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

Small Heat Shock Proteins (sHSPs) play crucial roles in protein homeostasis, the state of maintaining steady internal cellular conditions, despite changes to the cellular environment. As the “molecular life rafts” of the cell, sHSPs target partially misfolded proteins during stress measured as chaperone activity, and without consuming energy, prevent toxic aggregation. Mutations or malfunctioning of the sHSP, HSPB5 (B5), in humans are associated with neurodegenerative diseases such as Alzheimer's and Alexander's disease, as well as cancers, myopathies, and cataracts. As one of the ten sHSPs encoded in the human genome, B5 contains structural elements (the building block) common to all sHSPs: a highly conserved alpha-crystallin domain (ACD), that is flanked by variable, less conserved, N- and C-terminal regions (NTR and CTR, respectively). Previous studies determined that interactions between building blocks occur between a three amino acid region known as the I-X-I motif (a “knob”) in the CTR, and a hydrophobic groove (“hole”) in the neighboring block, similar to how two pieces of Lego come together to build a larger structure. Interestingly, in B5, there is an additional I-X-I motif in the unfolded NTR, but its role and structure are unknown. I hypothesize that the CTR and NTR motifs compete for binding into the hydrophobic groove, indicating the “knob” into “hole” interaction is loose, where the other “knob” can bind the “hole” when one leaves. To test this hypothesis, I prepared mutants containing CTR, NTR, and double motif deletions. I aim to uncover the effects of these mutations on chaperone activity and oligomeric size, by optimizing protein purification and using a combination of in vitro biochemical assays, and native (non-denaturing) gel electrophoresis on purified B5 mutants. These results will assist in demystifying the role of the NTR, direct future sHSP studies, and provide important insight for development of future therapeutic strategies.

The Lake Washington, and Sammamish basin contains a complex mix of life history strategies of Oncorhynchus nerka. These life history strategies include 1) Anadromous sockeye that remain in the lake for one or two years before migrating to the ocean and returning to fresh water as mature adults; 2) “Residual” sockeye salmon that breed with and are genetically a part of the anadromous population but do not migrate to the ocean, and 3) “kokanee” salmon that are genetically distinct from anadromous and residual sockeye. Kokanee salmon are native to the basin and are thought to have evolved when glaciers or other barriers restricted access to the ocean. Although once extremely abundant throughout the basin, native kokanee are now thought to be found only in Lake Sammamish. Large numbers of kokanee-like fish continue to occasionally migrate from Lake Washington into the Sammamish river and its tributaries. Intriguingly, these “mystery nerka” migrate and spawn later than the sockeye/residual population and may represent a fourth distinct O. nerka population (e.g. a remnant of native Lake Washington kokanee, or a newly evolved kokanee population derived from sockeye ancestors). Sockeye, residuals, and kokanee use gill rakers, bony extensions in the throat, to capture prey. In other cases where kokanee have evolved from sockeye ancestors, the number and size of gill rakers differs – a reflection of the of the different types environments they mature in and the different types of prey available in freshwater vs. saltwater. In this research we document the variation in gill raker number and length in the Lake Washington/Sammamish populations of O. nerka in an attempt to 1) investigate trophic adaptations within the basin associated with life history strategy and location of maturation, and 2) to assess the relationship of “mystery nerka” to the other populations known to occur in the basin.

Understanding an individual’s thought process as they encounter programming problems would enable the development of better techniques for teaching computer science and more comprehensive technical assessments. Prior work explored key stroke logging in writing research alongside the think-aloud study format using custom-built tools. We replicated this study format in the context of computer programming to gain insight into participant’s immediate thought process. We aimed to gain a better understanding of a participant’s mental model as they encounter computer science problems. In specific, we wanted to investigate pauses in coding and what students think before, during, and after these pauses. For this study, we used Codeitz, a custom programming tutor that allowed us to log all the participant’s timestamped input as they wrote code. We also collected audio and screen recordings of participants using the think-aloud strategy as they wrote code. We ran a pilot study that required participants (3) to answer eight programming questions, two of which involved writing code. We found some similarities in pause clustering for participants who answered the same questions. We also noticed that participants whose pauses were due to utilizing development environment affordances, identifying misconceptions, and identifying gaps in knowledge semantics exhibited more self-regulation as programmers.

A decline in effective mitochondrial functioning of cardiac cells is one the major underlying factors of aging. Many pathological conditions have shown to result in the peroxidation of the final electron carrier in the electron transport chain (ETC) known as cytochrome c. The ETC is constructed of a series of complexes responsible for the transfer of electrons from electron donors such as NADH through a continuity of redox reactions while coupling the electron transfer energy to the transfer of protons across the inner mitochondrial membrane, constructing a proton gradient to stimulate the production of ATP (Adenosine triphosphate). Peroxidation is known as oxidative degradation and causes cyctochrome c to lose its ability to act as an electron carrier through free radicals that steal the electrons from the complex. The SS-31 peptide works to bind to the inner mitochondrial membrane consisting of cardiolipin and prohibits the cardiolipin from converting cytochrome c into a peroxidase, an enzyme that catalyzes oxidation, and continue its function as an electron carrier. Additionally, administration of NMN (Nicotinamide mononucleotide) can help improve the overall bioenergenetics of the mitochondria through an enhanced production of NAD+, therefore increasing the amount of electrons donated into the ETC once NAD+ is reduced, leading to an increased production of ATP. Three different mice treatment groups were constructed for this experiment; the first group was treated with surgical incisions of pumps containing the SS-31 peptide, the second group was provided with the NMN drug administered through water pumps, while the third group was left as the control. Detection of bioenergenetic changes between treatment groups was evaluated through changes in the NAD+ stoichiometric peak evident through 31Phosphorous magnetic resonance spectroscopy. Administration of the SS-31 peptide and NMN through the mouse model provides a potential advantage in the treatment of age-related complications for human patients.

Autism Spectrum Disorder (ASD) is a developmental disorder in which individuals experience challenges with their behavior, social skills, and communication. There is a significant disparity between the numbers of males and females diagnosed with ASD; males are 4x more likely to receive a diagnosis, and it has been suggested that females with ASD are less likely to receive a diagnosis because they may “mask” their symptoms. Females with equally-high levels of autistic traits are less likely than males to be diagnosed with ASD, and females with ASD demonstrate enhanced social skills and higher levels of social motivation compared to males. Additionally, research by Parish-Morris shows that school-aged ASD females had stronger pragmatic language ability than ASD males. Pragmatic language is an individual’s ability to communicate verbally and nonverbally, understand and reciprocate social cues, and express appropriate social behavior. If females with ASD have stronger pragmatic language skills, it may serve as a linguistic camouflage and contribute to their ability to conform. The goal of this project is to examine sex differences in pragmatic language in children with ASD and explore what factors are related social communication differences between males and females with ASD. 15 male and 15 female participants with a confirmed diagnosis of ASD between the ages of 8 and 17 participated in this study. All participants completed a recorded conversational interview with a clinician. Videotapes were then rated by coders using the Pragmatic Rating Scale-Modified (PRS-M). First, we evaluated sex differences in PRS-M scores. We predicted that females with ASD will be rated as having better pragmatic language than males with ASD. Second, we investigated whether IQ, Age, and Autism Severity predicts PRS scores, and if Sex moderates these relationships. The results of this study shed light on sex differences in social communication in autistic children.

Increasingly, over the past half century, antibiotic resistant plasmids have spread to a large range of bacteria increasing the demand of new antibiotics. On average, once an antibiotic has been released into the public market, a strain that is antibiotic resistant evolves within a few years. Even though the constant production of new drugs and treatments provides some temporary solutions, a better solution would be to investigate and understand bacterial plasmid mechanisms. Through my research in the UW Biology Kerr Lab, I have been exploring how bacteria maintain plasmids that contain genes encoding for antibiotic resistance. Plasmids are extra-chromosomal pieces of DNA that require the host cell to allocate energy for their general maintenance. Prior theoretical research suggests that, to avoid this allocation of resources, the host should lose antibiotic resistant plasmids over time when the plasmid is no longer beneficial to the host’s fitness, for example when the antibiotic is no longer present. We found that many plasmids across multiple bacterial species persist in their hosts, even in the absence of selection for the plasmid. Currently, I am testing whether changing the environmental conditions experienced by the host/plasmid pairs, specifically from a nutrient-rich to minimal media, will affect the persistence of antibiotic resistant plasmids. This research provides important data that will allow us to have an easier time combating antibiotic resistance.  

Throughout the United States, children and adults are forced to engage in sexual acts and use illicit drugs against their will, in what many would call modern day slavery, commercial sexual exploitation, or sex trafficking. Victims are controlled through coercion, force, fraud, physical and sexual violence and they endure many emotional and physical consequences. Approximately 80% of victims access healthcare during their time of exploitation for health reasons such as acute injuries, sexually transmitted infections, and mental illnesses, such as depression, anxiety, trauma, and suicidal ideation. The emergency department (ED) is the frontline to these patients. To date, little is known about nurses' confidence or competence in identifying or caring for this vulnerable population in Seattle, WA. The aim of this study is to examine what current practices exist at emergency departments in three, large referral hospitals in Seattle to identify victims, and to assess facility and nurse readiness for improved identification. Nine ED nurses in Seattle were interviewed to gain insight into how they currently identify trafficking victims, their opinion of the acceptability of existing screening questions (compiled from nationwide piloted studies) in their ED setting, and whether they felt such a standardized screening tool may be effective in identifying victims and improving subsequent care. Through transcription of audio interviews, nurses’ responses were analyzed and coded for common themes. Improved identification of trafficking victims by nurses and other frontline health workers in emergency settings may lead to more efficient and effective linking with vital support services and resources to assist them in safely exiting the sex trafficking industry. Results from this study will be shared with the participating hospitals, as well as public health officials and stakeholder organizations in order to improve awareness of sex trafficking, victims, and provision of necessary care and resources to support this vulnerable population.

In 2015, the Laser Interferometer Gravitational wave Observatory (LIGO) received the first gravitational wave signal, shepherding a new era of discovering the universe in general, specifically, in the field of observing gravitational waves in astronomy. LIGO detected ten binary black hole mergers, and in 2017 the collision of two neutron stars, which enabled the multi-messenger observation of the merger and associated kilonova. To maximize the discovery potential for the new era of gravitational wave astronomy, a comprehensive approach to data analysis and parameter estimation was employed to identify and characterize gravitational wave signals. Therefore, great strides will be made in data analysis methods across the gravitational wave spectrum between groups, including LIGO, the North American Nanohertz Observatory for Gravitational waves, and the Laser Interferometer Space Antenna. This work will continue to expand the Bayesian data analysis strategy, which was successfully used in the first detection of gravitational waves across the gravitational wave spectrum. Specifically, we use Markov Chain Monte Carlo (MCMC) for parameter estimation. By coordinating and combining analyses across the full gravitational wave spectrum we will be able to move science beyond what could be accomplished by any individual group, alone.

The threat of influenza, Ebola, Lassa, and Zika (ZIKV) viruses are unprecedented in their current scale and spread, causing enormous global health and economic burdens. The need for effective drugs which are safe for use in humans, including during pregnancy and in children, is critical to addressing this worldwide threat. The antiviral drug Arbidol (ARB) is used clinically in Russia and China as an anti-influenza drug. ARB binds to the influenza hemagglutinin protein to block entry of the virus into human cells. ARB also blocks infection of cells by Hepatitis C virus (HCV), Ebola, Lassa, and ZIKV primarily by suppressing viral entry and potentially by inhibiting post-entry events such as viral replication. The purpose of this project is to optimize and quantitate immunofluorescent detection of the HCV NS5A protein to evaluate the efficacy of ARB against HCV replication. Various dilutions of primary and secondary antibody will first be tested to optimize detection of HCV NS5A in HCV replicon cells. The assay will be miniaturized in 96 well plates. Next, an automated microscope (Biotek Cytation 1) will be evaluated as a method for quantification of immunofluorescent detection by imaging wells for HCV NS5A. HCV replicon cells will then then be treated with various doses of ARB and the antiviral efficacy of treatment quantitated. Defining the various ways by which ARB suppresses different viruses may expand the drug’s use and, thereby, inclusiveness for addressing multiple global viral threats.

There has been significant concern regarding the global effects of climate change, especially on plant communities, which are influenced by individual plant species responses. Warming temperatures are having large repercussions for plant biodiversity, with rapidly changing environmental conditions causing shifts in species ranges and phenology. To better understand the implications of this phenomenon on plants, many studies have investigated responses of individual species to climate change. One approach that has grown in recent decades is the use of functional leaf traits, which are indicators of plant performance and reproductive capacity. Specific leaf area (SLA), the ratio of fresh leaf area to dry leaf mass, is one such trait that is attributed to plant growth and photosynthetic capacity, and found to be correlated with climate. We assessed the relationship between climate and SLA for Vaccinium ovalifoilum, a shrub that is prevalent in the montane ecosystems of Mt. Rainier. To accomplish this, we gathered SLA using samples from the Burke Museum’s herbarium collection whose distribution will be delineated across three elevational bands. Altitude was used as a proxy for climate due to variable environmental conditions found across elevation—namely temperature and precipitation—and the collection location of specimens allowed us to obtain temperature and snow accumulation data. With this information, we compared the variation between the three established elevational bands in which the specimens fell under. We hypothesized that as elevation increases, SLA will decrease, attributing this trend to a limited growing window to support high photosynthetic capacity as a result of later snowmelt and lower temperatures. Our results offered insight to understand how climate change may potentially affect plant functionality and guide future research to analyze how changes in individual species may influence community coexistence in the upcoming years.

Many plant species are known to undergo masting, where individuals within a species all produce a large amount of seed in a single year, with a sharp drop off in reproduction in the following years. Masting may be beneficial to plants by suppressing seed predator populations in low seed production years, allowing for seeds to escape predation in high seed production years. Masting is likely associated with climate, although this is poorly understood. In this study, I will use herbarium specimens to tackle questions related to masting in five plant species: Tsuga heterophylla, Pseudotsuga menziesii, Thuja plicata, Rubus spectabilis, and Rubus parviflorus. Specifically, I will note the number of cones, seeds or berries on herbarium specimens, as well as specimen size and the year it was collected. I will use these data to 1) examine patterns of masting in focal species as compared to field data from Mount Rainier. I hypothesize that herbarium specimens will show a similar pattern of masting as field data, with trees showing stronger patterns than shrubs. Next, I will use these data to 2) compare masting patterns to annual climate. I hypothesize that warm temperatures lead to masting the following year, and that masting has increased in frequency. Finally, I will 3) assess the relationship between masting and bird species that eat seeds and berries (e.g. grouse, jays), to determine whether masting influences population dynamics of higher trophic levels. I will do so by comparing masting patterns with bird count data from the Audobon Society. I hypothesize that population sizes of birds that rely on seeds and berries will be greater in mast years. This study provides additional information for how we might expect entire ecosystems to be affected by climate change, including resource distribution and population health.

The University of Washington High Enthalpy Flow Laboratory (HEFL) has constructed a purpose built laboratory for experimental research on Rotating Detonation Engines (RDE). This refit included the rebuilding of the lab apparatus, the assembly of the RDE and supporting equipment such as downstream piping, vacuum system, gas handling plumbing, and the redevelopment of the experimental instrumentation. The assembly of the lab apparatus consisted of the construction and mounting of fuel, oxygen, and nitrogen lines for the RDE, and the assembly of back pressure controlled exhaust tubes leading to a dump tank and an optical imaging port. A stand for the engine apparatus itself as well as much of the plumbing support equipment was also constructed. The assembly of the RDE consisted of the assembly of the various engine parts, followed by the connection of the various instruments such as pressure sensors, temperature sensors, ion probes to the engine itself. The hardware and software components of the instrumentation systems were also redeveloped to allow for very high instrument density for pressure and temperature sensors on the RDE. The software component of the instrumentation involved developing MATLAB scripts for valve actuation, data acquisition, and sensor calibration. The hardware aspect of the instrumentation involved selecting the sensors to be used on the engine based on their signal conditioning, as well as designing and building power supply and signal processing circuits to connect the sensors to a rebuilt data acquisition computer system.

Sleep in hospitalized children is disrupted by numerous factors including loud noises, light, assessments, medication administrations, and being away from their usual sleep routine and setting. Inadequate sleep can increase behavioral problems, increase stress, and increase length of stay. The goal of this project is to evaluate if an evidence-based sleep hygiene protocol in the Psychiatric and Behavioral Mental Health Unit at Seattle Children's Hospital promotes better sleep for the patients. The sleep hygiene protocol, a guided routine done prior to bedtime, is derived from a literature review on sleep routines in school aged children. A retrospective chart review will be conducted of seven patients from the unit ages 5-9 who use the sleep hygiene protocol. Data will include usage of sleep medication, hours asleep, and nighttime behavioral problems from before and after implementation of the sleep hygiene protocol. I am focusing on the effectiveness of the newly edited sleep hygiene protocol. Results from this study will be used to refine the sleep hygiene protocol so that it can be widely implemented in the PBMU and other units of the hospital. 

Asthma affects over 6 million children in the United States. Asthma management requires a high level of executive functioning and self-regulation, including attention, planning, problem solving, and self-control. Executive functioning deficits, therefore, may impair asthma management capacity. Therefore, the purpose of this study is to describe the executive functioning of school aged children with asthma. The executive functioning of 33 children ages 6 to 11 years with asthma was tested using the National Institute of Health Toolbox Cognition Battery. The battery assessed numerous executive functioning processes, including attention, inhibition, shifting, episodic memory, working memory, processing speed, receptive vocabulary, and language. Compared to the reference sample, children in this study exhibited significantly lower age-adjusted scores in attention and inhibition t(33) = 93.06, p = 0.001, shifting t(33) = 92.64, p = 0.003, and processing speed t(30) = 82.37, p = 001. They scored significantly higher in receptive vocabulary t(33) = 113.76, p = 0.000, and language t(30) = 119.80, p = 0.000. This study revealed significant differences in the executive functioning of school aged children with asthma, specifically deficits in attention, inhibition, and shifting. These functions can be instrumental in the consistent use of controller medications and as a result impact the effectiveness of asthma management. Implications of these findings may include developing asthma management strategies within the capacity of the child. Future studies should explore the possible causes for executive functioning deficits as well as interventions that align with the executive functioning capacity of school aged children with asthma.

Asthma is the most common chronic disease among children, affecting almost 10% of children in the US. Standard treatment for persistent asthma is inhaled daily corticosteroids to reduce airway inflammation. Adherence to these controller medications is poor, with less than 50% of children consistently using them. Poor adherence leads to worsened asthma control, causing increased symptoms, exacerbations, school absences, and decreased quality of life. Poor asthma control has also been associated with impaired family functioning. The purpose of this study was to analyze the relationships between quality of life, family functioning and asthma control among school-age children with asthma and their parents.  Thirty-three child-parent dyads (children ages 6-11 years) were enrolled in this study. Parents and children independently reported on asthma quality of life and the child’s asthma control. Additionally, parents reported on family functioning using the McMaster Family Assessment Device, which assesses numerous family functioning domains. Our hypothesis is that poor asthma control will be associated with impaired family function and decreased asthma quality of life and that parent and child reports of asthma quality of life will differ significantly. Results from this study will provide insight into new potential opportunities for nursing interventions for children with asthma and their families. 

Altrenogest (ALT) is a potent synthetic steroidal progestin commonly used as a veterinary pharmaceutical to maintain pregnancy in females, match estrus periods for breeding, or postpone the estrus period. ALT usage was estimated as several thousand kg across ~3,600,000 horses and ~66,000,000 swine; it subsequently enters the aquatic environment through agricultural runoff. ALT can act as an environmental endocrine disruptor because it has progestogenic and androgenic activity, however, little is currently known on its environmental fate, persistence, and ecological risks. Our study focuses on characterizing the biodegradation kinetics and product identification for ALT and its primary photoproducts.To evaluate altrenogest fate, we build microcosms by mixing altrenogest, water and growth media for mixed microbial communities collected from representative agro-ecosystems and municipal waste waters. We then concentrate water samples through solid- phase extraction and then use liquid chromatography and triple quadrupole mass spectrometry to analyze remaining ALT concentrations over time, to understand transformation kinetics. To identify transformation products, sample extracts are analyzed using high resolution mass spectrometry. Study results will aid in the risk assessment of ALT by improving our understanding of its environmental fate and management.

Bloodborne pathogens are wide spread and can pose risks to health care workers and vulnerable patient populations alike. Conventional diagnostic tests for bloodborne pathogens are costly and time intensive, so fast, affordable, and sensitive diagnostic methods are needed that can be performed under low-resource conditions by untrained personnel. Microfluidic self-digitization technology, developed in the Chiu Laboratory, provides the foundation for such low-cost diagnostics. As undergraduates, we work on the fabrication and optimization of cheap, robust devices used to load samples, as well as dPCR of samples required to detect diseases. As part of a larger research endeavor, we are developing a portable instrument that, in combination with our proprietary microfluidic chip technology, will expand rapid diagnostics to low-resource settings around the world. Expanding diagnostics for bloodborne pathogens will both help prevention as well as monitoring treatment of patients already infected.

Over 30 years after the Vietnam War ended, Quang Tri province was still affected by explosive remnants of war (ERW), which killed and injured more than 8,000 people, about 1.4% of its total population 2011 since 1975. Peacetrees Vietnam is an international non-profit organization, collaborating with local partners in Quang Tri Province to clear dangerous explosives from Vietnamese land, and return healthy land, and building sustainable communities. My internship at Peacetrees Vietnam in Seattle provided a value resources to accessing the impact of Community-based Explosive Remnants of Wars program in Quang Tri Province. Methodologically, I had informal interviews with the staffs, collecting statistics through their annual reports, read intensively literature reviews about remanats, and developed a visual population profile. I chose a qualitative interview method by developing questionnaire to understand the Peacetrees Vietnam's project. I traveled to Vietnam, Quang Tri province to interview and observe staff, mine clearance teams in Peacetrees Vietnam, the residents in Quang Tri Province, and others sustainable projects such as kindergarten, libraries, black pepper projects. In addition, I developed communication strategies for the organization to reach broader donors, by researching representatives who participated in UXO Caucus, then matched with donor's Peace trees Vietnam. The purpose was asking those donors representative to support for demining humanitarian program in Vietnam, particularly Peace trees Vietnam organization. 

Semantic ambiguity arises in language when a word or sentence can take on multiple meanings. The resolution process can not only greatly inform theories of language processing, but can also provide novel insights into human general cognitive abilities. There is evidence for basal ganglia (BG) involvement in semantic ambiguity resolution from a breadth of neuroimaging research and clinical populations. The current project focuses on bilingualism, which creates the higher cognitive demand of selecting, shifting, and inhibition information that is co-activated in two language systems. Our study tested 73 proficient bilinguals using a self-paced reading task that contained a lexical ambiguity manipulation. A probabilistic learning task was used as an index of BG functioning. We anticipate that bilinguals with a more balanced use of their two languages train their BG due to frequently managing interference between multiple languages, in comparison to bilinguals who have an imbalanced use of their languages. This should result in a better performance in resolving semantic ambiguities that arise due to low frequency word meanings. Specifically, we expect this better performance to result in smaller increases in reading speed, which reflect interference, for sentences containing low frequency word meanings, relative to control trials. Better understanding of the role of the BG in semantic ambiguity resolution in various bilingual populations will provide novel insights into the neurocognitive bases of human language processing and executive functioning. We see this as an exciting foundation for studies looking into bilingualism as a form of executive function training.

The idea of energy, matter, and motion has perplexed many philosophers and physicists from antiquity to modern physics, from Plato to Einstein. New and developing physical theories raise different interpretations of energy and matter but no complete theory of everything exists at present. However, there is a law we can almost take for granted - the Law of Conservation of Energy, it simply states that energy cannot be created nor destroyed although it can be transformed from one form to another. With an up-to-date history of the first law of thermodynamics, physicists in the field can have a sense of what has been done and what not. A complete overview of the rudimentary law would also provide a continuous timeline in which one can identify flaws in current theories. After establishing the foundational theory and history of conservation of energy, this literature review aims to provide a comparative study between the concept of mass and energy in two of the most profound physical theories - Quantum Mechanics and General Relativity. Subtle implication of numerous laws of thermodynamics and mass-energy equivalence like Dark Energy, Dark Matter, Higgs Mechanism and Blackhole Thermodynamics is studied in an introductory manner for potential history and correlate direct and indirect links to energy conservation.

Hybrid dynamical systems (HDS) are time dependent systems that have both discrete and continuous behavior, such as a bouncing ball or jumping leg. The BioRobotics Lab studies HDS in order to better understand locomotion and develop controls for robotics. As controllers are developed, they need to be tested in the hybrid dynamical system (HDS) either through simulation or implementing in physical robotics. While simulated system environments are useful in early controller development, they are unable to capture all the intricacies of a physical system. Thus, testing controllers in a physical system can provide better insights for future development. We developed a hopping robot for the purpose of easily implementing controllers through software. The hopping robot is designed to be modular and easily configured for different dynamics. Simulations of the robot were also developed so that researchers can use both simulated and physical environments. This tool will help researchers develop new controllers and could bring new insights to studying hybrid dynamical systems.

Stress-related disorders impact over 18% of the United States population. Further definition of the mechanisms behind stress responses in the brain is necessary for understanding and treating stress related disorders, such as anxiety and depression. Specifically, the lateral habenula (LHb) is a brain region known to modulate stress and anxiety responses, but the ways in which it modulates these responses is relatively unknown. In order to investigate potential mechanisms for this modulation, we examined differential gene expression in the pathways from the LHb to three brain regions: the ventral tegmental area (VTA), the dorsal raphe nucleus (DRN) and rostromedial tegmental nucleus (RMTg). Rats were stressed using a forced swim protocol and tissue from the LHb was homogenized in order to extract RNA using RiboTag. Using a combination of transgenic mice and a RiboTag viral vector we were able to extract highly specific RNA from complext brain tissue. We used a portion of our collected RNA to perform RNAseq, a molecular tool used to identify differential gene expression in certain pathways. Using the results from our RNAseq analysis, we used extracted RNA to perform quantitative PCR to verify the pathway specific genes found in the LHb. By determining the pathway specific patterns of differential gene expression, we propose a molecular mechanism for neuronal response to stress in the LHb.

Gravity remains one of the biggest mysteries in physics. Since Einstein’s Theory of Relativity not many new discoveries have happened. There are several big questions remaining about it such as: Why is it so much weaker than the other forces of nature? Is it mediated by a particle like the other forces? Is there a unifying theory between gravity and quantum mechanics? Does gravity have a place in the standard model? There are many theories proposed today which attempt to answer these questions, such as the presence of extra dimensions in string theory. If the effects of these theories exist, they would be present at small length scales (less than 1 mm). In order to test these theories, our lab uses a torsion balance experiment at sub-millimeter lengths. Our torsion balance experiment consists of an attractor mass on a turn table, and a detector mass hanging from a thin wire. Each has wedges cut out of it in the same pattern. The test is run by operating the turntable and measures the gravitational torque experienced by the detector mass. My project is to use a code that simulates the gravitational torque in order to investigate its dependence on different orientations and geometrical aspects of the experiment, as well as to improve on future runs of the experiment. This experiment will shed light on previously unknown aspects of Gravity and hopefully provide new discoveries to the field of gravitational physics.

Systematic measurements of the resistivity, susceptibility, and quantum oscillations are presented for single-crystal samples of the electron/hole-doped RAgSb₂ (R=Gd,Y,La). Doping the parent compound LaAgSb₂ with Gd and Y explores the effect of hole doping and electron doping the crystal. La_1−xGd_xAgSb₂ exhibits anti-ferromagnetic ordering around 14K, while La_1−xY_xAgSb₂ exhibits charge density wave ordering. This entire doping sequence is likely to create two quantum critical points related to these charge density waves and anti-ferromagnetic states. Such quantum critical points have been linked to high temperature superconductivity in cuprates, so the study of the similar RAgSb₂ crystals may lead to further insights about superconductivity. We use measurements of resistance versus temperature, magnetic susceptibility, and quantum oscillations to explore the effect of the chosen doping sequence. Part of this phase diagram has been determined, and no superconducting phase of RAgSb₂ has been found yet, but further doped crystals with finer spacing need to be grown to resolve the quantum critical points of interest. In addition to superconductivity, quantum oscillations in the crystal lattice are used to track changes in the material’s Fermi surface and effective mass. These oscillations are associated with the Landau quantization of electronic energy in an applied magnetic field. Magnetic-susceptibility data is also studied to locate the divergent temperature of the crystals follwing the Currie-Weiss fit.

Many children in the United States experience mental health issues that impact their performance in school. Evidence-based practices (EBP) have demonstrated effectiveness at improving student outcomes for students impacted by their mental health. However, many factors affect the successful implementation of these programs. Mental health services, particularly those for youths with the most mental health needs, typically involve multi-organizational processes to implement EBP. The Inter-Organizational Alignment study strives to examine these multi-organizational frameworks, and how they impact the school mental health services provided. The research study examined the association between race and the degree of inter-organizational alignment on climate for EBP implementation. Researchers surveyed 28 school mental health clinicians and 57 school staff in the states of Washington and Minnesota. The sample included 22 white or Caucasian participants and 14 non-white participants. Non-white participants were either American Indian or Alaskan Native, Asian, Black or African American, multiracial, or other. Implementation climate of EBP in school settings was rated on a Likert scale of 0 (not at all) to 3 (great extent) on a standard, multi-item scale. Researchers evaluated schools on a range from an open and positive implementation climate to a closed and negative implementation climate. The degree of alignment was determined between clinician and school staff scores, with misalignment defined as a difference of one standard deviation. Quantitative analysis of the results suggested more alignment in implementation climate between clinician and school staff of different races, which suggests that racial factors impact EBP implementation in racially diverse environments. An independent t-test determined that these differences were statistically significant. Consequently, these findings suggest that EBP may be impacted when implemented by more diverse organizations.

Fibrolamellar carcinoma (FLC) is a life-threatening variant of liver cancer affecting adolescents and young adults. FLC tumors do not respond to chemotherapy, thus, surgery remains the mainstay of therapy. FLC is characterized by a fusion event resulting in a novel chimeric protein that joins the N-terminal domain of DNAJ with the catalytic subunit of protein kinase A (PKAc). However, the underlying mechanism by which the FLC chimeric kinase drives FLC tumor growth remains unknown. Using CRISPR/Cas9 technology, the Scott Lab (UW) has re-created the human FLC fusion protein in a well-characterized and non-transformed hepatocyte cell line. The resulting cells retain hepatocytic differentiation while over-expressing DNAJ-PKAc compared with wild-type PKAc, akin to the human tumors. Using these model cell lines and a computational approach called, Kinome Regularization (KiR), I plan to uncover molecular mechanisms through which chimeric PKAc transforms hepatocytes in FLC. The concept of KiR is built around the fact that most kinase inhibitors are not specific but instead, affect a range of targets. By exploiting the property of polypharmacology in a set of well-characterized kinase inhibitors, we can make use of elastic net regression to compute and deconvolute the kinases that are responsible for a quantitative trait. To do so, we have identified a set of 30 broadly specific inhibitors that give us >85% coverage of the kinases studied. We can then test the effect of each of these 30 inhibitors on cell growth and use the results to identify the kinase important for cell growth. The KiR-based model will also be used to identify kinase inhibitors which can specifically reduce growth of FLC cells. Overall, these studies have a strong translational potential; a new therapeutic option for FLC could give unprecedented hope to the patients who currently face this disease with limited alternatives.

Fluctuating temperature patterns due to climate change could negatively impact the survival of species whose sex is determined by environmental cues rather than genetic factors. Species whose sex is determined by ecological cues or social interactions fall under the Environmental Sex Determination (ESD) category, while the Genetic Sex Determination (GSD) category includes species whose sex is determined by genotype at conception. There are numerous published examples of teleost fish species that rely on ecological factors for sex determination, but no studies have explored the extent to which the annual killifish Austrofundulus limnaeus, a species without sex chromosomes, relies on ESD. A. limnaeus inhabit ephemeral ponds in Venezuela, South America that experience extreme daily fluctuating temperatures. Climate change could affect this delicate lifecycle by disrupting seasonal temperature patterns that alter sex ratios or exposure to temperatures beyond their tolerance range. Therefore, it is essential to determine what impact temperature and social interaction may have on sex determination in developing A. limnaeus. To explore ESD, A. limnaeus larvae were exposed to constant temperatures of 20 and 30°C, and a daily fluctuating temperature regime from 20-30°C from hatching until the display of secondary sexual characteristics. Some fish were grown in isolation while others were grown in small groups. Fish grown in isolation at 30°C exhibited female-biased sex ratios with 64% developing as females whereas 69% in 20°C and 61% in fluctuating temperatures exhibited male-biased sex ratios. Ongoing experiments are being conducted to explore the possible interaction between temperature and social cues for determining the sex in this species. A. limnaeus has a relatively higher tolerance to fluctuating temperatures due to their ephemeral pond environment, and thus represents an opportunity to explore how even the most tolerant of species may respond to global climate change, especially in the context of ESD.

The nematode C. elegans is a common model organism for investigating cellular aging mechanisms and there is an extensive database of known genes which influence their lifespan. Protein kinases are regulatory enzymes which function in the cell as molecular switches. Here we use RNA interference to disrupt 11 classes of protein kinases to determine their role in 10 different C. elegans mutant backgrounds known to affect aging. With the included controls this involved over 120 individual lifespan experiments. In order to perform this many experiments we used a custom robotics platform called the Wormbot, a novel, high-throughput technique for measuring worm lifespans that our laboratory developed. We present here the results from 120 combinations of longevity mutants and inhibited protein kinases. The findings of this study may identify biochemical pathways or interactions which may play a role in the regulation of human aging or development of age related disease.

Traumatic fracture of the bone surrounding the eye (the orbit) can result in functional impairment of vision. Double vision, diplopia, is one such sequelae. The cause of diplopia in orbital fracture patients has most commonly been attributed to loss of orbital volume caused by an open fracture that allows the contents of the orbit to shift. However, in cases where the orbit is surgically repaired and orbital volume is restored, some continue to have diplopia. Our hypothesis in these cases is the anatomy of extraocular muscle pulleys is affected by the trauma. The aim of this study is to test this research question by analyzing computed tomography (CT) scans. Patients were selected from a previous study of orbital fracture patients in which all patients had CT scans available for review and consented to be part of a research study on orbital fractures. Locations of the extraocular muscle pulleys were measured relative to the center of the orbit in the lateral, anterior and superior directions. Pulley location was determined by a tangent plane drawn where the optic nerve meets the orbit and crosses the muscle. The measurements were input into Orbit, simulation software, to produce a prediction of visual changes in Lancaster plots. The Lancaster plots were compared to the data from the patient’s clinical visual testing to determine the accuracy of the prediction at each point in the visual field. Our results showed that the accuracy of our prediction varied, as the location of the pulleys is not the only factor that contributes to diplopia. Other factors that may contribute include weakened muscle, entrapment and damage that is not visible on CT. More research is needed to determine how the muscle pulley system is affected in orbital fracture, and to determine how clinical interventions including surgery may help improve diplopia.

