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.

The ability to regulate emotion does not develop completely until young adulthood, meaning teenagers are at risk for disorders associated with difficulties in regulating emotions. Identifying one’s emotions is essential for taking active steps towards regulating them; thus emotion differentiation is an essential skill that facilitates psychological well being. Although there have been multiple questionnaires developed to assess emotion differentiation, there are limitations of self-report. Behavioral tasks provide an opportunity to observe an individual’s ability to identify emotions. The Photo Emotion Differentiation (PED) task is a computer task designed to assess emotional differentiation, validated predominantly in adult populations. Participants are shown 20 standardized emotional images and are asked to report the intensity with which they experience each of the 19 listed emotions. The limitation to this method is that it has only been used once in child populations. We aim to validate the PED for use in adolescents by comparing it to a self-report questionnaire [the Levels of Emotional Awareness Scale for Children (LEAS-C)] that assesses emotion differentiation. The instructions for the LEAS-C ask youth to respond to 12 scenarios by indicating how they might feel and how the other person in the scenario might feel. A validated scoring system is used applying specific criteria to the emotion words used in the response. This is an ongoing study and we have currently recruited 14 participants from ages 13 to 16 who will come for a lab visit and complete both the PED and the LEAS-C. A positive correlation between the scores from the PED and LEAS-C will show that the PED is measuring the construct of emotion differentiation and can be used to obtain valid assessment in youth in subsequent studies. With this information, the PED can be used to examine the relationship between pain and emotion differentiation in adolescents.

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.

The use of Potentially Inappropriate Medications (PIM) in elderly is common and can lead to increasing risks for adverse drug events, morbidity, and increased utilization of health care resources. Early identification of PIM can improve the quality of care in elders and reduce hospitalizations. This study aims to identify PIM in a sample of N=60 people living with dementia who recently experienced a hospitalization and to evaluate what PIM are most common. We also aim to evaluate correlations between PIM and the number of patient’s chronic conditions and the total number of medications. Our hypothesis is that patients with higher burden of illness (more conditions and medications) can have higher number of PIM. We identified PIMs by evaluating medical records using the STOPP/START criteria. The STOPP/START criteria classify inappropriate medications that should be stopped as well as the appropriate medications that should be started instead.Descriptive statistics was used to describe the sample and the prevalence of PMI, chronic conditions and medications. Correlation analyses was used to explore relationships between the variables. Study findings will inform healthcare providers about the prevalence of PIM and help identify patients who are at higher risk of PIM.

Traumatic brain injury (TBI) afflicts people of all ages, with older adults having the highest rates of TBI-related hospitalizations and deaths among all age groups. Many of the issues and complications that TBI patients face are mediated by the immune response. Aging is a complex process which results in a decline of the immune system due to the altering of cellular production, proliferation and function resulting in an overall decline of immunocompetence. Injury sets off a chain reaction of immune cellular responses, the cell of interest in this project is TH2 cells, which have been shown to play a role in chronic inflammation. The purpose of this study was to explore if the age of an individual influences the TH2 cellular response in relation to traumatic brain injury. The TH2 cells used in the study were collected from younger (aged 21-64) and older (aged 65+) adult participants at < 24hours following mild/moderate TBI and at 3 months post injury. TH2 cells were stimulated with phytohaemagglutinin (PHA) and anti-CD3 and then incubated overnight. They were then analyzed for IL-5 production using the ELISpot assay. The number of cells producing IL-5 were counted, in triplicate, and the mean was taken to determine cellular response when stressed. The results were compared to determine if there is a difference between cytokine release amongst younger and older adults who experience TBI. By having a better understanding of how TH2 cell function is affected by age, we are exploring if overall outcomes following traumatic brain injuries are related to differential immune responses. This knowledge can potentially assist in identifying strategies to improve clinical outcomes.

In classical electrodynamics, accelerated charges emit electromagnetic radiation. The associated energy loss of the particle can be modeled as a radiation reaction force, proportional to the change in acceleration. Including this force in the usual dynamical equation for a charged particle yields the Abraham-Lorentz-Dirac (ALD) equation. For point particles, solutions to the ALD equation are problematic. First, they require additional initial conditions beyond those needed in regular Newtonian dynamics, but more concerning are the presence of unphysical run-away solutions and acausal trajectories. These problems arise in the point-like limit of the theory, so it is possible that quantum mechanics is the more appropriate framework with which to address the problem. In order to explore the similarities and differences of the classical and quantum frameworks, we compute classical trajectories of charged particles in the presence of a Coulomb field, including radiation reaction. We compare the associated classical cross-section with the quantum field-theoretic cross-section for Coulombic scattering, including radiative corrections. With these calculations, we will be able to assess when the field theoretic formulation of single-photon emission can approximate the classical radiation reaction.

The Collatz conjecture, named after Lothar Collatz, is one of the most deceptively difficult unsolved problems in mathematical number theory. The use of simple calculations and simple rules has left the mathematical community baffled for more than 80 years. Paul Erdős, a monumental 20th century mathematician, said that: "Mathematics may not be ready for such problems." He also offered $500 for its solution. In 2010, Jeffrey Lagarias claimed that based only on known information about this problem, "this is an extraordinarily difficult problem, completely out of reach of present day mathematics.” The Collatz conjecture’s simple rules are as follows; First, start with an integer. If it is even, divide by two. If it is odd, multiply by three and add one. Then, repeat this process for the result. Simple calculations. The conjecture states that every number will eventually reach one. For example: 5>16>8>4>2>1. This research aims to explore and observe the behavior of the Collatz problem as well as the “Collatz family.” The Collatz family are defined as iterative functions in the form: AX + B (X ≡ 1 (modulo Y)) and X/Z (X ≡ 0 (modulo Y)) Where X, A, B, and Y are integers. The Collatz conjecture is for the case: A=3, B=1, Y=2. This research does not attempt to find novel solutions to the problem using analytic number theory, rather we utilize computer programs to find structures and anomalies within the Collatz familly map. Hopefully, more discoveries surrounding the structure of the problem will give rise to its elusive patterns.

Drug addiction is a highly prevalent disease with common potentiating risk factors including stress-exposure, anxiety, and depression. A number of brain regions have been linked to behaviors that drive drug seeking and abuse, however little is known about how these regions communicate to regulate those behaviors. Currently, instruments can be used to record neuronal activity in vivo, however these devices are typically only able to record from one brain region at a time and don’t allow for specificity of neuronal stimulation. In order to improve the understanding of how brain regions communicate to drive behavior, there is a need to develop a multiple-site in vivo recording device that can record broad excitation signals while allowing optical stimulation of specific subtypes of neurons. In order to fill this need, I designed a dual-site optic delivering electrode or optrode. This device is small enough to mount on a mouse’s skull to promote naturalistic behavior with the ability to record non-specific electrical signals from the brain regions of interest, as well as optically stimulate specific subtypes of neurons. I also designed a program to process and analyze the data recorded by the device. If this device is successful, it will improve our understanding of how brain regions communicate to drive addiction-associated behaviors which could lead to therapeutic solutions for the treatment of addiction.

There is currently a lack of research in how transgender adolescent populations are affected by sleep and depressive symptoms. Sleep is incredibly important for teens, and there are links between depression and negative sleep outcomes. The purpose of this study is to examine correlations between gender, depression, and sleep in adolescents. I am using all data from a previous study that was comparing sleep and obesity in 100 cis-gendered adolescents aged 12 to 18. I am using this data to determine if a significant correlation exists between gender, objective sleep measures including total sleep time, sleep onset, wake after sleep onset, sleep efficiency (measured via Actigraphy), and depressive symptoms (measured via Center for Epidemiologic Studies Depression Scale, with scores of 16 or higher considered positive for significant depressive symptoms). An ANOVA test is being used to analyze for a significant correlation between gender, mean sleep time in minutes, and the presence or absence of depressive symptoms. The analysis of this data determines whether or not gender has a role in sleep and depressive outcomes, thereby determining the need for a further study of sleep and depressive symptoms in transgender adolescent populations.

Eclipsing binaries (EBs) are systems in which two stars orbit and pass in front of each other as observed from Earth. They are important astrophysical tools utilized in this project to directly measure the fundamental properties of stars, such as their masses and radii. We create a sample of 35 bright, detached EB targets from the Villanova Catalogue, based on high-quality photometry from the Kepler Satellite and spectroscopy from the Apache Point Observatory Galactic Evolution Experiment (APOGEE). Here, we present mass, radius, and orbital solutions for a subset of these EBs. For each system, we extract radial velocities (RVs), the speed at which each star in the system is moving away from the observer, from the APOGEE spectra. Then, we combine the RV with Kepler light curve (LC) information to simultaneously model the system light and line-of-sight speed as a function of time. Because our model has high dimensions with 18 free parameters, we first solve for the LC and RV solutions separately, and then simultaneously solve them. We use a nonlinear least-squares optimization method to determine the best fit solution and quantify the uncertainties in model parameters running Monte Carlo Markov Chain (MCMC) simulations. The model parameters that we find will further our understanding of fundamental stellar properties and binary star orbital parameters.

Past work have examined children's understanding of race, including their categorization of others based on race, racial preferences, and racial attitudes. Almost all of these studies have only investigated children's racial understanding based on Black and White individuals. In the current study, we wanted to examine whether 4- and 5-year-old White children categorize and hold preferences on the basis of race comparing Asian, Black, and White individuals. Participants were asked "Who do you like the best?" to determine whether they held preferences for individuals based on race, between paired pictures of different-race children. To assess categorization, participants were asked to match pictures of children to exemplars they thought looked most like the children in the pictures. Results demonstrate that children categorize based on race significantly greater than chance t(47) = 5.569, p < 0.001. In terms of preferences, children significantly preferred White over Black children, t(47)=2.801, p=0.007. However, they did not have a preference for Asian versus White children, t(47)=1.219, p=0.229 or Asian versus Black children, t(47)=1.070, p=0.290. Taken together, these results suggest White children have a fairly sophisticated understanding of race; not only do they differentiate between members of their in-group and out-group (significantly differentiating on race between White/Black and White/Asian comparisons), but they also differentiate between other racial groups (significantly differentiating between Asian and Black individuals). Although children categorize and recognize race, this does not mean they always form preferences based on race.

Sleep is crucial for producing higher levels of concentration, performance, and overall health and safety. Yet, teens, a vulnerable population, get far less sleep than the recommended 8-10 hours and continuously incur a sleep debt that negatively impacts their health. This troubling issue led to a national public health initiative to delay high school start times to benefit teens’ health. Though the Seattle school district recently accepted and implemented this initiative, it remains to be seen if the time change had the expected impact on the teens’ sleep quantity and therefore overall performance and health. The purpose of our research was to explore any correlation between the later school start time and positive outcomes of improved sleep, health and performance. In order to address this question, we created a 22-item survey which asks questions regarding quantity of sleep, self-reported measurements of mood and mental health, academic and extracurricular activity performance. We used convenience sampling and recruited from the community, specifically high schoolers within the Seattle school district who experienced the time change, to complete this survey. We expect to find that the later school start time increased the quantity of sleep high schoolers obtained, contributing to improved overall health and performance. If we obtain our expected results, we hope the data can be used to encourage other school districts to also adopt the time change and promote the health of the teen population.

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.

When you first walk into a classroom, do you think about the intent behind the design? This literature review examines the environmental psychology of classroom design through analysis of the connections between students and the physical characteristics of their surrounding learning environments to better understand what sort of structural, technological, and decorative features can be implemented to facilitate engagement and collaboration in modern classrooms. Physical features of educational facilities, such as lighting, acoustics, air quality, heating, the increased use of technology, the transition from lecture to collaborative learning, and the decor that educators choose for their classrooms to inspire their students are all key factors to consider when discussing the types of classrooms that improve and facilitate critical thinking. Accessibility to the resources necessary to provide the most optimal learning environment proved to be a concern, but my findings show that minimum structural quality and simple environmental cues like stimulating visuals that signal to students that they are valued learners can maximize educational outcomes for many students. My analysis of architectural, student, and teacher perspectives as well as evidence from academic journal articles concluded that learning environments encouraging creativity, reflection and the development of individual ideas are accessible simply by humanizing the institutional formality of the room—providing a safe and comfortable learning space while also supporting engagement and discussion facilitation through flexible furniture arrangements, displays of student work, and the effective use of technology. My findings will support further studies regarding the development of methods and implementation educational standards that focus on how to improve classroom designs and student experience. School classroom culture impacts students directly, therefore, the shift from traditional information-delivery lecture hall interior layouts to classroom that inspire critical thinking is essential when building or designing educational spaces for all students.

This research looks at the impact of elevated temperatures on rice biomass allocation, in the context of rice nutrient and contaminant uptake. Below-ground biomass allocation can influence the rate of mineral uptake, and above-ground biomass can influence how those nutrients are distributed. Rice was grown in four growth chambers set to different temperatures ranging from low (25.4°C) to high (33.0°C). Rice plants were harvested during two developmental stages, flowering and grain filling. The plants were sectioned into four components before storage and desiccation: roots, leaves, stems, and grain. A total of 256 rice plants were grown over two harvesting periods, thus each treatment has a sample size of 64 plants. To examine biomass allocation, each component is being measured on a high-precision scale accurate to the nearest 10^-5 gram. The impact of temperature will be quantified for the following groups: temperature treatment vs. component biomass, treatment vs. above- and below-ground biomass ratio, and treatment vs. total biomass. Rice is the primary staple food of over half of the world's population and is the main caloric and nutritional source in many developing countries. Increased global temperatures due to climate change may have significant impacts on rice growth, yield, and nutritional quality.

Past research has discovered a technique for photocatalyst synthesis utilizing never-dried cellulose fiber in order to produce non-agglomerating nanocrystals. This new technique allows the production of semiconductors in a flexible form. This form is useful in many areas, including in spacecraft technology, where solar panels must be kept in a compact form before deployment. One possible catalyst for this is gallium arsenide (GaAs), which holds many traits that are favorable to semiconductor devices in electronics. With a band gap that is receptive to visible light and many industry applications in radio frequency, light sensors and LEDs, gallium arsenide is an attractive candidate for storage in cellulose fiber. In particular, this storage method allows for the synthesis of long strands containing GaAs that are useful in solar cells. In order to form an electrostatic region necessary for electronic applications, a P-N junction must be formed within the compound. This is usually done by heating the compound and injecting ions into the structure so that P-N junctions are naturally formed. However, since the fibers are unable to be heated to the temperatures needed without compromising the storage, we instead propose that a magnetic field can be placed across the semiconductor during formation, with doping ions placed within the fiber so that the junctions naturally form within the GaAs structure. This new method for semiconductor production has the potential to offer a new strategy for electronic production that can exist in a flexible format.

Zebrafish have a higher regenerative potential than mammals, but the genetic differences between the groups that lead to their respective responses are not fully understood. Cross species analyses with mammalian models allows comparison of these genes with their mammalian orthologs to determine which genes show similar or different enrichment during bone regeneration processes. Information from microarray datasets for both rats and zebrafish provide information about the genome-wide transcription during regeneration in each model; the regenerative process in rats has a different timeline than zebrafish, so our lab has developed software to relate the two timelines so that gene expression can be directly compared. Using this information, I am performing two sets of analyses. In the first analysis, I am determining which genes show conserved expression in both models to identify deeply conserved genes essential for regeneration in both systems. In the second analysis, I am finding genes that are differentially expressed between rats and zebrafish during regeneration; pathway analyses of these genes can provide a better understanding of the differences in regenerative response, and potential ways to manipulate this response in both models. Determining the processes that involve these genes can help identify genetic targets associated with important regenerative functions, which can be applied to a mammalian model to potentially improve its regenerative response. Preliminary results for the similarly expressed genes’ ontology of shows involvement in skeletal development, phosphate transport, and organogenesis; the differentially expressed genes’ ontology shows involvement in morphogenesis, peptide linking, and organogenesis. The genes with similar expression affect ECM-receptor interactions and focal adhesion pathways, while the differentially expressed genes are affect nicotinate and nicotinamide metabolism and carbon fixation. Manipulating these pathways in zebrafish can show their distinctive roles in the regenerative process and provide a better understanding of the differences between the zebrafish and mammalian regenerative processes.

More than 40 million people in the United States have or are at risk for osteoporosis, a condition characterized by traits including low bone mineral density (BMD) and high fracture risk. Though genome-wide association studies have identified many candidate genes associated with genetic risk factors, genetic variations that are associated with osteoporosis-related traits, the causal genes underlying these risk factors remain undiscovered. My research centers around developing tools to assess bone morphology in a zebrafish model to identify specific genes that cause osteoporosis or other skeletal abnormalities. Because a trademark characteristic of osteoporosis is expanded bone diameter due to accelerated bone remodeling and increased resorption in the endosteum, I have developed tools to assess bone expansion in zebrafish vertebral structures. By using integral calculus and basic machine learning with the R programming language, I developed a predictive model for calculating approximate diameters for the centrum foramen, the hole in the zebrafish vertebral body. As a more direct alternative, I have also developed a program using image analysis tools in MATLAB that identifies the foramina of the centra, neural (superior) arches, and haemal (inferior) arches in binarized microCT stacks of zebrafish skeletons and calculates the cross-sectional area of each foramen. I am using these tools to retroactively analyze previously scanned mutant zebrafish to identify genes that have phenotypes consistent with abnormal foramina of the vertebral body and arches. I have determined that mutants with the bmp1a and plod2 genes knocked out separately have expanded centrum foramina. After compiling and analyzing a zebrafish data archive with data from other previously imaged mutant samples, my results will indicate previously undetected phenotypes. This data will aid in my lab’s efforts to determine the causal genes underlying osteoporosis genetic risk factors. This research may lead to discoveries that are used in future osteoporosis gene therapies.

The aim of this project is to investigate the effectiveness of medical translation for individuals who face language barriers in the doctor’s office. Translation services have made strides in bridging communication barriers yet some populations continue to suffer. This happens when medical terminology is difficult to translate to a language or if the Interpreter/Translator does not have knowledge of medical terms in the language to which they are translating. The research questions explored through this project are: Does the work of translation contribute to the marginalization of immigrant non-English speaking populations? How does poor translation contribute to the “letting die” of immigrant populations? How must we reconsider the role of language as it intersects the biopolitical field? This project focuses on the Urdu speaking population- most of whom have immigrated from South Asia and are at risk for heart disease. In Urdu, the word “disease” translates to “sickness” which could refer to something as minor as a cold or severe as heart disease. In this way, the severity of an illness is lost in communication and the patient is left filling in the blanks of how severe their sickness might be. This research aims to find gaps in understanding by asking native Urdu speaker to decipher the meaning of various medical phrases translated to Urdu from English. This provides insight into what medical phrases cause the most confusion when translated to Urdu so that it can be addressed in further research. Ultimately, the goal is that this knowledge can help improve translation techniques by creating a tool for patients to convey what was communicated to them during a visit to the doctor.

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.

There are various groups and organizations that affect the prosperity and integrity of women in India. Whether they are affiliated with a political party or village clans, women are typically placed at the bottom of the barrel. My research highlights how groups such as Hindutiva, Love Jehad, Triple Talaq, etc. oppress women or spark activism within their community. Women regardless of class, race, etc. are affected by some sort of familial system; expected to follow and obey traditional gender roles, and abide by their husbands. Women are also used as a unit of analysis in religious ideologies. A generalization is made that all women are either impacted or not impacted by Islam. For example, the more women do something, such as wear a veil, the more generalizations are made about their rights as women. To understand these issues, I interviewed domestic workers, young women who attend schools, and research activists in India. This research also explores how specific organizations made for women have fought for and implemented laws to strengthen the voice of the oppressed. This project will track the evolution of the women’s movement in India, from its origins to the present, providing insight into how women have worked their way up the ladder, the obstacles they faced, and what they hope to achieve in the future. Hence, it provides a different perspective on feminism—building on Third World Women in contrast to Western feminism.

In a region as tectonically and volcanically active as the Pacific Northwest, accurate models of tectonic history are essential to inform our understanding of modern tectonics dynamics. At present, very little is known of the history of the Olympic Mountain Range. Previous work has used fission track dating to date the onset of exhumation of the Olympic Mountains and has placed it around 18 Million years. Fission track dating as a method relies on the analysis of fissures in certain uranium containing minerals, in this case zircon and apatite, to determine when the rock body they inhabit cooled below the temperature at which that mineral is no longer able to chemically diffuse with its surroundings. This data is a proxy for paleodepth, however it gives little information about the topography at that time. In the past 20 years, newer, more precise methods have been developed such as Uranium-Lead dating of detrital zircon crystals. This method relies on analyzing zircon minerals extracted from sandstones and dating them using the radioactive decay of Uranium to Lead, and eventually comparing these ages with those of the potential sediment sources to reconstruct their provenance. Here, we analyze sandstones from the Seattle Basin and Olympic Peninsula to reconstruct the uplift history of this region. This approach coupled with stratigraphic techniques may be used to place a more precise age constraint on the onset of high topography in the modern Olympic Mountains: an event which tremendously impacted regional tectonics, ecology and climate in Washington State.

Speech-language pathologists (SLPs) evaluate voice quality using perceptual judgments, an important method for assessing voice disorders. Ideally, perceptual judgments exhibit both intrarater reliability, in which one listener rates voices consistently, and interrater reliability, in which different listeners rate the same voices similarly. In practice, several sources of perceptual variability confound reliability, including the scaling method itself. SLPs typically use visual analog scales (VAS), in which a response is recorded along a continuous scale between two endpoints (e.g., normal to severely breathy). While other scaling methods may be more reliable than VAS, they present challenges for practical application. Visual sort and rate (VSR) is a promising scaling method, in which a listener rates voice samples using a VAS, and each voice sample serves as a perceptual reference point for other samples in the set. My study will determine 1) whether VSR yields greater intrarater and/or interrater reliability than traditional VAS in ratings of speakers with voice disorders by inexperienced listeners, and 2) whether this effect occurs for both overall severity (OS) and an isolated perceptual dimension (breathiness). I recruited five SLPs (“expert listeners”) and 20 inexperienced listeners. I sorted fifty voice samples into six sets, with a variety of severity levels in each set based on ratings by the expert listeners. To measure intrarater reliability, I repeated 20% of the samples. I instructed the inexperienced listeners to rate the samples for OS and breathiness, using both VAS and VSR. I varied task order (VAS/VSR) and dimension order (OS/breathiness) to control for learning effects. I will analyze the inexperienced listeners’ ratings to determine whether VAS or VSR yields greater intrarater and interrater reliability. I hypothesize that VSR will produce more reliable ratings of OS and breathiness. Results of my study may support clinical application of VSR for voice assessment.

Everyday, human beings engage in prosocial behaviors, which are behaviors intended to benefit others. These include simple acts, such as holding doors for others, and costlier behaviors, such as donating money. Even young children help, share with, and comfort others. To gain insight into why human beings engage in prosociality from such an early age, it is critical to examine individual variability in children’s prosocial behavior. That is, why are some children more prosocial than others? One factor that may influence prosociality is social anhedonia, which is the reduced capacity to experience pleasure from social interactions. Adults with high social anhedonia are less prosocial; however, no work has explored if children’s capacity to experience pleasure from social interactions motivates their prosociality. The current work develops a measure of social anhedonia in early childhood and examines if variability in the capacity to experience pleasure from social interactions is related to children’s tendency to engage in prosocial behavior. To explore this question, parents of 4- to 8-year-olds report their child’s prosociality. They also report their child’s social anhedonia using the Child Social Anhedonia Scale, which I created based on a questionnaire assessing adulthood social anhedonia. This work is ongoing, but an analysis of 134 participants (57 females) revealed a significant negative correlation between children’s social anhedonia and prosociality, r=-0.32, p<0.001. This finding suggests that children who are less likely to experience pleasure from social interactions are also less prosocial, implying that perhaps enjoying social interactions serves as a motivation for children’s prosociality. This study is the first step in understanding the relation between pleasure from social interactions and children’s prosocial behavior. Future studies could further examine if this relationship is causal.

Autophagy is a process in which cells recycle their damaged or unwanted organelles. The process of macroautophagy encompasses a variety of selective autophagy mechanisms such as ribophagy, mitophagy, and lipophagy - each of which has a different specific target for degradation. These processes are initiated for multiple reasons, incuding ATP starvation and stem cell differentiation. During erythropoiesis, the process of hematopoietic stem cells differentiating into red blood cells, selective autophagy is known to be used to clear mitochondria in the terminal stages. Doulatov lab has recently identified the selective expression of BNIP3, a homolog of the known mitophagy regulator BNIP3 (NIX), in early erythroid progenitors. These preliminary data suggest that there may be an unnappreciated role for mitophagy in the earlier stages of erythropoiesis in addition to its late stage role. To better understand how mitophagy is involved at this time point, the level of expression of proteins BNIP3, BNIP3L (NIX), and another known mitophagy protein PINK1 will be evaluated at days 1, 3, 5, 7, 9, 11, and 15 of erythropoiesis by western blot. The expression of these proteins will be analyzed in conjunction with mitochondiral mass of the cells, which has been observed to rapidly decline following a sudden burst in mass at day three of erythropoiesis. We hypothesize that autophagy is responsible for this dynamic behavior, and investigating the expression of these proteins may implicate which specific mitophagy pathway is being used. After determining these expression patterns, we can use lentiviruses expressing shRNAs to seperately reduce and overexpress autophagy proteins in order to manipulate mitochondrial mass during erythropoiesis. Exploring the relationship between selective autophagy and mitochondrial dynamics during normal human erythropoiesis may eventually provide insight into pathologies in which erythropoiesis is impaired.

