation. Drawing on scholar Teresa Brennan’s interdisciplinary studies of the energetic, psychic, social, and economic aspects of modernity, I read the Elegies as presenting a theory of energy that is at once an affective, poetic experience of modernity in Western Europe. More specifically, I show how the Elegies map out and respond to a collective psychic exhaustion. Alongside Brennan, I argue that capitalist production in modernity—and the attendant accelerations in transportation and communication—is the main culprit. Collective psychic exhaustion finds its correlate in natural exhaustion—the depletion of natural resources extracted for commodity production—which, if not yet catastrophic in Rilke’s time, certainly is now. It should be noted that Rilke is a western, middle-class poet, and his work can by no means be read as speaking for all of ‘humanity.’ Yet with capitalism having only become more global, pervasive, and hegemonic since Rilke’s time, the Elegies offer illuminating insight into our own heterogeneous, global experiences—social, psychic, and energetic—of capitalism as it unevenly and differentially entangles, exploits, and mangles various parts of the world.

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.

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.

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!

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Hip hop is both a globalized movement and culture that gives marginalized community members an outlet to express themselves creatively. The hip hop community posits itself as one that welcomes individuals based on one’s credibility through the four pillars: rapping, DJing, breakdancing, and graffiti art. However, despite the “openness” the industry pushes forth, an individual’s race and gender, especially not being a Black, heterosexual male, complicates one’s access to opportunities. Asian Americans, in particular, must simultaneously subvert and reclaim their identities from controlling ideologies through their navigation of hip hop. In this study, I conducted a semi-structured focus group with Asian American hip hop artists from the greater Seattle area (all ranging in age). I conducted individual follow-up interviews with participants, utilizing a narrative inquiry methodology. The combination of the focus group and individual interviews enables me to outline the richness of participants’ hip hop experiences. My preliminary findings indicate that Asian Americans must not only face impositions by mainstream media outlets but also within the liminal spaces of hip hop. Renegotiations and reaffirmations of identity prove critical for Asian Americans because they correspond to a liberation from racialized and gendered scripts. Moving forward, one implication of this study is the limited scope of Asian ethnic representation within all four of the pillars of hip hop, and the need for Asian Americans to redefine themselves within hip hop.

The ability to recapitulate the dynamic presentation of signals in a stem cell's microenvironment remains a major hurdle in tissue engineering. By controlling cell growth and differentiation in 4 dimensions (i.e., time and 3D space) through biochemical and biomechanical cues, heterogeneous synthetic tissues could be produced that match the complexity of their native counterparts. By combining strategies in light-programmable hydrogels and recombinant protein engineering, we have demonstrated the ability to control the cellular microenvironment with a UV light mediated reaction that allows a covalent bond to form between a modified protein and the hydrogel. While covalent interactions form strong bonds, they are generally irreversible using mild, cytocompatible chemistries and pose potential temporal limitations. In addition, this technique uses UV light, which may be harmful to cells. Instead, by incorporating LOVTRAP into the photopatterning system, we introduce a greater amount of control by allowing for full reversibility using blue light. In the dark, LOV2 and Zdk1 dimerize to form a protein-protein bond with similar stability to an antibody-antigen interaction. Upon exposure to blue light, the dimer dissociates, allowing for fully reversible control over conjugation. A protein of interest can be tagged with the Zdk1 domain using recombinant protein engineering, while still maintaining its binding affinity for LOV2. LOV2 can then be conjugated throughout a hydrogel to make a light responsive protein binding material. By utilizing a light controlled dimerization event between proteins, the LOVTRAP system is fully reversible using only blue light. Thus far, I have been able to illustrate the photopatterning ability of LOVTRAP and am working towards demonstrating full reversibility. If successful, this technique could be used for tissue engineering applications that require mild treatment conditions and full dynamic control over the presentation of biochemical cues.

Current drug testing methods are unable to accurately predict and study the effects of drugs on human myocardial tissue. These methods are unable to accurately mimic the physiology and maturity of native cardiac tissue, and as a result, the tissues are unable to react to cardiotoxic drugs the same way that native cardiac tissue. Therefore, there is a need for physiologically accurate and mature tissue constructs in order to test clinical drugs for effectiveness, cardiotoxicity, and arrhythmic effects. To fulfill this need, we will use an electroconductive bioink containing decellularized extracellular matrix (dECM) from porcine cardiac tissue, reduced graphene oxide (rGO), and incorporated human induced-pluripotent stem cell (hiPSC)-derived cardiomyocytes to develop a more physiologically accurate cardiac tissue construct. This will result in more adequate cell maturation, and therefore, more accurate preclinical drug screening. The success of this project would lead to the development of high throughput production of biomimetic cardiac tissue models for use in accurate drug screening, along with improving the understanding of cardiac maturation.

The human brain is comprised of many billions of neurons, which then connect with each other many trillions of times. Modeling how these neurons function provides insight into language, thought, and behavior. However, neurons are not all identical, so an approach that performs well on some neurons will perform poorly on others. I focused on a learning system to detect and model neurons that use pattern-recognition in order to decide when to fire, which would not be expressed well under existing approaches. We researched a strategy for describing these process in a non-Markov state, which means that we do not have enough information to correctly model the neuron, by approximating to Markov models using a subset of the required information. This means that we produce a set of probabilities for the next state of the neuron given the previous state. We approximate the Markov model using Monte-Carlo Tree Search (MCTS) optimizing for smallest confidence interval to select sequences to measure. In order to calculate a confidence interval on a given sequence we apply A*, pronounced A star, which is a targeted pathfinding algorithm, in order to produce execution paths that in turn find confidence intervals. We use two strategies for pruning sequences; a MCTS to find the measured sequence that differs least from chance for long term learning, and exponential decay for short term learning. We assume that after we process information it cannot be recovered, so when we measure new sequences we only measure from the time of consideration onward. If our process successfully locates important patterns the neuron is looking for, it produces an accurate approximation for the neuron that can be rapidly evaluated.

TOPLESS (TPL) is a transcriptional co-repressor protein that plays a central role in the regulation of plant growth and development. In the model plant Arabidopsis thaliana, TPL acts in essential hormone response pathways, including that of auxin, a small signaling molecule. TPL acts in the auxin response pathway by binding another co-repressor from the Aux/IAA family (henceforth referred to as IAAs). In the presence of auxin, IAAs are degraded, relieving TPL repression and allowing for transcription of auxin responsive genes. Despite its central role, the molecular mechanism by which TPL confers repression is not well understood. Recent structural analyses indicate that TPL has interfaces for both homodimerization and homotetramerization. Synthetic assays have shown that TPL truncations in which the tetramerization interface has been deleted have a significant decrease in repressive function. To determine the repressive mechanisms of TPL, we created a structure-function map. We have created full-length TPL variants with point mutations at the dimerization and tetramerization interfaces, as well as serial domain deletions. We tested the repressive function of these variants in a yeast synthetic assay in which TPL represses expression of a fluorescent protein. Repressive function was then quantified from fluorescent reporter output with stronger repression corresponding to decreased fluorescence. We then validated the results of our synthetic assays in planta by expressing TPL-IAA14 variants that negatively regulate lateral root development. The repressive strength of each TPL variant will be quantified by measuring the number of lateral roots, with fewer lateral roots corresponding to increased TPL repressive strength. TPL homologs exist in many species. Defects in TPL homologues have been implicated in the causes of many cancers and developmental diseases, therefore a better understanding of the functional mechanisms of TPL will have broad implications across organisms, including humans.

Flowering plants exhibit striking diversity in their floral symmetry due to independent genetic changes throughout their evolutionary history. Diversity is also observed within the flowers of genus Rhododendron, which displays a variety of radially and bilaterally symmetric flowers across its approximately 1000 species. Floral symmetry is governed by an interaction between one TCP transcription factor, CYCLOIDEA (CYC), and two MYB-class genes, RADIALIS (RAD) and DIVARICATA (DIV). This interaction initiates when CYC is expressed in the floral meristem, leading to the activation of RAD in the dorsal domain. RAD then antagonizes DIV activity in the dorsal regions, leading to radial symmetry. In other flowering plants, duplications in CYC have been associated with changes in floral symmetry, but the role of RAD and DIV remain unstudied. A number of transitions to and reversals from radial symmetry have occurred throughout Rhododendron from a bilaterally symmetric ancestor. Focusing on RAD and DIV, the goal of this study is to better understand the evolutionary history of these floral symmetry genes in rhododendrons, and their correlation to floral symmetry changes. I sampled eight different species throughout Rhododendron in addition to various outgroups and reconstructed phylogenies of these genes. I obtained sequences from genomic and transcriptomic databases, and used these sequences to design primers for amplifying and sequencing these genes from laboratory samples from wild and cultivated specimens. I found two distinct copies resulting from one duplication, in both RAD and DIV. In future studies, we will expand our sampling of species to investigate the phylogenetic placement of the origin of these duplications in tandem with changes in flower symmetry, to determine whether duplications in RAD or DIV are associated with symmetry changes as has been shown for CYC.

Auxin is a hormone that is crucial for plant growth and development. Auxin promotes the activity of auxin responsive transcription factors (ARFs) that induce transcription of target genes. Though, we know a lot about auxin response in the model plant Arabidopsis, very little is known about ARF behavior in maize. It has been previously shown that auxin and ARFs mediate many diverse developmental responses in Arabidopsis and maize. We hypothesize this diversity of response may be caused by different ARFs binding to different promoters, allowing different genes to be activated. The goal of the project is to examine the activity of maize ARFs on different promoter structures. We tested if maize ARFs show similar rules of ARF-promoter interactions as Arabidopsis ARFs. By comparing Arabidopsis and maize ARF activity, we are be able to understand how the two species have evolved over time, and if ARF function and auxin response are conserved in the two species. Working on maize is also important because it such an essential food crop for people and animals and can help us resolve issues such as food shortage. To investigate how ARFs regulate the activation of genes, we used a synthetic yeast system to quantify transcriptional activation. We engineered yeast to express both a maize ARF and a synthetic auxin-responsive promoter regulating transcription of a fluorescent reporter. We quantified fluorescence, a readout of ARF activation of the promoter, by flow cytometry. We systematically tested how activation is impacted by the sequence, orientation, and number of cis-elements within a promoter sequence, and how these effects differ among different ARFs.

