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

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.

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.

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.

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.

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

The 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.

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.

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

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.

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.

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

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.

The goal of the Pulse Tectonics project is to apply the traditional Chinese practice of pulse diagnosis in the radial artery, to detect heart problems in a non-invasive manner. If we can detect heart disease early, we could potentially save hundreds of thousands of lives (there are 610 thousand deaths per year attributed to heart disease in the US alone), as in many cases it is only diagnosed after the first cardiac event (heart attack). Our research is to achieve diagnosis by capturing a short (5-10 second) video of the forearm. This video is then put through a video magnification algorithm developed by MIT, with different frequency and magnification parameters. By varying these parameters we can ‘tune in’ to the pulse in the radial artery and see it visually in full time. The pulse appears as a pattern of peaks and troughs which seem to change in response to a number of variables, from recent eating, exercise, health, etc. Currently we are working to synchronize these visual pulse readings with readings from an EKG and pulse oximeter to identify the information we can obtain from the videos, and thereby achieve diagnosis via visual pulse waveforms. This involves creating a baseline for a healthy pulse, and then identifying which parameters in the video correspond to different health readings. When successful, this technology would bring early heart disease diagnosis within reach of all people in an effort to mitigate heart disease related deaths.

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.  

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

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.

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).

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

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.

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

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.

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.

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.

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.

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

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.

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.

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.

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 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.

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. 

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

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

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

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

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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

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

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

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.

Flow is a mental state achieved by a person performing a task when there is a balance between skill and challenges, thereby evoking focused attention, full involvement, and enjoyment. For education applications, achieving a flow state may accelerate learning, retention and improve learning outcomes. Most current methods for assessing the extent of flow state use a self-reported questionnaire only when participants finish a learning activity. Alternatively, using objective real-time measurement such as electrophysiological techniques to assess the flow state, especially during a learning period, affords the possibility of timely adjustment of challenges to keep up with learners’ growing abilities. Such an adaptive approach may provide a more improved way to enter and sustain flow in learning activities. Previous studies also indicate that gamification is a proven way to induce the flow state, and virtual reality (VR) activities provide learners more immersive experience. The purpose of this preliminary study is to investigate an adaptive approach for assessing flow state during VR learning activities with electrophysiological measurement. This study used a NeuroSky EEG headset with a supervised machine learning algorithm to identify the features of attention, meditation, and eye blinks with flow state while performing VR learning activities. To evaluate the effects of the proposed approach, data collection was through an experiment with 10 UW students by assessing their flow state while playing VR educational games. The first version model trained by the three types of indicators is capable of determining if a learner performing VR learning activities enters the flow state. In turn, the result of this preliminary study serves as a metric for the follow-on research addressing the development of adaptive learning strategies to help each learner enter into a flow state and improve learning outcomes with the sustained flow state.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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

The research question for our study is, “Is a component of a multilevel intervention effective in promoting awareness of cardiovascular health and decreasing weight?” Within King County, an almost 10-year-difference in life expectancy exists between low- and high-income areas. While many factors may contribute to this disparity, cancer and cardiovascular disease (CVD) are the leading causes of mortality. Obesity and metabolic syndrome are major risk factors for both cancer and CVD, and disproportionally affects lower income populations. The Women Take Heart (WTH) study is part of a multilevel intervention that spans school, family, and individual levels, aimed at promoting awareness of positive health behaviors. The WTH intervention focuses on teaching women in the Renton community physical and nutritional health information. We hypothesize that targeted, weekly teachings by experts on complex health behaviors will increase health knowledge and decrease participant weight. We will assess the efficacy of WTH through quantitative methods. These include examining pre- and post-intervention values of physical and metabolic measurements, as well as pre- and post-questionnaire responses. We anticipate the results of our study will show increased health empowerment, increased knowledge of positive health behaviors, and decreased biologic markers of metabolic syndrome. If this intervention is effective, it could be implemented to address the high rates of obesity in low-income communities, which in turn could lower rates of cancer and CVD.

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.

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

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.

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.

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.