Beat poetry and rhythm tap are two interests I have had for several years.  Through my separated exposure to and analysis of both, I noticed a similarity in their manifestations of improvisation and rhythmic complexities.  Initially, I assumed these resemblances were due to the heavy influence of jazz music both beat poetry and rhythm tap dance underwent in their formulations.  However, when examining the jazz music more closely, it became clear that the characteristics of the specific form of jazz beat poetry emulated (bebop jazz) purposefully opposed the characteristics of the form of jazz rhythm tap was danced to (big band swing).  This research henceforth sought to find how the rhythmic complexity and improvisation in rhythm tap and beat poetry could manifest themselves so similarly despite their rootedness in fundamentally contradicting forms of jazz music.  Through analyzing the historical shift from swing jazz to bebop jazz, it was found that the contrasts between the genre were actually essential, as they allowed for a different relationship with jazz music to develop per art form: rhythm tap integrated itself into swing music, while beat poetry emulated bebop. Because of this, rhythm tap had the autonomy to add improvisation and rhythmic complexity atop mainstream swing music’s lack of both, while beat poetry could echo the improvisation and rhythmic complexity of bebop without losing its individuality. This resulted in both having sonic similarities to bebop: the unintentional musical bridge between between beat poetry and rhythm tap which resulted in the two mirroring one another.

Despite being individually uncommon, rare diseases are a heterogeneous set of nearly 7,000 diseases estimated to affect 6-8% of the global population, making them collectively common. Rare diseases are infrequent and their determinants are usually unknown which negatively impact clinicians’ ability to make an accurate and timely diagnosis. With the inception of consortia such as the Undiagnosed Diseases Network (UDN) and ontologies such as the Human Phenotype Ontology (HPO) there is now a wealth of information on rare diseases. This rich information has enabled researchers to infer gene-disease relationships and clinicians to assign genetic diagnoses. However, rare diseases that are caused by unique or uncommon gene combinations remain unsolved. In this study, we address this problem by assuming that a disease can be described by a combination of clinical features or phenotypes and, thus, a combination of genes. By developing a pipeline to incorporate known gene-phenotype relationships from publicly available resources such as HPO and using various combinatorial search algorithms, we can prioritize the most likely sets of genes to result in a given set of phenotypes. Integration of our pipeline with individual patient data is expected to further reduce the search space and produce higher quality predictions. We anticipate the results from this study to advance the quality and accuracy of gene-disease relationship predictions for rare and undiagnosed diseases associated with one or more genes. Our pipeline could be used as a tool for the diagnosis and discovery of likely oligogenic, rare and undiagnosed diseases that are normally turned away from consortia like the UDN.

The endothelial to mesenchymal transition (EndMT) has been identified as a key part of organ development as well as many disease pathways. EndMT is characterized by endothelial cells, which make up the inner lining of blood and lymphatic vessels and are adhesive and non-migratory, gaining mesenchymal markers and invasive, migratory behaviors. This overall change in phenotype is normal in embryonic development where EndMT is linked to development of organs but has also been linked to numerous diseases in adults including cerebral malformations, Alport nephropathy, fibrosis, heart disease, and bronchopulmonary dysplasia. Whereas it appears that EndMT does not discriminate by organ, it does by sex. The diseases mentioned previously have a significantly higher incidence in males. To understand the role that sex plays on the EndMT pathway, human neonatal pulmonary cells with a gestational age of 18 to 19 weeks from three female and three male donors were routinely cultured and monitored for changes in phenotype. Using angiogenesis sprouting assays, western blot protein analysis and immunostaining, we collected quantifiable data on the reversibility of the EndMT process in each donor. We found that cells from male donors had lower plasticity, characterized as shifting between the two phenotypes, and generally existed in an endothelial state until pushed into a mesenchymal phenotype through a stressor. Female cells were more likely to shift between phenotypes regardless of conditions and exhibited more angiogenic potential, suggesting a heightened ability to transition between phenotypic states. Future experiments include placing cells in environments with differing stressors to mechanistically determine what drives EndMT processes and monitoring cells with time-lapse imaging to quantify the dynamics of the transition.

With regards to most tissues, humans lack the ability to regenerate, instead scarring in response to injury. This often leads to poor patient outcomes, especially in the event of spinal cord damage. Xenopus tropicalis are capable of avoiding this scarring response as tadpoles but not as adults. They instead fully regenerate tail tissue and are thus an excellent model system for the investigation of how regenerative and non-regenerative organisms differ in their response to injury. Due to the complexity of this process, many transcription factors have been implicated to have a role in regeneration, though the precise roles of many such transcription factors remain unknown. Here, we focus on the transcription factor Hif1α, which is canonically involved in responses to hypoxia and oxidative stress. Using an Assay for Transposase-Accessible Chromatin (ATAC-Seq) we have found that over the course of regeneration, Hif1α response elements (HREs) increase in accessibility. To understand the role of Hif1α during regeneration, I have used echinomycin, a small molecule known to inhibit binding of Hif1α to HREs. Tadpoles treated with echinomycin fail to regenerate, indicating the necessity of Hif1α in regeneration. In order to determine the effects of Hif1α on gene expression, I have queried several genes known to be differentially expressed during regeneration through the use of quantitative polymerase chain reaction. I have shown that inhibition of Hif1α transcriptional activity via echinomycin significantly alters Wnt target gene expression, indicating that Hif1α regulates Wnt target genes. This provides an improved understanding of the regulatory processes that enable regeneration.

International adoption in the United States began during World War II. It was developed as a humanitarian act to aid those orphaned due to the war. Since then international adoption has remained an option for Americans looking to expand their family. The Hague Convention is an international organization aimed at uniting countries in their laws regarding international adoption policy with the intent to ensure the welfare of the child. Since its founding in 1983, the Hague Convention has influenced a total of eighty - three countries including the United States. Despite the intention of the Hague Convention and its member's international adoption still places a child's welfare at higher risk than those of domestically adopted children. International adoptees are victims of human trafficking, abuse, and untimely death. Even the Hague Convention intended to improve international adoption does not advocate countries to use international adoption as a solution to aiding their orphaned population. Permitting an international adoption is promoted as a last resort for the most vulnerable of an already targeted community. The primary intent of this paper advocates for stricter enforcement and potential temporary stall on future international adoptions within the United States. This stance is taken due to issues of lack tracking of international adoptees, the failure of enforcement of international adoption laws currently in place, and the negative impact of the overtly positive marketing of international adoptions. This work intends to bring further awareness of the systemic issues of international adoption that put a child's welfare at risk. Concerning international adoption, this is highly important due to its primarily positive reputation with the general public. This research also intends to provide a solution society may advocate for or further build upon in order to take the measures necessary to ensure the welfare of a child.

For years, scientists have been baffled by the imbalance between matter and antimatter in the universe. The properties of the neutrino, a subatomic chargeless particle, may ultimately help us explain this anomaly. Double beta decay takes place in an atomic nucleus, and it occurs when two neutrons spontaneously transform into two protons, emitting two electrons and two antineutrinos in the process. However, if the neutrino is its own antiparticle, the antineutrinos could annihilate each other, so that the two electrons are emitted with no balancing emission of antimatter. This is a postulated process known as “neutrinoless double beta decay.” The MAJORANA Demonstrator, a collection of germanium detectors, allows us to search for this creation of matter in a laboratory setting. However, there are naturally occurring background processes, such as gamma rays, which closely resemble that of the creation of matter. In order to accurately distinguish one process from the other, we must understand them extremely well. The Demonstrator relies heavily on the use of simulation software, called Geant4, in order to predict the occurrence of gamma ray backgrounds. Geant4 previously generated the gamma rays’ directions isotropically, but many sequences of gamma emission are emitted in correlated directions. We contributed new code that uses the computation of associated Legendre polynomials to correctly generate the gamma emission directions. This code used a recursive algorithm that was too slow for general use. A speedup was attempted using a cache, meaning it stored computations to avoid repetition. However, the cache was implemented inefficiently and incorrectly. Improved caching should speed up calculations. If it is insufficient, we will unwrap the recursive algorithm into a generative for-loop. For gamma emissions with extremely large angular momenta, the code may still be too slow. In that case, we will explore asymptotic formulae to speed up computations even further.

The United States presence in Africa is mostly militaristic and oil-driven, whereas China's recent foray into the continent has rattled the traditional conventions for doing business and investing on the continent. Through a series of Foreign Direct Investments, International Trade, Government Funded Contractual Projects and loans by the Chinese government, China has taken direct action to infiltrate the internal economies, politics and societies of many African nations. To frame where China lays in terms of economic investments and involvement, my research examines the current state of three African nations in which China invests. The markers within a nation include the profitability of a particular industry sector, previous political relations with China, the market size of an economy or nation, political security of a nation and geopolitical strategy. I focus on three Sub-Saharan nations in which China has previous practices or a history of investments, Tanzania, Zambia and Angola. Statistical data provided by loans or investments and first-hand accounts of events are used to support my arguments about China’s involvement in the affairs of these three nations. I discuss multiple value factors for a superpower to invest in a nation and how this influences that nation’s economy and politics. The end result takes the form of a review of China’s influence on these three nations. My study gives context and poses questions for future research on the economies and political strategy behind the investments made by world powers in African countries.

Is the neutrino its own anti-particle? This is a question physicists do not have the answer to, but if a process known as neutrinoless double-beta decay were observed then it could be said with certainty that the neutrino is indeed its own anti-particle. In an attempt to search for said process, researchers at UW have joined forces with researchers from a number of other institutions to form the group known as LEGEND (Large Enriched Germanium Experiment for Neutrinoless Double-Beta Decay). The source used for this experiment that undergoes double beta-decay is Germanium-76. This source is also used for the detector itself. When a beta decay happens in the detector a pulse proportional to the energy of the electrons emitted is produced. If these electrons have all the energy available from the decay, then it will be known that no neutrinos are present. What makes things tricky is that if this process occurs it does so with a half-life greater than 10²⁶ years. Thus, counting rates for this process will be very low, and very low backgrounds will be needed to effectively carry out the experiment. Currently at UW we are working on developing pulse rejection techniques that will allow us to get rid of unwanted background events that our detectors measure. The project I'm presenting on involves aiming a collimated alpha source at our detector, and the goal is to develop techniques that allow us to reject pulses resulting from alpha decays. A number of other collimated sources are also aimed at the detector in order to study rejecting the pulses that they give rise to. In order to help design this experiment I am running simulations in the Geant4 based application “g4simple” to determine collimator dimensions and materials that will work best for different radiation sources.

During a 2013 meeting of the Puget Sound Beekeeper’s Association, two major concerns were voiced regarding the rapid demise of bees. One was overwintering loss of honey bees and the other was Varroa mite infestations. The Puget sound area had an average closer to 40%, and overwintering loss for the nation averaged around 30%. This resulted in 2015 President Barack Obama issuing a “National strategy to promote the health of honey bees and other pollinators.” To reduce honey bee colony losses during winter, an effort was made to assess cause of death in honeybees. After the assessment was made, this sparked the creation of the “Mite Busters,” an elite team of students, and community members who shared their passion in beekeeping and biology. The goal of the “Mite Busters” was to assess the cause of death in honeybee populations during the winter months. The Mite Busters conducted an assessment of 15 characteristics of hives in 100 different colonies around Puget Sound in August 2016, and October 2016. Colony death rates were measured after the winter months had passed. The only measurement that allowed us to predict whether the colony would live or die was the mite counts from nurse bees. Before overwintering, colonies that had over 7 mites/100 bees had a 70% chance of overwintering death (30% survival rate). Colonies that had under 7 mites/100 bees mites had a 4% chance of overwintering death (96% survival rate). The results sparked the creation of the Mite Busters, which has put forth a variety of group based mechanisms to help all bee keepers keep healthy colonies together. Specifically, the focus is on treatment plans and methods to decrease infestation rates. The mite busters conclude that fewer varroa mites leads to better overwintering success rates for Puget sound honey bees.

According to the NIH, 76.2 million Americans have suffered from pain lasting more than 24 hours, with millions more affected by chronic pain. With such a high prevalence and impact on health and quality of life, the understanding of pain is essential to effective treatment. Exploring the mechanism by which our neurons set the gain for what is perceived as painful stimuli is one way to further that knowledge. Different populations of neurons have different thresholds for activation, and oftentimes alterations to these thresholds can result in aberrant pain signaling. Phospholipase C (PLC) is a promising target to study, as it has been previously shown to potentiate the activation of pain neurons expressing Transient Receptor Potential cation channel subfamily A, member 1 (TRPA1). TRPA1 channels are responsive to noxious stimuli such as mustard oil (AITC). This study explores the effects of PLC using a PLC activator (m3m3FBS) and an inhibitor (U-71322) to examine its role in response to the noxious stimulus, AITC. We performed a locomotor assay of zebrafish larvae to explore behavioral effects, as well as neuronal imaging experiments using transgenic zebrafish with fluorescent calcium indicators in neural cells. We hypothesize that both behavioral responsiveness to pain and neuronal recruitment will likely increase with activation of PLC and decrease with deactivation of PLC because of PLC’s ability to modulate TRPA1 channel activity. With data collected thus far, the results look consistent with our hypothesis. We observed increased locomotion in response to activation of PLC with painful stimulus (AITC) compared to control and inhibitor groups. Likewise, zebrafish exposed to PLC activators exhibited greater numbers of AITC responsive neurons than zebrafish exposed to control or PLC inhibitors. Together, these results indicate that PLC is an important factor in modulating the sensitivity of TRPA1 expressing neurons.

Chronic pain is debilitating for millions of people worldwide and our understanding of how the central nervous system processes painful information is limited. If we are to create more effective therapeutics to treat chronic pain, it will be necessary to develop a better understanding of the circuitry and functionality of the somatosensory system. Our lab is interested in the calcitonin receptor-like (CALCRL) receptor, which is expressed throughout the central nervous system and is known to respond to pain-inducing neuropeptides. We aim to profile CALCRL receptor-expressing neurons within the dorsal horn to elucidate their functional roles in nociception and to determine how they process painful information. This was done by 1) utilizing an adeno-associated viral vector (AAV) to preferentially infect and fluorescently tag CALCRL-positive neurons in the dorsal horn, 2) utilizing a retrograde, monosynaptic rabies viral vector to infect neurons that are synaptically connected to CALCRL-positive neurons, and 3) immunohistochemical staining and analysis to detect a variety of neuronal markers of inhibitory and excitatory neurons, laminar markers, and several other known dorsal horn neuron subtypes. Thus far, CALCRL-positive neurons were successfully infected via direct injection using both AAV and rabies vectors into the dorsal horn. In addition, we have also been successful in costaining for multiple neuronal markers. We have begun to profile and classify these neurons according to known neuronal subtypes. Our next goal is to modulate the activity of this specific neuronal population followed by behavioral testing to better understand its functional role in the processing of painful stimulus. If we are able to create a clear profile of these neurons, then we may be able to identify future targets for specific therapeutics.

Both acute and chronic pain are universal, often debilitating sensations that lead to significant physiological, psychological and economic costs. Drug development and research have worked to counteract these adversities, but current therapies are often inadequate and have dangerous side effects. Targeted drug development, which relies on pre-selecting a target that is subjected to in-vitro testing, has been difficult, costly and ineffective in producing a drug that works to effectively relieve pain with minimal unfavorable consequences. An alternative approach would be to develop an untargeted screen in a system that employs complex pain behaviors. It would act as a means of modeling the nociceptive processes, which are the neural processes of encoding and processing noxious stimuli, in the organism. We utilize an unbiased, behavior-based, novel assay that uses zebrafish larvae to better understand pain sensation. We have screened thousands of small molecules on zebrafish larvae to identify ones that have analgesic properties. The potential analgesics should block sensitized temperature aversion which changes the larvae’s temperature zone inclination meaning we observe no preference between the two zones. Thus far, our untargeted screen identified three novel molecules with analgesic properties. We then performed a series of pharmacology and behavioral experiments to understand the impact of the compounds and to narrow down their effects in order to confirm if it is truly impacting nociception and/or temperature aversion with the intent to validate the compounds as prospective analgesics.

Freshwater is one of the most valuable resources in Washington State. In recent decades, water supply has been affected due to climate change and population growth. Understanding changes in water supply and demand is crucial for ensuring an abundance of water for residential, economic, and industrial needs. The proposed research analyzes changes in the streamflow regime of the Cedar and Tolt Rivers which provide drinking water for the greater Seattle area. The main goal is to calculate the water budgets for the Cedar and Tolt watersheds and estimate how the inputs and outputs to these budgets change over the 21st century. An existing ensemble of streamflow projections for the Cedar and Tolt Rivers are used to analyze changes in water supply. The mean streamflow for each month is compared between a 30-year control period (water years 1971-2000) and a 30-year future period (water years 2031-2060). For each of these periods, I determine “optimistic” and “pessimistic” scenarios for the streamflow. For the “drought” month the highest streamflow value is considered as “optimistic”, and the lowest as “pessimistic” since the goal is to assess potential shortages. I use existing monthly demand values provided by Seattle Public Utilities and create different future scenarios, based on the predictions of population and employment growth. Supply and demand values are compared to evaluate (1) the potential for water shortage and (2) water management and conservation methods to satisfy the unmet demand. One potential water management method is the construction of a new reservoir. The results of the research are aimed at helping to inform society and water managers about the potential changes in the water system. Based on this information, they might be able to introduce changes in their future plans to accommodate the predicted needs.

Springsnails are a broad group of highly diverse North American gastropods, with the most speciose genus being Pyrgulopsis (139 species). These tiny aquatic gastropods are often found in thermally-influenced freshwater springs, where endemism is common. Restricted occurrence and narrow habitat requirements of many species has generated conservation concern because of anthropogenic threats to spring systems and associated aquafers. The Blue Point Pyrg is endemic to Blue Point Spring in Lake Mead National Recreation Area within the eastern Mojave Desert. Two other springsnail species also occupy this unique spring. Little is known, however, about the distribution, abundance, and habitat associations of these springsnails. As a first step in a larger study investigating these parameters, we addressed methodological questions associated with the use of artificial tile samplers for long-term monitoring of springsnail abundance. We determined that the area of our tile samplers was adequate for sampling these springsnails and that our multiple, replicate tiles did not produce significantly different measures of abundance within our one meter sampling areas. These results indicate that monitoring could be accomplished with fewer tile replicates. We identified all three springsnail species within our samples and determined that identification of adult springsnails by shell morphology under magnification appears possible; we are currently developing genetic markers to confirm the morphological assessment. The relative abundance of springsnails peaked at approximately four meters below the springhead, and then dropped precipitously further downstream. Limited numbers of springsnails downstream may be related to the presence of nonnative, predatory fishes. We are currently investigating this hypothesis, and the findings of our methodological assessment have allowed us to use half of our sampler replicates in a fish exclusion experiment to assess the impact of predation.

The waters surrounding the San Juan Islands in the Salish Sea near Washington state, USA, possess a variety of physical and chemical conditions that combine to support a rich multitude of marine organisms. Five constituents observed and analyzed in this project represent the larger food web found within the Salish Sea: nutrients, phytoplankton, forage fish, seabirds, and marine mammals. I tracked variability in these constituents during the fall over the course of twelve years from 2006 to 2018. This time range was selected to cover the years before, during, and after the North Pacific marine heat wave (2014-2016), and the subsequent return to normal temperatures in the Salish Sea since those years. The abundance and composition of these constituents varied over this time range. We found a significant decrease in both nutrient concentrations and fish condition in the fall of 2014, which had returned to previously observed levels by the fall of 2018. In contrast, the phytoplankton and marine bird and mammal observations remained comparably low in 2018, similar to values observed in fall 2014. The introduction of the marine heat wave into the Salish Sea during 2014 appears to have consequences that span across multiple years after its dissipation in the Pacific Ocean. As marine heat waves are anticipated to become more prolonged and common with global climate change, it’s crucial to understand their short- and long-term impacts on local marine populations. 

Conservative estimates suggest that food production must increase by 60-70% by 2050 to keep up with population growth. This challenge to global food security is compounded by a lack of knowledge of how crop species will respond to a changing climate. The Nemhauser Lab has been studying how the photoreceptor Phytochrome B (phyB) directs the allocation of plant resources in response to environmental stimuli like elevated CO2. I have focused on studying this phenomenon in Brassica rapa, a member of the mustard family that includes a large variety of popular vegetables such as broccoli, cauliflower, Brussels sprouts, as well as varieties used for oil production. B. rapa plants with mutations in the phyB gene make fewer seeds, have a lower chloroplast density, photosynthetic rate, total chlorophyll levels, and stomatal index. To better understand how phyB is involved in seed yield, I am characterizing ovules and gynoecia (female reproductive organ) development in phyB deficient B. rapa plants. To understand how phyB plays a role in other processes relating to or impacting resource allocation such as chlorophyll levels, I will identify genes differentially expressed between wild type and phyB deficient B. rapa plants. This will ultimately lead to the identification of potential targets for engineering more resource-efficient and higher-yielding crop varieties.

Biomimicry as a practice has generated a plethora of innovative technologies. By observing key processes that evolution has converged upon, we can improve and evolve manmade mechanisms. This literature review addresses the importance of vortices in biological systems and compares their locomotive purposes across a wide range of animal phyla. The development of particle image velocimetry (PIV) has enhanced our ability to study the vortex mechanics of remarkably fast or efficient animals. Such experiments have made great contributions to the human understanding of flow and kinematics. Vorticity studies, for example, have produced results that contradict the paradigm for animal motion-- particularly in how the inherent low-pressure zone associated with vortices can allow animals to maneuver through a fluid. Lampreys and jellyfish have shown to use vortex-based locomotive techniques to “suck” themselves through the water. Additionally, the “hyper-pitching" process of the zooplanktonic sea butterfly is controlled by pressure fields generated by leading edge vortices. Such findings have interesting implications for the future of biomimetic water and air travel, as the utilization of pressure as opposed to thrust may facilitate the creation of more efficient vehicles. Furthermore, comparative biological studies allow for a more in-depth interpretation of animal kinematics that have been difficult to study due to lack of proper technology. By creating qualitative analogies between air travel and water travel, we can reexamine how airborne creatures move.

Methane reservoirs are commonly found throughout the world’s oceans and the release of methane from seafloor reservoirs is thought to make up 5 to 10% of the global atmospheric methane. In fact, the greatest deep-sea mass extinction in the last 97 Myr during the Paleocene-Eocene Thermal Maximum (PETM) may have been caused by methane release from seep sites along the upper continental slope margin. Recently, methane reservoirs along this margin have been gaining attention due to their potential to accelerate current global warming. Changes in seafloor pressure and temperature could destabilize these seafloor deposits and cause methane bubble plume release into the ocean. At SHR, an extensively studied active seep site located ~ 90 km offshore Oregon, discontinuity in methane plume release was observed, but still not well understood. Hence, using Acoustic Doppler Current Profiler (ADCP) and pressure data archived by the Ocean Observatories Initiative (OOI) Cabled Array, we are investigating the potential correlation between tides and the presence of methane plume at SHR. Our study detects methane plume structures based on the proxies of echo contrast caused by acoustic-bubble interaction. By analyzing the derived plume structures and their correlation with 226 tidal cycles, we expect a trend of plume release triggered by low tides. Our study provides the first high-temporal-resolution analysis on the methane plume release at SHR using OOI acoustic data. 

The physics behind wave-driven mixing of river and ocean waters and current-driven wave breaking are not well understood. The current body of work surrounding river-ocean interactions focuses on large rivers. However, small rivers, which are much more strongly influenced by waves, make up the majority of such systems, and contribute significantly to global riverine discharge. Examining the momentum balance of river flow in opposition to wave-driven forcing from the ocean is necessary to understand how waves influence the travel and mixing of river water. One way to measure this interaction is using instrumental drifting buoys that follow the path of the river water and take temporal measurements of water properties. These leave gaps in our knowledge, as such buoys do not provide a description of the entire system, only specific points. To fill in these gaps, Unmanned Aerial Vehicle (UAV) footage was used to understand broader wave-current interactions at the Quinault River mouth, a small river that feeds directly into the Pacific Ocean. The town of Taholah, WA, is on its banks, and faces challenges due to wave-driven flooding. The size of the surf zone, the nearshore region where waves break at high frequency, was mapped with UAV footage, and related back to local environmental conditions, such as tidal phase. At low water, the momentum from the river is maximized, and so is the cross-shore extent of the surf zone. This decreases salinity around the river mouth, as freshwater is trapped by the surf zone. At high tide, these conditions are reversed, and fresh water streams can be detected past the surf zone, suggesting the river water has escaped from this region of high turbulence. The conditions under which these escapes occur are to be understood by combining analyses of UAV footage with drifter and tidal data.

New techniques in genome mapping have revealed a high degree of 3D spatial organization in the nucleus. Long-range loops connect enhancers to their gene targets to regulate expression. In order to assess the mechanisms and functions behind 3D spatial organization of the nucleus we need a system that allows us to engineer DNA loops. We use programmable CRISPR-Cas DNA binding domains to target specific sites in the genome. The CRISPR-Cas complex is tethered to a targeting domain (TD) that can dimerize with another TD at a distant DNA locus. To promote interactions between TDs that are bound to DNA, we have designed an allosteric switch that assembles the TD only when the CRISPR-Cas complex has engaged its DNA target. To validate that our switch proteins can act as a DNA sensor we have developed a simple reporter assay; upon successful switch protein activation on DNA a transcription factor is recruited to drive expression of a fluorescent protein. Our results indicate that the protein switches activate when they are recruited to DNA, effectively acting as a sensor for DNA binding. Future steps include optimizing our reporter assay design and modifying the design for DNA looping.

Synthetic CRISPR–Cas transcription factors enable the construction of complex gene expression programs, and chemically–inducible systems allow for precise, rheostatic-like control over the transcriptional dynamics. We have constructed a bio-orthogonal, chemically–inducible synthetic CRISPR regulatory system to activate and repress gene expression in yeast. By fusing chemically inducible transcriptional regulators to specific RNA binding proteins, we have expanded the tunability of this system of constructs. The RNA binding proteins are fused to half of one chemically-inducible system while the other half is fused to an effector. Upon addition of drug, the two halves come together to form the complete chemically-inducible system and either activate or repress the target gene. We use reporter gene assays to probe the dose-dependence, time-dependence, and reversibility of the systems. The use of multiple, orthogonal chemically-inducible systems and unique guide RNAs allows for more sophisticated, multi-gene programs that still maintain precise control of gene expression dynamics independently at different sites.

Precise spatiotemporal control over biochemical cue presentation is necessary to mimic the complex, heterogenous environments found in biological systems. Achieving this level of control within engineered microenvironments would allow for the manipulation of cell growth and differentiation, which could be utilized in tissue engineering and drug delivery. To this end, we developed a method that utilizes fusion proteins made from a novel PhotoCleavable protein linker (PhoCl) and a protein of interest (POI). This method allows for spatiotemporal control of POI release from hydrogels in response to cytocompatible violet light (λ = 405). This system is flexible, as PhoCl can be conjugated to many different POIs, including fluorescent proteins, enzymes, and growth factors, and was found to not affect protein function. Additionally, PhoCl undergoes a green-to-red transition after photocleavage, allowing for real-time tracking and quantification of POI release. As PhoCl cleaves in response to visible light, which is less damaging to cell function and has a greater tissue penetration depth than the traditionally used UV light, PhoCl fusion proteins hold promise for use in vivo. To demonstrate the feasibility of this system, PhoCl fusion proteins were formed with several fluorescent proteins (e.g., mRuby, sfGFP, mCerulean). Conjugating these fusion proteins into gels and exposing them to patterned light produced spatiotemporal localized release of proteins with micron scale resolution, which was demonstrated through fluorescent imaging of the photopatterned gels. To support the potential in vivo applications of this system, PhoCl was also used in mammalian cell studies with epidermal growth factor (EGF). These studies showed the expected increased cell growth in response to photomediated EGF release. This illustrates the potential versatility of the PhoCl system in biological applications, thus supporting the relevance of this novel system to tissue engineering and drug delivery methods.

Many environmental factors can influence foraging strategies of predators, such as availability of prey sources. Brown bears feed on many species of animals and plants but Pacific salmon are especially important to their diet. For example, brown bears in the Lake Aleknagik, Alaska ecosystem forage on sockeye salmon as well as other food items. Direct observations and motion-activated cameras have documented bears foraging on salmon but do not reveal variation among individual bears. This study used the distinctive carbon and nitrogen isotope signatures in salmon as a way to assess brown bear diet by processing samples of bear fur collected during the salmon spawning season. As fur sample collection is noninvasive, it provided the opportunity to “resample” bears (individually identified by DNA analysis) multiple times within a season and over the course of multiple seasons. This study demonstrated how various factors, including salmon availability, gender, and location, influence the extent of bear consumption of salmon over time. Understanding the association between brown bear diet and these factors can provide better insight into the importance of both sockeye salmon and alternative food sources to brown bears.

Acoustic signals are essential for communication, advertisement, and reproduction in a variety of organisms. However, their successful transmission is limited by the environment in which they are produced. My research investigates the acoustic adaptation hypothesis, which proposes that to maximize transmission efficiency, animals evolve vocalizations with characteristics that minimize degradation and attenuation (loss of volume) in their native habitat. This hypothesis predicts that birds of open habitats will exhibit vocalizations with higher frequencies and larger frequency ranges than birds of forest understory habitats, because fewer obstructions and more low-frequency ambient noise in open areas favor successful transmission of higher-frequency signals. I tested this prediction by recording and analyzing the vocalizations of 63 bird species living in open and forested habitats around Monteverde, Costa Rica. I found that on average, bird species of open habitats vocalized at significantly higher and broader ranges of frequencies than birds of forested habitats, suggesting that vocalization transmission efficiency helps shape avian communities and their response to habitat transformations.

My research topic is on Black student-athletes’ classroom experience at predominantly White institutions. As a Black student-athlete myself, I have been in classes where not only am I the only Black student, but the only Black student-athlete. The research shows that Black students are primarily affected by their perceived ability to succeed in college by the lack of Black representation in amongst their peers and professors, in the classroom. In my thesis, I build upon aspects of UCLA scholar, Tyrone Howard’s view of the critical race theory. In particular, I explore the idea that rather than race being biologically grounded and natural, it is socially constructed and functions as a means to maintain the interests of the White population. My thesis argues that Predominantly White Institutions set the “lay of the land” in terms of what is socially acceptable and deemed okay, and which often excludes Black student-athletes. The methods I use are surveys, individual interviews, and a focus group,  with an equal number of of Black men and women study participants. This qualitative data will show that Black student-athletes’ experience in the classroom at predominantly White institutions is directly related to whether they grew up being around White individuals.

My proposed research examines how sexual racism is experienced by LGBTQ+ community members in the greater Seattle Area who use Tinder and Grindr and other mobile dating apps. Sexual racism can be defined as a specific form of racial prejudice enacted in the context of sex or romance. My primary research investigates a series of in-person interviews that qualitatively analyze and articulate the various experiences of Black individuals, as well as focus groups to help to understand different and diverse manifestations of sexual racism. I use information/narratives from the in-person, and one-on-one interviews to analyze the experiences and compile them into a data set that can be closely looked at for trends and overlapping experiences. My research analyzing the effects of the experience of sexual racism as shown through mobile dating apps helps readers understand one form of inequity in our modern digital society that often goes unspoken. In addition, my research helps to identify how microaggressions work by the microagressor’s dismissing their racialized/sexualized comments as simply an issue of personal preference. While my primary research focuses on sexual racism in local communities, my secondary research draws on literatures that examine sexual racism both nationally and internationally. By working closely with a variety of people in the local community as well as drawing on research from other scholars focusing on the ideas of white privilege, constructed racism, and intersectionality, this research helps me speak up for Black LGBTQ+ individuals who are often marginalized by sexual racism.

Not only a form of self expression, fashion is one of many markers used by society to assign class, race, gender and sexuality. These assignments are made based on a set of norms which dictate which people are, or are not, privileged. Because of its power to assign privileged traits to an individual, it is also able to create a certain norm for what certain identities are meant to look like. In queer spaces, these norms are often thought to be challenged. This study engages with queer and feminist theories to analyze the ways queer individuals interact with the world of fashion. It argues that fashion should be viewed not only as a way through which individuals show self-expression, and explore identity, but also a form of powerful discourse. In order to do this, I have conducted 15 filmed interviews of queer individuals int the city of Seattle. These interviews seek to provide a platform through which participants can express the complexities of identity formation within a liberal, capitalist system as it relates to fashion. Interviews are collaborative and semi-structured, allowing for participants to share what they find important to their person and communities. From these interviews, this research engages with how the intersections of queer identities with race, class, gender, and sexualities work to form identities through fashion. This research and knowledge is then produced in the form of a thesis paper as well as a video. I have chosen to represent this research in a video format as there is something inherently visual about engaging with identity formation and fashion. This research and its methods are important in exploring and displaying the ways complex and multifaceted intersectional identities interact with systems of power through expression and fashion.

Within the past decade, scholarly and media attention regarding the “homelessness crisis” across the country has increased. However, recent developments in the field have problematized much of the previous research done on homeless identity, due to the fact that “homelessness” has been treated as an unambiguous defining characteristic of the individual. Past research relied on the assumption that these individuals saw themselves as homeless upon entering a state wherein they were without stable housing. Contemporary research seeks to revisit the conceptualizations of homeless identity, and this project will investigate how individuals without shelter, or at risk of being without shelter, come to define their situation and identify themselves -- as “homeless” or otherwise -- in relation to that status. This study focuses primarily on homeless identity as self-acquired, rather than ascribed, by researching an understudied group: homeless young adults. Studying identity within the dynamic frame of emerging adulthood provides a suitable environment for understanding identity development and adoption. This project utilizes ethnographic interview techniques conducted with individuals aged 18-25 with a range of time spent homeless. Analysis of these interviews seeks to examine key mechanisms in negotiation between socially-ascribed identity and self-acquired identity among homeless individuals, and to shed light on the mental reasoning that informs such a process. By determining how and why people come to see themselves as homeless, this research project will inform modes of early-intervention social service outreach while simultaneously complicating traditional lenses of viewing and researching homelessness.

Individuals with ambivalent and avoidant adult attachment styles are more likely to use negative coping strategies such as denial and disengagement, while individuals with a secure adult attachment style are more likely to use positive coping strategies such as reappraisal and support seeking. Certain negative coping strategies are linked with mental health problems such as depression and anxiety. Most research regarding the relationship between coping strategies and adult attachment style has been done on undergraduates and veterans. No research to date has examined gender as a moderator of the relationship between adult attachment style and coping strategies. However, research suggests that both coping strategies and adult attachment styles vary by gender. In the present study, a series of multivariate regression analyses were conducted to determine whether gender moderated the relationship between close, and anxious adult attachment styles and emotional support seeking, and substance abuse coping mechanisms. Participants (N=385) completed self-report measures of coping strategies and adult attachment styles online. This project may reveal that gender changes the relationship between adult attachment style and coping strategies. This information may help inform psychological interventions for individuals with maladaptive coping strategies and improve our ability to predict who might engage in maladaptive coping strategies.