This essay delves into the portrayl of fruit in Italian Baroque still life painting and its relationship to period botanical studies. By formally analyzing two seperates artists of the Baroque I hope to understand the importance of still life in scientific history. I focus my research on Caravaggio due to his cultural importance as a famous Baroque artist. In particular, the works of Caravaggio can be used as tool to understand the culture of fruit in Baroque Italy. I take a point of departure the high naturalism of Caravaggio, whose attentive depictions of fruit reflect seventeenth-century Italian domestic agriculture and import market. Botanical artist Giovanna Garzoni painted for Medici members of Florence specifically Grand Duke Ferdinando II and Grand Duchess Victoria. Garzoni provides an example of the fruit being grown in Medici botanical gardens. Medici botanical gardens are a prime example of horticultural practice within the seventeenth - century. By contrasting the depiction of the same species of fruit in Garzoni's painting Still Life of Birds and Fruit and Caravaggio's work Still Life With Fruit On a Stone Ledge, we can explore how the artists represented truth differently. Caravaggio paints from a specific subject by paying close attention to the detail of his subject in imperfections, which represent truth in specific form. This contrasts with Garzoni who a generalized truth of the species as a whole and not each individual subject. In this essay the contrast between these two artists will be explored to understand their different avenues of depicting truth in their artworks. Theatrical metaphor, sexuality, religion, and genre painting will all be employed to approach Caravaggios work. Comparitively Garzonis work will be viewed in the context of gender, class, and botanical collection.  Caravaggio and Garzonis seventeenth century still lifes explore how artists enter the discourse of scientific truth. 

While the population in America is becoming more and more diverse, the faculty that train our future workforce are not. At predominately white institutions (PWIs) across the United States, racial disparities amongst faculty are problematic. As of 2015, African Americans made up approximately 12.7% of the United States population. At that same time, male and female African American full-time faculty at degree granting college institutions made up only 3% of the workforce. With inadequate representation of African American male faculty, there are voids in the bonding experience between a student and professor. This study critically examines the limited representation of African American men in higher education, and the effects such representation might have on students and faculty, particularly regarding mentoring opportunities. The implications of racial disparities in higher education have been explored through in-person, semi-structured interviews with African American faculty members, graduate students, and undergraduate students. The results of this project have shown that the lack of representation amongst African American male faculty is negatively impacting the college experience for not only students but also staff at PWIs. This research has gained a better understanding of the importance of mentoring and the effects of limited representation and has added to the overall conversation regarding African Americans males in higher education.

Despite the intense coverage of the Syrian Civil War in US media, consensus about what started the Syrian Civil War is highly debated. The variety of explanations cited as leading to the Syrian Civil War range from: corruption, protests, sectarianism, climate change, and drought. My mixed methods research begins by exploring whether certain conflict explanations like the Arab Spring Protests are overrepresented in discourse whereas conflict explanations using climate change are underrepresented. A manifest content analysis of 134 American newspaper articles of causes for the conflict from the New York Times, Washington Post, and Wall Street Journal yielded that they did indeed favor Arab Spring protests but that the results varied by newspaper. The right-leaning Wall Street Journal failed to mention climate change in a statistically significant manner whereas the Washington Post repeatedly mentioned climate change as a major factor for the Syrian Civil War. Interpretations and analysis of the same conflict produced different ideas about what started the conflict. The second part of my research involved an inductive latent content analysis of these news sources to truly understand the perceptions that drove news organizations to report the way they did. Here I report two key findings: a better understanding of how causal factors for conflict are explained in American media and how media organizations justify and convey narratives of importance to them. Such research is important because climate change and conflict is an issue that is important to the stability of the globe. Understanding how and why it’s importance is overrepresented and underrepresented in news sources can help determine how popular geopolitics shapes perceptions and how to make discussions of climate change in the lens of conflict more acceptable.

Wealth inequality in the U.S. is at an extremely high level and continues to grow. In 2010, the wealthiest 10% owned 70% of total wealth, a percentage close to the level in 1930. The gross wealth disparity that characterizes the contemporary U.S. is one of the most pressing economic and political issues of our times. In this work, I present agapism as an alternate philosophical system of ethics to address the debilitating wealth inequality in the U.S. today. Agapism is an ethical system based on the commandment in the Pentateuch to love one's neighbor as oneself. Traditionally, academic philosophy has overlooked agapism as an ethical system because its foundational sources are of religious origin rather than grounded in philosophical texts. However, agapism is a robust ethical system that provides compelling moral reasons for government wealth redistribution. In my work, I detail the moral and philosophical reasons for wealth redistribution that arise from the agapist tradition and explore the kinds of moral obligations agapism imposes on individuals and communities. Though agapism’s foundational sources include those of Christian origin, I consider and respond to Christian arguments against government wealth redistribution and Christian arguments that make a weaker case for wealth redistribution than agapism calls for. I also consider and respond to arguments regarding the proper and just distribution of wealth from influential secular figures in contemporary moral philosophy, including John Rawls and Robert Nozick. Among other issues, I consider their perspectives on how wealth should be justly distributed, as well as the government’s role in wealth redistribution.

In 2015, Seattle voters overwhelmingly voted in favor of Honest Elections Seattle. A citizen-led initiative that significantly changed the way Seattle City elections were financed. By providing every resident of Seattle with Democracy Vouchers, four $25 credits that can be given to participating candidates, these reforms have provided a new opportunity for citizens to become political donors and participate in a process that has been dominated by wealthier and more educated elites. My research analyzes every political contribution made in the 2017 and 2015 electoral cycles for two city council races that are city wide. I break down the city of Seattle into ZIP codes and compare political contributions from each ZIP code in 2015 and 2017. I then use the American Community Survey data to compare each ZIP code by mean income, percent of residents with a bachelor’s degree or higher, and percentage of white residents. I predict that Seattle’s Democracy voucher program has significantly changed the profile of the average political donor in Seattle and made them more representative of the city as a whole. I hope to find that through publicly financing elections, we can create an electoral system where everyone can participate, not just the wealthy elite. This work is critical for evaluating the success of a multi-million dollar public program and whether it ought to be adopted in other cities throughout the United States.

Anthropogenic habitat modification is one of the most widespread and immediate threats to terrestrial biodiversity. One of the effects of this threat is the alteration of local microclimates, to which ectotherms are particularly sensitive. The shifts in spatial distributions seen following conversion, where some species decline while others persist in these modified habitats, may be in part explained by a change in the thermal conditions. However, understanding how thermal biology may affect species responses to habitat conversion has been addressed by relatively few studies. Here we examined how the change in the thermal conditions may affect the response of the poison frog, Oophaga pumilio to habitat modification by measuring three aspects of its thermal niche: field body temperatures, preferred body temperatures, and upper thermal maxima. We measured body temperatures in the field and behaviorally selected temperatures in the laboratory to determine if individuals in warm, pasture habitats have higher field temperatures and select for higher body temperatures than individuals found in cooler forests. Additionally, we measured upper thermal maxima to determine if individuals from altered habitats exhibit higher tolerances than those in forest remnants. Our results showed that individuals found in altered habitats have higher body temperatures than those in forest and also preferred higher body temperatures on average than those from forest. However, while there was considerable variation among individuals in thermal maxima, we found no significant difference of thermal maxima between individuals from the two distinct habitats. These results suggest that this species may be able to experience acclimation and/or selection on preferred body temperatures as individuals are exposed to novel temperature regimes in altered habitats but may not be able to cope with increasing temperatures if high daytime temperatures frequently approach their upper thermal tolerances.

Puget Sound is renowned for its biological productivity, but seasonal upwelling feeds this system with waters rich in dissolved CO₂ and consequentially accelerates the acidification of these ecosystems. In this region, aquaculture of bivalves has important economic and cultural roles that are threatened by ongoing changes in climate and water chemistry. For mussels and oysters, shell strength and integrity are the first defense in combating biotic and abiotic stressors but exposure to low pH can drastically weaken calcium carbonate shells. This study examined the effects of variable pH on the shell strength of the Mediterranean mussel, Mytilus galloprovincialis, and the Olympia oyster, Ostrea lurida. M. galloprovincialis and O. lurida were attached to ORCA buoys at three sites in Puget Sound, at either 5m or 20m depth on the buoy tether for three months. This spatial diversity exposed the bivalves to naturally occurring variations in pH which were continuously measured in situ by the ORCA buoys. The resulting shell strength was measured using an Instron Universal Testing Machine by puncturing a small hole in each shell. These results were evaluated using a two-way ANOVA between sites and depths. We expected that both species will have much weaker shells at deeper depths where pH is generally lower. This study can provide physiological thresholds of economically and ecologically important species under current and future oceanographic conditions.

A seed’s successful transition to a seedling depends on the suitability of the surrounding environment. All plants need water, sunlight, favorable temperatures, and soil nutrients to survive. On top of these essentials, interactions with other organisms through competition, herbivory, or disease may also have an impact. The goal of this study is to assess which factors influence tree germination in Washington’s temperate forests. Are there essentials without which seeds fail to complete the pivotal transition between embryo and tree? This question was explored using data collected since 2014 in a 25.6 hectare plot located in the Gifford Pinchot National Forest (WA). The dominant trees here, including Western hemlock and Douglas fir, were the focus species of this study. Forty seed traps distributed throughout the plot collected falling tree seeds so that they could later be identified to species and counted in the lab. Germinants and seedlings were recorded within a square meter adjacent to each seed trap, along with environmental factors such as soil moisture and sun exposure. Regression analyses were used to assess whether germination rates (the proportion of seeds that successfully germinated) were influenced by environmental factors, other organisms, seed densities, or year. While analyses and data collection are ongoing, results thus far indicate a negligible role for soil moisture and sunlight in germination. On the other hand, the presence of other vegetation decreased germination, while the presence of nurse logs increased it. Germination is an important and delicate life stage for every tree, and through their influence on it environmental factors may shape the species composition of these communities. Identifying relevant factors may also provide some ability to anticipate how these trees will respond to the warmer and drier conditions expected to define climate change in the Pacific Northwest.

Situated in the depths of a city’s music scene lies an underbelly of DIY (Do It Yourself) spaces. These spaces operate under the radar of the city’s commercial music scene found in for-profit venues, working to support experimental and small-scale artists who are often excluded from “legitimate” spaces. The DIY mentality developed from a desire to create venues that support musicians and audiences who refuse to adjust to the tastes of large music corporations. These communities host shows in spaces artists can afford, such as living rooms, basements, and warehouses. This project examines the creation and perpetuation of these underground music scenes, focusing on the development of a scene’s community and how identity is performed inside and outside of DIY spaces. This project explores how a city’s built environment (including its available housing, geographic layout, and ease of transport) impacts the way a scene functions and evolves. It teases out how these impacts are felt through observing how a scene’s social norms are performed at events in DIY spaces, examining the styles of music played within a scene, and other related factors. In order to determine how a scene's norms are specifically influenced by the spatial dynamics of a city, this paper examines the underground music scenes of Seattle and Philadelphia, a deliberate contrasting that shows how the differences and similarities in each scene can be attributed to both the cultural identity of the city as well as its unique urban environment. Whereas there are certain norms that arise out of the overarching DIY ideology (meaning they can be found in the scene of each city), there are disparate norms that are endemic to the each city’s scene. These latter norms prove a city’s built environment holds significant weight in the development of its underground scene. Ultimately, this data will provide evidence of the importance of these underground scenes within a city's arts community,advocating for their protection and support both locally and nationally. 

