The aviation industry is predicted to grow exponentially within the next few decades. With this growth in the industry comes a significant growth in carbon emissions; this increase will occur despite strides forward in jet engine and airline administration efficiency. With international concerns about environmental issues, it is critical that the impacts and detrimental effects of aviation usage are analyzed and mitigated. Although it is known to be environmentally damaging, many University of Washington faculty members are pressured to fly in order to develop and further their careers. Very little data has been gathered surrounding faculty members, particularly in environmental programs, and the correlation between their personal values and concrete actions. In attempts to quantify viewpoints, recent literature analyzes environmental beliefs and corresponding behavior within regular consumer populations. A majority of these studies observed and divided participants into categories depending on their behaviors. For those faculty members working in environmental and climate science fields, the question presents itself: How closely correlated are faculties flying habits and environmental beliefs? Through twenty open-ended interviews, this study will attempt to evaluate UW faculty members and their self proclaimed environmental beliefs and actions. I suspect that tensions will exist between faculty’s values and necessary career related travel. Analyzing these tensions, especially amongst those most educated in these topics, can aid in finding pathways to mitigate actions that are environmentally damaging

Stuttering is a fluency disorder which is characterized by prolongations, repetitions, and blocks, which disrupt the flow of speech (Guitar, 2014). There are multiple factors affecting stuttering, including physiological, psychological, environmental, and linguistic (Guitar 2006; 2016; Kang et.al, 2010; Sitek et.al; Smith & Weber, 2017). Self-disclosure has been shown to improve listeners’ perceptions and attitudes towards people who stutter in a positive manner (e.g., Byrd, McGill, Gkalitsiou, & Cappellini, 2017; Byrd, Gkalitsiou, McGill, Kelly & Reed, 2016; Lincoln, Brinker-Katz, 2017). Yet, limited research has explored the physiological and affective changes that speakers who stutter experience when they self-disclose (or do not self-disclose) their stuttering. Bowers and colleagues (2012) examined the relationship between anticipatory autonomic arousal and stuttering during reading tasks. They found that people who stutter presented with decreased skin conductance when stuttering was eliminated. They also reported that people who stutter exhibited increased final heart rate deceleration when a skin conductance response occurred. Bowers et al. (2012) concluded that physiological responses were best determined by the anticipation/possibility of stuttering, rather than speech outcome (fluent or stuttered). These results suggest the importance of further exploring the anticipation of stuttering and its effects on the speaker who stutters in a variety of contexts (other than reading). In the proposed study, we will ask participants to report speaking situations in which they feel least to most comfortable and we will monitor their physiological and affective responses within those situations. Participant self-report of speaking situations will enable ecological validity and inform our clinical practice. We hypothesize that speaking situations participants rate as “least comfortable” will elicit increased heart rate deceleration during a stuttering moment and decreased skin conductance when stuttering moment is finished.

We present optical and infrared photometry of the T Tauri binary KH 15D acquired in the 2017/2018 observing season. The data were obtained from the A Novel Dual Imaging CAMera (ANDICAM) instrument on the 1.3m telescope operated by the Small Moderate Aperture Research Telescope System (SMARTS) at the Cerro-Tololo Inter-American Observatory (CTIO). KH 15D includes two young stars (A and B, with 0.72 and 0.74 solar masses, respectively) orbiting their common center of mass, surrounded by an inclined precessing circumbinary disk. The recent data reveals Star B gradually emerging from the trailing “fuzzy” edge of the disk and is now in a stage that is completely unocculted for the first time since the system’s discovery in 1995. We use time-series photometry, or light curves, to probe the composition of the disk, derive parameters of Star B, and demonstrate the overall mechanics of the system. Recent data also shows reddening during the egress of the last eclipse, proving that the trailing edge of the disk is transparent and consists of dust-sized particles. Additionally, the most recent data displays Star B at a brighter magnitude than ever than before, allowing us to calculate an apparent I magnitude of 14.079, which is 12% brighter than previously computed.

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.

Legal theorists have long maintained that courts operate beyond their primary function of dispute-resolution and have problematized their characterization as “objective” bodies, noting their significance as powerful social and political actors bestowed with constitutive powers of meaning-making. Virtually absent in this scholarship is an analytical angle examining this constitutive power using theory or methods from performance studies. This is surprising, as courtrooms are highly theatrical spaces. My research seeks to fill this gap in scholarship by marrying theories and methods from sociolegal studies and theatre- and performance studies to examine how courts contribute to the construction of cultural meanings pertaining to identity. This essay treats the European Court of Human Rights (Court), the judicial organ of the Council of Europe and one of the most active, powerful international human rights courts in the world. How does the Court construct notions of identity – especially around nationality, European community, gender identity, and religion? More specifically, my project asks: How are these courtroom constructions conceived and legitimized through narrative performance, and how is their sociopolitical influence shaped by the mechanics of performativity? To answer these questions, I conduct an original research project analyzing both written judgments and video recordings of oral hearings held in the Court’s Grand Chamber. I form my own criteria to analyze these hearings as performances, and create a scheme to evaluate written judgments for their performativity. I also analyze certain structural characteristics of the Court, and some legacies of its case law, as symbolic and embodied performances, examining how identity narratives are reproduced by the Court’s composition as an institution and its behavior over time. In addition to demonstrating what can be gained by critically assessing courts holistically using performance theory and methodology, I hope to illuminate exciting intersections between sociolegal studies and theatre- and performance studies with this work.

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.

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.

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 abuse of opioids has become an epidemic in the United States. In 2017 the mortality attributed to opioid overdose was 70,237 individuals which is more than the death toll from the Iraq and Vietnam wars combined. Microdirect laryngoscopy (MDL) is a very common surgery performed among otolaryngologists with varying post-operative analgesia regimens. We aimed to characterize current opioid-prescribing patterns among otolaryngologists performing MDL by using a cross-sectional survey of otolaryngologists at a national meeting. Our eventual goal was to have a standard post-operative opioid prescribing protocol to improve safety and allow early identification of individuals that may be at risk of opioid misuse. We surveyed 57 practicing otolaryngologists: we found that 91% of surgeons routinely prescribed opioids, 84% of surgeons recommended non-opioid analgesics as adjunctive medications, and only 5% of surgeons report never prescribing opioids. When opioids were prescribed, patient preference, difficult exposure and a history of opioid use were the most influential patient factors. Concerns of opioid abuse, the physician role in the opioid crisis, and literature about post-operative non-opioid analgesia were also underlying themes in influencing opioid prescription patterns after MDL. Opioid stewardship should be a consideration for MDL. It appears that over 90% of physicians are prescribing opioids after MDLs, although many are also prescribing non-opioid analgesia. Armed with the knowledge of current practice and influences, otolaryngologists can work to decrease opioid prescribing patterns appropriately to improve patient safety and mitigate the contribution of post-operative prescribing patterns on the opioid epidemic.

Blood transfusion is a cornerstone of modern medicine, with a transfusion performed every 2 seconds in the United States. It is critical to accurately determine both patient and donor blood type prior to transfusion, as mixing non-complementary blood types can trigger life threatening reactions. While the ABO antigen system was first described over a century ago by Nobel Laureate Karl Landsteiner, to this day safe transfusion remains burdened by the nuance of blood type. Many of the current blood typing tests over simplify classification and often disregard ABO subgroups, despite widespread recognition of their significance. Moreover, our understanding of the ABO blood types (A, B, AB, and O) is still incomplete, as the full structure and microheterogeneity of these ubiquitous blood group antigens is not yet fully described. This project characterizes the biochemistry of ABO blood types through an interdisciplinary collaboration between UW Bioengineering, Medicinal Chemistry, and Bloodworks Northwest (the regional blood center). Our study employs exhaustive isolation of red blood cell (RBC) membranes from genotyped donors for comprehensive biochemical and biophysical analysis. The RBC membranes are treated with cocktails of enzymes - namely PNGase F, EGCase and Neuraminidase - to cleave glycan structures at specific locations. Reactivity to different antibodies and lectins provides insight into the structure of the glycan antigen. Results have shown that the clinical anti-A antibody binds disproportionally to N-linked associated antigens. These findings inform ongoing mass spectrometric and biosensing work to further elaborate ABO structure and bioactivity, with implications for transfusion and transplant medicine.

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.

The tools of mathematical modelling have been applied to many sports where athletes are searching for strategies to improve their performance. Downhill mountain bike racing is a sport that could benefit from mathematical modelling. My research is aimed at developing a computer algorithm that uses mathematical modelling to simulate downhill mountain biking. In a mountain bike race, racers compete for the fastest time to individually ride down a trail with turns and obstacles. The fastest riders are the most efficient at converting their potential energy to kinetic energy. These riders accomplish this by optimizing the amount of their energy expended on braking and friction so they are just below the borderline of crashing throughout the entire trail. The finishing times of the top 10 riders are often very close, indicating that they are approaching a physical time limit to complete the trail. By using mathematical modelling and the GPS profile of a downhill trail as input, I aim to develop an algorithm that optimizes braking at every point on the trail and outputs the minimum time to complete the trail. The results from this algorithm would provide insights into how a rider could improve their performance. In my work, I show that mathematical modelling can accurately simulate the motion of a downhill rider, explain the challenges in developing a computer algorithm that optimizes braking, and discuss the results of an experimentally tested algorithm.

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.

 I am an enrolled member of the Nor Rel Muk Wintu Nation located in Hayfork, California. My tribe has been fighting for federal recognition since 1986, leaving many of us in precarious situations without our sovereignty recognized by the federal government. Many tribes in California are seeking federal recognition due to the restrictions of services accessible, which hinders our access to beneficial federal policies such as the Indian Child Welfare Act of 1978 (ICWA). I understand the issues surrounding tribes that lack federal recognition and the problematic issues that arise without our sovereignty recognized, rendering our communities’ invisible. Due to this invisibility, my research focuses on the absence of knowledge pertaining to non-federally recognized tribes in California, such as the Nor Rel Muk Wintu, and our continued fight to utilize these policies, such as ICWA, while we remain sovereign with or without federal recognition. For my project, my methodology is a critical analysis of historical and contemporary policy; also examining the statistical data surrounding ICWA. Using statistical data gives me a framework to focus on the inclusivity of non-recognized tribal communities in California. Setting the foundation of settler-colonialism and Federal Indian Policy is essential to understand the precarious situations found in communities that lack federal recognition as these laws create barriers for tribal people. The ICWA as a federal law inhibits the help associated with non-federally recognized communities and leaves these children unprotected from historical known Indian child removal as an attempt to assimilate American Indian and Alaskan Native peoples into white society. As programs and research focus on the ICWA law, I have examined if they are inclusive of tribal communities that are not federally recognized. My preliminary results thus far have not included tribal Nations that lack federal recognition within their data.

Photoresist is a viscous light sensitive organic solution which is used to coat the surface of silicon substrates in nanofabrication processes. An essential step in nanofabrication is photolithography. During this procedure, photoresist is deposited in a uniform, thin film over the wafer surface using a tool called the Spin Coater.  The purpose of our experiment is to develop spin curves that will examine the correlation between the different speeds or RPM value that the wafer is spun at and the uniformity of the photoresist coated wafer. The thickness and uniformity are critical to determine the correct UV exposure dose and plasma etch times. We will analyze the results for both positive and negative photoresist. In the case of a positive photoresist, the regions that are exposed to light are dissolved in developer. On the other hand, with negative photoresist, regions that were not exposed to light are dissolved. After the wafers are spun, the uniformities will be measured by an automated thickness mapping system called Filmetrics. Filmetrics is a machine that allows for the surface to be measured at the nano-meter level. The spin curves experiment will allow researchers to obtain wafers using these photoresists to achieve photolithography with their desired thickness.

The natural history and morphology of blue mud shrimp, Upogebia pugettensis, burrows indicate that they farm their burrow linings. We tested the farming hypothesis by comparing carbon and nitrogen isotope, Carbon-13 and Nitrogen-15 ratios in tissues of U. pugettensis, their commensal clams, Naearomya rugifera and Cryptomya californica, and their isopod parasite, Orthione griffenis with other species and trophic groups co-occurring in the same mudflat, including the burrowing ghost shrimp Neotrypaea californiensis and Neotrypaea gigas, benthic clams and polychaetes. Ratios of these isotopes can indicate the relative trophic positions of organisms. We found similar isotope ratios among U. pugettensis and their commensal clams and that were different from isotope ratios in other clams and trophic groups occurring outside of the burrows in the same mudflat. The common isotope ratios among U. pugettensis and its commensal clams relative to these isotope ratios in other suspension and deposit feeding species in the same community are consistent with farming of the burrow lining.

In order to increase the success of students in mathematics, University of Washington Bothell’s Department of Undergraduate Learning has added a discussion section to “Precalculus II.” These discussion sections are primarily held by undergraduates who act as peer facilitators helping first years be successful in mathematics. At the beginning and towards the end of the course, the students are encouraged to take a “Mindset Survey.” The survey includes, roughly speaking, questions related to how students feel about mathematics in general. As a part of my research, I analyzed the survey results using a paired t-test on pre and post test scores. This study provides statistical evidence on the potential impact on students' learning and attitude toward mathematics. The result will help the department alter future courses to ensure the success of students in beginning math courses.

Photoperiod is utilized in plants to control seasonal responses such as flowering. Flowering of Arabidopsis is promoted in long day conditions (LD), late spring to summer, but not in short day conditions. Arabidopsis thaliana is our model organism because of its short generation time and simple genome which allows us to apply our findings to other species. One of the major factors that determines flowering time response to the different lengths of photoperiods is a gene, FLOWERING LOCUS T (FT). FT is induced around dusk in laboratory LD conditions. In natural LD conditions, there is an additional induction of FT in the morning. Although the molecular mechanism behind flowering regulation is the most characterized in Arabidopsis, the mechanism behind the expression of FT in the morning under natural LD conditions is not fully understood. Investigating these mechanisms will help us to understand how Arabidopsis plants flower in spring in nature and ultimately better the accuracy of experiments that are run indoors. The regulation of expression levels of transcription factors may be important for this FT induction. Through RNA sequencing analysis, we found eleven transcription factors within genes that were found to be differentially expressed between laboratory LD conditions and natural LD conditions. Analysis through quantitative polymerase chain reactions (qPCR) will hopefully yield results pointing toward a transcription factor that is important for the regulation of FT expression. 

The geriatric population is the fastest growing population in the U.S. Mental health is crucial to the quality of life of geriatrics and the family members who take care of them. While mental illness is a common health concern in the geriatric population, under-diagnosed and under treatment of mental illness creates challenges for the health and well-being of both elderly patients and their families. Unfamiliarity with psychiatric health, such as recognizing signs, symptoms, and providing appropriate referrals and treatment, may result in myths, the stigma of mental illness, and appropriate and timely psychiatric care. The purpose of this meta-analysis research is two-fold. First, the research provides a summary of the current evidence regarding the cause of geriatric psychiatric issues in nursing-related settings. Second, it highlights the possible solutions to the shortage of psychiatric nurse practitioners. As healthcare practitioners, nurses must have proper training in order to be aware and recognize geriatric mental health illness and provide appropriate care for our patients and their families. Providing patient education to the geriatric population and family members will allow them to assist in identifying the signs and symptoms of potential mental health problems. Lastly, the meta-analysis will examine possible solutions provided by current geriatric researchers for the best way to identify and treat psychiatric problems in the geriatric population.

First-passage and last-passage algorithms are two diffusion Monte Carlo methods that we can use to obtain the charge density distribution on a conducting surface. Usually, we use first-passage algorithms to obtain the capacitance and the overall charge distribution of the arbitrary-shaped conductor. On the other hand, the last-passage algorithms calculate the charge density at a point on a conducting surface by initiating the random walk at that point. The last-passage algorithm utilizes the dipole Green’s function to expedite the diffusion process which starts from the point. Past results determine the initial sitting using the largest hemisphere around that point with a radius that is contained in the surface, which inefficiently starts the random walk if the point is near the edge of the surface. Here, we derive the dipole Green’s function to start the diffusion process from a point on the hemisphere off-centered from the original point using weighted sampling to further expedite the computing process.

Pulmonary fibrosis is a disease marked by irreversible scarring and thickening of the lung tissue causing significant decline in lung function. Individuals afflicted will struggle to perform simple physical activities and often require mechanical assistance at some point in their lives. Currently, there are no permanent solutions for those with pulmonary fibrosis as most treatments only aim to slow down the progression of the disease. In these studies, we developed a novel therapeutic that could stop the progression through DNA modification of fibrotic gene targets using exosomes as a delivery vehicle. Additionally, regeneration of lung tissue is imperative for reinstating lung function and by using similar technologies we aim to target and overexpress critical regenerative genes. Using CRISPR Cas9 gene editing technology, we were able to knockdown key cytokine specific genes responsible for the development of fibrosis. We specifically targeted TGFß (Transforming Growth Factor ß) and Interleuken-6 (IL-6), both known to play a significant role in pro-inflammatory responses and fibrosis through exosome-mediated delivery mechanisms. CRISPR Cas9 vectors were designed to contain unique guide RNAs that could effectively target specific genes that the Cas9 complex could use to repress TGFß and IL-6. Cell lines were treated with the modified CRISPR Cas9 vectors and assessed for gene and protein expression. This study provides key insight into a novel therapeutic platform using a new delivery mechanism that mitigates and reduces fibrosis and promotes recovery of pulmonary function.

