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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

This project seeks to relate chemical composition of hop oil extracts to their measured sensory qualities. Sensory properties of beer are the result of their unique chemical makeup fingerprint. Feature selection implemented in this analysis allows subtle differences in composition to be related to sensory profiles. Separation and content identification of the extracts was achieved with gas chromatography – mass spectrometry (GC-MS) instrumentation. Data pre-processing and analysis were completed using MATLAB software and peak finding algorithms developed exclusively by in-lab personnel. Feature selection strategies facilitated the comparison of individual analyte peak heights to sensory data. Several selection methodologies were tested to compare their utility in finding correlations. These approaches included data tiling and peak table-based strategies. The mathematical nature of data correlation, linear or otherwise, was then investigated. Preliminary results suggest that there may be a complex relationship between the sensory profiles and chemical composition. Exploration in this research path will enable the use of data analysis methods developed herein to better determine which compounds present in food and drink contribute to unique sensory attributes.

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.

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.

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.

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.

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.  

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.

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

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.

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).

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.

Spinal cord injuries cause damage to the corticospinal tract which can lead to deficits in coordination and movement. This greatly alters and may decrease an individual’s quality of life. This project utilizes optogenetics to trigger action potentials in neurons, and tests the hypothesis that activity can promote regeneration of corticospinal connections. Co-cultured mouse spinal and cortical neurons serve as an in vitro model system. The spinal and cortical neurons are in separate chambers that are connected by a canal. Cortical cells are transfected with light- activated channels and stimulated with LED lights to trigger action potential firing. The canal connecting the chambers allows for the cortical neurons to form new synapses with the spinal neurons. In order to quantify the results, synapsin, a protein found in presynaptic vesicles, is labelled using immunocytochemistry, allowing us to quantify the number and size of synapses by measuring synapsin-positive puncta. It is expected that cells stimulated with light will show a greater number of synapses compared to those that were not. Different patterns of neuronal stimulation are tested to determine the best parameters for promoting synapse regeneration and strengthening. Once these have been determined, they will be validated in an in vivo rodent model, prior to testing in primates.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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 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.

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.

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. 

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.

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.

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.

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.

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.

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.

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.

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.

 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.

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.

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.

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.

STUDIO, a near-peer STEM (science, technology, engineering, and mathematics) mentoring program, fosters growth for both the mentors and mentees. In partnership with Neighborhood House, a local multiservice community-based organization, UW mentors support low-income, immigrant and refugee youth to develop motivation, interest, and identification with STEM education and careers. Mentors do this by creating units that provide youth opportunities to learn at the intersection of their stated interests and mentor expertise. This cultivates a community of learners that values youth and mentor agency. STUDIO focuses on both mentees and mentors, but our initial research and evaluation supported by National Science Foundation has focused primarily on mentees. In this study, we investigate mentor learning and growth. We are currently lead undergraduate mentors in STUDIO and are therefore positioned to reflect on our own and other mentors’ learning. Mentors are given the opportunity to advance their leadership and mentoring skills by documenting occurrences in program time, writing weekly reflections, creating and leading curricula, and participating in weekly seminars to share experiences and address issues important to increasing diversity in STEM. In this study, documentations, reflections, and interviews are analyzed to identify shared themes and unique personal stories that illuminate mentor learning, commitment, and collaboration in the STUDIO learning environment. In early thematic analyses, we have identified several emergent themes such as the powerful role of collaborating, relationship building, and mentors’ development through leadership that support their overall academic and personal connection with STEM. As students of color remain underrepresented in the STEM field, mentors empower youth to develop their identification with STEM, despite challenges they face due to persistent stereotypes and limited resources. This research will help us better understand mentor growth and learning so that we can continue to strengthen the STUDIO mentoring team.

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.

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.