This project considers how we might address barriers to coalition building across difference using interdisciplinary knowledge from social psychology, neuroscience, human centered design, and critical race theory. The first question this project asks is: how might we translate strategies from social psychology that are known to increase the self-other overlap into engaging, immersive virtual experiences (IVE) for coalition building? The concept of the self-other overlap relates to coalition building because of the breadth of research indicating empathy as a self-centric process wherein people are much more likely to feel empathy for people they see as like themselves. This project focuses on IVEs because of their unique ability to create interactive, low stakes environments in which participants can embody experiences outside of their own and play with abstract ideas, such as the social constructs of race, sex, and gender. Given these qualities, the project seeks to specifically explore how IVEs might facilitate compassion, and thus coalition building across identity differences, such as race, gender, and nationality. This project differentiates compassion as empathy with action and views compassion as a potentially proactive approach to social equity. Because of the complex ethics involved in this endeavor, this project must also ask: how might we use human centered, participatory design and critical race theory to ethically design these experiences while motivating and supporting audiences to engage? In this way, this project proposes to use a range of design tool fidelities to discover and design for barriers to coalition building, and thus forge a bottom-up pathway from the people being represented to their IVE representations. The products of this project include a literature review and a suggested protocol for the ethical production of IVEs designed to facilitate coalition building across difference using human centered, participatory design, and critical race theory.

Obstructive sleep apnea (OSA) is a condition estimated to affect 5% to 15% of the population, in which individuals stop breathing for extended periods while asleep. Treatment is usually successful when provided; however, the vast majority of OSA patients go undiagnosed, in part because the superficial symptoms of OSA in a wakeful state are varied and nonspecific, including drowsiness, hypertension, heart disease, diabetes, and depression. The current diagnostic gold standard is an overnight sleep study, which is expensive and requires access to a specialized sleep medicine facility. This motivates a need for a convenient and accurate technology to screen for sleep apnea in homes and clinics. A ubiquitous screening solution must be both sensitive to slight variations, and specific to apnea in spite of many interfering physiological factors; these challenges are further complicated by the constraints of low-cost sensing devices. Our approach is to detect persistent changes in the sympathetic nervous system that are caused by frequent apnea events; although these changes cannot be measured directly, they manifest in discernible changes to heart signals. To test our system we record cardiac and respiratory signals while participants execute a series of breathing maneuvers, such as breath holding and breath rate control. We record in parallel with (1) a smartphone running a custom application and (2) a commercially available wireless biomedical recorder. Using digital signal processing, we extract informative features from the locations and amplitudes of peaks and troughs in the PPG, SCG, and ECG signals. Equipped with these extracted features and the ground truth diagnoses provided for each patient by the Harborview Sleep Medicine Center, we use existing machine learning libraries to train a predictive model for apnea. We expect results to demonstrate a correlation between cardiac regulation and sleep apnea severity.

Parkinson’s Disease (PD), a neurodegenerative disorder, features accumulation and transmission of toxic species of the protein a-synuclein in specific brain regions. Because examination of such proteins in the brain is invasive and expensive, a robust diagnostic or predictive blood biomarker for PD is strongly required. Previous studies have observed that oligomeric a-synuclein was present in the red blood cells (RBCs) of PD patients, but it did not work well as a biomarker. Because toxic forms of proteins are secreted from cells to the extracellular space in membrane-bounded vesicles called exosomes, therefore we believe that the RBC derived exosomes could be an potential biomarker for PD diagnosis. Also, isolation of specific type of exosome could be equivalent for testing the originated cells. However, there are all types of exosomes in blood released not only by the RBC but also by most cell types, particularly large fenestrated organs such as liver and kidney. To test these vesicles, we have developed the technique of immunoprecipitation to purify distinct kinds of exosomes by targeting its novel unique markers, such as the RBC-specific membrane protein CD235a, and quantifying the amount and size by nanoparticle tracking analysis. My preliminary data have shown that the antibody of CD235a can successfully target the membrane proteins on RBC membrane and its derived exosomes and can collect pure extract of exosomes by immunoprecipitation. In sum, we think the RBC derived exosomes is a promising candidate for PD diagnosis that is worth further investigation. However, the ratio of CD235a positive exosome in whole plasma is still unknown and further tests need to be done on the amount and size distribution of RBC derived exosome in a PD cohort.

Nuclear coercion rests on the threat of force to compel a demand. Some strategists contend that nuclear coercion does not work between nuclear adversaries. The theory of the nuclear revolution posits that military victory is not possible in the nuclear era, and therefore military power cannot advance political ends. Others maintain that nuclear coercion is indeed possible, and the nuclear balance of power between adversaries shapes political outcomes. This study explores whether strategic superiority generates coercive leverage in crisis bargaining. It employs a qualitative case study analysis of Soviet decision making during the Cuban Missile Crisis to test rival theories of nuclear strategy.

The North Korean nuclear crisis is severe, with North Korea having developed missiles potentially armed with nuclear weapons that can reach the continental US. However, the international response has mainly been ineffective in stopping North Korea. Additionally, South Korea’s new attitude going towards negotiation with North Korea is an important game-changer. Through this research, I plan to explore the questions of why the international sanctions have been ineffective, how South Korea’s changing attitude can influence this issue, and what can be done to solve this issue completely. For this research, I have collected information from many sources both from the US and in Korea, including books, journals, and newspapers. Some of my findings are that there are loopholes to the sanctions, especially China not enforcing the sanctions and trading key goods with North Korea, especially oil. Additionally, the Moon Jae-In administration’s new strategy towards the issue, going more towards negotiation, may be catastrophic and must stop immediately. To solve this issue, South Korea must stop doing peace talks with North Korea, as such talks were catastrophic during the past, and stay on the same page with the US to motivate China from not trading with North Korea, especially oil which is crucial to its survival, as North Korea cannot produce its own oil. This may be enough to force North Korea to denuclearize. A better solution is to assassinate the dictator of North Korea, Kim Jong Un, which will lead to disorder in North Korea as Kim Jong Un does not have a successor currently, and South Korea and the US can use this opportunity to destroy the weapons of mass destruction in North Korea. This research is crucial for maintaining the peace and security not only in the East Asia region, but also for the entire world.

Before the Battle of Lepanto on October 7, 1571, the Republic of Venice’s relations with the Ottoman Empire were tumultuous and tentative. As the most powerful Mediterranean maritime force in the 16th century, it was Venice’s mission to protect Christendom from Ottoman Islamic armies. To fight this maritime crusade Venice employed privateers and corsairs, individuals who, in exchange for payments, supplied their own vessels to police the waters of the Eastern Mediterranean in search of Ottoman vessels. Since Venice relied on trade for basic provisions, Venetian authorities approached naval aggression as a necessary defensive measure. Venice’s lack of self-sustainability meant that protecting its imperial holdings was critical to the longevity of the city itself. As Venice won the Battle of Lepanto, destroying the Ottoman fleet, Venetians regained their sense of naval supremacy. Although Venice lost the larger Ottoman-Venetian war, as in the three previous was, the Battle of Lepanto marked a pivotal moment in Mediterranean history, driving Venetians to recapture some of what they had lost and to rebuild their once vast merchant empire. Confident in their naval prowess, Venice’s merchant galleys spread far and wide across the Eastern Mediterranean to forge new trade relations with the Ottoman Empire. Through these relations, Venice portrayed themselves as the gateway to the East by supplying themselves and Western Europe with exotic goods. I argue that The Battle of Lepanto ushered in a new era of economic expansionism grounded in a Venetian sense of naval superiority that allowed Venice to end its reliance on privateering and corsairing to protect its empire.

Rather than assuming the transhistorical existence of Kurdish nationalism, this paper identifies and explains the material motivations behind the formation of the short-lived Mahabad Republic in 1946. I argue both the tribal chiefs and urban elites of Kurdish society felt compelled to break from Tehran as they, along with the rest of Kurdish society, became more connected to a wider economy than ever before. Previous political movements within Kurdish society against unjust treatment from the Iranian central government had been led by the tribal chiefs whose hegemony over the rural areas had made them powerful forces to be reckoned with. In 1946, with the tribal chiefs undermined by anti-tribal policy from Tehran, and the urban population and wealth in Kurdish society growing at a rapid rate, the Mahabad separatist movement emerged as the first Kurdish rebellion to be directed and inspired by the urban elite. Yet the success of the movement still necessitated the cooperation of the landholding tribal elite, as they provided the military organization crucial for victory. Both groups, who held the bulk of power within Kurdish Iran, were motivated by adverse treatment associated with the Iranian state, including manifest corruption, cultural oppression, and economic recession. In that context, I argue, the landholding tribal chiefs and the emergent urban elite forged a secession movement away from Iran to establish the first successful Kurdish ethno-state.

Every nation state has its foundational stories and Afghanistan is no exception. Classical historiography and national myth contend that the Durrani Empire, founded in 1747 by Ahmad Shah Durrani, marked the beginning of the modern Afghan nation-state. As the fledgling polity subsumed all of present-day Afghanistan and Pakistan in addition to parts of Iran and the Central Asian republics, it found itself the object of ‘The Great Game’ in which the expanding Russian and British empires sought to control the region. I assert that, while it is certain that 'The Great Game' and Ahmad Shah influenced the growth of Afghan nationalism, traditional historiography fails to account for the deliberate, ruler-driven work that went into the Afghan centralization project. Rather than playing pieces propelled through their early centuries on a vast geopolitical Great Game board, the Shahs of the Durrani Empire and the Emirs of the Emirate of Afghanistan determinedly enacted policies furthering their goals and visions for the state. Concurrently, British India, governed by the Council of India, sought to shape the Afghan state to suit its own needs vis-a-vis Russia and Persia. I also maintain that while the early stages of the nation building project were a response to the political and military needs of Ahmad Shah, the relative power of each state shaped the later phases. The Durrani Empire initially had a military advantage, but later British territorial annexations in India facilitated power projection further into Central Asia, thereby imposing their image of Afghanistan over its local population. I argue fundamentally that Afghan national identity was shaped through a shifting relationship with Britain as a consequence of successful as well as abortive policy decisions from both parties which, when combined with the framework established by early Durrani rulers, coalesced to give form to Afghan nationalism.