This project deals with human robot-network collaboration for synchronization to desired reference velocities. A human interacts with the network of mobile robots by sending virtual source inputs to the leading robot. The information propagates through the network from each robot sensing its nearest neighbor. This research proposes a visual interface design to develop a real time, wireless communication channel between a human operator and the robot-network. The model developed introduces real time feedback from the human operator via a graphical interface of the relative positions of each robot in the network. The human operator’s ability to move the network cohesively with desired velocity trajectories require rapid information transfer, which is achieved using a delayed self-reinforcement (DSR) technique. We expect the human operator’s ability to move the network cohesively to improve with DSR hence enabling easier operation for the operator. The human-swarm interface designed has applications for semi-autonomous networks such as vehicle platoons. We can improve modern freight transportation safety and efficiency with a human remotely operating a robot-network of trucks.

The ability to eat our meals how and when we want is often taken for granted, but is not a reality for some with limited upper body mobility. Current haptic sensory inputs for autonomous robotic feeding systems are inconvenient and expensive. We propose using GelSight, a fingertip tactile sensor capable of providing rich haptic feedback. Built with silicone and 3D printed parts, GelSight uses a camera to track a grid of dots embedded in the silicone and estimate forces. GelSight is accurate and inexpensive to manufacture and overcomes many of the limitations of currently available and previously tested options. Based on laboratory tests and feedback from potential users we continue to improve our hardware and software, seeking to generalize our solution to any food.

Following the events of the 2016 United States Presidential election, evidence emerged of a Russian-led effort to influence the American people via social media. Through a Kremlin-backed organization known as the Internet Research Agency (IRA), computational propaganda was conducted against the American people on a variety of social media platforms including Facebook, Instagram, YouTube, and Twitter. As part of the ongoing Mueller Investigation and in the name of political transparency, Twitter released a data archive of Tweets and user information for bot and troll accounts linked to the IRA. Prior research completed by data scientists at the University of Washington has revealed that IRA accounts infiltrated the Black Lives Matter discourse community on Twitter. Building off of this work and using the publicly available Twitter dataset, I have analyzed the messaging tactics used by the IRA over time in relation to the Black Lives Matter discourse community on Twitter. I will randomly sample Tweets relating to Black Lives Matter, police brutality, and other related topics beginning in 2009 and ending in 2018, which is when the dataset ends. I use RStudio, Tableau, and other data analytic systems to identify trends, patterns, and messaging themes used by the IRA while they were infiltrating this online discourse community. As an area studies scholar, I provide a more comprehensive understanding of Russian tactics in addition to the data analysis. By examining the methods used by foreign agents when impersonating Americans on social media, I expand the knowledge base about this online effort and highlight themes or trends that could be used by similar groups in the future.

Memes have emerged in the last decade as tools for political commentary, and in some cases, a force for political mobilization. The purpose of this research is to add empirical and methodological data to the emerging field of memetic study by comparing and contrasting two case studies: (1) Britain leaving the European Union (i.e., Brexit) and, (2) the recent 2018-2019 US government shutdown. I collected memes from the social media blogging platform Tumblr from January to early April 2019. I then analyzed the stance and tone conveyed through the template, text, and visuals of the memes to yield insight into how memes impact internet communities that spread them. More importantly, I examine how the internet environment surrounding memes influence them. I expect the analysis of the data to show that memes have responded similarly in both case studies but their dissemination networks and spreading patterns are different. The implications of this study concern how people use online forums to react to perceived threats towards democratic institutions and the democratic process. The research also provides insight to how we consume and produce objects on the internet and how we might act as citizens as the borders separating the online-offline world erodes.

After the establishment of a new democratic government following the US invasion in 2001, the Taliban has provided a parallel court system across Afghanistan. Rebel forms of justice may appear highly coercive, but prove particularly appealing to civilians if they are quicker, more straightforward, easier to access, or more in line with their preferences than formal state courts. Under what conditions are citizens more likely to support the legal authority of the formal government’s judicial systems compared to rebel groups’ alternative forms of law? In this research, I expand the framework of competitive governance by focusing on the decision of individuals to support various legal institutions based on views of government legitimacy founded in the evaluation of public service provision. I hypothesize that as individuals view the government as more legitimate, they demonstrate support for the formal courts, and as they view the government as illegitimate, they are less likely to support the formal judicial system. I address this question by analyzing two data sources. First, I have identified active Taliban courts by district from 2011-13. Second, I have access to the ANQAR survey data, an extensive nationwide survey addressing perceptions of government legitimacy and rule of law. Preliminary findings suggest a zero-sum dynamic between the institutions - that successful rebel governance may not only increase compliance with the rebels, but may actually decrease civilian compliance with state institutions. The policy implications of this research are twofold. First, this informs formal governments that building a judicial system is not just a function of strength and access, but rather that civilians are assessing the government’s service capacity as a whole. Secondly, understanding civilian behavior and preferences will assist nascent democracies in determining how it is most efficient to spend their limited resources to increase the support of the civilians.

With more than a million arrivals in Europe in 2015, the mass migration has impacted the continent politically, economically, and socially. According to Europol, a law enforcement agency, in 2016 more than 90% of migrants going to the European Union have experienced some kind of smuggling during their journey. Many articles aggregate human smuggling with human trafficking. However, there is a lack of empirical examination and of different types of smuggling. In this study, I focus on migrant smuggling. Nevertheless, human smuggling is often seen as a crime that is organized, where a new “service” gets added to their principle activity (drug smuggling, money laundering…), as stated by Finckenauer, and performed by people who have never been involved in transnational criminal organizations. I assess this puzzle: How does human smuggling differ from human trafficking and organized crime, by examining primary and secondary sources such as scholarly literature and local newspapers? I argue that human smuggling has some traits of organized crime; however, considering entirely as it, limits the study of smuggling, as a business activity, and limits the prevention of illegal immigration. Human smuggling has traits of organized crime: the structure, the persistence, and violence have shown that these elements are not voluntarily present in the activity of smuggling. Nonetheless, the main purpose of this activity is treated as a business: where demand and supply meet and where price fluctuates depending on these factors. Migrant smuggling needs to be seen as a mutually consenting act between a migrant and a smuggler: the migrant is looking to flee because of instability in his/her country for the hope of a better life while the smuggler is considering smuggling as a business. This project aims to give a nuanced understanding of human smuggling to better intervene at the source of this mass migration.

Bitnation is a non-governmental organization which uses blockchain smart contract—an algorithm-based digital contract through a decentralized database—to provide Jurisdiction as a Service (JaaS) to its participants, or Citizens. This means that Bitnation Citizens enter contracts such as birth certificates, marriages, wills, company registrations, and passport through Bitnation’s own virtual scope of jurisdiction. Bitnation’s implementation of decentralized self-governance through blockchain and its promise to “outcompete” the nation-state model has attracted over 10,000 Citizens. In this research, I ask why such a big wave of people collectively decides to relegate nation-state citizenship—an institution which has been established and legitimized for centuries—and incline towards a stateless identity system. What could be the roles of the modern citizen perception of their rights and their access to emerging technologies, for example blockchain smart contract, in this deviation? My hypothesis is that one’s choice to opt in for Bitnation’s virtual jurisdiction, despite the standing establishment of the nation-states, is a product of modern identity politics and technological development. The increasing political and social interconnectedness worldwide have intensified importance and manifestation of identities. In addition, new technologies, particularly blockchain and smart contract, ensure anonymity in communications and contracting practices among Citizens worldwide, and attract those whose identities placed them in socio-economic and political disadvantages in their societies. To test this hypothesis, I conduct literature review on topics of the nation-state model, stateless virtual citizenship, and emerging technologies. Further, I conduct ethnography, surveys, and interviews on Bitnation’s online platform to find the correlation between the Citizen identities and interests in Bitnation and how the platform satisfies them. Through his study I hope to shine a light on the changing expectations in the state-citizen relationship as a contract and the role of technology in the evolution of governance model from centralized to decentralized.

High purity germanium (HPGe) detectors are an important technology in several leading experimental searches for dark matter and neutrinoless double beta decay. Understanding the interaction of various types of radiation on the different surfaces of HPGe detectors is essential to developing methods to reject unwanted signals from radioactive background sources. I have taken a leading role in the construction and use of the Collimated Alphas, Gammas, and Electrons (CAGE) test stand at the University of Washington, whose goal is to evaluate the response of an HPGe detector to different types of radiation on its various surfaces. CAGE is a vacuum cryostat with an internal system of motors that move a radiation source while keeping the detector active. It requires the operation of a liquid nitrogen cryostat, vacuum pump, temperature sensors, and various radioactive sources, all of which must be integrated into a single data acquisition (DAQ) system. We are currently constructing this system, fabricating and installing parts, and are planning to take initial data with the HPGe detector in the summer. In this talk I will present the current status of the CAGE detector, as well as preliminary data from radiation signals in the detector.

Our research group performs one of the highest-precision tests of Einstein’s equivalence principle, perhaps the most fundamental property of gravitation, using a sensitive rotating torsion balance. Among the leading experimental challenges are temporal and spatial temperature variation. Notably, horizontal temperature gradients across the apparatus, if not properly characterized, can emulate an equivalence-principle violating signal. We have implemented thermal shielding and run tests to measure the thermal effects on our measurement. Past tests have shown a need for both absolute and differential temperature sensors with higher sensitivity. Hence, my research project focuses on investigating the effect of temperature gradient on our experiments by constructing a thermal monitoring system. I have designed, laid out, constructed, and tested sensitive bridge thermistor circuits that can function as both absolute and differential temperature sensors. Current tests of our prototypes have shown that temperature sensitivities reaching 10 micro-Kelvin in one second (10^-5K/Hz^0.5). We are scaling-up these sensors and plan to deploy them in this academic year. Successful completion of this project will yield improved understanding of the temperature gradients within our experimental apparatus, allowing us to test the equivalence principle with yet higher precision.

Here at the University of Washington we are characterizing one ton of NaI[Tl] crystal scintillator detectors for use in the COHERENT project. NaI[Tl] scintillating crystals detectors work by producing photons from the kinetic energy of charged particles passing through the scintillating material. COHERENT aims to detect coherent elastic neutrino-nucleus scattering, a novel interaction between neutrinos and matter that was first observed less than two years ago. It employs a large scale of scintillator detectors in order to record these events at an appreciable scale. Our characterization campaign allows us to group crystals with similar outputs by voltage which will determine the setup of our detectors once at ORNL. During this characterization, the crystals exhibited behaviors that correlated with the ambient temperature of the lab. The temperature dependence was first noticed during voltage gain characterization tests taken at different times of the day in the uncontrolled temperature environment of our lab. We expect the gain of our crystals to fit to a curve function, which breaks down if data is taken at different times of the day. The goal of this study is to understand the impact of temperature dependencies on our characterization campaign, and in particular to derive a relationship between voltage gain and temperature. I will present the data gathered toward this goal, and also our larger body of data on the relationship between light yield, voltage gain, peak resolution, and waveform rise time, as well as the techniques used to re-characterize previous crystals gain curve based on the derived relationship from this study.

At the UW tandem particle accelerator located at the Center for Nuclear Physics and Astrophysics (CENPA), a program is searching for new physics though precision measurements of electron spectra from radioactive decays. The most sensitive searches require very pure Neon-19, which has a halflife of about 17 seconds. Accordingly, we have designed and constructed a system that produces Neon-19. We first bombarded Sulphur Hexafluoride (SF₆) with protons from the accelerator. We then metered the SF₆ and Neon-19 mix out into a cryogenic trap where it freezes only the SF₆. After the trap, we transported the remaining Neon-19 with a turbomolecular pump into the detector. Once the trap had filled with solid SF₆, it was valved off from the target, then heated, at which time the frozen SF₆ sublimated into to a storage tank before refilling the target. By using a pair of traps, the experiment can be run continuously; one trap thaws while the other freezes. Through models based on nuclear cross-section data from previous experiments, the system will produce on the order of 10¹⁰ Neon-19 nuclei per second. Our system will contribute to an effort to better describe the interactions of particles and refine the Standard Model of particle physics.

Mathematical knots are non-intersecting closed loops which may be tangled; links are knots that are possibly intertwined. These 3-dimensional paths often resist description, so mathematicians choose nice ways to describe them. One such way is to project them onto a plane. Even more, it is interesting to build knots in discrete ways such as placing them on tiles in a plane. In this poster we are considering hexagonal mosaic knots, knots that are projected on a plane tiled by the honeycomb hexagonal tessellation. In this way, knots can be built from a small collection of hexagonal tiles with loops. We create an interactive tool which presents hexagonal tile types, a grid on which to lay them, and options for analysis. The researcher uses a point-and-click tool to lay down a mosaic grid, and in so doing, creates an underlying data structure representing the segments contained in the mosaic. When requested, the software traverses this data structure like a linked list. In this manner, one may determine if the data structure represents a suitably connected hexagonal mosaic knot or if it contains dead ends or stray segments; that is, determine if a data structure represents a knot/link or not. This process helpfully assigns segments to their respective knots, distinguishing not only ‘over’ and ‘under’ but also ‘self’ and ‘other’. We hope to continue exploring automatic generation of information about knots from their tiled representations. Once more developed, we hope to be able to answer more questions about the knot or link represented by the data structure. We also hope to continue exploring the use of rapid, flexible feedback from prototypes in aiding exploratory research.

Orbital fractures are one of the most common facial fractures and often result in functional deficits if not treated appropriately. No prior reports have assessed dynamic visual acuity (DVA) in these patients, which is critical in visually tracking objects during head movement. Our research seeks to determine the effect of orbital fractures on DVA and assess whether DVA will change over time in those who undergo surgical reconstruction of the orbit. We hypothesize that DVA is adversely affected in orbital fracture patients and improves after surgical reconstruction. We designed a prospective pilot study at a Level I trauma center. Adult patients who presented with an orbital fracture between November 2017-January 2019 without prior ocular history were eligible. All enrolled subjects underwent static visual acuity (SVA) and DVA testing twice: once within one month post-injury before surgery, and another at least ten days following surgery. SVA was assessed using a mobile Snellen eye chart. DVA was measured by having the subject rotate their head at a standard frequency while again reading a Snellen chart. DVA is defined as abnormal if acuity falls more than two lines on the Snellen chart compared to SVA. Eleven patients have been enrolled and tested. Four(36%) patients exhibited abnormal DVA prior to surgery, compared to two(18%) after surgery. For all patients, the mean change in visual acuity (DVA logMAR minus SVA logMAR per subject) before surgery was 0.17 (SD=0.09). Following surgery, the mean difference in visual acuity across all patients was 0.07 logMAR (SD=0.07). Our data shows that, surprisingly, the majority of orbital fractures patients tested did not have abnormal DVA. In patients that did demonstrate abnormal DVA, half improved after surgery. The mean difference in visual acuity of all patients also improved after surgery. A larger study is needed to determine the prevalence of abnormal DVA in this patient population.

Modifiable psychosocial and behavioral factors place youth at risk for severe and persistent pain after major surgery. Opportunity exists prior to surgery to intervene with youth and families to prepare them for surgery including helping to manage distressing cognitions and teaching non-pharmacologic coping strategies, to reduce acute pain and prevent chronic post-surgical pain. This study aims to develop and evaluate a cognitive behavioral program in reducing acute and chronic pain in youth undergoing major surgery. In the pilot study, fourteen children ages 10-18 years (M= 14.5), 71.4% female, scheduled for major spine surgery, and their parents, were enrolled into the study. Enrollment rates were excellent with 88% (14 of 16) of families approached agreeing to participate in the study, with a range of 4 to 16 weeks (M = 6.3, SD = 1.3) until surgery at the time of enrollment. Teens and their parents completed three pre- surgical modules containing surgical preparation and relaxation tips during the month preceding surgery. Participants completed three post-surgical modules during the 6 weeks following surgery containing tips for managing pain and returning back to school and activities. Each module was accessed online and followed by a coaching phone call with a trained study team member to ensure comprehension of module content. All of the participants completed all pre-surgery and post-surgery modules within the prescribed time frame. Parents and teens completed assessments at four timepoints: 1 month pre-surgery, 1 week pre-surgery, 6 weeks after surgery, 3 months after surgery. The majority of parents and children (79%) completed the study phone calls within the prescribed time period. Preliminary results indicate excellent program feasibility. Further study must be done on patient outcomes to assess efficacy of the program in a larger population.

This presentation seeks to summarize a solution to helping the visually-impaired navigate new areas. While previous solutions have been relatively successful, many lacked two key features that we hope our solution addresses: being affordable and allowing customization towards those with compounding disabilities. Our solution consists of two main parts: (1) a user-interface created for Fusion 360, a popular 3D-modeling application, that is built upon an existing framework detailed in Hofmann (2018) called PARTs (Parameterized Abstractions of Reusable Things), and (2) an optimization algorithm to generate maps that are tailored for its users. Through PARTs, we developed different variations of modular pieces of map (e.g., roads, buildings, and sidewalks), which increases ease of customization. After the user specifies personal information and preferences through the PARTs UI—such as the width of their finger, their physical limitations, their understanding of braille, and their desired map features—the optimization algorithm will select the best combination of features from the PARTs database for that specific user. At the end of the process, users have a model of a tactile map in Fusion 360 which can be printed out with commercially-available 3D-printers. With 3D-printers becoming more affordable, this solution is significantly less cost prohibitive than other means of generating tactile maps, which required an initial investment upwards of a thousand dollars. Through user studies, we also test how blind users interpret these maps, which helps us guide design improvements in the future. In this presentation, we discuss the efficacy of our solution by comparing it to previous works and detail our plans to improve the system by making the PARTs user-interface more accessible and incorporating user feedback about the map itself. 

The Blue River of south-central Oklahoma is a spring-fed stream that drains much of the eastern Arbuckle-Simpson Aquifer, and is one of only two free-flowing rivers in Oklahoma with little to no anthropogenic influences on the flow of this river. Not much is known about the structure and composition of fish communities in the upper reaches of the Blue River. In collaboration with The Nature Conservancy, assessments of fish in riffle habitats of the Blue River were conducted adjacent to the Oka’ Yanahli Nature Conservancy Preserve in the summer of 2018. Fish samples collected were processed, individual fish were identified to species based on morphology, and biological metrics were calculated. A total of eighteen species of fish were collected from the riffle stream habitats in the upper reaches of the Blue River. The relative abundance of each species was calculated, and the Central Stoneroller (Campostoma anomaum) was highest in abundance, the Orangebelly Darter ranked second in abundance, and the Orangethroat Darter ranked third. The Orangethroat and Orangebelly darter were more likely to be found in areas in the riffles where river bed particles were in the small to large cobble size range (60 to100millimeters). The two darter species did not show any difference in preference for current velocity in the riffle habitats. The two darter species co-occurred in riffle microhabitats as indicated by the positive correlation between the numbers of each darter species collected across all seine hauls. Looking at biota in this river could give insight into how different habitats function in a free-flowing river, and more specifically, what is could potentially happen in riffle habitats of the Blue River because these areas will be the first stream habitats affected if flows are reduced from anthropogenic withdrawals of water from the Arbuckle-Simpson Aquifer.

Climate change will have significant impacts on Pacific Northwest hydrology. Rising temperatures and shifts in precipitation will lead to changes in snowpack, runoff, and streamflow timing, impacts that will have implications for water and environmental resource management. The Pacific Northwest’s Green River Basin is a valuable water supply and provides habitat to several cold-water aquatic species including the threatened Puget Sound Chinook salmon, but also has a major flood risk. Streamflow in the basin is seasonally regulated for flood prevention and ecosystem health, and changes in the annual hydrologic cycle will have consequences for flood risk and ecosystem habitat. To investigate the implications of climate change on streamflow, snowpack, and stream temperatures in the Green River Basin, climate sensitivity analysis and future climate impacts are simulated using two watershed models with varying spatial and process complexity: 1) the conceptual Snow17/Sacramento Soil Moisture Accounting model (Snow17/Sac) implemented with two elevation zones and 2) the process-oriented Structure for Unifying Multiple Modeling Alternatives (SUMMA) model implemented using twelve USGS HUC-12 subareas. Stream temperature climate sensitivities are modeled using the River Basin Model (RBM) Semi-Lagrangian Stream Temperature model. Future climate change impacts on basin hydrology and stream temperatures are assessed using an ensemble of statistically downscaled climate projections from 34 Global Climate Models (GCMs) run as part of the Intergovernmental Program on Climate Change 5th Assessment Report. The future warming scenarios show moderate changes in streamflow volume, shifts in streamflow timing, and reductions in snowpack, which differ depending on the watershed model. The presentation provides key results and findings from the study, and comments on potential impacts on stream temperature and fish.

Hybrid landscapes are the colonial, regulated plots of land (like reservations), that Native peoples have adapted to ultimately create new senses of Indian self-hood, through their ability to survive and thrive, despite the colonial process that displaces them to those regulated lands. The vanishing Indian narrative is one example of the colonial violence enacted through those regulated spaces as Western institutions and discourses confine Native peoples to notions of the past and primitivity, to ultimately claim that they have vanished in the wake of modernity. And while Western museums have helped perpetuate the vanishing Indian narrative, tribal museums have combated this harmful narrative. Museums, as institutions that present knowledge to the general public, are sites that can present counter-narratives and tribal communities can use these spaces to present proper representations of themselves. One such tribal museum is the site of my research project. The Suquamish Museum is located on the Port Madison Indian Reservation and opened in 1983. This research is interested in how this museum has made, and continues to make, a difference for the Suquamish community and particularly analyzes the Museum’s relationship to the reservation. Over several months I have spent time in the Museum and researched the Museum’s history through its grants, reports, programs, and exhibits. I argue that, as an institution that has continued to adapt to the community’s needs, the Suquamish Museum has facilitated the construction and continued development of the reservation as a hybrid landscape through owned representation as a means of confronting the vanishing Indian narrative, thus perpetuating Native agency and sovereignty. This research is important because looking at the Suquamish tribe as its own entity, with their own representations, addresses the colonial violence that treats all Indigenous peoples as homogenous, unadaptable peoples from the “past,” ultimately highlighting their agency as place-makers.

The purpose of this research article is to answer why Central Americans in the caravans of 2017 and 2018 seek asylum in the United States and not in Mexico. In order to understand this pattern, we will review the 1951 Refugee Convention and the 1984 Cartagena Declaration which provide the legal basis of refugee policy in the region, including commitments to peace, democratization, regional security, economic co-operation and the protection of refugees & asylum seekers in Latin America. However, it is essential to recognize that people do not make decisions based solely on international law. The voices of refugees can be found in news outlets’ interviews because the caravans received a surge of media coverage. Their statements indicate that this choice is a combination of gang/ drug violence, socio-economic opportunities, and family reunification that informs their decision to choose the United States. These motivations are not new. Central Americans have been coming to the U.S. for decades beginning with the civil wars in the region of the mid-20th century and the U.S. military, economic, and political interventions. This history created communities of immigrants that the current refugees are coming to join. Critics of the 2017- 18 caravans of refugees fail to consider the human priorities of familial and community connections created by the long history of migration of Central Americans to the U.S.

Pollution caused by large corporations is the primary reason for environmental degradation and the prison industrial complex is no exception. The purpose of this study is to contextualize the carceral system and its relationship to climate change from a critical ecofeminist perspective. Critical ecofeminism contends that the patriarchal nature of capitalism forces women to generate forms of resistance against essentialist systems--which attributes to their broader understanding of environmental degradation and the oppression of marginalized identities. Using the Fact Sheet Archive on Women in State Legislatures (1997-2016) which reports the percentage of women-identified legislators and governors in the US, this study will explore whether or not the independent effect of mass incarceration emissions decreases when more women are represented in legislative bodies. This work is meant to contribute to growing bodies of knowledge concerning critical environment justice studies, racial capitalism, and other intersectional frameworks.

Tuberculosis (TB) kills more than one million people annually. Bacteria of the Mycobacterium genus, including M. tuberculosis, build a complex cell wall containing mycolic acids. This cell wall is difficult to penetrate, so specialized antibiotics are needed. Even with newly developed drugs, bacteria adapt quickly and exhibit resistance at an alarmingly rapid pace. One adaptation that allows the community to survive is production of biofilms. Formation of biofilm is one of many quorum sensing behaviors known in pathogenic mycobacteria. This additional layer surrounds a microenvironment where bacteria can thrive with a very low concentration of antibiotic. Thus, one alternative method to treat TB is to control biofilm formation. In this research, a set of marine bacterial strains, including several bacteria that exhibited swarming behaviors and several from the same environmental samples that did not, were cultured, extracted, and analyzed by 1H NMR and LC-MS as well as in newly-developed biofilm and growth inhibition assays. Initial results showed one group of bacteria produced an organic compound that induced biofilm production in mycobacteria. This was an unexpected result. One representative strain producing a strong biofilm inducer was grown on large scale (10L) then extracted using progressively less polar eluents on a reversed-phase SPE column. The biofilm-inducing fraction was then separated using flask column chromatography. One major component was analyzed spectroscopically using 1D and 2D NMR techniques along with Mass Spectrometry. This compound could result in a strategy to interfere with biofilm formation in mycobacteria, thus making antibiotics more effective.

The ability of an organism to dissociate environmental cues for either safe or threatening situations is key for survival. Generalized fear is an adaptation in which behavioral responses for threatening stimuli are produced to non-threatening cues. In mice, discriminative or generalized fear responses are modeled using a fear conditioning paradigm of two shock intensities, 0.3 mA or 0.5 mA. Mice trained at 0.3 mA intensities could discriminate between safe and threatening cues, yet mice trained at a 0.5 mA intensities displayed generalized fear behavioral responses. Previously, we had identified that dopaminergic neural activity was critical for the ability to discriminate between cues when shocked at 0.3 mA. Dopamine neurons express Kv7.3 potassium channel subunits, which modulate neural activity. I hypothesized that Kv7.3 subunits on dopamine neurons would be critical to threat discrimination and mice that had undergone mutagenesis of Kv7.3 would show generalized fear discrimination. My approach used transgenic mice expressing Cre-recombinase and viral-mediated gene delivery of cre-inducible CRISPR-Cas9 plasmids targeted for the specific mutagenesis of Kv7.3. Mice underwent a three day paradigm known as fear conditioning. Baseline freezing behavior was assessed by playing two tones, A and B. This was followed by fear conditioning trials where at the end of tone A, mice received a shock of either 0.3 mA or 0.5 mA (CS+) and at the end of tone B, mice received no shock (CS-). On the third day, mice underwent a probe trial to assess final ability to discriminate between threatening and non-threatening cues. These findings could provide insights into the mechanisms underlying neurological disorders and serve as a guide for future pharmacological interventions.

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) have great potentials in biomedical research and can be used extensively in drug screening and heart simulations. To understand the cardiomyocytes, we need to perform functional analysis on these muscle cells. Therefore, we need a simple, controllable, yet biocompatible and high throughput tool to measure the cellular traction force. At the Sniadecki Lab, we are developing a new technique to measure the force generation of hiPSC-CM: dotted traction force microscopy platform. To create the platform, fluorescent proteins were first absorbed to a dotted polydimethylsiloxane (PDMS) negative and stamped onto a polyvinyl alcohol film. The film was then transferred to a soft PDMS substrate and subsequently dissolved using phosphate buffered saline solution while the patterned fluorescent proteins stained the substrate. Since the stiffness of the soft PDMS substrate is known, the force generation of the cardiomyocytes can be calculated in real time by optically tracking the deformation of the fluorescent dots. Currently, we are able to manufacture the platform with high fidelity and uniform alignment with a production time of less than 2 hours. Moreover, the cardiomyocytes can fully spread out to their in vivo state on the substrate which ensures the force measurement is valid and accurate. Potentially, this method is not limited to cardiomyocyte research and can be applied to study the interaction between force generation and cell performance of other cells. We are also exploring the possibility of automated manufacture and integration with 96-well to enable mass production.

Auxins are a class of bioregulatory hormones which impact nearly every aspect of plant growth and development. Indole-3-acetic acid (IAA) and one of its corresponding receptors (TIR1) have been shown to be involved in seed germination, lateral root formation, stem elongation, fruit set and development, along with numerous other developmental processes. In an effort to more effectively study auxin-dependent pathways, Torii et al. developed a synthetic version of the IAA/TIR1 receptor pair which was shown to act independent of the endogenous pair in Arabidopsis. Here, I extrapolate our synthetically engineered auxin-receptor pair into a model system with agricultural and environmental implications (e.g. Solanum lycopersicum- tomato) and aim to test whether we are able to 'hijack' endogenous auxin signaling in tomato to precisely modulate auxin-dependent, spatiotemporal developmental outcomes. These findings could shed some light onto the vastly complex, auxin-dependent developmental process in Solanum lycopersicum and provide a tool to study auxin's specific role in varying developmental processes such as stomatal formation, leaf morphology, temporal flowering and fruit setting.

We introduce Project Sidewalk, a new web-based tool that enables online crowdworkers to remotely label pedestrian-related accessibility problems by virtually walking through city streets in Google Street View. To train, engage, and sustain users, we apply basic game design principles such as interactive onboarding, mission-based tasks, and progress dashboards. In an 18-month deployment study, 797 online users contributed 205,385 labels and audited 2,941 miles of Washington DC streets. We compare behavioral and labeling quality differences between paid crowdworkers and volunteers, investigate the effects of label type, label severity, and majority vote on accuracy, and analyze common labeling errors. To complement these findings, we report on an interview study with three key stakeholder groups (N=14) soliciting reactions to our tool and methods. Our findings demonstrate the potential of virtually auditing urban accessibility and highlight tradeoffs between scalability and quality compared to traditional approaches.

Ischemic preconditioning (IPC) is a robust, neuroprotective phenomenon in which a brief ischemic exposure confers resistance to injury from subsequent prolonged ischemia. Characterizing IPC may provide insight into better treatment options for those at high risk of ischemic stroke. Microglia, the immune cells of the brain, play an important role in the immune response to IPC. Previously, our laboratory found that the type 1 interferon signaling pathway in microglia is important in IPC-mediated neuroprotection. This signaling pathway is dependent upon activation of Toll-like receptor 4 (TLR4) and type 1 interferon receptor (IFNAR1). We hypothesize that in this pathway, damage-induced molecular patterns (DAMPs), which are released by brain tissues under ischemic conditions, activate TLR4 resulting in a signal cascade that activates IFNAR1, leading to phosphorylation of signal transducer and activator of transcription 1 (STAT1). Phosphorylated STAT1 (pSTAT1) then forms a complex with other proteins and induces transcription of multiple interferon-stimulated genes (ISGs). ISG expression alters the microglial phenotype, leading to neuronal and axonal protection against subsequent ischemia-related brain injury. The kinetics of type 1 interferon signaling in microglia are not yet fully understood. We aimed to further characterize this pathway by culturing primary microglia from wild-type mice, exposing them to TLR4 agonists or type 1 interferons directly, and quantifying pSTAT1 levels using flow cytometry at multiple time points. A time course of STAT1 phosphorylation in response to innate immune stimuli will provide a clearer picture of the kinetics of microglial type 1 interferon signaling in the setting of ischemia. These findings will enable us to optimize experimental timing for future experiments involving more complex and physiologic stimuli. Optimization of the kinetics of the pSTAT1 assay will also allow us to investigate how genetic ablation of specific innate immune signaling pathways (like TLR4 or IFNAR1) might modulate the microglial response to ischemia.

Theiler's murine encephalomyelitis virus (TMEV) is a positive-sense RNA Picornavirus used to model epilepsy, poliomyelitis and multiple sclerosis. Previous research has demonstrated a dependence of some Picornaviruses on host glutathione (GSH) in order to produce viable progeny. GSH depletion in host cells has resulted in unstable viral capsids, reducing viral fitness due to a lack of oxidative homeostasis. The objective of this study was to investigate the dependence of TMEV on GSH and determine the consequences of oxidative stress in the host cell due to the absence of GSH. Incubation of TMEV at denaturing temperatures with increasing doses of reduced GSH demonstrated that GSH stabilizes viral particles and 54% viral infectivity was retained with doses as low as 25mM GSH. Using L-Buthionine-sulfoximine (BSO) to deplete GSH in host cells, a 3-fold decrease in viral production was observed when compared with untreated cells. Interestingly, when GSH was restored in BSO treated cells using cell permeable GSH ethyl ester, TMEV viral production was partially restored and viral plaque formation was comparable in yield to an untreated viral infection. Virus production and viability were quantified using plaque assays on host cell monolayers. Next steps include monitoring viral genome production via RT-qPCR and quantifying GSH levels using fluorescence plate assays. RT-qPCR will be further utilized to examine other host stress pathways. This project will use TMEV to look at a host-virus relationship as it relates to an important host antioxidant system interacting with the capsid, assembly, and genome replication of the virus life cycle.

As of now, mRNA vaccines have been deemed as a potent replacement for current vaccine models against infectious diseases for their improvements in B-cell and T-cell immune responses. Usually, when soluble, subunit antigens are delivered, they are scattered and randomly bind to B-cell receptors, often loosely. However, with a nanoparticle carrier for antigens, there would be more effective crosslinking with B-cell surface immunoglobins as there is a higher density of structurally ordered antigen arrays presented by the nanoparticle. As a result, the B-cell creates a stronger immune response. Additionally, the multivalent particles also favors the creation of long-lasting immunity against a given virus. My team and I are currently developing a self-assembling protein platform using dn5A and dn5B protein components as a carrier for an mRNA vaccine against the flu. My project mainly focused on optimizing the co-secretion of the two particles by exploring different models and combinations of both. This is important as the translated cage not only has to be able to self-assemble but also be capable of doing so without producing excess protein in order achieve its purpose. To do so, I investigated 12 different constructs of dn5A and dn5B through transfections and analysis with western blots and electron microscopy. We used the data collected to improve the dn5A/dn5b protein platform utilized alongside flu mRNA vaccines, helping them better achieve potency. Overall, if effective, the new vaccination model can be utilized for other infectious diseases, including HIV and meningococcus.

Information warfare is not a new Russian Federation tactic, or its predecessor state the USSR, but the digital age has allowed for a severe increase in the ease and ability to carry out operations. Information war, an overarching term that includes cyberwar, influencing policy outcomes with ill-gotten information, and propaganda campaigns. Russia’s operations are expanding and increasing in number with Russian state affiliated hackers, troll armies, and bots influencing the globe. In spite of the prevalence of this action, there is a lack of databases that track all Russia’s entire information campaign in its entirety. I am building a dataset using open source methods, including research in English, Russian, and French. The dataset currently contains 78 incidents spanning 30 countries. My initial findings indicate that Russian policymakers have three overarching objectives; (1) re-establishing Russian dominance in the post-communist/Russian sphere of influence, (2) undermining western economic, political, and cultural influence globally, and (3) expanding Russia’s political, economic, and military hegemony to all corners of the globe. I have found that although Russia's overall global strategy may seem somewhat straightforward, how that plays out in each region and country differs. The ways which Russia’s goals are customized on the basis of political landscape, historical background, culture, and religion. Often times, Russian actors will choose a simple disinformation campaign through the local media, but in other circumstances more intensive measures are used by way of hacker groups.