 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Anorexia nervosa (AN) is characterized by severe dietary restriction that results in significant malnourishment and weight loss. Regions in the brain related to appetitive drives and interoceptive awareness could be key biological factors that contribute to this severe dietary restriction. The insular cortex may be a particularly important region, as it is thought to be involved in a neural network that processes gustation and the integration of emotional valence with visceral input. A systematic review was conducted to explore links between AN and the insula using the following inclusion criteria: peer-reviewed fMRI studies that incorporated only adult samples of the AN population, were published in the last ten years, and measured activation in response to food-related stimuli. Eleven fMRI studies that addressed patients with current or past anorexia nervosa and the insula met inclusion criteria and were reviewed for qualitative analysis. Studies used a range of different methods, including different task paradigms, making it difficult to make between-study comparisons. Thus, although the insular cortex has been linked in the past to AN, if or how the insular cortex is implicated in restrictive eating in AN remains unclear. Additional studies are needed to clarify links between the insular cortex and AN to distinguish between disturbances that are present during the ill-state versus those that may occur prior to illness onset or following recovery. Studies that use larger sample sizes from both ill and recovered groups with AN will be necessary to further elucidate the potential insula dysregulation in AN and its role in food motivation.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.

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.

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.

Barium and Ytterbium ions are the forerunner ion species for quantum computation and quantum information in trapped ion systems. Ion chains of ytterbium and barium have been proposed for a scalable quantum computer with computation done on ytterbium ions and photonic coupling between different ion traps with barium ions. Ytterbium 171+ has a nuclear spin of ½ meaning it has a splitting of the 6S ½ ground state into 2 hyperfine manifolds separated by around 12 GHz. This allows for an easily addressable 2 level quantum system with a long coherence time. Barium 138+ does not have any nuclear spin, but an applied magnetic field causes Zeeman splitting of the 6S ½ state due to the interaction of the magnetic field and the atom's magnetic dipole moment, of which can be used as a qubit. In this poster I will discuss sympathetic cooling of ytterbium ions by barium ions which is caused by mechanical coupling of the ions from a harmonic electric field from the ion trap and the coulomb repulsion between the ion species, and the results of a recent experiment involving sympathetic cooling of the mixed ion chains of ytterbium and barium. The experiment itself consists of a linear chain of ions consisting of two barium and two ytterbium ions trapped in a four-rod linear Paul trap. Temperature of the ions is determined by performing Rabi flops between the ground state of barium 138+ to a higher energy state. Using the results from the Rabi flops you can determine the average thermal occupation numbers of the ions. I will discuss my role in the optical setup on a narrow line-width laser at 1762nm that it used to perform the Rabi oscillations, and collecting data during the experiment.

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.

This research will better illustrate the paralells of melanocyte harvesting as it has been shown in modern media, through the 2017 blockbuster, Get Out. Essentialy, Melanocyte harvesting is the process in which melanocyte cells are stripped from their host and then distributed for their various benefits. Many benefits of melanocyte harvesting is not only their monetary value, but their medical value. This research is important for the reassurance of the value of the brown and black body in a society designed on dismantling the institutions marginalized peoples represent. The methods of the harvesting initially come post mortem, however, the methodology of why is to be shown through the research. Not only will this research draw paralells with this film, but this research will also address the conversation of value, in regards to brown and black bodies. Using a psychoanalytic approach while analyzing this film, these very connections and paralells will be evident.  

Education on the current state of the food system can motivate individuals to create the food systems and generate demand for products they wish to see. With the idea that we are what we eat and how we consume, real food is the best medicine—for individual health, for society, and for the planet. The power of individual freedom does not mean anything goes, but rather informed, responsible choice that transcends to the global aggregate. Thus, respectful and healthy food systems begin with the individual, and have the potential to bring peace to communities and heal human relationships with land and each other, both locally and globally. Knowledge is power, and first starts with attention and awareness. Given the severe lack of transparency and multitude of socioenvironmental externalities within the industrialized food system, there is a need for adequate consumer education on practices and operations. Information on the consequences of these processes can influence attitudes to shift demand and create new vibrant systems. Here, the problem is the solution. To promote holistically healthy and nutritious systems, I created a disruptive advertisement campaign to highlight truths of the industrial system and its social and environmental externalities to inform consumers on cost and value of the products they are purchasing. This project juxtaposed the concepts of "farm to table" versus "firm to table," in additon to the applications of integrative sensory marketing tactics and culinary storytelling. Through the combination of art, music, poetry, and film, I sought to motivate people to think critically about the power of individual choice and what is behind a brand.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Seasonal stratification of the water column likely influences food availability to mussels grown at certain depths on aquaculture lines, as well as the environmental conditions experienced by the mussels. Fatty acids are important structural molecules that reflect the diet of the organism, such that fatty acid composition provides information on how the condition of mussels grown in different environments responds to food changes. Food sources vary based on a number of environmental conditions, including water temperature and turbulence, which differ between stratified water layers. Fatty acids in aquaculture mussels grown at 1m depth were compared to those at 7m in depth in the summer and fall of 2016 to test effects of varying environmental conditions between the depth layers. The results showed significant variability in the fatty acid composition of mussels grown at different depths in the summer months, but none in the fall. The difference between depths was contingent on the season. The variability in the summer months is likely due to stratification from increased surface temperatures, which decreases mixing and nutrient supply to mussels at lower depths. Stratification is then reduced in the fall and may explain homogenization of mussel fatty acid signatures from that period. In 2017, monthly sampling at the two depths was repeated and another experiment analyzing mussel plasticity was conducted in which mussels growing at 1m and 7m depth were switched during the summer and monitored at the new depth. Fatty acid signatures of switched mussels are predicted to adjust to become consistent with signatures of mussels established at the new depth by the end of the five-month sampling period. The results of this study will demonstrate the adaptability of mussels to new feeding environments and the effects of environmental changes on mussels as variable water conditions impact their algal food sources and overall health.