During embryonic development of the vertebrate central nervous system, innate immune cells, called microglia, migrate into the retina and brain. Microglia are responsible for phagocytosis, monitoring tissues for pathogens, and inflammatory signaling. Several studies in model organisms show microglia also have roles in neural development, particularly in formation of synaptic circuitry. Defects of the neuronal circuitry can lead to vision loss, therefore it is probative to investigate the role and mechanisms of microglia in wiring the retina. The purpose of this project is to investigate microglia migration and activity in the human retina, where very little is understood. To understand if microglia could have similar effects in human retinal development as in model organisms, we first needed to determine when and where microglia are found at different ages. We collected donated fetal tissues from as early as developmental day 40 through 132 to determine the number and distribution of microglia in tissue sections using Iba1, a microglia-specific antibody, and confocal fluorescence microscopy. To test whether microglia are necessary for retinal development we are using our lab’s fetal retina culturing technique that can be used to manipulate microglia populations. Retinal development can be visualized after deletion of microglia using markers for retinal progenitor cells (EdU) and various synaptic antibodies. So far, we have seen from whole retinal tissues that microglia are present as early as day 58, prior to the majority of synaptic development, and survive in retinal cultures. Earlier stages are being investigated, and we are currently determining methods that will deplete microglia in order to study the effects of their absence on retinal development. In conclusion, we know that microglia are present during synaptic development, and persist during retinal culturing. Therefore, microglia are potentially essential for human retinal development and could be targets for future disease research.

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.

Lung transplantation is currently the only treatment solution for end-stage lung disease in a large cohort of patients afflicted with a range of pulmonary issues including cystic fibrosis (CF) and idiopathic pulmonary disease (IPF). Despite the successes, a major setback is the development of chronic lung allograft dysfunction (CLAD). This is characterized by chronic inflammatory host responses towards the transplanted lung resulting in injury of the donor tissue. Currently, we are investigating the role of cell-derived vesicles or exosomes, in a range of immune responses such as chronic inflammation. The composition of exosome membrane components and internal signaling within exosomes depend on the cell type from where it was secreted and the current immune state. A major benefit is that unlike cells, exosomes do not change phenotype after being secreted by the parent cell due to environmental stimuli, making them ideal targets for biomarkers associated with immune responses. In these studies, we assessed exosome surface markers and investigated exosome function from retrospective patient serum, which provides insight into potential novel mechanisms in the development of CLAD. We developed a novel ExoFlow that qualitatively and quantitatively assesses exosomes at 1, 3, 6, and 12 months posttransplant using CFSE, traditional fluorescent antibodies for T cell and macrophage markers, and ImageStream to generate immune profiles. We then correlated these results to clinical outcomes. In a preliminary study, it appears that macrophage exosome profiles show significance in differentiating patients who develop CLAD, while T cell specific exosomes seem to be unremarkable. This could be attributed to the heavy course of immunosuppression posttransplant. Functional studies show insight in potential polarization capabilities of exosomes as immune modulators and provides another novel area of investigation into the complex pathogenesis of CLAD.

In the United States over 1 million people are living with HIV. In 2016, approximately 65% of those newly diagnosed were African American, 50% were aged 50 and older, of whom approximately 25% were women. The majority of these women are Black/African American (AA). Our study, Stress, Cognition And Quality Of Life In Women Living With HIV, sought to understand how HIV affects the mental, social and physical health of older women living with HIV. The overall goal of the study was to determine if changes in mental health, social health and physical health were associated with changes in cognition and quality of life. Between November 2018 and January 2019, we conducted in-depth, individual interviews with AA women aged 50 and older that were living with HIV. The interviews were conducted to understand whether stress, social interactions or changes in cognition impacted the quality of life as women age with HIV. Questions allowed participants to share their broad experiences of aging with HIV in relation to changes in their mental health, physical health, social health and overall experiences of aging with HIV. Preliminary results indicate that while emotional stress is not directly related to quality of life, instead physical stressors related to other chronic health conditions (i.e. arthritis, high blood pressure), mobility issues and deterioration of physical health due to aging had a direct impact on their quality of life. Patients also discussed how mental health and psychosocial (i.e. depression and social stigma) were intertwined with their HIV disease. Also, patients discuss how maintaining a positive relationship with their healthcare team, and surrounding themselves with a support system that encompasses family, religious organizations and members of support groups, help to maintain, guide and support their quality of life.

Hypoxic-Ischemic Encephalopathy (HIE) is a brain injury that commonly causes mortality in neonates. Current treatment consists of therapeutic hypothermia, but close to 50% of affected infants still have a poor outcome (death or severe disability). In order to discover new effective therapies, it is important to compare how different treatments affect the brain in animal studies. The research laboratory has developed a ferret model of HIE because the ferret brain has more complex gyrification compared to rodents. Animals underwent unilateral carotid ligation at postnatal age 17 days (P17), in which one side of the carotid artery was restricted temporarily and the other was restricted permanently. The animals then received periods of hypoxia and hyperoxia. To better quantify the extent of injury, a system involving measurements of the gyri, sulci, and cerebellar exposure was developed. Ex vivo brain measurements were collected from a population of 63 ferret kits at age P42, and adjusted by the weight and sex of the animal. These measurements included the lengths of: the longitudinal fissure (anterior and posterior), lateral sulci, suprasylvian sulci, coronal sulci, pseudosylvian sulci, ansinate sulci, cruciate sulci, presylvian sulci, lateral gyri, suprasylvian gyri, sigmoid gyri (anterior and posterior), coronal gyri, ectosylvian gyri (anterior and posterior), orbital gyri, and the exposure of the cerebellum. In injured animals, significant changes in the longitudinal fissure, ansinate sulci, left coronal sulci, cruciate sulci, presylvian sulci, posterior sigmoid sulci, and exposure of the cerebellum were seen compared to littermate controls. The implications of this measurement system include the ability to accurately characterize the degree of injury in animals with an hypoxic-ischemic brain injury, which will help to show whether potential treatments are neuroprotective.

Schistosomiasis is classified as a neglected tropical disease, ranking second only to malaria as the most common parasitic disease in the world. The two species of interest for this project are Schistosoma haematobium and Schistosoma mansoni, both of which can infect humans who come into contact with infested waters. The disease can manifest in urogenital (S. haematobium) or intestinal (S. mansoni) forms, leading to a variety of symptoms, including chronic pain, bladder and liver cancer, and – in extreme cases – death. Despite the extremely infective nature of schistosomiasis’ environmental stages and its complex transmission ecology, relatively little has been done to understand the effect of schistosome parasitism on the behaviors on its intermediate snail host. Expanding our understanding of snail behavior is necessary to explain the transmission dynamics of the disease and to reduce rates of human infection. In this research project, I examine snail choice behavior in infected and uninfected snails in a simulated lake habitat, and determine if schistosome infected and uninfected freshwater snails exhibit a difference in aggregation behavior, and where within a simulated pond environment infected and uninfected snails reside. I hypothesize that in a large population, both infected and uninfected snails will aggregate towards infected snails. I also hypothesize that infected snails will tend to linger closer to the surface of the water than uninfected snails and be less likely to quit the water, thus increasing the probability of transmission to a mammalian host. Understanding snail intermediate host behavior in the transmission of schistosomiasis gives us a way to control infection rates from an ecological perspective in addition to the traditional medical perspective.

Natural dermal armors are inspiring the development of advanced engineering materials and next generation flexible armors. Fish scales are an exemplary candidate and consist largely of laminated plies of unidirectional type I collagen fibrils. The mechanical properties of fish scales depend on the interpeptide bonds within the triple helix of the collagen fibrils. Adjusting the strength of these bonds to change the performance of the scales has applications to the design and functionality of bioinspired flexible armors. Here, elasmodine scales were exposed to polar solvents to adjust the extent of intermolecular bonding. Changes in the mechanical properties were evaluated in uniaxial tension and at two different strain rates. Results showed that the constitutive behavior was highly dependent on the intermolecular bonds. A significant increase was observed in elastic modulus (stiffness), strength and toughness as a result of increasing the extent of interpeptide bonding via solvents with low affinity for hydrogen bonding. A 300% increase was seen in the elastic modulus of scales soaked in acetone compared to HBSS at the highest strain rate. Furthermore, the importance of interfibril bonding was dependent on loading rate. Overall, results showed that the “protecto-flexibility” of fibrous armor materials can be improved by activating interfibril bonds and that this could spawn approaches for tuning armor performance.

Natural armors, like those found on animals, provide inspiration for the development of next-generation engineered materials. In this study, the microstructure and composition of the cuticle of the terrestrial isopod armadillidium vulgare was evaluated. The cuticle, composed of layers of mineral particles and chitin fibers, is multifunctional. It protects the animal from impacts, predation, and maintains internal moisture, while facilitating sensing of the environment. Prior literature has focused on mineralized portions or anatomical features, while this work integrates composition data with chitin fiber structure and orientation. Cuticles of the armadillidium vulgare were evaluated by scanning electron microscopy (SEM) and Raman spectroscopy. Cuticle cross sections were prepared by freezing individual tergites in liquid nitrogen, then sectioned by fast-fracture. SEM was used to image cross sections and view chitin fibers and ply orientations over the cuticle thickness. This data was used to understand fiber layer morphology and orientation throughout the cuticle thickness. Raman was used to evaluate the spatial dependence of composition across the layers. Results showed that the cuticle is actually a nanolaminate consisting of plys of chitin fibrils, and with ply thickness that varies through the cuticle. The stacking arrangement of the plies appears to follow a Bouligand structure, which is characteristic for other natural composites. Results of Raman indicate that the plies are mineralized chitin, however, it is unclear if there are changes in composition through thickness. This work is ongoing. An understanding of the ply arrangement and mineral distribution in this armor can be used to pursue new strategies for material design where resistance to impact and puncture are needed. Applying design principles found in this isopod, more efficient and effective materials can be designed for applications such as light-weight armors or protective coatings.

Dogs have been shown to use the direction of humans’ gaze to infer information about hidden food, a behavior referred to as social referencing. We might expect that social dependency towards a handler will be higher for dogs that are more dependent on humans’ presence, especially when faced with uncertain situations. We tested whether there was a relationship between attachment and dependency behaviors and social referencing in companion dogs. Dog owners completed an intake survey that included the previously validated Canine Behavioral Assessment and Research Questionnaire (C-BARQ), which gives a score for the degree of separation-related distress behaviors dogs exhibit which we used as a measure for dogs’ attachment and dependence on their owners. These owners then brought their dogs to participate on-location for our experimental set up. We taught the dogs a location-based discrimination task, in which subjects learned to expect a food reward in one location (the positive stimulus), and no reward in an opposing location (the negative stimulus). When dogs approached the positive stimulus faster than the negative stimulus, we intermittently presented them with ambiguous stimuli, i.e. intermediate between the positive and negative stimuli. We measured social referencing as the frequency of glancing behavior of dogs toward their owner or the handler for each trial. We analyzed social referencing by stimuli in order to assess whether dogs would treat ambiguous stimuli as they do the rewarded location or the non-rewarded location with respect to glancing behavior. We hypothesized that dogs with higher C-BARQ scores for separation-related behavior would exhibit higher proportions of social referencing behavior, particularly when presented with ambiguous stimuli. Our research has implications regarding potential effects of canine dependency on their owners in their decisions in certain situations, such as those that introduce ambiguity.

Forage fish such as Pacific herring, Clupea pallasii, are a valuable economic and ecological resource in marine food webs. Forage fish are integral species as they can drive both top-down and bottom-up effects in pelagic marine communities. Understanding population dynamics of herring and other forage fish species is essential to management. Although poorly studied, parasites of forage fish are of particular interest due to their potential effects on population dynamics and ability to predict the presence of anthropogenic contaminants in the environment. The goal of this study is to determine if parasite communities differ in composition and diversity between year-zero herring collected in offshore and nearshore (marina) environments in the Puget Sound. I am performing necropsies on 180 herring collected from 6 Puget Sound sites. I expect to find a greater abundance of parasites that use direct transmission in nearshore herring due to decreased stock mixing, as well as a greater prevalence of certain parasites due to closer proximity to anthropogenic contaminants. Parasites remain understudied in important forage fish like herring; and, this research can be used to understand population dynamics of herring in local marine environments as well as aid in fisheries management.

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!

Multiple studies have demonstrated an association between a long-term exposure to air pollutants and health outcomes in area of cardiovascular and respiratory diseases. However, there is suggestive, but insufficient, evidence linking the association between long-term exposure to air pollution and mental health outcomes, such as depression. In South Korea, a nationwide population-based, cross-sectional study investigated the relationship between long-term exposure to ambient air pollutants and mental health status. The study of 124,205 participants found a positive associations between Particulate Matter (PM10 and PM2.5 ), Nitrogen Dioxide (NO2), and Carbon Monoxide (CO) exposures and mental health status. The goal of this study is to determine whether the air pollution-depression relationship holds true in the ACT (Adult Changes in Thought) cohort by conducting a similar study to the cross-sectional study conducted in South Korea. In this study, I will consider air pollutants (PM2.5 and PM10) as exposure and depression as a measure of health outcome. The central working hypothesis of this study is that higher levels of PM2.5 and PM10 will be associated with an increase in CES-D (Center for Epidemiologic Studies Depression) score. Participants from the ACT cohort (members of the Kaiser Permanente in Seattle, Washington) who had an ACT study visit between 11/1/2000-4/1/2003 will be the study population. The primary analysis aims to evaluate the association between PM (PM2.5 and PM10) and CES-D scores using linear regression model after adjusting for age, sex, smoking, income, education, cardiovascular disease, and cerebrovascular disease. The secondary analysis aims to evaluate the effect modification of age, alcohol history and early vs. late onset of depression has on this association. It is hoped that the results from this study will expand our understanding of the relationship between air pollution and depression.

Small-angle neutron scattering (SANS) is a powerful tool that provides access to molecular-level structure in a variety of material, such as soft matter, colloids, and biomolecules. Currently, researchers must follow a manual and inefficient procedure to reduce and analyze data due to inconsistent meta-data storage and varying reduction processes. Thus, our project is aimed to improve the automated reduction of SANS data and streamline data flow at the experiment site by the use of machine learning (ML) and data science techniques. We propose a machine learning classification algorithm, trained on a historical SANS dataset, to automatically sort raw data into six categories of scattering profiles and relevant background measurements required for reduction. The first stage of our research project uses a feature reduction model to create a subset of most significant and relevant meta-data in the historical scattering data set. After pre-processing, we then explore different ML models (e.g. neural networks) to sort the data in a comprehensive, accessible, and maintainable form that can be easily applied to sorting data directly from experiment sites. In addition, we incorporate a Postgres database to improve data management as well as an interactive front-end to enable user interaction. Currently, we are building meaningful and useful data processing and management methods by starting with a small SANS dataset from the Pozzo Research Group at the University of Washington. In the future, these methods will be expanded to larger historical SANS datasets to train our machine learning models. By developing this machine learning algorithm that can utilize experimental information and scattering patterns for auto-labeling of raw data and relevant meta-data, we will enable more efficient storage, reduction, and analysis of SANS data for researchers in the future.

Sixty percent of adults in the US have a chronic disease (e.g., heart disease, cancer, diabetes) and forty percent of adults have two or more chronic diseases. Risk for chronic disease is strongly influenced by a short list of health behaviors such as tobacco use, physical activity, diet, and alcohol use. College students, as they become independent from their families, start to establish lifelong habits through their time in school. Students who experience high stress are more likely to engage in less healthful behaviors which can increase their long-term risk of chronic disease. The purpose of this study is to understand how stress and lifestyle behaviors among low-income and international college students impact risk for chronic disease. This is a survey study in which 300 undergraduate international and native students at Portland State University will complete questionnaires about health behaviors, stress, socioeconomic status and demographics. International student participants are recruited from different clubs and programs that provide support for international students. We expect our results to indicate that international students and students from low-income families experience higher than average levels of stress, which may negatively impact their engagement in health behaviors and further increase their risk for chronic disease.

I conducted analysis of data from 11 high-precision elemental abundance analyses of twin-star binary systems from previously published studies and included our own data for one additional pair. The goal of my analysis was to see if there were any new trends related to the differential abundances (Δ[X/H]) versus other common parameters in addition to condensation temperature. I did not find significant trends for surface gravity or effective temperature, but there is a weak correlation between the differential abundances and separation between the binary stars. As the separation between the stars increases, the absolute value of the difference in abundance increases for all chemical species. This suggests that less abundant chemical species tend to show higher star-to-star differences in abundance. This weak correlation could suggest inhomogeneity in the molecular clouds from which the binary star systems had formed.

 Domestic dogs express individual differences in personality and perception, affecting their behavior towards objects they encounter in the world. One of these differences is a form of cognitive bias called judgement bias. Dogs that approach an ambiguous stimulus at a rate closer to that of approach towards a rewarded stimulus demonstrate a positive judgement bias. Likewise, dogs who approach at a rate closer to that of a non-rewarded (or aversive) stimulus have a negative judgement bias. Some dogs refuse to approach the non-rewarding stimulus entirely, which can be defined as refusal behavior. We analyzed whether refusal behavior was related to companion dogs’ judgement bias and general fear and anxiety. Dog owners completed the Canine Behavioral Assessment and Research Questionnaire (C-BARQ), a previously validated questionnaire measuring a variety of individual differences in dog behavior, and, most importantly, fear and anxiety. Afterwards, dogs were brought in for in-person testing. We measured each dog’s latency to approach ambiguous stimuli and compared this to their latency when approaching rewarded versus non-rewarded stimuli. We would expect that dogs who refuse to approach ambiguous stimuli will also exhibit higher C-BARQ scores in fear and anxiety than dogs who do approach ambiguous stimuli. Refusing to approach may also suggest a negative judgement bias. These findings are extremely useful to not only further understand canine behavior and cognition, as refusal to engage with a stimulus may be a future tool to define a canine’s perception of ambiguous stimuli. They also have practical implications for both animal welfare and training efficacy, as individual cognitive differences among dogs may impact how they will respond in behavioral tests and training regimes.