The kinetochore plays a key role in aligning chromosomes during mitosis and helps ensure proper separation of duplicated DNA molecules into daughter cells. Some proteins that associate with the kinetochore regulate attachment to microtubules by destabilizing weak attachments and stabilizing strong attachments. In the model organism Saccharomyces cerevisiae, the Ipl1 kinase and Stu2 protein have similar effects on regulating tension on the kinetochore. Since Ipl1 is a kinase, and Stu2 is phosphorylated, we believe Stu2 function may be regulated by Ipl1. To test if Stu2 function is dependent on phosphorylation by Ipl1, we mutated possible Ipl1 phosphorylation sites and observed its effects on Stu2 function. Four Ipl1 target consensus sites within the Stu2 protein were selected for this study. We used site-directed mutagenesis techniques to alter these potential Ipl1 phosphorylation sites on Stu2 by mutating serine codons to alanine codons. We successfully constructed S40A and S430A/S593A mutations in Stu2 using the megaprimer whole plasmid (MEGAWHOP) cloning technique. We then introduced the mutated version of stu2 into yeast and conducted phenotype tests to determine if inactivating these putative phosphorylation sites affected its function. Our initial results indicated that phosphorylation at sites S430 and S593 may not be required for proper Stu2 function. We suggest that further testing of Ipl1 phosphorylation sites could reveal possible mutations that lead to malfunction of Stu2 that then affect the kinetochores ability to release improper attachments to microtubules. This would give insight into how signaling between kinetochore proteins can help to ensure proper chromosome segregation and avoid aneuploidy.

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne New World alphavirus, causing encephalitic disease in mammals. Increased circulation of VEEV in the Americas underlines the need to characterize alphavirus replication and develop countermeasures. The VEEV genome is a single-stranded RNA of positive polarity (+ssRNA). MicroRNA (miRNA) are small, cell-specific non-coding RNAs that aid in post-transcriptional regulation of gene expression. Previous studies have demonstrated that host miRNA can affect viral replication and pathogenesis by directly binding to the viral genome. Recent work on host miRNA in related alphavirus Eastern equine encephalitis virus (EEEV) found miRNA binding sites in the EEEV 3’ non-translated region (NTR). Binding of the host miRNA enhanced pathogenesis. Prediction software miRDB identified potential miRNA binding sites in the 3’ end of VEEV genome, including one for miRNA hsa-miR-1268. In this study, the impact of miRNA interaction with its putative binding site on VEEV pathogenesis was investigated. We performed site-directed mutagenesis of VEEV strain TC-83 to engineer point mutations at the hsa-miR-1268 binding site in the 3’ end. We are currently testing the impact of these mutations on viral replication by analyzing growth kinetics of wild-type and mutant viruses in cell culture. We anticipate that a mutation disrupting the interaction between hsa-miR-1268 and the predictive binding site on the +ssRNA genome will result in the decreased ability to replicate the viral genome and subsequently infect the host. Understanding the impact of the interaction may lead to novel mechanisms to prevent RNA virus replication.

Retinal diseases tend to effect specific neuron subtypes, ranging from age-related macular degeneration, which is caused by the deterioration of photoreceptors near the central portion of the retina (macula), to glaucoma, which identifies abnormally high intraocular pressure resulting in the death of ganglion cells. Unfortunately, adult mammals are not able to regenerate retinal neurons. Conversely, zebrafish, frogs, and various amphibians are able to completely regenerate their retinal neurons in many different animal models of damage, and restore retinal structure and visual function. The source of regeneration stems from the resident Müller glia cells, which normally provide neuronal support and span all three retinal layers. A critical gene for the initiation of transforming Müller glia into neurons was found to be Ascl1. This led our lab to hypothesize that the introduction and upregulation of Ascl1 in mammalian Müller glia might stimulate them to become retinal neurons after damage, as occurs in these other regenerating species. Indeed, after introducing Ascl1 into the Müller glia of mice, we found newly regenerated retinal interneurons (bipolar cells) that successfully integrated into the retinal circuitry and functionally responded to light stimulus. In addition to Ascl1, we have identified another transcription factor, that when introduced in combination with Ascl1, stimulates the generation of a different retinal interneuron (amacrine cells). Ectopic expression of a proneural transcription factor to stimulate retinal regeneration provides a potential therapeutic intervention for treating blinding diseases, that even now, have few modest treatment options. In contrast to prosthetic devices and stem cell-based therapies, neuronal regeneration via viral injections is advantageous in regards to host tolerance and reducing the invasiveness of a given treatment, since the patient’s own Müller glia are the source cell of the new neurons; and therefore, immunosuppression would likely not be required.

In recent years, researchers have dedicated much effort to overcoming the ~250 nm spatial resolution limit of light in order to reveal biological details that have been obscured by diffraction. A new form of super-resolution microscopy called expansion microscopy (ExM) relies on physically expanding a fixed specimen in a swellable hydrogel polymer and offers a simple, inexpensive approach to achieving ~70 nm resolution with conventional confocal microscopy. A critical and understudied step in this process is the homogenization of the embedded sample by proteolytic enzymes, enabling artifact-free expansion. However, in large and complex samples like Drosophila, enzymatic digestion is time-consuming and sensitive to experimental parameters such as fixation, hydrogel composition, and tissue type. To overcome the limitations of enzymatic digestion, I have explored parameter space for rapid peptide cleavage using air-tight stainless-steel vessels to achieve high temperatures and pressures not typically accessible in the lab. Additionally, a small-molecule digestion agent, dimethoxyiodobenzene, was tested in order to provide site-specific peptide cleavage and enhance tissue homogenization. The modified digestion process was first validated using standard immunofluorescent microtubules in cell culture. Next, Drosophila tissue was treated using thermal digestion to confirm the applicability of this technique in robust, difficult-to-expand tissues. This improved ExM protocol holds the potential to increase sample throughput, reduce expansion-related sample distortions, and extend ExM to be applicable to a wide range of previously incompatible tissues types, enabling pathologists to better analyze and assess diseases in human tissues.

Nearly 22 million HIV-positive people are receiving antiretroviral therapy in order to suppress their HIV infections. They need consistent viral load monitoring to track viral suppression and detect the possibility of viral rebound. Nucleic acid amplification tests (NAATs) are used to measure the viral load in a patient's blood. Traditional, laboratory-based NAATs require complex robotic systems to automate HIV RNA purification, amplification, and detection from blood. Since the majority of those living with HIV are located in low and middle income countries, there is a need for rapid viral load monitoring at the point of care (POC). We aim to provide accessible HIV viral load testing through low-cost, integrated POC NAAT devices. These proof-of-concept devices operate as a two-step assay to extract and detect nucliec acids in blood. An electrophoretic separation technique called isotachophoresis (ITP) separates HIV RNA from other components in a blood sample. An isothermal nucleic acid amplification assay amplifies the purified, concentrated nucleic acids in order to detect and quantify their presence. We present our development of a novel ITP system to remove potent contaminants from Proteinase K (PK) digested serum and extract highly pure nucleic acids automatically. Through computational modelling, a dual trailing electrolyte (TE) buffer system was designed to exploit the isoelectric point of PK for its removal, while simultaneously concentrating nucleic acids away from serum components. We demonstrate system control through comparison of experimental observations to model predictions by performing dual-TE ITP on pH paper. We also show that the dual-TE system improves upon previous limits of detection for DNA extraction and detection from complex samples. Our system processes 40 microliters of blood in 20 minutes using only simple buffers, a paper strip and an electric field - making it an ideal tool for use in a rapid NAAT for HIV viral load testing. 

Dysregulation of the dopamine system is a central mechanism driving substance use disorders. Our laboratory has shown that chronic cocaine consumption decreases dopamine release in the nucleus accumbens of the rat, which is a brain area that is important in reinforcement learning. This study also found that restoring dopamine transmission through the administration of the dopaminergic drug, L-DOPA, decreased their cocaine consumption. Recently, we have also shown that acute administration of L-DOPA decreases ethanol (EtOH) intake. Thus, the present study sought to examine the effects of chronic L-DOPA on operant responding for EtOH in adult male rats. Rats were presented with a 2-bottle choice between an EtOH (20%) solution or water, daily for 21 days. Next, animals made nose poke responses (FR1) for 0.2 mLs of an EtOH (20%) solution over 1-h daily sessions for 35 days. On Days 26-35, rats consecutively received either vehicle or L-DOPA (30 mg/kg) for 5 days, counterbalanced across days, and L-DOPA decreased operant responding for EtOH compared to VEH. We are presently examining the effects of L-DOPA on dopamine release during operant responding for EtOH. Together, these data may suggest the efficacy of L-DOPA as a treatment for patients with alcoholism.

Interferon-gamma Enzyme-Linked Immunosorbent Spot Assay (IFNγ ELISpot) is a laboratory technique that quantifies the number of cells producing interferon gamma (IFNγ) by utilizing antibodies that selectively bind to IFNγ molecules, resulting in spot formation corresponding to individual IFNγ-producing cells. Since cytotoxic T cells (CD8 T cells) and their helper Th1 cells (CD4 T cells) produce IFNγ to activate macrophages and inflammatory responses, quantifying IFNγ-producing cells allows for characterization of host immune responses. Our lab utilized a canine IFNγ ELISpot to test for immune responses against novel proteins expressed following gene therapy in dogs. Currently, we used a routinely given vaccine for canine flu, distemper, adenovirus, and parvovirus as a biological positive control. However, we tested our experimental proteins with peptides, making a whole-protein positive control, which required internal processing, flawed. Our goal was to optimize this ELISpot by identifying peptides from the vaccine that stimulates an IFNγ immune response in peripheral blood mononuclear cells (PBMCs) and splenocytes. Utilizing a commercially available canine IFNγ ELISpot, we stimulated PBMCs and splenocytes. These cells included lymphocytes (T cells) and macrophages, which acted as antigen presenting cells. We compared stimulation with the entire vaccine and various vaccine peptides in order to identify peptides that can be used as a biological positive control. These were compared to traditionally used mitogens that indiscriminately activated all lymphocytes. This optimization allows for greater confidence in the results obtained from our canine IFNγ ELISpot. The improved technique serves as a powerful tool to assist in preclinical trials of vaccine production and gene therapy. It is utilized in our lab to test for CD8 T cell-mediated immune responses against novel dystrophins following gene therapy in Duchenne muscular dystrophy dogs.

Flow Cytometry is a quantitative data collection method which utilizes a laser and optics system to measure forward and side-scattering light from single cells in a heterogeneous solution, which when analyzed describe the structure and internal complexity of the cells in solution. Additionally, varying wavelengths of light emitted from the cytometer excite particular fluorescent dyes that can be conjugated to known antibodies, so that when cells contain the known antibody’s antigen, the dye color will be present. This allows for cell identification and/or protein expression to be determined and quantified within a heterogeneous mixture of cells. With the given technology, we optimized a flow cytometry panel for the use of analyzing immune responses to gene therapy treatments in canines. We stained extracellular and intracellular protein markers on canine peripheral blood mononuclear cells (PBMCs) with fluorescent dye conjugated antibodies thought to recognize canine antigens. This entailed staining the extracellular markers with conjugated antibodies, fixing and permeabilizing the cell, and doing the same to intracellular markers. Once this had been carried out, the cells were run through a flow cytometer to excite the dyes with varying wavelengths of light to highlight separate dye colors. Analysis of multicolored dye presence in cells post-excitement allowed for identification and quantification of cell types. We identified antibodies that recognize canine antigens and developed a multicolor panel identifying T helper cells, cytotoxic T cells, T regulatory cells, and B cells in canine samples. Once optimized, we used this panel to characterize immune responses in dogs following gene therapy. With a reliable canine cytometry panel, future canine immune responses, both broadly and in isolated muscular tissues, can be characterized.

Establish-Maintain-Restore (EMR) is a professional development training for teachers to strengthen their relationships with their students. Previous studies have shown that the strategies presented in the training have significantly improved academically engaged time and reduced disruptive behavior among elementary and middle school students. The proposed study will examine 9th grade high school student perceptions of the appropriateness and effectiveness of the EMR strategies to improve student-teacher relationships within the school context. Additionally, this study will analyze whether there is a significant difference in these perceptions between the genders of students. It is predicted that male students will tend to perceive the EMR strategies as less effective and appropriate in improving student-teacher relationships compared to their female peers. A focus group was held to present the EMR strategies to 9th grade students at a racially/ethnically diverse high school in the Pacific Northwest. After the strategies were presented, students were asked to provide ratings and comments regarding the appropriateness and effectiveness of each individual strategy. The students were asked about the following items for each of the EMR strategies: appropriateness for school context, appropriateness for both students and teachers, and effectiveness at improving relationships with high school students. Findings from this study will offer insight for improving student-teacher relationships with consideration for the students’ genders. Research has shown that strong student-teacher relationships can serve as a protective factor against high school dropout, and this study may help provide information about culturally responsive strategies to reduce the dropout rates among students of color and male students.

Secondary metabolite chemicals are specialized chemicals produced by plants that serve specific roles in plant survival beyond aiding in growth or development. Sometimes, the presence of these chemicals negatively impacts surrounding species, a phenomenon known as allelopathy; an example of this is the inhibition of germination of neighboring species. One common non-native species that is known to have high concentrations of leaf secondary metabolite chemicals is Plantago lanceolata (ribwort plantain). Focusing specifically on prairies ecosystem implications, this experiment aims to test the allelopathic effects of Plantago leaf secondary chemicals on the germination of native prairie species. The predicted outcome of this experiment was that increased concentrations of Plantago extract would lead to decreases in germination quantity. To accomplish this, numerous extraction concentrations (including a controlled no-extract treatment) of Plantago leaf chemicals was applied to several prairie species. These species were additionally tested in the presence of high concentrations of yarrow and lettuce extracts; yarrow is another species that contains high concentrations of secondary chemicals, while lettuce leaf material lacks substantial secondary metabolites. Prairie seeds germinated in the presence of secondary chemical extracts include yarrow, Oregon sunshine, Roemer's Fescue, Blue wildrye, and Plantago. 1,400 seeds per species were placed in petri dishes and germinated in either spring or summer growth chambers based on each species' germination requirement. Germination data were analyzed to determine the significance of germination inhibition by each leaf extract. Because Plantago is a non-native and potentially invasive species, it is important to understand the potential for native ecosystem disruption. Additionally, since yarrow and Plantago seeds were germinated in the presence of extracts from their own species, we could determine whether extracts have stronger effects on disparate species than on the species that the extract is derived from. 

Air pollution due to traffic causes many human health problems including neurological disorders. Recently, compelling evidence from the literature has demonstrated that gut microbiome is a newly discovered organ that critically regulates the neurodegenerative disorders including Alzheimer’s disease (AD) via remote-sensing mechanisms. One of the major classes of microbial metabolites are the secondary bile acids. My research focuses on the relationship between TRAP (Traffic-Related Air Pollution) and bacterial metabolism of bile acids that might have significant implications on human health. Male and female wild Type (WT) and transgenic (TG; over-expresses two human AD risk genes [mutant amyloid precursor protein and presenilin-1]) rats were exposed to TRAP or filtered air (FA) for different time points. I focused on rats up to 10 months old that were exposed to TRAP or FA for up to 9 months and from their intestinal contents I extracted bile acids, DNA and RNA to compare which factors might affect gene expression. Bacterial gene and taxa abundance were measured by quantitative PCR (qPCR) and statistically analyzed for significance. Two-way ANOVA analyses were conducted separately among male and female rats; only male rats showed significant changes by qPCR. Exposure to TRAP increased levels of Lactobacillus reuteri in WT males, but conversely decreased L. reuteri in TG males. By understanding different factors affecting bacterial metabolism of bile acids, we are exploring if this could possibly affect human health as well. This can potentially help clinicians and environmentalists to improve clinical outcomes and policies regarding traffic-related air pollution.

Euphausiids (krill) are zooplankton that play a large role in Puget Sound’s marine ecosystem. They are widespread and numerous and have been suggested to play a large role in energy cycling and food web dynamics. Vertical layering of species is not uncommon, and patterns can persist between years, suggesting a significance to the layering. During the day, euphausiids form deep layers in the water column with a thickness in the tens of meters where ecosystem dynamics may differ between the top and bottom of the layer. These layers can be detected by acoustic systems, but characteristics of individuals cannot be resolved. In this study, we used net tows to sample euphausiids at different relative depths within a layer. We recorded the length, sex, and species for statistical analysis to assess the homogeneity of the layer. Comparisons against other locations in Puget Sound will allow us to see if vertical structures are consistent or if other factors such as the presence of predatory fish can explain for differences. This project will provide insight on ecosystem dynamics and carbon cycling.

Carbon dioxide concentrations have been on the rise since preindustrial times due to anthropogenic emissions. Understanding how past climates have responded to changes in the atmosphere is important to understand how our current climate will react to changes in our present-day atmosphere. Soil carbonates record the temperature at the time of their formation in their stable isotopic composition (called clumped isotope geochemistry). Ancient soil carbonates can record the temperature and allow us to better understand paleoclimates. Understanding what time of year soil carbonates form allows us to better interpret the temperature being recorded. The timing of changes in soil moisture is likely one of the most important environmental factors to consider. We test whether soil carbonates form during soil drying events using soil moisture and temperature data measured remotely by a satellite called Soil Moisture Active Passive (SMAP). This satellite has been gathering near-surface soil moisture data globally since 2015 at 35-65 km resolution. We compare the air temperature of the month with the greatest net negative soil moisture content month (determined from the satellite data) to the measured growth temperature of soil carbonates (estimated through geochemistry). We first compare the month of drying of three locales in North America, then extend the analysis globally to all locations for which soil carbonate clumped isotope data exist. Preliminary results suggest that the temperature of the month with the most drying agrees with formation temperature we estimated from clumped isotope geochemistry within one degree for a site in Nebraska and within seven degrees for a site in Wyoming. These results suggest that soil drying promotes soil carbonate formation in some environments. By using soil carbonates to explain past climates, we will improve temperature change estimates, which will help improve climate models for the future.

Maternal exposure to persistent environmental toxicants polybrominated diphenyl ethers (PBDEs) is associated with many human diseases, notably hepatotoxicity, thyroid disorders, and reproductive toxicity. PBDEs, previously seeded into manufactured products as flame retardants in the United States, were phased out during the 2000s. A 2017 study of women in California showed modest average annual percent increases in serum concentrations of PBDEs. Accordingly, the gut microbiome is increasingly recognized as the “second genome”, impacting crucial health-related factors like host xenobiotic biotransformation and energy homeostasis. Persistent dysbiosis may contribute to altered susceptibility of disease in adulthood. My goal for this study was to test the hypothesis that perinatal exposure to BDE-47, a common PBDE congener that can cross the placenta and enrich in breast milk, modifies the developmental trajectory of gut microbiota. Pregnant Wistar rats were orally exposed to BDE-47 (0.2mg/kg) from gestational day 8 to postnatal day (PND) 21. Fecal samples were collected from mothers at PND21 and male pups at PND65 and 120. I isolated Microbial DNA using 16S rDNA sequencing (n=5~9/group) and analyzed my data through QIIME. Perinatal BDE-47 exposure had minimal effect on the richness of gut microbiota in PND65 pups and mothers, but profoundly increased richness of gut microbiota in PND120 pups. In PND65 pups, only 4 taxa were persistently regulated by perinatal BDE-47 exposure. Interestingly, the effect of perinatal BDE-47 exposure was evident in PND120 pups, with an increase in 3 taxa in the Lactobacillales order and 11 taxa in the Clostridiales order. Targeted metabolomics has confirmed alterations of distinct microbial metabolites (short-chain fatty acids and secondary bile acids) corresponding to BDE-47-induced dysbiosis. In summary, the present study showed that perinatal BDE-47 exposure modified the developmental trajectory of the offspring’s microbiota, possibly producing delayed onset of diseases in adulthood.
 

When bacteria experience high salinity environments, such as the brines of sea ice, they take up compatible solutes to protect against osmotic stress. Examples of compatible solutes include amino acids, betaines, and other organic molecules that accumulate in the cells, balancing the osmotic difference between cytosol and external environment without impacting intracellular functions. I am exploring the mutualism of sea-ice bacteria and diatoms (an algal source of compatible solutes for bacteria), and the effects of salinity shifts on this dynamic. I have determined specific growth rates for five strains of bacteria at different combinations of temperature (–3°C to 1°C) and salinity (17 – 55 ppt) that mimic sea-ice conditions. Four strains derive from a collection of Antarctic bacteria found growing mutualistically in diatom cultures: 1) strain Fc1, most closely related (by16S rRNA gene sequence analysis) to Marinobacter psychrophilus strain i20041; 2) Fc4, closest relative Pseudoalteromonas arctica strain A 37-1-2; 3) Nl1, closest relative Glaciecola pallidula strain DSM 14239; and 4) Tr1, closest relative Colwellia rossensis strain S51-W. The fifth was isolated from Arctic sediments but has since been found in sea ice: Colwelia psychrerythraea strain 34H These strains were tested in a defined medium, composed of glucose, vitamins, and a nitrogen source (GVaN), and a complex medium, Marine Broth 2216. Those subjected to higher salinities could be tested at subzero temperatures due to the lowering of freezing point by the salts. During the incubations optical density and cell counts were determined and used for calculations. After determining permissive growth conditions from calculated growth rates, strains will be selected for experiments using specific compatible solutes and/or diatom exudates.

Spatial variation in soil abiotic conditions at plant range limits may be important in determining how plant range limits will respond to climate change. One reason for this is that plants are known to change many characteristics of the soil around their roots in ways that influence the growth of other plants.The range limit of subalpine fir is expected to shift into subalpine meadows as the climate warms. Our goal for this project is to describe the abiotic soil qualities of a subalpine forest habitat and a subalpine meadow habitat on Mount Rainier to explore how these characteristics may affect the predicted range shift. We hypothesize that soils from subalpine meadows will have less organic matter and therefore less phosphorus, a lower carbon to nitrogen ratio, and less water holding capacity than soils from the subalpine forest. We will develop a protocol for measuring water availability and implement it on soil samples obtained from around the roots of subalpine fir trees in both the forest and meadow sites on Mount Rainier. We will use standardized tests to obtain the organic matter and phosphorus measurements. If our hypothesis of lower nutrient availability and water retention in meadow soils is supported, this may suggest that subalpine fir growing in the meadows have a greater dependency on fungal symbionts for obtaining soil resources. This would have important management implications given that suitable fungal symbionts are expected to be rare or absent at range limits.

Emerging adulthood is a significant developmental period where individuals aged 18-25 years do not feel that they are adults, but on the path to becoming so. Individuals may describe their experiences within this life stage differently based on their racial identity. This research project asks: “How do young people of color in college describe their experiences of emerging adulthood compared to their white peers, and is this related to their mental health in different ways?” Within this study, I compare how students of color and white students view, experience, and navigate emerging adulthood and how this affects their mental health. Through interviews with young college students across racial groups at University of Washington (UW), I examine how they make sense of the stressors in their lives. Interview questions discuss significant areas of emerging adulthood, various social forces that could affect mental health, racial issues and socialization, and access to social support. I test the hypothesis that students of color describe their sources of stress as being more impacted by structural and institutional reasons, such as racism and xenophobia, while white students focus more on social and interpersonal reasons, such as families, relationships, and work. Emerging adulthood is a relatively new field of research and it is critical to understand how people of color experience this life stage. This research will contribute to current understandings and research of racial health disparities. It will also highlight areas for additional work addressing the significance and complexity of intersectionality within the emerging adulthood developmental period.

Ribonucleotides are essential components of the cell: they are the building blocks of RNA and DNA, key signaling molecules, and metabolic intermediates. Maintaining proper ribonucleotide balance is critical for cell survival. An essential, highly-conserved enzyme that regulates purine biosynthesis is IMP dehydrogenase (IMPDH), which catalyzes the first committed step in the production of GTP. In humans, there are two IMPDH isoforms: IMPDH1 is present in low quantities in most cells, and IMPDH2 is upregulated during proliferation. Both IMPDH isoforms form higher order structures in cells and assemble into filaments and bundles of filaments in vitro. Nine point mutations in IMPDH1 have been discovered that cause retinal degeneration and ultimately blindness in humans. Our current findings show that these point mutations in IMPDH differentially impact the protein’s ability to assemble into filaments in vitro. We hypothesize that the ability of IMPDH to polymerize will affect the protein’s activity because of the interplay between protein structure and substrate binding. We use negative stain electron microscopy to first characterize the polymerization behavior of IMPDH in the presence of different ligands: the substrates IMP & NAD+, as well as allosteric effectors ATP and GTP that promote polymerization. In addition, we employ kinetics assays that vary levels of substrate and GTP to quantitatively assess enzyme activity by measuring NADH output. Characterizing each mutant’s behavior will be the first step to understanding the molecular mechanisms that cause retinal disease in IMPDH. In a future study, we can use cryo electron microscopy to solve the structures of mutant protein.

Seasonal dark streaks on Mars known as Recurring Slope Lineae (RSL) propagate down steep, warm slopes and appear to be liquid water flows. However, the mechanism behind RSL formation is controversial, and both dry granular flow and percolating water hypotheses have been proposed. To determine if water is responsible for RSL formation, I investigated similar dark streaks generated by percolating water in the McMurdo Dry Valleys (MDV) of Antarctica, an extremely cold and dry Mars analog site. The goal of this research is to identify the source of water to the MDV streaks, and to compare the MDV streaks to Martian RSL. I characterized the MDV streaks by (1) analyzing a ~30-day time-lapse video of the streaks collected on site, (2) investigating the drainage hydrology, and (3) comparing hundreds of satellite images of the streaks from 2003-2017. My results show that the MDV streaks are very different from Martian RSL, which indicates that water is not involved in RSL formation. Unlike Martian RSL, I found that MDV streaks propagate downslope at much slower rates compared to Martian RSL, and do not grow and retreat seasonally. Furthermore, MDV streaks have distinctive patterns not apparent in Martian RSLs, and rapidly darken/lighten in response to relative humidity changes. Finally, MDV streaks form in response to extremely warm summer temperatures, conditions which are unlikely to prevail on Mars. These results are important for understanding how and if liquid water occurs on Mars’ surface.

The North American Nanohertz Observatory for Gravitational Waves (NANOGrav) uses an array of galactic millisecond pulsars to search for low frequency gravitational waves. The stability of millisecond pulsars allows their pulse time of arrival (TOA) to be used as precise clocks. Gravitational waves will produce timing delays that are are correlated across pulsars. In order to detect such correlations in TOAs, we must also understand the noise processes in the pulsar signal. Noise model selection aims to produce custom noise descriptions for each pulsar. Using NANOGrav's search code enterprise a Markov Chain Monte Carlo (MCMC) algorithm is used to search for the most favored model. A hyper model framework is used to explore across a set of models, which have different red noise and dispersion measure (interstellar medium effect) processes. The posterior odds ratio is then represented by the relative amount of time the chain spends in a model. An iterative approach is taken, where one model selection analysis is used to inform the next set of models from which to choose. The resulting noise descriptions will aid in mitigating its effects within the pulsar signals, increasing chances of gravitational wave detection.

Recurring slope lineae (RSL) observed on Mars appear to be flows of liquid water because they seasonally propagate down sunny slopes in the spring and fade during the winter. Liquid water suggests the potential for life on Mars’ surface and has implications for future exploration; however, recent hypotheses contend that RSL form via dry sand avalanches. To test wet vs. dry flow hypotheses, we analyzed images and topographic data from Garni crater taken by the High Resolution Imaging Science Experiment (HiRISE) during the Martian summer and winter. Our results show that RSL size correlates with areas where we expect high windblown sand deposition, such as on the SE lee side of the crater, or in small gullies below large headwalls. Additionally, RSL do not appear on the wind-scoured NW side of the crater. These surface relationships indicate that RSL in Garni crater form via a dry process in which windblown sand is deposited by prevailing NE winds and seasonally avalanches down steep slopes. To further test our conclusions, we are examining additional confirmed RSL sites on Mars to see if they display the same behavior.

A series of ultraviolet exposure tests were conducted on a high-oil content, paraffin-based wax binder used in an operational U.S. Thoroughbred horse racetrack to simulate multi-year outside exposure. This type of hydrocarbon binder is commonly used in synthetic granular composites used in North American Thoroughbred horse racetracks and other equine sports surfaces. The function of the binder is to hold together the sand, polymer fiber, and rubber particles that constitute the surface. Previous research on this binder extracted yearly from the same racetrack over a six-year pear period, during which the track was not altered compositionally, showed that environmental oxidation increases over time. This degradation can potentially affect the mechanical performance of the overall surface which may impact the safety of both horse and jockey/rider. The goal of this work is to demonstrate how accelerated aging, in a short period of time, can mimic multi-year exposure using an UV-A equipped oven, and test results from fourier transform infrared spectroscopy (FTIR), gas chromatography (GC-FID), and differential scanning calorimetry (DSC).

By their second birthday, toddlers help others. Moreover, infants as young as 9 months of age can detect others’ needs. Yet it is unclear if early helping behavior is based on and motivated by an underlying assessment of others’ needs, or motivated by other factors, like the desire to socially interact or affiliate with others. Here, we investigate whether toddlers utilize an experimenter’s needs when helping. We presented N=24, 24-month-old toddlers with two helping tasks: a puzzle and hunger-or-thirst task. In the puzzle task, toddlers watched an actor fail to complete a puzzle due to a missing puzzle-piece. Toddlers then had the opportunity to help the actor by either bringing her a puzzle-piece that fit the puzzle (need-fulfilling) or a puzzle-piece that did not fit the puzzle (not need fulfilling). Overall, toddlers were more likely to help with the puzzle-piece that fulfilled the actor’s need than the puzzle-piece that did not fulfill the actor’s need, p=.008. In the hunger-or-thirst task, the actor told toddlers that she was either hungry or thirsty. Toddlers could help the actor by giving her one of three different items: (a) cereal, (b) water, or (c) a shoe. Here, toddlers brought the needed item (e.g. cereal if she was hungry) at chance, p=.11. However, toddlers were more likely to bring the needed or the thematically related item (e.g. water if she was hungry) significantly more than chance, p<.001. Our findings provide initial evidence that 24-month-old toddlers are motivated to help based on others’ concrete needs: toddlers brought the needed puzzle-piece. However, toddlers have a harder time helping appropriately when the actor’s need is internal and therefore more abstract; hence, the equal likeliness to help with the needed and related item during the hunger-or-thirst task.

Chimeric antigen receptor (CAR) T-cell therapy is the latest treatment option available for those suffering from certain forms of cancer such as lymphoma and leukemia. These engineered cells are able to recognize specific proteins found in tumors, and subsequently induce CAR-T cell proliferation, cytokine secretion, and lysis of the cancerous cells. Despite its promise, a percentage of patients who receive this treatment develop a range of neurotoxic symptoms. My research project tests the hypothesis that endothelial activation of vascular tissue in the brain, which would allow for increased permeability of immune cells through the blood-brain barrier, is contributing to the development of these clinical symptoms. Using a technique called immunohistochemistry, I used the antibodies claudin-5 and cd31 to fluorescently label tight-junction proteins and adhesion molecules of endothelial cells from brain tissue harvested from a developed mouse model. This mouse model received CAR-T cell injections and underwent behavioral testing to confirm the presence of neurotoxicity symptoms. I then used microscopy skills to visualize the labeling of the endothelial cells and proteins. If my hypothesis is correct, I expect to see a quantifiable decrease in the number of cerebral tight-junction proteins connecting endothelial cells along the blood-brain barrier, as compared to negative control tissue that received no CAR-T cell injections. In order to make these comparisons, I will use a software program such as Image-Pro Premier software (Media Cybernetics) to help me quantify the positive fluorescence labeling of endothelial cell proteins and adhesion molecules in both the control and experimental tissue. Tissue with less tight-junction proteins and adhesion molecules would permit the influx of foreign particles into the CNS. Understanding the cause of CAR T-cell related neurotoxicity will be first step in promoting prevention and increasing the effectiveness of this new cancer immunotherapy.

 Adults use many forms of information when deciding how to act in any situation. We are investigating the types of information infants use when determining how to act in a novel reaching task. We are looking at costs (how far they must reach; Study 1) and the social value of the object they are acting toward (Study 2). In Study 1 (ongoing), we tested 6-month-olds (n=25) and 9-month-olds (n=14). Infants completed a warm-up task to measure their maximum reach. During test trials, they were presented toys at 3 different distances: one inch away (Easy condition), one inch past maximum reach (Hard condition), and 27 inches away (Impossible condition; Figure 1). Infants reached more in the easy (93.2%) than the hard (72.6%, β=-1.90, p<0.0001) and impossible conditions (19.3%; β=-5.45, p<0.0001; Figure 2A). Infants also reached more in the hard than the impossible condition (β=-3.5, p<0.0001; Figure 2A). A within-subjects one-way ANOVA revealed a main effect of condition on infants' latency to reach F(2,73)=127, p<0.0001. The average latency increased from easy (2.61+/-2.05seconds), through hard (4.93+/-3.21seconds), to impossible (9.29+/-1.13seconds; Figure 2B). This indicates that infants are less likely to reach for objects when costs are high. In Study 2 an actor will manipulate one toy to be exciting (“I love this toy!”) and one toy to be boring (“Eh”), 3 times, 10 seconds each. We hypothesize that if infants use social value in their decision-making process, they will persist more when reaching for the exciting toy, particularly in the hard condition when reaching is costly. Even though infants engage in less complex decisions than adults, we are able to see evidence of decision-making processes in infants’ actions, supporting the idea that humans’ ability to perform these processes may emerge during early infancy.

Marine mammal strandings can serve as an indicator of marine ecosystem and mammal population health, providing an opportunity to learn about the life of individual animals prior to their deaths. Existing stranding networks are focused on response to opportunistic reports of stranded or beached marine mammals, which limits their usefulness in establishing baseline data. The Coastal Observation and Seabird Survey Team (COASST) engages volunteers along the western coast of the United States in collecting and reporting data for two effort-based programs, beached birds and marine debris. Looking to the future, COASST hopes to complement information gathered by marine mammal stranding networks by expanding their effort-based surveys to include marine mammals. COASST has already begun this process by asking volunteers to report sightings of marine mammals along with pictures of their beached bird or marine debris finds. These pictures can be used for species identification, and by looking at these photos in correspondence to other survey data such as region, beach, and survey date we can learn about species distribution along the western coast of the United States. We found at least 300 beached pinnipeds, through photo identification we were able to place them into at the least the families Otariidae or Phocidae. Using current literature on marine mammals, pinnipeds specifically, and their identifying characteristics, I aim to map pinniped species distribution and locate hotspots to ultimately test a pinniped species identification key that will be used by COASST volunteers. With this distribution and hotspot identification we will be able to idenify whether pinnipeds follow already established beaching patterns of beached birds or if they differ. These differentiations could lead to more information about the death of marine mammals and allow future research on the death of these animals in more focalized areas. 