Diatoms are small photosynthetic organisms that are important in global carbon fixation and help provide a base to the oceanic food web. Viruses are known to play a role in the overall life and death of diatoms but the extent of this role is not fully understood. A previous member of the Rocap laboratory has isolated a virus (PmDNAv) known to infect diatoms of the species Thalassiosira pseudonana. This virus is infectious in six out of the seven cultured strains kept in the lab; a seventh, CCMP 1012, is resistant. Each of the seven strains has a microbial community that propagates with the diatom cells as they are kept in culture. I hypothesized that the T. pseudonana CCMP 1012 was able to survive the viral inoculation because a beneficial microbe absent in the other strains was able to confer viral resistance. To test this hypothesis, I confirmed the previous results that showed viral resistance in the CCMP 1012 strain and susceptibility in another cultured strain. I then treated the diatoms with antibiotics to remove the microbial community. With the newly microbe free CCMP 1012 culture I performed infection experiments to test if the axenic strain would behave similar to the nonresistant strains and die, or if it would remain resistant to the virus. When the microbial community was removed from the previously resistant CCMP 1012, the strain was susceptible to viral infection. The most likely explanation was that the microbes were conferring resistance to the diatom strain. This implies that microbial interactions can lead to drastic changes in the dynamics at the base of the food web. Future work includes experiments questioning if the microbial community from the resistant strain can confer viral resistance to other strains and analyzing how the microbial communities differ genetically among resistant and susceptible strains.

Skeletal reduction is a common feature among deep-sea fishes that have diversified from shallow-water relatives, such as snailfishes. These skeletal reductions may be an adaptation to environmental conditions of high pressures, low temperatures, declining luminosity and limited food availability. Snailfishes (family Liparidae) are found across a large bathymetric range (0 –>8,000 m), with intertidal ancestors giving rise to a large clade of deep-sea species. We used microcomputed tomography (micro-CT) to estimate average bone mineral density and examine jaw, pectoral girdle, and neurocranium morphology. Our results suggest at least three mechanisms of skeletal reduction: (1) reduction of bone size, (2) reduction of bone density, and (3) loss of skeletal elements. First, using phylogenetic generalized least squares (PGLS) analysis, we found that the change in cranial dimensions with depth was not uniform. While the size of the maxilla, dentary, and pectoral girdle decreased with greater depth, length of the upper premaxilla and the neurocranium did not vary with collection depth. Second, average density of the lower jaw decreased with increasing depth. Lastly, the ventral suction disc has been lost multiple times within the deep sea lineage. While all three methods are seen in snailfishes, other groups may use some or all of these mechanisms to different extents. Some mechanisms of skeletal reduction may be more advantageous than others. The extent to which a structure is retained in deep-dwelling fishes may indicate its functional importance. Variable skeletal reduction in the family Liparidae provides insights into the physiological adaptations that allow fishes to survive in deep-water environments. We conclude that some skeletal elements are maintained at the expense of others as fishes balance the functional demands of life in the deep sea.