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

PEDOT:PSS is a conducting polymer that is very promising as the next generation materials for the transparent electrode. PEDOT:PSS-based organic electrochemical transistor (OECT) has been widely used for various sensing applications such as glucose, antigen, DNA, and pH sensing thanks to the much lower working voltages, typically less than 1 V, and known biocompatibility of a PEDOT:PSS. OECT comprises three electrodes (source, drain, and gate), a PEDOT:PSS channel between source and drain, and electrolyte solution of analytes. Electric current flows through the conductive PEDOT:PSS channel. However, upon the application of a positive gate voltage, cations from the electrolyte are injected into the channel, decreasing a conductivity of the PEDOT:PSS. Hence, electric current decreases as a gate voltage becomes more positive. In our previous work we examined the impact of double-in-plane gate electrode on the OECT performance and found it to have a much higher transconductance of 35 mS as compared to 13 mS of a single gate. Now we investigate if applying heat can further improve the device performances such as sensitivity and response time of the OECTs. To test this, we have integrated a micro heater made of ITO on top of the glass substrate then covered the heater with aninsulative layer on which all transistor electrodes are fabricated in the same plane. High conductivity PEDOT:PSS was used to create a channel between source and drain. Fisher brand pH meter calibration solution was used as the electrolyte with pH values of 4, 7 and, 10. A drop of electrolyte was placed just over the channel and the gate electrodes. Once fabrication has been completed the OECT’s are tested and characterized at various temperatures by resistively heated micro-heaters. This work is important as it will allow the development of highly sensitive portable OECT arrays for various chemical/biological sensing applications.

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.

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

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.

PEDOT:PSS is a conducting polymer that is very promising as the next-generation materials for the transparent electrode. An organic electrochemical transistor (OECT) can control the amount of current flow in a conductive channel through an electrochemical reaction in the PEDOT:PSS channel assisted by an applied electric potential at a gate electrode. PEDOT:PSS-based OECT devices are widely used for biological and chemical sensing applications due to their high sensitivity, low cost, flexibility and lower operating voltage, typically less than 1 V. In addition, OECT has shown improved sensing performance when the gate electrode is modified with biocompatible polymers, such as Nafion. Nafion can lead to a more highly selective OECT-based sensor. A key feature of OECT is that both ions and electrons are used as charge carriers. This is of particular interest and importance for chemical sensors. For example, by combining a proton-conducting electrolyte, a simple Nafion-based OECT humidity sensor can be implemented as Nafion changes its conductivity upon exposure to humidity. In previous work we examined the impact of a double-in-plane gate electrode on OECT performance and found it to have a much higher transconductance. Branching off from that, we now investigate the impact of Nafion on OECT performance. Particularly, we want to investigate whether OECT sensitivity depends on the presence of Nafion film. In order to determine that, we fabricate several devices in which all transistor electrodes are in the same plane. High conductivity PEDOT:PSS is combined with Nafion in order to create a channel between source and drain. Once fabrication is complete, we plan to test and characterize the OECT’s to determine whether OECT performance is optimized with Nafion film. This work is important as it will allow the development of highly sensitive portable OECT arrays for various chemical/biological sensing applications.

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.

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.

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

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. 

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.

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.

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.

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.

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.

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

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.

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

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

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

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. 

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

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.

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.

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

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

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

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

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

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

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.

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.

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

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

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

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

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

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

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

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

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.

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.

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

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

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.

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.

Despite the large number of gametes that clams release, very few offspring survive to reproductive age and harvestable sizes. There are several ways that aquaculturists try to protect young settlers, including adding gravel on top of fine sediment. We tested whether the addition of gravel helped decrease the mortality rate from small crabs in lab experiments. We tested predation rates on juvenile manila clams, Ruditapes philippinarum by the hairy shore crab, Hemigrapsus oregonensis in different sediments. Clams were placed in tubs with no sediment (NS), fine sand (FS), or sand with gravel on top (SG). After allowing time for the clams to burrow, crabs were added to each tub and given 24 hours to consume the clams. Crabs consumed some clams in all treatments although there was high variation among individuals. Gravel addition did not reduce predation rates compared to fine sand alone, but there was a trend for more predation in no sediment than with sediment. We also tested the ability to consume small clams of different predators that live in the same sediment habitat as R. philippinarum. The worms, Nereis brandti, Paranemertes peregrina and Hemipodus borealis all showed no predation on clams within a 24-hour period. The snail, Alia also showed no predation on juvenile clams. By understanding multiple factors that lead to juvenile clam mortality, fisheries can improve upon their methods to increase harvestable populations.

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.

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

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.

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.

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.

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. 

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.