In the last decade, a large amount of studies have been done using virtual environment (VE) because of the increased control over the sensory stimuli used and the detailed observation of the associated behavioral and sometimes neuronal responses. In this study, we placed honeybee in a VE and exposed them to visual stimulus in closed-loop. We showed that honeybees are able to fixate the stimulus regardless of the level of feedback fed to the sensors(e.g., the gain between the animal motion and the stimulus motion on the VE). Our next step is to investigate how different neuromodulators such as the octopamine and dopamine, may be important for fixation and adaptation to the different level of sensor feedback. Octopamine (OA) is key in modulates physiological process in invertebrates including honeybees. Recent studies have identified OA neurons that are critical for visual behaviors and that increase their activity during active behavioral state. To identify the effects on octopamine and dopamine (DA) on honeybee’s ability to fixate, we are injecting bees with OA, DA or their respective antagonists in a visual processing brain area. Potential results of this study will impact the fields of neuroethology, providing insights on the modularity of neural processes and the feedback between sensory and motor pathways.

During the last ice age outburst floods from glacially-dammed lakes incised canyons across eastern Washington, transporting large amounts of sediment ranging in grainsize from silt to boulders. Around Ephrata, floodwater channeled through Grand Coulee escaped the confinement of the canyon and deposited much of this sediment in the Ephrata Fan. Deposited at the mouth of Grand Coulee extending 45 kilometers south across Quincy Basin to the Frenchman Hills, this deposit is up to 90 meters thick. Older, high-standing deposits within the fan are cut across by successively younger scarps and channels to produce a stepped landform that records many episodes of flooding. The aims of my project are to date the deposits forming the oldest surfaces, and to determine the source of the granite boulders contained within these steps.
I made elevation, slope and aspect maps of the Ephrata Fan using digital elevation data and ArcInfo Geographical Information System (ArcGIS) software in order to distinguish the relative age of deposits within the fan. I collected samples from granite boulders on surfaces of different ages for exposure dating with cosmic-ray-produced beryllium-10 (Be-10). I am currently separating quartz from these samples. Quartz will be dissolved, and beryllium will be extracted and purified for isotopic analysis, to determine the concentration of cosmic-ray-produced Be-10. The abundance of this isotope measures the exposure time of the samples. The range of dates from the oldest to youngest surfaces in the fan will constrain the age and duration of the floods epoch. Furthermore, granite samples from the sequence of deposits will be compared to granites exposed in the floor of upper Grand Coulee. If found, the appearance of this specific rock type in the Ephrata Fan deposits will help determine when floods eroded the canyon to its present depth offering an insight into its development.

Morality has significant social importance as it influences the way we interact with others. We know that adults and children (aged 3-11) expect all groups to follow moral norms such as fairness, but only in-group members to follow non-moral norms like certain food preferences (Liberman, 2017). It remains unknown if this applies to infants. Studying infants’ moral sensitivities will shed light on the origins of morality, and it will give us insights on its socialization. We are investigating infants’ expectations about in-group and out-group members performing actions that are consistent/inconsistent with moral norms (i.e., distributing resources fairly/unfairly) and actions that are consistent/inconsistent with non-moral norms (i.e., using an object according to its established function or unconventionally). In Study 1, 24-month olds (N=32, testing ongoing) are first familiarized to a storyteller speaking English (in-group) or Spanish (out-group). Infants are then shown the storyteller doing a fair (equal) or an unfair (unequal) distribution of cookies to two third parties. We are measuring, via infants’ visual attentiveness, whether they expect fair or unfair resource distributions. We predict that infants will show enhanced attentiveness to the unfair event, thereby suggesting what they saw violated their expectations. During piloting, infants in both conditions looked longer at the unfair distribution (English-Unfair: M=32.44 seconds (SE=9.09), Fair: M=28.8 seconds, (SE=15.4), Spanish-Unfair: M=27.8 (SE=15.2), Fair: M=17.3 (SE=5.39), providing preliminary support for our hypothesis. We are also testing how non-moral norms translate across group boundaries. After the same familiarization events as before, the test trial shows an unconventional action (ie. brushing your hair with a fork) pitted against a convention one (ie. eating with a fork). We predict that non-moral norms will be group-specific because they should be seen as culturally dependent and not encompasing. In sum, these findings will provide important new insights into the origins of morality.

During the Last Glacial Maximum (LGM), the Cordilleran Ice Sheet advanced into the northwestern United States and dammed the Clark Fork river in western Montana, forming Glacial Lake Missoula. The ice dam in the valley repeatedly broke, sending at least 100 massive outburst floods known as the Missoula Floods into eastern Washington where they incised deep canyons forming the Channeled Scabland. During the period of flooding, the Okanogan Lobe of the Cordilleran Ice Sheet crossed the Columbia Gorge onto the Waterville Plateau, diverting floodwaters away from the Columbia River into Grand Coulee, before blocking Grand Coulee itself. My research project examines the timing of glaciation of the Waterville Plateau and how it influenced the paths of the successive floods. To determine the timing of glaciation, my advisers and I studied glacially transported boulders that began to accumulate the cosmic ray produced isotope beryllium-10 (10Be) after they were exposed by ice sheet retreat. In the lab, we separated and dissolved quartz from our samples, purified beryllium, and then measured 10Be/⁹Be ratios using Accelerator Mass Spectrometry (AMS). From AMS measurements, we calculated the exposure ages of our samples. We expect the ages to fit within the established sequence of ice advance across the Columbia River, redirection of floodwaters down Grand Coulee, and eventual ice retreat to north of the Columbia River. Following this sequence, we expect our samples from the northern edge of the Waterville Plateau to be younger than the last floods down Grand Coulee (15,300 years) but older than samples from the Omak Plateau north of the Columbia Gorge (13,900 years). Along with dates from previous studies, the new exposure dates from this project explain how the Okanogan Lobe guided Missoula floodwaters and influenced landscape evolution in eastern Washington.

Cardiovascular disease (CVD) continues as the leading cause of death worldwide. The underlying cause of CVD is atherosclerosis, characterized by fatty plaques in the inner walls of the artery, and exacerbated by oxidative stress, inflammation and immune cells. The high-density lipoprotein (HDL)-associated enzyme paraoxonase-1 (PON1) plays a significant role in protecting against CVD. However, the mechanism of PON1’s protection is not well understood. Our laboratory and others have reported a progressive decrease of PON1 activity in several diseases. Our goal is to understand how PON1 prevents oxidative stress and its potential measurement as an early biomarker of risk of disease. Our hypothesis is that oxidative stress inhibits PON1 enzymatic activity, leading to progression of the atherosclerotic process in CVD. The objective of this research is to generate a mouse model to allow us to study the human enzyme PON1 in induced atherosclerosis in vivo.  Starting from two strains of knockout (KO) mice, we have generated the Pon1/apolipoprotein E (apoE) double KO mouse, known to be susceptible to atherosclerosis. We are now crossing this double KO mouse with Pon1 KO mice that express human PON1 (transgenic human PON1 mice, tgHuPON1). We collect ear punches for DNA extraction and blood from the saphenous vein for activity assays. We use polymerase chain reaction (PCR) genotyping methodology, which amplifies DNA, to identify mice that are KO for mouse Pon1 and apoE and that express human PON1. We run enzymatic assays to determine activity levels of the human PON1 in mice. Once we have created the tgHuPON1/apoE KO mouse, we will feed mice with an atherogenic diet, which will induce subclinical atherosclerosis. This knowledge will contribute to understanding the relationship between PON1 and CVD, and will likely generate a useful biomarker for risk of disease.      

Field research is an important way to understand complex ecosystems and the roles of individual wildlife species within these systems. As climate change and other human factors continue to affect our global patterns, studies must be conducted to assess the health of current populations and predict future trends. Many studies involve direct or indirect contact with the focal animals, which may impact the fitness of study animals despite efforts of researchers to minimize cost. Long-tailed Jaegers (Stercorarius longicaudus) in Denali National Park, Alaska were captured and fitted with satellite-linked GPS trackers to study migratory routes. The birds were tagged by other researchers while on their summer nesting grounds caring for eggs or recently hatched chicks. This disturbance has potential to affect the nesting success of the jaeger which is thought to already be in decline in the area. A long-term study of the nesting success of jaegers and other shore birds in DNP is being conducted to assess the suggested decline in these species. What impact did radio tagging nesting jaegers have on nesting behavior and success? I collected behavioral data in the field during a four-week period in July of 2018. With a UW grad student, I directly observed 2 breeding pairs of jaegers that had been tagged and 3 that had not. We observed the birds from over 150 meters away, recording parental feedings, chick protection, and vigilance. Preliminary analysis suggests that the two subsets of jaeger behaved differently during chick fledging. This could have impacted the way chicks were raised and the nesting success rate of tagged parents. Further analysis into the feeding rates and protective behavior is underway to determine the complete impact of radio tags on the population.

The interactions between pollinators and plants have a strong correlation to the fitness and reproductive success of both parties involved. These interactions are responsible for most of plant reproduction by seeds and they also drive evolutionary diversification of both plant and pollinator species. Wind turbulence plays an important role in navigation by smell, which is important for many pollinators while locating flowers. Climate change may alter wind patterns, which in turn may affect the ability of pollinators to locate flowers. The goal for this project was to determine the effect of wind on pollinator success. We determined the visitation rate of pollinators at Oenothera pallida flowers in the field by analyzing infrared camera videos recorded last summer at a field site in Grant County WA. Next we ran a multiple linear regression to determine the effects of wind speed, temperature, humidity, and ozone levels on floral visitation rates. Pollinators of Oenothera pallida include the hawkmoths Hyles lineata and Manduca sp., various bee species including Andrenids, Apids, Lassioglossum sp. and Megachilids, Bembix wasps, and various flies. Wind speed is the strongest variable that affects pollinator visitation at different times of day, which implies that changing wind patterns significantly impact plant-pollinator interactions.

Although Asians and Asian Americans are often classified as belonging in the same social category, these two groups may perceive and think about the world differently. This project examined whether UW students who are Asians and Asian Americans hold different viewpoints regarding social identities and social statuses. Primarily, we examined group differences in Status Legitimizing Belief, Perceived Racial Discrimination, and Racial Identification. Status legitimizing belief is a set of beliefs (measuring protestant work ethic, perceived system permeability, and system legitimacy) asserting that if individuals work hard, are motivated, and are talented, they can improve their social statuses. Perceived racial discrimination measures the extent to which racial minorities believe that they are targets of discriminations. Racial identification measures individuals’ beliefs and perceptions that their racial group matters and is central to how they perceive themselves. Through meta-analyses of self-report surveys across 13 academic quarters, we found significant differences between Asian Americans and Asians across all measured variables. First, we found that Asians have higher status legitimizing belief than Asian Americans. Asians also perceive lower racial discrimination than their Asian American counterparts. And finally, Asians are less likely to identify with their racial in-group than Asian Americans. This research demonstrates that while both groups are often classified or perceived as the same social group, they, in fact, hold different perspectives regarding their identities as well as their statuses. Understanding how these two groups rationalize and perceive legitimacy and discrimination offers insight into intergroup relations.

Sexual harassment is pervasive yet many people underestimate its prevalence or often do not believe victims when they come forward. The current research examines a potential source of this bias. Specifically, we theorize that people assume and misperceive victims of sexual harassment as prototypical women (i.e., those who fit the stereotypical, idealized image of women), and those who deviate from this prototypicality are less likely to be believed as victims. In this study, participants read a vignette describing a woman named Anna who was either sexually harassed by a male boss or not (control group). Importantly, we manipulated her prototypicality using photographs obtained from previous research. After reading the vignette, participants rate how likely they think Anna experienced sexual harassment. This is a 2 (prototypical vs non-prototypical images) x 2 (harassment vs control) between-subject design. We are primarily interested in the interaction between the two conditions. If the interaction is significant, then we will examine the non-prototypical vs prototypical within the harassment condition as well as in the control condition. We are trying to see how the interaction effect works for women who are prototypical or not when they have been harassed because we believe that prototypical women will be more likely to be believed than non-prototypical women. We do not expect this pattern to repeat in the control condition because prototypicality should not influence women who are not harassed. This research will allow us to understand how perception of harassment can be influenced by women’s resemblance to the prototypical image of womanhood.

Alzheimer’s disease (AD) is characterized as an irreversible, progressive brain disorder that gradually destroys memory and thinking skills, and eventually the ability to perform simple everyday tasks. Despite many decades of research focus on AD, the cause and mechanistic understanding of the progression remains enigmatic. Identification of amyloid beta plaques and hyperphosphorylated Tau in post-mortem analysis of brain biopsy is viewed as definitive for diagnosis of AD. Dr. Su-in Lee’s lab has developed a machine learning method that integrates brain tissue pathology metrics with gene expression analysis from the same patient samples. Their analysis identifies genes and pathways that are statistically-associated with the concordance of pathological AD phenotypes. Working with researchers in the Kaeberlein lab, we are using the nematode C. elegans to directly test the impact that these genes have on the progression of human tau-induced neuronal dysfunction and death. The Kaeberlein lab previously identified a subset of genes in complex I of the electron transport chain (ETC) that are highly correlated with human amyloid beta-induced paralysis. We are now extending that work by examining the relationship of these ETC genes in the lifespan and healthspan of human Tau-model nematodes. Our preliminary results suggest that reduction of Complex I activity increases the lifespan of human tau-models nematodes. We are conducting further studies to determine the replicability of these findings as well as disrupting ETC function with RNAi from other genes. Through directly testing nematode orthologs of human genes that are statistically-associated with AD neuropathology we will generate a better understanding of the cellular mechanisms that influence normative aging and Alzheimer’s disease.

Sleep deprivation has serious health consequence with disturbances in cognitive function and metabolism, and increased risk for age-related diseases such as Alzheimer’s disease. Intervention strategies are therefore of interest, especially in individuals unable to routinely obtain healthful sleep time hours. This study was designed to investigate the effects of the repurpose drug phenylbutyrate (PBA) on learning impairment in a mouse model of short-term sleep deprivation. Histone deacetylase (HDAC) is activated by neuronal stress resulting in decreased gene expression and under-acetylation of histones linked to decreased cognitive function. As an HDAC inhibitor, PBA would be expected to alleviate cognitive dysfunction associated with sleep deprivation. Further rationale for testing PBA was provided by showing the drug enhanced expression of acetylated histones in mouse and human neuronal cell cultures. Nine CB6F1 male mice, 17 months of age, were started on treatment with PBA in the drinking water at a concentration of 6 g/L for twelve weeks. Nine control mice were provided drinking water with diluent only. During the last week of treatment, mice were maintained in an awake state 4 hours during the day for 4 days using a non-stressful protocol. All mice were then immediately tested in a box maze learning paradigm consisting of four successive trials to find an escape hole. Control mice had variable escape times over the four-trial test, while mice treated with PBA showed a consistent decrease in escape times with each successive trial. This observation suggests that pretreatment with PBA can prevent learning impairment induced by short term sleep deprivation in mice. Since PBA is already clinically approved to treat urea cycle disorders in children, there are intriguing implications for repurposing this drug for experimental trials in individuals with primary or secondary sleep disorders.

The most recent National Vital Statistics Report reports that approximately 9.85% of babies in the United States are born preterm, with 72% of those born late-preterm (at 34-36 weeks of gestation). Using neonatal ferrets at age 17 days old, the Juul lab in the Division of Neonatology at the University of Washington Medical Center has developed a preliminary model of brain injury to mimic late-preterm neonatal injuries. In this species-specific adaptation of the Vannucci Model, the left carotid artery is permanently ligated, along with a temporary (4h) occlusion of the right carotid artery. Ferrets are then exposed to periods of hypoxia and hyperoxia. By looking at data and outcomes from our surgeries, I aim to examine the effects of certain surgical parameters on ferret mortality. These parameters include: time the animal is exposed to isoflurane, the length of surgery, and the amount of time the animal is given to recover between surgery and hypoxia. Aside from mortality, I will also analyze the effects of these parameters on respiratory rate after surgery as well as gross brain injury and data from behavioral testing in an attempt to discern the level of injury in living animals and the most common predictors of death in those that died prior to their determined endpoint.

Autism Spectrum Disroder (ASD) occurs in one in every 59 children, yet the causal mechanisms remain widely unknown. Research is advancing through genetic testing as well through speculation of external environmental influences. Recent stuides have examined in greater depth gene by environment interactions and have found an impact on severity symptoms of ASD. This research follows the two-hit model of gene by enviornment effects and investigates the link of auoimmune disorders, specifically thyroid disfunction, Likely Gene Disrupting (LGD) mutations to genes related to ASD, and the relation to IQ and regression. Behavioral and cognitive data are collected using clinician-administered questionnaires and assessments. Those who carry an LGD mutation with exposure to maternal thyroid dysfunction lean towards a trend that show more severe behavioral phenotypes than those without an LGD mutation. These results spotlight the importance of gene by environment contributions in addition to mechanisms involved in the disorder. These findings may help improve future treatment and intervention for those with ASD. 

Mosquitoes primarily navigate using their olfactory system, and can use this system to form “memories” that influence their choice in hosts. When a mosquito encounters an odor, information is sent through the antennal lobes in the brain to the mushroom bodies, which are structures responsible for learning and memory consolidation. This odor-learning pathway is mediated by neurotransmitters like dopamine and serotonin. Recent research has shown that the mosquito Culex quinquefasciatus has extremely low levels of dopamine in the antennal lobes compared to other species, and is unable to learn to avoid odors associated with a negative response. This led us to predict that dopamine is essential for aversive learning in mosquitoes. We hypothesized that Cx. quinquefasciatus differed from other mosquitoes in learning ability because they were previously tested in the light and they are the most nocturnal of the originally tested species. To test this hypothesis, we conditioned the mosquitoes in the absence of light in an aversive learning paradigm to measure how frequently they chose to avoid the conditioned odor. An inability to learn regardless of light condition would indicate that the role of dopamine as a neuromodulator in the antennal lobes evolved partly to allow diurnal mosquitoes to avoid defensive hosts. Next, specific neurotransmitters in the antennal lobe were mapped using confocal microscopy, revealing their concentrations which may explain behavioral differences from other mosquitoes. Most mosquito species show some plasticity in host selection, which can lead to the transmission of animal diseases, like West Nile Virus, to humans. Mosquitoes are the world’s deadliest disease vector, killing over 700,000 people globally each year, so understanding how and why this adaptation occurs can help us understand the framework that underlies the spread of mosquito borne diseases and bring us one step closer to solving this global issue.

Understanding prosocial behavior, the concern for the welfare of others, is critical to navigating the social world. Here, we investigated the nature of infants’ understanding of prosociality by asking whether they expect those who are fair (i.e. those who distribute resources equally) to also be trustworthy (i.e. respect someone else’s property). We showed 32 22-month-olds videos of two actors, one who distributes goods fairly (3:3) and another who distributes goods unfairly (5:1). Using eye-tracking, we captured infants’ active and passive expectations about the trustworthiness of these actors when both were warned by a third character, a toy-owner: “Don’t touch my toy”. When she left the room and came back to find the toy missing, she asked “Where is my toy?”. We predicted that more infants would give anticipatory looks towards the unfair actor than towards the fair actor, suggesting that infants expected the unfair actor to have stolen the toy (i.e., active expectations). Next, infants either saw the fair actor steal the toy (n=16) or the unfair actor steal the toy (n=16). Here, we predicted infants would look longer at display when the fair actor stole the toy, a signal that this event violated their expectations (i.e. passive expectations). Additionally, we were interested in how social-environmental factors may influence infants’ expectations. Thus, we also investigated the influence of siblings on infants’ expectations. Findings revealed that infants with siblings looked anticipatorily at the unfair actor while infants without siblings looked anticipatorily at the fair actor. Additionally, infants who saw the unfair actor steal the toy looked longer at the display. This may be explained by infants looking longer at the actor whose behavior they found most interesting. Together, these findings provide insight into infants’ understanding of various sociomoral traits and how this understanding may be influenced by social-environmental factors.

Progeroid syndrome is a group of genetic disorders characterized by accelerated aging. Molecular mechanisms of progeroid syndrome include abnormalities in genomic stability, nuclear structure, lipid and carbohydrate metabolisms as well as mitochondrial functions. Genomic instability is a major category of progeroid syndromes in humans. Prototypical example is the Werner syndrome caused by the mutations in the WRN gene which encodes a DNA helicase. Cells derived from progeroid syndrome patients generally exhibit phenotypes of accelerated cellular senescence with a very limited replicative lifespan. International Registry of Werner Syndrome recruits progeroid syndrome patients from all over the world for the genetic study. Among the subset of those patients, a recurrent disease mutation has been identified in the POLD1 gene. The POLD1 gene encodes a catalytic subunit of polymerase delta, a major replication polymerase which is also involved in translesion DNA synthesis. The POLD1 mutation is known to cause MDPL (mandibular hypoplasia, deafness, progeroid features, and lipodystrophy) syndrome. In our study, cellular model of MDPL syndrome was generated by expressing mutant POLD1 cDNA in human fibroblasts via lentiviral system. Consequences of the POLD1 mutation are determined by various assays including cell growth, accumulation of DNA damage and sensitivity to genotoxic agents. The eventual goal is to develop therapeutic approaches that ameliorate cellular disease phenotypes. We plan to test candidate therapeutic approaches using established POLD1 cell lines and assay methods. More recently, a mutation in the SMAD4 gene, was identified in one progeroid patient. SMAD4 gene encodes a crucial member of the cellular transduction pathway. The wildtype and mutant SMAD4 are being expressed in human fibroblasts to determine whether cells expressing mutant SMAD4 exhibit phenotypes of accelerated senescence. This project would provide us with an understanding of recently identified progeroid loci and likely sheds a light on the previously unknown mechanisms of normal aging and age-related disorders.

Zea mays (maize, corn) is an essential crop plant; important to global agriculture and the U.S. economy. However, maize productivity and yield can be drastically affected by abiotic environmental stress. Therefore, a priority for many plant breeding programs is to select for crops displaying phenotypic traits of enhanced tolerance to abiotic stress. A subset of abiotic stresses induce the plant hormone, abscisic acid (ABA). The mediator of paramutation1 (mop1) gene encodes an RNA-dependent RNA polymerase that functions in the RNA-directed DNA methylation (RdDM) pathway. The mop1-1 mutation results in the loss of DNA methylation which in turn causes a variety of genes to be expressed abnormally. We determined how a mutation in a mop1-1 affects RNA expression under abiotic stress by conducting a computational analysis of multiple RNA-seq datasets of stress-treated maize seedlings. We compared RNA-seq data from mop1-1 and WT seedlings treated with exogenous ABA control (no ABA treatment) with a publicly available dataset of WT maize plants treated with heat, cold, drought, salinity, and control (no stress treatment). Genes commonly down-regulated in the four stresses and in MOP1 WT ABA, but up-regulated in mop1-1 ABA represent genes potentially silenced under stress that require MOP1 for gene silencing. The presence of these genes in the given stress treatment allows us to identify the abiotic stress responsive genes that require ABA and MOP1 mediated regulation.

Wireless power transfer has many applications, from powering biomedical implants to wireless sensors. For more practical use, however, several challenges must be overcome, such as a lack of efficiency and power leakage to other nearby electronics. These issues become especially difficult to tackle with a moving receiver. To combat these problems, an array of magnetically coupled coils was designed. Previous work has shown the capabilities of this system when one coil of the array is supplied with power. In this work, I explore the possible benefits of having two coils in the array driven with power instead, studying the interaction between the different coils. By adjusting parameters such as the phase relationship between the two transmitters’ signals, we aim to optimize power delivery to specific targets and simultaneously minimize leakage to other areas. I tested different configurations of the system in a series of experiments and analyzed measured data to determine which setup is most favorable. Afterwards, I evaluated the efficiency of the configuration compared to the previous single-transmitter case. This provides better insight into how the coils in the array magnetically interact with one another, which will inform future design decisions. It can also eventually lead to better solutions for delivering high power to selected targets within a given space. This can create flexible, efficient, and safe wirelessly charged electronic implants for a variety of biomedical applications, enabling further research in the field and the development of novel solutions.

The 6He experiment located at the North Physics Lab aims to reach sensitivity 10 ^-3 or better in searching for beyond standard model tensor currents that violates chirality. The Fierz interference coefficient (little b) is linearly depended on tensor couplings and can be experimentally extracted by precisely measuring the 6He beta decay spectrum. The technique of cyclotron radiation emission spectroscopy from Project 8 (A neutrino experiment located at the UW Physics building) will be used to reconstruct 6He beta spectrum by measuring the cyclotron radiation frequency of the decayed electrons. Each piece of the energy spectrum will be measured separately by varying the magnetic field strength. Since the total number of 6He atoms entering the decay volume can vary over time, each part of the spectrum needs to be normalized to the same scale before combination. This requires a monitoring system that counts the total number of 6He atoms over each data taking period. As part of the effort to prepare for the upcoming 6He experimental run, this project is to develop this monitoring system so that it maintains its stability at the level of 10 ^-3 . The test was done on three experimental setups including a pair of gas counter plus silicon detector, a pair of scintillators and a single silicon detector under vacuum. Of the three setups, the single silicon detector reached desired stability on the most recent experimental run although more validations are needed. A successful setup of the monitoring system will help the experiment to reach desired sensitivity with spectrum normalization. And the detection of tensor currents implies the existence of symmetry breaking with chirality in beyond standard model theories.

Geothermal flux, the amount of heat from the Earth’s interior that reaches the Earth’s surface, is an important boundary value used when modeling ice sheets in Antarctica and estimating future sea level rise. However, geothermal flux is difficult to measure directly. This research project used a numerical ice and heat flow model to estimate the upper bound for geothermal flux under ice domes in Antarctica. We applied this model to ice domes with identifiable Raymond arches, structures in the internal stratigraphy which form only when the ice is frozen to the bed. We estimated the geothermal flux at which an ice dome’s modeled basal temperature reaches the melting point, thus setting an upper bound, using site-specific values for the accumulation rate, surface temperature, and ice thickness. Where measured basal temperatures are known, we made more precise estimates of geothermal flux. Uncertainty values for the modeled flux values were derived by testing the uncertainty of each input value. Model estimates were compared with Martos et al. (2017) and An et al. (2015) geothermal flux estimates derived from remotely sensed data. Comparisons show that in regions such as the Siple Coast, estimates disagree significantly, while they mostly agree in the Antarctic Peninsula. The results of this project set an upper limit on geothermal flux values that can be used to support past and future geothermal flux estimates at these locations.

Nanopore sequencing is a “third-generation” sequencing approach in which a constant electric voltage is applied across a nanoscale pore and the changes in the ionic current flow through the pore are measured as single molecules such as RNA or DNA pass through it. It is our goal to expand and adapt this sensing technology to enable single-molecule proteomics. Specifically, being able to characterize protein post-translational modifications at the single-molecule level is important for quantifying protein complexity and understanding how different protein mod-forms contribute to cellular processes such as differentiation and the progression of disease states like cancer. In this project, we modified a model protein to contain a protein kinase A phosphorylation motif with the purpose of demonstrating the ability to discriminate the modified protein from the unmodified with the Oxford Nanopore MinION, a high-throughput nanopore sequencing device. We hypothesize that the observed ionic current pattern will change upon phosphorylation and enable direct quantification of modified peptides. Ultimately, these analyses will inform us of the general ionic current signature that phosphorylated residues generate, which can then be added to our growing library of nanopore signal signatures that are informative of protein sequence and structure at the single-molecule level.

Methanol is a common pollutant in freshwater ecosystems due to its widespread use in industrial operations, fuel, antifreeze, paints, and insecticides, and being a result of the burning of garbage. As a bioindicator species, Daphnia magna health indicates changes in aquatic ecosystem health. They are an important part of the food web, eating algae, and as a food source to insects and fish. No previous studies have examined the effects of the pollutant methanol on Daphnia heart function and mortality. This experiment examined the effects of varying methanol concentrations on heart function and mortality of Daphnia magna. It was hypothesized that methanol significantly affects the heart and mortality rate of Daphnia. Fifteen experimental biospheres were used in each trial, with three jars for each of the five concentrations. The biospheres were filled with deionized water and methanol in concentrations of 0 ppm (control), 822.6 ppm, 1644.5 ppm, 3289.0 ppm, 7119 ppm. In a second trial, the concentrations were 0 ppm, 822.6 ppm, 1644.5 ppm, 205.7 ppm, and 411.3 ppm. Heart and mortality rates were observed and recorded for each trial over 4-8 days. For each jar, videos were recorded for 15 seconds each and heart rate was counted, and mortality counted every other day. Based on the survival and heart rate differences, it was concluded that as methanol concentrations increase, the heart rate of Daphnia varied but didn’t respond linearly to concentration levels. Additionally, higher concentrations of methanol negatively affect survivability, although the initial control groups had somewhat high death rates. This study highlights the negative impact of methanol pollution on Daphnia because a negative impact on Daphnia affects the whole freshwater ecosystem. Indeed, in Lake Washington, Daphnia represent a major source of nutrients for juvenile Sockeye Salmon, making Daphnia indispensable for their growth.

Mitosis is an essential cellular process in which a cell divides to produce two genetically identical daughter cells. When this process becomes dysregulated cells divide uncontrollably leading to diseases such as cancer. Polo-like kinase 1 (Plk1) is a key enzyme that is necessary for coordinating numerous events during mitosis. When Plk1 becomes dysregulated or mislocalized, mitotic spindle assembly, protein organization, and mitotic timing impairments may occur. One of the many subcellular locations where Plk1 carries out essential mitotic functions is the kinetochore. The kinetochore is the interface between the chromosomes and the mitotic spindle and is critical for ensuring proper DNA to microtubule attachments early on in mitosis. Historically, the small-molecule inhibitor drug BI2536 has been used to inhibit the activity of Plk1 in order to study its role in regulating various mitotic processes. However, traditional inhibitor drugs turn off entire protein kinase populations, inhibiting the activity of Plk1 all throughout the cell, not just at the kinetochore. This can lead to unwanted side effects and limits our understanding of Plk1’s role at specific subcellular locations. To improve the specificity of BI2536 drug delivery, we utilized SNAP-tag, a tool in which a self-labeling enzyme can irreversibly react with substrates linked to a chloropyrimidine (CLP) functional group. By genetically manipulating human bone cancer (U2OS) cells, we expressed a kinetochore localizing SNAP. We also generated a BI2536 conjugated to a CLP group. By treating our genetically modified cells with CLP-BI2536, we can target Plk1 inhibiting drug to the kinetochore to study Plk1’s role at this specific location. Using super-resolution structured illumination microscopy (SIM), we demonstrate that we can effectively target fluorescently labeled CLP substrates to kinetochores in our cell line. In future work, we will target our CLP-BI2536 drugs to the kinetochore and investigate how local Plk1 inhibition affects mitotic timing.

Insect pollination is crucial to agriculture and conservation, but little is known about the ecology and evolution of floral scent, which is one of the strategies that plants use to attract pollinators. Flowers that rely on insect pollinators have floral scent compositions that attract certain types of pollinators more than others. Oenothera pallida is a plant which is pollinated by both daytime and nighttime pollinators, so examining its floral volatiles gives us an idea of what attracts the different pollinators to this flower. My research examines how floral scent emissions from Oenothera palllida differ between the day and nighttime, and how these differences in floral scent emission affect the attractiveness of the flowers to different pollinators. I extracted the floral scent from Oenothera pallida that is grown in the lab. I used Porapak traps to sample volatiles from each plant for six-hour periods in the evening and in the morning, which allowed me to see the change in composition depending on the time of day. I analyzed the floral scent samples using gas chromatography - mass spectrometry (GCMS). Then I created artificial scent blends in mineral oil that reflected the scent compositions of daytime and nighttime floral scent emissions. I exposed the hawkmoths and honeybees to the different scent compositions in a wind tunnel and observed the different responses of the two species. Finally, I determined what proportion of the moths or bees were able to locate the scent source by counting the number of individuals that flew upwind and landed on the artificial flower. 

Rats produce ultrasonic vocalizations (USVs) in a range from 20-kHz to 95-kHz that vary in frequency and shape across social and motivational contexts and can correspond to the affective state of the animal. To assess these USVs accurately and efficiently, our lab created DeepSqueak, a novel machine learning software package that expedites the detection and analysis of rat USVs by using neural networks to differentiate them from noise. DeepSqueak also allows for automatic and unbiased classification of USVs into discrete categories using call parameters such as shape, frequency and duration. Prior to this unbiased categorization method, identified 14 subjective categories in 50-kHz rat vocalizations that could be manually identified by a trained experimenter. These categories have received some limited study, but the excessive labor and time needed for manual classification restricted broad adoption. We aim to use neural networks to quickly and automatically classify USVs into these categories to promote broad adoption and better our understanding of the relationship between USVs and behavior. The process of training our neural network to differentiate between vocalizations was approached in two ways. Audio files were converted to sonograms through DeepSqueak and manually labeled. Thousands of these labeled calls were then inputted as training data for the neural network. This method allowed the network to learn using a large set of labeled vocalization data. The second method is based around the manual selection of an optimal call for each subtype using DeepSqueak's "call clusters" function; the neural network was then trained around how closely vocalizations matched the optimal calls. We now plan to compare DeepSqueak's automated calls and clustering to manual scoring in order to develop the best possible system that reliably categorizes USVs, thus allowing for more specific analyses of USV categories and behavior.

Polymorphisms in the gene, FKBP5, and its resulting protein, FKBP51, are associated with stress-related disorders. Although FKBP51 inhibitors may have antidepressant-like effects, the relevant brain regions mediating this effect are still unknown. We found that FKBP51 expression is elevated in serotonin neurons of the mouse dorsal raphe nucleus (DRN) after stress, so we tested whether FKBP51 inhibition in the DRN by the novel FKBP51 antagonist, SAFit2, has antidepressant-like effects. First, we implanted guide cannulas into the DRN of wildtype mice stereotaxically, then we habituated the mice to 2.5% sucrose-containing bottles in their home cages overnight. On the following two days, the mice were stressed through repeated forced swims after receiving either SAFit2 (n=8) or a vehicle (n=7) to the DRN via the cannulas, prior to each swim session. That evening, the mice underwent a sucrose preference test to assess motivation by quantifying sucrose versus water preference using lickometers. On the next day, the mice were tested in a three-chambered social interaction test, where one chamber contained a wired cup enclosing another mouse of the same sex and the other chamber had an empty wired cup. Our results show that the SAFit2 and vehicle mice had the same immobility time during the forced swim stress, signifying that SAFit2 did not interfere with our immediate stressor. The SAFit2 mice demonstrated an increased preference for sucrose after stress compared to the vehicle mice, indicating greater motivation to consume a pleasurable liquid. However, there was no significant difference in the time spent interacting with the same sex during the social interaction test. This suggests that SAFit2 may have blocked stress-induced anhedonia by inhibiting FKBP51 activity in serotonergic neurons, as measured by the sucrose preference test. Further studies of FKBP51 inhibition in the DRN can lead to potential therapeutic treatments of neuropsychiatric disorders.