One of the most significant problems facing modern agriculture is climate change. Plants thrive best within a fairly narrow range of temperatures. Outside of that range they have significantly reduced crop yield and significantly increased mortality. This imposes limitations on where certain crops may be grown. Due to rapidly growing populations, the industry must be allowed to expand into new regions, but climate change is reducing available regions. One possible solution is amplified heat tolerance due to symbiosis with endophytes. Endophytes are symbiotic microbes which live in the intercellular space within plants, and which may be used to improve plant fitness through stress tolerance, nutrient supply, and many other mechanisms. We chose a poplar tree which likely hosted beneficial microbes to alleviate heat stress due to its harsh environment, and have been working to isolate the relevant endophytes. I am using a plant-based isolation procedure using species such as rice and kale. By exposing the plants to the endophytes and then to heat stress, I assure that the endophytes have a broad host range because they must be able to survive in more than just their host plant, and I allow the plant to choose the most helpful endophytes to alleviate stress. Through multiple repetitions of this isolation procedure, I can increase the presence of heat-tolerance-conferring endophytes within the microbiome. These endophytes may eventually be used to expand growth into regions which are outside of conventional temperature ranges, or to remain in current regions in which temperatures are increasing.

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.

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.

Eelgrass (Zostera marina) is a vitally important organism to the Puget Sound that exists along the shallow, muddy seabed. Many different living creatures of all trophic levels rely on the eelgrass beds to survive and absorbed contaminants could be a real threat. Toxics metals in the eelgrass, sediment and water column could have critical implications to the ecosystem. The heavy metal concentrations in the eelgrass, sediment and the water column of two locations in the Possession Sound (Mukilteo and Buoy) were analyzed in order to determine the specific levels of metals and contaminants that travel up through the trophic pyramid. The study endeavors to determine the metal absorbance ability of eelgrass and check if factors including temperature of the water column, seasonality or time of day influenced heavy metal uptake by eelgrass. A sediment grab was utilized to collect the sediment and eelgrass samples. Sample analyses were conducted at the Everett Environmental Laboratory and in partnership with a University of Washington trace metals laboratory to find the concentration of the metals arsenic, copper, lead, zinc and cadmium in the surrounding water column and the eelgrass. It was predicted that greater concentrations of copper and zinc would be found near Buoy because they are legacy chemicals and due to anthropogenic influences near the Everett Port of Everett. It was also hypothesized that a higher concentration of metals would be found in the eelgrass during the spring and summer as more direct sunlight leads to greater primary productivity and uptake of chemical constituents. Determining these types of correlations and catalysts is significant to the entire Possession Sound ecosystem as it would lead to possible strategies on how to prevent further contamination of eelgrass. Furthering our understanding of the connected network of interactions here can only benefit the future inquiries.

Microbes that live within plants, called endophytes, are being heavily researched on their ability to assist host plants in processes from nitrogen accumulation to drought tolerance. Two endophyte strains named WP5 and WP9 are known to colonize Populus trees. Previous research has shown that the presence of WP5 in a host plant allows for greater colonization by WP9 subsequently. This research is directed at replicating these results with more robust molecular biology techniques. Methods for experimentation include the growth of the endophytes in selective media and varying the optical densities of these liquid cultures before inoculating the poplar clones. The plants co-cultivate with the inoculum for 24 hours, at which point they are removed, washed and placed in limited nutrient media. After removal from the inoculum as well as at 7 and 14 days hence, the host plants will be sampled by performing genomic DNA extractions and subsequently analyzed through Digital Droplet PCR to quantify endophyte presence. Additionally, these strains have been marked with fluorescent tags to enable imaging under a microscope. The two endophytes were labeled with different colors, one red and one green, so that they could be visualized concurrently. Along the same sampling timeline, root samples will be taken to image through microscopy in order to visually investigate the colonization process of the two strains. The results of this research will help to shed light on the colonization abilities of these strains, and allow for the optimization of bio-fertilizers comprised of endophytic consortia.

The Eocene-Oligocene Transition (EOT) 34 million years ago was one of Earth’s most dramatic global cooling events from a hothouse with no ice caps to our current icehouse world with intermittent glaciations. It is important to understand the details behind the EOT in order to understand the mechanisms that can drive such significant climate change as well as the magnitude of the effects such a shift could cause to modern ecosystems. Here, we apply geochemical methods to organic-rich rocks from the Yaw Formation in the central Myanmar to reconstruct its paleoenvironments and gain a better understanding of Eocene climate in Southeast Asia. The ratio of the stable Carbon isotopes C12 and C13 (d13C) from plant matter in rocks can be used as a proxy for changes in the amount of woody cover in tropical ecosystems as well as mean annual precipitation (MAP). Using mass spectrometry on coals and sandstones of various ages, we are able to see how the d13C values have evolved over time in order to observe possible trends in Myanmar’s paleoenvironment. Preliminary results show an increase in d13C values over time which could indicate aridification in the environment.

Plants are affected by various abiotic and biotic stressors such as pollution, high salinity, drought, and pathogens which can inhibit growth or cause disease. High salinity, a type of abiotic stress that decreases crop productivity and quality, is especially widespread with nearly half of the world’s cropland facing salinity stress in 2010. This is problematic because there are very few plants that can tolerate high levels of salt and the process of remediation is water and energy intensive. However, endophytes, the beneficial bacteria that live within plants, have shown potential in helping plants tolerate these stressors in a more natural way either by directly reducing the stressor or indirectly by modulating the plant’s response to the stress. The main goal of this study was to isolate and test endophytes to determine whether they colonize other plants and help these plants tolerate high salinity conditions. In this study, a total of 15 salt tolerant endophytes were isolated from pickleweed and wild wheat growing in a marine estuary. These strains were then tested on bush beans and poplar to test salt tolerance conference. There were visible signs of higher stress tolerance in bush beans inoculated with endophyte SSP1 and poplar inoculated with SSP8. The results for the remaining endophyte strains are pending. By improving plant growth under abiotic stress, these bacteria will help promote sustainable agriculture practices and bioenergy production.

This study explores the sustainability performance of international companies in the food and beverage industry. The research goal is to investigate whether sustainability performance is correlated (positively or negatively) or is not correlated with financial performance. The Global Reporting Initiative’s sustainability reporting framework, called GRI, provides principles and metrics for reporting corporate environmental and social responsibility impacts. The Financial Accounting Standards Board financial reporting framework, called generally accepted accounting principles (GAAP), is used to prepare corporate financial reports. Both the GRI and GAAP frameworks provide consistency, so report users can analyze a company’s performance over time as well as in comparison to competitors. The Sustainability Performance Assessment (SPA) System developed by Paun (2015) incorporates GRI and GAAP measures for reporting triple bottom line performance (i.e., financial, environmental, human rights, labor practices, product responsibility, society, economic). Using the SPA System, data was extracted from 2016 sustainability and financial reports and analyzed in terms of the following multi-dimensional performance variables: environmental, human rights, labor practices, product responsibility, society, economic, revenue, leverage, and profit. The sample companies are based in Europe and the U.S. Their 2016 revenues ranged from $8.9 billion to $91.5 billion and employees ranged from 42,000 to 328,000. Data was analyzed using descriptive statistics (e.g., performance mean, degree of transparency, transparency weighted performance mean). Preliminary research findings suggest that correlations exist among the triple bottom line sustainability variables. This research reveals broader trends about the impacts of multi-national companies on the consumers they support and environment they influence.

Nanoparticles have begun to see wide adoption in commercial application particularly in fields relating to medicine and electrical engineering. While their small size provides unique properties furthering advancements in these field, their effect on human health are still relatively unknown. As their use increases, their potential to cause health effects will need to be considered. This is especially true for workers who manufacture engineered nanomaterials (ENM) and who use them in commercial products. Quantum dots (QD) are an emerging application of nanoparticles using their semiconductor properties for optical imaging. To determine the effects of QD to human neural development, an in-vitro model was established using an adverse outcome pathway (AOP) framework. This methodology provided observations of QD on their ability to alter cellular morphology and developmental endpoints. H9 human neural progenitor cells were cultured and maintained in vitro for up to 21 days in 96 well plates. Normal morphology and biochemistry was characterized under both proliferating and differentiating conditions. H9 cells were then treated with two different QD, Qtracker non-targeted QD and Qdot ITK carboxyl QD, under the concentrations of 0, 2.5, 5, 10, 20, and 40 nM at culture day in vitro (DIV) 1, 6, 13, and 20. After 24 hours of exposures, cell viability was evaluated for dose-response relationships using LDH and MTT assays. H9 cultures undergoing proliferation saw resistance towards Qtracker non-targeted QDs, however cell viability declines with increasing concentrations of ITK carboxyl QDs. H9 with differentiation media under DIV 1 and 6 saw declining cell viability towards accumulative exposure to Qtracker non-targered QDs. Nonetheless, H9 cells with differentiation media showed resistance towards ITK carboxyl QDs. In the future, we will investigate the resistance of our cells to various Q dots by assessing dosimetry of QD uptake under our test conditions.

Utilizing the Type III Secretion System (T3SS), Shigella spp. uses a cascade of proteins to manipulate, penetrate, and colonize host eukaryotic cells. Inducing epithelial necrosis, Shigella spp. infection is responsible for moderate to severe diarrhea in millions of children and immunocompromised individuals — the majority from under-developed communities. Previous translational research on Shigella spp. has been limited due to the lack of proper in vitro and in vivo models. Understanding infectivity of Shigella spp. heavily relies on imprecise estimations of intracellular Shigella spp., which ultimately impacts vaccine and antibiotic efforts. This project aims to address this problem by developing a novel red intracellular reporter to quantify successful invasion of Shigella flexneri. By using a series of polymerase chain reaction (PCR) assemblies, we aim to construct a plasmid with a RFP reporter to be expressed during successful invasion of Shigella spp. The IpaH9.8 MxiE promoter, which has been shown to be expressed upon cell entry, has been integrated within the pUltra RFP plasmid through a Gibson-Reaction assembly and cloned using PCR. The new DNA replicate was electroporated into a streptomycin-resistant S. flexneri strain. We  initially tested each strain in vitro by inoculating HCT-8 cells with the newly engineered S. flexneri and monitored for selective RFP expression by intracellular S. flexneri. The outcomes of this project will provide an accurate and efficient method of quantifying invasive S. flexneri. in vitro and in vivo, as well as quantifying efficacy of new antibiotic treatments. The implications of this project are crucial to the advancement of shigellosis research and in furthering the efforts of the international community to abate the rates of disease mortality and burden.

Managing chronic pain is difficult, as pain mechanisms and relief strategies are poorly understood. Chronic pain afflicts many adults nationwide, diminishing functional activity, and quality of life. Recently, opioid therapy has become a treatment option for chronic pain, increasing prescription opioid use and related public health issues. Additionally, pain education among providers, prescribers, and clinicians is generally insufficient. Providers require education in alternate pharmacological strategies, and effective non-pharmacological strategies. Telehealth technologies developed recently can span geographic distance to improve quality of pain care for patients by improving provider knowledge of pain-management. The question remains: is telehealth-based pain education effective in improving provider’s knowledge and management of pain? We hypothesized that clinicians who attend weekly Telepain sessions will demonstrate improvement on their quarterly evaluation of pain-medicine knowledge and confidence, and the KnowPain-12 questionnaire. Providers (N=128) participated in or observed a weekly video-conference, orchestrated by pain specialists representing internal medicine, rehabilitation medicine, addiction medicine, psychiatry, social work, nursing, and anesthesiology. Telepain sessions are divided into two segments: a didactic lecture on a pertinent, evidence-based topic related to pain, and case presentations and discussion by clinicians. Participating providers completed a quarterly questionnaire critiquing the conference, as well as self-report questionnaires related to pain management knowledge (KnowPain-12; mean score of 1-5) and perceived competence (mean score of 1-7). To determine if Telepain attendance led to improvements in pain knowledge and perceived competence, a generalized linear model (GLM) was fit, where KnowPain-12 mean total scores were the outcome variable and Telepain attendance time was the predictor variable. A generalized estimating equation was used. Results of the GLM indicated improved pain knowledge with increased Telepain participation time (coefficient = 0.002, 95% confidence interval = -0.0002, 0.0044, p = 0.08), suggesting that telehealth interventions such as Telepain may be an effective option for delivering advanced provider pain education remotely.

The population of refugee and immigrant families in Seattle's Lake City neighborhood has grown significantly in the last decade.  Despite the health challenges these families often face, no one has performed a systematic assessment of the health needs specific to this population.  Our project aims to provide preliminary data about the health needs of refugee and immigrant children and families in the Lake City neighborhood, as well as resources available to assist them.  This analysis is timely and relevant for community stakeholders, such as the non-profit Refugee Women's Alliance (ReWA), who are currently expanding services for refugee and immigrant children in Lake City.  We used mixed methods to assess the health and health-related resources relevant to preschool age children of refugee and immigrant groups in the Lake City neighborhood.  These methods included key informant interviews with individuals knowledgeable about the health of refugee and immigrant families in Lake City, as well as analysis of publicly available secondary data.  Interpreting the interviews using relevant secondary data provides a holistic initial picture of the physical, socio-economic, educational, cultural, and community factors contributing to the health and wellbeing of refugee and immigrant children and their families in Lake City.  We anticipate our research findings will reveal a culturally diverse community with distinct needs, as well as many existing community resources—assertions confirmed by preliminary results.  The results of this study will both inform ReWA's early childhood education programming, and give healthcare providers and community organizations in the area a more comprehensive understanding of refugee and immigrant needs.  Because this project has stimulated community interest in further research relating to these populations, this study can also serve as a platform for future work in the area. 

Osteoarthritis and disturbed sleep negatively impact the daily life of many older adults (65+) in the United States. While previous research shows that physical activation can improve osteoarthritis and sleep disturbances, it is often a challenge to motivate older adults to engage in daily physical activity. Walking is the most common and affordable form of physical activity and therefore provides a practical target for health behavioral interventions. The objective of this study is to examine if, in older adults with osteoarthritis and sleep problems, a wearable wrist-worn device (Fitbit) combined with infrequent motivational text messages and phone calls targeting physical activity improve participants step count and sleep. To examine this question, we recruited 20 older adults over the age of 65 who have clinically diagnosed osteoarthritis, have a sleep deficiency (defined by a score greater than or equal to 12 on the Insomnia Severity Index) and were judged to be underactive (doing physical activity less than 30 minutes a day). This data is then analyzed to see if there is a change in participants step count and the effect of this change on their sleep symptoms. Preliminary results show that step count improved over time such that there was almost a 400 step increase per day between baseline and week 14. Ultimately, this work will increase our understanding of mobile interventions and their potential effectiveness in helping patients to engage in more physical activity as a cost-effective way of improving sleep.

Myanmar, in Southeast Asia, has recently opened access to foreign geologists; however, most of the Burmese geology still remains to be studied. At the western edge of Myanmar, the Indo-Burman mountain ranges today form a prominent topographic high. One of the big mysteries in geology of Myanmar is the precise timing of the Indo-Burman Ranges uplift, which is currently estimated to be in between the early Cretaceous (~140 million years ago) and the Neogene (~20 million years ago) periods. Here, we present preliminary sedimentary provenance in river and sedimentary basins between the Indo-Burman Ranges and the central Myanmar low plains. We use Uranium-Lead radioactive ages of detrital zircon crystals from dated sedimentary rocks, revealing the source of the sedimentary input which resulted from the uplift of the surrounding mountains. Our results will indicate the timing of sedimentary input to our study basin sites, and when the uplift of the Indo-Burman Ranges occurred. Dating the Indo-Burman Ranges uplift will contribute to understanding tectonic activities in the past, which would have affected the regional climate evolution, such as the Asian monsoons.

American Foulbrood (AFB), a disease of honeybee larvae caused by the bacterium Paenibacillus larvae, has global economic significance. AFB spreads through colonies killing the next generation of bees. AFB has traditionally been treated with antibiotics or by burning infected hives and exposed materials. The former method is complicated by antibiotic resistance and bacterial sporulation, while the latter method carries severe financial liability for beekeepers. One alternative treatment is the use of bacteriophages, viruses that infect and destroy bacteria. Bacteriophages are host-specific and co-evolve with their host, unlike antibiotics, thus making resistance and collateral damage a non-issue. Characterizing these phages will be key to future treatments of infected hives. The P. larvae phage Willow, isolated in our lab, is both lysogenic (allow the infected bacterium to survive) and lytic (kill the infected bacterium). Currently, we have confirmed Willow lysogeny in P. larvae strain 3650. This relationship presents a model system for investigation. A comprehensive understanding of the host-pathogen interactions between Willow and P. larvae will aid in the effective targeting of P. larvae in the field. Our laboratory also seeks to determine the relatedness of four P. larvae phages to Willow to further characterize the genes responsible for lysogenic/lytic decision making. In sensitivity assays, lysogens (bacteria with integrated phage) are plated to form a lawn and dilutions of a different phage are spotted onto the plate. An identical wild-type plate is made, and comparison yields plating efficiencies. Plating efficiency determines what degree of protection is offered by the integrated phage. I hypothesize that genetic sequencing will show measurable genetic differences in the putative C1/Cro region of the phages under investigation, and that all genome sequence similarity will correlate directly with established plating efficiencies. Furthermore, I used sequence alignment, product alignment, and dot-plots to illustrate the degree of sequence similarity between phages.

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.

Infective endocarditis (IE) is a life-threatening bacterial infection of heart valves. In comparison to treating other diseases, IE treatment is especially difficult to treat due to an increased resistance to conventional antimicrobial agents as well as a continuously high shear environment of the endocardium wall. Even after receiving prompt therapy, patients with streptococcal endocarditis often develop complications- including heart failure, progressive valve destruction, and stokes. Though the interactions between adhesive bacteria such as streptococci group of viridians (the major cause of IE) and platelets are known to facilitate bacterial vegetation in damaged heart valve, it is not well known how the bacteria bind through hitchhiker binding events (a specific interaction of platelets with streptococcus group viridans). Mainly, it is unclear whether bacteria bind to platelets and then to heart valves, or if the bacteria bind to platelets which are already found on inflamed heart valves.  To successfully characterize these spatial and temporal events, we used a parallel microfluidic device to develop a model. Specifically, we used our humanized in vitro model of infective endocarditis to understand the initial stages of the disease. We are demonstrating that the number of adherent bacteria can be measured after bacteria mixed with various blood components is washed through to the device, with sufficient accuracy to test hypotheses regarding the adhesion phase. Finally, we quantified the number of bacteria in vegetation after a growth phase following the adhesion phase. The findings from this design can potentially lead for the development of novel molecular therapeutic mechanisms. These will have implications not only for infective endocarditis, but also all other endovascular infections with a shear environment.

Vagus nerve stimulation (VNS) involves the delivery of electrical stimuli to the vagus nerve, which is associated with several brain regions and functions. VNS is currently used as auxiliary treatment for some types of epilepsy and there is significant interest regarding its potential in the treatment of other illness as well as for cognitive augmentation and promoting plasticity. The goal of this project is to investigate the differences in ipsilateral and contralateral cortical responses to different vagus nerve stimulation protocols, as well as to compare the responses to invasive versus noninvasive VNS delivery methods. Data was collected from a non-human primate using dual electrodes (with epicortical and intracortical contacts) placed in the prefrontal, premotor, supplementary and primary motor and parietal cortical areas, as well as a nerve cuff placed on the left trunk of the vagus nerve. Data analysis focused on the cortical evoked potentials elicited by VNS and recorded at cortical sites both ipsilateral and contralateral to the VNS. VNS was delivered to both the auricular branch of the vagus nerve in the noninvasive protocol and through a nerve cuff on the left vagus nerve trunk for the invasive protocol. This work is related to a larger project focused on establishing protocols for noninvasive VNS to augment targeted neuroplasticity and enhance cognitive performance in normal nonhuman primates. This nonhuman primate study will be directly applicable to the development of noninvasive VNS technology that can be used to enhance neuroplasticity and cognitive performance in healthy adult humans.

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.

Immunization for children is a global health priority as 19.5 million children are not vaccinated every year. According to the World Health Organization (WHO), the coverage of global immunization of diphtheria–tetanus–pertussis-3 (DTP-3) has increased to 78%, but the African region has been constantly falling behind. Owing to the high cost of maintaining immunization supply chains (iSC), optimizing the distribution of vaccines is a high priority. The subsequent goal of this research is to optimize the healthcare of children in Africa through the distribution of time-sensitive vaccines whilst utilizing limited resources (e.g., vaccines, vehicles, refrigerators). This research will focus on the transportation of vaccines to rural villages, sometimes referred to as last mile logistics. The optimization model will consider two objectives. The first objective is to maximize the number of children who receive vaccines. The second objective is to minimize the overall effort of achieving scheduling and routing for last mile distribution of vaccines. A linear program will be presented and solved using the CPLEX optimizer. Specific case studies in the literature will be used as inputs to the linear program. Anticipated results are alternative transportation routes and modes (e.g. car, bicycle, walk, boat) to local health facilities and improvement of their associated performance in terms of number of children receiving vaccines in a timely manner. This work is important because it can improve vaccine distribution, and manage available resources efficiently. This work also has applications to other last mile logistics to deliver time sensitive goods, such as perishable food, to further optimize goods received by those in need amidst numerous constraints.

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.

Cortical plasticity is the substrate for learning and memory. It is the basis of an organism’s ability to adapt in response to a changing environment and is central to functional recovery after an injury involving the nervous system. Vagus nerve stimulation (VNS) has already been shown to be effective in altering neuroplasticity. Most VNS research has been conducted on epileptic animals and thus offers little information on how VNS may affect a healthy human brain. The final goal of this project is to establish a minimally invasive VNS protocol aiming to augment neuroplasticity and enhance behavioral performance in a cognitive task. Non-human primates are implanted with cortical electrodes and also receive a stimulating cuff electrode around the vagus nerve in the neck. By delivering current through the cuff, vagal evoked potentials (VEPs) are elicited on the cortex. In order to measure how VNS affects cortical excitability, we pair the stimulation of the vagus nerve with stimulation of a somatosensory nerve (i.e. median nerve) and we quantify the effects on the cortical activity by measuring the magnitude of the evoked responses generated on the cortex. Preliminary results from one animal showed a suppression of cortical activity in the primary motor area (M1) when the delay between the vagus stimulation and the median nerve stimulation ranges between 100 and 150 msec. Four additional animals have received vagus nerve cuffs and neural implants targeting multiple cortical areas. These neural implants give us access to recording not only from M1, but also from prefrontal, premotor, supplementary, and parietal cortical areas. In this way we will be able to characterize the physiological effects of VNS on the cortical excitability of different brain areas, generating data and insights never before obtained and directly applicable to the development of neuromodulation technology in humans.

Among the many cultural treasures within the Burke Museum collections is a full-size sailing outrigger canoe from the island of Chuuk in Micronesia. This canoe is not currently on display but will be part of the Ethnology exhibit of the new Burke opening 2019. The basis of our research was to understand and analyze how Chuukese knowledge about canoes was reflected in cultural aspects such as canoe design, songs, myths, and language. To deepen our understanding of the Chuukese canoe we researched cultural aspects through methods such as literature review, community interviews, and collections analysis. Our aim for our research was to give a greater understanding and contextualization in order to unlock the knowledge of the outrigger canoe from Chuuk within the Burke collection. Our hopes were that this research would give visibility to the Chuukese community as well as educate all Burke visitors and staff members.

How is the representation of Yapese knowledge brought to the forefront of musuem spaces? How is Oceanic knowledge recognized as a way of life, through what Epeli Hau'Ofa draws from interconnectedness between community, family, and beyond the Western concept of Yapese outriggers being represented as: Just a boat? Our reserach dives into the history of the Yapese canoe, the spirituality behind its meaning, how it is constructed, and how the outrigger connects to resources and sustainability. Through interviews done with Yapaese youth and elder within the community, analyzing material culture, and participartory knolwedge through the emerison of Yapese dance, we were able to bring Yapese voice into the display that will be at the Burke Museum. We aimed to connect the modern knowledge we have today with the cultural context surrounding daily Yapese society. The importance behind bridging these two forms of knowledge is to expose and provide a deeper understanding to those who only have access to non-indigenous studies of the Yapese culture.