One out of every two-hundred schoolchildren lives with type 1 diabetes. Type 1 diabetes is a chronic illness that requires monitoring blood glucose, calculating insulin needs, meal planning, and monitoring for and treating hypoglycemia and hyperglycemia. Effective coordination of care between school nurses, health care providers, parents, children, and school staff is critical to promote diabetes control and prevent adverse health outcomes. The purpose of our project is to describe parent and school nurse perceptions of care coordination in the care of children with type 1 diabetes. Our project is part of a larger project that aims to identify facilitators and barriers to effective care coordination in Washington state schools. Focus groups were conducted with parents of type 1 diabetics in urban and rural settings throughout the state that represent the diversity of resources and school nurses across the region. We recorded, transcribed, categorized, and analyzed verbal and written responses to identify themes. Our preliminary findings suggest that parents and nurses identify inadequate communication between school nurses, parents, and providers, and difficulties organizing care as a significant barrier to effective care coordination. Strong communication and involvement between all parties contributes to successful care coordination. Results from the larger project will be used to develop a care coordination model to inform interventions to improve the care of children with type 1 diabetes in schools.

Advancements in fabrication of manufacturing and medical systems is focusing on using computer-aided fabrication methods, also called additive manufacturing or 3D printing. In civil engineering, we still rely on traditional methods of construction. Although there are researchers and companies investigating 3D printing of concrete, most focus on form, not on engineering properties. This research project has begun to remedy that by investigating mix design methodologies, new extrusion techniques and use of large-capacity testing equipment to advance engineering of 3D printed concrete structures. The first phase has investigated extrudable and stable (in its fresh state) mix design(s); a new protocol is being developed to test the engineering properties, including stiffness, strength of the extruded material, as well as multi-layer adhesion and deformation. The second phase will investigate the hardened properties. The research is funded by Pactrans, with the ultimate goal of printing components for multi-modal concrete structures, such as pedestrian and bicycle bridges.

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.

Lift-off is a subtractive process used in wafer fabrication of Micro-Electrical-Mechanical-Systems (MEMS) devices to pattern deposited films, often metal, that are challenging to dry etch. To achieve a successful lift-off, the lift-off process begins by depositing and then patterning a photoresist masking material onto a silicon wafer using photolithographic techniques. An important characteristic of the photoresist is undercutting the resist sidewalls after developing, protecting them from being coated with metal during deposition. After deposition, the photoresist and metal layer is removed via solvent. The purpose of our research is to allow for a more varied range of fabrication using positive tone photoresist. Negative tone photoresist is typically used for this lift-off process because after development, this resist naturally forms the desired undercut. Alternately, positive tone photoresist is characterized by a tapered sidewall that is difficult to not coat with the metal film layer, making the removal step via solvent problematic. We hypothesized an advantageous undercut is possible with positive tone photoresist using a white light diffuser that would allow light to enter at angles through our mask during the exposure step. We evaluated resist undercut using the Nikon microscope and resist/metal sidewall characteristics using the Scanning Electron Microscope. We will assess the new resist exposure technique using both line-of-sight evaporation (physical vapor deposition in which a target material’s atoms precipitate into solid form, when heated up under high vacuum, coating everything in the vacuum chamber) and sputtering (metal deposition involving particle ejection of ions) to deposit a thin metal film. We anticipate evaporated metal to lift-off easily with the new technique, which indicates a crowning demonstration of success.

Self-assembling synthetic nucleocapsids have been at the center of increasing development as a medium for targeted drug delivery. By identifying certain cell markers of tumor cells, researchers at the Baker Lab have been evolving desired characteristics to this protein assembly by attaching different functional domains to specifically target cells. This screening of functional domains is possible because of the nucleocapsid’s ability to encapsulate its mRNA sequence, thereby linking genotype to phenotype. Moreover, this enables us to evolve desirable features in these functional domains through library selection. However, subsequent attachment of functional units to its exterior surface proved to decrease its mRNA packaging efficiency, thus limiting applications like mRNA delivery and evolution of functional units. This project aims to enhance the amount of encapsulated mRNA by mutating certain interior amino acids. Methods include cloning our I53-50-v4 protein assembly gene into Escherichia coli (E.coli) strains and over-expressing the proteins through IPTG induction. After the cells were harvested and lysed, proteins were purified through Immobilized Metal Affinity Chromatography (IMAC). RNA encapsulation levels were measured through Quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) to compare between the original and mutated nucleocapsid. Promising results would demonstrate an increase in RNA concentration per nucleocapsid when compared to the original assembly across different constructs. The success of this project would allow for attaching multiple domains for evolution without compromising the nucleocapsid’s capacity to retain its biomolecular cargo. This research would greatly expand the utility of these nucleocapsids for evolving displayed proteins for desirable characteristics as well as enhance their efficacy for drug delivery applications.

Despite the yearly development of a vaccine, influenza (flu) still causes annual epidemics and is responsible for tens of thousands of deaths in the United States. Current flu vaccines are not fully effective in preventing viral infection because they protect people against a finite number of flu strains, which people may or may not be exposed to during a particular flu season. To address this challenge, we are engineering new protein therapeutics to increase the efficacy of flu vaccines. The two major proteins that flu viruses use to infect host cells, hemagglutinin (HA) and neuraminidase (NA), structurally parallel the two proteins that constitute a de novo designed nanocage. De novo protein design allows researchers to create proteins that are more stable than those produced in biological systems via evolution. The focus of this project is to use this designed nanocage to scaffold a more potent flu vaccine through a process called pseudo-symmetrization, which will allow the cage to display many different strains of HA and NA. To pseudo-symmetrize proteins, we used a modelling software to determine which protein components to modify to build a pseudo-symmetric protein. Then, we use molecular biology techniques to make modifications to regions of the protein that interact with other proteins when it self-assembles. As a result, the pseudo-symmetric protein is composed of building blocks that are all slightly different from one another, but can still assemble to create a nanocage with the same structure. So far, we have identified several variants of the modified cage component that can self-assemble, and we are continuing to test more interaction sites that make pseudo-symmetric proteins. These results, and continued experiments, will help us create new vaccines capable of displaying more flu virus antigens, thus protecting people from the flu using a single universal flu vaccine.

Current methods of drug delivery include the use of antibody drug conjugates (ADCs), lipid and polymeric nanoparticles, and top-down modified viruses. While successful in certain applications, these delivery platforms involve laborious production methods and have limited engineering opportunities. Synthetically designed proteins are viable drug delivery candidates that can be precisely modified to overcome the engineering challenges associated with other delivery platforms. Specifically, synthetic nucleocapsids (synNCs) are computationally designed icosahedral protein assemblies evolved to have virus-like genome packaging. The linkage between the encapsulated mRNA (genotype) and exterior proteins (phenotype) allows for directed evolution to be achieved through library selection. The synNC was evolved to increase the in vivo circulation half-life from less than 5 minutes to over 4.5 hours. The next step is to optimize the targeting ability of synNCs toward specific organs. We performed site-directed mutagenesis to introduce several mutations on the exterior of the synNC, performed two rounds of in vivo library selection, and identified several mutations that favored specific organs. Our current work involves producing five promising synNC mutants, biochemically characterizing the mutants, and examining their biodistribution in mice. The ability to target specific organs will be a successful step towards utilizing nucleocapsids in drug delivery and other biomedical applications.

Designing conducting biomaterials capable of long-range electron transfer for the development of bioelectronics and biosensor remains a challenging and unsolved problem in protein design. The overarching goal of this project is to design protein fibers and template redox-active cofactors for long-range electron transfer. Recently our lab developed a method to design proteins that assemble into long fibers with a tunable diameter. We are using these fiber materials to assemble redox-active cofactors within 10-15 of each other. We are using a helical segment of a natural cytochrome-C protein as the electron transfer conduit. First, We docked this helical fragment inside the fiber molecules previously designed in our lab. Promising docks compatible with distance constraints for effective electron transfer (generally within 10-15Á of each other) were chosen for further design calculations to accommodate the cytochrome-C molecule. We ordered 11 proteins from the first round design calculations to characterize experimentally. Proteins were expressed using the usual E. coli. expression system and purified using Ni-NTA affinity chromatography. 9 out of 11 designs expressed and were soluble. For the helical cytochrome-C fragment, we expressed the native protein in E. coli. and obtained the heme-containing helical fragment by trypsin digestion. To ensure that the heme cofactors are incorporated in the intended positions of the fibers, high-resolution cryo-EM will be performed after cofactor incorporation. The redox potential of these fibers will then be measured using cyclic voltammetry (CV). If successful, this will lay the foundation for the development of a wide range of redox-active biomaterials capable of long-range electron transfer.

Nowadays teamwork is becoming more and more important in business, and we may need to work together to fulfil projects’ goals. However, we still cannot find the exact reasons why some teams collapse. However, we think referent power and trust, in part, be likely culprits because it affects the way teams communicate to share knowledge about the project. Referent power is a form of reverence gained by a leader who has strong interpersonal relationship skills. Trust refers to a strong belief in the honesty and goodness of someone. Past research suggest that if the referent and trust are relatively low, it will affect the effectiveness and efficiency of communication or even no communication at all. Without communication, the team work will likely collapse. To test this contention without negatively affecting real-world teams, we used an agent-based modeling and simulation approach. Agent-based models are an impactful tool to study team phenomena because it can model the complex behaviors and probability of interactions and effects in a closed environment. So in our research, we analyzed the referent power and trust of a team by using agent-based models. We created a model for our research with two components “referent power and trust”. We 1) tested a mix of referent power and compared high referent power with low member trust, versus low referent power with high member trust to see what is the best scenario and 2) the results showed the scenarios when a team had higher effectiveness and efficiency in team work. Also, we share our NetLogo agent-based model code for other researchers to leverage.

At present, there is a disconnect between people’s awareness of environmental crises and their motivation to act on this knowledge. Novel ways of fostering a sense of connection with the environment are currently being explored to address this problem. Dance, among other artistic disciplines, has the potential to motivate pro-environmental actions because it appeals to people’s emotional centers through empathy-inducing experiences, community building, and non-traditional communication. Using members of the Seattle dance community as a case study for environmental dance, this research explores whether and how environmental activism through dance is manifested in Seattle, if barriers exist to engaging in environmental dance, and if current forms of environmental dance effectively motivate action. To execute this exploration, I will conduct several one-on-one semi-structured interviews with members of the local dance community; interviews will last between 0.5-2 hours. Interviewees will be selected to represent varying degrees of participation in environmental dance--from minimal to explicit environmental dance activities--and will include internationally recognized dance creatives to rising entrepreneurs. These discussions will inform a qualitative analysis of how dance has or has not been used as tool for promoting environmental action locally. Furthermore, they will provide the context for my own choreographic pursuits on environmental dance. Based on relevant research and my 10+ years of involvement in the Seattle dance community, I predict that environmental dance can be identified as choreographic productions, site-specific explorations, embodied knowledge, sustainable practices in the arts, and collaborations between scientists and dancers. The results will be communicated to a performing arts audience through creative demonstrations of key research findings and through excerpts of my choreography. I hope, by engaging with both the environmental science and dance communities, to promote a dialogue within and between these communities and to inspire further environmental dance endeavors beyond the scope of Seattle.

Botox (botulinum toxin) is commonly used to reduce facial wrinkles, but it is also injected into the masseter muscles, the main jaw closing muscles, for cosmetic reasons or pain reduction. Botox blocks neurotransmission, leading to partial muscle paralysis and atrophy. Although these effects are considered safe and temporary, we previously found that a single treatment of the rabbit masseter with Botox caused muscle atrophy persisting for at least 12 weeks. However, some muscle fibers were unaffected or even enlarged. The purpose of this study was to determine if the changes observed were more or less severe in specific regions of the masseter, and if differences in fiber size correlated with the regional electromyographic (EMG) response to nerve stimulation. Rabbit masseters were injected unilaterally. Regional EMG was recorded before euthanasia at either 4 (n=4) or 12 weeks (n=5) post-injection. The regions corresponded with the three sites of injection, anterior, middle and posterior in the inferior part of the muscle. Superior regions were also examined for the 12-week sample. Least fiber diameter was measured in histological sections (40-60 fibers/region). Linear regression was used to correlate EMG and fiber diameter. In general (6/9 treated muscles) the region with the largest fibers showed the highest EMG, but at 4 weeks there was no linear correlation; all regions showed both atrophied fibers and low EMG. At 12 weeks, all regions of treated muscles had larger average diameters and some also had increased EMG. Positive correlations between fiber size and EMG were seen anteriorly (r2=0.66) and posteriorly (r2=0.43) and in the muscle as a whole, both inferiorly (r2=0.36) and superiorly (r2=0.76). These results indicate that Botox injections have adverse effects long after the initial injection. Although no regions are consistently more affected than others, there is a general correlation between fiber recovery and signal strength.

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.  

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.

For more than 4,000 years, paper has been made from cellulose, the most abundant natural polymer, for the purpose of recording information. With the incorporation of fillers, such as carbon nanotubes (CNTs) and cellulose nanofibers (CNFs), conventional paper can exhibit enhanced strength, electrical conductivity, and high sensitivity to external stimuli (e.g. strain, temperature, humidity…), which has a great potential for applications in portable electronics and wearable devices. The present research consists of me spinning one or multiple strips of smart papers into highly robust yarns. I also prepare different strips of dried and wet paper. They are prepared from bleached soft wood pulp and are twisted into densely compacted yarns. I then exam their pore structure and strength properties using analytical methods. Results indicate that paper yarns made out of two strips exhibit the highest tensile strength, while the incorporation of additional strips shows only limited strength improvement. This work is important because it can let us know more about the physical ability of smart papers and nanotechnology and how to improve them in the future using yarn method.

The narrative of nuclear patriotism was heavily promoted to justify the construction of plutonium production facilities like Hanford, as well as the use of plutonium-based atomic bombs against Japan. Nagasaki, bombed only days after Hiroshima, does not fit into this patriotic narrative and has subsequently been overlooked by the public. Just like the government minimizes the attention on Hanford in the United States, the bombing of Nagasaki is not as well known as the bombing of Hiroshima. As a result, Nagasaki victims have endured health disparities of equal magnitude in silence. We researched this topic further by conducting interview analysis, discourse analysis, critical film analysis, and literature review. We wish to connect Hanford and Nagasaki by focusing on downwinders and atomic bomb survivors. While Hiroshima has had more public exposure than the Nagasaki bombing, we want to bring to light the equally devastating impact of the bomb on the citizens of Nagasaki. Hanford and Nagasaki are tied together not only by association to nuclear weapons and radiation, but also by the silencing of their association to these weapons. These impacts are closer to home than one would expect, and it is essential to bring awareness to the unseen struggles within our international community. Cleanup of nuclear sites and nuclear regulation need to be regarded as national responsibilities to global safety, to ensure that history will not repeat itself.

From the years 1946 to 1958, the Republic of the Marshall Islands (RMI), a sovereign nation in free association with the United States, endured the nuclear detonation of 67 atomic bombs conducted by US military. As a result of the nuclear testing, many Marshallese were gravely affected by the radiation exposure: suffering multi-generational health problems as well as being displaced from their homes. The unprecedented amounts of nuclear contamination have inevitably forced the Marshallese to abandon their lands, which has severely disrupted their cultural practices and lifestyle that has been passed down for years. The people have suffered countless traumas including birth defects and miscarriages, cancer, and autoimmune diseases. Through interviews, literature reviews, documentaries, and other modes of anthropological discourse, we will be demonstrating how the Marshallese have been affected by the US Government Nuclear Testing Program, and how this may parallel to the detrimental health effects of the people living near the Hanford Facility in Eastern Washington. Given the severity of health problems and involuntary migration in the RMI, we argue that the US government should take more responsibility and initiative to ensure that the Marshallese are granted proper restitution for the irreparable damages these nuclear test operations have caused to them and their culture. By implementing codes of ethics as well as more access to healthcare, we believe the health and wellbeing of the Marshallese will begin to thrive once again.

The research question this study addresses is: How do community-based promoters contribute to the delivery and utilization of health insurance among marginalized populations in India? The subject of investigation for this study is the insurance delivery model of VimoSEWA, an organization based in Ahmedabad, India that provides health and other social insurance services to self-employed women with limited prior access to financial protection. To address the research question, I investigated the successes and difficulties experienced by VimoSEWA community-based insurance promoters, called aagewans, through field visits and personal interviews in Ahmedabad and nearby rural districts in Gujarat. Both aagewans and insurance members were interviewed during this study to develop a comprehensive understanding of the importance of community-based promoters in health insurance delivery and the various factors that impact their role. The role of VimoSEWA aagewans in promoting and delivering health insurance to self-employed women in Guarat is significant because insurance improves the financial stability of these women and their families. Furthermore, health insurance is effective in decreasing high out-of-pocket healthcare expenses and improving access to quality healthcare services. However, the findings of this study indicate that the benefits of health insurance can only be attained by marginalized populations if insurance is made accessible to these communities through proper delivery methods and sufficient social support systems. VimoSEWA aagewans perform a fundamental role in establishing trust between the community and the insurance provider, making health insurance accessible, and adapting services to the community's needs. 

The Hanford nuclear site is a 20th and 21st century example of America’s ongoing military industrial complex. Its ties with the aftermath of the Manhattan project shows that its harm was not unidirectional, but rather multidirectional since harm was done to the people of Nagasaki and to the communities within and around Hanford, Washington. Migrant workers have had ongoing misrepresentation regarding the nuclear site’s post-communal health impact; especially within oral and scholarly accounts. In this study, we explore what factors have had short-term and long-term impacts on the health, socioeconomic status, and autonomy of Hanford migrant workers. We use literature review and discourse analysis to understand these complexities affecting migrant health, and by developing these frameworks we reveal to the reader how such human and unalienable rights were undermined for the purpose of global control.

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.