Photovoltaic (PV) electricity generation has become much cheaper in recent years and as a result is becoming a larger percentage of total energy production. However, growth is limited due to the high capital expenditure (CAPEX) required to build new PV factories with current technologies. Solution processing techniques (spray coating, roll-to-roll, etc.) to deposit thin-film absorber materials such as CuIn(S,Se)₂ and Cu(In,Ga)(S,Se)₂ represent a much lower CAPEX alternative to current PV processes. Using simple metal chloride precursor salts dissolved in polar aprotic solvents, our group has shown solar power conversion efficiencies of 13.4%, which is a world-record for solution processed CIS. Understanding the complexation chemistry of precursor salts in solution is essential to making stable solutions which produce homogeneous absorber layers after thermal annealing. Using solubility experiments and calorimetry to examine interactions between the precursors in anhydrous dimethylformamide (DMF), we were able to infer participating molecules and stoichiometry of the complexes formed in solution between the metal chlorides, thiourea, and solvent molecules. We have also made CIS absorbers under various thermal annealing conditions, and studied the resulting changes in 1) elemental composition profiles using glow-discharge optical emission spectroscopy (GDOES) and energy-dispersive X-ray spectroscopy (EDX) and 2) film morphology using scanning electron microscopy (SEM). These results represent steps forward in improving solution processing techniques for low CAPEX solar cell manufacturing which will increase the prevalence of renewable energy to combat global warming.

Werk Student Quasar Absorption Disgnostisions (Werk SQuAD), a group of undergraduate students led by astronomy professor Jessica Werk, aims to assemble a database of identified absorption features present in 230 nearby quasars. The purpose of this database is to provide astronomers studying galaxy evolution more information about the circumgalactic medium (CGM) of galaxies. The CGM is a giant halo of matter gravitationally bound to dark matter surrounding a galaxy, acting as a recycling hub for galactic outflows and accreting material. A major limitation to observing the CGM is that it is so diffuse, it is impossible to observe directly via emission. In order to learn more about the CGM, we must rely on other light sources. As light is emitted from a background quasar, the light passes through the CGM of galaxies in its line of sight as it travels to us in the Milky Way. Every CGM the light passes through leaves a sort of fingerprint, as ions from the CGM absorb some of the original light from the quasar, leaving trenches in the data. By figuring out where those absorptions happened and what ions were present, we can gain insight into what systems of gas were encountered on the quasar’s journey to us. With the use of a specialized GUI, we are able to search for ion absorption features in the spectrum. We look for recognizable signatures such as the Hydrogen Lyman series, while checking for other ion absorbers as well. When there are multiple absorbers at a particular redshift, this is often an indication that we are viewing part of a nearby galaxy’s CGM. By identifying these absorptions and linking them to particular galaxies, we are able to better understand the cycle of galaxy evolution.

With the spread of large digital painting collections, the demand for automatic theme classification has risen in both academic and commercial fields. Many researchers have investigated various techniques to implement automatic painting classification and developed several approaches to improve classification accuracy. SURF is one of the most commonly used local invariant feature descriptors for painting classification. However, the common method of classification based on traditional SURF local feature description makes the color feature information not comprehensive. Also, the feature space is high dimensional and sparse which will result in low classification accuracy, data redundancy and a time-consuming process. To overcome this drawback, we suggest a new method of classifying painting styles with bag of words (BOW) model based on the RGB-SURF algorithm. First, split RGB channels into separate images for each painting. Then, independently calculate key points and descriptor of each RGB channel using SURF and combine descriptors of each channel to obtain overall RGB-SURF feature for each painting. This approach is to compensate the loss of color feature brought by traditional SURF descriptor which mainly treats colorful images as gray images. Next, construct the visual vocabulary by reducing the number of features through quantization of feature space using K-means clustering to obtain BOW model. The histogram described by appearance frequency of the visual words is used to represent the content of the image. As a result, every image is viewed as a bag full of visual words. Finally, establish the support vector machine (SVM) classifier based on radial basis function (RBF) with the data above for training and testing. Compared to classification method based on the traditional SURF feature descriptor and other painting classification approaches, BOW method based on RGB-SURF algorithm shows the highest average classification accuracy, which means this method produces the most consistent automatic classification results with manual classification.

Anthropogenic climate change is gradually reducing snowpack and shifting the timing and volume of streamflow in the Columbia River Basin. Mountain snowpack plays a key role in the water cycle by storing water in the winter and releasing it as snowmelt runoff in spring and summer. Snowmelt and the resulting streamflow are critical for a variety of sectors: irrigation, hydropower, flood risk management, and ecosystem services, particularly regarding salmon. There is a large network of reservoirs along the Columbia River and its tributaries that water managers use to store water from snowmelt to satisfy the needs of industries and communities. Snow can also be thought of as a reservoir, as it delays the streamflow response to a precipitation event. With anticipated increases in temperature due to a changing climate, the size of that snowpack reservoir is expected to decrease. We will analyze projections of changes in the amount of water contained within the snowpack and determine the volumetric size of the snow reservoir that will be “lost” due to a warming climate. We will compare it to existing reservoirs in the western United States. As the basis for these analyses we will use an ensemble of 160 different hydrologic projections included in the Columbia River Climate Change dataset. We will relate these changes in snowpack to changes in streamflow timing. The results of this study may help inform discussions about the need for changes to reservoir operations on the Columbia River.

Microplastics are polymers < 5mm, varying in shape, color, chemical composition, and density. Manufactured plastics are primary microplastics which include pellets, fibers, and microbeads. Secondary microplastics are plastics fragmented through photodegradation and/or mechanical weathering. Research has documented microplastics in high densities (e.g., 100,000 items per m3) in marine environments, but little work has been conducted in riverine environments. Our study is focusing on the Puyallup River Watershed, located in Washington State, and its role in microplastic transport. The Puyallup River and its two principal tributaries, the White River and the Carbon River, drain a watershed of approximately 1,040 square miles and stream from several glaciers located on Mount Rainier, including the Puyallup Glacier. During our preliminary research, samples were collected monthly, both upstream and downstream of municipal wastewater treatment plants, from five cities in the lower reaches of the Puyallup River Watershed. Fibers, fragments, and foams were identified, characterized and quantified. Only 1-foam and 5-fragments were found, with the majority being fibers. The concentration of fibers, ranged from 0 to 204 fibers/L, with an average of 22-fibers/L in each sample collected. Results were statistically inconclusive to determine if wastewater treatment plants were a point source of plastic pollution to the Puyallup River Watershed, although more fiber numbers were located upstream than downstream at most sites.

Understanding how extracellular environments facilitate the differentiation of stem cells holds much promise for the field of regenerative medicine. Non-muscle myosin II (NMII) plays an important role in cell morphology and also generates forces that alfter biochemical signalling. It has been shown that the activity of NMII controls mechanoreceptors and integrins facilitating stem cell fate. More specifically, mechanotransduction of transcriptional coactivators YAP/TAZ facilitate differentiation of mesenchymal stem cells (MSCs). YAP and TAZ are responsible for upregulating genes associated with stem cell differentiation. Under external stresses mesenchymal stem cells differentiate into osteocytes whereas softer extracellular conditions favor the differentiation into adipocytes through mechanotransduction of YAP and TAZ.To further explore the role of physical forces determining the fate of stem cells, we used a computationally designed self-assembling homo-polymer called 2E01, generated by the Institute for Protein Design (IPD). Mechanical stress and the physical activity of NMII can be mimicked by controlled expression of the length of the E01 protein fiber. We introduced the 2E01 gene under a doxycycline-inducible promoter into the AAVS1 "safe harbor" locus of the induced pluripotent stem cells (iPSC). Expression of the E01 fiber in iPSCs lead to changes in colony morphology and subsequent differentiation of those cells, suggesting that changing the morphology of cells can change their fate. I want to see if I can use the 2E01 fiber as a tool to accelerate differentiation from IPSCs to neuronal cells and cardiomyocytes. In addition, we expressed 2E01 in mesenchymal stem cells, a cell type currently used in lab, and observed the activity of YAP and TAZ as an indicator of differentiation. Utilization of the 2E01 fiber could be benefical to the field of regenerative medicine as a directed agent of physical manipulation towards desired stem cell fate.

In Washington State, the goal of the Washington Fish and Wildlife Department’s gray wolf (Canis lupus) conservation and management plan is to not only help wolves naturally re-establish a sustainable population across the state, but also to reduce the conflicts with humans, livestock and other wildlife. A successful implementation of this requires us to understand how the public values wolf management and what factors could shape this kind of value. The purpose of this study is to examine Washington State residences’ willingness to pay for wolf-livestock coexistence projects from a statewide survey including an attribute-based choice-experiment. Willingness to pay shows the maximum amount of money an individual wants to sacrifice to procure a good or service, it can be influenced by personal interests, preferences, incomes and demographic background. In this study, I explore the survey data using random utility maximization (RUM) models to identify both heterogeneity and homogeneity factors that may affect Washington residents’ willingness to pay for wolf-livestock coexistence. I also apply Machine Learning to select covariates that help to generate highly accurate prediction models. An individual’s willingness to pay for wolf-livestock coexistence projects is expected to increase as their income, knowledge about wolf conservation status, and attitudes to wolf conservation increase. The aims of this study are to have a comprehensive understanding of people’s willingness to pay for projects designed to promote human-wolf coexistence and to provide implications for conservation groups and organizations to find alternative funding sources in the future.

The North American beaver (Castor canadensis) is a keystone species and ecosystem engineer, capable of modifying the landscape and creating diverse habitats for other species. Through dam-building, beavers impound streamflow and create ponds and wetland complexes behind dams. The presence of beavers has been shown to increase biodiversity, reduce downstream flooding, and improve water quality. While beavers alter landscapes greatly, often in ways beneficial to native habitats and species, their dam-building can also create conflict with human land-use and infrastructure. One way to reduce human-beaver conflict is to adopt non-lethal approaches such as the use of pond leveler devices. Pond levelers, consisting of a pipe through the beaver dam with a cage around the inlet, control the water level of the pond by establishing a desired level while allowing beavers to persist, thereby reducing flooding. Little observational evidence exists on whether pond leveling devices create fish barriers or otherwise impede fish passage for migrating salmon. The objective of this research was to evaluate whether migrating salmon can pass through or around beaver dams fitted with standard pond leveling devices, under high flow conditions. We tested this by observational analysis collected from five pond levelers on Big Spring Creek, King County, Washington during the 2017 autumn salmon migration. Target migrating species include Chinook (Oncorhynchus tshawtscha) and Coho salmon (Oncorhynchus kisutch). During prolonged precipitation events it was determined that stream stage overtopped dams, providing unhindered passage in our study areas. Additionally, during the 2017 migration period, over-dam stream velocity and through-dam velocity (i.e. within the pipe) were passable by salmonids during 100% of the flows we observed.