The Marshall Islands are often recognized as the victims of US nuclear weapon testing, leaving a lot unsaid about who they are as a people. This dark past often times overshadows the resilience and ingenuity within the Marshallese culture. This research project is aimed to gain a better understanding of Marshallese culture through their canoes and navigation techniques. The way that they navigate and construct their vessels plays a large role in their lives; their voyages, their developed culture, language and livelihood. Our methods include interviewing Marshallese community members within Seattle, analyzing navigation articles, wave charts and using the Burke Museum collection database for information on Marshallese canoes. We anticipate that this project will result in the general public walking away knowing the strengths of the Marshallese and a better grasp of one of the cultures in Oceania that is often underrepresented. It is important to look into other cultures, especially those we do not know a lot about, because you can learn so much from them. We also anticipate making relationships with those we interview and by understanding the views and values of their culture. By the end we hope to have opened the door for future research in this realm to encourage people to explore this on their own and participate in clubs and organizations.

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.

In Samoan culture the va’a alo, the word for canoe, represents Samoan culture and indigenous science. The relationship between the canoe and the people who continue to use them reflect Samoan mana (cultural spirit). To understand the meaning of the canoe, it is important to understand the complexity and interconnectivity between the va’a alo and the natural world as well as the activities of the people on and off the canoe. Much of the history and resources about the va’a alo that are accessible to students have been tainted by a colonial lens and we strive to counteract these practices and bring forward the beauty and relevance of indigenous knowledge connected to the va’a alo. Our research emphasizes the importance of how Samoan culture connects its people to the canoe. We examine the cultural significance of the canoe design and the role of each person on the canoe. To understand the Samoan canoe, we must also understand its people and cultural values as reflected in canoe practices. Our research methods include lived knowledge of ceremonies and spiritual beliefs as well as interviews with Samoan elders, analysis of mythology, tattoos, proverbs, siva samoa (dance), and published voyages. We are conducting this research to educate the Seattle public through the Burke Museum of the importance of indigenous canoes and their value in Samoan culture throughout history and still today. We hope our results will help current Samoan generations, and even non-Pacific Islanders, to keep in touch with their Samoan traditions and ancestors. Maintaining this indigenous knowledge for the future is also a prominent goal that we hope to pursue. We want to keep this Samoan and the traditions of the canoe alive.

International Transracial Adoption (ITRA) is something that became popular in the 1950’s and adoptions from Asia has accounted for approximately half. International adoption occurs when a child from one country is adopted into another. Transracial adoption is the phenomena of adoption across racial and ethnic identities. While popular, the effects of ITRA on racial and adoptee identity formation are still unknown. The study focuses on the Adoptee Mentorship Program (AMP) and AMP’Lified Program that teach International Transracial Adoptees (ITRAs) from Asia about racial and adoptee identity while building community. This study aims to understand how a mentorship program could affect the adoptee and racial identity formation process for other adoptees ages 5-18. The study used a series of program evaluation surveys to determine the effects of the mentorship program on adoptee and racial identity formation. It is hypothesized that the mentorship program will allow ITRAs to develop a stronger sense of their racial and adoptee identity. This was measured through several short answer and likert scale questions focusing on how the adoptee identifies themself as an Asian and as an adoptee. Questions measured self-esteem, knowledge around race and adoption, and whether or not the ITRAs felt a sense of community from the mentorship program. The pre and mid-way survey were conducted in November and March respectively. It is believed that data from these two surveys will show a positive correlation between the AMP and AMP’Lified Programs and the racial and adoptee identity formation for the youth. The final survey will be conducted at the end of the program in June and researchers hypothesize the program will continue to strengthen the racial and adoptee identity of ITRAs. Understanding the effects of mentorship programs on adoptee and racial identity formation for ITRAs will allow for better post-adoption resources and services for adoptees.

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.

During the formation of the early embryonic zebrafish body, bipotential neuromesodermal progenitor cells (NMPs) that are located at the posterior end begin to differentiate via regulation of the Wnt pathway. Relatively higher Wnt-signaling activates the expression of the tbx16 gene, which in turn inhibits the neural fate and commits cells to a mesodermal (muscle) fate. The aim of this study is to understand the downstream effects of tbx16 on the rate and mechanism of anterior migratory transitions of mesodermal cells as they leave the progenitor region and travel to the somite-forming mesoderm region. We have previously shown that successful anterior migration and differentiation of mesodermal cells is dependent upon tbx16 downregulating the expression level of two Arhgaps, a Rho GTPase-activating protein. Hence, we heat shock hsp70: Arhgap29 and hsp70: Arhgap35 zebrafish transgenic lines at early somite stages in order to compare and contrast the effects of sustained Arhgap activation during the critical period of mesodermal cell anterior migration. At 24 hours post-heat shock, embryos are sorted by wild-type and transgenic, with transgenics having severe defects in their posterior somite formation. Followed by immunocytochemistry for a muscle antibody, confocal imaging on whole-mount embryos captures the shape and number of somites from each transgenic line. My results show that while Arhgap29 affects both the number and morphology of somites, Arhgap35 only affects their morphology. This suggests that these two Arhgaps do not have overlapping roles in the control of mesodermal cell migration. I am currently performing a separate in-situ hybridization experiment to help me understand the role of these Arhgaps on the essential genes involved in muscle cell differentiation. This study contributes to understanding early vertebrate development as a model for human embryogenesis.

Flowering plants have coevolved with insect pollinators in a mutualistic relationship; plants provide nectar to insects and insects in turn cross pollinate flowers. Plants have employed a range of colors, scents and shapes to attract their insect pollinators. Vision, olfaction, and mechanosensation all have roles in the identification and interactions with flowers. While the roles of vision and odor sensing have dominated the literature, recent work has shown that mechanosensation plays as much a role as vision in ensuring that moths stay engaged with a moving flower. Moths use their straw-like proboscis to probe a flower, using the overall shape of the flower as well as tiny grooves in the petals to guide the insect’s mouthparts toward the nectary. Using the feeding behavior of the nocturnal hawkmoth, Manduca sexta, we ask how moths use mechanosensory information to find the nectary opening in flowers. We combine 3D printing technology--to generate different 3D flower curvatures, with micro-sensing technology--that allows us to detect the proboscis tip inside nectary, and computer vision techniques--to detect the motion of the hovering moth, to test the relationship between flower shape and efficiency in locating the nectary. We find that flower exploration depends on its 3D curvature. Moreover, over repeated trials, moths take less time to find the nectary across all curvatures suggesting that moths use tactile exploration to learn flower shape. Mechanosensation is one of many inputs used by moths in the wild to interact with their environment. In future studies we wish to explore the integration of mechanosensation with other sensory information, and the salience of each modality.

The south Puget Sound region has a history of smelting activity, notably the ASARCO smelter that operated in Ruston, WA. Despite the smelter being closed, the consequences of this smelting activity are still felt today. Due to high levels of arsenic contamination in the region’s soils, the area was designated a SuperFund site. Preliminary research conducted in 2014 indicated that several urban lakes in the Tacoma/Federal Way area also have high levels of arsenic in their sediments. If the arsenic is mobilized into the water column, where it can be taken up by lake biota and biomagnify up the food chain, it could potentially affect human health and ecosystem health. We examined two lakes, Angle Lake and Lake Killarney, that have the same amount of arsenic in their sediments, but different physical properties likely impact the release of arsenic into the water column. Angle is seasonally stratified, while Killarney remains well-mixed all year. Consequently, the bottom waters of Angle Lake stay at a relatively stable temperature of 4-10°C and consistently have arsenic concentrations between 30-100 ppb year-round. In contrast, bottom waters in Lake Killarney warm significantly from 4°C in the winter to 21°C in the summer and arsenic concentrations increase from 75 ppb to 700-1000 ppb. We hypothesize that temperature is the primary control on the release of arsenic from the sediments. To test this hypothesis, sediment cores were taken from each lake and placed into plastic tubes. To test this hypothesis, sediment cores were collected from each lake in the winter when all lakes have low bottom water temperatures. The cores were placed into two different temperature treatments, 10°C and 20°C. Samples of the water overlying the cores will be taken every week and measured using ICP-MS to determine the flux of arsenic out of the sediments.

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.

Indoor Environment Quality (IEQ) is a vital topic to address in today’s studies as it presents a significant role to the overall well-being of professionals who work indoors. IEQ adheres to overall human reactions to cleanliness/dirtiness, surrounding temperatures, and other irritants that may exist. While studies of IEQ in office environment have been well documented, less is known about IEQ during construction of an interior renovation. There are numerous possibilities of exposure to contaminants and pollutants both during construction and renovation to workers and building occupants, whom become vulnerable to the dusts and odors from construction. Currently there are no enforceable indoor air quality (IAQ) standards targeted specifically for office environment, so it is vital to address these topics and increase awareness, advocate the practice of applying minimal toxic materials, and prevent health concerns. In order to promote productivity and bridge the gaps in awareness concerning IEQ and health in office buildings, this three-phase project at the University of Washington Tower (UW Tower) aimed to addressed and advocated the importance of providing satisfactory IEQ, sustainable renovated workspaces, and shared IAQ strategies that could be implemented during indoor construction and renovation projects. Overall, three phases were implemented in this project. Phase-One took place four weeks before retrofitting. Phase-Two occurred during the construction. Phase-Three occurred after moving to the retrofitted workspace. This project involved collecting and analyzing IEQ data as well as surveying employees at the UW Tower to assess their psychological state, regarding each individuals enjoyment, well-being, at their workspace before and after construction. Future investigations should be directed at understanding what types of construction practices should be used to reduce pollutants, airborne toxins to maintain satisfactory IEQ.

Chronic low back pain (CLBP) poses a major public health burden, affecting 31% of the general population and 54% of older adults. Among individuals with CLBP, multisite pain increases the risk for persistent pain and can lead to physical and mental impairments. Despite this, multisite pain research is limited and little is known about its relationship with health-related quality of life (HRQoL). This study describes the effect of multisite pain on HRQoL and the association between multisite pain and falls in older adults with CLBP. We conducted a secondary analysis using the Back Pain Outcomes using Longitudinal Data (BOLD) registry. BOLD consists of 5,239 participants, ≥65 years, from three health systems, with new primary care visits for back pain. We identified 899 participants with CLBP (>2/10 pain intensity, 6 months after new visit) and assessed comorbid pain at 6 pain sites, including widespread pain. Outcomes of HRQoL (EQ-5D, scored 0-1) and falls prevalence in the past 3 weeks were evaluated 6 and 18 months after participants met the chronic pain criteria. We used linear and logistic regression models to test the relationship between number and type of pain sites with outcomes, adjusting for demographics and health characteristics. Widespread pain (b=-0.035; CI: -0.058, -0.012) and pelvic/groin pain (b=-0.027; CI: -0.050, -0.004) sites were associated with lower HRQoL. For each additional pain site, HRQoL scores decreased an average of 0.013 points (95% CI: -0.020, -0.007) and odds of a fall increased 30% (OR, 1.30; CI: 1.12, 1.51) with nearly all falls occurring in those with >1 pain site (>95%). Number of pain sites had stronger associations with decreasing HRQoL than individual pain sites. Multisite pain increased the risk for falls. Clinicians and researchers should assess multisite pain as a potential risk factor for low HRQoL and falls in older adults with CLBP.

The way adolescents describe their emotions shapes how they view themselves, peers, and the world around them. Observational and experimental studies have shown feelings of gratitude in particular to be linked to an increased sense of well-being, academic performance, and prosocial behavior. Previous studies have defined “gratitude” as an appreciation of what is valuable or a state of appreciation. This study explored 1) how gratitude varies across different peer interaction scenarios and ethnic groups, and 2) how adolescents explain the emotion gratitude. Studies have yet to examine how ethnically diverse students interpret the emotion. Our sample size consisted of 300 students from ages 12-18, evenly divided between African, European, Mexican, and Native Americans across Washington state. Students provided explanations of times where they were an actor and recipient in four different scenarios: calming, amplifying, avenging, and reconciling a peer. In each scenario students rated how grateful they felt and why. Quantitative analyses demonstrated that students’ levels of gratitude varied by role and scenario, but did not vary by ethnic group (all ps < 0.001). This suggested that adolescents’ definitions of gratitude could vary in different roles as well. To understand influences on gratitude in adolescents, we coded students’ explanations for their actions across all four scenarios to see if different definitions of gratitude were being used in each role. We also present results of demographic analyses relating to gratitude levels (gender, ethnicity, grade level). The results of this study contribute to research on adolescent mental health and peer relationships in school contexts, and could also help school practitioners work towards learning environments that promote student well-being and more stable peer interactions.

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. 

Building relationships with students may not be an easy task as a teacher, because students are coming in with a diverse range of differences which includes students’ backgrounds (i.e. life outside of school, race, socio economic status), perspectives, behavior, and interests. Teacher-student relationships may help increase student engagement, increase their sense of belonging, and help foster a safe environment which can have a significant impact on their success. Unfortunately, research has shown that many teachers are unprepared to teach students from diverse racial and cultural backgrounds. One reason may be that teacher preparation programs have not been as successful in changing teacher's values, attitudes, and dispositions related to teaching culturally diverse students. In my research, I examined the structure and content of the University of Washington Elementary Teacher Education Program (ELTEP) to better understand how teacher candidates transfer knowledge from their course work into their field placement, focusing on classrooms that are situated in culturally, racially, and ethnically diverse Seattle public schools. I analyzed how teacher candidates took up strategies for building teacher student relationships from their coursework into their field placements. I did so through interviews and ethnographic observations, analyzing teacher student communication patterns (i.e. one on one interactions, positive and negative reinforcement, humor, body language, etc.) in their field placements. My findings have significant implications for improving ELTEP coursework focused on building teacher-student relationships and ultimately improving student success in Seattle public schools.

Using a climate model, we changed the Earth’s rotation direction from counter-clockwise to clockwise, keeping the period of 24 hours the same. The purpose of this experiment was to better understand how various climate variables are affected by Earth’s rotation. The results give insight into patterns of today’s climate, and help to frame discussion of future climate changes. The model used was GFDL CM2c, a course climate model that utilizes coupled ocean-atmosphere physics. The model was run for a 100-year control simulation, followed by a 700-year reverse rotation simulation. Model output revealed drastic changes in many of Earth’s climate variables. The main effect was that atmospheric flow pattern switched directions, with westerlies becoming easterlies, and vice versa. Because of this, ocean currents switched to opposite sides of ocean basins and there was a new distribution of sea surface temperature. As a result of these changes, global precipitation and temperature patterns were greatly affected. Some dry areas, such as the Sahara Desert, were now wetter, and some wet areas, such as the southeastern U.S., were now deserts. Albedo and ice coverage increased in the Northern hemisphere, possibly due to the ocean circulation changes. Unexpectedly, the thermohaline circulation weakened significantly in the Atlantic Ocean while a similar circulation developed and strengthened in the Pacific Ocean. These results are fascinating and important for testing current knowledge of the climate system.

Ocean acidification is projected to put coral reefs in a state of net dissolution by the end of the century. Coral reef ecosystems are important habitats, supporting 25% of marine biodiversity in less than 0.1% of its surface area. As humans continue to burn fossil fuels, adding CO2 to the atmosphere and oceans, local mitigation approaches become increasingly important to consider for preserving these vital ecosystems. Bubble stripping is a geoengineering approach to ocean acidification that has been modeled and tested in the laboratory as an effective means of enhancing air-sea gas exchange in coastal ecosystems. Bubbling of CO2-deplete air through the water column allows dissolved CO2 to diffuse into the bubbles and, ultimately, the atmosphere. Bubbling is strategically timed to occur at night, when organisms are respiring and CO2 is not removed by photosynthesis. By increasing the rate of air-sea gas exchange, the ocean and atmosphere equilibrate such that concentrations of CO2 do not reach the extremes that would otherwise occur in the water column. In this study, we used airstones (bubble diffusers) and a test tank to confirm the results of an earlier bubble stripping experiment. Bubbling increased pH and decreased dissolved inorganic carbon (DIC). Its effectiveness could be optimized by testing parameters like bubble size, air flow rate, and water column height. However, obtaining and expelling compressed air is an energetically expensive process, so bubble stripping would likely be useful only for stabilizing seawater chemistry in specific, small sections of reef.

Increased specialization within the forestry industry has led to the rise of a distinct industry known as forestry services. Whereas logging historically encompassed this work, a separate population increasingly participates in the remote grooming and tree planting of forest lands. Physically demanding, dangerously hazardous, and low paying, forestry services work in the Pacific Northwest predominantly employs Mexican and Central American immigrants. As an extension of my honors project at the UW School of Nursing, I examined how occupational injury among this group of workers with correlates with attitudes that workers and employers hold about their work environments. Performing a secondary analysis using survey interview data collected by the UW Pacific Northwest Agricultural Safety & Health Center, and the Northwest Forest Worker Center, I identified top risk perceptions and barriers to workplace safety as reported by workers, as well as by a set of employers and supervisors. Not only was there variation in the prevalence of worker injury between different employers, there was also variation in the perceived attitudes about workplace safety. In future research, it will be possible to link the experiences of workers with the attitudes and policies of those who employ them.

In educational and research settings, Tetrahymena thermophila is a fresh water protozoan that serve as an excellent model organism for elucidating phagocytosis and ciliary motion. As a step towards determining how Tetrahymena thermophila adapt to environmental changes, we developed new, practical, inexpensive approaches that label organelle changes in fixed and living cells. To address our research objective, we pursued the following experimental approaches: One, a novel heat fixation method was used to fix Tetrahymena thermophila prior to doing a Wright stain and different conditions of Wright stain were performed and observed with a light compound microscope; two, to observe cells that have loss of plasma membrane integrity, we pre-incubated 20µM of Sytox green dye for three hours and observed for green fluorescence in the macronucleus (MAC) and micronucleus (MIC). We used a new portable battery-operated inverted fluorescence microscope designed by Dr. Rebecca Richards-Kortum’s research group and Cellcams for acquiring images and time-lapse movies. We found that heat fixed Tetrahymena thermophila followed by a Wright stain labeled organelles at different stages of their life cycle. We conclude that using Wright stain and Sytox green fluorescence dye in combination with heat fixation are novel low-cost applications that allow phenotypic analysis in Tetrahymena thermophila. In the future, these useful approaches can be applied broadly into many lab inquiry settings, such as toxicology and molecular genetics.

A consequence of the rising opioid epidemic in the United States is the dramatic increase in the number of infants born with a drug dependency known as neonatal abstinence syndrome (NAS). Treating NAS often requires lengthy hospital admissions and presents a range of challenges to both nurses and mothers caring for these newborns. While the nurse-mother partnership carries great potential to improve treatment outcomes for the infants, it is frequently hindered by stigma and poor maternal engagement. The purpose of this study is to better understand the nursing and maternal-level factors that affect the nurse-mother relationship and to identify the needs of both parties to partner in infant caregiving. We collected data through surveys given to nurses and mothers at Swedish Medical Center First Hill and Ballard campuses. Data analysis of the nurse surveys focused on the relationships among knowledge and comfort with NAS, stigma, and compassion while analysis of the mother surveys focused on the relationship among trauma history, parenting confidence, and maternal engagement. We hypothesized that greater knowledge and comfort with NAS among nurses was associated with decreased stigma and increased compassion towards families affected by this syndrome. We also predicted that extensive trauma history and lack of parenting confidence was negatively associated with the mother's ability to engage with her infant. In creating a better understanding of the nurse-mother relationship, we hope to guide future research on developing interventions that will improve the nursing care and maternal engagement in families affected by NAS.

One potential benefit of vegetated building rooftops, called ecoroofs or green roofs, is reductions in outdoor air pollution levels. However, there is little empirical data on real roofs that would enable evaluation of air quality impacts of ecoroofs. We developed and tested a low-cost dynamic flux chamber for characterizing ozone (O3) deposition on the vegetation and substrate typically used for ecoroofs. Ozone flux measurements were determined in the lab using ecoroof substrate; the next phase of testing uses ecoroof vegetation called sedums. To measure flux, a 6.59 L acrylic chamber is injected with ozone to elevate chamber O3 levels. Ambient air is drawn through the chamber by a vacuum pump. The decay of O3 levels are measured by an ozone monitor. Separate tests are conducted using an inert tracer gas, CO2, to measure the chamber air exchange rate. Preliminary results show the chamber had an air exchange rate of 0.17 ± 0.023 min-1. Minimization of errors between O3 measurements and mass balance models yielded deposition velocities (vd) for both the acrylic chamber and substrate, which were 0.16 m/hour and 5.66 m/hour respectively. Future experiments will characterize substrate and vegetation across a range of temperature, moisture content, and lighting conditions. These results will constrain models of rooftop pollutant dynamics, enabling estimates of impacts of rooftop vegetation on both urban and indoor air quality.

As the field of genomics continues to grow, there is an overwhelming need for robust ways to assemble entire genomes, yet there is little guidance on what software best achieves this goal. An assessment of available genome assemblers is needed to improve assembly procedures. Genome assemblers output draft assemblies consisting of DNA scaffolds that are permeated with errors inherent to sequencing data, like wrong number of repeats, misjoins, inversions, missing sequencing, and extraneous sequences. These draft assemblies can then be input into an experimental assay called HiC that attempts to fix and orient the assemblies by taking into account chromatin contact interactions to elucidate genome architecture. The resulting genome is then more accurate and useful for research purposes. However, given the plethora of genome assembly and HiC software available, navigating each available software is time consuming and often requires extensive testing before actual use can begin. To improve this process, we aim to review several HiC scaffolding software tools for performance and quality, and fine tune their parameters for optimized outcome. This will allow us to suggest which software work best for a range of genomic data as well as provide summary statistics and accuracy measurements for each genome assembler tested. We tested several genome assemblers, including GRAAL and SALSA, which utilize HiC libraries to scaffold draft assemblies. After being produced and corrected through assemblers, these assembled genomes can then be used to advance research in functional genomics, genetic epidemiology, and many other fields reliant on genomic data. It is our goal to improve genome assembly procedures so that more researchers can use open source software to build and understand entire genomes and further the field of genomics.

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.

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).

Smoking is the world's leading preventable cause of death and it is responsible for millions of deaths annually. Smoking costs the United States billions of dollars each year due to medical care and lost productivity. There is very little research that addresses Hispanics working in agriculture jobs. This study evaluates whether and to what extent smoking is a coping mechanism for Hispanic males to manage agriculture work-related stress. This qualitative research study includes 5-10 short formal interviews with Hispanic males residing in Wenatchee, WA who smoke and work in agriculture. Results are analyzed using thematic analysis. Expected results are that Hispanic males who experience agriculture work-related stress use smoking as a coping mechanism, and experience negative health effects caused from either stress and/or smoking. This project will help health centers create programs that promote awareness on smoking and work-related stress that Hispanic males may be experiencing due to job roles.

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.

The three essential structures of life are RNA, protein and a lipid bilayer membrane. We hypothesize that these three structures formed co-dependently in an aqueous environment, as opposed to forming independently in diverse environments. In our scheme, a vesicle (membrane) formed and bound nucleobases and amino acids, the building blocks of RNA and proteins, respectively. Then, the resulting confinement and conformational constraints imposed by the membrane on the nucleobases and amino acids facilitated the formation of RNA and proteins, leading to the origin of life. The work presented here addresses one part of the hypothesis: “Do amino acids increase vesicle formation?” An increase in vesicle formation due to the addition of amino acids would support the hypothesis that membranes and proteins evolved co-dependently. It would suggest that amino acids stabilize vesicles, increasing the likelihood that fatty acid membranes and amino acids co-localized. Our experiments used decanoic acid, a prebiotic fatty acid that spontaneously forms membranes when dissolved in water. In the first part of the research, we added aqueous solutions of amino acids to a solution of decanoic acid at pH 6.83 and determined the extent of vesicle formation by measuring light scattering with a spectrophotometer. In the second part, we added amino acids to a decanoic acid solution above the pH at which vesicles form, and then slowly acidified the solution until vesicle formation began; again, we used light scattering as a measure of the extent of vesicle formation. We found that specific amino acids do in fact increase vesicle formation and also have an effect on the pH at which vesicles form. The next step in this research will be the addition of multiple types of amino acids and peptides additions in order to search for combinations that increase vesicle formation the most. The results contribute to the the possible driving mechanism behind the emergence of protocells.