Within the dimensions of temperament, effortful control (EC) is the ability to regulate urges over certain actions and adapt to the demands of an environment.  EC is salient to study for its contributions to socio-emotional development, regulations, and child adjustment. It is instrumental to further examine the role of EC as it allows the caretaker to handle the child and take actions to alleviate their undesired dilemma. In this secondary correlational study, we examined the positive association between children’s (N= 301) EC levels from kindergarten to second grade and adjustment to school, including their academic performance and peer relationship quality. Measures include reports from both parents and teachers of children’s peer relationship, effortful control, the relative level of chaos in the classroom, and children’s standardized assessment of academic achievement. We analyzed whether classroom chaos based on teacher reports modified the relations between EC and children’s adjustment. We predict that for children in low chaos classrooms, EC would correlate to stronger academic performance than for children in high chaos classrooms. For children in high chaos classrooms, we predict that EC has a stronger association to peer relationships than children in low chaos classrooms.

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

Portland, Oregon takes the lead in the highest strip clubs per capita, however, strip clubs in Portland have gone unregulated, allowing for poor management and oversight of health and safety issues. When violence and exploitation occurs, exotic dancers have scarce resources to turn to due to the continued stigma of being a sex worker. Past research has explored limited issues related to exotic dancers, including drug use, sexually transmitted infections, and mental health problems, but few have questioned what safety measures are needed to protect women in this industry. This study aims to explore the exploitation and abuse that exotic dancers experience in order to improve the laws and regulations of strip clubs. Through this qualitative study, I will use semi-structured interviews in order to better understand experiences of interpersonal violence against exotic dancers including various forms of violence from clients, employees and law enforcement in Portland. Data will be analyzed using thematic analysis in order to establish working themes. The anticipated results of this study is that the interviewed participants will express various experiences of interpersonal violence and that there may be common variables to violence experienced in strip clubs such as race, age, structural safety features in clubs, and the availability of outside resources to report violence. It is also expected that violence perpetrated by clients and club managers will be among the highest reports by the participants. Lastly, it is hypothesized that women who have not experienced abuse and exploitation (or limited amounts) while at work will still fear experiencing it, which is still a cause for concern. This study provides a platform for exotic dancers’ voices to be heard, while also attempting to improve better working conditions of adult entertainment establishments.

Steeped in ritual, The Autopsy of Jane Doe walks viewers through the (mediated) processes of a clinical autopsy with the subject being a young, recently-deceased woman in pristine condition. Psychoanalysis of this film reveals deep interconnections of Freud’s structures of the mind and cultural portrayals of gender power dynamics. Dillman  explores the concept of a “dead-beginning”, where women play active roles in story development, yet experience a halting of “temporal progression”, reinforcing the objectification and exploitation of women’s bodies. What starts as a routine procedure, beginning with cataloguing of biometric data, quickly turns into chaotic mania as dead bodies are reanimated, flash floods trap the inhabitants and a dead woman seems to have taken control of the building. Using a psychoanalytic approach, this paper illuminates major connections between the id, ego and superego while also identifying the preconscious, conscious, and unconscious functions of the brain. As expressed through character interaction and symbolic relation, this paper posits that the continued shallow practices of female representation contribute widely to a culture built on systematic oppression and the exploitation of women as sexual objects. Furthermore, Jane Doe’s retaliation over her circumstances echo traits of the #MeToo movement and the crucible of men in positions of power.

Sexuality acts as a societal arbiter; the further away one is from the norm, the more marginalized one becomes. As a result, sexuality forces us to ask the question of,  “who deserves love, and who should we extend it to?” These questions become paramount in stories that present love towards nonhuman subjects. Lars and the Real Girl, a movie about a man who falls in love with a sex doll; The Shape of Water, a fantasy romance between a mute woman and an amphibious man; and The Goat, or Who is Sylvia?, a play that features a man who has an affair with a goat, will be the base texts being analyzed. These stories question the structures we have in place for what we do and don't tolerate as love: what's wrong with loving a goat? To answer this question, I imagine love as a scale, with all the things in between the most normative love - white, heterosexual, and cis - and bestiality examined. Where do we draw the line between good, valid love and bad, invalid love and why? Using queer theory, a framework already populated with these questions, I analyzed these texts. There is a pervasive idea that writing about love has become a cliché and naïve pursuit. However, this thought has stifled the nuances that exist within the concept and erases the populations it has already marginalized. It is a delicate situation, but examining our desire, from the possible to the impossible, may illuminate what we believe is ethical. For without straying into the uncomfortable, we cannot challenge a norm. Rethinking perspectives and coming to a more complete and inclusive concept of love can be the value of these narratives of nonhuman desires.