Parametric models are used in demographic research to reduce the number of parameters over those found in a life table, smooth and correct inadequate mortality data, and provide insight into the underlying processes of aging and mortality. One difficulty with many existing parametric mortality models, such as the Siler model, is that they assume that mortality risk is homogenous. We developed the mixed-Makeham model to explicitly model heterogeneity in mortality in the youngest ages. The model divides mortality risk at the youngest ages into “low-risk” and “high-risk” subgroups, as well as a parameter that specifies the fraction of newborns in each subgroup. Senescent mortality in both subgroups is a shared 2-parameter Gompertz model. We apply the model to cohort life table data from 11 European countries from 1876 to 1925 published in the Human Mortality Database. When mortality is decomposed this way, the proportion of high-risk infants declined and the mortality risk for low-risk infants declined for later cohorts, as anticipated. The mortality hazard for high-risk infants, however, increased for later cohorts. These findings suggest that, over time, medical and public health improvements shifted some fraction of infants from the high-risk category to the low risk category. The shift toward higher mortality hazard in the high-risk infants is likely explained by heterogeneous risk in the high-mortality pool, where medical and public health improvements are less effective on infants at the highest mortality risk.

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.

Epilepsy is a neurological disorder in which abnormal brain activity causes spontaneous seizures, and behavioral comorbidities including anxiety, depression, and cognitive deficits. Epilepsy can result from many different inciting events, including infection, genetic background, or neurological damage. For example, status epilepticus (SE) is a clinical emergency defined as continuous seizures lasting longer than five minutes, which can increase susceptibility to developing epilepsy. Clinical studies in patients with epilepsy have shown that seizures of different severity can occur at discrete times of day or night, suggesting that there may be circadian patterns of seizure incidence in humans. In this study, a post-SE model of temporal lobe epilepsy (TLE) was used to first establish whether there are any notable circadian patterns of seizure activity in a preclinical rat model of epilepsy that is commonly used for antiseizure drug development. Male Sprague Dawley rats were implanted with cortical electrodes one week prior to the systemic administration of the chemoconvulsant, kainic acid, to induce SE insult. The rats recovered from the SE insult and then went on to develop spontaneous recurrent seizures days to week later. The onset and severity of spontaneous seizures were then continuously monitored for 6 weeks, with seizure segregated by time of day in which they occurred: light vs dark cycle. Preliminary data suggest that rats from this model more frequently experience seizures during the dark phase, i.e. the active period of this nocturnal animal. Results from this study will establish the circadian pattern of spontaneous seizures in the post-kainic acid SE model of temporal epilepsy in rats. Further, this study provides the basis on which to then determine if chronic administration of prototype antiseizure drugs can be optimally administered prior to periods of peak seizure incidence to more effectively reduce long-term seizure burden in this model.

Epilepsy is a neurological disorder that affects over 65 million people globally. The initial identification of antiseizure efficacy and tolerability of any investigational agent is routinely defined in mouse and rat models of epilepsy. C57BL/6 mice are a commonly used inbred strain for antiseizure drug discovery, while CF-1 mice are a commonly used outbred strain. Although there is established data on the median effective anticonvulsant doses (ED50) of common prototype antiseizure drugs (ASD) in mice, there is limited quantitative data pertaining to the acute impact of anticonvulsant doses of ASDs on locomotor activity in an open field, which may inform on the potential for adverse effects in a clinical setting. This study aimed to provide a quantitative evaluation of the impact of ASDs on locomotor behavior to provide an added way to compare investigational agents to ASD standards-of-care. Male C57BL/6 or CF-1 mice (n = 8/treatment group/strain) were habituated to an open field 24 hours prior to the testing day. On the day of testing, mice were administered prototype ASDs (valproic acid, carbamazepine, levetiracetam, lamotrigine, phenobarbital, diazepam, ethosuximide, phenytoin, gabapentin) or vehicle by the intraperitoneal route. Mice were then allowed to explore the open field for the 30 minute period encompassing the time of peak effect of each ASD. Endpoints of locomotor behavior in the open field included time spent in the center of the field, vertical rearing, fecal boli, and total distance traveled. In CF-1 mice, diazepam generally reduced all measures of exploratory behavior whereas gabapentin increased the total distance traveled. This study establishes a comparative pharmacological profile of the effect of prototype ASDs on exploratory locomotor behavior of male outbred CF-1 and inbred C57BL/6 mice.

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.

Communication on online platforms has become one of the primary methods by which people communicate with one another. Regardless of conversation space, either online or offline, arguments can arise. Through our research, we are studying the ways in which the design of a platform influences the tenor of a conversation and the factors that lead to fights and reconciliation. We conducted in-depth in-person and phone interviews with 23 adults to understand how arguments arise online, how they end in different circumstances, and received input for possible design ideas. We followed up with the interviewees to gather demographic information about them. Through affinity diagramming, we qualitatively analyzed the 23 interview transcripts to uncover recurring themes, such as the role of time, the stages of an argument, the way people move arguments from public to private spaces, and differences between images and text in sparking arguments. Based on these themes and design suggestions from participants, we made sketches for potential design ideas that can be implemented in social media platforms to encourage constructive discourse. We are planning to use the design sketches to create prototypes to test with participants for iteration, which we will describe in a research paper to share our findings and design ideas broadly.

In neurons, microtubules are critical for cellular and developmental functions including neurite outgrowth and maintaining stable wiring of the nervous system. Tau, an intrinsically disordered protein, plays important roles in microtubule assembly and stabilization. However, tau can dissociate from microtubules and form amyloid fibrils in a set of neurodegenerative diseases termed tauopathies, which includes Alzheimer’s disease and frontotemporal dementia. Mutations in the tau sequence cause the disease FTDP-17T, providing evidence that alterations in tau alone can cause tauopathies. Most mutations occur in or near the microtubule-binding domain of tau, which suggests that mutant protein may be deficient in its capacity to stabilize neuronal microtubules, more prone to aggregate, or both. In particular, the disease-associated mutation P301L appears to enhance tau’s propensity to aggregate into fibers and alter its pathological activity. Molecular chaperones are responsible for maintaining protein solubility, promoting proper folding, and preventing atypical aggregation. The chaperone HspB1 delays wild-type tau fibril formation by weakly interacting with early species in the aggregation process. It is able to recognize aggregation-prone motifs within the microtubule binding repeat region of wild-type tau. Therefore, we used fluorescence spectroscopy to test the affinity and activity of HspB1 against wild-type and mutant models of the tau microtubule binding region, to see whether changes in the tau sequence alter interaction with the chaperone. In addition, tau oligomers are known to disturb lipid bilayers, a harmful interaction that could lead to potential cell death. Using a vesicle permeabilization assay, we tested the interactions between artificial lipid membrane with our tau constructs, and whether HspB1 can counteract these harmful interactions. This will extend our understanding of the characteristics and behaviors of disease-associated mutations of tau and the ways in which chaperone target aggregation-prone tau species.

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.

Previous research has found descriptive drinking norms (i.e., how much someone thinks others drink) are associated with increased risky drinking and intentions to drink among college students. However, this research has mostly focused on self-reports of typical drinking, whereas some students report low levels of drinking except on specific high-risk events such as birthdays. This study expands on previous research by examining how descriptive birthday drinking norms moderate the relationship between drinking on a previous birthday and intentions to drink on an upcoming birthday. We hypothesized a positive relationship between previous birthday drinking and intentions to drink that would be more pronounced in students with increased norms. A total of 248 University of Washington students (aged 18-24) who reported at least one heavy episodic drinking event (5+/4+ drinks for Males/Females) and three alcohol-related consequences in the past month were assessed. Participants reported the number of alcoholic beverages they drank on their most recent birthday, how much they intended to drink on their upcoming birthday, and the number of drinks they thought a typical University of Washington student drinks on their birthday. Results from moderated linear regression demonstrated both previous birthday drinking and birthday norms were positively associated with intended birthday drinking (b = 0.477, SE = 0.063, p < 0.001; b = 0.189, SE = 0.054, p = 0.001, respectively). The cross-product of birthday norms and intended birthday drinking also had a significant effect (b = -0.036, SE = 0.013, p = 0.005), such that the effect between previous birthday drinking and intended birthday drinking was strengthened in those with higher norms, supporting our hypothesis. This research contributes to critical literature addressing high-risk alcohol use among students and helps to better understand the role of norms and high-risk drinking events, such as birthdays, in research.

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.

Worldwide, there are currently more than 50 million people living with dementia and this number is projected to exceed 135 million by 2050. Unfortunately, negative stereotypes and misconceptions about dementia continue to exist, which can result in harm, isolation, and stigma towards those living with dementia. Dementia Friends is an anti-stigma and educational campaign that trains volunteers called “champions” to host informational sessions out in the community. During these sessions, champions educate local community members about the impact of dementia and what they can do to help. These community members are known as a “dementia friend” and are encouraged to help those with dementia live welll. Although Washington state is the fourteenth state to adopt the Dementia Friends program from the United Kingdom, limited research is available about the effectiveness of the program. This study seeks to evaluate the effectiveness of the Dementia Friends program in training the champions in Seattle and Yakima by comparing pre-training and post-training questionnaires. Results from this study will guide the expansion of the Dementia Friends program in other cities. Online questionnaires were distributed to 15 champions before and after the training session via RedCap. In order to assess the champions’ attitudes, perceptions, and experiences about dementia, participants were given 20 subjective statements about dementia and a 7-point Likert scale to assess the degree to which participants agree or disagree with each statement. We anticipate that Dementia Friends will be effective in educating community members and reducing misconceptions regarding dementia. If efficacious, we recommend Dementia Friends to be adopted across Washington to de-stigmatize dementia by educating community members.

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 purpose of the UW-EXP research study is to understand the first-year UW student experience in a data-driven manner to create a cornerstone for institutional change. This study extends focus to investigating stressful life events of first-year students. Phase 1 data collection is complete, and we are in Phase 2 of the project. The UW-EXP research study is researching the overall well-being of first-year students. Can we detect stressful life events in students using passive technologies (mobile phone data, Fitbit and Social Media)? Which technology is a better indicator of a stressful life event or do they complement each other? Phase 1 data used a participant sample size of around 200 University of Washington first-year undergraduate students (around 50% pre-/engineers). Data consists of both active and passive collection methods: participants actively respond to Qualtrics surveys, with questions investigating stressors, and passively via our phone software and Fitbits. The stressors are defined as stressful events in the students' relationships, health, living situation, finances, and if they experienced discrimination, relationship violence, and assault. The following information collected from our phone software and Fitbits are number of steps, location, sleep, App usage, and when in conversation and with whom in generic terms (friend or relative). I have used the data collected in Phase 1 to answer my research questions. We identify critical data that can be analyzed to advance the science of behavioral health and trauma. This data is unique in providing a picture of student behavioral changes after stressful experiences. Additionally, this advancement in science can become a basis for institutional change for improving student wellness. As the first-year population is only a slice of the overall student experience, we hope to expand this study further by encompassing the graduate student experience and the full four-year college experience in addition to a larger sample size. We will help improve the lives and success of University of Washington students.

Reactive oxygen species (ROS) such as the superoxide anion (O₂-) and hydrogen peroxide (H₂O₂) are produced by enzymes such as NADPH oxidases (NOX), which have been identified in most cell types and tissues. Additionally, ROS is identified as a second messenger which regulates the activity of G-protein-coupled receptors. For example, ROS decreases the sensitivity of the kappa-opioid receptor (KOR), a signaling pathway in the brain involved in drug addiction. Thus, a fluorescent ROS sensor protein would allow us to monitor KOR signaling in animal models of drug addiction. However, the best performing ROS sensor called HyperRed is not suitable for in vivo studies due to the weak amplitude of fluorescent signal output. Therefore, the overall goal of the project is to increase the magnitude of fluorescent change of HyperRed, ease the detection of low H₂O₂ concentration, and decrease the time of fluorescent response after the addition of H₂O₂. First, using the structure-based engineering approach with the help of Dr Berndt, I construct a library of thousands of semi-randomized HyperRed variants, where mutations are only introduced to the amino-acid linkers between the main domains. Then I test the fluorescent output of all the variants in the library at high throughput utilizing a novel protein engineering platform. This approach allows me to rapidly identify the best performing ROS sensors and optimize their signal amplitude in several rounds of repeated mutagenesis mimicking an accelerated evolutionary process. The expected result is to detect one variant with the signal amplitude having at least a 100% change of fluorescence over baseline values which has been determined to be the minimum for applications in animal models. The improved sensor enables direct measurements of ROS signaling during drug-seeking behaviors and could potentially facilitate the development of novel therapeutic approaches.

The release of chloride in response to the binding of the neurotransmitter GABA to the ligand-gated ion channel GABAAR mediates neurotransmission that plays critical roles during early development. Disturbed chloride homeostasis in early neuronal circuits results in imbalances in neuronal differentiation, cell growth, and synapse formation that are thought to trigger irreversible paths into neuropathological brain states associated with autism, epilepsy, and schizophrenia. However, the pathogenesis and fundamental physiological mechanisms underlying these disorders are unknown. To dissect these diseases, researchers must understand, in neurodevelopment, the specific role that chloride-mediated neurotransmission plays in triggering the imbalances of inhibitory and excitatory neuronal pathways observed in neuropathological states in adulthood. Zebrafish serve as a powerful model, as the fundamental mechanism of neurotransmission and the microarchitecture of neuronal circuits are preserved among vertebrate. Furthermore, the zebrafish central nervous system is accessible for experimental manipulation from early development. I aim to precisely control chloride-mediated neurotransmission during early development through the creation of versatile transgenic zebrafish lines in which GABA-producing (GABAergic) and glutamate-producing (glutamatergic) neuronal subtypes express the light-activated chloride channel iC++. We are currently designing DNA constructs encoding iC++ and UAS, a promoter element that binds to the yeast transcriptional factor Gal4, to be injected into embryonic wild-type zebrafish. Upon successful integration of these transgenes, Gal4 driver lines that express the transcription factor in specific neuronal subtypes such as GABAergic (Gal4:gad1b) and glutamatergic (Gal4:vglut2a) cells will be crossed with our UAS response line to achieve our desired expression. Ultimately, I will non-invasively activate iC++ in live animals through light stimulations to drive chloride signals with millisecond precision at any time throughout the embryonic and larval stages. This approach will serve as a high-throughput system, allowing us to collectively study a large number of conditions that trigger permanent neuropathological impairments.

As climate change progresses, increasing temperature is expected to have community and population-level consequences. The temperature-size rule predicts shifts in both community and population structure to favor smaller bodied organisms over larger bodied organisms as temperatures increases. We investigated this hypothesis in the context of rocky intertidal invertebrate communities on San Juan Island, and examined changes in community and population structure over the past 45 years. We replicated historical ecology studies on the abundance of six intertidal species; three of which body size data was also collected. These species included grazing and predatory molluscs (Katharina tunicata, Nucella lamellosa), anemones (Anthopleura elegantissima), and crabs (Hemigrapsus nudus, Pugettia gracilis, Pagurus sp). Additional abundance data was collected on smaller molluscs (limpets, littorine snails). Predicted decreases in body size were not apparent in populations of K. tunicata., N. lamellosa, and A. elegantissima. However, when comparing abundances, shifts in community structure towards smaller-bodied organisms were apparent. We observed an increased abundance of smaller-bodied gastropods and crustaceans (limpets and Pagurus sp), but a decrease in K. tunicata abundance, one of the largest grazers in this system. This research highlights the potential for a variety of community and population responses including both stability and variability in the face of climate change.

Our project took place at the Wilson Botanical Garden, Las Cruces Biological Station, Costa Rica. The strata of the garden which were identified were sky, canopy, mid strata, low shrub and ground. Bird species and their behavior such as flying over, flying through, eating and perching were observed. Numerical field keys were developed for both strata and behavior. 96 species and 220 total number of birds were identified. There was a significant difference between the number of species and the total number of birds in the sky. This reflects the big flocks of vultures, parrots and swifts. The larger number of birds in mid strata correlates to the flowers and fruits there. The greatest family of birds in mid strata were the tanagers. The least number of birds which were observed on the ground correlates to no fruit or flowers there. Birds are often indicator species regarding changes in ecosystem or relating to climate change. This data can be compared to past studies and future stories to see any trends. Traditional Ecological Knowledge (TEK) can also be integrated with the research.

There is a common thread among contemporary circus art disciplines that is unique in the performance world. It is a blend of theater, dance, and acrobatic skill that can produce amazingly complex and captivating works. When comparing the choreographic processes of these performance mediums with the creative practices of solo contemporary circus artists, do new choreographic themes exclusive to circus arts become visible? Or does the essence of contemporary circus lie in the combination of standard techniques adopted from theater, dance, and acrobatics? An analysis of well-known work provides viewable examples of contemporary circus choreography, while local artist interviews provided seasoned, close-to-home examples of solo circus act creation on a professional level. In summary of my findings, I discuss the implications of choreographic methods in contemporary circus from the viewpoint of a solo artist and choreographer.

Gravitational wave research comprises an emerging field in physics, as many institutions around the world rely on measurements from the Advanced Laser Interferometer Gravitational Wave Observatory (LIGO), and other interferometers as a vital source of data. Wave parameters provide valuable information about the astrophysical source properties, such as sky localization, source mass, spin, luminosity distance, and orbital inclination, and can also be used for an independent determination of the Hubble constant and tests of general relativity, and the nature of gravity itself. For these reasons, enhancing the absolute accuracy of gravitational wave detectors is essential. The accuracy of these parameters is fundamentally limited by calibration uncertainty. Accordingly, this project researches methods of enhancing the absolute accuracy of gravitational wave measurements to augment the data obtained by interferometers such as Advanced LIGO, to advance gravitational research. One current calibration method relies mainly on photon pressure calibrators (PCals), which are based on the measurement of test mass displacement generated by a periodic force via radiation pressure from the reflection of a power–modulated laser. The technological limit of the absolute calibration uncertainty corresponds to a few percent due to uncertainty in power, and thus limits accuracy in source parameters. The LIGO affiliated Eot-Wash team at the Center for Experimental Nuclear Physics and Astrophysics (CENPA) works to minimize fundamental systematic uncertainty in calibration methods through extended analysis of the combination of gravity field calibrators (GCals) and PCals. GCals make use of a gravity gradient to achieve modulation of the test mass displacement for calibration, providing an alternative source of accurate actuation. The combination of the two calibrators could reduce the systematic uncertainty in GW strain measurements and improve astrophysics with LIGO.