Glutathione S-transferase (GST) is an enzyme that is present in most organisms. Its primary function is the detoxification of xenobiotic compounds. In mammals, some GST isoforms have a role in modulating the MAPK signaling pathway. The GST protein from Schistosoma japonicum (26 kDa) is also an important tool used in biochemistry labs as a tag for the isolation of proteins via affinity chromatography. Reduced glutathione (GSH) is a substrate for GST that binds to its G-site with a high affinity, and this interaction can be exploited to purify GST-fusion proteins on agarose beads containing a GSH moiety. In the research presented, GST was expressed in E. coli, purified, and dialyzed to remove GSH ligand completely. The protein concentration of the purified, dialyzed GST sample was quantified using Qubit™ fluorescence spectroscopy. Isothermal titration calorimetry (ITC) was utilized to measure the dissociation constant and thermodynamic properties of the binding of GSH to GST. ITC is a highly sensitive analytical method that monitors changes in heat produced from noncovalent chemical associations. In order to obtain accurate ITC measurements, various concentration ratios of GSH/GST were explored. Quantifying the binding affinity and thermodynamic properties of GSH binding with GST provides useful information for investigators who use GST as a fusion tag or who are interested in reactions between the GSH-GST complex and its substrates.

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.

Can arts administration be an artistic act? Can curation itself be considered a performative art? These are two questions swirling in my head as I prepare to embark on a post-undergraduate journey of freelance art making and arts administration. My theory is that these two things do not need to be conceived of as mutually exclusive, specifically, that there is an art to simply making art happen. Through an experiential research process, I, as a performing artist, shall perform the role of art curator, undertaking contemporary concerns, processes and logistics in the field as such, and will produce an exposé of art by other artists as well as a research paper detailing my experience and a performed ‘curatorial talk’ about the featured work. Via this process, I hope to better understand the balance of generating and producing opportunities that mutually enhance both my individual art practice, and the practices of others. While, ultimately encouraging more working artists to invest in the wider conversation of what kind of work should be shown in this moment.

 Functional morphologists examine the anatomy of organisms to elucidate how they are adapted to various habitats and behaviors. These type of studies have also led to intense research and speculation about the specific behaviors associated with the morphologies of now extinct species. Can we predict the hunting behavior of a predator from its skeletal morphology? In this study, we examined both femur morphology and the calcaneus to femur length ratios in extant members of Carnivora, with the goal of finding a link between these traits and a species’ hunting strategy. We categorized hunting strategies from videos and previous accounts by taking note of the presence and timing of each species’ attacks of live prey. To quantify hind limb bone morphology across species with different hunting strategies, we measured the length of the calcaneus and femur, and the minimum bone diameter of the femur. Our sample included 12 extant species from several hunting strategies. We expect to find femurs with a greater minimum diameter in species that have strategies that require greater muscle force during the prey capture period. This type of anatomy would provide the support necessary for attachments of larger running muscles. For femur to calcaneus ratio, we expect to find a lower value in species with longer chase periods in their hunting strategy. This would be due to a greater need for longer strides and contact time to reach the speeds necessary to catch their prey. This study will allow scientists to more accurately predict the hunting behaviors of extinct animals based on measurements that can be easily obtained from an intact fossil.

Humans have limited ability to regenerate many tissues. In instances such as limb loss or spinal cord injuries there is a dramatic decrease in quality of life and there are few therapeutic options to help recover from these serious injuries. My research characterizes how epigenetic changes affect tail regeneration in the frog, Xenopus tropicalis. Xenopus tadpoles have significant regenerative abilities when they are developing but that ability is lost as they age and undergo metamorphosis. This transition in regenerative ability makes them a great model for understanding the molecular differences between tissue that can regenerate and tissue that can not. Other advantages of Xenopus for epigenetic studies of regeneration include a well-characterized diploid genome and many well-established molecular tools. Previous work by our group has shown that the accessibility of chromatin undergoes drastic remodeling in which many of the genes are made inaccessible shortly after injury in the Xenopus tail. These genes are then reopened during regeneration. These changes are likely due in large part to histone deacetylases (HDACs) and histone acetyltransferases (HATs). We hypothesize that HDACs are necessary for causing the initial inaccessibility of the chromatin and that HATs are necessary for the reopening of chromatin for regeneration. We used an Assay for Transposase-Accessible Chromatin and sequencing (ATAC-Seq) to show that the chromatin does not undergo its normal shift toward inaccessibility over the course of regeneration when tadpoles are treated with HDAC inhibitors, coupled with a reduction in regenerative ability. This study will help us identify how histone acetylation directs changes in chromatin accessibility. Additionally, with immunohistochemistry we can study specific sites of histone acetylation and validate these antibodies for future epigenetic research. Our study of large-scale epigenetic changes during regeneration will help characterize how epigenetic gene regulation enables regeneration.

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.

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.

Homeless service providers often provide care and support to homeless individuals and families with experiences of trauma. Through hearing their client’s trauma stories and witnessing the pain, fear, and suffering that their clients endure, homeless service providers may be at risk for developing secondary trauma. Secondary trauma occurs when a helping professional develops symptoms of post-traumatic stress disorder through empathetic engagement with someone who has firsthand trauma experiences. A recent study revealed that 25% of homeless service providers reported high levels of vicarious traumatization. Amid a growing homelessness crisis and the challenges of ongoing budget cuts that homeless service agencies face, the percentage of homeless service providers with secondary trauma is likely to increase. The purpose of this investigation is to gain a better understanding about homeless service providers’ exposure and experiences of secondary trauma in their work environment. Participants of this study are homeless service providers that were recruited through convenience sampling from a large homeless service organization in King County. Participants completed demographic questions, a highly validated scale measuring Professional Quality of Life (ProQOL), and open-ended focus questions that explored occupational health challenges as well as personal level protective health factors. All measures were collected using an online survey application. We anticipate to find associations between secondary trauma among homeless service providers and high cumulative exposure to working with survivors of trauma, low engagement with self-care practices, a perceived lack of social and organizational support, and high work-related stress. Information gained through this research may be used to identifying ways to protect, sustain, and empower homeless service providers so that they can provide safe and quality care for their clients. The results of this investigation will be used to support occupational health policies and guidelines that promote the health and wellbeing of frontline workers in the homeless sector.

With a society that consumes pharmaceuticals daily, the need to develop more efficient syntheses of bioactive molecules is vital. Organocatalysis is a field in chemistry that has been looked upon to have immense potential to succeed in this area. A type of organocatalyst that has been gaining notoriety is the bisphosphorylimide, which is a stronger acid and more sterically hindered than chiral BINOL-derived phosphoric acids. This upsurge can be attributed to the simple preparation and functionalization of bisphosphorylimides. In this investigation, several bisphosphorylimide organocatalysts are prepared and their performance in a Friedel-Crafts reaction between sesamol and benzylidenecarbamates will be presented. Ultimately, the enantioselective products synthesized from this research may serve as bioactive components in the preparation of pharmaceuticals such as trabectedin, an anti-tumor drug.

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.

In the United States, international education and multicultural education are both discussed and implemented in many schools. International education is a form of education that aims to increase student’s knowledge of world regions and international affairs. It also promotes multiple language learning. One argument for international education is to promote global identity (Parker, 2008; Stewart, 2008). Meanwhile, multicultural education aims to transform the education system into one that provides diverse perspectives, histories, and values (Parker, 2008; Stewart, 2008; Banks, 2008). It focuses on a national civil rights narrative that is inclusive of ethnic identities within the United States (Banks, 2008). It promotes a national identity by focusing on the diversity and history of the United States. These two forms of education present global identity, national identity, and ethnic identity in education. The United States' education policy is profoundly connected to nationalism and largely concerned with unifying American identity (Hutchins 2016). The movements for international education and multicultural education bring into question the tensions over identity-formation and the role of education in influencing students’ identities. Should students mainly become national citizens or global citizens? Both? Neither? The purpose of addressing these questions is because modern education is closely related to liberal democratic nation-state development administered by the state through mass education (Hutchins 2016). The tensions of implementing both or either international education and multicultural education is because of this relationship. A change in education is a change in identity which relates to how domestic issues like minority rights and international issues like international peace and economics are handled. The purpose of this project is to consider the impact of these two programs on identity-formation in the United States by how they affect the legitimacy of the nation-state and how it could alleviate unchecked and dangerous nationalism in domestic and international policy.

Cystic fibrosis-related diabetes (CFRD) complicates up to 50% of adult cases with CF. However, its pathogenesis is poorly understood. One thing that has been shown, however, is that amyloid deposition occurs in the islets of 60% of subjects with CFRD, which is known, from data in other forms of diabetes, to be toxic to insulin-producing islet β-cells. Currently existing animal models do not reproduce this feature of human CFRD, since islet amyloid deposition requires the expression of an amyloidogenic form of the islet peptide islet amyloid polypeptide (IAPP). To address this gap in the field, our group is generating a CF mouse model that expresses the human amyloidogenic form of islet amyloid polypeptide (hIAPP). To do this, we have generated a double transgenic mouse from a male homozygous for the CF mutation and a female hemizygote for the hIAPP transgene. Mice will be followed for up to 12 months, or until hyperglycemia develops. During this time, body weights and non-fasted blood glucose levels will be measured monthly. When hyperglycemia is identified, animals will be euthanized in order to determine if islet amyloid is present in the pancreas. We are expecting to find that mice bearing the CF mutation and expressing the hIAPP transgene will develop increased and/or accelerated amyloid deposition in their islets as compared to the control mice generated by the cross. In addition to this, we expect that these mice will also show increased glucose levels (hyperglycemia) and decreased β-cell mass. There are currently 16 mice on study, and data collection is ongoing, with additional animals being enrolled approximately every two weeks. The goal of this study is to generate a new model of CFRD, which better reflects the human disease state, and can be used to develop and test improved therapies for human CFRD.

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.

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.

Infants born prematurely often suffer from hypoxia-ischemia and inflammatory responses that can lead to cognitive delay and behavioral problems. A novel rodent preterm brain injury model is being developed to simulate histological and behavioral changes seen in preterm brain injury. It was hypothesized that injured pups {in-utero hypoxia-ischemia followed by post-natal lipopolysaccharide (LPS)} will have a significant early behavioral deficit compared to controls. The rodent model of preterm brain injury includes: intrauterine hypoxia at embryological day 18, with postnatal LPS administration from Postnatal (P) day 2 to P4. In order to assess behavioral changes I conducted early reflex and motor skill tests on rat pups from ages P8 to P13. Early reflex testing included: righting reflex, negative geotaxis, and cliff aversion. Early motor testing included: ambulation, front limb suspension, hindlimb suspension, and grip strength. There was no significant difference seen in early reflex testing between control vs injured. Significant difference (P<0.05) was observed between control (n=19) vs injured (n = 11) in early motor testing: grip strength impulse, ambulation, hindlimb suspension and front limb suspension. Based on these findings, the novel preterm brain injury model is producing a motor deficit in the injured groups compared with the control group. Going forward, we will continue to repeat this experiment to verify the results and further elucidate what aspects of behavioral development are impacted most by this injury model.

Chronic pancreatitis (CP) is a condition in which the pancreas is consistently inflamed, resulting in pain, malabsorption of nutrients, and irreversible organ damage. CP-related pain can be severe and is associated with decreased quality of life and impaired psychosocial functioning. Treatment options for CP, particularly for pain management, are extremely limited in both scope and efficacy. It is imperative that additional pain therapies be made available to the CP population. Cognitive behavioral therapy (CBT) is a non-pharmacological treatment that has shown benefits in helping people cope with painful conditions. This study aimed to 1) adapt an established online CBT program (The Pain Course) for people with CP pain, 2) assess feasibility and acceptability of the program, and 3) conduct a pilot randomized controlled trial to determine preliminary efficacy of the program. We first adapted The Pain Course through careful review of the existing five lessons and case stories to insert information about CP and its symptoms to increase the relevancy of the program for CP patients. In the second phase of the project, 10 CP patients will receive access to the modified online course (The Pancreatitis Pain Course) and will complete the intervention to learn cognitive-behavioral pain coping skills. Patients will provide qualitative feedback regarding their experience and the acceptability of the intervention through interviews, and the course will be modified further. In the final phase, 30 patients will be randomized (15 patients will receive CBT and 15 will receive waitlist control condition). Outcome data on pain, psychological functioning, and quality of life will be obtained at baseline, 8 weeks, and at three-month follow up to assess treatment efficacy. Ultimately the goal is to develop a safe, economical treatment option for those who suffer from CP pain that will alter and expand current clinical practice of CP pain management.  

Alzheimer’s disease (AD) is a debilitating neurodegenerative disease that currently affects >5 million individuals. We have previously demonstrated genetic and neuropathology-based variation across cognitively-defined AD subgroups. Here we sought to determine whether patterns of vascular risk factors differed across cognitively-defined subgroups. We used data from the Adult Changes in Thought (ACT) Study and the Religious Orders Study/Memory and Aging Project (ROS/MAP). These are prospective cohort studies of individuals who are dementia-free at enrollment. We used cognitive data at the time of AD diagnosis to determine scores for memory, visuospatial abilities, language, and executive functioning. We used these scores to determine each individual’s average cognition and then domain-specific deficits below that individual average. We used these data to define six groups: no domain with a substantial relative impairment; isolated substantial relative impairment in memory, in visuospatial functioning, in language, or in executive functioning, and multiple domains with substantial relative impairments. We evaluated risk factors for these six groups from self-report and/or diagnosis data on vascular conditions, including diabetes, stroke, hypertension, atrial fibrillation, cholesterol levels, and coronary artery disease. We used multinomial logistic regression models with the no prominent domain group as the reference. To account for multiple comparisons, we present tests of the null that each risk factor is unrelated to each subgroup, and an omnibus test of the association between each risk factor and any subgroup. The proportion of individuals in each subgroup differ between the two studies. Our results suggest possible differences in risk for specific cognitive domain deficits associated with stroke history, HDL cholesterol, and treated diabetes. Subsequent work will attempt to understand possible mechanisms behind these associations through literature review. These results support additional efforts to further understand cognitively-defined AD subgroups.

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.

Fetal ultrasounds are frequently associated with joy and happiness for expecting mothers, however, women seeking termination can be subjected to emotional and financial distress due to mandatory ultrasound screenings. My literature review examined how different ultrasound laws and healthcare coverage impacted women in Washington and Texas. These states have very different regulations and coverage for ultrasounds during pregnancy or termination. To do this, I examined laws in each state regarding fetal ultrasounds to see if there were benefits or disadvantages for women choosing to carry their pregnancies to term versus choosing to terminate. My findings showed women seeking termination in Texas undergo a mandatory viewing of their fetal ultrasound before they can access termination, whereas, women in Washington are not required to do so. Payment coverage for ultrasounds also varied between states. Differences in required payment for private insurance and Medicaid disadvantaged women in Texas, but not Washington. My findings showed Texas Medicaid did not cover the mandatory ultrasound before termination, whereas Washington Medicaid covered all termination services. Texas Medicaid was also shown to offer less coverage for women intending to carry their pregnancies to full term than private insurance. Depending upon geographical residence and health insurance status, the ultrasound experience will vary significantly, especially for women seeking termination. With this research, I hope to increase awareness of the effects of mandatory ultrasound laws and gaps in payment coverage for women covered by Medicaid. Drawing attention to this issue and starting a conversation is the first step in moving towards an equitable health care system.

Energy efficiency of important industrial chemical reactions is a motivation behind scientific research across a wide range of disciplines as a response to the growing energy crisis. Electrocatalysts play a crucial role in improving energy efficiency in the interconversion of electrical and chemical energy, and are essential components in any sustainable solar fuels conversion scheme. An issue in the widespread use of renewable energy sources is the fluctuation between energy demand and energy supply. This issue can be solved by using the renewable energy source to generate chemical fuels, storing the energy from the sun or wind in energy-dense chemical bonds to be released on-demand. One such fuel is molecular hydrogen, H2. Molecular [Ni(PNP)2]2+ catalysts are highly active catalysts for the hydrogen evolution reaction (HER) that employ pendant amines—an end group that assists with hydrogen production by allowing for efficient proton transfer. However, as molecular species, these catalysts suffer from low stability and low potential for scalability. The primary focus of this research is to develop an efficient nano-scale Ni2P synthesis based off prior syntheses in the literature, that incorporates cooperative ligands for HER on the surface. Our end goal is to determine the best method to synthesize Ni2P nanoparticles with enhanced activity due to the cooperative effects of pendant amine functionalities to create a nanomaterial catalyst with properties that meet and surpass the molecular [Ni(PNP)2]2+ catalysts for HER.

During the time in between large earthquakes, smaller seismic events, or microseismicity events have been detected along the Cascadia plate boundary. This microseismicity represents the accommodation of small stresses along the margin, and may provide information on the location of high stresses or zones of weakness in the crust and upper mantle, or along the plate boundary. Studying the distribution of microseismicity and comparing it to known structural models based on seismic reflection profiles may help us to better understand the overall faulting process at subduction zones. In this research, I compared the spatial distribution of microseismicity along different parts of the subduction zone with structural features from seismic reflection images. I used earthquakes dataset that are recently compiled using regional seismometer located within the subduction zone as part of the Cascadia Initiative. I presented a depth profile of Cascadia subduction zone forearc, a margin between the oceanic trench and the continental plate, to investigate whether current depth estimates for recent earthquakes are more consistent with upper plate seismicity within the North America Plate, along the plate boundary, or within the down going oceanic plate. The results of this study will help us to better visualize the spatial distribution of microseismic events and draw its relation with the damage zone or other fault structures along Cascadia subduction zone.

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.

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.

 The student population in higher education settings continues to become more diverse by increasing the number of Hispanic, Asian/Pacific Islander, Black, and American Indian/Alaska Native students, but the college graduation rate continues to be lower compared to their white counterparts, except for Asian students (National Center For Education Statistics, 2015-2017). The purpose of this research is to understand if student's academic self confidence correlates with various student identities. The principal research questions for this study are: 1) Is there a correlation between student academic self confidence and their racial/ethnic identity? 2) Is there a correlation between student academic self confidence and whether they are disabled or not? 3) Is there a correlation between student academic self confidence and their socioeconomic status? 4) Is there a correlation between student academic self confidence and whether they’re first generation or not? 5) Is there a correlation between student academic self confidence and their gender? A secondary data analysis will be conducted. This analysis will test the correlation between student's academic self confidence and their various identities. I hypothesize that there is a positive correlation between students having academic self confidence and identifying with the dominant student population. Furthermore, I predict a positive correlation between students not having academic self confidence and identifying with the minoritized student population. Results from this study can be used by higher education professionals to build identity-conscious leadership development programming in order to promote student self confidence and have a positive impact on graduation rates of students of color.

Craniofacial sutures are fibrous joints which connect adjacent skull bones. The sutures are sites of growth but are probably zones of mechanical weakness compared to the bones. The suture’s ability to transmit compressive and tensile loads therefore affects both cranioskeletal growth and stress distribution. I compared tensile mechanical properties of four adjoining sutures, two longitudinal (interfrontal; n=5; internasal, n=2); and two transverse (coronal, n=2; nasofrontal, n=8). Coronal (n=6) and nasofrontal (n=1) were tested in compression. The suture specimens were extracted from the heads of young pigs used in unrelated experiments. All sutures exhibited a “toe area” where substantial strain occurred at a low load relative to the elongation. This region presumably represents the stretching of relaxed fibers. The stress-strain curve showed a linear region that began almost immediately following the toe area, in this “elastic region” the suture can recover its original length when unloaded. At high stress the response began to deviate from linearity. With further strain, the load ceases to increase, the sutures experienced plastic behavior presumably representing increased load bearing by the remaining intact fibers, when even a slight drop in force was seen. The sutures were reshaped permanently, cycles of elastic and plastic behavior continued until a final softening phase and suture failure. The mechanical properties measured were similar at all four sutures under tension and compression. Ultimate stress was variable, ranging from 0.1-4.3 MPa and an overall average of 1.32 ± 0.88 MPa (n=22). Eliminating the highest and lowest values resulted in a more accurate mean of 1.23 ± 0.54 (n=20). These values are considerably less than bone (over 100 MPa). Ultimate strain was more consistent, averaging 5.9 ± 4.3 % (range 2–14%, n=22). These values are considerably more than bone (less than 1%). Thus, sutures are more flexible but less strong than bone.

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. 

Every year, approximately 18,000 children and adolescents are diagnosed with cancer in the United States, and many of these diagnosed children will have siblings. Some studies indicate that siblings suffer from high rates of post-traumatic stress reactions, school absenteeism, behavioral problems, and declines in academic performance. Preliminary results from “Parenting in the Face of Cancer: Non-ill Child and Parent Relationships" indicate that children have misconceptions about the cause of cancer and contagion. They are also reluctant to share their feelings and concerns with their parents, and wonder what their role is in helping their sibling with cancer. The aim of this study is to develop a children’s book to facilitate communication between parents and their non-ill children. We reviewed the published literature about the effects of cancer on school-age non-ill siblings, and conducted interviews with child life specialists who work in cancer care. We also analyzed interviews of school age (7-12 years) non-ill siblings of children with cancer. Analysis focused on sibling’s perspectives of what caused the cancer, contagion, worries and concerns, and the perceived availability of their parents. The siblings’ perspectives and misconceptions were used to develop a story that provides a simple description of cancer, addresses the siblings’ misconceptions and concerns, encourages them to share their feelings and concerns with their parents, and suggests ways they can play an active role in their sibling’s treatment. A future study will be designed to evaluate whether this interactive children’s book alone, or the book with a short nurse coaching session, will improve emotional and behavior outcomes in non-ill siblings of children with cancer.

Nationwide older adults experiencing homelessness is on the rise. In Seattle, over 11,000 individuals are homeless and over 20% are over the age of 50. People experiencing homelessness face a variety of barriers in attaining and maintaining physical and mental health. These barriers are often insurmountable for older adults. The purpose of this investigation was to explore the facilitators and barriers to wellbeing in a sample of male adults over age 50 who are homeless and utilizing a night shelter in Seattle. We used an interpretive phenomenological approach with a photovoice methodology. Participants were asked to take photos that captured their response to the questions, "What supports your wellbeing and what are barriers to your wellbeing?" Additionally, we collected demographic variables such as age, gender, duration of homelessness, and age first homeless. Following the collection of photographs, we held two semi-structured focus groups approximately three weeks apart. At the first meeting, we discussed the meanings captured by their photos. The meeting was audio recorded, transcribed verbatim, and themes were extracted utilizing Dedoose software. We anticipate that older adults have unique unmet needs. A lack of established services tailored to this population, coupled with recent cuts to services has impacted access to programs that foster good mental and physical health. These findings have important implications for nursing practice, gerontology, and public health. Information gained from this project can serve as a tool to inform policy change towards efficacious person-centered solutions for older adults experiencing homelessness.

Elevated mutation rates due to mutations in the POLE gene, encoding DNA polymerase (Pol) Epsilon, drive a subset of colorectal carcinoma and endometrial cancers, and may accelerate tumor malignancy and pharmacological resistance in other cancers. Work with Saccharomyces cerevisiae revealed that classic mutator alleles encoding defects to Pol Epsilon proofreading mutators rely on the S-phase checkpoint, which regulates dNTP (deoxyribonucleotide triphosphates) levels by controlling the expression and activity of ribonucleotide reductase (RNR). This raises the question, do human POLE cancer alleles share this dependency on the S-phase checkpoint? And if so, do they activate the S-Phase checkpoint by creating replication stress? To investigate these questions, we created mutator yeast strains that mimic human POLE cancer alleles and deleted the S-Phase checkpoint kinase gene, DUN1, which works by indirectly controlling the expression of RNR, and thus dNTP production. Here we show that there is a consistent suppression of mutation rates in diploid strains lacking DUN1 compared to those with one or two working copies. We further extended these studies by monitoring key indicators of checkpoint signaling and replication stress. Our work suggests that targeting dNTPs in order to modulate the mutator phenotype represents a potential therapy for POLE mutator driven tumors.

Mutator phenotypes due to mutations in genes encoding DNA polymerases or mismatch repair proteins lead to increased error rates during DNA replication that accelerate the evolution of cancer cells. Work in the yeast Saccharomyces cerevisae indicates that excessive DNA replication errors lead to error-induced extinction (EEX), where every cell within the population dies due to the random loss of essential functions. One escape route from this lethality is the acquisition of antimutator alleles that lower the overall mutation rate. A possible direction for cancer therapy, then, may be to exploit these antimutators in order to modulate the mutation rate of mutator cells with drugs – either to increase mutation rates to a lethal level or suppress mutation rates to the baseline level of non-cancerous cells, thus slowing the rate of tumor evolution. Our lab has identified several different antimutator mutations in genes that regulate the production of dNTPs, the building blocks of DNA. Examination of cancer genomes from mutator tumors reveal numerous candidate antimutator mutations in the corresponding human genes. We reverse-engineered these candidates into mutator yeast strains to test whether they indeed confer an antimutator phenotype. Evidence that mutations exist in mutator driven tumors that confer an antimutator phenotype would suggest that the unrestrained mutator phenotypes may be lethal to cancer cells. These findings raise the possibility of new methods of human cancer therapy by which specific genes can be targeted to manipulate mutation rates.