The goal of the project is to determine whether ma-N 1420 photoresist can be used with Heidelberg laser direct write tool, and to optimize the ma-N photoresist sidewall profile. The process starts by applying a negative photoresist onto a surface of a silicon wafer followed by an exposure to an ultraviolet light using a Heidelberg laser tool. The 410nm laser is applied directly to the photoresist without the use of a photomask, which is normally used for the purposes of exposing the wafers. The Heidelberg process is optimized in a manner that has not been possible previously at UW. This requires studying the thickness of the photoresist using reflectometry and optimizing the spin speed during spin coating. Various exposures on the Heidelberg system are then tested to make sure that the ideal exposure conditions have been achieved. The next step is to deposit a thin metal film on top of the photoresist. The deposition is achieved via an evaporation of metal inside the chamber of the device in which the metal is melted and evaporated by high speed electrons and is then deposited on a cooler silicon surface. The undesired metal is then stripped away from the surface of the wafer by removing the photoresist from under the metal film in a process the engineers refer to as “liftoff.” The optimization part of the project refers to testing different development times to make sure the development gives ideal photoresist overhang for the liftoff process. Finally, the sidewalls of the photoresist mask are analyzed using Scanning Electron Microscope (SEM). An SEM is used as the thickness of photoresist can be thinner than 1µm. The research was performed to verify that ma-N photoresist is suitable to use with Heidelberg system to complete a nanofabrication process.

 Polyethylenimine (PEI) is considered as the most promising alternative gene carrier to viral vectors. PEI-based carriers minimize unwanted immunogenicity and promote loading capacity. However, PEIs’ nondegradable nature determines their high cytotoxicity. To minimize the toxicity and improve gene transfection efficacy, biodegradable cross-linking agents have been screened to synthesize biocompatible PEIs. Various cross-linkers have been linked to low molecular weight PEI (MW = 800) and tested across multiple cell lines (xPEI). N,N'-Methylenebis(acrylamide) (NDA) showed the lowest toxicity and highest transfection rate among all cross-linkers. To further optimize gene transfection efficacy, xPEIs were modified with increasing amount of fluorocarbon (xPEI-FC). DNA that expresses red fluorescence protein are bound to xPEI and xPEI-FC and then incubated with cells for 48 hours. Green florescence light is later used to examine the presence of RFP. xPEI-FC has demonstrated higher biocompatibility as well as higher transfection rate in vitro with higher level of RFP. The best-performing candidates for xPEI, PEI-FC and xPEI-FC based on toxicity and transfection efficiency will be selected for nanoparticle (NP) modification. Selected candidates will be conjugated with Chitosan-poly(ethylene glycol) (PEG)-catechol copolymer (CCP) and then grafted onto iron oxide nanoparticle (IOCCP-PEI). The resulting nano-vector delivery system will be tested in vitro. Ultimately, in vivo test will be performed to evaluate its transfection efficacy in living organisms.

Quantum information systems are reliant on the fidelity of the spectra of their qubits. Diamond nitrogen vacancy centers present many of the best traits among qubit candidates and show promise for scalable quantum computing. Preferential lattice orientation of these nitrogen vacancy centers is a technically difficult, yet essential step to improve the signal to noise ratio of quantum sensing and the efficiency of quantum computing. My research seeks to test our theoretical knowledge of nitrogen vacancy center orientation changes through annealing diamonds at high temperature. I present the techniques I use to return to the same single atomic defects to compare, through confocal microscopy, orientation changes as a function of annealing temperature. I show our preliminary data in relation to the nitrogen vacancy density distributions and orientation changes throughout the diamond to test current theory regarding vacancy diffusion through the diamond lattice near substitutional nitrogen. Finally, I discuss some unexpected results from our first run of this experiment and share our remaining questions and future efforts to preferentially orient nitrogen vacancy centers.  This research is contributing to progress through the Noisy Intermediate-scale Quantum era with reduction of noise generated by local strain near qubits and better signal-to-noise for quantum sensors.

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.

Patients and providers are beginning to use patient generated-health data (PGHD) to collaborate to understand patient routines, identify health problems, and tailor treatment strategies. However, current technology designs fail to support key aspects of collaboration, including planning, data collection, review, and analysis. Among all the health data people track, food data is essential for preventing and managing many health concerns. Although numerous tools exist to help people track and understand their diet and its consequences, these tools are often high burden, can lead people to focus on what is easily tracked rather than what is most relevant for their health, and fail to support effective collaboration between providers. In this study, we designed, developed, and deployed novel food tracking diaries to support healthy eating and the management of irritable bowel syndrome (IBS). Eighteen people with healthy eating goals used the food diaries for at least two weeks, and then worked with their health providers to plan changes to their diet. Sixteen IBS patients used the IBS version of the diary for at least nine days and then worked with providers to identify food triggers and plan changes. We interviewed patients and providers and observed their collaborations. The photo-based food diaries we designed supported patient-provider communication for both healthy eating and IBS. Compared to traditional food diaries, the photo-based food diaries make data collection, review, and analysis easier for patients and providers. However, patients and providers described scenarios when specific nutritional information -- beyond what they can see in photos -- helped the diagnostic or management process, such as when identifying IBS triggering nutrients. Our research will lead to better use of PGHD to give patients more tailored, accurate, efficient and informed treatment plans. Our results also inform the design of  food diaries that will better support people with different various health goals.