The first-year population, with students transitioning from high school to college, is full of novel experiences. These experiences, be they academic, social, etc., influence the well-being of the student. The purpose of the study is to understand the first-year experience in a data-driven manner to create a cornerstone for institutional change. Although replicating a previously piloted study at Carnegie Mellon University in Spring 2017, this study extends focus to investigating stressful life events of first-years. Over the 2018 Winter and Spring quarters, a participant sample size of around 200 UW first-year undergraduate students (around 50% pre-/engineers) contribute data to the study. Data consists of both active and passive collection methods: participants actively respond to Qualtrics surveys, with questions investigating stressors, and passively via our phone software and FitBits. The two quarters of this study will yield tangible data that can be analyzed to advance the science of behavioral health and trauma. This data is unique in providing a picture of student behavioral changes after stressful experiences. Additionally, this advancement in science can become a basis for institutional change for student wellness. As the first-year population is only a slice of the overall student experience, we hope to expand this study further by encompassing the graduate student experience and the full four-year college experience in addition to a larger sample size.

Active learning has often been described as the key to increase retention rates among undergraduate STEM majors because students are engaged in meaningful learning. Common activities associated with active learning include completing worksheets in groups, clicker questions, or discussion questions followed by reporting out by random call during class. Random call differs from cold call as the instructor allows discussion time where students can work together to formulate an answer prior to random call. However, previous research has demonstrated that implementing active learning principles may increase student anxiety. Specifically, answering questions in class, either by volunteering or random call, may cause the highest level of anxiety for students. We have conducted a study investigating how student demographics impact the likelihood of students responding to random call. Our study was conducted in an Introductory Biology course with 576 students, in a lecture-hall style classroom. The instructor utilized random call, then recorded which students either gave a response or passed the question when called upon. A binary logistic regression was performed to create a best fit model in which student demographics could predict which students were more likely to answer or pass. Students who are the first in their family to go to college (1st generation students) were 57% less likely to respond to random call questions compared to other students, even when controlling for incoming GPA. This result indicates that students with diverse demographics participate differently in some active learning activities and further investigations are necessary to determine if this has an impact on their learning. To bridge this “responding” gap between 1st generation and Non-1st generation students, instructors should implement additional techniques such as group random call as opposed to individual random call to increase student comfort during random call, thereby increasing the likelihood of students responding regardless of student demographics.

Pregnant women often get their bellies touched without their permission by people ranging from family members, to coworkers, to strangers. While usually well-intentioned, people who touch pregnant bellies are unaware that their actions may be unwanted and invasive. Previous works, such as Asta Roseway’s Printing Dress, have shown that wearable computing can bring attention to social issues by provoking discourse. Those works lead us to our wearable design that highlights the issue of personal space for pregnant women. We implemented a maternity shirt that reacts to inappropriate touches upon contact in various ways, such as displaying messages, vibrating, and setting off an alarm. We plan to deploy this shirt on experimental participants and gather qualitative data in addition to the quantitative data collected through the shirt about when and where touches occur. Moreover, findings from the experiment will provide insight into pregnant women’s experiences, and how to design wearables that benefit to pregnant women. Our future goal is to have the shirt deter the toucher as they approach the belly. Through this interactive design piece we hope to raise awareness and provoke conversation around themes of consent, inappropriate touching, and women's bodies.

 Fault zones are dynamic structural regions in the Earth’s crust that can constrain fluid flow in the subsurface. The presence of fluids in fault zones changes local stresses and can result in coevolving relationships between fluid migration and faulting. Because of this complex behavior, fault zone architecture is difficult to define, but two broad regions of deformation can be differentiated by material differences to describe permeability and other fluid-rock relationships. The fault core is the narrow, highly pulverized, often impermeable area of the fault closest to the slip surface. The damage zone is the wider, fractured, outer region of the fault which can allow fluid flow through fault-related cracks in the host rock. Although these these definitions describe general fluid-rock properties across fault zones, they do not fully capture the complex nature of fluid migration and compartmentalization in faults. Because fluids are difficult to observe in the Earth, mineral precipitates can be used as geochemical tracers for fluids. We analyzed carbonate precipitates in fault rocks from the fault cores and damage zones of three normal faults in Central Italy to characterize the fluids present in the area and the structural influences of fault architecture on fluid compartmentalization. Preliminary ¹⁸O and ¹³C standard stable isotope analysis aided initial fluid characterization and informed carbonate powder sampling for D47 clumped isotope analysis, which allowed us to reconstruct fluid temperatures and compositions. We present a spatial analysis of fluid compositions relative to structural units within the three fault zones.

At one point or another, every student is faced with some sort of academic failure that can in turn have negative impacts on self-esteem or future academic performance. Being able to overcome such obstacles requires resiliency and the ability to view failure as a learning opportunity. Growth Mindset (GM) interventions aim to shift a student’s perception of intelligence as a quality that can be developed over time and enhance their approach to overcoming barriers. Originally, the GM was developed as an evidence-based intervention to be delivered by trained professionals. However, bringing this intervention into the real-world calls for a more feasible and accessible model. To bridge this gap, the current study utilizes the role of teachers as a valuable resource in building capacity within schools to attain sustainable, long-term goals regarding student success. The purpose of our research is to explore how a GM intervention delivered by teachers affects students’ beliefs about the brain’s ability to change (neuroplasticity). This project utilized a randomized control design with longitudinal follow-up to evaluate the efficacy of the GM intervention in comparison to curriculum as usual delivered in a rural district in the Pacific Northwest region. At two separate time points, middle and high school students completed an online self-report survey that assessed three constructs: theory of intelligence (whether intelligence can be changed), effort beliefs (the relationship between effort and outcomes), and learning goals (goals towards improving academic abilities). We hypothesize that students assigned to the intervention would show more positive implicit attitudes towards malleable intelligence, beliefs about effort, and learning goals. By understanding how students view themselves within an educational context, we can improve the measures taken to further engage and empower students. Future research should evaluate the quantitative outcomes of academic performance (i.e. grade point average) in relation to a GM intervention.

Environmentalism has often been considered a moral commitment. However, this paper investigates the hypothesis that environmentalism is not just a moral commitment, but a highly logical economic commitment. I argue that environmentalism is not contrary to economic motivations: instead, states fund their departments of ecology when they stand to gain economically from doing so. This paper compares the percentage of each state’s budget that went towards funding their ecology department to the tax revenue generated by two types of state resources: the outdoor recreation economy in each state and each state’s proven crude oil, shale gas, and natural gas reserves. When states receive more tax revenue from the outdoor recreation economy, they allocate a larger percentage of their budget to ecology departments. On the other hand, the presence of proven crude oil, shale gas, or natural gas reserves will decrease the amount of funding for state ecology departments because states generally gain more economically from the exploitation of those resources than from the outdoor recreation economy. Broader implications of this paper include the conclusion that the best way to ensure that states will be environmentally conscious is to make it economically advantageous to do so as states act primarily on economic incentives. This study uses data sets from Ballotpedia and American FactFinder and is supplemented with data from the National Conference of State Legislatures and the Outdoor Industry Association.
 

On top of being iconic symbols of climate change, glaciers integrate year-to-year precipitation and temperature variability, which can mask their response to a climatic trend. For this reason, it is vital to identify the variability in their records to better detect regional climate change. With time-varying sea-level pressure (SLP) and sea-surface temperature (SST) fields, we examine the influence of natural climate variability on 14 glaciers in the North Atlantic region by using a statistical method called dynamical adjustment. The SLP and SST fields each explain 50-60% of variance in the winter mass-balances and 30-40% in the summer mass-balances of the maritime glaciers. The continental glaciers are less closely linked to oceanic variability, with SST explaining roughly 30% of variance in winter and summer mass-balances. The glaciers located further south fluctuate with the North Atlantic Oscillation (NAO) in the winter, while glaciers near the Arctic show influence from the Atlantic Multidecadal Oscillation (AMO) in the winter. To investigate how this variability affects glacier trends, adjusted mass-balances are compared to observational mass-balances with no signs of variability forcing trends. The observed and adjusted summer mass-balance trends of the southern glaciers are significantly negative, while the observed and adjusted winter mass-balances of the northern glaciers are significantly negative. This indicates that winter trends are more likely to emerge in glaciers near the Arctic, while summer trends are more likely to emerge in glaciers further south which is consistent with surface temperature time of emergence for global warming.

In recent years, researchers have dedicated much effort to overcoming the ~250nm spatial resolution limit of light in order to reveal biological details that have been obscured by diffraction. A new form of super-resolution microscopy called expansion microscopy (ExM) has enabled ~65nm image resolution or better by physically expanding fixed specimens in a swellable hydrogel polymer. While ExM allows researchers to achieve high resolution with standard microscopes, the technique requires the use of water-immersion lenses, rather than higher-resolution oil-immersion objective lenses, when imaging more ~5 µm deep due to spherical aberrations caused by refractive index mismatch with oil lenses and water-based hydrogels (n=1.5 vs n=1.3). Oil-immersion lenses also collect more signal than water-immersion lenses, enabling higher signal to noise with oil-immersion lenses under the same excitation conditions. I have developed an index-matching technique that significantly reduces spherical aberrations when imaging with oil lenses and expanded specimens, facilitating improved resolution (~1.12x lateral improvement and 1.5x axial improvement) for depths of up to 25 μm. Expanded specimens are index-matched by simply incubating the specimen in a high-index iohexol solution which equilibrates with the specimen in approximately 18 hours. A modest ~17.5% shrinkage of the hydrogel is produced as a result in the current implementation, which I can in principle compensate for by tuning the hydrogel recipe to achieve a slightly higher expansion factor. I found that the iohexol solution on its own accelerated the rate of fluorophore bleaching and led to some fluorophore quenching. However, the addition of the triplet-state quencher n-propyl-gallate effectively mitigated this chemical bleaching. Ultimately, this iohexol-facilitated index-matching procedure not only combines the utility of ExM and the high collection efficiency of oil immersion objectives but allows researchers to use common chemicals and readily available instruments to obtain images that reveal a previously inaccessible wealth of information.

A common post-translational modification of microtubules is glutamylation, which is a covalent bond between glutamic acid and a residue on the C-terminus of tubulin. Microtubule glutamylation is catalyzed by tubulin tyrosine ligase-like (TTLL) enzymes which modify microtubule functions such as, regulation of centriole stability, neuronal outgrowth, and cilia motility. How these enzymes regulate glutamylation remains unsolved. Caenorhabditis elegans (C. elegans) have five glutamylating enzymes (TTLL-4, -5, -9, -11, and -15) and lack glycylation, making them a good model for studying the function of TTLL enzymes. All five TTLL enzymes have an extended TTL domain suggesting glutamylation activity, TTLL-4, -5 and -11 have cation-enriched regions (cMTBD) which can make direct contact with microtubules, TTLL-9 and -15 lack cMTBDs and may require additional mediating factors to interact with microtubules. In a previous C. elegans study, ttll deletion mutations showed that the loss of an individual TTLL enzyme does not affect embryonic viability or spindle function, which is most likely due to redundancy. However, the triple mutation: ttll-4(tm3310); ttll-11(tm4059); ttll-5(tm3360), results in a male mating deficiency which suggests that glutamylation is required for proper microtubule function during male mating. To further investigate the role of tubulin glutamylation in male mating, we are generating mutant strains that contain deletions in multiple TTLL enzymes and a him-9 mutation to increase the incidence of males. Genetic crosses between hermaphrodites containing mutations in the TTLL enzymes and a male containing the him-9 mutation in the background will be performed. Phenotypic assays addressing the efficiency of male mating and other phenotypes will then be performed in the mutant strains.