Autistic Spectrum Disorder (ASD) is a heterogeneous disease characterized by varying degrees of social dysfunction. Several studies by the CDC show that 1 in 68 children in the United States are affected by ASD, this number could be 1 in 45 according to the newest studies by various government resources. So far pharmacological treatments are not effective in most cases, only treating a few symptoms at best rather than the whole. Several theories exist for the pathogenesis of ASD; however, much is still unknown despite multiple studies. Investigators often tend to research the pathology of ASD based primarily within their scientific discipline, and we feel this narrow view limits a deep understanding of the disorder. This literature review explores neurostructural, neurochemical, and genetic disciplines, synthesizing an overall hypothesis of the pathogenesis of the disease. Specifically, we explore specific groups of genes known to have a causal effect in ASD and focus on how they might interact to produce the disorder. We analyze these genes to see how they affect different neurotransmitter systems and impact different structures of the brain. We are restricting our database search using terms such as “genes”, “synaptic transmission”, “brain areas” and “homeostatic/compensatory mechanisms” associated with ASD. The literature suggests that genetic aberrations in ASD are quite numerous and cause cascading effects throughout the brain, affecting synaptic transmission in many regions. Our analysis suggests that ASD is a polygenetic disorder where numerous small changes in protein function occur in multiple brain regions. Homeostatic and compensatory mechanisms cannot correct these cellular and connectivity deficits, and ASD develops. We hope this review helps researchers take a broad view of the various genes, neurotransmitter systems, and anatomical structures implicated in ASD as they embark on future studies.
 

One of the main science goals of the Large Synoptic Survey Telescope (LSST) is to further understand the relationship between dark energy and the universe's expansion. In order to achieve this scientific goal of the LSST, accurate estimates of photometric redshifts, which are used as a proxy for cosmological distance, for galaxies are required. To improve its estimates of photometric redshifts, the LSST could incorporate near-infrared data from other surveys along with its optical measurements of galaxy brightness. In order to understand how photometric redshifts improve with the addition of near-infrared (NIR) data, we statistically compare the quality of photometric redshifts using simulated galaxy catalogs with optical-only and optical-plus-NIR data. In my poster, I quantify the expected improvements to photometric redshifts when LSST optical data is combined with NIR data from the future ESA Euclid or NASA WFIRST space telescopes. In general, WFIRST has less outlier galaxies because WFIRST’s NIR filters have a redder band and can cover deeper in the IR spectrum.

The prevalence of alcohol use disorder (AUD) and associated alcohol-related health conditions is disproportionately high among individuals experiencing homelessness. This disparity results in relatively high use of publicly funded services, particularly high-cost healthcare (e.g., emergency department and inpatient hospital services). A recent study of harm-reduction treatment for alcohol (HaRT-A) showed it was efficacious in reducing alcohol-related harm. The objective of this secondary study was to test whether HaRT-A had effects on inpatient and emergency department service utilization as well. Participants (N=167; 24% women) in this secondary study were recruited from community-based clinical and social services settings and were randomized to receive the HaRT-A intervention or services as usual. Outcomes were post-pre differences in number of inpatient and emergency department visits from 6 months prior and subsequent to study participation. There were no significant group effects on changes in emergency department and inpatient visits (ps > .78). HaRT-A did not precipitate significant changes in utilization of emergency and inpatient services by individuals experiencing homelessness and AUD. The study time frame might have been too short to document changes in such statistically rare outcomes. It is also possible that healthcare outcomes are too distal to show the impact of such a brief intervention. Future treatment trials should include longer data collection time frames to test treatment effects on more distal yet important health-related outcomes.

The Vava'u Archipelago, Kingdom of Tonga, is an island group located in the central south Pacific Ocean. The waters within the archipelago have abundant and diverse marine zooplankton that are a critical part of the local, and likely regional, food-webs. Invertebrate zooplankton and ichthyoplankton form the biological foundation of the reef ecosystem. They are prey for each other and larger organisms. As such, they are key components of energy transfer throughout the food web, and their dispersal can determine the settlement of many species. Any changes to the plankton assemblage has the potential to damage the higher levels of the ecosystem. Assessing the condition and composition of these groups provides key insights into the health of the community. However, the composition and seasonal cycles of Vava’u’s zooplankton communities have never been studied. This information is needed to establish baseline data for detecting impacts to the zooplankton and surrounding marine ecosystem caused by the current progression of environmental stressors in the region, such as global warming, ocean acidification, and local development-related water pollution. Through assemblage and genetic analyses of samples made in April 2017, I estimated the general zooplankton composition of the area. 

Spinal cord injury (SCI) currently affects approximately 285,000 people in the U.S. with more than half experiencing incomplete tetraplegia. Currently, there are no effective treatments, leaving patients with devastating lifelong ailments. This project investigates a new implant to aid treatment and recovery after SCI by mimicking the mechanical properties of the native spinal cord tissues and improving neuro-regeneration through modulation of macrophage phenotypes. Results previously produced in the Ratner Lab for engineered biomaterials research show that scaffolds with a specific porous structure create pro-healing and anti-scarring effects. Based on these results, we hypothesize that when the porous structure is paired with suitable mechanical properties, the macrophage response will be strongly indicative of a pro-healing environment. Proper mechanical properties have been achieved through variation in the chemical composition, water content, and methods of synthesizing the scaffold to preserve the microstructure. Now, the stiffness is tunable over several orders of magnitude and has been matched to the softness of spinal tissue. The scaffold also demonstrates very good biocompatibility, verified through cytotoxicity and endotoxin tests, as well as in literature. To test how cells interact with the implant, I seeded macrophages into the 3D structure and observed the response. If the cells integrate healthily into the softer 3D scaffold, this implies that the material may be a useful tool in treating SCI. To further test this, our collaborators in the Hofstetter Lab will implant the material in rats to investigate the influence on SCI recovery.

The vaginal microbiome has a mutualistic relationship with the immune system and can have a major impact on health and immunity to diseases, specifically its role in prevention against STI’s and Bacterial Vaginosis (BV). BV has been found to be associated with the prevalence and incidence of multiple STI and HIV. We hypothesized that changes in bacterial composition would correspond to changes in inflammatory cell frequencies in the vagina and examined this using rhesus macaques (RM) treated with various antibiotic regimens.12 rhesus macaques were administered paromomycin (n=3), enroflaxin (n=3), clindamycin (n=3), or cephalexin (n=3). Vaginal biopsy samples were taken twice before antibiotics (ABX) and at 5 timepoints post-ABX. DNA was extracted according to standard protocol and bacterial 16s rDNA was amplified and quantified by PCR and sequenced using Illumina kits and the Illumina MiSeq platform to determine abundances of relative bacteria. Flow cytometry was performed on cells isolated from matched biopsies to assess inflammatory cell frequencies. For animals treated with cephalexin or paromcyin, we found that CD4+ T cells and CD8+ T cells spiked after treatment around day 14 and declined to normal levels by day 63. Additionally, we found that neutrophil abundances spiked between days 28-63. Animals treated with clindamycin increased CD4+ T cells and CD8+ T cell counts around day 28 through necropsy while neutrophil levels stayed constant. Those given enroflaxin spiked in CD4+ T cell and CD8+ T cell counts at day 14 then returned to baseline, while neutrophil levels spiked between day 14-63. We observed alterations in bacterial composition that was dependent on the ABX regimen given and observed associations between these changes and the immune cell changes we observed. Taken together, these data show that altering the vaginal microbiome results in changes in inflammatory cell frequencies that could have implications for STI risk.

Hydrogen Sulfide (H₂S) has potent physiological effects. In large doses, it is a deadly toxin, but in small doses, it acts as a signalling molecule with a wide range of physiological effects. The worm C. elegans is a good model organism for the study of H₂S because of its short lifespan, ease of genetic manipulation, and ease of maintenance. In C. elegans, H₂S induces a stress response pathway, coordinated by the HIF-1 and SKN-1 transcription factors, that plays a role in extending lifespan and improves resistance to various stresses. A previous screen in our lab identified several mutations that suppress the requirement of hif-1 for survival in H₂S by increasing SKN-1 activity. One SKN-1-upregulated transcript, rhy-1, was sufficient to rescue hif-1 lethality in H₂S. RHY-1 is an integral membrane protein that is localized in the hypodermis, intestine, and some head neurons of C. elegans. It has predicted acyl transferase activity, but its specific molecular function is unknown. The role of RHY-1 as a hif-1 lethality suppressor indicates that it acts in a hif-1 independent H₂S response pathway. The goal of this study is to better understand the role of RHY-1 in this hif-1 independent response pathway. In order to identify its binding partners and elucidate its role in cellular signalling, we performed immunoprecipitation of RHY-1 for use in tandem mass spectrometry. This approach allows for the identification of its binding partners under baseline and H₂S stress conditions, which may further define the role of RHY-1 in the stress response to H₂S. Defining the role of RHY-1 will enhance our understanding of how the H₂S stress response leads to increased lifespan in C. elegans. Since several members of this pathway are well conserved in humans, this work may provide a mechanism for the therapeutic use of H₂S in human medicine.

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.

Along with the surge of white supremacy across the U.S. there has been an equally strong and more robust anti-racist/racial justice social movement. For white folx, widely publicized killings of young black men have awakened a collective populace to the injustices that communities of color experience and have been fully aware of for generations. Social Identity Theory suggests that individuals create and define their place in society by which groups they belong. It also suggests a divide between in-groups and out-groups, each with their own lived experiences of oppression. This project investigates how white anti-racist activists and activists of color come to know and understand structural systems of oppression. We utilize semi-structured interviews from seven white anti-racist activists and seven activists of color in the Puget Sound Region of the U.S. to identify the processes by which each group comes to understand systemic oppression and how they frame systemic oppression. Our findings suggest that people of color learn about these systems through personal experiences, whereas white activists see the experiences in these systems as a third party. Our research suggests that awareness and education about systemic oppression may indicate a pivotal point in which individuals decide to take action and become activists. We present findings along with theoretical and practical implications for anti-racist activism. 

Atomic Force Microscopy (AFM) images of peptide self-assembly on two dimensional atomically-thin inorganic solid substrates have features that are difficult to extract because of the diverse conformations these peptides have on the surfaces from nanoislands, no nanowires to confluent films and disorganized nanostructures. Analysis of these images can produce parameters such as thickness, aspect ratio, order/disorder ratio, and orientation distributions quickly and accurately. The first step is to input data in a table and convert it into an array. The images are then converted into a grayscale version, its background noise subtracted and subsequently renormalized. User determined edge detection techniques are then used to delineate the edges in the images. Appropriate segmentation methods are then used to separate different types of nanostructural textures and phases, and coupled with the edge information. Several further parameters such as percent area and volume fraction of each phase (surface coverage), percent-ordering in the long-range ordered phases, their shape and orientation distributions, as well as relative sizes are identified and quantified from the images. The sets of unique parameter are then used as the bases for assigning specific labels for the degree of molecular recognition of the substrate by the peptides and eventual orientation relationships between the peptide nanostructures and the crystalline lattices of the 2D atomically thin solid substrates. These labels are then used to train a machine learning algorithm to cluster these images and relate them to processing parameters associated with them via a relational database. The eventual goal here is to parameterize the images so that we can predict the ordering characteristics of any peptide-substrate pair to accelerate design of future technologies, e.g., bionanosensors, emanating from these hybrid material systems. 

Chronic pain is a perplexing and complex disease that may inflict physical disability or psychological impairment on individuals due to a medical illness or intervention, acute injury, or in the absence of physical illness or injury. Yet while chronic pain affects individuals across all age ranges, certain groups are disproportionately represented in chronic pain research. In particular, limited chronic pain research has focused on adolescents and young adults (AYAs) roughly between the ages of 16 and 25, leaving unanswered questions about how and when AYAs with chronic pain achieve developmental milestones such as gaining employment, forming romantic relationships, and living independently. The focus of this project is to investigate the effects of chronic pain on AYAs and aims to answer the following research questions: (1) Does the age of onset of chronic pain influence how AYAs achieve developmental milestones, (2) What developmental milestones are achieved by AYAs with chronic pain and how do they compare to controls who experience no chronic pain, and (3) Are commonly applied psychological measures ascertaining the most important information from AYAs? To answer these questions we performed a secondary data analysis of a data set of AYAs reporting to a tertiary pain center in the United Kingdom. This data set is courtesy of Dr. Hannah Twiddy of the University of Liverpool. Our analysis includes questionnaire data in the form of validated measures for impacts of pain on lifestyle, disability, depression, and self-esteem among others.  Results of this study describe the developmental milestones achieved by AYAs suffering from chronic pain and will help psychologists understand the nature of chronic pain in AYAs, and potentially develop more effective treatment plans in the future.

This research seeks to assess the feasibility of sustainable community engagement amidst urban planning projects. It seems like every other day there is city construction taking place in hopes of becoming the next major metropolis; a new public park here, a microbrewery opening right down the street -- when do we draw the line between neighborhood revitalization and gentrification? When a city government agrees to sponsor a revitalization project, we must consider the following questions: who will take on the responsibility of which roles? What level of city intervention is actually appropriate and in which spaces? More importantly, we must ask if there are concrete strategies moving forward; what other actions can be done in order to ensure the continued development of this project? I assess these questions more broadly through a case study comparison between two ongoing urban development projects: the Lincoln District Revitalization Project (LDRP) happening in Tacoma, Washington, and the Bayview-Hunter’s Point Redevelopment Project (BHPRP) taking place in San Francisco, California. I explore not only the ways in which city administrators provide accessible opportunities to ensure community involvement, but also the potential resources that can be established to sustain future collaboration amongst city and community. Two types of populations from both cities are assessed: local residents and municipal government actors. I spend my time in various project sites where city members and community members frequent, conducting both unstructured and semi-structured interviews of these two populations over the course of 10 months. My findings show that distinctions upon the relationship between cultural vitality and economic vitality are essential in ensuring effective development that engages all stakeholders.

Alzheimer’s Disease (AD) is one of the leading causes of death in the United States. Studies suggest that the root cause of AD is due to two proteins, Aβ1-42 and tau, which accumulate and aggregate into amyloid plaques and neurofibrillary tangles, respectively. Current studies on the heritability and genetic foundation for AD are not well resolved. In order to understand which genes are best able to resist the effects of Aβ1-42 and tau, we utilized an AD fruit fly model. More specifically, we used a mutant line of Drosophila melanogaster, which we call R32, in which human transgenes of Aβ1-42 and tau are expressed in the fly eye. We used this reagent to express AD proteins in the Drosophila Genome Reference Panel (DGRP), a set of 200 fully sequenced, inbred lines derived from a wild population, in order to simulate a model of natural genetic variation. Aβ1-42 and tau proteins lead to degradation in the eyes causing fusions and irregular shaping of ommatidia. Accordingly, we imaged fly eyes at 28 days of age. We found significant genetic variation in ommatidial circularity and area, two measures of eye quality. We performed a genome-wide association study to identify specific single nucleotide polymorphisms (SNPs) that act as markers signaling degradation in the ommatidia. Significant SNPs were found linked to genes associated with neurotransmitter receptors, neural signalling, and photoreceptor differentiation. Further studies will try to validate the effect of the identified genes and quantify the effects of the SNPs on the degenerative eye phenotype. Additionally, metabolomic studies as well as a model that expresses the AD-related proteins in the brain would be utilized to study the effects on lifespan, memory, and locomotion.

Insulin is a medication that requires training, safety, and care in administration due to potential serious outcomes if administered incorrectly. Under Washington State Law, long-term care workers (LTCW) are permitted to administer insulin in community-based and in-home care settings with the oversight of a nurse delegator, a registered nurse who is responsible for the nursing care of a client and supervises an unlicensed person to perform selected tasks for that client. The current model of training for LTCWs lacks a standardized method to assess their competency in administering insulin. The purpose of this research study is to explore methods of assessment to inform the development of a standardized, comprehensive tool for evaluating competency in insulin administration. The aims of this study are to determine the utility and feasibility of this tool. I developed the “Insulin Delegation: Competency Evaluation Tool” by researching methods of training and evaluation and through student-mentor collaboration. The tool incorporates entrustment scores, reflection, and competency-based education. Prior to testing, the tool was reviewed by content experts, including Washington State Nurse Delegation Program Managers and a nurse researcher who helped develop and evaluate nurse delegation regulations in Washington State. The tool was tested in the field by nurse delegators contracted with the Department of Social and Health Services to assess delegated LTCW competency of insulin administration. After that testing period, feedback on the utility and feasibility of the tool was obtained by an online survey with Likert-type scale and free-text items. I expect to find that the tool is effective in assessing competency in insulin administration and applicable to the workflow of nurse delegators. This tool has potential use as a standard resource for nurse delegation training and an ongoing safety and quality measure in community-based and in-home care practice.

Antibiotic resistance, drug cytotoxicity, and lengthy treatment regimens are major barriers to ending the tuberculosis epidemic. Host-directed therapies (HDTs) that avoid direct targeting of Mycobacterium tuberculosis (Mtb) while enhancing macrophage clearance of the bacteria may overcome such challenges. Because host protein kinases (PKs) regulate multiple innate immune signaling pathways involved with Mtb clearance, we hypothesized that host PKs are HDT candidates. We investigated a group of ATP analogues with specific activity against parasite serine/threonine protein kinases called bumped kinase inhibitors (BKIs). BKIs inhibit few mammalian PKs, so they offer HDT potential while avoiding broad activity that could result in toxicity. To assess the effect of BKIs on Mtb growth within monocyte-derived macrophages (MDMs), MDMs from healthy donors were infected with a luminescent Mtb reporter strain (Mtb-lux) in the presence or absence of BKIs and daily luminescence readings were recorded. We found three BKIs that limit Mtb intracellular replication in MDMs at a final reaction concentration of 10-20 µM. Interestingly, none of these compounds inhibited Mtb-lux growth in 7H9 broth culture. To examine possible mechanisms, we measured the effect of the BKIs on pro-inflammatory cytokine release in MDMs in response to various stimuli including Toll-like receptor agonists, virulent Mtb, and the attenuated vaccine strain Mycobacterium bovis BCG. In response to all of these stimuli, the BKIs potently inhibited TNF secretion and moderately inhibited IL6 secretion by ELISA. In contrast, the mRNA expression level of antimicrobial peptide cathelicidin was maintained in the presence of the BKI tested. Since pro-inflammatory cytokine induction and cathelicidin expression are generally host-protective in early Mtb infection, it is unlikely that the effect of the BKIs on these pathways are responsible for inhibiting intracellular Mtb growth. We are currently evaluating the effect of BKI treatment on other antimicrobial pathways that restrict Mtb infection, including phagosomal uptake and autophagy.

Under Washington State law, nurse delegation is a process in which a registered nurse, known as a nurse delegator, provides training and management for delegated care tasks to be performed by long-term care workers (LTCWs) within in-home or community-based care settings. State law requires that clients who receive care through nurse delegation must be in a stable and predictable condition (SPC). In our previous study, we determined that nurse delegators need more specific criteria than the definition in Washington State law to assess SPC. The purpose of this project is to provide additional clarification to the determination of SPC by developing an instrument for nurse delegators to use for comprehensive assessment of SPC and describing the instrument’s utility and applicability. Methods to reach those goals included: 1) reviewing published literature and policy reviews of federal and state-by-state laws on potential alternative definitions for SPC; 2) consultation with nurse delegation content experts (two Washington State Nurse Delegation Program Managers and a nurse researcher, whose work helped establish state regulations for nurse delegation in Washington State) regarding the clinical applicability of a SPC assessment instrument; 3) development of the instrument based on relevant clinical evaluation guidelines and instruments content expert feedback; and 4) collection and analysis (via phone interviews and qualitative content analysis, respectively) of feedback from nurse delegators on the utility and applicability of the developed instrument. We hypothesize that nurse delegators will view the instrument as a useful clinical resource for determining SPC within the nurse delegation process. The results of this study can be used to implement the instrument independently or in conjunction with other evaluation methods, as standardized practice to assess SPC and effectively meet this state requirement for clients to receive care under nurse delegation.

Microaggressions are reoccurring derogatory messages that degrade one’s identity. While invisible and unknown to many, they remain visible and apparent to those impacted by them. The research questions for this project are: (1) What microaggressions do Queer Black men experience within larger society? (2) To contrast with larger society, what microaggressions do Queer Black men experience within Black communities? Using in-depth interviews, I will examine the intersectional microaggressions that Queer Black males experience in their own community and in larger society. After conducting my interviews, I will adopt Derald Wing Sue’s taxonomy of microaggression themes to translate the underlying messages behind delivered microaggressions. The results in this study will aid in addressing a gap within intersectional microaggression literature by documenting how Queer Black males experience these muted, normalized insults and invalidations in society.

Few studies have attempted to figure out how humans may alter their behaviors when faced with trade-off decisions surrounding convenience and risk. Walking is still a primary mode of transportation for many humans, and in this study, we aimed to try to understand how pedestrians behave while engaging in risky behavior, specifically jaywalking (here defined as crossing at a crosswalk but against the green light). Subjects were observed at different intersections in Seattle as they crossed the streets while we recorded various characteristics, including speed, group composition, and gender. The video footage was collected using an iPhone; distance was measured using a Kestrel wheel; and the video footage was analyzed using Kinovea software. Statistics were done in SPSS 25. People (N= 652) were more likely to walk faster when they were jaywalking (p=0.006), and were more likely to check the surrounding environment (p<0.001) when crossing against the light. People walking in groups were less likely to walk quickly (p=0.001) (than people walking independently), and less likely to check the surrounding areas when crossing the street (p=0.034); however, groups were also less likely to jaywalk than individuals (p=0.013). Jaywalking and walking-safety data are regularly used by city planning and development committees to determine how to allocate city resources to pedestrian safety measures. Additionally, this study can be used as a foundation for better understanding humans’ walking and movement decisions surrounding risky behaviors, and how walking in groups might increase walking safety and change people’s risk assessment.

Parkinson's disease (PD) is degenerative disorder of the nervous system that primarily impairs motor function along with other cognitive functions due to a specific loss of striatal dopamine neurons. The most challenging aspect of treating PD is that there is no explicit cause or any definitive long-term treatment. Current therapies restore dopamine levels in brain to alleviate the symptoms of PD. In this study, our goal is to address and identify possible markers of PD by studying the action of dopamine using functional MRI (fMRI) data. Resting-state fMRI allows us to examine the patterns of neuronal firing in vivo. We performed fMRI in 26 PD patients (age = 68 +/- 8 years) before (OFF group) and after (ON group) administration of dopaminergic medication to understand which brain regions showed altered neuronal firing with dopamine therapy. We applied the Integrated Local Coherence (ILC) approach to study temporal coherence of neuronal fluctuations within regions. High ILC corresponds to coherent neuronal fluctuations or recruitment of larger number of neurons as baseline. Low ILC corresponds to reduced temporal coherence in neuronal fluctuations due to neurodegeneration. ILC was computed in the cortex and compared between the ON and OFF groups using a paired t-test. Significance was considered for a voxel-wise threshold of p=0.001 and a Family-Wise Error correction for multiple comparisons at p=0.05. ILC measures were higher bilaterally in the superior parietal lobe, angular gyrus, and precuneal regions in the OFF compared to ON group. These results support another study where increased temporal coherence was observed in the same regions in PD patients compared to healthy controls. These regions are also part of the PD-related disease pattern network involved in motor dysfunction. With this work we believe that administration of levodopa reduces the excessive recruitment of neuronal regions during rest in PD patients.

Identity is constructed by the intersection of many different categories that are supported or marginalized by the society depending on variables such as context, time, place and group values. This study sought to investigate how the categorical intersections of identities as sociological concepts were informed, challenged or supported  through the experiences of integration and marginalization of Asian Pacific Islander American artists in the progressive city of Seattle. In the micro level, it is experienced through daily social interactions within the community and on a macro level through educational programs and social policies. These mixed methods studies developed 1- a quantitative statistical descriptive analysis disaggregating 9 APIA subgroups by residential dispersion on tract level and basic socioeconomic parameters in King County and 2- a qualitative research focusing on 12 in-depth interviews with self-identified APIA artists contrasting race and gender identities by heterosexual and LGBT. The APIA racial category unique experience is understudied in the field and I sought to address this gap by contrasting current pervasive narratives and stereotypes. This was addressed via unpacking the reality of personal experiences of artists providing intimate insights on the shifting dynamics negotiationing these identities. The study controlled for similarities of experiences and outcomes framing analysis through the grounded theory methods of ulilizing data and inquiry to derive theory. In order to understand experiences of multiple marginzalizations, it's important to address a multitude of intersecting categories. In short, until we see it, it dones't exist. I expect to find that experiences of marginalizations increase when intersecting race/ethinicity of APIA artists with non-heterrosexual gender and sexual identities.