Placentation, the formation of the placenta, is a dynamic process which is vital for the development of a fetus. A key structural feature of placenta in ruminants, such as sheep, is a placentome. Placentomes are thickenings in tissue that form along both the maternal and fetal sides of the placenta. During pregnancy, placentomes generally begin with the same type of structure, called Type A. Over the course of a gestation, Type A placentomes are found to convert to functionally more efficient forms (Types B, C, or D). Prenatal stress (PS) has been shown to reduce uterine blood flow in pregnant sheep model. This would influence placental blood flow, supply of nutrients, clearance of metabolites and exposure to stress hormones. Undernutrition accelerates the placentomal conversion in pregnant ewes of certain breeds as an adaptive response to maintain the fetal developmental growth curve, while other breeds are not able to adapt. We hypothesized that placentomal conversion is influenced by PS. We modeled chronic PS in the last trimester in pregnant sheep through reoccurring and unpredictable bouts of maternal isolation over a period of 30 days, a validated paradigm to model human PS. At ~136 days of gestation (full term is 145 days), the placentomes were collected, weighed, and sorted according to their morphology. The weights of Type B, but not Type A, placentomes were found to be lower for the stressed sheep when compared to the control. These findings confirm our hypothesis that PS reduces the degree of the placentomal conversion from Type A to a more advanced form, Type B. This may be caused by a chronic reduction in placental perfusion (blood circulation) during PS. The found reduction in placentomal conversion may be one of the missing mediating factors linking PS to known postnatal developmental abnormalities in metabolism and phenotype.

This presentation examines emperor Nero’s use of food and dining practices as a way to invert social class in public and private life. Through an examination of accounts by the ancient authors, secondary scholarship, and archeological evidence of the Domus Aurea, it is evident that Nero had a complicated reign, but his actions related to dining practices and public life made an intentional effort to equalize Roman social class while including the common Romans in aspects of life to which they were not previously privy. The investigation is separated into three sections: the first examines the history and basis of the ancient authors with respect to their relationship with Nero; the second looks at the public spectacle and how that contributed to the change in public and private life; and finally the third demonstrates the scale of the gestures in which Nero partook, thus illustrating how he was courting the non-elite and simultaneously debasing the elite. Each section is supported with overlapping evidence; however, certain aspects are highlighted within each section. The first focuses primarily on examining the perspective of the elite authors with some support from secondary arguments. The second uses some archeological evidence but mostly uses secondary analysis with some support from the contemporary authors. Lastly, the third uses a combination of the three, but it mostly focuses on the Domus Aurea and the impact of this space. With these three clearly identified points of examination, the complex reign of Nero is emphasized while further discussing his intentional use of food and dining to promote his agenda. Nero worked to change public and private life in order to put himself forward as the sole ruler of Rome. Most important, all of his actions were intentional and calculated in order to create his new empire through food and dining.

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.

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

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

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.

This research aims to examine the effects of nanoparticle-mediated inhibition of the phospholipid glutathione peroxidase (GPX4) pathway in mesenchymal state cells on radio-resistance in glioblastoma (GBM) therapy. GBM is a particularly deadly cancer with poor survival rates and relatively low treatment success, despite aggressive surgery and radiotherapy. Recent research has shown that biocompatible, tumor-targeted iron oxide nanoparticles (NPs) can serve to enhance radiotherapy through production of secondary electrons and subsequent reactive oxygen species (ROS) within the tumor volume. The presence of these NPs in the tumor during radiotherapy has shown to decrease damage to the healthy surrounding cells and prolong survival in mice with GBM tumors. This approach however, has not demonstrated the ability to eliminate the cancer completely, in part due to the presence of mesenchymal state cancer stem cells. The GPX4 pathway has shown to effectively kill mesenchymal state cells in sarcomas by inducing ferroptosis, an iron-dependent form of cell death. Here we plan to evaluate the efficacy of a range of GPX4 inhibitors on silencing of the GPX4 pathway and the ability to induce ferroptosis in primary human GBM cells. Inhibitors identified as effective silencers of the GPX4 pathway will be combined with a NP delivery vector to provide targeted delivery to GBM. The radioenhancement capabilities of iron oxide NPs in conjunction with targeted therapy against mesenchymal state cancer stem cells may provide a means to overcome radioresistance in GBM therapy.

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.

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.

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

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.

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

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

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.

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.

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.

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

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

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.

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

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.