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

Many genes have been found to be associated with microcephaly, a condition characterized by a smaller head size. Through exome-sequencing, we identified two de novo missense mutations in an actin polymerization gene, ARPC4, in four patients with microcephaly, mild developmental delay, and mild intellectual disability. To understand the molecular mechanisms that lead to the disease phenotype observed in the patients, I used a variety of genetic and biological assays. I began by using CADD, a measurement used to predict the deleteriousness of single nucleotide variants. The mutations identified in the patients were shown to be in highly conserved loci, indicating they might be pathogenic. We proceeded to study the functional effect of the pathogenic variants in actin polymerization. Actin is an essential component of a cell’s cytoskeleton which gives the cell its structure and aids in cell movement and cell division. I was able to establish fibroblast (skin) cell lines from two patients and perform an immunofluorescence assay staining for actin in patients and control fibroblasts. Additionally, I used western-blot, a technique used to detect a specific protein in a sample, to further quantify the amount of actin present in the patients’ cells. We were able to observe a greater abundance of actin filaments in the control sample compared to the patients’ cell. The results from this study elucidate the impact of ARPC4 in actin polymerization, establishing actin deficiency as a clinically recognizable cause of microcephaly.

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

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

Viral infection is associated with asthma exacerbations. Normally, viral presence is detected by Toll-like receptor 7 (TLR7)—an innate immune receptor in airway epithelium that responds to single-stranded RNA viruses (like influenza) and triggers an immune response to infection. TLR7 is also expressed on airway sensory nerves, but its specific role is unknown. Here, I tested the role of TLR7 on sensory nerves and identified which sensory nerve populations express TLR7 using nerves isolated from dorsal root ganglia from female Hartley guinea pigs (~400 g). Ganglia were isolated, plated onto matrigel, and treated with a TLR7 agonist R837 (0.1-100 microM) for 16 hours. Neurite number per cell was not changed by stimulating TLR7, but neurite length, and the number of branch points were significantly increased. Separate experiments measured which types of sensory nerves expressed TLR7. Vagal and dorsal root ganglia were isolated and fixed in zinc formalin. Nerves were immunolabeled with antibodies against TLR7 and either neurofilament-1 (NF-H) to identify A𝛿 fiber sensory nerves or transient receptor potential V1 (TRPV1) to identify C-fiber sensory nerves. I found that airway sensory nerves originating in the vagal and dorsal root ganglia expressed TLR7. However, TLR7 was expressed predominantly on small TRPV1-expressing C-fiber neurons, but not on large NF-H-positive A𝛿 neurons. In conclusion, TLR7 is highly expressed by airway sensory C-fibers nerves, and its activation stimulates neurite growth. These findings suggest TLR7 may increase airway C-fibers supplying the lungs which may enhance airway reactivity and be a mechanism for virus induced exacerbations of asthma.

Many biochemical processes rely on the conversion of electrical energy into chemical energy. Tryptophan is one aromatic amino acid that facilitates electron transport through proteins by means of reduction and oxidation reactions, allowing for the energy conversion to occur. The ability for a protein to tune the reduction potential of tryptophan is critical to its function in reactions within enzymes such as cryptochromes, which are involved in regulation of circadian rhythm, and photolyases, which are involved in DNA repair. This tuning of the reduction potential is achieved by modulation of the microenvironment surrounding tryptophan residues within a protein. In order to study the relationship between protein environment and tryptophan oxidation, we have designed and synthesized a series of model peptides to engineer specific environments which have the same geometry but differing charge states and levels of solvent exposure. The reduction potential of each peptide was determined via differential pulse voltammetry over a pH range from 1-7.5 in order to determine how the pH dependence of tryptophan's reduction potential responds to changes in its microenvironment. The results indicate that the reduction potential of tryptophan at the physiologically relevant pH=7.5 increases with increasing positive charge in the surrounding microenvironment. The results across the entire pH range indicate that the pKa of oxidized tryptophan increases with decreased solvent exposure. Finally, our entire series of peptides indicates that the tryptophan oxidation reaction does not directly follow the expected Nernstian behavior for pH dependence of a single proton-coupled electron transfer reaction and thus indicates that the oxidation process may have differing degrees of reversibility in difference environments.