With only a handful of species known to the general public, many of the 4000 bees endemic to the United States go unnoticed. As crucial pollinators, bees are incredibly important to the environment. There is a notable lack of data regarding bees in the United States, thus data collection about bee species diversity and abundance is prudent. Citizen science, or the use of volunteers in ecological studies, is a relatively new concept, introduced only a century ago by ornithological and astronomical sciences. The invention of digital single-lens reflex (DSLR) cameras makes it easy for novice photographers to take quality pictures, and they have become more accessible to citizen scientists in recent years. Our research introduces methods using visual observation and digital photography to study bee species diversity and abundance. It is impossible to identify most bee species without a microscope so we have taken a morphogroup approach, adapted from Xerces Society monitoring protocols, to gather data about bee species without needing an identification expert. We group bees into eight categories according to key characteristics visible to the naked eye, as similar-looking species are often closely related. Using digital cameras we implement two timed survey protocols, one tallying abundance and one “capturing” as many species on camera as possible. Two years of preliminary data has yielded information regarding the abundance, diversity, and phenology of bee groups on the UW Bothell/Cascadia College campus. Our surveys revealed the presence of all eight morphogroups on campus, 23% representing honey bees and 77% other bee species; bumble bee species (Bombus sp.) dominated in abundance representing 55% of all bees seen in 2018. Research has thus far informed improvements to monitoring protocols, identified bloom gaps on campus, and has resulted in the creation of UW digital photo archive documenting the findings of the research.

 In recent years, the University of Washington has promoted itself as a leader in sustainability and has made significant strides towards increasing sustainability efforts on campus. One area in which the University has not focused heavily in sustainability is in the curriculum. To address this gap, I am developing a framework for what measures can be taken to implement a sustainability requirement at the University of Washington. In developing this framework, I am researching sustainability requirement policies at other institutions and sustainability policies and initiatives at the University of Washington. My research shows that a sustainability requirement has been implemented at several universities around the nation, some of which are scale-comparable or peers institutions to the University of Washington. Furthermore, a sustainability requirement would support several of the University’s goals and initiatives. Using this research and the UW Diversity Credit as a case study, I am developing a report detailing recommendations and an action outline to details next steps to implement a sustainability graduation requirement. In addition, I am forming a student coalition to gain campus support and work with administration to pass the policy through the appropriate channels. If a sustainability graduation requirement can be implemented, it will not only help the University of Washington emerge as true leader in higher education sustainability, but it will also help develop future generations of graduates who understand sustainability; its applicability to their lives, decisions, future careers, and fields of study; and enable them to tackle the emerging global challenges.

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.

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.

Prior studies suggest that a dynamic shared care plan for children with medical complexity (CMC) may help meet the information needs of their diverse care teams. However, little is known about how these care plans should be implemented and kept updated; the primary objective of this study was to explore the optimal collaborative management model of a dynamic care plan which engages both parents and providers based on CMC parents’ perspectives. Following a user-centered design methodology, we conducted interviews with 21 CMC parents between 3/16-1/19 to elicit their preferences for engagement in the maintenance of a dynamic care plan. Between sessions, we conducted content analysis of interview transcripts to understand themes related to parents’ preferences for care plan (1) ownership, (2) reviewing, and (3) editing, as well as electronic alerts. CMC parents emphasized that the care plan owner should have the medical expertise necessary for caring for the child, a holistic understanding of the child’s health conditions, and frequent contact with the child. Since no one individual on the care team possessed all these qualities, we developed a “core team” model composed of the parent, as well as a parent-chosen physician representative and care coordinator, who would together oversee care plan content. Parents generally believed that healthcare providers had the necessary expertise to update medical information but desired the ability to review all sections of the care plan and edit family-related sections (e.g. care preferences, home nursing, social history). They also desired automatic alerts prompting them to obtain medication refills and review care plan updates made by other providers, as well as customizable alerts to help them keep track of appointments. Future usability studies will test parent engagement with a dynamic care plan through this model.

Inflammasomes are multimeric protein complexes involved in innate immune responses. Inflammasomes include a protein sensor, such as NLRP3 or pyrin, linked to the enzyme caspase-1 via the adaptor protein, ASC. Active caspase-1 is responsible for release of the cytokine interleukin (IL)-1ß and triggering inflammatory cell death. Inflammasomes are crucial in defense against pathogens. However, excess inflammasome activation is linked to diseases such as Alzheimer's, atherosclerosis, and other inflammatory conditions. Although inflammasomes are linked to several diseases, we do not fully understand how inflammasomes are activated. We are researching the role that potassium plays in inflammasome activation. To detect inflammasome activation, I measured released IL-1ß using enzyme-linked immunosorbent assays (ELISAs). I determined whether inflammasome activation requires potassium efflux by measuring IL-1ß released from cells stimulated in high extracellular potassium, which prevents potassium efflux. I found that IL-1ß release triggered by NLRP3 inflammasome activators is prevented when cells are stimulated in high extracellular potassium. However, IL-1ß release triggered by the pyrin inflammasome was not affected by high extracellular potassium. From these results, we conclude that the NLRP3 inflammasome is dependent on potassium efflux from the cell, whereas the pryin inflammasome is not. The implications of our research are two-fold. First, our findings argue against a long-standing hypothesis that high extracellular potassium blocks ASC binding. Both NLRP3 and pyrin need ASC, but our data show that only NLRP3 is affected by potassium concentration. This suggests that potassium affects NLRP3 activation at an unknown point. Second, understanding the role of potassium in regulating inflammasome activity provides a potential therapeutic target. There are drugs that regulate ion concentrations by controlling ion channel activity. Knowing whether an inflammasome pathway is potassium efflux dependent could be beneficial in limiting excess inflammasome activation that is linked to a variety of human diseases.

Abstinence-based treatment has long been considered the standard of care for people with alcohol use disorders (AUD). However, abstinence-based treatment fails to engage severely affected populations (e.g., homeless people affected by AUD) because many are not yet ready, willing or able to stop drinking. A recent randomized controlled trial tested the efficacy of a lower-barrier harm-reduction treatment for alcohol (HaRT-A), in which participants could define their own harm-reduction and quality-of-life (QoL) goals. The aim of this present secondary study was to describe participants’ own harm-reduction and QoL goals and document their achievement of these goals over the course of HaRT-A. Participants were people currently experiencing homelessness and AUD (N = 86) who attended the 4-session HaRT-A, during which interventionists elicited participants’ own harm-reduction and QoL goals. The Safer-drinking and Harm Reduction Efforts (SHaRE) form was administered to elicit and record participant-generated harm reduction goals, which were entirely participant-driven with no suggestions from study interventionists for any specific drinking-related goals. Directed content analysis was performed to classify participant-generated treatment goals. Results indicated that goals fell into 7 primary categories, the top 3 being drinking-related goals, quality of life goals, and health-related goals. These findings suggest that a client-driven, goals-setting approach could inform accessible and appropriate treatment and QoL-enhancing interventions for people experiencing homelessness and AUD.

DNA polymerase (Pol) proofreading and mismatch repair (MMR) cooperatively guard against DNA replication errors and cancer. Defects in these activities produce “mutator” phenotypes characterized by elevated levels of base-substitutions and frameshifts. Haploid yeast with combined defects in these activities rapidly go extinct, in a process termed error-induced extinction (EEX). Organisms adapt by duplicating their genome without dividing (polyploidization) or by lowering their mutation rate via antimutator mutations. In evolution experiments with haploid mutators that display a synthetic-sick phenotype due to Pol ε proofreading and MMR defects we found that polyploids routinely beat out antimutator mutants. To investigate whether polyploids arise during the evolution of mutator diploid strains, we propagated diploids defective in Pol δ proofreading and base-base MMR, which have a mutation rate an order of magnitude below the diploid error threshold. Our mathematical modeling predicts that EEX mutants will overtake mutator cultures by 250 generations. We found only a single tetraploid in 89 independent cultures evolved for 300 generations. We then measured mutation rates of isolates from cultures that remained diploid and repeatedly found antimutator phenotypes. Whole genome sequencing of independent isolates from each culture revealed a single dominant antimutator clone that caused significant changes in mutation spectra. Thus, spontaneous antimutator alleles and polyploidization rescues haploid and diploid cells from EEX with markedly different efficiencies. Differences in the relative frequency of each escape mechanism may reflect the nature of the mutator alleles, the starting ploidy of the cells, or the magnitude of the initial mutation rate. Our findings in diploids suggest that mutator cancer cells near the edge of error-induced extinction may similarly be under selection for spontaneous antimutator mutations and polyploidization. 

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.

c-fos is an immediate early gene that is commonly used to mark cell activation and can be identified using immunohistochemistry techniques. In this project, we optimized immunohistochemistry conditions for a phosphorylated c-fos antibody in brain tissue obtained from the rat lateral habenula (LHb). Male, Long-Evans rats (n=4) were injected with cocaine (10 mg/kg) or saline. Ninety minutes following intraperitoneal injections, rats were perfused with 4% paraformaldehyde. Brains were dissected and 40-micron slices across the rostro-caudal axis of the LHb were collected. We tested two dilutions of the rabbit phospho c-fos antibody (1:500 and 1:800), three blocking agents (normal goat serum, donkey serum and bovine serum albumin) and two secondary Alexa Fluor antibodies (goat anti-rabbit Alexa Fluor 488, and donkey anti-rabbit Alexa Fluor 488) to determine which combination allowed for the best visualization of c-fos in the LHb. Fluorescence microscopy analysis of the tissue sections is underway, and imaging is expected to show differences in brightness and visibility of c-fos with respect to the varying conditions. These results will identify the optimal conditions for more accurate identification and quantification of cell activation in the lateral habenula.

The goal of the Laser Interferometer Gravitational-Wave Observatory (LIGO) detectors is to detect faint ripples in spacetime caused by the merger of massive compact objects, like black holes and neutron stars, using a Michelson interferometer with Fabry-Pérot cavities in the 4-kilometer arms. Because the detectors have length change sensitivity on the order of 10^-20 meters, there are many types of unwanted transient signals that affect the calculated gravitational wave strain signal and interfere with searches for real gravitational waves. These are referred to as glitches; finding the cause of a glitch category is the first step to eliminating it. I searched for the source of 60-200 hertz range glitches known as “scratchy” glitches. I found a correlation between elevated ground motion and detection of scratchy glitches, then estimated false alarm rates for their observed coherence. My research supports on-site efforts to eliminate scratchy glitches.

WMlife Network Technology Company Ltd builds shared bookcases located in kindergartens to rent picture books at a low annual fee. WMlife builds bookcases of different sizes based on the number of students in the kindergartens. For all existing kindergartens in the system, WMlife has been choosing the same set of books for every kindergarten. However, now they are considering supplying different book sets to different kindergartens and exchanging books between them each year to provide new books while reducing total cost. To minimize the time investment by WMlife, we modeled the problem as a periodic traveling salesman problem and used a modified Prim’s algorithm and brute-force to find the route with the shortest traveling time. We also constructed a feasible book exchanging algorithm. With our new strategy, WMlife could get a dynamic instruction for book exchanging instantly with kindergarten locations and starting locations as input. WMlife can exchange books easily according to our instructions and significantly reduce cost by 30% in book reallocation approximately. As WMlife expand their services in more cities in China or adding more new kindergartens to the existing city, they could have a smart start of purchasing the book for future cost saving. The system not only solves a one-time problem but also can support WMlife to provide better books and more book types for kindergarten children, help them to form reading habits, widen their horizon and raise Chinese average reading rate.

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.

The impacts of climate change may be partially ameliorated by positive interactions among species, such as native plants and arbuscular mycorrhizal fungi (AMF). Sea level rise caused by climate change will detrimentally impact saltmarsh habitats by increasing the elevation and rate of terrestrial salt water inundation, thereby reducing effective functionality of ecosystem services provided by saltmarshes. Facilitations, positive interactions between species, is key in determining which species can survive in habitats characterized by abiotic stress, such as salt marshes. Halophytic plants within salt marshes can benefit from symbiotic AMF facilitations through increased inundation tolerance, greater nutrient availability and uptake, and relief from saline stress. This study identifies the presence of AMF across multiple saltmarsh plant species and measures the impacts of AMF within Oregon’s Salmon River Estuary at Cascade Head. I have extracted samples from four monoculture plots within high and low marsh elevations across four species that grow at both elevations: jaumea (Jaumea carnosa), Lyngbye’s sedge (Carex lyngbyei), pickleweed (Salicornia virginica) and salt grass (Distichlis spicata). I have centrifuged soil samples from each plant, and calculated AMF spore abundance at each sample location. I am also processing soil samples for percent water in the sediment, soil salinity and pH. Additional samples from both elevations within polyculture plots have been collected to develop a secondary index to cross-reference my primary findings. Through this research, land managers developing sea-level rise mitigation plans will have data supporting which plants will be most resilient to sea level rise. Potential inoculation of host plants could protect estuaries from sea level rise and increased frequency and intensity of storm events in coastal regions. In identifying plants which host beneficial AMF, fungal inoculation of plants in marshes could help plants grow further into lower marsh elevations, increasing sediment accretion and decreasing erosion and soil degradation.

Hybrid organic inorganic perovskites are a promising highly efficient photovoltaic material that can be solution processed at low temperatures enabling an inexpensive solution to rising renewable energy demands with high-volume, scalable manufacturing of solar cells. Small scale perovskite devices are successful using spin coating; however, this needs to translate to larger scale deposition systems such as roll-to-roll slot die printing. Understanding the crystallization and morphology dependence of these materials is essential to enabling slot-die coated perovskite films on scalable systems and transitioning this technology to the market. In order to model crystallization rates of printed layers, we used in-situ optical and photoluminescence microscopy during printing of perovksite films to determine crystal growth rates and evaluate perovskite conversion. Printing parameters were manipulated through variation of temperature, atmospheric conditions, ink recipes, and substrate surface energy generating a model to achieve desired grain size and morphology of the perovskite layer across an array of relevant potential perovskite photovoltaic device stacks. Following classical models, we determined the necessary parameters to translate these fundamentals to perovskite crystallization and grain growth. We further explored the conversion and degradation of the perovskite phases through the printing process, which plays a significant role in device performance, through in situ photoluminescence microscopy, as well as verification through X-ray diffraction. Verification of the observed grain sizes and morphology was also done through scanning electron microscopy, to ensure optical measurements and analysis were accurate. With efficiencies of perovskites approaching current industry standards of silicon, perovskites are increasingly becoming the clear answer to solar industry demands. This research is essential in enabling scalable methods with the potential to revolutionize the solar industry with large scale fully printable devices.

High rates of early dropout or premature termination in university psychology training clinics adversely affect both patients and clinicians. Prior research suggests that among clients seen at training clinics approximately 70% terminate prematurely and approximately 55% do not report reliable change at the conclusion of treatment. To help assess the generality of this issue, we are investigating the rate of premature termination in a university-based clinical psychology training clinic in the Northwest. Using the Reliable Change Index (RCI) as a marker of recovery, we calculated the RCI for 3 outcome measures: the Patient Health Questionnaire (PHQ-9), Generalized Anxiety Disorder 7 (GAD-7), and the Brief Adjustment Scale-6 (BASE-6). Additionally, the training clinic in this study practices Measurement-Based Care (MBC) which involves the systematic administration of symptom rating scales known to increase treatment efficiency and effectiveness by assisting with clinical decision-making and informing patient progress. The hypothesis was that there would be a higher rate of reliable improvement and lower rate of deterioration at the end of treatment. Our examination of the test-retest reliability within 2 weeks of these outcome measures found the total scores of all three scales to perform adequately. Within the training clinic, 18.18% reliably improved using the GAD-7, 21.51% reliably improved using the PHQ-9, and 27.27% reliably improved using the BASE-6. These results did not support the hypothesis and instead found a lower rate of reliable improvement than the published norms. Potential reasons for the discrepancy will be discussed. This study will benefit those suffering from ineffective treatment outcomes and those struggling with untreated debilitating mental disorders. It will also add to the growing literature on the benefits and obstacles of MBC which has been gaining increasing recognition recently. 

An often conceptually difficult topic learned in early engineering courses is known as the angle of twist. The angle of twist is necessary for two reasons: to analyze reactions along a shaft where traditional equilibrium equations do not suffice, and in designing a shaft when twisting is restricted. In this project, the purpose is to design and build a device that will be an aid in classroom demonstrations of the concept and applications of the angle of twist. The prototype of this device is designed to test foam shafts of a certain length and with a constant applied torque. The device will need to support, hold, and twist foam shafts while providing precise measurements of the applied torque and the resulting angle of twist. Two markers will be put in place before twisting. The shaft will be fixed at one end, where one marker will be in place, and twisted at the opposite end where the mobile marker will be used to determine the angle between the two. It must be durable to withstand regular classroom handling and have an appropriate interface for students of varying levels of proficiency in the topic. Its design must also be inexpensive and replicable so that it can be built and used within a low classroom budget. Students will be able to calculate, measure, and observe the applications of polar moment of inertia, angle of twist, and torque using the measurements from the apparatus. From the measurements, the shear modulus of the shaft material will be experimentally determined, allowing for an active learning experience of this key concept.An often conceptually difficult topic learned in early engineering courses is known as the angle of twist. The angle of twist is necessary for two reasons: to analyze reactions along a shaft where traditional equilibrium equations do not suffice, and in designing a shaft when twisting is restricted. In this project, the purpose is to design and build a device that will be an aid in classroom demonstrations of the concept and applications of the angle of twist. The prototype of this device is designed to test foam shafts of a certain length and with a constant applied torque. The device will need to support, hold, and twist foam shafts while providing precise measurements of the applied torque and the resulting angle of twist. Two markers will be put in place before twisting. The shaft will be fixed at one end, where one marker will be in place, and twisted at the opposite end where the mobile marker will be used to determine the angle between the two. It must be durable to withstand regular classroom handling and have an appropriate interface to be used by students of varying levels of proficiency in the topic. Its design must also be inexpensive and replicable so that it can be built and used within a low classroom budget. Students will be able to calculate, measure, and observe the applications of polar moment of inertia, angle of twist, and torque using the measurements from the apparatus. From the measurements, the shear modulus of the shaft material will be experimentally determined, allowing for an active learning experience of this key concept.