Previous research on JNK-mediated stress signals demonstrated that stem cells in the posterior midgut of Drosophila Melanogaster only undergo compensatory proliferation or apoptosis. However, our group discovered that the stem cells can also undergo the process of basal extrusion and dissemination, resulting in the cells being eliminated from the tissue into the hemocoel, the blood containing intertissue body cavity. The JNK signal promotes the cells to exit the epithelium of the gut, move through the muscle layer, and be released to the hemocoel, which resembles the process of metastasis in human cancer. In order to understand the mechanism of this extrusion process, we carried out an RNA Interference (RNAi) screen and sought to find genes that are necessary for the stem cell extrusion in the JNK activator, HepCA, expressed flies. We used the ESG-GAL4, UAS-GFP, TUB-GAL80TS(EGT) genetic system to study the knockdown effect from the RNAi of each gene. We selected 215 lines of kinases and phosphatases of flies to test if the knocked-down gene results in suppression of cell elimination by the JNK stress signal. After 4 days of inducement, which is the sufficient time for the JNK signal can promote complete extrusion of the intestinal stem cells, the intestines were dissected, fixed, mounted, and examined with a fluorescent microscope for any presence of stem cells. Through this screen, we could find 33 lines that had strong suppression of cell elimination, 39 lines that had a moderate effect. Our results suggest that the knocked down genes with strong suppression of cell elimination are involved in the mechanism of basal cell extrusion, and future research dictates an investigation into the molecular function of each of these genes.

Wintertime air pollutant emission trends are poorly understood in comparison to emission trends in the summer mostly due to a lack of available and analyzed data on precursor air pollutants in the wintertime. This creates uncertainty in current atmospheric chemistry models. “WINTER 2015” was an aircraft research campaign launched in February 2015 that was executed to measure pollutant concentrations in addition to other data. All of which were relevant to the transportation, distribution, and chemical kinetics of pollutants and aerosols across the northeastern United States. The colder temperatures as well as lack of available sunlight have significant effects on chemical kinetics in the atmosphere. In particular, during the daytime, nitrogen oxides tend to produce ozone (O₃), a criteria pollutant regulated by the U.S. EPA, but nitrogen oxides destroy ozone at night. Longer nights, and lower sunlight during the day may mean that nitrogen oxides net destroy ozone for much of the winter. Current air quality models do not accurately simulate the nighttime chemistry of nitrogen oxides. I am examining the wintertime relationship between nitrogen oxides and O₃ using data taken in the WINTER 2015 campaign to gain insights into the extent to which wintertime nitrogen oxide emissions produce or destroy ozone. This information will then improve atmospheric chemistry models that are used to forecast air quality in various regions. It is expected that in the wintertime, the amount of reactive nitrogen oxide is limited relative to hydrocarbons. This nitrogen limited regime would mean that reactive nitrogen oxides have a greater role in the destruction of ozone, than the production of ozone.

Aerosol particles, solid or liquid particles suspended in the air, can affect Earth’s climate by scattering and absorbing sunlight. PM_2.5, particles less than 2.5 micrometers in diameter, are largely responsible for degraded visibility and easily traverse respiratory system pathways causing adverse health effects in humans. Often, a majority of PM_2.5 is composed of organic matter formed through photo-chemical reactions of hundreds of volatile organic compounds (VOC). This process depends on nitrogen oxide radical (NO_X = NO + NO₂) concentrations in the atmosphere, now predominantly contributed by anthropogenic emissions. NO_X and VOC react to produce organic nitrates, thought to be significant contributors to PM_2.5, but for which measurements are generally lacking. My project involves developing a concrete assessment of the role of organic nitrates as contributors to PM_2.5. I am developing an analytical method to thermally desorb organic nitrates from atmospheric particles collected on filters and promptly decompose them into nitrogen dioxide (NO₂). The resulting NO₂ is measured with a Cavity Attenuated Phase Shift (CAPS) spectroscopy instrument. I am establishing whether there is a direct correlation between the concentration of organic nitrates in PM_2.5 and desorbed NO₂. The goal is to quantify organic nitrates without individually measuring each of the likely hundreds present in the ambient atmosphere. Moreover, the thermal desorption process provides information on the physical properties of organic nitrates, such as effective saturation vapor pressure, needed for air quality computer models to accurately simulate their contribution to PM_2.5. As a result, I will help develop a better understanding of how natural and anthropogenic emissions affect the composition of the atmosphere by allowing assessments of how PM_2.5 levels have changed in response to NO_X emission reductions by the Clean Air Act.

Plasma, the fourth state of matter, is created by introducing a gas - in this case, helium - to an electric field. This field ionizes the helium atoms, which in turn ionize other molecules, creating a wide variety of highly reactive species. Previous work at Edmonds Community College demonstrated the efficacy of an atmospheric pressure plasma jet (APPJ) in killing endospores of Bacillus atrophaeus for the purpose of spacecraft sterilization for NASA (Bernard et al., 2017). With increasing rates of antibiotic resistance, there is interest in using an APPJ in healthcare settings to eliminate harmful pathogens and therefore promote wound healing. However, given its destruction of endospores, it is unclear if the APPJ would damage living tissue. The purpose of this research was to analyze the effect of an APPJ on multicellular eukaryotic organisms. The impact of different exposure times of the APPJ upon both germinated and ungerminated Zinnia elegans seeds, and the effects on plant growth, was studied. The optimal exposure time for germinated seeds was between one and two minutes, while treatments greater than 2 minutes may increase germination rate.

Retinal pigment epithelial cells (RPE) normally reside on the photoreceptor side of the retina; however, they can become dislodged as a result of trauma and surgery. A condition called proliferative vitreoretinopathy (PVR) can occur when these cells undergo an epithelial to mesenchymal transition (EMT) and form contractile scar tissue that results in retinal detachment. PVR is a common complication of retinal detachment surgery occurring in about 10% of cases, and there is currently no effective non-surgical treatment. In-vitro models of PVR have previously been created from surgically excised tissue, but these cultures are difficult to create and maintain. However, one recently isolated primary cell line, fRPE #51, has been noted to spontaneously form contractile bands similar to those found in other PVR models. The goal of this study is to characterize this cell line to determine if it has the potential to serve as a reliable in vitro model of PVR. To fully characterize this fetal RPE cell line, we stained the cells for known markers of PVR. We also completed several assays for proliferation ability of the cells to assess for functional changes consistent with PVR. Finally, in order to characterize changes to the structure of these cells, we assessed the formation of tight junctions by measuring transepithelial resistance (TER) of cells grown on filter membrane inserts and performed transmission electron microscopy to look for other structural changes. Our preliminary data indicate that the candidate cell line fails to establish normal tight junctions. In addition, an initial proliferation assay demonstrates enhanced ability of the candidate cell line to proliferate and migrate in comparison to control lines. Establishing an in vitro model of PVR will allow for screening of potential drugs and other small molecules that may inhibit the formation of PVR.

Incorporating research into the undergraduate experience provides students with opportunities to develop transferable skills by engaging in the process of science. Historically, most students who have participated in research did so through apprenticeships in faculty research labs. However, the apprenticeship model limits the numbers of students who have access to authentic research experiences early in their academic careers. In contrast, Course-based Undergraduate Research Experiences (CUREs) engage larger numbers of students in firsthand research investigating questions that are relevant to the scientific community. CUREs provide access to undergraduates who might not otherwise have the awareness, confidence or social capital needed to pursue scientific research opportunities through traditional pathways. The University of Washington (UW) Introductory Biology CURE provides students with authentic research experiences studying the evolution of antibiotic resistance in E. coli through credit-bearing lab sections. We investigated the CURE’s impacts on students’ personal development as scientists along with their mastery of fundamental biological concepts and principles of experimental design. At the beginning, middle, and end of the first two quarters of the Introductory Biology series, CURE and non-CURE students completed concept surveys to detect changes in their: (1) attitudes about science and their own abilities, (2) competency in experimental design, and (3) conceptual understanding of key evolutionary concepts, such as the relationship between genotype, phenotype, and fitness. Although all students in this study attended the same lectures, we anticipate that students who participated in the CURE lab modules will attain greater gains relative to their peers enrolled in the non-CURE labs. Specifically, we predict that CURE students will demonstrate greater understanding of the mechanisms of evolution via natural selection, and improved ability to design controlled experiments and reason scientifically. In addition, we expect that alumni of the CURE will gain an increased sense of belonging and enhanced retention in science-related fields.

Understanding the principles that underlie physiological problems can help students succeed in the mastery of a wide range of physiology topics. Understanding the principle of flux, which governs pressure gradients, can greatly improve a student’s ability to solve problems related to bulk flow and pressure in a variety of physiological systems. In general terms, the principle of flux describes the rate of movement of a substance from one compartment to another. It is defined as the magnitude of the driving force (gradient) divided by resistance. We examined how students in an introductory physiology class think about flux in the context of a pressure gradient within the cardiovascular system. We began by incrementally refining a variety of gradient-related questions through successive rounds of think-aloud interviews with individual student volunteers. Using these responses, we generated a cardiovascular pressure gradient question that elicited a wide variation of student answers. We collected responses from 200 introductory physiology students both before and after relevant course content to be sure our question captured both novice and advanced reasoning. We examined the responses and constructed a rubric to categorize student responses into a hierarchy of response sophistication and completeness. Generally, level 1 represents the most novice responses, while level 5 represents the most advanced. In our rubric, level 1 answers relied on vague reasoning relating to homeostasis, equilibrium, or intuition. Responses categorized at levels 2 and 3 showed an understanding of the components that contribute to pressure without successfully identifying how they connect to changing pressures. Lastly, answers at levels 4 and 5 showed an understanding of these components as well as the ability to successfully relate them to changes in pressure. Identifying patterns in student responses to a pressure gradient problem can give instructors a starting point from which they can target common misconceptions to ensure conceptual mastery in their classrooms.