Astrocytes are a type of glial cells in the central nervous system, play a critical role in protecting neuronal signaling by regulating brain homeostasis, synaptic plasticity and transmission, and blood brain barrier functioning in central nervous system. Accumulating evidence has indicated that abnormal behaviors of astrocytic functions, including astrodegeneration and astrogliosis, are implicated as the primary factors contributing to a number of chronic neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Kir4.1 is an inwardly rectifying K+ channel expressed on the projections of astrocytes, which serve important roles in the neuroprotective function of astrocytes, such as maintaining K+ homeostasis and regulating extracellular glutamate. Abnormal expression of Kir4.1 has been reported in certain neurodegenerative diseases, including Amyotrophic lateral sclerosis (ALS) and Huntington’s disease (HD), suggesting a vital role in the development of pathophysiology. However, the association between the molecular mechanism and expression of Kir4.1 and the underlying pathogenesis of AD and PD has been largely uninvestigated. In this study, we have had the critical opportunity to access human post-mortem brain tissue, provided by the University of Washington Alzheimer’s Disease Research Center, and conducted confocal microscopy studies. Through a quantitative immunofluorescense staining approach, we expect to demonstrate a distinct expression pattern of Kir4.1 in various brain regions of AD and PD post-mortem tissues when compared to control subjects. Determining the role this protein has in neurodegeneration may provide new insight into the development of therapeutic targets to ameliorate the progression of AD and PD.

Barcoding of physical objects with molecular tags holds an advantage over traditional paper or electronic barcodes in that they are discreet, durable, and difficult to falsify. Here, we developed a DNA tagging system that labels objects to verify their authenticity and trace their origin. We chose DNA as our tagging medium due to its information storage capacity and chemical stability, allowing us to generate a wide variety of unique barcode sequences that can be read by Oxford Nanopore’s MinION sequencing device. The MinION contains an array of thousands of nanopore sensors that are capable of sequencing single strands of DNA. The nanopore sequencing process creates distinct disruptions in the ionic current through the sensors that are indicative of the DNA sequence. However, the DNA basecalling software that processes the raw ionic current is computationally expensive, making it impractical when our goal is to quickly “scan” and identify a tagged sample. Because of this, we designed our barcode sequences to generate unique current patterns that are identified using a simple classification algorithm as opposed to arduous basecalling. So far, we have synthesized and classified a set of 96 barcodes that can be indiscriminately combined to create multi-bit tags. In a given tag, each bit is defined by the presence or absence of a particular barcode, and in practice, we have assembled and read up to 16-bits. We have also explored increasing bit capacity by independently varying barcode lengths, which adds another dimension to the barcode space. We also tested the durability of our barcodes by drying them onto filter paper and sequencing them 24 hours later, proving that our barcodes could survive in a dehydrated state. Future experiments will aim to lengthen this duration and expose the barcodes to different environments, in order to better simulate intended tagging conditions.

What started as a recovery account on Instagram, about four years ago, quickly grew into something so much more. As I became transparent about my struggles with an eating disorder and mental health, after being sexually abused, this account became an avenue of guidance for others. Through this process I realized the disheartening need for support that was free of any fiscal burden that so often is unjustly required. My project, currently funded by a Mary Gates Leadership scholarship, aims to raise awareness while giving community and support to victims of sexual abuse. I contacted SARVA (sexual assault and relationship violence activists) on campus to receive volunteers to collaborate in my project. With their consent, I am drawing them with their eyes removed to create a conversation of the overwhelming number of individuals who've been assaulted. The censorship of the eyes allows a layer of anonymity for the volunteers as well as an unsettling feeling to the viewer. I am drawing them using ink on a 5”x7” aquaboard. I meet with each survivor to present a healing opportunity where they can disclose their story to me. During this time, I take their picture and use that as my reference to draw them, capturing a powerful moment in that meeting. As of right now I have ten portraits to show, but underneath those ten portraits are hours of research, late studio nights, and forty previous paintings. I have written numerous essays just on Jenny Saville, but also researched Paula Rego, Marlene Dumas, Tracy Emins, and more. This process is crucial as it informs my practice and keeps me knowledgeable about previous works. With that said, there is another component to my project; psychology. These situations are extremely sensitive and my previous studies and research in psychology have been invaluable.

Jacques-Louis David's 1789 The Lictors Bringing Brutus the Bodies of His Sons stages a harrowing scene from Roman history. Consul Brutus, upon discovery of his sons' treasonous plot to restore the monarchy, sanctions their deaths in defense of the Republic. Debuted in the 1789 Paris Salon and shortly after the fall of the Bastille, the political meaning of the colossal painting would have been explicit. In painting the return of the sons' bodies, David's composition reinforces the grave but necessary cost of revolution. Representing an event of classical antiquity as a moral exemplar, Brutus is firmly anchored in period conflict, evincing David's personal revolutionary values. This presentation is a survey of current art historic scholarship surrounding David’s Brutus as a dramatic tableau that synthesizes antiquarian interest and theatricality. The purpose is to understand the aesthetic, social and historic influences of the painting and its presentation as a cathartic, timeless exemplar of nationalistic virtue told through the myth of Brutus.

This presentation examines Sir John Everett Millais’ 1851 Mariana, paying special attention to the ways in which the painting embodies and represents nostalgic desires. A hopelessness that provokes the historical encounter of distant past pervades the piece, which takes its inspiration from a 1830 poem that uses the characters from Shakespeare’s play Measure by Measure. Moreover, the aesthetic vision of Millais, like many of his pre-Raphaelite contemporaries, is one framed by a trans-historical dialogue with tradition. The painting depicts Mariana with an arched back and an outward gaze, reminiscing on her past love. Overall, the painting invites the viewers to reminisce about their personal and artistic past while getting lost in the details this painting offers.

Current artificial neural networks (ANNs) use an archaic view of neurons based on oversimplification of their biological computations. This has allowed optimized computation through GPUs, leading to the widespread adoption of ANNs in deep learning but losing important biological features. In this research we create a new model for artificial neural networks that incorporates more realistic aspects of biological neural networks such as stochastic vesicle release in neuronal synapses and dendritic computation. It has been shown that animals learn models of the environment when introduced to a new situation, but this type of learning is often not incorporated into reinforcement learning models in AI. The goal is to have the new, biologically realistic ANN learn models of environments in simulation frameworks like OpenAI Gym and AI2Thor so that given past frames/images and an action taken by the agent/player the network can predict how the environment will react over time. We compare the performance of this network with that of traditional ANNs (e.g. recurrent neural networks with long-short term memory) to demonstrate the capabilities of the new network. Our results have implications for recent efforts to move toward biologically inspired models of learning in the fields of artificial intelligence and computer vision in robotics. We expect the model learning algorithms we present to more efficiently learn an environment and select actions to achieve arbitrary goals within that environment. This is different than traditional reinforcement learning models, which aim to complete a single goal and can take a long time to train. The novelty of this work is the increased biological realism without the computational complexity of simulating real neurons, the temporal aspect in neural processing in addition to the spatial aspect, and prediction based on actions instead of pure video prediction.

By the late 1520s, Henry VIII’s lack of a legitimate male heir had led to a succession crisis in England. Eventually this culminated into a procession of legal and scholarly battles broadly referred to as "The Great Matter", which was the quest for the annulment of Henry VIII's first marriage. Criticisms over these proceedings by historians often decontextualize the events of the Great Matter. Moreover, the Great Matter is often portrayed as a vanity project; one that was wholly unnecessary because Henry VIII had a legitimate daughter from his first marriage. There are many flaws with this presentation of history. For one, it ignores most of the historic precedent up to the point of Henry VIII's reign for how female leadership was received, and what that reception could lead to– namely rebellion, usurpation, forced abdication, civil war, and instability. I argue that, rather than a vanity project, the Great Matter was absolutely understandable within the context of the time and place it occurred. I also argue that, rather than the near and distant future proving Henry’s anxiety over the reception of female leadership as unwarranted; such anxiety demonstrated a remarkable sense of awareness and an extraordinary prescience. My research includes the Letters and Papers of Henry VIII and a collection of other various primary source quotes relevant to the matter of female succession in the sixteenth century, and the Great Matter in particular. These were analyzed through a social and cultural lens, and also analyzed through contextualization and comparison to later relevant events.

This project looks to understand the role of women in the second rise of the Ku Klux Klan in the 1920s to understand why this manifestation has been categorized as the largest right-wing movement in the history of the United States. I argue that the addition of women as active participants in Klan activity, unlike the first rise during Reconstruction which was a strictly fraternal society, transformed the movement from a domestic terrorist organization into a political club with immense social influence on the white Protestant population in America. Primary sources used to build this argument came from Klan documents such as pamphlets and newsletters as well as local and national newspapers from across the U.S between 1918-1927. Women in this time period were emboldened to participate in politics after their victory with the suffrage movement, and those who employed racist and nativist ideology easily transitioned into the white supremacy of the Klan, who desperately sought to recruit blocs of voters. Using coded language such as "100% American" to describe themselves, the Women's Ku Klux Klan (WKKK) utilized issues such as poor education, alcoholism, and immigration as a silk screen to vilify their ever-growing list of "enemies" (a tool used to recruit membership from a larger base) among them Catholics, Jews, Bolsheviks, blacks, labor unions in the North, and immigrants. The addition of women allowed the Klan to become an organization that supported nuclear family structure and encouraged all to be involved, including children, which served to develop “Klan culture” to recruit and retain members by building community. While Klanswomen were different from their male counterparts, they worked within social networks that maintained consistent growth, starting chapters in almost every state and amassing political and social influence on a local and national level.

The nineteenth century saw the British empire rapidly expand around the globe, with the British military facing conflicts in Spain, Crimea, India, Central Asia, and across the African continent. This rapid expansion culminated in the largest of Britain’s many nineteenth century colonial conflicts: the South African War (1899-1902), otherwise referred to as the Second Anglo-Boer War. While Britain had been engaging in military conflicts nearly continuously throughout much of the nineteenth century around the globe, its intelligence apparatus was, at both the strategic and the tactical levels, largely ad hoc and underfunded. Because of this, those in the British military tasked with gathering intelligence regularly relied upon nonmilitary people for intelligence. My research seeks to analyze the structure of British tactical intelligence networks during the South African War, focusing specifically on the British military’s often unacknowledged reliance on people it deemed outside of itself, such as volunteers, prisoners, journalists, and black South Africans to gather and communicate military intelligence. Drawing on primary sources such as newspapers, diaries, parliamentary testimony, and memoirs, I have crafted a view of British tactical intelligence networks during the conflict which focuses on the biases and prejudices which influenced their development and structure, as they simultaneously reified and questioned the dominant racist and sexist hierarchies of the time. I argue that the diverse composition of British tactical intelligence networks in South Africa demonstrates that these networks were intersectional spaces, where politics of race, sex, and knowledge determined the methods by which intelligence was gathered, communicated, and analyzed throughout the war. In contextualizing the tactical intelligence networks of the South African War as intersectional spaces, I seek to demonstrate that the study of intelligence networks in wars of imperial expansion affords a unique opportunity to analyze the relationship between colonial armies and the peoples they fight amongst.

I present a baseline assessment of the plant family Melastomataceae along an elevational gradient of the Llanganates-Sangay ecological corridor in central Ecuador. Conservation efforts within this corridor aim to preserve the high levels of diversity and endemism present in the region. Melastomataceae, as the third most diverse plant family in Ecuador, contributes valuable biodiversity, biomass, and ecological services to the ecosystems of this corridor. On Cerro Mayordomo (max elevation: 3,383 m), 300 m transects were established at four different elevations, and six 5x5 m plots were assessed along each transect (600 m² assessed total). All melastome species encountered in plots were grouped and counted based on morphological characteristics. My findings reveal a positive correlation of melastome diversity and abundance with elevation up to 2,500 meters. At 3,000 meters, species diversity decreases sharply, but total abundance remains high. Jaccard, Sorenson, and Morisita-Horn similarity indices indicate dramatic changes in melastome community composition over even slight differences in elevation. Eighteen species of flowering melastomes belonging to four genera were found, revealing a subset of the family's astounding diversity in this region. The results of my study will be used to inform future conservation efforts and ecological studies in this incredibly unique and important Andean corridor.

Pacific sand lance (Ammodytes personatus) are important to the diets of sea birds, other predatory fish, as well as mammals. Microplastics (plastics < 5 mm) have been found in spawning and deep-water habitats for these organisms. This project explored if microplastics are found on beaches near Friday Harbor Labs on San Juan Island, WA., and if so, to determine their concentration and distribution. Nine sediment samples were collected from two beaches (Jackson and South) and a wave field known to be Pacific sand lance habitat in this area. Samples were processed according to NOAA’s Microplastics Methods Manual. Presence, abundance, type (fiber, fragment, film, pellets) and size class (< 0.5 mm, 1-5mm, 6-10mm, > 10mm) of microplastics were determined from sediment samples collected. Microplastics were found in all samples. Microfibers were the most abundant microplastic type (86%), and Jackson beach had the highest concentration of microplastics (17 microplastics/m2). On average the sizes were between 1-5 mm, and the number were 13 microplastics/m2 in the study area. Larger pieces (5-10 mm) were not present at the wave field located on the seafloor, although found at both beaches. This research helps connect microplastic presence to Pacific sand lance habitat. Considering the main prey type of Pacific sand lance and microplastics found in their environment overlap in size classes, it is highly likely that Pacific sand lance are consuming microplastics.

Dysregulation of the dopamine system is a central mechanism driving substance use disorders. Our laboratory has shown that chronic cocaine consumption decreases dopamine release in the nucleus accumbens of the rat, which is a brain area that is important in reinforcement learning. This study also found that restoring dopamine transmission through the administration of the dopaminergic drug, L-DOPA, decreased their cocaine consumption. Recently, we have also shown that acute administration of L-DOPA decreases ethanol (EtOH) intake. Thus, the present study sought to examine the effects of chronic L-DOPA on operant responding for EtOH in adult male rats. Rats were presented with a 2-bottle choice between an EtOH (20%) solution or water, daily for 21 days. Next, animals made nose poke responses (FR1) for 0.2 mLs of an EtOH (20%) solution over 1-h daily sessions for 35 days. On Days 26-35, rats consecutively received either vehicle or L-DOPA (30 mg/kg) for 5 days, counterbalanced across days, and L-DOPA decreased operant responding for EtOH compared to VEH. We are presently examining the effects of L-DOPA on dopamine release during operant responding for EtOH. Together, these data may suggest the efficacy of L-DOPA as a treatment for patients with alcoholism.

Drosophila alpha-tubulin acetylase (dTat) is an enzyme that covalently modifies microtubules by addition of acetyl groups to the microtubule lumen. Prior studies demonstrated dTat is essential for mechanosensation in Drosophila. Mutation of alpha-tubulin lysine 40, which is covalently modified by dTat, similarly compromises mechanosensation, but our preliminary results suggest that alpha-tubulin 40 mutation and dTat mutation differentially affect some forms of somatosensation. Consistent with this observation, recent studies suggest that dTat may additionally regulate microtubule stability independent of its enzymatic activity. Whether this non-enzymatic function of dTat influences neuronal function remains to be determined. In my studies, I aim to determine the relative contributions of enzymatic and non-enzymatic functions of dTat to somatosensory function in Drosophila larvae. To this end, I have assayed requirements for dTat function in a variety of larval mechanosensory and thermal responses, which are governed by defined classes of somatosensory neurons. For each of these behaviors, I used transgenes to resupply dTat function to dTat mutant flies, comparing the ability of wild type and enzyme-dead versions of dTat to support neuronal function. Results from these studies provide an entry point to understanding enzyme-independent function of dTat.

Gut Microbiome is increasingly recognized as a pivotal player in toxicological responses, thus dysbiosis or microbial imbalance may worsen chemical-induced adverse outcomes such as inflammation, metabolic syndrome, and cancer. Early life exposure to environmental contaminants may produce long term toxicities in adulthood, and little is known to what extent early life exposure to environmental contaminants modulate the gut microbiome beyond adulthood. Therefore, this study tested the effects of perinatal exposure to 3 human health relevant environmental contaminants (BDE-47, TBBPA, and BPS), on the composition and functions of the gut microbiome of perinatally exposed adult male mice. CD-1 mouse dams were orally exposed to vehicle (corn-oil, 10ml/kg), BDE-47 (0.2mg/kg), TBBPA (0.2mg/kg), and BPS (0.2mg/kg) once daily from gestational day 8 to the end of lactation (postnatal day 21). Feces from male pups were collected at 12-weeks of age (n=14-23/group). Microbial DNA was isolated, subjected to 16rDNA sequencing, and analyzed using QIIME. Microbial biomarkers for each chemical exposure were predicted using LefSe. Microbial functions and key taxa that drive functional changes were predicted using PICRUSt and FishTaco, respectively. None of the 3 chemicals markedly altered the overall richness of the gut microbiome in adult male pups. However, principle coordinate analysis showed a distinct separation among different exposure groups, and especially between BPS and vehicle exposure groups. A total of 73 taxa were persistently altered by at least 1 chemical exposure, among which 12 taxa were commonly regulated by all 3 chemicals. The most representative microbial biomarkers for each exposure condition were Clostridiales for vehicle, S24-7 for BDE-47, Rikenellaceae for TBBPA, and Lactobacillus for BPS. Together, these observations suggest early life exposure to these human health relevant environmental contaminants produce persistent gut dysbiosis in adult male offspring, leading to functional shifts that may play important roles in regulating certain diseases of the host.

Mouse adenoviruses (MAdVs) are non-enveloped double stranded DNA viruses. There are two different types of MAdVs with different tropisms or ability to infect particular cells or tissues. MAdV-1 infects macrophages and endothelial cells and causes encephalitis. MAdV-2 infects intestinal cells but causes no disease. Although, the MAdV fiber capsid proteins are important for attachment of the virus to host cells, it is not known if they are the major determinant of tissue tropism in the mouse. To address this question, I use recombination-mediated genetic engineering to make chimeric MAdVs, wherein I keep most of the genome of one strain but replace the fiber protein with that of the other strain. I then use transfection to introduce the DNA of the chimeric virus into a mouse cell line to allow the virus to replicate. I am currently designing and testing the proper chimeric fiber construct that will result in a replication-competent virus. Ultimately, I compare infection of the chimeric virus to that of the parent viruses in intestinal organoids, a tissue culture model that allows us to faithfully test tropism without the need for mouse studies. These experiments may reveal general principles of AdV tropism that will allow us to understand why different human AdVs cause disease in specific organs.

Mouse adenoviruses (MAdV), like human adenoviruses (HAdVs), have specific tissue tropisms. MAdV-1 infects macrophages and vascular endothelial cells, which can result in encephalitis, while MAdV-2 infects epithelial cells of the intestine but does not cause overt disease. The viral protein that determines MAdV tropism is unknown; however, for many viral families it is the viral attachment protein that is critical. For MAdVs, fiber is the viral attachment protein, and the receptors used by MAdV-1 and MAdV-2, although unknown, are distinct. To test whether MAdV receptor usage dictates tissue tropism, I constructed a MAdV-2 chimeric virus, replacing its fiber protein with that of MAdV-1 using a gene-editing recombination system. The chimera was used to infect a 3D culture model of the intestinal epithelium called “enteroids.” As expected, MAdV-1 does not replicate in enteroids and MAdV-2 does, consistent with their in vivo tropisms. Remarkably, the chimera replicated efficiently, indicating that the fiber protein is not the sole determinant of MAdV-2 intestinal tropism. Although fiber is not the main contributor to tropism, its interactions with host factors are still likely important for productive infection. A recent study identified N-acetylglucosamine (GlcNAc) as a specific ligand for MAdV-2 fiber. We have shown that GlcNAc is not the primary receptor for MAdV-2; however, binding to GlcNAc may aid in adhesion of MAdV-2 and penetration through the mouse intestinal mucus layer. To test this hypothesis, I mutated the GlcNAc interacting residues in MAdV-2 fiber to prevent GlcNAc binding. I am currently comparing the infectivity of this mutant virus to wild type MAdV-2 in both epithelial tumor cells and enteroids. Unlike tumor cell cultures, enteroids contain mucus-secreting goblet cells which will recreate the in vivo context more accurately. Together, these studies of MAdV may help us to understand why different HAdVs infect specific tissues.

Human alpha defensins, a component of the innate immune system, are small cationic peptides that possess antiviral activity against non-enveloped viruses. The effect of defensins on human adenoviruses (HAdV) is serotype-dependent, infection by some serotypes is enhanced while for others it is neutralized. Enhanced infection correlates with increased cell binding; however, the mechanism of increased binding is unclear. One hypothesis is that defensins mediate receptor-independent binding. Inhibitor studies support this hypothesis, although formal proof is still needed. To test this hypothesis, we used CRISPR/Cas9 lentivirus to knockout the primary receptor, coxsackie adenovirus receptor(CAR), in A549 lung cells. In order to vet these cell lines, they were infected with different HAdV serotypes that use either CAR or an unrelated molecule, sialic acid, as their primary receptors. As expected, the sialic acid-utilizing but not the CAR-utilizing serotype was able to infect the CAR KO A549 cells. We have used these cell lines in combination with integrin co-receptor inhibitors to measure binding and infection of wildtype and mutant adenoviruses in the presence and absence of defensins. These experiments allowed us to determine the extent to which defensin-mediated attachment and entry is receptor-independent.
 

Bacteria inhabit a world filled with threats, including antagonism from other species throughout different environmental conditions. One mechanism microbes employ as protection from these hazards is the type VI secretion system (T6SS) - a system bacteria utilize to inject toxic proteins into neighboring cells, leading to cell death. The H1-T6SS of Pseudomonas aeruginosa comprises 7 pairs of toxins and cognate immunity proteins (which prevent self-intoxication). I hypothesized that each of these toxins could be maximally effective against specific kinds of competing bacteria, however the function of many effector proteins is unknown. My research focuses on characterizing the protein Tse7, encoded by the gene PA0099, and elucidating its potential role in species-specific antagonism. To begin, I identified its key functional amino acids and the gene encoding its immunity protein. I designed and created mutant strains with several genes adjacent to PA0099 deleted and co-cultured these with wild-type Pseudomonas aeruginosa to identify any mutants with a loss in competitive fitness. This lead to the discovery that the gene PA0100 encodes the cognate immunity protein. To determine key functional residues, I identified potential candidates using conserved motifs in the toxin’s amino acid sequence. By creating mutants of these residues and analyzing their change in competitive fitness compared to wild type, I recognized histidine 230 as the residue vital for Tse7 function. Going forward, I will attempt to determine whether Tse7 improves fitness of P. aeruginosa against any specific families of bacteria, indicating the toxin targets that particular bacteria. Almost one-third of Gram-negative bacteria have T6SSs. These systems largely dictate the ability of bacterial species to compete with one another, dramatically affecting bacterial community structure and the landscape of human infections. Therefore, this deepened understanding of its function could further our knowledge of and ability to manipulate bacterial interactions’ impact on environmental and human health.

 Twelve replicate populations of the bacterium Escherichia coli have been evolving in Lenski's Long-Term Evolution Experiment (LTEE) for over 67,000 generations in a shared nutrient limited environment. The evolved bacteria grow 70% faster than their ancestor but experience a decrease in number produced during a growth cycle. This is consistent with a trade-off between growth rate and yield (here defined numerically). We explore if populations are constrained by their previous ecolution, and if populations with high growth rate can evolve to have a higher yield (and if so, does this happen at a cost to growth rate?). We do this by adding population structure to growing populations, where selection is relaxed on growth rate and strengthened on yield. Water-in-oil emulsions provide a structured environment where millions of nutrient-filled droplets are isolated by an oil phase. We manipulate population structure by inoculating droplets with either one bacterial cell (low starting density) or more than two bacterial cells (high starting density). We observe that selection acts on faster growing cells in our high density emulsion treatment and higher yield cells in our low density emulsion treatment. We also observe a change in cell size: cells in the high density emulsion treatment get bigger over time, and cells in the low density emulsion treatment get smaller. We explore if there is a relationship between cell size and growth rate/yield trade-off.

Extra chromosomal pieces of DNA, called plasmids, exist within bacterial populations. Many scientists believe that the relationship between plasmids and their bacterial hosts is mutually beneficial. Plasmids use replication machinery from their host to ensure their continued persistence. Meanwhile, the plasmid carries genes that can benefit the bacteria, such as genes that can provide resistance to antibiotics. In environments that contain antibiotics, bacteria that contain plasmids with antibiotic resistance genes would have a higher fitness and be able to survive and reproduce at a higher rate compared to bacteria that don’t carry plasmids. Contrary to popular belief, research by members in our group showed that different plasmids actually persisted in bacterial populations when they were not under selection. The purpose of this project is to see if the trend of plasmid persistence would continue in a nutrient limited environment. We performed a long term evolution experiment on three types of bacteria containing plasmids in a nutrient limited environment. Next, grew the evolved descendants in an environment containing antibiotic to see what portion of the population is still containing the plasmid. The results of this experiment will help scientists have a more holistic understanding of plasmid biology which could have implications on antibiotic treatments.

One method of comparing strain fitness is to compete strains head to head; over time, the competitor with a fitness advantage will increase in frequency in the population. To track the frequency of each strain, they must be differentially marked such that their frequencies can be measured by plating the culture and counting colonies of each type - a time and labor-intensive process. One common marker used by our lab and others is using pigment production to produce colonies of different colors. My project is to create a continuous culture monitoring device named a chromostat that uses a color sensor to measure the relative abundance of different colored strains in solution, removing the need for plating and increasing the automation of competition experiments. By comparing the color of the individual yeast strains to the color of them mixed together, the chromostat can calculate, in real time, the relative abundance of each strain in solution and determine which strain is more fit and by how much. I built the chromostat on a raspberry pi minicomputer using an open source Java library, pi4j, to control the attached color sensor. This sensor converts light waves to red, green, and blue color values, which are then converted to frequency values for each strain and displayed to the user. The chromostat is controlled through a text-based interface that operates on the command line and has a variety of functions to modify data acquisition to increase overall accuracy and allow for data analysis. It will be used as part of a high school teaching laboratory in which students conduct evolution experiments and later compete different yeast strains against each other to generate fitness data.

Companion-affected mass loss complicates our understanding of evolved stars; for example, theoretical models predict up to 70% of all main-sequence O stars interact with companions at some point during their lifetimes, but the details of mass loss and transfer in binary systems are poorly understood. V367 Cyg is an eclipsing, low-mass binary system with a complex geometry that offers a unique opportunity to better understand mass transfer processes; the primary star has overflowed its Roche lobe, resulting in an accretion disk that surrounds the secondary star. Using new spectropolarimetric data of V367 Cyg taken with the University of Wisconsin’s Half-Wave Polarimeter (HPOL) at the Pine Bluff Observatory, I have resolved the behavior of the accretion disk by determining the position angle and intensity of the polarized light from the system as a function of orbital phase. Here, I will present an analysis of this data and discuss their implications for the mass-loss geometry of the system. By constraining the properties of this interacting binary, we can more precisely study the details of stellar mass transfer.

 As the number of American students who identify as mixed race or biracial continues to grow, the American education system still has yet to make the necessary changes that are responsive to the needs of this shifting demographic. While identifying students on their own terms is important for all students, for mixed-race students, the questions and potential disconnect between racial labelling and how one defines themselves is fundamental. This study examines the roles biracial categorization plays in today’s classrooms through lived experiences as remembered by college students. Many classrooms still struggle to incorporate the achievements of minorities, and, in some cases, the mixed identity of a historical figure is overlooked entirely. The inability to see themselves in the curriculum may be causing mixed-race students to feel invisible in the classroom and disconnected from their education (Joseph-Salisbury, 2017). Drawing on findings from survey results, focus groups, and individual interviews, this research project contributes to studies focusing on the schooling experiences of mixed-race students. Maria Root (1996) and Kristen Renn’s (2003) models of biracial categorization are used as a framework for the study, as the project re-assesses the inclusivity and adequacy of the biracial categories introduced. In the classroom, seemingly small interactions and events may be forcing students to choose one aspect of their identity, rather than celebrating both. Focusing on how the classroom setting impacts identity has the potential to make the classroom a more inclusive space that is responsive to the myriad of ways biracial students may or may not choose to identify.

For many high schoolers having a mentor can significantly alter their life course. For marginalized youth, research has shown that quality mentoring increases the likelihood for high school graduation, addresses socio-emotional needs, and improves mentee’s behavioral skills. Mentoring is one of many interventions schools might use to address students with multiple risk factors such as poverty, housing instability, food insecurity, and discrimination. These many risk factors, in turn, lead to a disproportionately negative high school experience and higher rates of socio-emotional and behavioral issues than students with fewer risk factors. However, increasingly schools have turned to more punitive carceral approaches to manage these negative behaviors by increasing the presence of police officers, security guards, or school resource officers into public school settings. One Portland program works to address this issue by implementing a community care based mentoring program. This study seeks to understand the experiences of both policing and community care mentoring for freshman and sophomore students at three urban public high schools. This study will take on a mixed-methods approach. A survey will be composed to collect quantitative self-report data, as well as semi-structured interview guide to collect qualitative data in the form of open ended questions. The findings from this study will inform the power of community care in high school in relation to mentoring students of color vulnerable to the school-to-prison pipeline, which can be used to inform the argument to remove police from schools and for the continuation of mentoring programs and the allocation of increased federal funding to provide further support for this program and ones similar.

Periodic orbits provide an underlying structure to chaotic attractors, which provides order and low-dimensionality to complex, chaotic systems. The trajectory of chaotic systems proceeds to infinity for an arbitrary initial condition; for this reason, periodic orbits are useful as a finite set of finite mathematical objects to characterize the infinite, complex behavior of a chaotic system. In particular, the mathematical framework of chaos, chaotic attractors, and unstable periodic orbits allow for a new understanding of self-organization in complex physical systems like turbulence. In this study periodic orbits as an organizing principle will be examined in the Lorenz system and the double pendulum system. This study will find the unstable, periodic orbits of the Lorenz system and the double pendulum system using Newton’s method. The expected results of the study are that periodic orbits of both systems will both be found. This study presents an opportunity for an understanding of chaotic behavior which will lead to engagement with the current research on turbulence.

Single electron devices (SEDs) are electronic devices that can isolate individual electrons along a conducting path. SEDs have potential applications in the field of metrology [science of measurement] and quantum computation. However, the devices have issues with performance, uniformity, and stability that must be addressed before these applications can be realized. To investigate these issues with SEDs, this work focuses on low-frequency charge noise, much less than 1 Hz, called charge offset drift. Previous studies have shown that the geometry of the device impacts charge offset drift. In this talk, I will describe our efforts to extend these studies, performed at 2.5 Kelvin, to millikelvin temperatures to further our understanding of these issues.

With the increased development of space programs globally, more space probes are being funded for sample-return missions. Versatility and power limitations are some of the critical issues that these extraterrestrial sampling rovers are seeking to overcome in order to reliably deploy autonomously. Exploring the rough and unpredictable surfaces of other celestial bodies requires more adaptable and energy efficient robotics, which is what makes bio-inspired origami structures so appealing. Leaf-like origami is reconfigurable, which means that it can walk, jump, grasp, and actuate other useful motions all within the same device. Typical robots have redundant actuators and structural systems, but origami devices can build up potential energy before converting it into a mechanical motion. Due to this, rigid origami design approaches have the potential to be more compact, versatile, and energy efficient than conventional devices. Studying reconfigurable origami-based robotics can lead to devices that can be transformed into multiple configurations for various tasks. To design a versatile origami-based structure, I followed up on the research that Professor Jinkyu Yang and the members of his research group had on leaf-like origami, specifically leaf-out origami. This origami structure shows multi-transformable features. This means that the structure can be configured in a stable-stored or stable-deployed shape without having an external power supply maintaining its configuration. By finalizing the design, fabrication method, and discovering the optimized folding patterns for jumping and grasping motions, we will be able to start implementing the structure into more complex systems. Designing more structurally efficient systems may be the most practical solution we currently have to combat power and versatility limitations for autonomous space probes.

We investigate recent developments in the foundations of mathematics, particularly homotopy type theory, to determine their viability as foundations of mathematics. Related foundations such as Martin-Löf type theory, topos theory, and category theory are also discussed. We evaluate the possible benefits of a type-theoretic formulation of mathematics and the nature of constructive axiomatic foundations. The research involves a review of the existing literature in these areas and a comparative analysis of the methods used across frameworks. This research is the first step towards the development of languages easily used by computers and mathematicians which incorporate the power and flexibility of nonstandard deductive procedures.

Increasing energy demand coupled with over-reliance on fossil fuels and other non-renewable energy sources has created a need for alternative renewable energy sources. The sun is one of the most promising sources and photovoltaic cells are one way to capture solar energy. Halide perovskite thin-films have recently emerged as ideal materials for solar cells due to low fabrication costs, bandgap tunability, high extinction coefficients, and high carrier mobility. Moreover, they have demonstrated rapid gains in power conversion efficiencies from 3.8% to 23.7% in nine years. Halide perovskites have the molecular formula ABX3, where A and B are cations while X is a halide. Past research has shown that methylammonium(MA) lead triiodide, a commonly used perovskite, can be changed into formamidinium(FA) lead triiodide by exchanging the A-site cation in a formamidinium iodide solution. This highlights high ion mobility and interchangeability in perovskites. However, in perovskites with mixed-ion composition, high ion diffusion adversely affects the device performance due to ion segregation, but little is known about inter-diffusion of different ions in perovskites. Here, we investigate the inter-diffusion of A-site and X-site ions in halide perovskite films by creating a lateral heterojunction of the ions. We confirm the creation of the gradient using UV-Vis and steady-state photoluminescence (PL) measurements. We further confirm that there is no change in the film morphology and crystallinity as evidenced by SEM and XRD, respectively. With PL line scans across the lateral gradient, we image the inter-diffusion of the ions as a function of position and time. Using Fick’s Diffusion equations to fit the PL line scans, we determine the ion inter-diffusion coefficient and extract the activation energy using temperature dependent measurements. This study demonstrates a facile quantitative method of probing the ion inter-diffusion in halide perovskites and furthers understanding of mixed-ion perovskite compositions.

As the only bus that runs from the University District to Mount Baker across Seattle’s Eastside, the 48 provides a unique perspective on accessibility. Through a research paper, and map of the 48’s route I analysed the access to various forms of economic and social capital, such as grocery stores, schools, medical centers, and community centers. Access to forms of economic and social capital were analyzed through their relative proximity to the 48 bus route, or the walking distance from homes in the Central District. The purpose of my project was to start a conversation about the access provided by the 48 bus, and to create a map and record of what is in the quickly changing Central District, as well as Mount Baker and Capitol Hill neighborhoods relative to the 48. All to ask where can the 48 take you? With the Mount Baker Transit Center and University of Washington as end caps, all of the destinations in between mark different issues Seattle faces such as development of single family homes, food deserts, and access to community centers. Focused through the perspective provided by public transportation a new perspective is provided on these issues through the lens of public transportation.