The Arbuckle karst system consists of caves, microfractures, and hydrogeologic barriers. Isopods in the genus Caecidotea inhabit the pools of water within the groundwater system. Young Caecidoteas travel through microfractures, and small populations move from one cave system to the next. Over the time these fractures close, causing the populations of Caecidotea to be isolated and potentially drift genetically. The sampled distinct populations have become morphologically distinct, but it is yet to be determined if they also have become genetically distinct species. Genetic classification may also provide a more timely identification of fracture closing. DNA Barcoding using the Cytochrome Oxidase subunit 1 (COX1) gene will provide the percent of divergence in the samples obtained from different populations/locations; however, the chitin-heavy exoskeleton of isopoda could make it difficult to have DNA extractions that are “clean” (without protein) and decent yield. An extraction method was used proteinaseK (protK) and high salt to release the DNA followed by ethanol precipitation to concentrate the extract. For DNA Barcoding, the COX1 gene sequences need a PCR protocol with the robust primers is crucial. We plan to explore various primer sets for the optimal amplification.

Memory formation, or plasticity, is the brain’s ability to change and adapt in response to new information through altering the strength and effectiveness of communication at the synapse. Synaptic plasticity plays a major role in the brain’s capacity to incorporate past experiences into stored memories and it has become one of the most intensively researched subjects in neuroscience. Neuroscientists typically evaluate synapse function using enriched, homogenized preparations of synapses, called synaptosomes. However, synaptosome preparations contain a mix of neuronal and non-neuronal contamination along with active and inactive synapses that are impossible to separate, making it difficult to draw specific conclusions about synapse activity. To address these challenges and understand the molecular mechanisms behind synaptic plasticity, my lab has developed a synaptic TAG- an engineered protein that localizes to recently active synapses. The TAG construct, containing an extracellular CD4 protein whose expression is driven by activity-dependent regulatory elements, will be electroporated into the developing motor cortex of mice in utero. The mice will later be trained to run on a rotarod, a test commonly used to assess motor learning. After the mice have learned this task, the differences in their synapses will be evaluated by sectioning and staining the motor cortex with fluorescent antibodies. The number of distinct fluorescent TAGs on the synapses on a given number of neurons will be counted through confocal imaging. My hypothesis is that I will see an increase in the number of TAGs on the synapses of a trained mice, which will demonstrate that the TAG is synaptic in vivo and activity dependent. The completion of this experiment will allow my lab to identify learning-associated proteins using magnetic cell sorting, mass spectrometry, and RNA sequencing. Understanding learning-associated protein interactions will shed light on how their malfunctions contribute to Autism Spectrum Disorders or neuropsychiatric disorders.

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.

Young adults are susceptible to a whole range of psychological disorders. Approximately 39.6% of young adults (ages: 18-25) in the United States have had a heavy drinking episode in the past year, and 9.6% of young adults have had a major depressive episode in the past year. Previous research has shown that young adult males tend to drink more alcohol, while females have higher rates of anxiety and depression. There is, however, limited research about the extent to which certain groups of young adults, based on living situation and college enrollment, may exhibit higher alcohol use and poorer mental health. The purpose of this research is to examine differences in alcohol use, alcohol-related consequences, and mental health by demographic characteristics (i.e. attending 4-year college or not, living with parents or not, biological sex) among a community sample of young adults (ages 18-23). Analyses use baseline data (N=764; 55.9% female, mean age 20.6 (SD = 1.72) from a larger longitudinal study on health behaviors. Outcomes will be alcohol use, alcohol consequences, depression, and anxiety. Separately for each outcome, an analysis of covariance (ANCOVA) will be conducted. The sample includes 352 4-year college students and 412 individuals not attending a 4-year college, 468 individuals not living with parents and 296 individuals living with parents, and 428 females and 336 males. We hypothesize that higher alcohol use and consequences will be found for males, individuals not living with parents, and individuals enrolled in a 4-year college. We also hypothesize poorer mental health for females, individuals not living with parents, and individuals enrolled in a 4-year college. Results from this study will provide a better understanding of which young adults are experiencing poorer mental health and higher alcohol use, thus providing valuable information to guide interventions.

The receptor human protein kinase EphA2 has emerged as a therapeutic drug target for cancer and infectious diseases. However, the dearth of selective EphA2 inhibitors in the field is hampering EphA2-based research and therapies. Our lab recently developed a novel selective small molecule EphA2 inhibitor I268 using medicinal chemistry. Surprisingly, we observed the same inhibitory effects on cell proliferation paradoxically when inhibiting EphA2 with I268 or activating EphA2 with its agonist EphrinA1. We hypothesized that both I268 (inhibitor) and EphrinA1 (agonist) may lead to the same protein-protein interaction network of EphA2 that caused this paradoxical inhibition. We used a chemical proteomic method developed in our lab called “co-clickable precipitation (Co-CP)” to study the interaction network of EphA2 in colon cancer cell line HCT-116. We observed that the onset of inhibitory effect by I268 concurred with the association between EphA2 and a protein interactor called c-RAF, a key player in activating proliferation pathways in cancer cells containing Ras mutations such as HCT-116 cells. We are currently performing confirmatory experiments to characterize whether upon inhibition by I268 or activation by EphrinA1, EphA2 sequesters c-RAF in a form unable to transmit proliferative signals downstream. Our results may demonstrate a possible mechanism for inhibitory effects of EphA2 inhibition on cancer cell growth. These results validated EphA2 as a drug target and may provide novel ways for treating cancer cells by inhibiting cell proliferation pathways indirectly using EphA2 inhibitors.

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.

In microbiology, matrix-assisted laser desorption/ionization time of flight (MALDI/TOF) is a method used for the identification of a wide variety of micro-organisms such as bacteria or fungi directly from the selective medium used to isolate them. The technique uses laser energy absorbing matrix to create ions from proteins with minimal fragmentation. It is a three-step process where first, the microbial sample is mixed with suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. Finally, the analyte molecules are ionized in the hot plume of ablated gases and accelerated into the mass spectrometer. The mass spectra generated are analyzed and compared to stored profile using a dedicated software. Species diagnosis by this procedure is much faster, more accurate and cheaper than other procedures based on immunological or biochemical tests. Consequently, MALDI/TOF is becoming a standard method for species identification in medical microbiological laboratories. Bacteroides fragilis and Escherichia coli are two bacterial species that MALDI/TOF can accurately identify directly from the media they are growing on. Certain strains of enteropathogenic B. fragilis and E. coli ETBF and EPEC respectively, cause severe enteric disease manifesting by watery diarrhea and colic. On the other hand, non enterogenic strains of B. fragilis and E. coli such as NTBF and DH5 alpha are completely benign. Using MALDI/TOF technology and virulent and non-virulent strains of B. fragilis (BFT and BFT) and E. coli (EPEC and DH5 alpha), we hypothesize that a correlation between peaks and virulence proteins can be made conferring to MALDI/TOF the potential to predict virulence of bacteria based on the expression of proteins mediating virulence.

c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinases (MAPKs) family that are derived from three genes: Jnk1, Jnk2, and Jnk3. JNKs have been implicated in several cellular responses to homeostatic insults, including inflammation and apoptosis. We previously reported in a chronic epilepsy rat model significant elevated levels of phosphorylated JNKs (pJNKs), which indicate increased JNK activities. Additionally, we demonstrated that pharmacological manipulations of JNK proportionally affected seizure frequency. In this set of experiments, we attempted to identify which of the JNK isoforms (JNK1, JNK2, JNK3) contribute to the overall increased pJNK levels in our animal model of epilepsy. This would provide us insights as to the role(s) of JNKs in this disease. We measured the phosphorylation levels of the individual isoforms after pJNK enrichment from the CA1 hippocampal tissue of chronic epileptic rats and their age controls. The amount of protein was normalized by pJNK levels between experimental and control samples. We found a significant increase in activation levels of JNK2 in chronic epilepsy at 130 ± 9% (n=6, p=0.018) when compared to naïve, nonepileptic controls but insignificant changes in activation levels of JNK1 (97 ± 14%, n=5, p=0.83) and JNK3 (98 ± 17%, n=6, p=0.92). Previously, we had found in rats that JNK1 predominantly exists in the 46kDa size; JNK3 predominantly exists in the 54 kDa; and JNK2 exists in both sizes equally. We further analyze which of the JNK bands (46 kDa and 54 kDa or both) contribute to the elevated phosphorylated JNK levels. Given the previous pharmacological observation that JNK manipulation does influence seizure frequency in epilepsy, this investigation is imperative as it will allow us to narrow our focus to a specific JNK isoform to study further.

Physical resilience is a measure of healthy aging, but current assessment methods are underdeveloped, relying on a frailty panel of subjective tests. A quantitative, reliable test for resilience using endpoints aligning with healthy aging is needed to provide a standardized measurement of resistance to age-associated decline. The chemotherapeutic drug cyclophosphamide (CYP) is an immunosuppressant used in clinical medicine for certain types of cancer and autoimmune diseases. Precursor neutrophils are especially sensitive to this chemical stressor, such that a single low-level dose stops cell cycling with a decrease in mature neutrophils, but neutrophils rebound as the drug is eliminated from the body. This study sought to characterize the neutrophil rebound response in aging mice as a biological sensor for how an organism might respond to physical stress with increasing age. One intraperitoneal dose of CYP at 100 mg/kg was given to groups of mice at various ages. White blood cell differential and total counts were enumerated to monitor cellular response over a 25-day period. A robust and predictable drop in neutrophils occurred across age groups five days after injection of CYP, followed by a robust increase in neutrophils beyond baseline measurements at day seven in an age-dependent manner. Strength of the neutrophil rebound had a moderate correlation with strength and stamina as measured by rod hanging time, a test that corresponds to hand grip assessment in humans as an indication of frailty. This observation suggests that the neutrophil rebound response to the chemical stressor CYP in young adult mice can predict resilience to aging in older adult mice. The clinical implications are that an in vitro bench test could be developed using CYP-induced rebound response of human precursor neutrophils to predict resistance to frailty and produce a more accurate assessment of resilient healthy aging in older adults.

Three generations of immigrant history have led up to my personhood. I’ve inherited the struggle of my mother and my grandmother before her, who have worked themselves to the bone to provide me security. This inheritance is the driving question in my research project RATSKIN, a theatrical play that is in development. How does one honor one’s immigrant history but also break free from the ideologies that were made to trap immigrants within a cycle of destruction? RATSKIN is my intervention. Incorporating literary and theatrical traditions with historical, archival research, the play is an exploration in how to weave together personal experience, genre, cultural theory, and history into a narrative that can be shared to a community in a productive, discussion generating way. RATSKIN draws inspiration and theoretical groundwork from Borderlands/La Frontera by Gloria Anzaldúa; One Hundred Years of Solitude by Gabriel García Márquez; Neo-Marxist theories by Ngũgĩ wa Thiong’o, Louis Althusser, Evelyn Nakano Glenn; Tacoma’s immigrant history; and my own family’s immigrant history. The plot and construction of the story itself is an attempt to physically manifest and represent racialization, assimilation, and the trappings of harmful ideology that is expanded upon in the theoretical foundations. With these lenses, RATSKIN is a presentation of immigrant history and how the theatrical and literary traditions can help reveal how families continue to be affected by immigration. How can this history be refracted within a single family? What are these effects? How have they evolved through generations? How can we make sure these effects don’t limit the growth of our families?

 Developmental epileptic encephalopathies (DEEs) are a group of severe neurological disorders that present with seizures in early infancy and developmental delays. A genetic cause can be identified in up to 50% of affected individuals and is most commonly a de novo genetic change. However, for some patients a genetic change is not evident through DNA sequencing. In this research project, we are using RNA sequencing to search for and identify abnormal splicing events that may be due to splice-altering variants in the genome of previously undiagnosed patients. Splicing occurs naturally in unaffected and affected individuals; it is the process of introns being removed from mRNA transcripts and exons being joined. The process of RNA sequencing allows us to discover abnormal splicing errors by looking at splice junctions, which are sites on the intron and exon border where splicing normally occurs. We search for abnormal splicing defects using RNA sequencing by comparing the splice-junctions from our patients to a reference database of healthy controls (Genotype-Tissue Expression Project), filtering out common splice junctions, allowing us to identify unique and abnormal splice junctions. If we identify abnormal splicing, we will also investigate the genome of the patient to determine whether there is an underlying DNA change. Using RNA sequencing, we hope to provide a genetic diagnosis for a subset of our undiagnosed patients and for more individuals affected by DEE in the future.

Many smartphone users engage in compulsive and habitual phone checking which they find frustrating, yet our understanding of how this phenomenon is experienced is limited. We conducted a semi-structured interview, a think-aloud phone use demonstration, and a sketching exercise with 39 smart phone users (ages 14–64) to probe their experiences with compulsive phone checking. Their insights revealed a small taxonomy of common triggers that lead up to instances of compulsive phone use and a second set that end compulsive phone use sessions. Though participants expressed frustration with their lack of self-control, they also reported that the activities they engage in during these sessions can be meaningful, which they defined as transcending the current instance of use. Participants said they periodically refect on their compulsive use and delete apps that drive compulsive checking without providing sufficient meaning. We use these findings to create a descriptive model of the cycle of compulsive checking, and we call on designers to craft experiences that meet users’ definition of meaningfulness rather than creating lock-out mechanisms to help them police their own use.

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.

About 75% of women experience sleep disturbances during pregnancy. Sleep problems during pregnancy are associated with prolonged labor, preterm birth, an increased risk for cesarean delivery, gestational hypertension, glucose intolerance, and depression. To our knowledge, no research has explored the experience of sleep difficulties in pregnant women of color, despite the evidence that racial and ethnic minorites have an increased risk for poor sleep quality. The purpose of this study is to describe the sleep experiences in pregnant women of color during the second half of their pregnancy and to examine the personal and systemic contexts for their sleep. We conducted qualitative semi-structured interviews with 10 women recruited from a local prenatal clinics. Questions explored the internal physical and emotional challenges as well as the external challenges to getting sufficient quality and quantity of sleep during pregnancy. We audio recorded interviews, transcribed verbatim, and analyzed data using qualitative description methodology. We expect that health disparities faced by women of color will be manifested as personal, enviromental, and systemic factors that contribute to their difficulty sleeping during pregnancy. Findings from this study will have implications for the design of culturally appropriate prenatal interventions to facilitate improved sleep for minority women. 

Gastric dilatation volvulus (GDV) is a life-threatening condition that occurs in large breed dogs. Previous research investigating three candidate genes of major histocompatibility complex (MHC), DLA88, DRB1 and the innate immunity gene, TLR5 found diagnostic markers that could be used to identify Great Danes at risk for GDV. The Endoplasmic Reticulum Aminopeptidase 1 gene (ERAP1), is now known to be an important up-stream component of the antigen-presentation system of the MHC, and human polymorphisms in this gene have been linked to the same inflammatory disorders. I hypothesize that Great Danes with certain ERAP1 single nucleotide polymorphism (SNP) variants on exons 3,7,12,13,16 associate with the risk for GDV in Great Danes. We conduct the experiment on two groups of Great Danes; eighty dogs are recruited for this study. Half comprise a GDV group consisting of dogs that have undergone emergency surgery for GDV, and a second age-matched gender-matched control group is dogs with no history of gastric problems. We perform polymerase chain reaction (PCR) and sequencing on subjects from both groups in the variable regions of the ERAP1, evaluating alleles from the gene for association with GDV while controlling for dog family, ages, and diet intake. The goal of this work is to establish a list of specific “risk”or “protective" alleles of ERAP1 that are associated with GDV in Great Danes. If the dominant genotype that predisposes dogs to GDV can be determined, this canine GDV model marker will provide a means to detect at-risk animals, especially in Great Danes. Early genetic testing, probiotic, drug-based approaches and gastropexy (a surgery to prevent GDV) could reduce the incidence of GDV.

Rehabilitation research has demonstrated the benefits of early powered mobility intervention for children with disabilities, from improving developmental skills to empowering children to better participate in family and community life. However, traditional powered mobility devices are often stigmatizing, costly, and require specialized transportation due to their size and weight. One alternative early powered mobility option that has sought to address several of these concerns, The Go Baby Go Mobility and Socialization Project, provides children with disabilities a means of socially welcoming, early independent mobility experiences through custom safety and accessibility modifications to commercially available toy ride-on cars. The Go Baby Go project has resulted in promising pilot research along with community-based outreach and education in collaboration with families, clinicians, and engineers. However, a means to efficiently track car performance in real-world environments without the presence of a researcher has been lacking. Therefore, the purpose of our project was to develop a customized data logger and companion Arduino code with the ability to collect real-time data from the cars as families use them in their homes and communities. Our multidisciplinary team has created and implemented a system which gathers car performance data automatically via integrated sensors, including the number and duration of switch activations, frequency and duration of use, outdoor location, distance traveled, and driving terrain. Housed in a simple, waterproof food storage container, the data logger is integrated into the car’s electronics and powered by the car battery, with data stored on a micro-SD card. Preliminary analysis of results from eight cars in local communities is ongoing and will be shared; initial feasibility of our system for real-world tracking without undue research presence or caregiver reporting burden is promising. Future research goals include full quantitative analysis of car use patterns to improve technology design and implementation in community settings.