The catalytic activity of many metals can be increased when the catalyst exists as tiny nanoclusters as opposed to large bulk-like metal particles. Thus materials, or supports, that facilitate the growth of nanoparticle catalysts are highly desired. Of these supports, the most widely used are metal-oxides. The growth of catalysts on these supports can be better understood by studying the chemical bonding at the metal-oxide interface. The Mallouk group has found a calcium niobate nanosheet, HCa₂Nb₃O₁₀, that when used as a support both resists and reverses the coalescence of metal-oxide or hydroxide nanoparticles on the surface. These nanosheets are of additional interest because they are smooth on the atomic scale, similar to single crystal surfaces, with a large ratio of terrace sites to edge sites. Here, calorimetric measurements of the adsorption energies of silver and copper vapor on oxide thin films composed of four layers of these nanosheets are directly measured using adsorption calorimetry in ultrahigh vacuum. The initial heat of adsorption of silver atoms was found to be ~112 kJ/mol which closely resembles the predicted density functional theory (DFT) values for silver monomers. The growth mode of silver was determined using a surface sensitive spectroscopy technique, low-energy He+ ion scattering spectroscopy (LEIS). The number density of silver particles, as estimated from the LEIS data, was found to be ~2.2x10¹⁰ particles/cm² at 1.7 monolayer silver coverage. This is much lower than the particle densities on other metal-oxide supports and is attributed to the lower density of step/nanosheet edges on this support. The evolution of the LEIS signal indicates that silver grew as 3D nanoparticles. This data encourages further investigations of the adsorption calorimetry of different metals on this interesting support.

This paper analyzes a collection of letters and postcards hand written during World War II, authored by German crystallographer and volcanologists Ferdinand Bernauer to his son. The analysis draws on aspects of critical theory of the epistolary genre, while keeping in mind that the collection is a set of artifacts, not a fiction, as they were never published or intended as a work of literature. Their analysis provides a unique insight into the decisions and repercussions of a strong refutation of Nazism by a distinguished man of science residing in Hitler’s Germany. His greatest contributions to the academic world – proof of Continental Drift through his studies in Iceland and a crystal growing method now lost to mankind – attest to his considerable intellect and dedication. Yet it is his letters that uncover a life worthy of investigation for what they illuminate about the human psychological faculty of weighing the risk of death with the ethical reward of fighting for one’s values. The epistolary lens allows the reader to grasp aspects of the text not explicitly written such as intentional self-censorship, introspection upon one’s choices and moral stance, and stylistic choices made because the intended recipient was his son. The letters, unlike actual epistolary novels, need no omniscient narrator to provide a historical backbone upon which the narrative may play out, because it has been provided largely by World War II records. Therefore, this work facilitates a strong identification between Ferdinand Bernauer and the reader in an absorptive reading experience typical of an epistolary novel, without vast holes in historical perspective. This analysis explores a method of reading letters written under political oppression that enables one to understand the real difficulty in making the choice between standing against an immense malevolent power, and portraying one’s resistance quietly among the chaos.

My research focused on the question: What can be learned about 19th century Middle Eastern and European medical practices from the personal diaries of Joseph Mattia Svoboda, a European resident in Iraq from 1860 to 1908? Joseph Mattia Svoboda’s diaries document a very detailed account of daily life and information in the Basra and Baghdad regions of modern day Iraq. Joseph himself suffered from a chronic gastrointestinal disease and frequently wrote about the medication prescribed to him by doctors and self-selected which he then self-administered. I used this information as a basis to piece together common medical practices and medications utilized in the 19th century. Using digital transcriptions of the diaries, I used data-mining techniques to extract references to medicines, doses, and usages. Then, using contemporary European newspapers, medical journals, advertisements, and historical records I traced these medicines and their ingredients back to their origin. I examined modern research on these medicines’ ingredients to look at the effect these medicines had on the body compared to the expected results of the time period. I found the medicinal practices of the time, especially in relation to patent medicines generally stem from Europe with many medications being produced and sold there. This allowed me to identify some of the ingredients and usages. However, some of the ingredients and medications were not native to Europe, indicating a larger trade system and medical practices from around the globe influencing medicine in Iraq. Future projects stemming from my research could look into the influence of Asian, Middle Eastern, and Native American herbalism and indigenous practices on 19th century medical practices and medicine trade. Regardless, I hope my work encourages others to explore beyond the eurocentric narrative of developing medicine in the 19th and 20th centuries.