 Alzheimer’s disease (AD) is a severe neurodegenerative disease and the most common cause of senile dementia in the United States. AD affects approximately 5.7 million Americans. Presently, there is no treatment for the disease and the mechanisms underlying the development and progression of the disease are not well understood. Human induced pluripotent stem cells (hiPSCs) are a promising technology for the study of Alzheimer’s disease pathogenesis, but current stem cell maturation methods, used to produce functionally mature neurons for accurate disease models, are too time-consuming to allow for the efficient study of disease mechanisms. Therefore, there is a need for a more rapid maturation method to produce cultures of functional neurons without the extended time commitment that is standard for common differentiation protocols. To achieve accelerated neuron maturation, optogenetic stimulation will be used to periodically stimulate neural stem cells according to an optimized stimulation protocol. To accomplish this, we have created a lentivirus using a construct that expresses the channelrhodopsin, Chronos, under an EF1α promoter, designed RT PCR primers to measure Chronos expression, and collected RT PCR data on transduced cells. This virus will then be used to transiently transduce hiPSC derived neurons that have previously been gene edited to express a NeuN (marker of maturity) RFP (Red Fluorescent Protein) tagged fluorescent reporter that will function as a cell maturity readout. This stem cell line will be used to develop an optimized protocol for the light driven maturation of stem cells in vitro. The maturity of the neurons will be measured using electrophysiology to evaluate cell function and RT PCR to monitor gene expression. The success of this project will allow for more efficient study of Alzheimer’s disease in stem cell based disease models, which could lead to the discovery of disease mechanisms, revolutionizing the understanding of this burdensome disease.

Polycystic kidney disease (PKD), commonly caused by defects in polycystin-1 or polycystin-2, results in the formation of fluid-filled cysts and progressive loss of kidney function. Our laboratory has established a cellular model for ADPKD using kidney organoids, multicellular tissue that functionally and structurally resembles the organ of interest, derived from gene-edited human pluripotent stem cells (hPSC). To address the need surrounding a cure for PKD, we have also discovered a basis for a form of treatment involving myosin. Non-muscle myosin is a protein that controls cell protrusion and adhesion; we have established that lack of adherence increases cystogenesis dramatically. We discovered blebbistatin, a non-muscle myosin (NMMII) inhibitor, is a robust inducer of cystogenesis. Our previous finding begged the question if activators of NMMII have the opposite effect and reduce cystogenesis in PKD organoids. To better understand the role of myosin, we differentiated kidney organoids from human PKD hPSCs in a 24-well plate coated with Matrigel. We proceeded with microdissecting the organoids at 3 weeks before they formed any cysts and transferred the organoids to suspension culture where they were treated with either DMSO as a control or a pharmacological myosin activator for one week. The organoids were then imaged and number of cystic organoids were quantified. The treatment using the myosin activator compound resulted in decreased cystogenesis, in terms of the size and number of cysts. Although we have yet to clarify myosin’s effect in the PKD pathway, we have identified a myosin activator as a potential inhibitor of cystogenesis. Further experimentation is to be done with other compounds such as actin activators, and proceeding with experimentation on ex vivo kidneys of mice. Our current findings suggest that the polycystin proteins positively regulate actomyosin’s contractility, therefore myosin may be an important factor for keeping kidney tubule integrity and preventing cystogenesis.

Polycystic kidney disease (PKD) affects nearly 600,000 people in the United States and it is caused by mutations in the genes that encode polycystin-1 (PC1) and polycystin-2 (PC2). These modifications are responsible for the growth of fluid-filled renal cysts that can impair kidney function over time, and lead to end stage renal disease. PC1 and PC2 have also been localized to the mitochondria, suggesting that they are responsible for regulating cellular metabolism and energy production, which can lead to mitochondrial dysfunction and increased PKD progression. Our lab uses human pluripotent stem cells (hPSCs) to generate kidney organoids that can be used to study the advancement of PKD, which contain the major proximal structures of the nephron including podocytes, proximal tubules, distal tubules, and endothelial cells. Orgnaoids that lack both PC1 and PC2 will develop cysts that can grow large enough to be seen by eye. Unfortunately, these organoids lack a collecting duct (CD) system, a crucial component of the kidney that expands greatly in PKD. To address this need, we developed a protocol to differentiate hPSCs into ureteric bud (UB) cells, the precursors of CD cells. First, we identified Dolichos biflorus agglutinin (DBA) as a key CD lineage marker in developing kidneys through immunofluorescence analysis on human kidney tissue. Then, we took undifferentiated hPSCs and investigated their ability to express DBA by treating them with a concentration gradient of small molecules known to induce kidney lineage cells. The resulting cells were stained with DBA and GATA 3, an additional, early CD marker, and we found that both markers were expressed in vitro. We will continue modifying this protocol to better study the increased metabolic rates seen in PKD, its effects in CD cells, and the mechanism behind the PC1 and PC2 pathway that leads to cyst formation.

Alzheimer's disease (AD) is the most common cause of dementia, a general term for memory loss and other cognitive abilities. Although this disease has been a major research focus since the 1980s the pathologic mechanisms are still not understood, and therapeutic interventions have been ineffective. The most definitive method for classifying AD is through identifying accumulations of toxic proteins amyloid-beta and tau proteins in post-mortem brain tissue. Dr. Su-in Lee’s lab has developed a machine learning method that integrates the pathological tau phenotypes with gene expression levels in the same brain tissue. This analysis highlights the genes with expression level changes that correlate with the pathological protein aggregation phenotypes. For this proposal I will directly test the impact of these candidate genes on cellular pathologies resulting from aggregating human tau protein with a new C. elegans AD model in which human tau is expressed in the worm’s muscle. This tau expression will likely result in premature paralysis because previous nematode AD models with human amyloid-beta have shown this phenotype. The results of my genetic screening will lead to a better understanding of the human genes that are dysregulated in human AD brains and provide a basis for genetically-dissecting the pathways that influence the mechanisms of tau toxicity.

Journalists play a vital role in science communication. As media coverage of science is the gateway for the general public to engage in scientific issues, journalists are responsible for presenting understandable and reliable scientific news. What journalists report on and the underlying tones of their depictions largely shape how lay audience perceive science. Peer-reviewed journals serve to be journalists’ main source of information. The ongoing replication crisis in studies of life and social science, however, indicates that publication in a scholarly venue is not enough to acknowledge the validity of a study anymore. This leads to the question of how journalists determine whether the result of a study is robust enough to communicate to the public. The goal of this research is to understand how journalists interpret scientific findings and how uncertainties in scientific research impact journalists' decision-making. To understand these questions, I have interviewed journalists about their evaluation criteria of assessing the reliability of scientific findings in their depictions. I have also delivered surveys to draw insights about how journalists interpret quantitative reports from scientific researches, and how different factors, such as statistical significance mean or sample size, may affect journalists' judgement about the reliability of the studies they report on. This study, qualitative in nature, contributes to understanding how aware journalists are to uncertainties in science as well as to possibly suggesting ways to improve accuracy and reliability in science news.

The 2016 United States presidential election illustrated the pervasiveness of foreign information campaigns - state-backed operations aimed at influencing political discourse within a target nation state. Twitter has uncovered several such campaigns and has released datasets containing tweet activity of over 4,000 accounts identified as information operatives. The work presented here utilizes these datasets to study the interactions these campaigns have with science, scientific discourse, and the broader public understanding of science. A primary objective of these campaigns is to weaken a foreign adversary through information warfare. For example, one strategy might be to reduce vaccination rates. One way this is accomplished is by sparking debates in politically controversial scientific claims, such as the safety of vaccines, by referencing pseudo-scientific and predatory literature. To understand the extent of this strategy, we utilize document clustering to measure the concentration of engagement - total tweet frequency - around these controversial topics, comparing against a baseline random sampling of tweets from the Twitter real-time data stream. In addition to this, we perform exploratory analysis to detect references to both legitimate and illegitimate scientific articles, leveraging data from the Web of Science (WoS), a bibliographic database of more than 50 million papers across all disciplines since the mid-19th century. We expect the proportion of tweets mentioning controversial scientific topics to be higher in the Twitter data disclosure than in the random sampling of tweets. Of those tweets mentioning science related issues, we expect a small proportion of tweets to be direct references to scientific papers, which will likely be studies that are either controversial, disinformative, or directly related to foreign policy interests. Our goal for this study is to assess the strategic role that science disinformation plays in these campaigns and to contribute to the growing body of research aimed at detecting and preventing misinformation.

Auxin is a plant hormone that promotes root branching which allows improved anchoring in the soil and nutrient acquisition. At the molecular level, auxin promotes the activity of auxin responsive transcription factors called ARFs. I hypothesize that AGL42, a MADS box transcription factor works with ARFs during lateral root formation. I used CRISPR to remove the entire AGL42 gene from the genome and characterize lateral root phenotypes in the mutant. I characterized that AGL42 is regulated by auxin signaling. This was done by spraying Arabidopsis seedlings with auxin and measure AGL42 expression levels by RT-qPCR. I predict that increasing the levels of auxin will positively impact AGL42 levels. Alternatively, AGL42 may not be an auxin-responsive gene but may itself interact with the ARFs to affect downstream auxin signaling. To test this hypothesis, I performed a co-immunoprecipitation (Co-IP) assay to determine whether the AGL42 and ARFs interact with each other. By better understanding the lateral root specification, specifically the role of AGL42, we can learn how to improve the architecture of different crop plants, increasing their ability to thrive even in harsh environments.

Spinal cord and traumatic brain injuries (SCI and TBI) result in secondary injury causing further damage to neural cells, due to mechanisms of inflammation and cytotoxicity. Though some anti-inflammatory drugs have shown promising results in reducing secondary injury in animal models, their use is controversial in clinical practice due to systematic side effects at the required high dosage with questionable efficacy. An electrically controlled drug release system will allow for spatiotemporal control of drug delivery and might solve some of the issues with systemic dosing. We designed and fabricated a polypyrrole (PPy) microneedle array for control release of dexamethasone for application to the nervous system. Using micro-scale 3D printing, microneedles design were 3D printed in photoresist and sputter coated in gold to form a conductive surface. PPy was electrodeposited onto the microneedle arrays from a monomer solution of pyrrole and dexamethasone. Dexamethasone can then be released from the PPy layers by applying a negative potential. Dexamethasone release was quantified using absorbance spectrometry, after purification through high pressure liquid chromatography. Dexamethasone PPy arrays were then tested in an in vitro model of neuroinflammation. One hour after inflammation activation, cells received treatment. After 48 hours of incubation, cells were assayed for nitric oxide and cytokine production. Experimental results show sufficient release using electronically controlled dexamethasone release from PPy microneedles to decrease nitric oxide. There was a trend towards decreasing inflammatory cytokine release, but future experiments with higher sample sizes will be needed to prove significance.

Labeling objects with DNA-based tags can provide a secure, difficult to fake identifier that is particularly useful for objects of high value or those that cannot be physically tagged. In this problem setup, a tag is a bit string, where each bit represents the presence or absence of a DNA strand containing a particular barcode. Our goal is to consistently and accurately identify the tag. These DNA barcodes were designed for use on a MinION nanopore sequencer, which outputs a time series signal corresponding to the DNA sequence. Ideally, each barcode should generate a dissimilar signal, which makes it easier to distinguish from other barcodes. We designed 96 barcodes that are signal orthogonal (i.e the signal output from the MinION was as dissimilar as possible), and detected them using signal processing algorithms. Using this system, I created an error analysis pipeline to ensure that we can identify tags both quickly and accurately. In order to optimize the time it takes to identify a tag, it was important to minimize the number of sequencing reads we needed to observe on the MinION, without sacrificing accuracy. I found that using a subset of the reads produced approximately the same error rate as a full run. Therefore, we can run the MinION for a shorter amount of time, and still identify tags at a similar error rate compared to a longer runtime.

Hemoglobin A1c (HbA1c) is an important marker to aid in the diagnosis and monitoring of diabetes, as it is a measurement of average blood glucose concentration over the previous two to three months. The current instrument used at Seattle Children’s Hospital to measure glycated hemoglobin is the DCA™ Vantage Analyzer. The DCA™, being a point of care (POC) device, can only run one sample at a time and requires a significant amount of tech time to run a batch of samples. With that, there is a desire to validate HbA1c on the Vitros 4600 as it would improve utilization of tech time and potentially provide more accurate and precise results. A correlation study was first done by running 30 different samples across the Analytical Measurement Range (AMR <14%) on the Vitros 4600 and compared to the original values run on the DCA™ using the statistical program in EP Evaluator. The overall bias of the two methods was -3.265%, but after closer analysis, the bias <9% HbA1c was -0.509%, while the bias >9% HbA1c was -5.026%. Another method comparison was done by running high HbA1c samples (8-14%) on the DCA™ and Vitros 4600 compared against ion exchange HPLC, which is the gold standard for the measurement of HbA1c. The Vitros 4600 had a better correlation with HPLC (bias of 1.075%) on the high end for HbA1c compared to the DCA™, suggesting the DCA™ actually has a high-end bias with higher HbA1c values compared to HPLC. Thus, by using the Vitros 4600, there can be more accurate results for HbA1c levels especially when managing diabetes, while also increasing productivity by having the ability to run multiple samples compared to a POC device.

Many of the world’s most important countries are experiencing large increases in their populations of older adults (e.g. Japan, China, Italy, Germany). Such longevity is requiring a greater need for long term care. However, societies can not afford to pay for formal care, so informal (unpaid family) caregivers (CGs) are becoming increasingly important. Unfortunately, many CGs are at high-risk for psychosocial/health problems. Moreover, caregivers with pre-existing health problems are particular risk. Our goal is to examine factors that may make cancer caregivers vulnerable. We used a vulnerability (have a cancer history or not) by exposure (being a caregiver or not) model, and stratified our participants into four groups: Cancer Caregivers, Non-Cancer Caregivers, Cancer Non-Caregivers, and Non-Cancer Non-Caregivers. At baseline and 15-18 months later, we measured indicators of life quality and caregiver demands: satisfaction with support, well-being, perceived support, loneliness, and hours spent caregiving. Cancer Caregivers reported poorer social supports and more time caregiving. This is important because previous work has shown that Cancer Caregivers have more negative and fewer positive life experiences and that these are related to the ability to fight tumor growth. Despite innovations, this study only included white Americans. Also, to increase participation among persons with cancer, we only included those who were not treated for at least one year and who had not suffered from serious forms of cancer. Our results would probably have been stronger had we included persons with more serious cancers, but such individuals might not have participated or been able to be caregivers. Given the rapid rise of cancer in China, we suggest that research examine cancer and caregiving in China and that cross-cultural research be done in the U.S. and China. To understand the dynamics of caregiving, health and well-being, one needs to study these processes cross-culturally.

2D cell models have traditionally been used in labs to test the effects of new drugs on certain cell types due to the ease and convenience of use. While 2D methods are great, they often simplify the cell-to-cell interactions and may not accurately represent cell systems in humans. 3D methods show the complex cell communication systems and better simulate actual organ systems. Research comparing these two methods can inform scientists on the benefits of 3D models which can help efficiency in creating new drugs. Our lab looked into various 3D models to determine their effectiveness and reliability and looked into the differences in perceived cell mechanics and functionality between 2D and 3D methods. We tried Corning Matrigel and Corning 3D Spheroid microplates for 3D cell modeling using HEK293 cells, which are human embryonic kidney cells that were grown in lab. They are known for being easy to grow and transfect. We used SNAP-Gels, which are protein assays that show the protein levels in the cells, to ensure that the protein levels were similar between the 2D and 3D systems. We then did florescent imaging to determine cell localization and EPIC dynamic mass redistribution (DMR) to determine cell functionality. We found Matrigel to have inconsistent results, so we focused on using the spheroid microplates. Based on our initial results, we saw increased functionality and expression levels for full-length protein cells compared to cells with a truncated N-terminal protein in the 3D method. This increase in functionality and expression levels was not seen in the 2D method. Our results show that 3D modeling methods can be reliable, and do show results that differ from 2D models. This is important for future studies that require cell modeling because 3D models can provide a more accurate and reliable modeling system to create novel therapeutics.

The Large Synoptic Survey Telescope (LSST) will be capable of observing objects of 25+ magnitude across the u, g, r, i, z, y broad-band filters. At these extremely dim magnitudes the survey will turn up a large number of unresolvable red point-like sources. With some variation depending on the filter, beyond roughly 25 magnitude these filters will lose the ability to provide data accurate enough for an observer to reconstruct the parameters of the objects being detected. In other words, past that point it will become difficult to tell whether an object is a nearby low mass main sequence star, a far away giant, or a high-redshift galaxy. The simplest possible solution to this problem is to add some more filters, specifically ones with narrower band width. If these narrow band filters allow for accurate data to be collected at higher magnitudes than their broad band counterparts can, it would not only solve the problem, but do so without necessitating a longer survey or requiring any great feat of engineering to implement. A simulated LSST field consisting of roughly 127,000 stars was used to explore this possibility. The (simulated) observed magnitudes and colors of each star were compared to a catalog of each star’s true magnitudes, with a nearest-neighbor algorithm applied in an attempt to recover that star's true effective temperature, surface gravity, and metallicity. This process resulted in accurately-recovered stellar effective temperatures out to far greater magnitudes than allowed by the broad band filters. Unfortunately, improved parameter recovery seems for now to be unique to effective temperature, as this initial test has not shown any great improvement in the recovery of gravity or metallicity over the broad band filters.

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multi-organ inflammation and damage, including skin and kidney. Ultraviolet B light (UVBL) is the only environmental factor known to precipitate both skin and kidney disease. How UVBL-triggered sterile inflammation in the skin influences kidney injury remains a pressing question for SLE patients, about 70% of whom suffer from sensitivity to UVBL. We previously demonstrated that neutrophils are the first immune cells to infiltrate the inflamed skin tissue after exposure to UVBL. To investigate the neutrophils’ role in UVBL-induced kidney injury, C57BL/6J mice were irradiated with a single dose of UVBL (500mJ/cm2). Cells in the bone marrow (BM), skin, blood, and kidney were characterized using flow cytometry. Gene expression of inflammatory mediators and adhesion molecules was evaluated using qPCR. Following acute exposure to UVBL, we observed a 10-fold increase in skin neutrophils, associated with a decline in neutrophils from the BM and a 5-fold increase in circulating neutrophils relative to baseline (no UVL). Relevant to SLE, neutrophils increased up to 10-fold in the kidney after skin UVBL injury (vs. no increase in monocytes/macrophages). Local skin response was characterized by rapid induction in inflammatory cytokines (IL1b, TNFa, IL6, IL33) and neutrophil chemoattractants (G-CSF, CXCL1, LIX) (day 1-2) that returned to baseline by day 6 after UV. Neutrophil infiltration into the kidney was accompanied by endothelial activation and inflammation: increased VCAM1, E-Selectin, IL1b, Ngal, and s1008/9 gene expression, markers of kidney injury in SLE, as well as by transient proteinuria. Neutrophils recruited to the kidney demonstrated two phenotypes: early activated CXCR2hi (day 1-2) and late aged CXCR4hi (day 2-6), which followed expression of CXCR4 ligand CXCL12, another marker of kidney injury. Together, our findings propose a novel neutrophil-dominated skin-kidney axis of pathogenesis and provide a model for UVBL-triggered disease UW flares in SLE.

In Arabidopsis thaliana the plant signaling hormone auxin is a major regulator of plant growth and development including the formation of lateral roots. Auxin controls the development of lateral roots by regulating the activity of transcription factors, known as Auxin Response Factors (ARFs). Because ARF7 and ARF19 mutants shows reduced formation of lateral roots, they are identified as master regulators of lateral root development. Using these ARF mutants, my project aims to understand how these regulators control early stages of lateral root development and gain insight into the role of auxin signaling in developmental specification. To investigate this, reporter lines are crossed with plant mutant lines of ARF7, ARF19, and both ARF7/ARF19 exhibiting a range of lateral root phenotypes, enabling accurate identification of lateral root specification and initiation stages. In mutants, we use bend assays to induce the lateral root developmental program in a synchronous manner. Seedlings are grown vertically on agar plates for 4 days, then turned 90° eliciting a gravitropic bend response at the root tip and leads to an eventual emergence of a lateral root at that the bent region. In mutants, temporal dynamics of lateral root program is quantified using fluorescence microscopy of reporters in synchronously induced lateral roots. Based on collected data thus far, the arf7 mutants (compared to wild type) exhibit slower onset of the specification reporter, suggesting the mutation has a temporal delay on developmental processes. As this project progresses, we will focus on temporal differences in expression of reporters that identify early specification and initiation stages of lateral root development via use of bend assays along with microscopy. Insights gained from these experiments will help us focus on stages and events in lateral root development that are impaired in arf mutants and thereby indicate on how auxin controls the developmental processes.

The Zwicky Transient Factory (ZTF) is a telescope located at Caltech in southern California. It is part of a new generation of wide field survey telescope programs. With its 47 square degree field of view and the ability to cover 4200 square degrees per hour of the night sky, ZTF is equipt to complete its survey of the Northern hemisphere. ZTF takes photometric data in multiple color bands including visual (r and g) and (i) bands increasing the accuracy of data collected on an observed body. It’s limiting magnitude is ~21 allowing us to see deeper into our universe. We constructed a pipeline of code which pulls photometric data from ZTF and fits light curves for asteroids with previously reported orbital parameters. A light curve is a recorded fluctuation in light intensity of a variable body. As an asteroid rotates its albedo or surface reflectivity varies producing the variation in flux we measure as a light curve. From a light curve you can calculate many properties of the body such as period, diameter, and mass. Our pipeline fits the observed light curve for its period and, for a subset of the asteroids with previously known periods reported in the Light Curve Database (LCDB), we test the accuracy of the fitting process. Of the initial ~4000 asteroid samples, 437 had periods reported in LCDB. In this subset we matched ~60% of the reported rotation periods within 5%. We continue improvements on the pipeline, specifically in outlier rejection, in hopes to use our pipeline in future telescopes like the Large Synoptic Survey Telescope. As well as data collection hoping to fully resolve the Jovian Trojans, two asteroid groups that co-orbit with Jupiter.

Secondary nucleotide messengers are used by all domains of life to sense and respond to the changes in their environment. In bacteria these secondary nucleotide messengers play a role in regulating several signaling pathways such as cell wall homeostasis, motility, and the expression of virulence genes. The nucleotide cyclic di- 3, 5’ adenosine monophosphate (c-di-AMP) was recently added to the list of secondary nucleotides. C-di-AMP is found in many bacteria such as S. aureus, S. pneumoniae, B. subtilis, and L. monocytogenes (Lm). C-di-AMP has been best characterized in Lm, a well-studied intracellular pathogen. Lm has adapted to survive and replicate in the host cell cytosol by evading host cell defenses through use of key virulence factors. In Lm, synthesis of c-di-AMP is catalyzed by the diadenylate cyclase dacA and degradation is coordinated by the phosphodiesterases, pdeA and pgpH. Studies using Lm mutants that lack both pdeA and pgpH contain abnormal c-di-AMP levels that cause growth and virulence defects of about four logs compared to wild type Lm. This highlights the importance of c-di-AMP regulation for bacterial virulence and growth, but we still know very little about c-di-AMP regulation and toxicity. Our goal is to further understand the toxicity of high levels of c-di-AMP during bacterial infection. We aim to create a transposon library in the double phosphodiesterase KO (ΔΔ Pde) background to identify suppressor mutations. Previous approaches to analyzing suppressor mutations in the ΔΔ Pde strain has not been thorough or cannot be utilized in vivo. Therefore, we have created an amenable phosphodiesterase mutant that knocks out the phosphodiesterases in Lm (pdeA and pgpH) to grow in vivo successfully to investigate c-di-AMP regulation. Understanding the regulation of c-di-AMP could result in targets for novel treatments against Lm and allow for ways to investigate regulation methods of c-di-AMP in other organisms.

All around the world, humans depend on cultivating plants for medicine, food, landscaping and building materials. Understanding how plants grow helps people make more informed decisions about what to grow and how best to grow it. The plant hormone auxin plays a key role in determining almost all aspects of plant growth and development. The Nemhauser Lab has previously determined that two versions of the receptors for auxin, TIR1 and AFB2, function at different speeds in the model plant Arabidopsis thaliana. Currently, we do not know how this speed disparity affects specific plant functions. My hypothesis is that there are measurable differences in organism functions caused by this difference in molecular speed. In the past, full knockout mutants for TIR1 and AFB2 did not exist, making it difficult to answer this question. To complete my research, I developed these mutant plant lines, determined functions that can be quantitatively measured, and collected and analyzed the data. Because the auxin-signaling network affects so many plant functions, any additional information we can gain about how this network functions in the model organism helps us move towards a more complete understanding of plant growth. This could positively improve the efficacy of agriculture and other plant-based industries, as well as moving us towards other new discoveries in the field of plant growth.

Proper development of an organism relies on the tight regulation of gene expression in cells and errors can lead to diseases or improper growth. Corepressors interact with DNA-binding proteins and inhibit gene expression. In the model plant Arabidopsis thaliana, the corepressor TOPLESS (TPL) is a member of a deeply conserved Gro/Tup1/TLE family. I am studying which helices in TPL monomers are necessary and sufficient for homotetramerization. Additionally, I’m investigating what proteins TPL interacts with to control repression, especially mediator components and histone deacetylases (HDACs), which previous studies have identified as potential interactors. I am using a protein-protein interaction assay known as the cytoplasmic split-ubiquitin system (Cyto-SUS). In my assay, a bait (TPL) and prey proteins hypothesized to interact with TPL are attached to two halves of ubiquitin. If the bait and prey successfully interact, then ubiquitin is reformed and a ubiquitin-specific protease cleaves a transcription factor to induce expression of genes producing adenine and histidine. Successful interaction is measured qualitatively by observing growth of yeast on plates that lack adenine and histidine. Only certain helices of TPL are observed to interact with full length TPL. Specifically, truncations that are sufficient to drive repression in a synthetic yeast assay are insufficient to multimerize. This means that the multimer state is not required for repression. Secondly, we found that the N-terminus of TPL directly interacts with mediator through MED21, suggesting that TPL regulates recruitment of RNA Polymerase II. Other corepressors of the Gro/Tup1/TLE family, like Tup1 found in yeast, and the mammalian homolog Transducin-like enhancer of split (TLE) are known to homotetramerize and interact with similar regulatory elements like TPL, including: HDACS and mediator components. Understanding homotetramerization of TPL and its role in repressive mechanisms is pivotal for comprehending how corepression works across eukaryotes.

2-deoxy-ATP (dATP) is a nucleotide used in DNA synthesis and its presence has been seen to improve the magnitude and rate of contractions in heart muscle cells. However, levels of dATP are naturally low in mature cells. As an attempt to develop a novel treatment for heart failure, methods to increase the expression of ribonucleotide reductase (RNR), a key enzyme in the production of dATP are being investigated. RNR is regulated by ubiquitin-proteasome degradation of the small subunit of RNR, the Rrm2 subunit. We constructed a variant version in which two regions were changed to prevent ubiquitination. This new variant should lead to higher levels of RNR in cardiomyocytes, which also indirectly increases levels of dATP. Our preliminary results show a successful increase in levels of both RNR protein and dATP in cultured neonatal rat cardiomyocytes. Although levels of RNR and dATP were increased, the level present in our cultured samples are much higher than expected for adult rat and mice cells. Therefore, we are currently testing this RNR variant in vitro in cultured adult rat cells, as well as in vivo in aged adult mice. These models are more representative of a therapeutic use. Preliminary results have been promising toward identifying a more effective method of increasing dATP levels for improving cardiac function.

Microbial toxins are a molecular weapon involved in pathogenesis, immune evasion, and bacterial competition. A prime example of such microbial toolkits are polymorphic toxin systems, which consist of multi-domain proteins and are widespread in all major bacterial lineages. A polymorphic toxin system called MuF has been newly identified and is the first to be discovered in temperate phages and their bacterial hosts. Though it is highly abundant in the human gut microbiome, its biological role has not been defined. To better understand the toxin system, our team is studying a model species Enterococcus faecalis, a commensal bacterium encoding a two-domain MuF toxin protein on one of its phages, consisting of an N-terminal MuF domain and a C-terminal toxin domain. The toxin domain is predicted to be an ADP-ribosyltransferase (ART), which post-translationally attaches ADP-ribose moieties to its target molecules and can profoundly impair cell processes, leading up to cell death. Using genetic approaches to generate phages with malfunctional ART activity, I have found that the mutations change phage infectivity and the morphology of the plaques formed (clear zones in a cell layer formed due to lysis by phage). Moreover, heterologous expression of the toxin domain in E. faecalis results in cell aggregation. From this, I hypothesize that the MuF toxin is delivered by phages to help infection and ensure phage DNA incorporation into host genomes. To further dissect the mechanism by which the MuF toxin system operates, our team is currently developing a fluorescent protein reporter system to investigate and track the detailed process of phage infection. In addition, by applying X-ray crystallography and electron microscopy, I aim to uncover structural information on the toxin, which may lend insight into the mechanism of MuF toxicity and its larger role in the human microbiome.

Magnetic Resonance Imaging (MRI) is an invaluable imagining modality that allows physicians to quickly analyze the anatomical and physiological processes of the body. To improve contrast efficiency, MRI contrast agents are frequently administered to patients. However, the most commonly used T1 contrast agent – gadolinium-based contrast agent (GBCA) – has been associated with many adverse health effects, such as reduced white blood cell count, increased serum levels of inflammatory cytokines, and vacuolar degeneration. As such, there is an urgent need to design a T1 contrast agent that has a short half-life and that does not produce toxic endpoints in patients. To address this need, the present study developed an iron-oxide nanoparticle (IONP)-based T1 contrast agent by synthesizing 4 nm oleic acid-coated IONP and reacting them with phosphine oxide-PEG. Next, this study characterized the biological and the magnetic properties of the generated IONP system in vitro in order to determine its suitability as a T1 contrast agent. Finally, this study also analyzed the synthesized contrast agent’s use in other biomedical applications, specifically targeted drug delivery. Previous research has shown that cells can undergo ferroptosis – a regulated form of cell death – upon loss of activity of the lipid repair enzyme glutathione peroxidase 4 (GPX4). As such, a silencing RNA (siRNA) that can mark GPX4 mRNA for degradation was conjugated to these IONPs in order to downregulate GPX4 expression in mesenchymal stem cell – a type of stem cell that are particularly involved in cancer progression and that are especially resistant to radiotherapy – and sensitize them to radiotherapy. Ultimately, the findings of this study not only offer a safer alternative to GBCAs but also provide a foundation for a versatile, tunable IONP system that can be used in a variety of biomedical settings.

Modification of biomolecules is responsible for the regulation of cellular activities in all organisms. A type of enzyme, named ADP-ribosyltransferase (ART), plays a crucial role in such modifications by transferring one or multiple ADP-ribose moieties onto its target molecules. Some bacterial ART proteins are toxins that serve as virulence factors that enable pathogens to disrupt host cell functions during persistent infection. However, it was unclear if ARTs play roles in interbacterial interactions. Here, I report the discovery of the first interbacterial ART toxin encoded by a Serratia proteamaculans strain, a commensal bacterium isolated from plant root. Growth competition assays showed that the toxin is capable of conferring a higher fitness for S. proteamaculans. Subsequent analysis by microscope revealed that target bacterial cells became elongated, leading up to cell lysis. Together, my results offered new insights into the complex question of how bacteria compete against each other. The finding expanded our knowledge of the diverse roles of ART proteins and their cellular activities.

This project showcases how the works of organizations and individuals have advanced the efforts to achieve justice for the crimes against humanity committed throughout 20th century Latin America. By conducting in-depth research on how organizations have advanced cases of disappeared persons through forensic anthropology and criminal prosecution, we answer the question of how specific organizations and individuals have revolutionized the fields of forensic anthropology and human rights in the pursuit for justice. Our research investigates newspaper articles, court cases, and other media resources to identify how forensic evidence has been used to hold human rights abusers accountable. We also compare the human rights crises in Latin America to other global human rights crises to identify similarities between their initiation and subsequent movements for justice. We expect to find similarities in the cases of forced disappearances in Latin America and gain detailed information on how different methods of justice have been pursued across the region. Our research will be culminated on a central website that depicts the background, development, and ongoing movements of Latin America’s human rights history. By presenting this information in an accessible form, we hope to increase the public's knowledge of forensics and human rights, and to explain the value of these fields in attaining justice in Latin America and ultimately around the world.

Obstructive sleep apnea (OSA) is the condition of repetitive stops of breathing during sleep due to complete or partial occlusion of the upper airway. OSA affects around 34% in men aged 30–70 years and is associated with significant cardiovascular mobility. Studies have indicated that retro-palatal region is the most common site of upper airway collapse leading to OSA. However, few studies have addressed the respiratory dynamics of soft palate, tongue base, and epiglottis during sleep. The purpose of this study is to analyze the respiratory motions of soft palate and its relation to oropharyngeal structures during drug-induced sleep in verified obese/OSA and non-obese/non-OSA minipigs. The hypotheses is that obese/OSA minipigs would have larger variance of soft palate motions and altered motion pattern as compared to non-obese/non-OSA controls, which may contribute to OSA. Four obese and two non-obese minipigs were first revived live sleep monitoring using wireless BioRadio system to verify OSA, and all 4 obese showed different degrees of OSA by apnea/hyponea index (AHI) while 2 non-obese did not. Sleep videofluoroscopy was performed under sedation when subjects were places in the prone and lateral positions. The ImageJ was used to trace the movements of soft palate tip in inhaling and exhaling phases. The static reference was defined to be the intersection of mesial surface and occlusal plane of upper second molar. The purpose of reference is to compare relative location of soft palate tip and its relation to other oropharyngeal structures. Dynamic movement of soft palatal tip presented significantly larger variance in obese/OSA than non-obese minipigs. Going forward, I will further map the dynamic shape changes of the soft palate and to define how spatial relationships between soft palate, tongue base and epiglottis lead to oropharyngeal airway patent or collapse during respiration.

Analysis of plant foods and medicines is a growing field within archaeological research. However, few scholars have examined plant foods among Native American communities in colonial settings. This project combined archival and archaeological data to better understand plant use within the Grand Ronde community during the late nineteenth and early twentieth centuries. Field Methods in Indigenous Archaeology (FMIA), a community-based research partnership between UW and the Confederated Tribes of Grand Ronde Historic Preservation Office, has collected macrobotanical remains from the Grand Ronde Reservation in northwestern Oregon. I explored how and why these remains were used within the community. Knowing this information will provide a better sense of local environmental contexts and cultural lifeways. To study this question, I selected ten plants that have been recovered during FMIA’s excavations and examined ethnographic, archaeological, and documentary sources from the region to understand each plant’s cultural context. I found that most plants found on the reservation were used as food sources, though some also had medicinal and spiritual significance. This work sheds new light on the relationships between Native communities and plants in the Pacific Northwest over the past two centuries, helping us understand how people navigated the challenges and opportunities introduced by colonialism.