Globally, poor and underserved countries tend to have an elevated incidence of infectious disease, often contributing to increased mortality rates. One health issue resulting from this is diarrhea, the 6th leading cause of mortality in developing countries.  Because pregnant women are already vulnerable to infections due to an immune system that is rapidly adapting to a developing fetus, they may be more susceptible to diarrhea and the complications that come with it.  We sought to identify whether diarrhea during pregnancy was associated with adverse birth outcomes, such as preterm birth and being small for gestational age. We used data from a prospective longitudinal study of maternal influenza immunization of pregnant women and their infants conducted in rural Nepal from 2011-2014. Diarrhea episodes were defined as three or more watery bowel movements per day for one or more days. The chi-square test, two-sample t-test, and log-binomial regression were performed to evaluate baseline characteristics and the association between diarrhea during pregnancy and adverse birth outcomes. From our study, we found that average weight and BMI at enrollment for women with diarrhea was significantly lower than those without diarrhea during pregnancy (47.6kg vs. 48.5kg, p=0.01, 20.72 BMI vs 21.06 BMI, p=0.01) and women with diarrhea during pregnancy were significantly more likely to have small for gestational age infants (42.6% vs. 36.8%, p=0.03). We also found that the incidence of non-live birth, preterm, and low birth weight did not significantly differ between mothers with and without diarrhea. By understanding the risks diarrhea during pregnancy poses for both mothers and infants, we can assess the severity of this problem, and whether or not a possible means of prevention should be prioritized. Further research should examine whether methods to improve weight and BMI during pregnancy prevents diarrheal illness and thus negative birth outcomes. 

The US/Mexico border is a politically polarized and militarized place where each year millions of people cross, both with and without authorization. As a militarized border that divides two nations, the border region is prone to violence for at least two reasons: the presence of armed state officials on both sides of the border, and the presence of drug trafficking. National treaties such as the North American Free Trade Act (NAFTA), soon to be replaced by the United States–Mexico–Canada Agreement (USMCA), impact industries in Mexico. NAFTA removes trade tariffs, creating investment opportunities for the United States in their border countries (Canada and Mexico). These industries employ high numbers of womxn in their facilities. Notably, there is a history of high rates of murders and disappearances of womxn in border towns such as Tijuana, Ciudad Juárez, Mexicali, El Paso, etc. Many of these murders, disappearances, and other acts of violence are ignored or denied by local and state officials. My research explores the violence that is enacted through the actions and inactions of state and local officials. I will conduct an analysis of declassified documents, released by the United States and as well as related research publication. My research contributes to a larger conversation about how accountability can be upheld for the victims of violence who have been dismissed by state officials and the media. I also hope to contribute to a larger conversation about how to prevent such violence. Keeping a research focus on these questions also mitigates against the further violence of forgetting about the victims and their families.

Glycans are ubiquitous in biology and play a crucial role in cell to cell signaling, immunity, and disease. The A, B, and O blood groups are differentiated by different glycan structures and linkage patterns presented on either glycoproteins or glycolipids. To date, the exact glycan structures that differentiate blood types remain unknown. A clear understanding of these structures would increase the success of transfusion procedures and reduce the risk of complications. Our lab is currently examining glycans from glycoproteins isolated from red blood cell membranes, however we do not have the enzymes needed to remove glycans from glycolipids. ECGase I is an enzyme that was recently shown to effectively cleave glycans from a wide range of glycolipids. We have cloned the gene for ECGase I into a GST fusion vector for recombinant bacterial expression. With this we have been able to generate high yields of purified ECGase I. The EGCase I produced was more active than commercially available product. The ability to grow EGCase I enables large scale investigation of glycolipids involved in the ABO blood group system.

Water temperature is one of the largest factors of hatchery efficiency, and this can vary greatly depending on the source of the water. Warming waterways is thought to be a problem with salmonid hatcheries in the Pacific Northwest. For this study, we compared the effects of water source (Lake Aberdeen vs VanWinckle Creek) as well as temperatures on the mortality rates of Oncorhynchus mykiss. Water temperature data was collected from 2015, 2016, 2017, and 2018 to compare the effects of temperatures and water source on the mortality rates of O. mykiss. Microscopy was also used in an attempt to find and identify Tetracapsuloides bryosalmonae, the parasite known to cause Proliferative Kidney Disease in salmonid fishes. This parasite is believed to be a major contributor to high summer mortality rates. We collected multiple morbid and recently deceased juvenile O. mykiss, and examined these samples using a hematoxylin and eosin staining of the kidneys and gills. Initial findings suggest no significant impact of lake versus river water for this specific disease, however gram staining and biochemical assays indicated a presence of a bacterial fish pathogen: Flavobacterium columnare. Because of this, future directions include broadening the scope to a greater variety of infectious diseases. If factors influencing development of PKD can be identified, preventative actions can be taken to lessen the mortality rates and allow for a larger amount of fish to be successfully raised each year.

A hatchery’s purpose is to supplement falling populations of wild fish, mitigating human impact. However, the effect operating a stream-based hatchery has on the immediate stream environment is not well understood. Varied hatchery designs make it difficult to find a consistent way of assessing an establishment. This project used the idea that consistency is key to evaluate the impact hatcheries made by examining water of the the influent and effluent flow. Water was sampled from where it entered, transitioned, and exited three different fish-bearing hatcheries. Hatcheries were classified into three general water-system types, gravity-fed, spring-fed, and flow-through. Water status was evaluated by measuring electric current, dissolved oxygen, pH, temperature, and bacterial content. In addition to unique location characteristics, containment mitigation measures and extenuating circumstances were considered when evaluating the data. The results showed the trend of influent to effluent water in all three hatcheries increased in temperature while the levels of dissolved oxygen, electric current, and pH decreased. Similar result trends were also found between alike water-system types, although with the small sample results are inconclusive. This study is not meant to be a stand alone. With the inclusion of more locations the data will begin to form an averaged scale which could be referenced for the effectiveness of certain hatchery designs and contaminant mitigation techniques. Having this data-set would eventually serve as a resource for future hatchery construction projects.

Hydrogen sulfide (H₂S) is a common cause of workplace injuries and deaths for industrial workers. In our project, we use Caenorhabditis elegans (C. elegans) as a model organism for investigating how cells behave under an environmental stressor and the long-lasting effects of that behavior. Previous work in our lab has shown that early exposure to low H₂S (50 ppm) enable C. elegans adults to survive a much higher subsequent exposure by forming a cellular memory known as a “bookmark.” Bookmarked animals survive at high H₂S (150 ppm), while animals without previous exposure do not. In a genetic screen, we identified various epigenetic factors that are involved in this process; however, it is still unclear when in the “life” of the bookmark and where in the animal these factors are required. The required bookmarking gene swsn-4 is part of the SWI/SNF complex, a group of proteins that regulate compaction of DNA and thus the accessibility of genes. We are interested in assessing the spatial requirements for swsn-4 by rescuing mutant animals that lack this chromatin-remodeling factor. For the first part of the project, we use Gateway recombination cloning technology to enable tissue-specific expression of swsn-4. In the next part of the project, we test whether introducing swsn-4 in specific tissues rescues bookmark retention. A recent study identified hif-1, a transcription factor, to be broadly needed to rescue animals exposed to both low and high H₂S, suggesting that the response is needed in most cells to ensure survival of the animal. Because swsn-4 is also present broadly in the body of C. elegans, we predict it will be needed in a similar way to hif-1. We hope that our investigation would lead us to discovering methods in which we can utilize the properties of H₂S as a chemical messenger to help patients.

Tooth sensitivity is a common affliction that leads to discomfort or even pain when teeth come in contact with a variety of stimuli, such as cold drinks or brushing. The pain is a result of the tooth's natural protective enamel layers wearing down over time, exposing microscopic channels in the teeth known as dentin tubules. These dentin tubules transmit sensation from the tooth surface to the nerves, which is why exposing them leads to greater sensitivity in the tooth. The goal of this study was to evaluate the effectiveness with which a mineral dentin desensitizer could cover and seal the dentin tubules, thereby decreasing tooth sensitivity. Samples of human teeth were cut into disks to expose the dentin tubules and applied with the desensitizer. One treatment group was immediately processed for imaging using a scanning electron microscope, while the other was stored in simulated body fluid for four weeks before imaging. Cross sectional and surface images were taken of the dentin samples, at several magnifications. Both treatment groups showed effective coverage and mineralization not only over the open tubules, but also penetrating into the tubules. These results suggest such treatments may be an effective way to treat patients with tooth sensitivity caused by exposed dentin.

Pollution from human influences is a growing problem in the Chehalis River and tributaries causing deleterious effects on stream health. Stream microbiomes are composed of diverse collection of microbes that play an important role in keeping the surrounding riparian zones and life within the streams healthy and thriving. Stream water has been facing a decline in quality from the leading cause of pollution from agriculture and manufacturer run-offs. Although there have been many studies relating to run-off pollution affecting streams, there are few in-depth studies done on the taxonomy and functionality of microbes in urban water ecosystems, so it is important for this to be further investigated. With the use of 16s rRNA sequencing, each sample site presents two years of data included to indicate differences both by season (Fall, Summer) and sample site. At the phylum level, every season consists of a primary microbial signature shared amongst the sites. These phyla are Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, and Tenericutes. From the family data, common to nearly all sites are the Flavobacteriaceae, Comamonadaceae, and Oxalobacteraceae. Families prevalent at many sites in various combinations include Flexibacteraceae, Crenotrichaceae, Chitinophagaceae, and Verrucobacteraceae. This project presents a two-year microbiome analysis of Alder and Fry Creek to develop trends for the seasonal variation in urban water ecosystems due to human impacts.

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.

The cooling process for aluminum cast molded parts impacts the material properties and quality of the final product.  Understanding what microstructure and properties produced by a given mold is critical for the mass production and design of consumer and industrial parts.  This research analyzes the cooling of a pure aluminum cast molded part under variable corner geometry, in order to predict properties of the finished aluminum product.  This project goal was to create a flexible, three dimensional model of the cooling process for an aluminum cast part, using finite volume analysis. The model takes into account both static and dynamic material states and properties.  The model's goal was to be robust and flexible enough to be utilized for a wide range of material properties, as well as various corner geometries, including chamfer, fillet and a 90˚ corner.  In order to verify the accuracy of the model, and assess microstructural effects, the cast geomtry has been tested with a real mold and aluminum.  Temperature readings for the mold are taken in order to assess the models accuracy.  We predicted that the fillet geometry will cool the slowest of the three geometries, with the chamfer being second and the 90˚ corner being the fastest. With this in mind we predicted that the fillet will have the the greatest cooling continuity, with the chamfer being second and the 90˚ corner being last.

The blood brain barrier (BBB) is an almost impenetrable obstacle for therapeutic delivery, hampering the treatment of many neurological diseases. By exploiting natural transport mechanisms utilized by the brain such as iron import via transferrin receptor (TfR), researchers have been able to transport therapeutic molecules into the brain, albeit with a low efficiency. TfR is a transmembrane protein that is highly expressed on the BBB where it binds its ligand, Transferrin. Transferrin-bound iron binds on the blood side of the BBB, is subsequently endocytosed and trafficked through the cell before being exocytosed on the brain side. We have computationally designed a protein that, like the transferrin ligand, can bind TfR and pass the BBB in in vitro BBB models. The goal of my project is to attach existing protein nanocages to this binder which have previously been shown to package therapeutic molecules. I have generated constructs by fusing the binder to these cages, purifying the cages, analyzing their stability, and testing their binding affinity to transferrin receptor. We currently have one cage fusion that successfully binds the transferrin receptor and is being tested for BBB traversal. We are continuing our work to create more variants that can successfully cross this barrier. Using computationally designed de novo proteins has many advantages over traditional protein engineering approaches such as hyperstability and a high degree of customizability. In the future, this project could provide new opportunities for treatment of many neurological diseases.

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.

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. 

In countries with developing economies, economic activity and progress are often considered only in numeric terms such as wages, Gross Domestic Product (GDP) or utilization of credit. Proponents of economic empowerment as a vehicle for economic development emphasize the social and educational aspects of development such as financial education, gender equality and agency. I investigate how existing research defines “economic empowerment,” in the context of economic development, and observe various programmatic approaches to economic empowerment in Kenya. For this project specifically, I focus on how one organization, The Hope Foundation for African Women (HFAW), fosters economic empowerment through financial education and financial services. In addition to advocating for gender equality, HFAW provides finance and literacy trainings primarily for women using the “Popular Education” model and “Social Change Communication.” The organization provides programming in five counties located in Southwestern Kenya. The goal of this project is to highlight existing financial education methods used by HFAW to empower communities and individuals, and to prompt discussion regarding vehicles of economic empowerment. This paper highlights effective teaching methods within the organization and illuminates areas where further research might help improve outcomes for HFAW participants. Based on areas of need identified by HFAW staff in interviews, and informed by my background research, materials will be provided to support the organization’s financial education programming. Funding is made possible by the Ottenberg-Winans Fellowship. This project will foreground further research that can identify and improve upon effective future economic empowerment programming.

Spanish is one of the fastest growing spoken languages in the United States. In 2017, the US census reported that about 41 million residents (13.4%) speak Spanish in the home. Since the number of Spanish speakers increases annually in the United States, it is important to research how Spanish heritage language (HL) learners and Spanish second language (L2) learners interact with each other. Many assume that speaking with a Spanish HL learner will improve the quality of the L2 learner’s Spanish. The goal of my project is to analyze the amount of English spoken between the two types of students and the opportunities for learning created during their interaction by correcting each other’s grammar or helping each other to use different vocabulary words. To this end, I have transcribed the Spanish conversations between two Spanish L2 students and formatted them using the F4/F5 transcription software. I am currently coding them using a qualitative data analysis program called Atlas.Ti, with the addition of three other transcriptions that had already been transcribed. I predict that our results will demonstrate that, while some learning will occur between the HL and L2 students, a majority of the learning will occur among Spanish L2 learners. Since the research is still ongoing, I predict that due to the greater level of comfort a Spanish L2 learner has while talking to a fellow Spanish L2 learner, they will work together to solve more language issues than with a Spanish HL learner. This research is important due to its implications for improving how Spanish is taught in schools across the United States.

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.

 During development in most animals, tubes form as precursors to complex organs such as the neural tube, digestive system, and vasculature. To create a tube, cells within a sheet, or epithelium, must coordinate specific shape changes and movements. This coordination requires each cell to establish and maintain directional identity, thereby distinguishing the ‘top’ of the sheet from the ‘bottom’. While extensive research on a group of proteins, called ‘polarity proteins’, has elucidated how cells establish directional identity, little is known about how they maintain that orientation during the shape changes and rearrangements that occur during tube formation. To address this gap in our understanding, I am studying how these polarity proteins contribute to proper tube morphogenesis during the formation of specialized structures on Drosophila melanogaster eggshells called dorsal appendages (DAs). These appendages, which provide the developing embryo with oxygen, are formed from an epithelium that wraps into a tube, elongates, and then fills with eggshell protein. The epithelium sloughs off when the egg is laid, leaving the appendages as a visualization of the earlier tube formation. I used RNA interference (RNAi) to assess the role of 24 candidate proteins in DA formation. My initial results led me to hypothesize that one protein, Crumbs (crb), regulates the tube’s directional elongation. To explore this role, I am studying crb protein localization during tube elongation, assaying DA defects after knocking down expression using RNAi in subsets of cells, and analyzing the distribution of adhesion, motor, and other polarity proteins when crb is completely absent in null clones. These analyses will add to our understanding of the role of polarity proteins in the conserved development of epithelial sheets into tubes.

Age-associated diseases, like neurodegenerative disease, cancer, heart disease, and metabolic dysregulation limit healthy human lifespan. In recent years, biologists researching aging and longevity have turned their attention towards maximizing healthspan, the healthy portion of one’s life before the onset of age-related disease. By delaying age-associated diseases, we can fundamentally improve quality of life globally. Natural products and other pharmacological interventions hold particular promise as interventions to extend healthspan and lifespan. We seek to identify novel compounds that extend lifespan using the invertebrate model system Drosophila melanogaster (fruit fly). We have tested an extract made from Pterocarpus marsupium (PME), a tree native to India and Sri Lanka with uses in Ayurvedic medicine. PME extends cellular lifespan in budding yeast, another invertebrate model system. We also tested pterostilbene, a compound found in Pterocarpus marsupium extract. As a positive control for lifespan extension, we are treating other cohorts of flies with rapamycin. Rapamycin is a specific inhibitor of the nutrient sensing mechanistic Target Of Rapamycin (mTOR) pathway, a known longevity regulating cellular pathway. Using multiple fly genetic backgrounds, performed a dose response to identify concentrations of PME and pterostilbene that extend Drosophila lifespan. Through pharmacological methods, we seek to delay aging and minimize human vulnerability to age-induced diseases. Discovery of specific compounds that prolong lifespan is a first step in developing therapeutic methods to delay human aging and health decline.