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.

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.

Forefront Cares is one of services provided by Forefront Suicide Prevention, a center at the University of Washington School of Social Work. Suicide loss survivors receive care packages and have the opportunity to be connected to mentors, who are also suicide loss survivors and are specially trained to provide support to new loss survivors. The goals of Forefront Cares are to offer support to suicide loss survivors and to help them find resources that are appropriate for their individual needs. The purpose of this study was to examine participants’ perceptions of Forefront Cares, including what is helpful and what could be improved, through an online satisfaction survey which I created. I then sent e-mails to individuals who received a Forefront Cares package between January 2013 and December 2017, inviting them to participate in the study. Those who participated completed a brief anonymous online survey, which involved rating experiences with Forefront Cares. Questions addressed how helpful they found the package they received and what they found most or least helpful. Participants who had a Forefront Cares mentor were asked to rate how helpful that experience was. The data collection ended in mid-April, and I analyzed data with assistance from my mentor. Results will help determine what participants found more and less useful, as well as the acceptability of the Forefront Cares package and mentor process. It is expected that findings will indicate the importance of community support in the grief journey of newly bereaved suicide loss survivors. The creation of the satisfaction survey was intended to be a starting point in establishing ongoing analysis of Forefront Cares, as Forefront currently lacks permanent evaluation tool to assess their services. Information obtained will help improve the Forefront Cares process for future participants.

Water pollution is a serious problem that not only threatens wildlife, but also the health and safety of human populations around the world. While the commonly held perception is that water pollution only affects vulnerable groups in developing countries, the 2014 water crisis in Flint, Michigan is a stark reminder that even developed nations are not impervious. Given the scope and weight of this problem, there has yet to be an accurate and affordable way to reliably test for heavy metals and other water-soluble contaminants. Current solutions such as handheld digital instruments can be expensive and require calibration and electricity, making them less practical in low-resource settings. Test strips, while deployable, are often inaccurate. Hence, our aim is to create an inexpensive, deployable yeast-based diagnostic tool that can detect various water pollutants with high sensitivity and report results with a fluorescent or color output. At the beginning stages of our project, we are using Next-Generation RNA Sequencing and experimenting with various analysis techniques to screen for genes in Saccharomyces cerevisiae that exhibit a unique and differential expression profile after exposure to a particular contaminant. For now, we are limiting the scope of our research to zinc, copper sulfate and caffeine because there are existing gene sets in literature for us to reference, but as more data are acquired, we hope to apply this pipeline to a wider range of chemical pollutants, including pesticides, toxins and hormones.

Our current project is one stage in a larger research goal: to build multiple yeast strains capable of detecting toxic water contaminants. We searched for the optimal contamination concentrations for yeast response to obtain robust, accurate RNA sequencing analysis results. This data will then be used to determine which contaminants elicit a strong enough genetic response for promoter attachment. The fluorescent yeast will emit a recognizable signal in this manner, and allow for reliable water assessment without the use of expensive equipment or testing services. Thus, we investigated the optimal times for RNA extraction, when the cells are expressing the most contaminant-induced genes but are still sustaining metabolic processes. To this end, we must consider factors such as contaminant concentration and time after exposure. At this stage, data collection involves the use of a plate reader, which periodically measures absorbance of the yeast solution. Absorbance, which is proportional to population density, is limited by the solution’s carrying capacity. We then generate population trend graphs and identify the greatest instantaneous growth time in each sample. Through repeated experimentation, we compile a spectrum of contaminant types, concentrations, and yeast carrying capacities. Analysis of these growth curves indicate the time of incubation at which RNA expression is ideal for sequencing. Future work will involve identifying additional contaminants of interest and additional modification of our algorithms to obtain more precise, accurate, and meaningful data.

Water can have many contaminants that are harmful to humans and animals alike. Since water is so essential to life on this planet, it is important to know whether or not a water source is contaminated. However, testing water samples can be expensive. In order to make it easier to test water for contaminants, we are working to create a device to sense this contamination within a matter of hours by using yeast that produce a fluorescent protein in the presence of various water contaminants. In order to make the yeast easier to transport, we first need to dry the yeast before packaging it, similar to dry yeast that can be bought at the grocery store. To test a sample, the device utilizes a light to frequency sensor to convert the intensity of light from the glowing yeast into a signal that can be processed by an arduino board contained within the device. Our device can be used as a reusable, low cost diagnostics machine for testing water for contamination. This could provide access to advanced technology in parts of the world that don’t have access to expensive testing equipment, as well as  be used by an ecologist in the field.

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.

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.

QRS-like artifacts are present in ECG recordings during CPR but have not been described previously. We coin these artifacts compression induced complexes (CICs). They prevent accurate real-time cardiac rhythm characterization during CPR compressions. Additionally, we hypothesize that CICs may be an early prognostic tool for return of rhythm (ROR), return of spontaneous circulation (ROSC) and an indicator of cardiac health. The objective is to characterize and describe these QRS-like complexes quantitatively and create an algorithm that distinguishes CICs from native cardiac activity. CIC characteristics that are being measured are a) amplitude, b) sharpness, and c) temporal relationship with CPR compressions. Custom software was used to analyze the ECG data from King County Emergency Services with CICs annotated by expert review. 50 cases were used to determine the range of features specific to CICs, to include: a) amplitude as measured at CIC peaks, b) sharpness as quantified by measuring the peak of the second derivate at CIC locations and wavelet transform analysis to measure the range of frequencies present in CICs, c) the temporal relationship between CICs and CPR compressions as measured using peak finding algorithms and comparing the delay between the impedance peaks from CPR compressions and CIC peaks. Ten CICs from each case for each feature were analyzed using standard deviations to define quantitative parameters for a CIC detection algorithm. After development, this algorithm was tested to determine the percent of CIC complexes that are detected in a test set. It was also used to examine the association of CICs with ROR and ROSC. This algorithm can potentially aid in advising pre-hospital care tailored to the patient’s cardiac condition.

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.

Arthropods represent 29 percent of the world’s animal biomass and comprise over 500 million years of evolutionary diversity. Arthropods such as spiders and moths constitute a perfect milieu for the discovery of multitudes of highly diverse RNA viruses of unknown pathogenic potential. Sequencing and characterizing these viruses is of immense value for understanding many basic science questions about viruses. The sequences obtained and described can also provide great insight into future zoonotic outbreaks. We sequenced RNA extracted from 10 moths and 6 spiders collected from western Washington. We developed a custom bioinformatics pipeline for automatic discovery and characterization of completely new viruses. The custom software also automates the process of depositing viral sequences into the National Center for Biotechnology Information’s Genbank archives, the main database in which DNA and RNA sequences are shared among scientists and researchers. A total of 12 novel viral genomes were discovered in these 16 samples. These new viruses belong to 4 highly different viral families, all of which contain species known to infect humans. We also present what is likely a completely new viral clade within Picornavirales, the viral family that contains polio and many other diseases afflicting humans. This new viral clade has a never seen before genome organization and contains a highly divergent RNA dependent RNA polymerase. New and highly divergent strains such as the ones outlined here provide extremely valuable insight into the inner workings of viral biology and genetics.

Heterotopia are organized structures consisting of mixed elements of neurons, glia and neuronal progenitors arranged in an architectural pattern inappropriate to the considered tissue. Heterotopia are observed in pathological preparations of the cerebral cortex and the cerebellum as a feature of many neurological disorders yet the mechanisms driving their development remain unclear. We have analyzed 28 Dandy Walker Malformation (DWM) human fetal cerebella and found that more than 40% of cases contain heterotopia. DWM is the most common structural birth defect of the human cerebellum and is characterized by hypoplasia and foliation defects. A subset of cases are caused by loss of FOXC1, a transcription factor expressed in the mesenchyme adjacent to the developing cerebellum. We previously reported that in mice, loss of FOXC1 causes loss of the mesenchyme-secreted factor SDF1-alpha. Further, loss of SDF1-alpha is sufficient to cause cerebellar heterotopia, highlighting the importance of mesenchymal signaling in the maintenance of the highly stereotypical laminar architecture of the mature cerebellum. We hypothesized that granule neuronal progenitors (GCPs) adjacent to the mesenchyme are the primary cellular target of SDF1-alpha mesenchymal signaling and thus, the primary cell type driving heterotopia formation. To test our hypothesis, we specifically deleted the SDF1-alpha receptor from just GCPs using a Cre-loxP genetic scheme in mice. We determined that loss of SDF1-alpha in just this one cell type caused their premature migration into the developing cerebellar anlage and secondarily caused other cerebellar cell types to form structured heterotopia. We also observed defects in cerebellar foliation in the treatment group. Our data further highlights the importance of SDF1-alpha dependent mesenchymal signaling in cerebellar development and identifies heterotopia as a new phenotype in DWM.

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.​

The Kaeberlein laboratory utilizes the budding yeast Saccharomyces cerevisiae to study aging, a progression characterized by the gradual deterioration of cellular components and bodily functions. Aging is a progression every organism eventually undergoes, and by better understanding the molecular mechanisms behind it, we can determine how to delay its progression and increase our healthspan, the portion of our lifespan in which we are healthy and free from serious disease. S. cerevisiae functions as an effective model organism because it contains many conserved biological processes, making lifespan simple and fast to measure. The replicative lifespan assay (RLS) is used to quantify the lifespan of the yeast. Individual yeast cells undergo asymmetric mitotic division producing a daughter cell that is distinctively smaller than the original mother cell. Yeast are incubated on growth promoting plates, and the yeast produce daughter cells that are microdissected, counted, and moved away. The cycle repeats until the original mother cell can no longer produce a daughter. The total number of daughter cells produced by individual mother cells is then used to understand the effect of the gene on the lifespan of the yeast. This technique aids in developing models that can be used to understand the conserved biological pathways that influence longevity. Aging is an underlying risk factor for many non-communicable diseases such as Alzheimer’s Disease, Cancer, and heart disease. Our laboratory has performed thousands of gene knockouts on S. cerevisiae and has identified several genes that modulate replicative lifespan. This research is focused on identifying the genes that play a role in reducing the rate of aging to delay the onset of age associated diseases. By understanding how specific genes play a role in aging, we can apply this research to other organisms, with the ultimate intent of increasing the length of a healthier human life.

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.

Alzheimer’s Disease (AD) is a progressive brain disorder that results in middle to late life dementia. AD, the most common form of dementia, is the sixth leading cause of death in the United States, and the third leading cause of death for older people over 65 years of age. AD is pathologically characterized by the accumulation and aggregation of an alternatively spliced amyloid-beta (Aβ) and hyperphosphorylated tau, which lead to the formation of neuritic plaques and neurofibrillary tangles (NFT’s) in the brain and ultimately to decreased neural function and cell death. Previous studies indicate that the extent to which an individual is affected by the interaction of these proteins and the severity of AD is largely influenced by genetic variation. However, the specific genes involved, their regulation and expression remain largely unknown. Our ongoing project explores the genetic variation underlying Drosophila susceptibility to severe eye cell degeneration caused by human Aβ and tau. We express Aβ and tau in the fly eye through the UAS-GAL4 system to create our AD model Drosophila, and cross them with a panel of flies (the Drosophila Genome Reference Panel, DGRP) that allows us to map natural genetic variation for resistance to Aβ and tau. Our preliminary results show significant variation in neuronal eye cell degeneration among DGRP lines, implying that neurodegeneration would also differ between DGRP lines if Aβ and tau were expressed in the nervous system. Based on current progress, this new project will continue exploring variation in DGRP lines, but this time we will express them in the fly brain. I will measure how different genotypes shape the effect of brain-specific Aβ and tau on lifespan and protein aggregation, and will use Genome Wide Association Studies to identify single nucleotide polymorphisms associated with variation in expression of Aβ and tau.

The key to understanding the obesity epidemic may be in the role of incentive motivation and reward mechanisms in eating behaviors, thus sugar-sweetened beverages are commonly investigated. Though explicit reports of food choice and behavior are typically used, reward processes likely influence intake through implicit mechanisms. Cognitive load, or the use of mental energy, influences eating behavior by decreasing mindful eating. The present study examines hedonic liking and motivational wanting with three tests, Greenwald and colleagues (1998) Implicit Association Test (IAT), the Personalized IAT (“I like”), and the Extended Personalized IAT (“I want”) in participants under cognitive load. As our ability to self-regulate is dependent on cognitive resources, the cognitive load manipulation should influence implicit liking and wanting, but not the traditional IAT. We predict that due to the cognitive load manipulation, 1) participants will demonstrate significantly greater implicit liking and wanting as compared to traditional IAT scores and 2) implicit wanting, but not implicit liking, will serve to predict participant beverage selection. The prediction of feeding behavior is important given that many efforts taken to combat the obesity epidemic have failed; therfore, understanding the underlying psychological processes that explain over consumption may be the key factor in abating the obesity epidemic.

The incidence of many human diseases, such as cancer, Alzheimer's and heart disease, increases with age. Studying the aging process could provide insight into new treatments and therapies for these aging-related diseases. Our research uses the yeast species, Saccharomyces cerevisiae, as a model organism to explore the effects of specific genetic and environmental factors on aging. Aging in yeast can be measured in terms of replicative lifespan, which is the number of progeny (daughter) cells produced by a parental (mother) cell. In order to measure the replicative lifespan, we utilize a microdissection microscope outfitted with a fiber optic needle that is used to separate individual mother cells from their daughter cells in order to quantify the number of daughter cells produced. The total number of daughters produced by a mother cell is the replicative lifespan of that cell. To determine which genes play an instrumental role in yeast replicative lifespan, our lab has studied the lifespan of 4,698 yeast mutants containing single gene deletions. Many mutants were identified that increase the lifespan of S. cerevisiae. In this study, we have re-evaluated our data to identify potential false-negative results from our initial work, in order to identify additional genes that may influence lifespan. Identifying the false-negative results will be beneficial in finding genes that may play a role in the aging process and had been previously overlooked. This will allow future research to continue in developing treatments that target the prevention of age-associated disease in humans, potentially allowing people to live healthier lives and decreasing the prevalence of cardiovascular disease and cancers. 

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.

Pollution from human influences is a growing problem in the Chehalis River and tributaries causing deleterious effects on stream health. Pollution runoff happens when rainfall or snow melt pick up and carry human-made or natural pollutants and are then deposited into streams, lakes, and rivers. With a better understanding of microbial populations within streams you can correlate the role that the surrounding environment is playing on overall stream health. Stream water has been facing a decline in quality from the leading cause of pollution from agriculture and manufacturer run-offs. Previous studies have linked increasing industrialization to ecological losses. Pollution entering a stream can influence and alter the abundance and diversity of aquatic life, especially at a microbial level. Although there have been many studies relating to run-off pollution affecting streams, there are no in-depth studies done on the taxonomy and functionality of microbes in urban water ecosystems, so it is important for this to be further investigated. For this project, overall stream health was measure by assessing seven locations along Alder and Fry creek. Environmental factors, percentage of man-made covering, and potential pollution runoffs were all considered and analyzed. A stream microbiome analysis was done along all sites sampled using 16s sequencing. The microbes present are a strong indicator of the health of the ecosystem. From this information, future studies can draw how to improve stream restoration efforts based off the abundance and diversity of organisms within streams facing variation in levels of human impacts.

Stream microbiomes are composed of diverse collection of microbes that play an important role in keeping the surrounding riparian zones and life within the streams healthy and thriving. The Chehalis River provides habitats in favor of fish spawning and juvenile development, but fish return populations upstream haves decreased in recent years. The aim of this study was to identify and characterize microbes within the Chehalis River tributaries, in correlation to fish populations, that are causing part of an invisible fish barrier. An invisible fish barrier is an undefined barrier that is blocking or preventing the return of fish. When water conditions are altered by human impacts or water quality is poor, it can result in microbial communities to shift. These communities can become harmful and potentially pathogenic to the surrounding hosts and environment. Microbial identification specifically within the stream in relation to fish populations could help to find ways to improve overall water quality for fish health. This analysis may provide a holistic indicator for necessary renovation and restoration of fish passages. Sites that lack species diversity in their riparian zones, and were closer to urbanization, show diversity in potentially harmful microbes like Camplyobacter, Sanguibacter and Shewanella, in correlation to low fish population. Continued monitoring will help correlate trends that are influencing riparian zones, water quality conditions and fish populations during the process of stream restoration.

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.

In this study, I investigate how students with different racial identities -- white students and students of color -- think and interpret their own value of their debt as they near graduation and thus, begin their journey of repayment. Knowing that students of color take on a higher debt burden than white students, I want to look at these two groups of students and see if there is a difference in how students perceive their debt in accordance with their life, racial identity, and social experiences. I will investigate this using in depth interviews of students with $20,000 or more of student debt. This research will provide insight about the intersection of socioeconomic status, race, and student debt within American colleges. This will expand our understanding of how different people place a value on and expand on their student debt. As the student debt burden increases in the U.S., it is crucial that we understand how people make sense of that debt within their lives.

The importance of understanding the inflammatory response in the lungs is underscored by the fact that pneumonia and influenza illnesses led to an estimated 12,000 deaths in the 2015-16 U.S. flu season. Our research investigates the expression and regulation of versican in response to lung infections, both viral and bacterial. Versican is a chondroitin sulfate proteoglycan present in the extracellular matrix; it is expressed in lungs during embryonic development, mostly absent during healthy adulthood, and re-expressed in instances of inflammatory lung injury or infection. We are interested in understanding the pathways that result in versican upregulation, as preliminary data suggest that versican can be either pro- or anti-inflammatory, depending on the type of cell it arises from. My research project investigates this differential regulation phenomenon - recently, I have incorporated chromatin immunoprecipitation (ChIP) of versican transcription in both viral-stimulated macrophages and lung fibroblasts to explore the epigenetic factors that control expression. ChIP allows us to establish and quantify interactions between proteins and DNA; in our case, we are interested in transcription factors that follow interferon beta signaling (IFNb), which has been shown by our lab to be a key mediator of versican expression. IFNb itself is a known anti-viral cytokine, suggesting that versican may also follow this response to viral infection. If we can determine which transcription factors, if any, lead to an increased response of versican, we will have identified a signaling pathway by which to manipulate versican expression. The ultimate goal of this work is to develop a lung inflammation therapy by driving production of versican in an anti-inflammatory state. Utilizing versican's power as an immunomodulatory molecule could be a new tool for fighting severe inflammation associated with respiratory illnesses.

The recent launch of bike-share programs in Seattle has brought to light a pertinent issue in public health that will continue to grow as their distribution increases across the city. While bike-shares promote physical activity and provide an alternative commute option, they also seem to be associated with decreased helmet use, which is associated with an increased risk of head injuries. The purpose of this study is to explore the issue of helmet use among bike-share riders on the University of Washington campus. By implementing a campus-wide cross-sectional survey, I gained important information about how Seattle's unique bike-share and helmet issue can be addressed on UW campus in the future. Participants in this study included UW students, faculty, and staff who were recruited by convenience sampling through email distribution. The survey was written with Catalyst WebQ online and had 21 questions evaluating participants general bike and helmet utilization habits on campus, barriers to helmet use with bike-shares, and awareness of Seattle's mandatory helmet law. I anticipate results to confirm a decrease in helmet use among bike-share users and reveal several barriers to wearing a helmet with bike-share bicycles. I will utilize the information from this research study to create a targeted helmet promotion campaign on UW campus in the Spring. In addition, this valuable information will be shared with local public health officials to inform health promotion endeavors over the coming years as bike-share programs continue to expand in the Seattle area.

The rising cost of attending four-year colleges and universities concerns students and parents across the nation, calling for an explanation and possible educational alternatives. One such alternative may be trade schools, which offer a shorter path from secondary education to the workforce. In deciding which post-graduation path to pursue, students (and their parents) may be interested in the rate of return to each of these options. Many estimates have arisen calculating the rate of return to a four-year degree, but comparatively little has been done for trade schools and short-term professional programs. This study is a preliminary attempt to fill this gap. I focus on beauty schools as a specified form of trade school, and compare tuition and early-career salaries from twenty-three beauty schools in the state of Washington to pre-calculated Washington averages for four-year universities. If the labor economy is operating at maximum efficiency, the rate of return for trade schools should be equal to that of four-year universities, i.e. the same benefit to cost ratio. An efficient labor market that includes beauty schools at a higher rate of return than four-year universities could indicate an occurence of social stigma, encouraging unprepared high school students into a longer program than would be economically efficient. The expected result would be an increase in students capitalizing on the program with the higher rate of return. While preliminary results suggest a higher rate of return for four-year programs, I plan to continue the study with expanded data sets.

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.

This research deals with the specific dynamic pricing strategy of fashion products sold online. The pricing method works under the condition of a pre-determined quantity of inventory with stochastic demand functions on a limited time horizon, which is formulated as an optimization problem. To achieve the maximized profit, it is essential to balance between the extra marginal revenue earned by setting a high selling price and the cost lost from unsold items. In order to find the solution, we first develop and estimate a pricing model that captures the important characteristics of the fashion apparel market. Afterwards, we use data from a leading Taiwanese fashion retailer to examine the accuracy of our model. The final purpose of this research is to provide an insightful conclusion of the dynamic pricing policies that would generate the highest retailer revenues.

Monte Carlo simulations employ random probability distribution statistics to estimate areas and volumes. Here, we employ Monte Carlo simulations to estimate the numerical value of π. We inscribe a circle in a square board and throw N darts using random values for both x and y. The probability that the dart lies within the circle = area of circle/area of square. This relationship allows us to estimate π. We wrote EXCEL/JAVA code for this research. The accuracy of estimated π is improved as the number of darts N --> ∞. This research allows us to combine mathematics, computer programming and data visualization to estimate π. Important applications of Monte Carlo simulations to find areas and volumes of complex objects including rivers, landscapes and organisms which cannot be represented by analytic functions will be discussed.

For those interested in understanding more about fatal shootings of civilians by police, a natural place to start would be data on the events. Such data is, however, surprisingly hard to access. There are no official sources, but there are several crowd sourced data sets available online. These data sets each contain some common and some unique fields, and they are stored in very different formats. Hence, these data sets require preprocessing before the data can be used for other practical purposes like analysis and visualization. In this research, we focus on cleaning such heterogenous data sets using statistical methods with major focus on data matching. Data matching refers to matching data from different sources and recognizing the matching entities. It is an essential step in data cleaning that helps in resolving the conflicting information provided by the data sets---clerical errors, missing data, differently stored data, etc. Traditional statistical procedures and classification algorithms are based on supervised learning which requires training data. However, it is quite common that the training data is not available at hand and it might not be cost effective to prepare one from scratch. We explore a two step unsupervised learning algorithm that might achieve the same performance as the supervised counterparts. In the first step, it prepares a seed data set containing data points that are relatively extreme matches and non-matches based on discriminating fields. This prepared data set can be used as training data to train classical classification algorithms---k-nearest neighbors, Support Vector machines, Random Forests---which in turn can be used to classify the remaining data points. In the process, we examine missing data, geocode matching, and feature selection methods that increase classification accuracy by selecting the most discriminating fields. Finally, we examine the prospect of generalizing this approach to suit differently aligned data.

Distributed Denial of Service Attacks (DDoS) have been a prevalent threat to information security across organizations. Moreover, the rise of botnets has provided a lucrative environment for DoS attacks to evolve and increase at an alarming rate. Hence, it is crucial for organizations to integrate security policies and infrastructure within their operations. Various security products such as Intrusion Detection/Prevention systems (IDS/IPS) and firewalls help address this need. However, acquiring and configuring these products can be time-consuming and costly. Furthermore, configuring & integrating such systems together requires technical expertise in information security. This research study suggests a novel approach to developing a lightweight and low-cost sensor for early detection of DoS attacks. The sensor communicates over a distributed network, with an IPS system which responds by reducing the impact of DDoS attacks. Such a configuration also allows the solution to be scalable i.e. the IPS could be configured to manage data from multiple sensors. The project is being conducted in 3 phases: (1) Identify, implement and test the technologies required for monitoring and logging traffic to and from insecure device, within a virtual environment. (2) Extend configuration to the production environment including Raspberry Pi(s) acting as the sensors. (3) Add usability enhancements such as an interactive console or Graphical User Interface (GUI) for system configuration. With development in progress, it is anticipated that this project will open various avenues to explore the potential for effective use of remote devices to detect DoS attacks.