Neurodegenerative diseases, such as Alzheimer’s (AD), Parkinson's, and Huntington’s, affect millions of people. In AD, prior studies indicate the formation and accumulation of amyloid-beta proteins may play a crucial role in the pathology of the disease. The Herpes Simplex Virus (HSV-1) encodes an alkaline nuclease (UL12.5) known to cause degradation of the mitochondrial genome. HSV-1 infection has been previously associated with AD brain pathology. We hypothesize that UL12.5 activity in the brain may predispose an individual to amyloid-beta aggregation and AD neuropathology. Here, we controlledl the amyloid-beta protein aggregation using a degron attached UL12.5, which is induced by the plant hormone auxin through a molecular signaling pathway known as auxin-inducible degron. We have engineered an auxin UL12.5-degron construct in order to precisely control the temporal and cell type expression of UL12.5 in Caenorhabditis elegans (C.elegans). This construct was microinjected into the worms and by using auxin, we controleld the expression of UL12.5 and tested its effects on amyloid-beta and Huntington protein aggregation. Here, we have elucidated the relationship between HSV-1 infection, UL12.5 expression, and neurodegenerative disease which may form the basis of novel treatments.

Tetramerized viral proteins are a powerful tool for examining the immune response to infection and vaccination. However, the field lacks a clear understanding of the stability of these tetramerized proteins over time and varying temperatures. One such viral protein, Respiratory Syncytial Virus (RSV) fusion (F) protein can degrade from a prefusion (preF) conformation to a postfusion (postF) conformation. The stability of tetramers of the RSV preF protein is tested by 1) freeze-thawing; 2) incubating for 1, 2, 4, 8, and 12 weeks; and 3) storing at -20°C in glycerol, 4°C in PBS, and room temperature in PBS. RSV F in the preF versus the postF conformation is measured using bio-layer interferometry (BLI) to assess how these different variables affect tetramer stability. This study aims to define ideal conditions for the storage of tetramerized viral proteins. This crucial information will ensure reagents used to study the immune response to vaccines and infections are robust and will also help minimize the cost and time of producing these reagents. The findings could also allow the implementation of these reagents in resource-limited settings.

Microphysiological systems (MPS), also known as “organs-on-chips,” provide a novel, ex vivo approach for evaluating the risk of drug induced toxicity and the impact of environmental toxins. Evaluating the chronic impact of exposure to environmental toxins in humans is difficult, due to ethical concerns, but the MPS provide an approach to examining the toxicological effects on human cells, without the need for human subjects. Aristolochic acid I (AA-I) is a potent, plant-derived nephrotoxin and carcinogen that has been implicated as the causative agent in both Balkan Endemic Nephropathy and Chinese Herb Nephropathy. The contribution of hepatic metabolism to the bioactivation of AA-I was previously demonstrated by microfluidically linking a hepatocyte containing MPS and a human renal proximal tubule eptileial cell (PTEC) containing MPS. PTECs are kidney cells from the nephron that lie between the glomerulus and the Loop of Henle. We studied the cytotoxic effects of AA-I on PTECs and human hepatocytes in MPS by exposing the MPS to concentrations of AA-I ranging from 0 µM to 10 µM for longer than seven days. AA-I was perfused into the MPS into either a linked hepatocyte-PTEC MPS or an unlinked PTEC only MPS. The chronic, low-dose effect of AA-I resembles Balkan Endemic Nephropathy, where individuals were exposed to low concentrations of Aristolochic acid from tainted wheat. Both PTEC only and linked hepatocyte-PTEC MPS provide experimental methods for further investigating how organ-organ interactions affect drug metabolism and xenobiotic toxicity.

From November 2015 through March 2016, the Olympic Mountains Experiment (OLYMPEX) was conducted on the Olympic Peninsula to study the evolution of wintertime clouds and precipitation in frontal systems passing over this coastal mountain range and to validate satellite-derived precipitation measurements from the U.S.-Japan Global Precipitation Measurement (GPM) mission. While most OLYMPEX research has focused on precipitation processes on the windward (usually southwest) side of the Olympic Mountains, this study uniquely examines the leeward (usually northeast) side of the mountains where there is climatological rain shadow (i.e. a minimum in precipitation relative to the windward side). The vertical structure of the frontal systems over the northern Olympic Mountains is examined using data from a radar managed by Environment and Climate Change Canada on Vancouver Island (EC-XBAND), including intensity inferred from radar reflectivity. Using environmental data from North American Regional Reanalysis on the windward side of the mountains, this study classifies the leeside radar data based on upstream large-scale conditions. The cloud and precipitation structure on the leeward and windward sides of the mountains are compared utilizing the Doppler on Wheels (DOW) radar in the Quinault River Valley, and the EC-XBAND radar. Cloud and precipitation particles measured by in situ aircraft over the windward and high terrain illuminate situations when particles are lofted over the mountains to the leeward side, reducing the rain shadow. These findings will inform local studies of snowpack and water supply in the Olympic Peninsula as many reservoirs there 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.

Fragile race avoiding is defined as the tendency to refrain from talking about race or racial issues to hide one’s bias due to sensitivity concerning the topic. Some even demonstrate discomfort or incoherence when directly talking about racial issues. This is common amongst whites who want to avoid conflict regarding racism. Although white people may believe that avoiding racial topics stops disagreements from arising, fragile race avoiding can promote ignorance about stereotypes and inhibit cultural awareness. We believe that this is a method in which individuals suppress their discomfort towards blacks. Therefore, we predict that a higher score on fragile race avoiding will correlate with higher levels in overall racism. We tested this prediction in a study in which UW undergraduate students talked about various scenarios with a research confederate to prompt a discussion about current day racial issues. Coders watched these taped interactions and rated various categories of microaggressions on a scale from zero to three. Scores of zero for fragile race avoiding indicates that the research participant is comfortable talking about racial issues and brings up race without being prompted by the confederate. Meanwhile scores of three indicate that the participant actively avoids mentioning race and shows palpable discomfort throughout the interaction. For the scores on overall racism, coders considered the interaction as a whole and determined how black individuals would feel when in a room with the participant. A score of zero represents comfort and understanding of the racial implications these topics were created to induce, while a three shows that the participant’s racist beliefs are explicit and clear. We hypothesize that there will be a positive correlation between the scores on fragile race avoiding and overall racism, indicating that fragile race avoiding is a modern form of racism in which individuals suppress their discomfort among blacks.

For women to have protection from unintended pregnancy and human immunodeficiency (HIV), current lead prevention options use oral antiretroviral drugs (ARV) for pre-exposure prophylaxis (oral PrEP) along with a form of contraception. Failure to adhere to these drug therapies will increase the risk of contracting HIV or pregnancy. We have proposed to integrate drug-eluting materials onto a copper-intrauterine device (IUD) that could provide both HIV prevention and contraception. We will evaluate two methods to formulate a matrix release drug delivery system. Injection molding is a method to inject material into a mold that can be used for constructing drug-eluting medical devices with low drug degradation. For our purpose, we injected a polymer and drug combination into a mold to construct a solid slab. Whereas, electrospinning is a method that uses electric force to formulate stable and high surface-to-volume ratio nanofibers with high drug encapsulation and porosity compared to the molded slab. Both delivery systems will be used to administer ARV drugs to the female genital tract for a year. We optimized the molded slab and electrospun nanofibers technique for maximum polymer-loading, and used 3-D printing and nanofiber wrapping technique as a process for slab integration and fiber integration onto the IUD respectively. The polymer and drug combinations for both electrospun nanofibers and molded slabs were chosen to have the maximum drug-loading and stable mechanical properties. Drug release was measured in vitro to predict daily release rates out to three years. The ideal matrix release drug delivery system method for the dual HIV prevention and conception IUD is determined based on the mechanical properties and drug release rate of the polymer and system combination. We also investigated the drug delivery systems for cytotoxicity to verify dosage safety.

In the era of new technologies, the functions of mobile apps cover all aspects of our lives. Social networking apps expand our social and business groups, as well as increase job and entertainment opportunities dramatically. Other types of apps, such as travel and buying & selling apps, enable people to get both tangible and intangible products without leaving home. The fast development of mobile apps, however, made it difficult for elders over 65 to understand and learn, and the physical condition of elders presents barriers to operating new technologies. Overall, the lack of accessible design on mobile apps has caused elders to not have the equal opportunity to obtain information and enjoy the same conveniences as other age groups; and new technologies have gradually made the older generation feel abandoned. In the past six months, I conducted a competitive analysis of the current situation of using mobile apps by the elderly to gain a broad view on the user experience of mobile apps for elders. I designed and distributed a questionnaire survey among members of the Yakima Serious Table Tennis Club to understand the barriers they encountered when using various types of mobile apps. I interviewed two retirees from different fields of employment and cultural backgrounds about their views on the usability of different kinds of mobile apps. Ultimately, referring to my collected data and the Web Content Accessibility Guidelines version 2.1, I analyzed possible changes that could be made by some popular apps to improve the accessibility for elders. I created interface templates of an accessible mobile social media for elders using Adobe Experience Design; then I edited it to a final version while doing usability tests on the templates. The conclusions from this research could be used to help design applications that are suitable for more age groups, and to ultimately make society more inclusive by letting elders have equal opportunity to enjoy new technologies.

Autism Spectrum Disorder (ASD) is a collection of neurodevelopmental disorders characterized by social-communicative and behavioral impairments that affects approximately 1 in 59 children in the US. Children with ASD, on average, exhibit increased rates of externalizing behaviors compared to their typically developing peers. Studies have shown that children with relatively low familial risk for ASD are more likely to develop ASD if they have a history of pregnancy complications and that presence of pregnancy or birth complication can exacerbate the severity of externalizing behaviors. In typical development, pregnancy complications are associated with a number of child psychiatric disorders and externalizing behaviors and males have increased levels of externalizing behaviors compared to females. In a sample of children with ASD, this study (1) investigated the relationship between pregnancy complications and externalizing behaviors and (2) compared sex differences in externalizing behaviors. The study involved 200 children with and without pregnancy complications, between the ages of 8 and 17 years. Pregnancy complications were provided by the parent during a medical history interview and refer to a wide range of complications including, among other things, health concerns for the mother or child, difficult birth, or coexisting pregnancy diagnosis such as gestational diabetes or preeclampsia. To assess for externalizing problems, parents of participants completed the Behavior Rating Inventory of Executive Functioning (BRIEF) questionnaire about their child. We predict that ASD children (1) with pregnancy complications (compared to those without complications) will demonstrate more externalizing behavior problems and (2) males with ASD will exhibit more externalizing behavior problems than females in the subscale mean scores. The results of this study provide insight to the connection between pregnancy complication and externalizing behaviors in children with ASD.

At the terminus of every robotic manipulator is an end-effector. Sensors mounted at the end-effector provide egocentric perception, enabling the robot to touch and see the world from a unique viewpoint. Our existing wireless perception module has been able to stream visual (RGBD) and force (haptic) data wirelessly to other devices and is integral to our autonomous feeding robot application. As our robot applications have grown in scope, the demand for more sensors with higher quality and greater frequency has increased too. This research focuses on identifying the bottleneck of the data transmission speed of multiple sensors and implementing task-driven data extraction and compression methods. The module compresses the sensor data with optimized processing methods, such as real-time object detection, face detection, and pressure prediction. Additionally, this project involves a hardware design portion which improves the previous design and aims to easily exchangeable mounting technique and sensors. This research uses the Nvidia Jetson TX2, which is able to complete more complex tasks in shorter computing power than the Intel Joule used in the last version. The new embedded board mainly uses Python to run deep learning instances and uses low-level packages and hardware encoders to interact with sensors and cameras. This project also compares processing speed with different deep learning frameworks on Jetson infrastructure and results in a faster and more accurate solution. The sensor module becomes a processing node in the robot network, freeing the robot to focus on task-level computation rather than lower-level perception calls.

Causal inference is a large and long-standing field that attempts to answer a very fundamental question: does X cause Y? This question arises in many fields such as healthcare, genomics, biology, and econometrics. The complex systems analyzed in these fields often have many interacting components mathematically represented as nodes and edges (connectivity) of a network. Network inference is the study of the time-dependent behavior of these nodes to reverse-engineer the network connectivity. The theory of causal inference has many contending definitions of causality such as state-of-the-art techniques Granger Causality (GC) and Convergent Cross Mapping (CCM). These algorithms are computationally tractable and easy to use but require strong mathematical assumptions. We simulate networks of harmonic and Kuramoto oscillators and attempt to reconstruct their ground-truth network structure using observations of oscillator displacements over time. Our analysis investigates the performance of inference methods on Erdos-Renyi and scale-free random graphs. We show that the GC and CCM inference methods systematically fail to determine network structure by returning overly sparse or dense connectivity results. These findings challenge the applications of such top-down inference approaches to physical and biological systems. Using a few basic assumptions, we demonstrate how networked systems of coupled oscillators can be successfully reconstructed if perturbations of the system are allowed. We propose a Perturbation Causal Inference (PCI) algorithm that uses systematic perturbations and tracks how perturbation cascades spread through the network. Using changepoint detection, correlation, and windowed variance statistics, we predict causal relationships between nodes in the graph. Our analysis shows that PCI works at scale and efficiently returns high accuracy reconstructions of large networks with varying coupling strengths and connectivity structures. We conclude by proposing future applications of perturbation inference methods into neuroscience and make a connection with Hebbian learning rules.

Hair cells are sensory receptors responsible for hearing and balance in the auditory and vestibular systems. These cells are surrounded by supporting cells, which are non-sensory cells similar to glia. In non-mammals, hair cells get replaced after damage through conversion of supporting cells. Recent studies have shown supporting cells can also transdifferentiate into type ll hair cells in the vestibular system of adult mice. The signals that control hair cell regeneration in mammals are poorly understood. It is known that the transcription factor Sox2 is utilized for specification of hair cells in the neurosensory domain of the otocyst. This project tests the premise that Sox2 is required in adult supporting cells for their transdifferentiation into type II hair cells after damage. We used time specific gene deletion technology, CreER-LoxP, to delete the gene encoding Sox2 in supporting cells prior to damage. The mice used include the following alleles (genetic segments): 1) the floxed Sox2, or Sox2loxP/loxP allele, which enables Sox2 deletion when Cre is active; 2) the Sox9CreERT2 allele, which targets Cre expression to supporting cells; Sox9CreERT2 is tamoxifen-dependent, so the timing of Sox2 deletion is controlled by tamoxifen injection; and 3) the Pou4f3DTR allele , which enables hair cell killing upon injection of diphtheria toxin (DT). Hair cells were identified and “typed” using several markers, including antibodies to myosin VIIa, neurofilament, and ßIII tubulin. I compared the number of regenerated hair cells of Sox2 expressing supporting cells and Sox2 negative supporting cells. Sox2 deletion in supporting cells resulted in a significantly reduced number of type ll regenerated hair cells. This result provides evidence that Sox2 is required for transdifferentiation of supporting cells. Understanding the function of Sox2 will give insight into potential downstream molecules that can become prospective targets for future research in understanding cellular regeneration in adult mice.

Self-disclosing personal stress is an effective way of managing stress. Previous research has shown that high school students disclose more when prompted by robot that discloses vulnerability. Thus, disclosure reciprocity in human-robot interaction (HRI) provides a promising way of offering stress intervention. The current study examines how different types of disclosure from a social robot affect reciprocal human disclosure and other user outcomes through a stress-disclosing activity. Using a between-subject design, 36 young adults were randomly assigned to converse and engage in a stress-disclosing activity with a robot that shared technical facts (technical condition), feelings from other users (by-proxy condition), or feelings from itself (emotional condition). We hypothesize that emotional robot disclosure will elicit longer and deeper participant disclosure, and higher robot attributional ratings (such as likeability, perceived safety, user satisfaction, and intention for future use) than technical disclosure or by-proxy disclosure. Participant self-disclosure was measured by word count and depth of response during the robot interaction. User satisfaction, intention for future use, robot likeability, and perceived safety were captured using 5-point Likert scales. Our multivariate generalized linear model revealed that participants who experienced the technical robot disclosure condition gave the robot significantly higher rating for perceived safety, but no significant differences in other variables, such as length and depth of participant disclosure among robot disclosure conditions. Surprisingly, we found that people with higher perceived stress significantly disclosed less in both breadth and depth, and rated the robot as less likeable, had lower future intention to use and user satisfaction. This study demonstrates the complexity of designing robot for stress-intervention and the importance of capturing perceived stress as a predictor for stress intervention in HRI. Future research will examine how high stress and low stress group might perceive and interact with a social robot differently in long-term repeated interactions.

The Yerkes-Dodson law suggests that performance is optimal when physiological arousal is moderate. Prior research has shown that arousal induced by listening to music will affect task performance on a cognitive task. The goal of this study was to test whether different music tempos would affect arousal levels and performance on a cognitive task. We recruited 16 UW undergraduates and exposed them to different tempos of the same song while performing a math test. We tested their accuracy, completion time, and recorded their heart rate. Results suggest that accuracy was higher under moderate music tempo than slow but there was no difference between moderate and fast. Interestingly enough there was no difference in completion time or physiological arousal. Although we failed to establish an effect of arousal and completion time the fact that participants did better on accuracy when music tempo was moderate is in line with what we predicted. Music tempo could still be influential to performance and future research can be done to understand these effects by operationalizing performance differently. Future directions about ways to improve the study will be discussed especially whether music/music tempo affect people subjective arousal and physical arousal differently.

In human-robot interaction, virtual reality (VR) provides strong potential to aid in the design of social robots. In order to understand teens' perceptions of, and interactions with social robots, we utilized a human-centered design methodology to develop a collaborative VR game for teens. The design process involved interaction studies with a local high school in three phases: (1) Brainstorming and Sketching environments on Paper, (2) Card sort game play for exploring robot design options (3) Developing and usability testing the low-fidelity VR game play. The design goals were to create an inviting game context for teens to engage in collaboration and to elicit and capture the details of teen-teen and teen-robot interactions within VR. From the design process, we found that (1) the human-centered design process engaged teens in the design process (2) teens expressed positive emotions during collaboration and (3) the asymmetric design of the VR game allowed for not only strong engagement, but also unexpected role play as teens identified themselves as the robot during gameplay. Through the design and development of this VR game, we recognized the effectiveness of a VR platform as not only a design tool, but also as an engaging collaborative platform for gathering interaction data from teens. Given this potenial, we anticipate several future applications for the study of teen-teen interaction through VR collaboration.

The influenza virus is known for its rapid evolution, or the ability to fix many mutations over a short period of time. Some of these mutations lead to amino acid substitutions in regions of the virus targeted by the immune system. Such changes are often selected for because they confer a fitness advantage by allowing the virus to "escape" immune response. This pattern of repeated immune escape is a detriment to public health because it necessitates an annual update to the influenza vaccine. Therefore, identifying sites on the influenza virus which are targeted by the immune system could help predict which influenza strain will circulate in the future, inform vaccine design, and help understand basic evolutionary questions. Using molecular phylogenetic techniques, we can identify sites potentially targeted by the immune system by looking for "positive selection", a phenomenon which manifests as a higher than expected rate of evolution. To identify sites evolving faster than expected, we defined a null expectation of the evolutionary rate of influenza in the absence of immune pressure. This null model is defined using empirical measurements from a high-throughput functional assay known as deep mutational scanning. This null model differs from traditional phylogenetic models in that it describes the constraints on influenza on a site-specific basis and, as a result, has been shown to be a more accurate and powerful null model. I have implemented an empirical Bayes approach to identify sites which deviate from the null model by an unexpectedly high evolutionary rate, suggesting positive selection. Preliminary results show that my method outperforms other methods for identifying sites under positive selection. Next, I will apply these methods to the influenza virus surface protein, hemagglutinin, which is a major target of the immune system.

There has been growing concern regarding rising carbon dioxide concentration in the atmosphere because CO₂ traps excessive heat and warms the planet through the greenhouse effect. One strategy to mitigate this problem is through the capture and conversion of CO₂ via hydrogenation to fuels and chemical feedstocks that are currently produced from fossil fuels. Given the complexity of these multi-electron, multi-proton transformations and the multitude of products that can result, catalysts are required to lower the energy barrier and direct the selectivity of CO₂ conversion reactions. One catalyst currently under development is a Ru(II) bis-(protic N-heterocyclic carbene) phosphine catalyst, which incorporates protic N-H wingtips adjacent to the metal center. The N-H wingtips are an interesting feature due to their ability to activate CO₂ through metal-ligand cooperation, their accessibility as a proton source near a metal active center, and the likelihood that they aid in splitting H₂ between the metal center and the nitrogen. Preliminary results have shown moderate turnover numbers (TONs) for both formate (130) and methanol (7), the latter of which is a rare transformation in a single catalyst system. In order to improve catalytic TONs and understand the role of protic N-H wingtips, a library of catalysts with varying ancillary ligands, including 2,2’-bipyridine, 4,4’-dimethoxy-2,2’-bipyridine (electron donating), 4,4’-dibromo-2,2’-bipyridine (electron withdrawing), and 1,2 bis(diphenylphosphino)ethane (sterics), is synthesized and screened under high pressure and temperature conditions using THF solvent and varying additives (e.g. Li₃PO, K₃PO₄, KPF₆) and additive concentration. It is expected that the ancillary ligands, bound trans to the bis-carbenes, will influence the proton donor ability of the N-H wingtips and catalytic turnover.

Thermoregulation, the maintenance of core body temperature in a constantly changing enviroment, is a critical aspect of homeostasis. Despite its importance, the neural mechanism by which thermoregulatory processes occur is not very well understood at the circuit level. Afferent skin temperature information travels through the spinal cord to the parabrachial nucleus (PBN), where it passes on to the preoptic area of the hypothalamus (POA). A subset of prodynorphin (Pdyn)-expressing neurons in the PBN (PdynPBN neurons) are activated when mice are exposed to warm environments, and 80% of these neurons project to the POA. The exact role of PdynPBN neurons has not been characterized, however, and their full projection profile is not established. Using genetic and viral techniques, we inserted a Cre-dependent designer receptor exclusively activated by designer drugs (DREADD) into mouse PdynPBN neurons and labeled their synaptic projections with GFP-bound synaptophysin, an abundant synaptic vesicle protein used for neurotransmitter trafficking. The use of Cre-dependent DREADD and synaptophysin-GFP allowed us to specifically label and activate PdynPBN neurons. We found that activation of these cells increases tail-skin temperature with a concurrent drop in core-body temperature. These data suggest that PdynPBN neurons may convey environmental temperature information that is sufficient to activate heat-defense responses. Establishing the genetic identity of neurons in a circuit that helps to maintain constant core body temperature will allow for the elucidation of downstream nodes in this circuit.

Dynamical systems are ubiquitous in science and engineering. Inferring the mathematical laws that govern dynamical systems typically requires a 'scientist-in-the-loop' to guide the discovery process, via their expert knowledge and intuition about the system. Getting computers to perform this task automatically, without the guidance of a domain expert in the loop, is a grand challenge in the field of data science. A number of algorithms have been developed to infer such laws. One leading algorithm is Sparse Identification of Nonlinear Dynamics (SINDy), which applies simple linear regression coupled with sparsification to optimize a model over a large library of candidate functions. This algorithm is purely data-driven and makes no use of information that may be known previously about the dynamical system, such as symmetries and conservation laws. In this work, we develop a framework for incorporating and enforcing symmetries and conservation laws in SINDy so that the inferred models are consistent with prior domain knowledge. We analytically show how to propagate symmetries and conservation laws through the SINDy function library, and from this analytically derive linear constraints on the resultant linear regression. These constraints can be incorporated into the regression problem using options available in standard quadratic optimization packages. We implement this method and show that it provides improved accuracy and robustness on the task of inferring several canonical dynamical systems.

Autism Spectrum Disorder (ASD) is neurodevelopmental disorder that impairs an individual’s social, communicational, and behavioral skills. Boys are 4.5 times more likely to be diagnosed with ASD compared to girls. A potential cause for differences in diagnostic rates may be that girls tend to be more socially focused, allowing them to better camouflage their autism symptoms. Puberty is a period in an adolescent’s life where teens experience significant changes in social experiences and expectations. While puberty often increases social motivation, it’s unclear if males and females improve in the same ways or at the same rates. The goal of this study is to investigate sex differences in the relation between autism behaviors and stages of pubertal development. Participants included 140 children (70 males, 70 females) between the ages of 8 and 17 with a diagnosis of autism. Participants or their parents completed the Pubertal Developmental Scale, which provides a score of the child’s physical progression through puberty. Parents of the children also completed the Social Responsiveness Scale (SRS-2) which scores their child’s social and autism-related impairments. Our analyses (1) Compare SRS scores between youth with ASD based on their pubertal groups (pre/early/mid/late/post). We expect an increase in social awareness, motivation, and cognition for children going through puberty or in post puberty relative to those who have not yet started puberty. (2) Examine sex differences in SRS subdomain scores within each pubertal group and in the pattern of differences between pubertal groups. We expect to find no sex differences before puberty, but lower SRS scores in girls during and after puberty. Investigating the relationship between puberty and social behaviors could help us develop better supports for youth with ASD that incorporate biological and physical changes that come with development and consider how that might impact the youth’s social environment.

Hydra vulgaris are some of the simplest animals with neurons and have only two thin, near transparent layers of tissue: myo-endodermal and myo-ectodermal layers. Each cell in the animal can be examined simultaneously due to their small size, simple body pattern, and stereotypical (regular and defined) behaviors. This makes Hydra great animals for examining simple signal transmission pathways from which the complex pathways in vertebrates derive. Cells in the ectoderm and endoderm use calcium signaling to coordinate contractions and cause the animal to move, but how this mechanism of cell-to-cell calcium signaling functions is not well understood. Invertebrate gap junctions, intercellular proteins that cells use to send signals to adjacent cells, are coded from the innexin gene family. It has been found that the genome of Hydra magnipapillata has fourteen predicted innexin genes. Recent data suggests some of these innexins are expressed in the ectoderm, specifically innexins 1,4,5, and 13. I hypothesize these proteins are necessary for the animal to perform coordinated contractions. To determine the role of these proteins, I used shRNA techniques to knockdown innexin expression. After examining wild type Hydra, I examined an existing line of transgenic Hydra which express GCaMP in ectodermal cells to identify when cells use calcium to signal other cells. In these animals, signals can be viewed as a wave of fluorescence passing across the ectoderm. I knocked down the genes by electroporating shRNA molecules into adult animals who express GCaMP, and will image these animals’ behavior. There should be quantifiable differences in the fluorescent waves, as I postulate that some cells will be excluded from these waves if an innexin is knocked down, and analyzing these differences should clarify the role of innexins in gap junction signaling.

Platelets seal wounds in blood vessels in order to prevent blood loss. When there is an exposed vascular matrix, platelets bind at the wound site through the glycoprotein (GP) Ib-IX-V complex. Glycoprotein receptors allow platelets to initiate homeostasis by forming attachments to the damaged tissue. Platelets use their glycoprotein receptors to form bridges between other platelets and the surrounding proteins that form the clot within the blood vessel. Aspirin, a common household medication, produces its effects through inhibition of thromboxane production which prevents the formation of these blood clots by meddling with platelet aggregation. Standard doses of aspirin for an adult are 81mg, 325mg, and 500mg. However, there could be differences between male and female platelets, indicating that there may be different amounts of glycoprotein receptors between males and females. Here, we evaluated the force of single platelets without aspirin in males and females and single platelets with aspirin in males and females by using a reference-free traction force microscopy (TFM) platform. This TFM platform contained a grid of a fluorescent protein at known locations and was coated with von Willebrand Factor (VWF) to mediate platelet binding. Immunofluorescent staining and fluorescent imaging was conducted to visualize to platelet f-actin, a cytoskeletal component, and GPIb. Platelet binding, spreading, and contraction is observed on these substrates. By placing the platelets on the substrate, we are able to measure the deflection of the grid and determine the force a single platelet generates. In the future, we hope to measure the force of platelets at 0mg, 81mg, 325mg, and 500mg between men and women and hope to elucidate how GPIb expression, platelet mechanics, and response to aspirin varies in males and females.

The tumor microenvironment (TME) dictates the outcome of many immuno-oncology therapies for solid tumors. To better understand the dynamic milieu of the TME, new multiplexed, spatially-resolved histologic techniques are being developed. A key limitation to evolving these techniques is identifying specific and selective antibodies that perform well in an immunohistochemistry (IHC) platform. The over-arching goal of this project is to develop a flexible, high-throughput platform to empirically test the IHC staining characteristics of antibodies in formalin-fixed paraffin-embedded (FFPE) tissues with improved throughput and lower test volumes. Essential elements in our platform design include: 1) flexibility to test a variety of biologic materials, which is dependent on the test antigen, 2) compatibility with manual and semi-automatic tissue microarray (TMA) builder, 3) easy use for pathologic assessment, and 4) future compatibility with fully-automated tissue staining instrumentation. Using computer-aided design software, and a stereolithography printer, we prototyped a guide template to build recipient TMA FFPE blocks. To screen for a variety of antigens in TMA "cores", we prepared cell lines, and acquired mouse tumor xenografts and human tissues. Standard IHC techniques were used to screen hybridoma supernatants generated from mouse immunizations. We have designed and tested six different multi-well slide-based IHC screening platforms. The current format consists of a six by four array of 2 mm cores. We have screened antibodies from two different mouse hybridoma campaigns. Thus far, we have identified candidate IHC antibodies for exogenous epitopes to identify chimeric antigen receptor T cells used to treat solid tumors, and a fusion protein hypothesized to be an oncogene in pediatric liver cancer. This project developed a single-slide antibody screening prototype for IHC. The device offers the flexibility to test multitude of tissues, and is built with design considerations for future automated tissue staining compatibility.

Mycobacterium tuberculosis (Mtb) is a bacterium that can cause both latent Mtb infection (LTBI) and tuberculosis disease (TB). LTBI affects one quarter of the world’s population of those who are LTBI positive, 5-10% develop TB disease which left untreated can be fatal. Most individuals who are highly exposed to Mtb develop LTBI and show positive results for the tuberculin skin test (TST) or interferon-g release assay (IGRA). The Hawn lab has followed a cohort of Ugandans with heavy exposure to Mtb within the household but test negative by the TST and IGRA tests and define these individuals as Mtb 'resisters'. The presence of these Mtb ‘resister’ genes suggests a possible pathway for host directed therapies. Using transcriptomic profiling to compare the ex vivo Mtb response in LTBI and resister monocytes, several candidate resister genes were identified. We hypothesized that these candidate resister genes modulate antimicrobial functions through an effect on pro-inflammatory cytokine secretion which restricts Mtb growth. Individual ‘resister’ genes were inactivated by CRISPR/Cas9 gene editing in THP-1 cells and then differentiated into macrophage-like cells prior to various stimulations. Macrophage signaling pathways were stimulated with LPS (Toll-like Receptor 4 (TLR4)), PAM3 (TLR2/1) as well as with whole cell lysate from Mtb. I measured pro-inflammatory cytokine secretion in supernatants after 24h (IL-6, IL-1b, and TNF-a). We identified two genes, SETDB1 and NFIL3_03, that may differentially regulate pro-inflammatory cytokines compared to the control THP-1 cells. By uncovering the function of these genes, we hope to better understand how Mtb infections can result in variable immunopathogenesis.

The study of the behavior of multiple agents, specifically human and machine, in a dynamic environment is challenging due to the unpredictable individual behaviors. Humans will naturally formulate beliefs about the machine’s behavior, which would directly affect their future decisions. Our research aims to develop a framework for the study of human-machine dynamic interactions. With the imperfect information humans and machines have about each other and their environment, a game-theoretic approach was done to study the natural model of their interactions. We derive theoretical models for steady-state (i.e. equilibrium) and transient (i.e. learning) behaviors of humans interacting with other agents (humans and machines). We also design experiments to validate our theory. A haptic testbench, in the shape of a robotic arm, is used as a dynamic simulation platform for studying the trajectories of the human/machine interaction, allowing us to study both theoretically and experimentally. The robotic arm has a position control system that supports a wide variety of human/machine experiments. The user is provided with visual and haptic feedback, which allows for experiments to be designed to study the sensorimotor learning processes. The robotic arm is built using direct-drive brushless motors, force sensors, an open-source ODrive motor controller, and an arm lever. The motor firmware is designed in C/C++, and integrated with a user-interface in Python. With the wide variety of potential applications, we hope our research will give insights into the different natures of human motion and be a fundamental platform for technological breakthroughs in the medical field.

About 3.1 million adolescents are diagnosed yearly with depression. Adolescent onset of depression is associated with acute or chronic difficulties in physical, mental, and psychosocial functioning. However, over 60% of adolescents with depression do not receive mental health care, and, among those who do, treatment engagement is low. Behavioral Activation (BA) is an evidence-based psychosocial intervention for individuals with depression. While BA holds promise as an effective treatment, researchers have found that adolescents may be better reached and engaged through social and mobile technologies. In addition, BA requires frequent interaction from patients over time, which can be difficult and costly to administer in-person. There is an opportunity to improve the usability of and engagement with EBPIs via online technologies. Asynchronous Remote Communities (ARC) is a promising technology-based approach for engaging adolescents that leverages technology’s reach while providing support, social interactions, and motivation. ARCs are private online groups on which researchers can deliver weekly research tasks to participants and gather information about their perceptions in a format that is lightweight, accessible, usable, and low burden. We have used ARC to both discover design requirements and to design/build a platform for administering BA, which we have tested with clinicians and adolescents. We used ARC with 10 mental health clinicians specializing in treating teens with depression to discover their needs. Specifically, we worked with mental health clinicians to better understand their needs and to identify facilitators and barriers to adapting BA to ARC. We used the Slack online platform to create an accessible, anonymous environment where we posted 20-minute long design activities each week for 10 weeks to be completed asynchronously. We were then able to recruit teenagers to understand their needs. Based on the results, we are adapting BA to ARC settings and then testing out the feasibility.

Previous research has established extracellular vesicle (EV) signaling as a ubiquitous cell-signaling modality used by all cells. In this modality RNA, peptide, and protein signals are packaged together in small vesicles and directed to specific downstream cell targets. In addition to being necessary for healthy physiology, EVs can also contribute to pathological processes such as neurodegeneration in Alzheimer’s disease through carrying toxic proteins tau, Aβ and β-synuclein between cell types. Recent research in the Kaeberlein and Mendenhall labs has shown that when human tau is specifically expressed in neurons of C. elegans, there is a significant increase in HSP90 chaperone and proteostatic stress reporter expression in the intestine. I hypothesize that the induced human tau neuron-to intestine stress signal is conveyed by the extracellular vesicles. To determine the signal pathway, extracellular vesicle signaling was disrupted specifically in neurons of a transgenic nematode line with neuron-specific human tau and fluorescent intestinal proteostatic stress reporter (daf-21::GFP). RAL-1 is a small GTPase that has been shown to be necessary for EV signaling in the C. elegans hypodermis and intestine. Therefore, RAL-1 function is disrupted though knocking down neuron-specific expression with either a double-stranded RNA ral-1 construct or a dominant-negative form of RAL-1 The degree of daf-21p::GFP expression was compared between the reporter lines and those with disrupted ral-1 function. Many studies utilizing C. elegans have shown that neurons send cellular stress signals to other tissues which strongly affect lifespan, metabolism, and proteostatic stress. Therefore, the results from my experiments contribute to determining whether EV-signaling carries neuronal stress-signals induced by human tau and establish a methodology for using C. elegans as a model for studying this important signaling pathway.