This project seeks to understand tidal circulation between Puget Sound and the Pacific Ocean using data captured by sensors on board Washington State Ferries traveling across Admiralty Inlet. As the most important passage between Puget Sound and the Pacific Ocean, understanding circulation across Admiralty Inlet is critical to monitoring water quality in Puget Sound. Data from this research is being used by the Washington State Department of Ecology to manage water quality issues such as nutrient enrichment, algal blooms, dissolved oxygen concentrations, and transport of toxic chemicals across the region. In addition to managing existing data, my role has been to develop a tidal-energy dissipation map of Admiralty Inlet. While site specific energy dissipation has been calculated in areas of Admiralty Inlet, a cross-channel model has never been developed. Understanding tidal-energy dissipation at the mouth of Puget Sound will benefit future large-scale tidal-energy research by assisting tidal-energy forecasting, characterization, and assessment.

Oncolytic adenoviruses such as serotype 5 adenoviruses (Ad5) selectively infect and destroy cancer cells and are widely used in preclinical and clinical trials for gene therapy. However, Ad5 has many downsides including preexisting anti-Ad5 immunity in humans, and the Ad5 receptor (CAR) is known to be down regulated in many aggressive tumors. Species B adenoviruses which use a different receptor than CAR are an alternative which shows great promise. These vectors avoid the immune response against Ad5 and show different cell tropism. Our lab has identified desmoglein2 (DSG2) as the main receptor for a group of species B adenoviruses, including Ad3. DSG2 is an epithelial junction protein and is highly expressed in malignant tumors. During Ad3 infection, binding of Ad3 fiber to DSG2 triggers the transient opening of these intercellular junctions and thus supports the lateral spread of the progeny virus. Our lab has recently developed an Ad3 fiber knob mutant (Y250F) which has an enhanced affinity to DSG2. We have shown that an increased affinity is correlated with a stronger ability to open these junctions. In this study, we developed an Ad3 based oncolytic vector containing fibers with enhanced affinity to DSG2 (> 400x higher than wild type Ad3.) We developed this vector using PCR site-directed mutagenesis and cloning the recombinant gene in E. coli. By inserting our gene into a Ad3 plasmid it allowed us to transfect the plasmid into human embryonic kidney cells (HEK 293 cells) and to amplify and recover the mutant oncolytic virus. We are working on in vitro experiments and in vivo tumor xenograft models to test our hypothesis that the oncolytic virus with an enhanced affinity to DSG2 will be translated to a significant improvement to the spreading of progeny virus, and thus a significant improvement to the effectiveness of oncolytic virotherapy.

HRI is a serious health risk for agricultural workers that can result from prolonged exposure and overexertion in hot temperatures. The four different types of HRI in increasing severity are heat rash, heat cramps, heat exhaustion, and heat stroke. These conditions are preventable using simple approaches such as proper hydration and limiting one's time in the sun. To better equip agricultural supervisors and safety trainers responsible for conveying heat safety to their workers, I collaborated with members of University of Washington’s Pacific Northwest Agricultural Safety & Health (PNASH) Center to develop a modular flipbook that will serve as training material, covering the following topics: symptoms, risks, and treatments, clothing, hydration, and other preventative measures; as well as where and how to cool off in the home and community. I helped advance this project by taking the lead on the production of the flipbook content under the direction of the Research Scientist. I collated images, researched instructional designs, and developed prototypes of the flipbook, as well as edited the written instructions for facilitators. The educational activities in the book consists of an interactive portion, guiding questions for the facilitator to pose to the group, role-play scenarios, take-home points to reinforce the educational messages, and 3-dimensional educational charts. Modules also contain a “Knowledge Evaluation” section with questions for the facilitator to ask participants both before and after the activities to gauge their change in knowledge and to ensure the material has been understood. As a final product, the flipbook will be a portable and convenient resource for safety trainers to use in the field. My goal is to ultimately make this flipbook accessible to the general public, as it is not only a great safety resource for agricultural workers, but also for their families and surrounding community.

Computer science and neurobiology have an undeniable entanglement with one another in the 21st century with the advent of advanced artificial intelligence and attempts to understand the black-box model of a brain. However, most neurobiology research has revolved around understanding existing behaviors in large animals, with commonly researched organisms including zebrafish and mice. Introducing novel behaviors to animals in a controlled environment is undeniably attractive in modern neurobiology. With the use of mass data-collection in the online Aquarium lab environment, this study shows the potential to model and produce novel behaviors in Hydra vulgaris (freshwater anemones with simple nervous systems). We aim to create a high-throughput, data-oriented, model for gene-based behavior analysis and editing in neurobiology research. By creating a single controlled environment to perform all research jobs on mass-produced H. vulgaris strains with clockwork husbandry, extraneous factors affecting the organisms are significantly reduced. By taking data on the success of every modification of these Hydra, we can model the effects of specific factors on these animals and progress toward creating a model organism for neurobiology research akin to knockout mice in medicinal genetics. With these methods we have been able to produce a significantly more efficient process of gene editing in Hydra and with several different kinds of DNA integrants. Over the long term, the wide availability of the online Aquarium lab can yield the discovery of unknown trends in genetic knockouts and the discovery of novel behaviors through analysis of all data collected in this controlled environment. Here we highlight successes thus far and future developments necessary to make this system a viable model for gene-based neural engineering over this century.

River ecosystems depend on services salmon populations provide. Coho salmon, Oncorhyncus kisutch, supply valuable nutrients for mammals and birds and offer economic benefits for the Pacific Northwest. Salmon rely on water quality in freshwater streams during successful seasonal spawning. However, for over the past 15 years, research determined that urban stormwater results in the mortality of Coho salmon. Exposure to urban stormwater is toxic to Coho salmon, killing them in hours. This phenomenon is known as pre-spawn mortality (PSM), and it kills salmon before they reproduce. If this phenomenon continues, Coho salmon could go extinct. Previous studies have linked highway runoff and pre-spawn mortality. However, they indicate that basic water quality parameters such as temperature and pH and “typical” stormwater toxicants such as metals and pesticides are not the cause of PSM. Current hypotheses point to an unknown organic contaminant that is linked to urbanization and is probably present from roadways or cars. Previous studies have also shown that bioinfiltration of stormwater through a mixture of sand and compost can protect Coho salmon. The goal of this study was to investigate removal of organic contaminants in a pilot-scale compost-amended bioswale (CABS). The pilot-scale CABS was based on a field-scale bioswale that is operated by WA DOT and located on SR-518. In this study, we developed methods to extract water with suspended sediment (whole water), as well as extract filtered water and total suspended sediment (TSS) separately. Whole water and filtered water were extracted by solid phase extraction (SPE), using Infinity® SPE cartridges. TSS was measured using EPA Method 160.2, and captured solids were extracted with methanol. Extracts were then analyzed by liquid chromatography-high resolution mass spectrometry. These methods were then applied to evaluate removal of organic contaminants in the bioswale, including performance at multiple hydraulic retention times.

Diversity structures within organizations (e.g., diversity awards, diversity training) can create illusions of fairness: the perception that a company is treating all employees equally because of the mere presence of diversity promoting intiatives without confirmation they are being enforced. This leads to both minority and majority group members perceiving organizations as more procedurally just and less discriminatory even in the face of contradictory evidence. This research expands upon such findings by examining how diversity awards influence what types of information people use in determining if sex-based discrimination disadvantaging women is occurring at an organization. Preliminary analyses show that individuals exposed to diversity awards (vs. control condition) are less likely to perceive sexism-disadvantaging women occurring within a company. Additionally, diversity structures lead women and men to seek out different types of information: women are more likely to perceive information relating to formal discrimination as more informative whereas men are more likely to perceive information relating to informal discrimination as more informative. These findings provide insight into what types of information regarding discrimination are acknowledged versus ignored, and they reinforce prior findings that diversity initiatives lead to the perception of a less discriminatory workplace without actual evidence affirming these beliefs.

 Microbially Induced Calcite Precipitation (MICP), or bio-cementation, is a bio-mediated soil improvement process that can improve the engineering properties of granular soils through the precipitation of calcite on soil particle surfaces and contacts. In the urea hydrolysis driven process, soil microorganisms containing urease enzymes can catalyze a hydrolysis reaction that degrades urea, producing total ammonium, dissolved inorganic carbon, and hydroxide ions. In the presence of sufficient soluble calcium, the resulting carbonate production can supersaturate solutions with respect to calcite and initiate precipitation. The process has shown significant promise as an environmentally-conscious alternative to traditional ground improvement methods, which oftentimes rely on high mechanical energy and energy-intensive materials to improve soils. Despite many recent advances in MICP, environmental concerns regarding the fate of nitrogen by-products have remained largely unaddressed. In this study, soil column experiments were performed to examine the transport, removal, and transformation of nitrogen by-products following MICP. Columns were 7.6-cm in diameter, 17.8-cm long, and contained a poorly-graded sand material. Soil columns received identical treatment solution injections over 14 days targeting a post-treatment calcite content of 4% to 5% by mass. During treatments, non-destructive geophysical measurements were completed to monitor changes in soil stiffness and pore fluid compressibility resulting from carbonate degradation. Aqueous samples were obtained from all columns in time to examine changes in solution chemistry related to microbial urea hydrolysis, calcite precipitation, and ammonium sorption and transport. Following cementation treatments, columns received rinse injections of differing ionic strengths and pH values to investigate the effect of rinse solution chemistry on by-product removal. The results of this study will address critical knowledge gaps currently limiting practical application of MICP technology and will guide future efforts to model the transport and removal of ammonium by-products following bio-cementation.

Interactions between HIV-1 and dendritic cells (DCs) have been suggested to play a role in HIV-1 pathogenesis. DCs are antigen presenting cells that take up, process, and present foreign material to T-cells. Previous research suggests that HIV-1 can exploit this process by binding to DCs, allowing HIV-1 virions to relocate to lymph nodes where infection of T-cells can occur. HIV-1 mediates this interaction through binding of the HIV-1 envelope glycoprotein (Env) to DC-SIGN, a glycan binding protein located on the surface of DCs. Env contains a high amount of oligomannose glycans, enabling Env to act as a binding partner for DC-SIGN. Due to high sequence variation, HIV-1 strains exhibit variability in glycan presentation. A gap remains in our knowledge of where DC-SIGN binding occurs and how glycan presentation across various isolates modulates these interactions. In this study, we applied a combination of biophysical and structural approaches to characterize Env:DC-SIGN interactions across multiple HIV-1 strains. Biolayer interferometry experiments measuring binding affinity demonstrate that DC-SIGN binds with strong affinity towards Env from different isolates. This suggests that DC-SIGN is capable of recognizing different oligomannose glycan presentations and may not have a well defined epitope. However, preliminary results using electron microscopy illustrate that Env glycoprotein structure can be disrupted and altered via binding to DC-SIGN. This appears to be an isolate-specific response, as some strains remain unchanged. Using single particle approaches, we identified potential epitopes in heavily glycosylated regions of Env where additional densities are attributed to DC-SIGN. We infer that in addition to binding HIV Env, DC-SIGN may shield key neutralizing epitopes within these glycosylated regions. Our results provide further insight into the interactions that occur between HIV Env and DC-SIGN, and suggest a mechanism where HIV-1 hijacks DC’s normal immune function allowing HIV-1 trafficking while shielding neutralizing epitopes.