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

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

The years between 1889 and 1922 saw great archaeological activity in Egypt, a period known as the 'Golden Age' of Egyptology. Our research seeks to answer the question: “What were women’s experiences during the ‘Golden Age’ and what impact did their work have?” Mrs. Emma B. Andrews and Mrs. Helen Winlock are unique characters, choosing to escape the rigidity of Victorian society and pave their own way on the dusty roads of Egypt. Their letters and diaries bear witness to an exciting period of history. Our survey begins with the record of travel and excavation kept by Mrs. Emma B. Andrews and Helen Winlock, wife of Herbert Winlock, Director of the Metropolitan Museum Egyptian Expedition. They describe challenges of archaeological missions in Egypt, recounting issues of site and workforce management, as well as their interactions with diverse explorers and adventure. From scans of original handwritten letters, we transcribe frequently challenging handwriting and record Andrews’ and Winlock’s unique observations. These include descriptions of difficulties of daily life on site, of managing large groups of workers, and offer insights into the personalities and characters of eminent archaeologists. The results of our work are open source and offer important insights into the lives of the foremost Egyptologists and their families. We utilize technology such as iPads, Basecamp project management, and collaborative software to facilitate transcription. Ultimately, we will produce output that is accessible online to encourage collaborative engagement with others researching this ‘Golden Era’ of excavation. This information is stored in a database and will be freely available on our project website, to encourage collaborative engagement with others researching this ‘Golden Era’ of excavation. In doing this, we aim to recreate the world of archaeology from a bygone era, seen and described through the eyes of women who were ahead of their time.

Cancer, the leading cause of death worldwide, results from a combination of mutagenesis and selection for malignant phenotypes. Mutations from DNA replication errors may initiate as many as two thirds of all human cancers. Accurate DNA replication requires proofreading domains found on the major DNA polymerases as well as mismatch repair (MMR) proteins that detect and repair replication errors after DNA synthesis. Cancer-causing defects in proofreading and/or MMR lead to “mutator phenotypes”, marked by elevated mutation rates and increased cellular mutation burden. Such mutator cells occur spontaneously and drive evolution by generating mutations that enhance population survival. However, mutator cells also accumulate detrimental mutations that compromise fitness. Combined defects in polymerase proofreading and MMR cause error-induced extinction (EEX), which imposes a strong selection for cells with “antimutator” mutations that suppress the mutator phenotype. Using yeast (Saccharomyces cerevisiae), we isolated mutants that survived EEX and mapped the underlying determinants to candidate mutations (APC1, MCM5, PMS1). We are engineering these mutations into yeast strains to test whether they confer an antimutator phenotype. Understanding how mutator cells suppress elevated mutation rates will give us insights into how cancer cells survive and thrive in the face of strong mutagenesis and may suggest novel therapeutic strategies to combat this disease.

Tyrosine kinases are critical drug targets in oncology due to their role in tumorigenesis. Accordingly, the treatment of specific cancers has been revolutionized by the development of tyrosine kinase inhibitors (TKIs). However, the long-term effectiveness of TKIs is undermined by the emergence of drug resistance, often caused by mutations that prevent drug binding. Understanding whether a given mutation confers drug resistance can enable physicians to tailor treatment based on the patient’s tumor genotype. Current methods to identify resistance mutations are laborious and can only interrogate a small subset of possible mutations. To overcome this limitation, I have designed an assay to identify all possible single drug resistance mutations in the oncogenic kinase ALK in a single experiment. A key feature of this functional assay is that it can accurately discriminate between drug resistant and drug sensitive mutations. Moreover, this assay leverages the Ba/F3 cell line, a mammalian cell line that only proliferates when an active oncogenic tyrosine kinase variant is expressed. Thus, when treated with a TKI, cells expressing drug resistant kinases continue to proliferate while cells expressing sensitive kinases die. As a first step, I have genetically engineered the Ba/F3 cell line to enable single-copy integration of tens of thousands of ALK variants. Additionally, I have cloned ALK into a mammalian expression vector and have optimized transfection conditions for the Ba/F3 cell line. Next, I will transfect the cloned vectors into Ba/F3 cells and measure the growth rates of each transfected cell line. I anticipate that only cells harboring active ALK will grow, while those with inactive variants will not. This result would lay the foundation for further development of a system for the exhaustive identification of drug resistance mutations in oncogenic kinases.