National interest in the fatal shooting of civilians by police is growing, driven in part by several high profile cases that were captured on video. Several news organizations, including the Washington Post and the Seattle Times, have done in-depth reporting on local or national trends. While the data these organizations used has been made public, the technical skills needed to access and analyze the data present a barrier to public use. This project seeks to develop browser-based software that will support simple access to the data, along with tools for Exploratory Data Analysis (EDA), that will make it easier for others to learn from these data. For this project we are working in the programming language R, writing a shiny app to provide the browser-based interface to R’s powerful EDA tools. Shiny apps involve writing two software components: the underlying R code for analyzing the data, and a user interface (UI) that provides a simple point and click tools for running the code. For the R code, we will focus on graphical exploration of the data: time series charts at different levels of spatial aggregation, interactive maps where users can zoom in and view online links for individual cases, choropleth maps to visualize racial disparities, and animated cartograms. For the UI, we will develop a webpage with tabs for each graphical option, and a range of filters and aggregation options on each tab. Users will be able to easily view and interact with each visual and modify it to display what they are interested in. Our codebase will follow the guidelines for reproducible research, and be uploaded to a public GitHub repository. This will support both public use and public development; users interested in contributing to the codebase can clone our repository, and submit suggested edits via pull requests.

Here we explore applications of multivariable calculus for studying three dimensional wave media in our environment. We employ regression based methods to derive analytic formulae for real wave. Using multivariable optimization methods, we derive the maxima, minima and saddle points of three dimensional functions. We use advanced data visualization methods to study the divergence and curl and illustrate how these can be used to study ocean waves- including their vorticity and circulation. The project provides hands on exploration of real world environmental science problems with advanced data visualization and shows how divergence and curl can be used to measure circulation and vorticity parameters of real wave media involving ocean waves. Real world manifestations of scalar and vector fields in our environment are also presented.

Mass shootings are becoming a common occurrence in the media. Often times, in an effort to cover mass shootings, reporters are putting out information as soon as possible. The coverage often encompasses victims, suspects, death tolls and gruesome details. That practice leaves room for victims to become statistics and leaves many questions unanswered, which may result in insensitivity. The media has a duty to report the facts to the public, but what precautions should be taken when reporting on an issue that requires the lense of ethics? In an effort to better understand the perspective of journalists, a focus group consisting of media personnel was conducted. The focus groups allowed for open conversations between media personnel about the professional requirements of reporters during field reporting and the privacy expectations of victims. The focus group consisted of four media personnel who had been in the industry for several years and came from different backgrounds. The focus group was given five guided questions and the discussion was recorded. This study hopes to open up a discussion about the ethical coverage of mass shootings. These results could yield future guidelines that pertain to the ethical coverage of mass shootings.

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.

South Korea’s rapid industrialization and democratization led to policy reforms that allowed women to invest more heavily in their education, career, and leisure beyond the domestic sphere. Consequently, these women became active participants and consumers of the goods and services within their society, as exemplified by their consumption of media. Given that Korean women in their twenties and thirties have embraced strategies to improve their status as citizens who operate in society in ways that transcend traditional normative, restrictive spheres of action, we would expect them to explain their consumption habits in terms of how the cultural objects resonate with their own experiences. Instead, they reveal ambivalence with regards to the value of these dramas as accurate representations of Korean society. Why? I argue that the widespread consumption of Korean dramas replete with mixed messages that call into question these women’s self-fashioning aspirations can be explained as a function of their ability to detect and stand apart from the submissive qualities reflected in female characters whose behavior represents a capitulation to traditional gendered norms. Through open-ended interview questions about professional women’s viewing habits and career objectives, I demonstrate how the critical distance attendant upon drama consumption is an agentive coping mechanism beyond a passive act of acquiescence to gendered discrimination, and is premised on self-perceptions of critical acumen nurtured by their academic and vocational background. Such knowledge resulting from women’s intense focus on education derives from their perception of education as a conduit for the actualization of career aspirations, which equipped them to interrogate gendered power relations that pose challenges to their success. Critical acumen is viewed as the source of their capacity to recognize and distance themselves from popular media’s representation of gendered socio-economic inequality and the broader patriarchal discourse in Korea that perpetuates norms of women’s submissive position.

In The Ecstasy of Communication, Jean Baudrillard states that the invention of television and internet radically changed the perception of reality. As Baudrillard puts it, we no longer exist in three-dimensional space with clear boundaries separating one another. Reality is now a two dimensional plane, a flat reflective surface, within which boundaries have collapsed and the most intimate parts of our lives are exposed. This is what Baudrillard categorizes as obscene, an oversaturation of information and the all too visible. Many artists address similar concerns in their artistic practices. For example, through his unnerving puppet works and the series, Eyes, Tony Oursler explores surveillance. Blatantly exposing the increasing lack of privacy in current society, he highlights the realities of Baudrillard's claims. I contrast artists James Turrell and Olafur Eliasson to Oursler in their use of technology, showing the illuminating nature of electronic communication. Eliasson's Din blinde passager and Turrell’s Ganzfeld, enhance the physical realm through light and color. Reinforcing a three-dimensional awareness, Eliasson and Turrell offer a solution to Baudrillard’s obscenity. In comparing these artists, I show technology’s ability to critique our society of increased surveillance through self-awareness, as well as demonstrate the potential positive relationships that technology can foster between individuals.

Google Street View operates as a global surveillance system. While it periodically gets updated, GSV constantly remains a tool available for any and all individuals with access to the internet. This means that even though photo quality increases, the scope of the database widens, and its various applications multiply. Over the last decade, various new media artists have explored the possibilities that come with GSV’s all-encompassing database of images. Artist Mishka Henner has “appropriated” stills from GSV. Turning temporary online data into physical art, Henner subverts the notion that surveillance systems only serve as momentary fragments of information. In his series “No Man’s Land”, Henner documents roadside prostitutes captured by the GSV camera in rural Italy. His cropped images engage with the notion that as a public surveillance system, GSV captures bits of everyday life and turns them into data. In framing stills from GSV as aesthetic works of photography, Henner toys with concepts of privacy, detachment, and most importantly, modern surveillance. In this project, I explore the ways in which Henner uses Google Street View as a tool to make a commentary on the database system. Focusing on the globalization of public surveillance, Henner addresses worldwide issues of privacy in the internet age. His photography makes us think about the permanence of online data in an ever expanding information system. He suggests that through GSV we become data coded in 0s and 1s, forever part of the database. 

Public Broadcasting Service (PBS) is using its children's programs to promote STEM career tracks. My research project sought to analyze the representation of male and female identifying characters in PBS science-based programs for children ages 4-10. I collected both quantitative and qualitative data from the following four shows: Cat in The Hat, Magic School Bus, Cyber Chase, and Wild Kratts. These 30 minute animated shows are presented as gender neutral and science focused. My research examined the following questions: 1) The number and ways male-identified versus female-identified characters are represented in leading and supportive roles; 2) How STEM fields are presented as future careers for both genders; 3) The number of STEM learning opportunities presented within each episode; and 4) How children view the gender roles and relationships between characters. Data was collected through two processes. First, I watched multiple episodes of each show and gathered quanitiative data, for example; how often females are in leadership roles, how often they generate their own ideas, and are viewed as capable of completing a task. I then co-viewed episodes of each show with children in the intended age range. While co-viewing I made observational notes and asked a set of verbal questions used to engage with the child during the show. Through the co-viewing process and dialogue, I gained insight into how children view gender representation within these shows. This research project further examined the messages children receive regarding STEM learning and careers during the critical time when self image is being developed. In addition, this research highlights the opportunity for further research across multiple television networks, analyzing gender representation within STEM fields.

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.

Herbivorous fishes feed on stems, leaves, flowers, seeds, fruits, and nuts of diverse aquatic plants, as well as algae. In the Neotropics, many of these fishes have intricately tied ecologies with their prey plant’s life history and facilitate seed dispersal; including the herbivorous cousins of piranhas, pacus. Most pacus experience fluctuation in their diet that reflects the changes in seasonality and plant part availability. A few species of pacus, however, exhibit a specialized feeding strategy known as phytophagy; solely consuming the plant material of Podostemaceae (riverweed). This trend of dietary specialization may be paralleled by a similar shift, away from general herbivory, and towards a specialized phytophage morphology. To investigate the link between diet and morphology within the greater scope of herbivory, we examined four coexisting species including: the seemingly specialized phytophage, Ossubtus xinguense; the generalized phytophages, Tometes kranponhah and Tometes ancylorhynchus; and a facultative phytophage, Myloplus rhomboidalis. We compared the gross morphology of these species with several other serrasalmids using micro-computed tomography scanning to measure functional jaw characteristics, as well as using geometric morphometrics to compare body shapes. Jaw biomechanics indicate that O. xinguense produces the weakest jaw leverage potentially as a result of its sub-terminal mouth. However, we also concluded that the phytophagous species as a group, do not overtly differ from the more generalized herbivorous pacus in terms of jaw mechanics (but remain distinct from the piscivorous piranhas). Body shape analyses also show little divergence among phytophage and herbivore body shapes, suggesting that many herbivores share a similar bauplan adapted for fast flowing waters. With the exception of O. xinguense, phytophagous pacus appear to be equipped with a general herbivory feeding morphology sufficient for a specialized diet. This suggests that phytophagy is not a particularly challenging feeding strategy, but performance may be augmented by additional morphological specialization.

Belted Kingfishers (Megaceryle alcyon) are widely distributed across freshwater and marine environments of North America, but the species’ feeding ecology remains poorly studied in marine habitats. In summer 2017, we investigated the behavior and feeding ecology of Belted Kingfishers in the nearshore marine waters of San Juan Island. Our objectives were to assess differences in feeding strategy and success among birds of different ages, to calculate time budgets, and to examine the effects of dynamic environmental factors such as tide and current speed on kingfisher feeding. We conducted focal behavioral observations of adult and juvenile birds at two locations on San Juan Island. Observations on individual feeding success were collected opportunistically during study periods. Overall, adult birds showed a higher success rate and longer average prey length than was observed for juveniles. Feeding success for all age categories was higher at Jackson Beach than at Friday Harbor Labs, suggesting that prey abundance or accessibility may be site specific. Feeding success was fairly consistent over all current speeds but was highest during low tides. Feeding success also showed a diel pattern (highest from 1200 to 1400), differing from prior research in freshwater habitats. Our results are intriguing and demonstrate the need for continued research on how life stage, currents and tidal stage influence marine based Belted Kingfishers and their role in coastal ecosystems and food webs.

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.

Dungeness crabs (Cancer [Metacarcinus] magister) hold commercial and cultural value in Washington State, yet little is known about the effects of climate change on their population--even less is known about their competitor, the graceful crab (C. [M.] gracilis). To investigate the effects of temperature and size on feeding rate, we conducted consumption experiments in aquaria at multiple temperatures and across a variety of sizes (70-100mm carapace width) of Dungeness and graceful crabs. We investigated their weight-specific feeding rates, egestion, and excretion via a basic mass balance bioenergetic equation in which consumption must equal respiration, egestion, excretion, and growth. We measured the egestion and excretion components of consumption by collecting unconsumed food material and fecal material, respectively. This multi-species comparison evaluates size and temperature-dependent feeding patterns that have implications for future spatial distributions and energy requirements of Dungeness and graceful crabs across Puget Sound. Future management of the fishery and ecological impacts under changing conditions are discussed.

Among the most robust determinants of fitness within the animal kingdom are successful feeding techniques that enable adequate energy acquisition. The need to maintain a steady food supply is especially crucial in mammals who have high metabolic demands in order to maintain a homeostatic internal body temperature. Within the Class Mammalia, the Order Cetacea consists of whales, dolphins, and porpoises, and includes some of the most derived and specialized aquatic carnivores. Of the three Cetacean suborders, Odontoceti retains the ancestral condition of having teeth rather than baleen for filter-feeding as in Mysticeti whales. This allows odontocetes to consume many prey types, ranging from cephalopods to large vertebrates. The aim of this study is to investigate if interspecific differences in bite force and gape size evolved in tandem with the consumption of specific prey types in odontocetes. To achieve this goal, we used skull specimens from the Burke Mammalogy Collection at the University of Washington to take a variety of linear measurements of the cranium and mandible. We used these measurements to estimate gape size and bite force by applying mathematical equations, and then contrasted these values across species that differ in diet. We expect to find that odontocetes evolved cranial adaptations to 1) increase bite force as a means to consume harder prey and 2) increase gape size as a means to consume larger prey. Developing a better understanding of how species maximize energy gain is imperative to determining the factors that drive evolution and species adaptation. This knowledge can also help inform future conservation efforts, improve the general understanding of Odontoceti evolution, and serve as a reference for future studies of mammalian cranial morphology and biomechanics.

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.

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.

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.

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.

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.

Cystic Fibrosis (CF) is a genetic disorder that is characterized by recurrent pulmonary infections and a progressive decline in lung function caused by increased inflammation. While the host immune response can help fight these infections, an overzealous inflammatory response in the lungs may be harmful. Inflammation can be induced by multimeric proteins called inflammasomes, which catalyze the maturation of pro-inflammatory cytokines and pyroptosis. Our laboratory is interested in investigating genetic variants that alter the response of the NLRP3 inflammasome in human CF patients as a means of identifying potential targets for host-directed therapies. Preliminary data from the EPIC study has identified two genetic variants in CF children that is associated with colonization by P. aeruginosa, a common bacteria in the lung that can induce deleterious inflammation. We hypothesize that genetic variants in the NLRP3 inflammasome will increase the inflammatory response to bacterial infection and will lead to worsened pulmonary outcomes in patients with CF. First, we used CRISPR/Cas9 and gene editing techniques to knock out the NLRP3 gene in human cell lines. We then inserted NLRP3 genetic variants and stimulate the NLRP3 inflammasome using Pathogen associated molecular patterns such as Nigericin and ATP. The extent of inflammation was measured using ELISA (Enzyme Linked Immunosorbent Assay), and results were compared among NLRP3 genetic variants and wild type controls. The ultimate goal of this investigation is to learn how genetic variants are associated with the clinical outcomes of CF patients. Future studies can involve harnessing host-directed therapies to target specific inflammatory pathways in order to reduce harmful inflammation in CF. Finding the relationship between the NLRP3 inflammasome and CF is critical to generating an effective treatment for CF.

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.

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.

Conservation is a pressing and widely discussed topic. There are many people and organizations involved in the issue, meaning there are many different perspectives and opinions. In his paper “Conservation in the Anthropocene,” Peter Kareiva presents controversial ideas about modern day conservation. Based on my rhetorical analysis of his paper, I argue that he takes advantage of the controversy by presenting his ideas in a purposefully more provocative way than he needs to. In this paper we see him attacking conservation icons and ideals as well as putting forward arguments against currently held ideas in the conservation movement and directly attacking traditional environmentalists. This enrages much of his audience, and through that controversy he brings more attention to his paper and his ideas. This paper analyzes how he uses rhetoric to emphasize the controversial aspect of the ideas he presents in this paper to attract more attention to his argument and to open up a discussion about the issues he presents.

Theodosius Dobzhansky was a prominent 20th century scientist, who proved to be an eloquent rhetor, catalyzing the interdisciplinary synthesis of modern theories of evolution by bridging the great divide between Mendelian and Darwinian schools of thought. In March 1973, The American Biology Teacher published his essay “Nothing in Biology Makes Sense Except in the Light of Evolution.” This sentence has become the memorable line from the essay, often used anecdotally against religion and in support of evolutionary theories by the scientific community. However, this use directly contradicts Dobzhansky’s goal of persuading readers that science and religion aren’t mutually exclusive, through arguing for evolution as proof of God’s greatness, attempting to unite these two disciplines. Theories of evolution have long been tied to and in confrontation with religion. This contention prevails today; in 2017 alone multiple bills were introduced into the U.S. House lobbying for equal time spent teaching both evolution and creationism in public schools. I argue that Dobzhansky’s rhetorical eloquence allows him to appeal to two audiences. Through the use of prolepsis, anecdotes, and devoutness to God he is able to address his religious audience while simultaneously giving educators persuasive tools for teaching evolution in a religious context. Going forward, we can pull from Dobzhansky’s rhetorical strategies to facilitate productive conversations between polarized schools of thought, such as seen today in the American political climate.

Young people spend two-and-a-half as much time watching Internet videos as they do traditional television. Business concerns aside, questions remain about other effects of this change in media consumption. One such concern is of celebrities and their influence. Research demonstrates that celebrities are influential, in part because people consider them credible sources, even with regard to political information. Research also shows that a credible source is more effective at changing one’s attitude and behavioral intention than a low-credibility source. These research findings might alter what was previously perceived as the influence of traditional celebrities – movie stars, pop groups, and the entertainment industry as a whole. With the growth of particular participatory platforms and social media sites, a new type of celebrity exists: microcelebrity. Defined as an act of bolstering digital self-representation through media and technology, the term microcelebrity has since evolved to include individuals who construct self-representation and garner popularity online. Although there is a great deal of research demonstrating that microcelebrities are also influential, especially regarding consumer good purchases on social media, the question of microcelebrity influence on politics remains. In a two by two experiment, this study starts with a literature review on credibility, traditional celebrity, their political influence on audiences, followed by an introduction to microcelebrities and their influence, with a method section that leads to a few hypotheses. First, according to past literature, it is hypothesized that traditional celebrities are evaluated as more credible than microcelebrities. Second, male celebrities (both traditional and microcelebrities) are expected to be evaluated as more credible than female celebrities. Third, traditional male celebrities will be more credible than any other kind of celebrity. Given credibility is deemed by scholars as a crucial component of persuasion, assessing microcelebrities’ credibility provides a better understanding of their societal and political mpact.

Cosmos was a widely popular TV show that presented science to general audiences in the United States. It first aired in 1980 as Cosmos: A Personal Voyage, with famed astrophysicist Carl Sagan spearheading the making of the show, hosting it and becoming one of the most popular scientific spokesmen in the late 20th century. The show was redone in 2014 as Cosmos: A Spacetime Odyssey, hosted by Neil deGrasse Tyson. The revival season featured mostly the same subject matter as the original and had some of the same writers and producers, so the differences in presentation are mostly due to new scientific discoveries and new public perspectives towards science. While many rhetoricians of science have analyzed the shows, no comparison has been performed to see how rhetoric in public science presentations has changed over time. In this presentation, I will analyze corresponding episodes of Cosmos, one from each season, to determine how the presentation of scientific topics has changed for the better and to rediscover past rhetorical strategies which could be employed once again in contemporary scientific discourse. A tone of wonder and awe permeates the 1980 Cosmos while one of excitement is present in its 2014 counterpart; it is this change in particular that may have detrimental effects if the two tones are not merged in public rhetoric going forward.

Many children with Autism Spectrum Disorder (ASD) suffer from decreased gut motility that manifests as debilitating chronic constipation, leading to an unhealthy aversion to food. We hypothesized that the same neurological defects that cause the hallmark cognitive impairments in ASD also negatively impact the enteric nervous system controlling gut peristalsis. Within the autism spectrum, we chose to study one particular condition called Phelan-McDermid Syndrome (PMDS), because every patient with the diagnostic chromosome 22 micro-deletion has a dramatic decrease in gut motility. Evidence suggests that the gene-of-interest in the deleted region is SHANK3 because mice with SHANK3 haploinsufficiency show decreased postsynaptic density of neurotransmitter receptors. The overriding goal of this project is to develop novel drug treatments for patients with PMDS and ASD. Finding new compounds that can increase (or bypass) postsynaptic receptor density could alleviate these patients’ gut motility problems. However, models to study the enteric nervous system either involve invasive biopsy procedures to remove enteric tissue from patients or the use of animal models that fail to replicate the pathology observed in humans. Therefore, the objective of this study is to create a human disease-in-a-dish model of enteric nervous system dysfunction by generating stem cells from PMDS patients and differentiating them into enteric neurons (ENs). We predict that molecular characterization of SHANK3-deleted enteric neurons will identify aberrant signaling pathways suitable for therapeutic intervention. Preliminary experiments from our laboratory have demonstrated the feasibility of differentiating patient-derived induced pluripotent stem cells (iPSCs) into neural crest (NC) cells, which are necessary precursors to making enteric neurons. NC plus smooth muscle co-culture experiments will then be used to drive fluorescently labeled normal and SHANK3-deficient NC cells to enteric neurons, thus enabling phenotypic characterization of the disease phenotype in vitro.

Streptococcus mutans is an acidogenic bacterial species that predominates in the oral microbiome. S. mutans binds to the salivary pellicle, a layer of proteins that forms on the tooth surface and forms acids after metabolizing sugars. Accumulation of S. mutans biofilms leads to cavity formation, and when the bacteria travels to and infects the heart, can lead to infectious endocarditis. Therefore, decreasing accumulation of S. mutans is a key concern. Recent evidence suggests that S. mutans is among the bacterial species that utilize functional amyloid fibrils in its biofilms. Amyloids are insoluble fibrillar protein aggregates with a cross-ß structure, and functional amyloids are used by bacteria to provide structure and strength to their biofilms. While functional amyloid systems in bacteria such as E. coli and S. aureus have been investigated, very little is known about the mechanism or purpose of S. mutans functional amyloids. Polyphenolic small molecule epigallocatechin gallate, or EGCG, is an amyloid inhibitor in S. mutans biofilms. Previous results from our lab suggest that amyloid fibrillization progresses via an intermediate that adopts a unique secondary structure, an alpha-sheet. Alternating L- and D- amino acid peptides adopt an alpha-sheet secondary structure and have been shown to inhibit amyloid formation in multiple mammalian systems by binding to soluble alpha-sheet-containing oligomeric species. Inhibition of amyloid formation by alpha-sheet peptides suggests presence of an alpha-sheet intermediate species on the pathway to functional amyloid formation. To investigate the mechanism of functional amyloid formation in S. mutans, alpha-sheet peptide inhibitors were compared to EGCG for their ability to inhibit fibril formation of S. mutans adhered to an artificial salivary pellicle.

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.

Type 2 diabetes (T2D) is a disease associated with pancreatic islet β-cell failure; especially, the loss of β-cell mass. Approximately 75% of patients who start with one medication will need multiple to control the progression of this disease. With no cure and numerous secondary complications - blindness, kidney failure, heart attack, and stroke - T2D places an enormous burden on our society and healthcare system today; The disease is projected to be the seventh leading cause of death by 2030. Islet amyloid polypeptide (IAPP) deposition is observed in approximately 90% of T2D patients. While human IAPP (hIAPP) is amyloidogenic, forming amyloid fibrils and deposits, IAPP from rodents is not. Our group’s previous findings suggest that T2D and other amyloid diseases form soluble toxic oligomers through a non-standard α-sheet secondary structure. We propose a peptide-based therapeutic to combat T2D via utilizing synthetic α-sheet compounds complementary to the amyloid-associated α-sheet structure to target the toxic oligomer form of hIAPP. In this study, we addressed the efficacy of this peptide-based therapeutic through inhibiting the aggregation of hIAPP via a Thioflavin-T assay and neutralizing the hIAPP oligomer cytotoxicity via a MTT cell viability assay in a human-derived pancreatic cell line. The preliminary results suggest that our peptides are effective in reducing hIAPP aggregation and oligomer cytotoxicity. Moving to a more biologically relevant model, we evaluated the effects of our compounds on reducing amyloid formation in the islet of Langerhans from transgenic mice; the preliminary results are encouraging. The α-sheet platform provides a novel potential therapeutic for treating T2D and other amyloid diseases.

The misfolding and aggregation of free light-chains into amyloid fibrils is the hallmark of antibody light-chain (AL) amyloidosis, a fatal disease associated with the accumulation of amyloid species in tissues throughout the body, including the heart and kidneys. Current treatment options, including chemotherapy and bone marrow transplant, do not address the causes of aggregation on a molecular level. Molecular dynamics (MD) simulations were used to investigate misfolding pathways in the aggregation of two light chain monomers, Jto and Wil. These simulations showed that under amyloidogenic conditions, conversion from beta-sheet to alpha-sheet secondary structure was observed in both Jto and Wil. Misfolded conformations, obtained from the MD simulations, were used to guide the design of alpha-sheet peptides, which have been used previously to inhibit amyloid formation in diverse systems. The designed peptides were evaluated computationally by docking them against misfolded conformations of Wil, and the best performing peptide was chosen for future experimental work to explore its potential to limit aggregation.

Alzheimer's disease affects millions of individuals worldwide, yet there is an astounding lack of marketed treatments that can effectively slow the neurodegeneration associated with the disease. In the past few decades, evidence has emerged that small, soluble aggregates of beta-amyloid (Aβ) peptide known as oligomers are primarily responsible for toxicity in the brain, which has sparked research to develop inhibitors targeting the toxic oligomers. However, the actual structure of Aβ oligomers remains unknown, in large part because traditional methods used to determine protein structure are ineffective due to the dynamic and heterogeneous nature of these oligomers. This in turn has greatly hindered therapeutic development. Interestingly, a designed α-sheet peptide known as AP3 displays striking behavioral similarities to Aβ under low pH, making it an ideal model for understanding amyloid protein behavior. In addition, AP3 aggregation and toxicity are potentily inhibited by other amyloid species. The interactions between this synthetic amyloid and naturally-occurring amyloid species, including Aβ, are being explored both experimentally and via computer simulation, and the data are being used to design a de novo peptide inhibitor. This inhibitor is being tested for its ability to inhibit amyloid aggregation and toxicity, as well as whether it can specifically bind to heterogeneous populations of Aβ even at low concentration. The successful completion of this project wil result in significant progress towards understanding amyloid behavior and aggregation. This may eventually lead to novel applications of the α-sheet structure in treatments and diagnostic assays for Alzheimer's.