Oil-spills are a widespread hazardous environmental issue, often caused by mistakes when drilling or transporting crude oil. The effects are devastating to the ecosystem. There are very few ways to quickly clean up an oil spill efficiently, at low cost and without additional environmental damage, as often they are cleaned by using expensive chemical dispersants. We conducted research on an environmentally friendly and inexpensive solution to this problem by using pearl oyster mushroom mycelium. The pearl oyster mushroom has a lignin decomposing basidiomycotina that produces a set of extracellular ligninolytic enzymes that have bioremediation properties. Our hypothesis is that, oyster mushrooms can be used to clean oil spills. We cultivated the mushroom mycelium in straw on trays with different amounts of oil on them. We grew this in a greenhouse with controlled temperature and allowed 4-6 weeks for the mycelium to eat the oil. We are currently observing the results. After 6 weeks, we will filter out the remaining hydrocarbons with a solvent and determine if the mycelium reduced the amount of hydrocarbons or consumed them entirely. Our anticipated results are that the mushroom will clean up the oil in six weeks. For future work, we plan on conducting this same experiment but in a salt water environment to explore applications for mycoremediation in a simulated ocean environment.

The dinoflagellate Alexandrium sp. is a source of paralytic toxins in Puget Sound shellfish and a potential cause of paralytic shellfish poisoning in consumers. Paralytic shellfish poisoning not only threatens the livelihood of our Puget Sound and neighboring ecosystems, but largely affects the health of those ingesting marine invertebrates. An individual ingesting shellfish containing concentrations of paralytic toxins might experience mouth and limb numbness, serious illness or death. The University of Washington Tacoma and Washington State's Department of Ecology have partnered together through the Puget Sound Ecosystem Monitoring Program to monitor the presence of Alexandrium cysts throughout the Puget Sound. The Alexandrium cyst research involves processing sediment collected in Bellingham Bay. The sediment samples are sonicated, sieved, preserved using formalin, solubilized using methanol, and stained using Primulin. The samples are then prepared onto a Sedgewick-Rafter slide and cysts are counted using an epifluorescence microscope. Through the identification of cyst distribution throughout the Puget Sound, our research strives to preemptively assess and predict Harmful Algal Blooms and, ultimately, the risk of paralytic shellfish poisoning in consumers. Through our research efforts, we hope precautionary measures can be taken toward preventing paralytic shellfish poisoning in consumers of Puget Sound shellfish, benefiting the health of all Washingtonians.

X-ray diffraction gratings are an array of equally spaced structures with defined width designed to diffract optical waves. These waves create a spectrum that allows for the characterization of the wavelength or angles created by each diffraction. X-ray diffraction is commonly used in x-ray crystallography, where x-rays are diffracted off crystal lattices and give information about its three-dimensional structure. The goal of this project is to develop a microfabrication process for high aspect ratio x-ray diffraction gratings. These devices will expand the x-ray diffraction capabilities of the University of Washington and the National Nanotechnology Coordinated Infrastructure (NNCI) at large. In developing this process, our main objectives are to attain smooth vertical sidewalls for the grating features, minimize gold waste in the plating process and to be highly repeatable. For our research, each fabrication step will be tested, troubleshot, and documented for future use. The microfabrication steps required in our process include photolithography, etching, grinding and polishing, wafer bonding, and electrochemistry metal plating. The main challenges of this project are producing a photoresist pattern thick enough to withstand deep etching without affecting the sidewall profile, attaining precise grinding thicknesses and overcoming wafer bonding complications. The work towards maturing each process through inspection and troubleshooting for fabricating high aspect ratio x-ray gratings will be discussed.

An Inductively Coupled Plasma fluorine (ICP-F) reactor is used to anisotropically etch silicon dioxide with octafluorocyclobutane (C4F8) and argon (Ar) gas. Microelectromechanical system (MEMS) and microelectronics applications require several micron wide features with high-resolution and precision features made on silicon wafers. The ICP-F is a fundamental of the pattern transfer process called a damascene process where a precision pattern is formed and then filled with metal and planarized to remove excess metal and leave the intended pattern. This step of the damascene process consists of lithographic resist patterning and subsequent plasma etching of the underlying material. In this work, C4F8 plasma with Ar additives are used to etch silicon dioxide to create patterns in the oxide that will later be used molds for copper electroplating. In this design, the ICP-F must have a consistent etch rate with high selectivity to achieve constant depth for the copper layer with high resolution patterns. Variables such as DC bias, Ar flow, and O2 flow were optimized to achieve a repeatable etch rate. Furthermore, wafer stress was measured at every step in the process as the varying stress of the IPD could adversely affect the electronic circuits that the IPDs are connected to. Compared to Discrete Surface Mount Devices (SMD), IPDs allow for high-density trench capacitors, Metal-Insulator-Metal Capacitors, and high-Quality inductors which are enabled by ICP-F technology. In addition, new radio frequency (RF) circuits for 5G applications are employing the use of Integrated Passive Devices (IPDs) for making RF filters.

Deep Reactive Ion Etching (DRIE) is used for high aspect ratio etches in silicon wafers. The process is effective at achieving deep etches with high anisotropy and selectivity, however more process development is required such that side wall profile angle is selectable based on etch parameters. The goal of this study is to manipulate process variables (including pressure, etch time, and temperature) to allow the production of tapered, reentrant, or vertical side walls as needed. The SPTS-DRIE will be used to etch silicon targets with a repeating array of test patterns using a standard etch and deposition recipe. The standard etch recipe used will cycle between polymer deposition steps and plasma etching steps at low pressure using C4F8 and SF6 gases. Etch depths will be verified using a Bruker DekTak profilometer and sidewall angles will be measured using a Jeol scanning electron microscope. The parameters of the etch recipe will then be adjusted depending on the previous etch profile. Depending on the profile and aspect ratio of the etch, different parameters will be studied, including the process pressure, temperature, gas flow rates, and etch/deposition times. This process will be repeated until results within a reasonable margin of the target are reached. The goal will be to obtain an etch profile with sidewall angles of 90° ± 0.1° for use in industry and to determine parameters for reentrant and tapered profiles.

Brain tumors are the most common form of pediatric cancers after leukemia. Deregulation of the family of MYC (avian myelocytomatosis viral oncogene homolog) transcription factors in some forms of pediatric brain cancer correlates with very poor prognosis. It is believed that overexpression of MYC may play a role in sustaining aggressive brain tumor cell populations in diffuse intrinsic pontine glioma (DIPG), medulloblastoma, and atypical teratoid/rhabdoid (AT/RT) pediatric brain tumor types. A targeted therapy capable of inhibiting MYC transcription factors may be a promising option for children with MYC-upregulated brain tumors. We addressed the role of MYC genes in the tumorigenesis of several patient-derived pediatric cell lines with upregulation of MYC transcription factors. Via a lentiviral delivery agent, we attempted to knock down MYC transcription factions through the expression of doxycycline induced omomyc—a 90 amino acid, MYC-derived, polypeptide that interferes with normal MYC activity by outcompeting for the enhancer binding sites that MYC normally binds to. We found that MYC inhibition, using omomyc, halted the growth of tumor cells in over half of the patient-derived primary cell cultures with MYC overexpression. 6 out of 11 lines showed significant inhibition of tumorigenesis through the induction of omomyc. This suggests that the mechanism of action of omomyc, as a MYC inhibitor, may serve as a model for drug development against MYC for pediatric brain cancer.

Etching is one of the critical process steps in the fabrication of micro- and nano-scaled devices. Prior to etching, a pattern, usually defined in a temporary photo-sensitive polymer mask material called photoresist, is transferred onto a silicon wafer. One way to etch material, is through the use of plasma. Inductively Coupled Plasma (ICP), is distinct for its coil that shapes plasma and DC bias coupling for directionality. The machine has high etch rates and is used to etch oxide. Specifically for this project ICP-F (Fluorine) has been used. During etching, a photoresist reticulation problem has occurred. With this reticulation, features on the wafer are degraded, when reticulation is wide spread, the whole wafer must be stripped and restarted. This problem affects the speed and quality of production of wafers. In attempts to fix this problem, different variables such as the DC bias, chuck temperature, He backing, and RF power are monitored. Furthermore, the effects of varying pre-etch conditions, such as wafer bakes and different wait times, are examined to determine if there is a correlation between moisture in the photoresist film and resist reticulation or if the issues are predominately related to the etching system. Different inspection steps are made to ensure the quality of the etch, such as visual inspections and measurements of etch depths. These inspection steps concludes how much reticulation has occurred and what it has affected. ICP-F etching is just one step of the process in of fabrication of micrometer scale inductors and capacitors directly on the top of silicon wafers referred to as Integrated Passive Devices (IPD). This process decreases the amount of space used and increases the bandwidth of radio frequency (RF) analog filtering and the speed of digital information transfers. 

In the fabrication of integrated circuits and microscale devices a technique known as electroplating is often used to deposit thick layers of metals such as gold and copper. The electroplating process requires a conductive layer to facilitate electroplating, commonly referred to as a “seed” layer. In many cases, the seed material will not bond well with the base materials, necessitating the use of an intermediate “adhesion layer” to improve adhesion between the substrate material and the plated metal. In this project, Electron Beam Physical Vapor Deposition (EBPVD) was investigated as a means to deposit a 25nm titanium adhesion layer followed by a 300nm copper seed layer to promote the adhesion of electroplated copper to a silicon dioxide substrate. EBPVD is a process in which a collimated beam of high energy electrons is used to boil metal atoms off of a target and deposit them on a substrate. These systems operate in high vacuum to increase the mean free path of metal atoms ejected from the target surface, allowing for highly anisotropic deposition on the substrate. The stress states of EBPVD deposited seed layers and electroplated wafers were also observed as residual stress can adversely affect the performance of active circuitry that IPDs are bonded to. The deposition of this seed layer, followed by electroplating of copper, is but one step in the fabrication of prototype signal filtering devices for mobile applications. These micrometer scale inductors and capacitors, referred to as “Integrated Passive Devices,” are built directly atop silicon wafers, with the intent of eliminating the need for larger surface mounted signal filtering devices in applications where working volume is at a premium, such as in mobile phones and tablets. We hope our research will allow for production of higher quality prototypes and accelerate development of this emerging technology.