We are using yeast to investigate how the DNA helicase mutation mcm4^Chaos3 interferes with the early events leading to DNA replication and how these replication defects may lead to its role in cancer development. Mcm4^Chaos3 encodes a mutation in a subunit of the MCM helicase, an essential complex required for unwinding double stranded DNA during replication. Mcm4^Chaos3 mice exhibit genomic instability and more than 80% of female mice homozygous for Mcm4^Chaos3 developed mammary tumors (Shima et. al 2007). Further work in yeast identified an origin-specific minichromosome loss phenotype, suggesting the mcm4^Chaos3 mutation may have particular sequence requirements at origins, where DNA replication initiates. To determine the basis of origin sequence specificity in mcm4^Chaos3 function, we had previously performed a plasmid maintenance competition assay using a mutARS317-seq library, containing 500+ plasmids with random single mutations within the ARS317 origin sequence. This assay identified 5 origin sequence variants that performed better in mcm4^Chaos3 yeast than wild type ARS317. To investigate mcm4^Chaos3 interaction with ARS317 variants, I first measured the loss rate for wild type ARS317 plasmids in mcm4^chaos3 vs wild type yeast. As predicted, wild type cells maintained the plasmids better than the mcm4^Chaos3 mutants (16.8% loss rate/generation compared to 5% in wild type). I am currently characterizing the 5 sequence variants, and based on the competition assay data, am predicting to see differences in plasmid loss rates across the ARS317 variants. Understanding the cause for this origin specificity could help us develop a greater understanding of the mechanics involved in DNA replication, genome stability, and cancer-causing mutations.

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 and contribute to chemotherapy resistance. Work in the yeast Saccharomyces cerevisiae indicates that excessive DNA replication errors can lead to error-induced extinction (EEX), where every cell within the population dies due to a random lethal mutation. Thus, a possible direction for cancer therapy may be to target antimutators, which can modulate mutation rates of mutator cells and suppress mutation rates, in order to slow the rate of tumor evolution. In a screen isolating antimutators, we identified an EEX mutation in Chromosome Transmission Fidelity 18 (ctf18-K666fs). Ctf18 directly associates with the N-terminus of DNA Polε, including part of the proofreading domain, and thus may influence mutation rates by directly affecting Polε function — a novel finding that would expand our understanding of mutator polymerases. In the current study, I determined whether Ctf18 exerts its antimutator phenotype independent of the S phase checkpoint pathway, the pathway by which all other previously isolated antimutators, such as Dun1, are known to modulate mutation rates. To accomplish this, I compared the mutation rates of double mutant strains, dun1Δ ctf18-K666fs and dun1Δ ctf18Δ, to their respective single mutants in pol2-L439V cells, where lower mutation rates would indicate additive antimutator effects from independent pathways. I also observed the degree of activation of this pathway by fluorescently tagging Sml1, a protein downstream of Dun1 in the S phase checkpoint, expecting to see decreased expression of Sml1 in cells in which the S phase checkpoint was activated. Expanding our understanding of mechanisms by which antimutators can modulate mutation rates may contribute to novel approaches for cancer treatments by targeting the mutator phenotype.

Breast Cancer type 1 gene (BRCA1) was first linked to a high risk for breast and ovarian cancer over two decades ago, yet much remains elusive about its functional mechanism and how inheritance of a variant of the ubiquitously-expressed gene can lead to markedly increased risk for tissue-specific cancers. A gene found in the nematode C. elegans was demonstrated to be homologous to human BRCA1 including at the protein product level. Its protein product was shown to have the same type of enzymatic activity as the human protein product of BRCA1, and to be involved in the same DNA repair pathway. Using purified protein products and both structural analysis via Nuclear Magnetic Resonance and in vitro biochemical enzyme activity assays, I have shown that the C. elegans and human BRCA1 share some structural similarities and that the enzymatic activity is conserved. These results suggest that C. elegans could be developed into a model system that would allow for experimentation to directly move between in vitro biochemical studies and in vivo genomic/genetic studies. My current work has focused on furthering the development of the C. elegans model system by using it to identify other protein-protein interactions, including the identification of new protein targets. Additionally, my work explores the effect that cancer associated variants have on the enzymatic activity of the C. elegans BRCA1. The development of C. elegans as a model system could lead to new insights into conserved functions of BRCA1 and a fuller understanding of its biological and developmental importance.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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