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.

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.

 Scholars in many disciplines have used the concepts of charisma and charismatic authority to describe leaders of prominent terrorist groups. These researchers do not give the breadth and depth these topics require when attributing them to casual relationships between leaders and followers. As a field, the study of terrorism is lacking in substantial work on the subject. This leads to an absence of deep conceptual understanding and incorrect or ill-defined usage. I will address the gap created by these missing definitive parameters to build a clearer understanding of the concepts. Through systematic comparison of the social tools employed by the leadership of Al-Qaeda and Boko Haram I will explore the characteristics of charismatic authority. I will analyze comparative parameters of group leaders, local demographics, institutional structures, and major national or regional events that precede violence. This goal will be achieved through historical document analysis using primary and secondary sources. Primary sources include documented speeches and interviews, documents released by the groups, and personal documents of leaders. Secondary sources include news stories, scholarly articles, and other academic literature. The purpose of this research is to set the stage for those with access to their followers to adequately explore the potential causal relationship between charismatic leadership and the actions of their followers.

Sexual assault is a serious public health problem on college campuses. Nationally, an estimated 20% to 25% of college women experience some form of rape victimization during their college years. This problem is not limited to the United States. In Brazil, a woman is raped every eleven minutes and 700,000 live with regular aggression and assault. However, Brazil has formed innovative interventions such as specialized Women's Police Stations and court systems to respond to violent crimes against women. They have established Women's Right's Councils at the national, state, and city levels. Northern feminists have paid little attention to learning about or adapting models from Latin American countries. My hypothesis is that Brazilian students will have greater awareness of intervention strategies than University of Washington students. This project proposes a cross-cultural comparison on student perceptions of intervention strategies for sexual assault victims to evaluate the awareness, accessibility, and effectiveness of these services. I utilize a combination of qualitative and quantitative data collected from 245 surveys and interviews with students at the Methodist University of Sao Paulo, the Federal University of Mato Grosso do Sul, and 245 surveys and interviews at the University of Washington, Tacoma. I employ Feminist and Post-colonial theory to analyze policymaking and the globalization of local women's agendas. Findings indicate a greater lack of knowledge of resources at the University of Washington. Brazil's experience suggests that implementing Women's Rights Councils in the United States may create space within the municipalities of our country for women's participation in elaborating public policies as well as in advising and supervising executive actions. Under a gendered lens and within a global perspective, Brazil serves as a leading case study in an ongoing movement toward the institutionalization of women's equality. 

It has long been known that certain species possess the capacity to regenerate bony appendages following amputation through a process called epimorphic regeneration. For instance, zebrafish possess the ability to regenerate their tail fin bones. Early regeneration involves the formation of a blastema, similar to the blastema that mediates limb regeneration in salamanders. After the blastema forms, the bone regeneration process resembles the bone developmental process in humans. Thus, a better understanding of epimorphic regeneration holds promise to enhance our understanding of regenerative biology, allow for medical advances in bone tissue engineering, as well as increase understanding of the skeletal developmental processes. A challenge in understanding the regeneration process is the inability to immobilize fish to generate time lapsed images of various stages of regeneration. Typical methods for anesthesia in zebrafish only enable 10-20 minutes of sedation. Several studies (including those by our lab) have developed specialized methods to do long-term imaging with the use of Tricaine Methanesulfonate and Benzocaine. However, both anesthetics are sodium channel inhibitors, which inhibit the regeneration process itself. In order to circumvent this problem, we designed a chamber for lower anesthetic plane imaging with a restraint system, as well as a glass-bottom window to facilitate imaging. The chamber is coupled to peristaltic pumps so water and anesthesia can flow in and out. In pilot studies we have found the zebrafish quickly acclimate to the chamber, and have remained in the chamber for two hours. We have been able to image sp7, NADH and birefringence simultaneously for the first 2 hours of regeneration and have found stability in these signals over time. Our studies indicate that this long-term imaging chamber may allow us to see details of dynamic processes that unfold during bone regeneration, which currently can only be seen through snapshots of short-term imaging.

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.

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.

Giardia, a protozoan parasite which resides in human intestine, can cause Giardiasis, a common parasitic disease associated with severe diarrhea. It possesses a simple life cycle including the motile trophozoite stage and infectious cyst stage. Once a human consumes unsanitary drinking water or food with Giardia cysts, the low pH in stomach drives excystation to release the trophozoites. When they perceive stimuli from the high bile and alkalinized pH environment, they will initiate encystation by turning on the Cyst Wall Protein gene to form cysts. Our purpose is to understand the spatiotemporal encystation process and the encystation rate of Giardia in a physiological environment (murine intestine) via observing the ratio metric change of encysting and non-encystation cells in the Dual-color Bioluminescence Imaging (BLI) System. BLI is essential to monitor noninvasive biological processes in living organisms via detecting photon emissions that requires the enzyme luciferase to catalyze a substrate, usually luciferin, with oxygen, ATP, and magnesium. To test if dual-color BLI can report the ratio metric change of encysting and non-encysting cells in vitro, we have generated the in vitro encystation assay. The promoter of Glutamate Dehydrogenase, a constantly expressed gene at all stages of Giardia, is combined with a luciferase gene to represent non-encysting cells when transcribed in normal media. The promoter of cyst specific gene, Cyst Wall Protein 1, is combined with another luciferase gene to represent encysting cells when expressed only in encystation media. By successfully observing the ratio metric change of luciferase expressions in vitro, we can then proceed to future mouse experiments. Once the technique has been confirmed feasible in the mouse model, it can be applied to monitor the life cycle of all cyst forming parasites and understand when and where they are at infectious stage, thereby improving the accuracy for alternative drug screening.

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.

As one of the five leading causes of blindness, uveitis is the reoccurring inflammation of the uvea, demonstrating pathological changes in the eye. In recent years, optical coherence tomography (OCT) has been recognized as the leading, clinically accepted imaging modality for diagnosing major human optical diseases. Despite this, research on the clinical usage of OCT, primarily spectral domain OCT (SD-OCT) and swept source OCT (SS-OCT), for uveitis diagnosis remains sparse due to the lack of a quantitative-based set of parameters to assist with OCT image analysis. As a result, there is a need to develop an index of parameters that quantifies the microvasculature and structural changes associated with uveitis. To address this need, a novel five parameter quantitative-based metric consisting of distance of retinal detachment, retinal thickness, vessel area density, vessel diameter, and vessel perimeter was evaluated. Through layer segmentation of SD-OCT and SS-OCT scans, application of optical microangiography, and quantitative analysis of structural and microvasculature changes for healthy and uveitis cases, the clinical potential of SD-OCT and SS-OCT for diagnosing uveitis was evaluated. This project introduced a metric for evaluating changes associated with uveitis in a qualitative and quantitative manner to further understand the abnormalities that accompany the disease. Assessing the clinical efficacy of SD-OCT and SS-OCT for uveitis detection can provide insights on the most effective method for diagnosing this disease.

Small RNA molecules called microRNAs (miRNAs) are translational repressors and are involved in a variety of processes important for normal cell development and function. Previous studies in our lab showed that miRNAs are required in early (embryonic) stages of retinal development. After depletion of miRNAs in early retinal progenitor cells (RPCs), late RPCs and their progeny, such as Müller glia (MG) which are the primary glial in the retina, are not generated. Instead, only early born neurons are produced. The depletion of miRNAs can be obtained through deletion of an enzyme that generates mature miRNAs called Dicer. Since we know that miRNAs are crucial for early retinal development, this study investigated if miRNAs are also important for proper late (postnatal) retinal development. We used a Sox2 reporter mouse which allows visualizing late retinal progenitors (Sox2 is a gene expressed in RPCs) and selectively deleted Dicer in RPCs at postnatal day 2-6. The tissue was analyzed 2, 4 and 7.5 weeks after Dicer deletion and compared to normal retinas using immunofluorescent staining of retinal cross sections and confocal microscopy. We found massive disruptions in the retinal architecture such as the formation of rosette/ bubble-like structures, indicating that miRNAs are required for proper formation of the retinal layers. Since MG play a role in maintaining the retinal structure, in a second series of experiments we induced Dicer deletion specifically in MG at postnatal day 11 –14, when the retina is almost completely developed. The tissue was analyzed 8 and 20 weeks after Dicer-deletion and compared to normal tissue. We found an atypical location of MG and disruptions in the layered retinal structure, indicating that miRNAs are also required for accurate MG location in the retina, which is essential for normal retinal architecture.

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.

For more than a century, Drosophila melanogaster (fruit flies) have been an invaluable and versatile tool to further our understanding of cell signaling and survival mechanisms. To this day, they continue to shed light on the endogenous pathways that cancer cells can hijack in order to proliferate, metastasize, and recur following remission. The molecular conservation of these pathways invites parallels between the germline stem cells in D. melanogaster and the cancer stem-like cells in human carcinoma. In the same way that a tumor can relapse following a period of dormancy, Drosophila germline stem cells are capable of repopulating their niche after insult from Ionizing Radiation (IR). Utilizing this powerful model, we have conducted a small molecule drug screen of 512 compounds that we have narrowed down to eight candidate drugs that appear to increase cell death in Drosophila germline stem cells. Having already characterized the wild type Drosophila germline stem cell response to IR-induced DNA damage, we  probed how drug treatment and gene knockdown affected the germline stem cells' ability to recover from insult. Previous work in the Ruohola-Baker Lab has demonstrated the critical importance of the mechanistic target of rapamycin (mTOR) and the Tie receptor pathways in regulating regeneration after insult in the Drosophila germline. The Tuberous Sclerosis Complex (TSC), a heterodimer comprised of Tsc1 and Tsc2, is a known negative regulator of mTOR. Additionally, the Tie receptor is central to anti-apoptotic signal transduction in the Drosophila ovary. We have screened four candidate drugs to see if they effectively increase stem cell death in Tsc1-knockdown and Tie-null flies, in order to ascertain whether our drugs affect stem cell survival mechanisms through mTOR and/or Tie signaling. Our findings may shed light onto how to mitigate the quiescent threat of tumor relapse.

Characterizing biological functions on a single molecule scale increases understanding of biological functions by providing information about the indiviual contributions which combine to create larger scale functions. Single molecule measurements are a crucial part of characterizing molecular interactions. Although atomic force microscopy (AFM) and magnetic tweezers are able to measure the response of single molecules to mechanical force, it is challenging to ensure single molecules are being measured. In this project, a precise DNA Origami structure was used to space molecules for single molecule force measurements. Base pair association between DNA nucleotides allowed specific nanostructures to be designed and fabricated. Molecules of interest self-assemble to specific sites of the structure. AFM was used for imaging and obtaining force measurements. This research investigates the strength of adhesion for double stranded DNA when subjected to different loading rates as a proof of concept. In the future, this structure will be used to determine force properties of diverse molecular interactions like platelet and bacterial adhesions.

Gene amplification can be associated with genetic disorders such as cancer and varying types of autism. One such form of amplification is a neochromosome where a chromosomal segment is amplified and these two segments are joined at an inverted repeat. There are two models to explain how this event could occur: double stranded break and repair and origin dependent inverted repeat amplification (ODIRA). ODIRA hypothesizes that a replication fork error occurring near short inverted repeats could cause the leading strands to erroneously become ligated to the lagging strands and produce an extrachromosomal palindromic DNA intermediate. Because both models produce identical neochromosomes, I have worked to find which pathway produces them. To do so I utilized CRISPR/cas9 to induce breaks at commonly observed junctions, and analyzed the resulting intermediates using gel analysis of whole yeast chromosomes. If the neochromosome were to occur via the double stranded break and repair model, I expected that providing the break should increase the frequency with which these neochromosomes arise. Alternatively, if the neochromosomes were occurring due to the ODIRA model, I expected the frequency to remain unchanged. I followed this initial analysis with DNA sequencing to give further support to either outcome. In particular I verified that the CRISPR system was working by sequencing across the junctions where cas9 was cutting. If cas9 was indeed cutting, then when comparing the sequence from the cas9 survivors to that of the yeast genome, the survivors had an altered cut site. My work provides insight to the etiology to this fascinating class of chromosome rearrangements.

Antibiotic resistance is an intractable clinical challenge that disproportionally affects much of the world’s most impoverished populations. A critical driver of resistance stems from DNA mutations. Therefore, insights into how mutations arise in the genome is critical to understanding the development of antibiotic resistance. Our lab is currently identifying factors and environmental conditions that promote mutagenesis and bacterial evolution. Utilizing mutation rate analysis, we have identified factors and conditions that promote mutagenesis in divergent bacterial species. Additionally, using short-term evolution experiments, we have found that these factors promote the development of antibiotic resistance over time. This work provides novel mechanistic insights into mutagenesis and antibiotic resistance development in bacteria.

Staphylococcus aureus is responsible for large numbers of patient morbidity worldwide. However, studies of this important pathogen have suffered from the lack of a robust toolset for scalable genetic and genomic manipulation in the organism. Our goal for this study was to develop an efficient, simple, and inexpensive system for precision genome engineering in S. aureus. Our strategy employs ssDNA oligonucleotide recombineering coupled with CRISPR/Cas9-mediated counterselection to address these needs. We first identified a single-stranded recombinase protein, EF2132, derived from Enterococcus faecalis, which can successfully integrate single-stranded DNA oligonucleotides into the S. aureus genome. Our results showed that EF2132 readily mediates recombineering across many different laboratory strains and primary clinical strains, normally yielding thousands of recombinants per transformation. We proceeded to expand the generality of our genome editing system by incorporating lethal counterselection, enabling efficient recovery of recombineered isolates lacking a selectable phenotype. We constructed a temperature sensitive, two-vector system that enables conditional recombineering and CRISPR/Cas9- mediated counterselection in S. aureus without permanently introducing exogenous genetic material or unintended genetic lesions. Our findings indicate that our system effectively targets and edits genes with both specific mutations and large-scale knockouts by utilizing inexpensive, commercially synthesized oligonucleotides as substrates for inducing and counterselecting precise genomic changes. Since our system utilizes cheap synthetic DNA oligonucleotides as substrates for recombineering and counterselection, it provides a scalable, precise and inexpensive tool for producing isogenic strain in S.aureus. Because of this, our system can be used to effectively facilitate future studies to investigate the genetic mechanisms of many different biological phenomena. As our study progresses, we hope to introduce refinements to further improve the scalability and efficiency of this methodology.

DNA replication is critical to cellular reproduction. In bacterial and eukaryotic cells alike, DNA replication occurs in immobile, discrete complexes (so-called “factories”) enriched for replication proteins. However, the size of these replication complexes is well below the optical diffraction limit (~250 nm), making them difficult to study using conventional microscopy. Using Escherichia coli as a model organism, the goal of my project is to create an ultrastructural model (50-nm resolution) of the bacterial replication complex. To this end, I have developed an expansion microscopy (ExM) protocol that is compatible with bacterial cells. In short, E. coli cells harboring fluorescent fusions to replication proteins are embedded in a swellable polymer gel and physically expanded by a factor of four. The expanded specimen is subsequently visualized at high-resolution using a conventional fluorescence microscope. Unlike more traditional super-resolution methods, ExM is compatible with simultaneous imaging of up to four replication proteins, which I expect will be critical in determining the overall organization of the replication complex. Although ExM is established for eukaryotic cells, I am the first to apply the method to visualize the interiors of bacterial cells. I expect that this project will not only contribute a new super-resolution-microscopy method for bacterial cells, but also reveal the structure of the replication complex with unprecedented detail, perhaps providing insight into the mechanism of the fundamental process of DNA replication. This, in-turn, could lead to new therapies for combating diseases associated with replication defects, including cancer.

DNA origami nanotechnology has evolved rapidly since its conception eleven years ago. Both two-dimensional and three-dimensional nanostructures have been created with potential applications in targeted drug delivery, “smart” diagnostic technology, and the study of cell behavior. By annealing “staple” oligonucleotide strands to a single-stranded DNA scaffold we can effectively fold the DNA onto itself to build the nanostructures of interest. One of the primary physical limitations to what one can build is the scaffold. The most commonly used scaffold is derived from the bacteriophage M13mp18 and has a length of 7,249 nucleotides. Its length has previously been varied; however, an overlooked limitation is the secondary structure DNA naturally exhibits. These are sites in which the scaffold binds to itself, thus creating competition for staples to bind during folding reactions. To predict the impact that a designed sequence with little secondary structure could have, we analyzed the first 6,000 bases of the M13mp18 DNA sequence using NUPACK, a nucleic acid sequence analyzer, for their minimum free energy (MFE) at storage, manipulation, and maximum folding reaction temperature. Preliminary data shows M13mp18 exhibits less secondary structure at a high temperature (65°C) than at a low temperature (4°C) and increasing the concentration of divalent salts linearly increases the amount of secondary structure. Additionally, alternative, shorter sequences have been engineered and their secondary structure is being analyzed at varying conditions. To further determine the effects on yield and stability, structures will be folded using the designed sequence and the standard sequence as a scaffold. These will be compared through agarose gel electrophoresis and transmission electron microscopy. The results from this preliminary data could help us move us toward using a scaffold with decreased secondary structure present at folding temperatures which could potentially result in higher yields, shorter folding reactions, and increased stability.

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.

 The so-called DREAMers are the current generation of largely undocumented youth named after an unrealized piece of Congressional legislation known as the Development, Relief, and Education for Alien Minors or "DREAM" Act. These youth, many of college-age, are the source of an unrelenting voice for the advancement of immigrant, civil, and human rights throughout the United States. Their movement mirrors earlier struggles that resulted in significant social, economic, and political change; taking the form of direct-action protests and involvement with state, national, and transborder organizing campaigns through social media networks. This ethnographic research project explores the DREAMers' Movement in terms of activists' enunciations of identity, subjectivity, and civil disobedience in the context of the State of Exception created by the Trump Administration's engagement in biopolitics. I address the principal research questions: Are new radicalized political subjectivities emerging from the widely shared daily-lived experiences of precarity among the self-identified members of this movement? How does this subjectivity shape DREAMers' perceptions of and engagement with identity politics and civil disobedience in their rebellion against their status as bodies without rights? These questions were research through ethnographic methods, such as one-on-one interviews and participant-observations. Ultimately noting new forms of engagement in activism and the creation of new identities and ideologies surrounding civil disobedience, this project will provide a scholarly space for reflections on the DREAMers' Movement and its prospects for transforming national and transborder narratives of self, citizenship, and belonging in this political era.

Ethnic and religious violence on the border of western Myanmar’s Rakhine State and Bangladesh displaced approximately 647,000 Rohingya (residents), a stateless Muslim minority in Myanmar since August 25, 2017. The fact that this crisis has not been fully addressed by the Burmese majority is very alarming especially under the administration of Aung San Suu Kyi, the prominent political figure of Myanmar. Hence, the initial purpose of my research was to examine the factors contributing to this humanitarian crisis by conducting interviews, oral histories, and online surveys among resettled Rohingya women in the Greater Seattle area. I employed a transformative feminist theoretical framework to understand the relationships between political subjectivity and gender violence and colonialism, military dictatorship, and patriarchy. However, while recruiting participants for my project, I encountered silence and reticence rather than enthusiasm from the Rohingya community. This wall of silence and the absence of Rohingya community even among the small Burmese populations in Greater Seattle Area has been a significant turning point in my research. Perhaps this silence itself indicates Rohingya fears that even the researcher-researched relationship could expose them to further racism and discrimination from Burmese here in Seattle on top of their sufferings from political trauma and sexual violence in Myanmar. Therefore, I am currently implementing an auto-ethnographic approach to excavate the role my own and other majority Burmese immigrants' perceptions of and ways of representing the Rohingya, and how this has contributed to the current distrust, silence and fear between women in two communities who have both experienced sexualized military violence. By doing so, I hope my research will begin a process of facing Burmese internalized racism, sexism, and religious discrimination towards the Rohingya community and serve as the stepping stone towards inclusive community-building with cultural humility here and in Myanmar.

This project seeks to highlight and archive the lives, stories, and experiences of queer and trans people of color at the University of Washington. Queer movements have historically rested on the labor of queer and trans people of color, however, these histories are often whitewashed. The experiences of queer and trans students of color are not ones that are often archived or given space to be told. Through this project I seek to give space to stories and lives that are pushed to the side and silenced. I also seek to find commonalities among different yet similar student experiences. This project is based in one-on-one, in-person interviews with induvidual students. As an interviewer, I ask the interviewees questions about experiences include upbringing, familial structure, cultural context, coming into queerness, finding queer of color spaces in and outside of the university context, looking to the future, and ways of healing from traumas. My methods include in-depth audio and visual recorded interviews, and full detailed transcripts of each interview. As a member and leader of the Queer People of Color Alliance at UW, I am a part of and have access to queer communities of color at UW. This project highlights the importance of induvidual narratives, as they inform larger understandings of queerness and community. In addition, this project builds an archive of queer and trans student of color experienes that, among other things, highlight the importance of institutional spaces within the university campus that supports queer and trans students.

The space program is a quickly expanding industry that promises trillions of dollars within the next 20 years. Countries are scrambling to cultivate space programs as the opportunities, both scientifically and economically, develop before our eyes. The United States leads the pack in the global space industry, and Washington State is a strong contender as front-runner in the US space program. With 26 federally recognized tribes, it is easy to see First Nations people being left behind in this lucrative business. How can we, as First Nations peoples, indigenize the space program by contributing our vast amounts of historical knowledge and re-appropriating the industry to reflect our unique views and histories? Do indigenous groups even want to be involved in the space program? And finally, how do tribal governments benefit from the financial benefits of the space program? By doing archival research of tribal views on space, the space program, conducting a field study based on the geography and economics of Spokane Tribe of Indians, and considering my own knowledge as a Native American identifying woman, I was able identify issues and formulate policy recomendations. Unfortunately, it is all too easy to see this important demographic becoming overlooked by this financially profitable opportunity. If First Nations groups will ever feel comfortable becoming part of the space program, their voices and sacred views need to be respected and valued. The US government also needs to make sure that indigenous people are able to have the opportunities that allow them to participate and share their views. Lastly, tribal governments need to find ways to indigenize the space program and make sure our communities see the economic profit that can be yielded from this extremely important industry.

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.

As general circulation models (GCMs) increase in complexity, the number of physical processes representing the climate system increases. A central goal of climate science is to understand how uncertainty in these physical processes, translates into uncertainty in the system response. But the very complexity of the GCMs generates a troublesome question: how do you properly define a stable and unchanging reference system with which to compare constituent elements and characterize their uncertainties? To navigate around this, we introduce a simple energy balance model (EBM) that accounts for the transport of both sensible and latent heat in the atmosphere. We demonstrate that the EBM accounts for approximately 90% of the inter-model spread in the temperature response for an ensemble of GCMs subjected to increasing CO2. We then calculate the unique model patterns of ocean heat uptake, radiative forcing, and radiative feedbacks and demonstrate that 100-years after an abrupt quadrupling of CO2 above preindustrial values, the largest source of uncertainty is the pattern and amplitude of radiative feedbacks. Using this, we identify regions of high feedback uncertainty and show how this can bias temperature responses in other regions.

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.

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.

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.

Phytophthora alni is a species complex of pathogenic oomycetes (water molds) that can cause lethal disease in alder trees, Alnus spp. One variant, P. alni subsp. alni, is widespread across Europe, devastating stands of alder since the 1990s. One less lethal member of the species complex, P. alni subsp. uniformis, has already been found in the wild in Alaska and Oregon, but not in Washington State. Recently, it has been detected in potted alders in nurseries in Pierce County. It is currently unknown whether any member of the P. alni species complex is in the wild in Washington, either naturally or through introduction from nursery plants. To begin efforts to detect Phytophthora alni in Washington State, a risk assessment map will be created using Geographic Information System (GIS) techniques. The spatial analysis will involve examining the environmental factors that increase infection susceptibility, such as slope, soil grain size, and flooding, and correlating with the distribution of alders. Important questions that could be revealed are whether high risk areas are upstream, where infection could spread, or downstream, and whether high risk areas correlate with urban or agricultural land use. The risk assessment will provide a starting point for choosing sampling sites, which is the next step in detecting the existence of P. alni. Additionally, the final analysis will inform forest management practices, as the highest risk areas could be inspected for symptomatic alders and mitigation measures could be enacted if any are found. The assessment will also have implications for restoration sites, where native trees such as alder are planted from nursery stock.