The average number of coronary artery bypass surgeries performed annually in the United States is roughly half a million. Recently, extensive research has been conducted on the use of acellular tissue engineered vascular grafts which could be implanted into the body to replace the blood vessels that fail due to cardiovascular disease. The Ratner lab is working on creating a novel vascular graft based on a pro-healing porous material which is best suited to guide native blood vessels to heal into the material so that the vascular graft can transform into a living blood vessel. However, a paradox in this design is that right after the graft replaces the blood vessel, before the healing happens, the pores in the graft could give rise to bleeding if not monitored properly. This project addresses that problem by creating a hydrogel that seals the pores, preventing initial bleeding, while degrading at a rate in sync with the rate of healing and is ultimately replaced by vascular tissue. Initially, a series of hydrogels with varying crosslinker levels were made. Subsequentially, an in-vitro degradation assay was used to test each hydrogel in a cell culture medium. This assay showed that the higher the concentration of crosslinker, the slower the hydrogel degrades. In addition, the hydrogel was implanted under the skin of a mouse and the observed degradation of the hydrogel in vivo closely matched the in vitro data but was slightly slower. In the future, the hydrogel with the optimized crosslinking will be applied to a vascular graft for large animal experiments in sheep and pigs and the healing and degradation rates will be observed to measure the effectiveness of the hydrogel as a sealant.

With their small genomes, fast evolutionary rates, and clinical significance, viruses have long been fodder for studies of whole genome evolution. One common need in these studies is the analysis of viral evolution over time through longitudinal sampling. This analysis is relevant to basic scientists to understand viral evolution in different model systems, to drug manufacturers to understand antiviral resistance development, and to clinical researchers to understand viral evolution within hosts across space and time. However, there exists no simple tool to automate such analyses. We created a simple command-line visualization tool called LAVA (Longitudinal Analysis of Viral Alleles) originally to survey HPIV1 and HPIV2 adaptations to culture. Our hypothesis was that the culturing process selects for mutations in viral entry proteins (hemagglutination-neuraminidase and fusion) that are never seen during growth in humans. Previously done manually, LAVA cut down the workload for analysis of minor allele variants significantly, and furthermore visualized the results to instantly show that the primary regions of HN and F in which many of the mutations took place were different than those found in the previously studied HPIV3. Further development on LAVA allowed it to grow into a critically useful bioinformatics tool in virology. LAVA allows dynamic and interactive visualization of viral evolution across the genome, over time, and within three-dimensional protein structure. Results are easily shared via a single HTML file that also allows interactive analysis based on read depth and allele frequency. LAVA requires minimal input and runs in minutes for most use cases. LAVA is programmed mainly in Python and is compatible with Mac and Linux machines. LAVA is a user-friendly command-line tool for generating, visualizing, and sharing the results of longitudinal viral genome evolution analysis. Instructions for downloading, installing, and using LAVA can be found at https://github.com/michellejlin/lava.

In the last two decades, the number of dual-language learners (DLL) in the United States has increased dramatically, with a significant portion being children. With the growing ubiquity of smartphones and tablets in a technology-driven society, there has also been a rise in the popularity of smartphone-based language learning apps, such as Duolingo. As a newer concept in the field of language acquisition, there is a lack of research on the effectiveness of using a language learning application to aid in a DLL’s language development. The purpose of this project was to evaluate how individuals utilize language learning apps, and predict the applicability of Octo, a language app designed for caregivers of Mandarin-English DLLs. Differing from the format of traditional language learning apps, Octo is designed to be a way for caregivers, who have little to no exposure to Mandarin at home, to add Mandarin into the learning environment of the DLL during daily interactions. By surveying the general population using an online survey, we had discovered the range of perspectives regarding parental use of language learning apps with their children. The survey also provided data regarding the user interface and content of the Octo app itself, which will provide additional information on the applicability of this particular app. By evaluating the general views of language learning apps and the user experience of Octo, we were able to predict the likelihood of use for caregiver-implemented language learning apps for children, specifically Octo. By understanding the public views surrounding language learning apps and their use with young DLLs, there can be a deeper understanding of the applicability of DLL language learning applications as well as the general patterns of development in bilingual children.

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.

English sole Parophrys vetulus is a species of benthic flatfish that is commercially and tribally exploited off the coast of Washington State. The commercial value of English sole can decrease if the fish is infected with parasites, which degrade their appearance and health; in fact, widespread parasitic infection contributed to the closure of the commercial fishery in south Puget Sound in 1948. Clavinema mariae is a trophically transmitted nematode parasite that has increased in abundance by eight-fold since 1930 in Puget Sound. Since C. mariae is a nematode that infects hosts via ingestion, I used a diet analysis of English sole to: 1) assess the types of prey that sole consume, and 2) correlate the prey type abundance to C. mariae abundance. I evaluated the gut contents of contemporary sole collected in 2017 and historical sole collected over the past 80 years and held in the UW Fish Collection. I categorized gut contents to the lowest taxonomic family. Sole are hypothesized to primarily consume invertebrates, and C. mariae is transmitted by copepods, thus we expect copepods to represent a larger portion of the diet in more recently collected, more heavily infected sole. Knowing the type and number of organisms that English sole consume will improve our understanding of how sole interact with the Puget Sound food web; specifically, how they are initially infected with C. mariae, which would offer insight to their observed increase in abundance in sole over the past 80 years.

The meteorological conditions across the North of Iceland regulate snow metamorphic processes and are therefore the driving factors behind melt-freeze crust formation. The North Atlantic Oscillation (NAO) is a climate system that controls these meteorological conditions. By analyzing the cumulative NAO index over the past two decades, the influence of climate change on Icelandic meteorological conditions can be established: the shifting climate system is stimulating heightened precipitation and increased northern storm cycles. The association of these climate trends with the historical patterns of avalanche cycling in Iceland can help understanding of the causes of melt-freeze metamorphism and can demonstrate the expected effects climate change will have on these processes. According to the cumulative NAO index and the Icelandic avalanche data from 1995 to 2018, melt-freeze metamorphism frequency increased in the early and late months of winter seasons across the North of Iceland and remained less relevant in mid-winter months. The alteration in frequency and seasonality of melt-freeze metamorphism poses challenges to Icelandic communities possibly facing increased risk of slab avalanches and to the vulnerable ecosystems of Iceland. Increased observation and availability of reliable data is paramount to understanding how snow metamorphism will evolve with climate change and consequently what individuals must adapt to.

The relationship between greenhouse gas emissions and climate change and the dangers of global warming are widely documented. The 2030 Agenda for Sustainable Development was signed by all United Nations Member States in 2015 and calls for the “widest possible international cooperation aimed at accelerating the reduction of global greenhouse gas emissions” with the aim of “holding the increase in global average temperature below 2 °C”. What role do counties have in reducing greenhouse gas emissions? This project aims to develop a granular model of carbon storage and flux in Multnomah County to inform policy interventions that bring the county closer to meeting the goals outlined in the 2050 Climate Action Plan adopted by the City of Portland and Multnomah County in 2009 with a goal of reducing community-wide greenhouse gas emissions 80% by 2050, with a more ambitious goal of being a net-zero emitter of greenhouse gas. One of the first steps in developing a jurisdictional level greenhouse gas accounting is an inventory and projection of carbon stock change. Our study hopes to assess the feasibility of various methods in predicting carbon storage and flux on forested lands in Multnomah County, compare our results against Forest Inventory Analysis (FIA) estimates and gain a better understanding of carbon storage and flux as it relates to land ownership and management on public and private forest lands.

Aging is characterized by the loss of physiological and cellular functionality, however the mechanisms that underlie this deterioration are still unclear. Emerging evidence indicates that aging is associated with increased cell-to-cell variation in gene expression within tissues: homologous cells within tissues start expressing the same gene at varying levels. The causes of this age-related variation of gene expression are not known. Here, we aim to investigate this age-related dissimilarity in gene expression using C. elegans as a model system. We hypothesize that increase of gene expression variation is an early event during aging that may therefore underlie subsequent deterioration of tissues functionality. By characterizing aging in C. elegans, we hope to provide further insight into the molecular characteristics of aging in humans, and possible points of intervention. Previously, we have found that young C. elegans animals exhibit nearly identical stoichiometry of independent genes expression with very little difference between individual animals of the same genetic background. Our initial results support the idea of increased cell-to-cell and animal-to-animal variation of gene expression with age in C. elegans. Here, I use quantitative microscopy to measure animal-to-animal and cell-to-cell variation of genes expression in middle aged C. elegans using fluorescently-tagged proteins and quantitative microscopy. In addition, I use the methodology of molecular cloning and transgenics developed by the Mendenhall lab to create new transgenic strains of C. elegans. These transgenic strains will be also be used for quantitative microscopic analysis. By examining existing strains and developing new ones, I will determine if increase of gene expression variation represents early event in the aging of C. elegans.

Widespread distribution of dissolved uranium (U) from natural and anthropogenic sources poses a challenge to both environmental and human health. Some bacteria are known to reduce highly soluble U(VI) into more insoluble U(IV), limiting the rate it may leach into subsurface environments. Therefore, understanding how this metabolism functions in situ is vital for predicting subsurface U transport. Any thorough understanding of microbial metabolisms must compare different means of energy production (i.e. catabolic reactions). This means the metabolic processes involved in U(VI) reduction must be compared to those where an alternative terminal electron acceptor (TEA) is used. The facultative anaerobic bacterium Shewanella putrefaciens strain CN32 has been the focus of many recent studies on U, but there has yet to be a detailed study of its metabolic efficiency across multiple TEA’s. This work quantitatively examined the metabolic efficiency of Shewanella putrefaciens CN32 by comparing the ratio of cells produced to the total mass of protein produced when growing on three different TEA’s: O2, Fe(III), and U(VI). Furthermore, the overall health of the culture was evaluated by measuring the size of cells grown with each TEA. Initial results indicate that both a larger average cell size and larger ratio of cells to protein mass correspond with potential Gibbs energy of each catabolic reaction (in decreasing order: O2, Fe(III), U(VI) reduction). Gaining a further understanding on bacterial U reduction will allow for hazard mitigation methods to be developed and used in at-risk areas around the world. 

Transient receptor potential vanilloid-1 (TRPV1) ion channels are polymodal signal integrators of noxious stimuli including heat, vanilloids such as capsaicin, peptide toxins, acid, and inflammatory mediators. It is unknown whether activation of TRPV1 by different stimuli is achieved through the same structural mechanism or if different stimuli activate the channel through different structural mechanisms. Clinical trials using TRPV1 antagonists resulted in patients exhibiting hyperthermia, suggesting that TRPV1 plays a role in maintaining body temperature, and highlighting the need to ensure that therapeutics targeting the channel do not disrupt thermal homeostasis. Hence, knowledge of different structural mechanisms for channel activation would aid in the design of therapeutic agents targeting TRPV1. To address this, we have expressed a series of functional single-cysteine rat TRPV1 channels for spectroscopic analysis, with techniques such as electron paramagnetic resonance, double electron-electron resonance, and Förster resonance energy transfer spectroscopy. By probing several structural regions within TRPV1 we can determine which regions of the channels move during activation and whether those are the same for different noxious stimuli.

National calls have been made to strengthen our nation’s STEM workforce by improving preparation and increasing graduation rates. At Portland State University (PSU), Oregon’s largest urban university, over 60% of students transfer from community colleges and the large majority do not live on campus. Transfer students may perceive a loss of support and a drop in GPA during their first term post-transfer, elements of what is known as “transfer shock.” As part of a newly-awarded NSF S-STEM grant, we aim to measure if high-impact STEM support programs can mitigate factors related to transfer-shock and support student sense of belonging. Direct impacts of the S-STEM program are being assessed qualitatively (e.g. focus groups, reflections), and preliminary results for our first cohort of S-STEM Scholars indicate strong bonds among the cohort and feelings of success. To examine how students supported by the S-STEM and other high-impact STEM programs compare to other PSU STEM students, a survey measuring self-efficacy, scientific identity, scientific values, STEM involvement, and sense of belonging was broadly disseminated to students in Fall 2018 and will be repeated in Spring 2019. Initial survey results (n=933) allow us to compare student responses for students supported (n=93) or unsupported (n=840) by programs such as the S-STEM. We will also compare traditional four-year students (n=291), community college transfer students (n=398), and four-year college transfer, returning, and post-baccalaureate students (n=240). Preliminary results indicate that students supported by high-impact STEM programs such as the S-STEM report significantly higher sense of belonging, both at PSU and in STEM groups. Efforts implemented by the S-STEM program to improve STEM student experiences academically, financially, and socially, particularly to the most vulnerable populations, will ultimately improve and diversify the STEM workforce.

Methodological advances have made it possible to generate predictions of brain activity using functional magnetic resonance imaging (fMRI) for cognitive architectures, such as Adaptive Control of Thought—Rational (ACT-R), thus expanding the range of model predictions and making it possible to distinguish between alternative models that produce otherwise identical behavioral patterns. However, for tasks associated with relatively brief response times, fMRI predictions are often not sufficient to compare alternative models. Presently, we outline a method based on effective connectivity, which significantly augments the amount of information that can be extracted from fMRI data to distinguish between models. We show the application of this method in the case of two competing ACT-R models of the Stroop task. Although the models make, predictably, identical behavioral and fMRI predictions, patterns of functional connectivity favor one model over the other. Finally, we show that the same data indicates, provided reasonable task constraints, that we may be able to automatically generate modifications to our models using measures of effective connectivity, further increasing the validity of our models and opening new avenues for model development. We see this an exciting opportunity for future research.

American Indian / Alaskan Native (AIAN) communities assert their rights as sovereign nations by integrating their cultural values and community-wide protections into research regulations. This increasingly includes the creation of tribal research review boards to oversee research conducted in their communities. Understanding where these boards exist and the unique considerations of their application processes is essential to conducting ethical research with tribal communities. A central registry of tribal research review boards does not exist, so we first sought to locate them throughout the U.S. We conducted a search of the Office for Human Research Protections’ online database of Institutional Review Boards (IRBs) to find registered IRBs serving tribal communities. Through multiple online searches, we then located other non-registered tribal research review boards. We created a new dataset of tribal research review boards and mapped their locations in relation to the federally recognized tribes in the U.S. From this new dataset, we chose six current tribal research review boards for an in-depth comparison of their application processes. Our content analysis revealed important requirements for all applications including approval from agencies within the tribal community, determination of potential risks and benefits to individuals and communities, and board approval prior to dissemination of findings. Most processes also required researchers to report their findings to the tribal community and some explicitly established tribal ownership of research data.  This work begins the process of locating tribal research review boards in the U.S. and presents trends found in six of these boards’ application processes. This information is useful to researchers seeking to ethically partner with tribes and to tribes wanting to establish their own research review processes. Moreover, these analyses demonstrate tribal sovereignty within the field of Indigenous ethics and research regulation.

This work replicates previous research used to criticize the use of principle component (PCA) and exploratory factor analysis (EFA). Factor analysis is often used when research is being conducted in a new area and there is limited background knowledge about what one might expect to find. It’s useful because of its ability to reduce the number of variables in a dataset by examining the correlations between items and identifying latent dimensions that account for measured item variance and covariation. A criticism of this method is that it detects patterns in random data where there is no underlying structure. We tested this criticism by replicating the methods in a 1981 paper by Robert Vierra and David Carlson. We generated random data in R Studio and looked at the variance accounted for by the factors identified by EFA and PCA. We also examined the Type I error rate in sample correlation matrices tested with Bartlett's test. Additionally, we have begun a literature review looking at the modern methods similar to exploratory factor analysis, including machine learning, in order to understand how these criticisms have been addressed by these modern approaches.

Our criminal justice has an extremely high rate of recidivism, i.e. the rate at which those who are released re-enter prison (more than half within one year, more than three-quarters within five years). The prison system is a harsh environment, ineffective at rehabilitating inmates for release in several aspects, including education and mental health care. Virtual reality (VR) is an immersive technology with multifarious applications. Inmates at a local prison sought to utilize this technology to solve issues in prison. The inmates, along with UW students and the Reality Lab, collaboratively identified three application domains in which virtual reality is potentially an effective solution. These applications areas are (A) hands-on education and vocational training; (B) exposure to day-to-day experiences; and (C) mental health skills/ relaxation.We have currently developed prototypes for applications (B) and (C), and are in the process of designing a method to measure their efficacy. We hope that this will provide a foundation for the development of future applications and facilitate deployment in a local prison. 

Culturally competent interventions are essential to recruiting and retaining ethnic minority populations. Latino communities are the fastest growing population in the United States. Despite their growing numbers, Latino communities are dramatically underrepresented in clinical trials. As a result, the data from those clinical trials are not representative of the Latino population. There are many factors that make Latino communities very diverse, even amongst themselves. They do not share the same languages, customs, and socioeconomic status. There is a need to investigate the barriers and facilitators of the recruitment of Latinos into research. A survey was developed for Latino families in Oregon. The survey items were informed by a literature search around barriers and facilitators of clinical trial participation for minority and disadvantaged populations. This survey has been translated in both English and Spanish. After finalization of the survey, it was piloted with three representatives from the local community to get qualitative feedback. It will be administered to low-income parents of children enrolled in head-start settings in Oregon over the next five months and expect to have 200 responses. The anticipated results will contribute a better understanding of what commonly impacts recruitment among the Latino families participating in clinical trials and what strategies address those issues. This project can serve as a resource for the wider scientific community that seeks to recruit and study the Latino population for research purposes.

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.

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.

Transportation infrastructure like freeways provides an excellent lens through which to look at the issue of environmental justice. There is legislation in place that should prevent or at least draw significant attention to environmental justice, yet new freeways are still being proposed which continue to worsen environmental justices as decades past. With grassroots opposition as a primary form of resistance, this paper investigates the tools available to activists, as well as the ones most effective in ensuring the success of the movement. This paper is based upon three case studies of recent freeway proposals across the United States – the successful resistance to the Harbor Bridge Project in Corpus Christi, Texas; the unsuccessful resistance to the Central 70 Project in Denver, Colorado; and the unsuccessful resistance to the South Mountain Freeway Project in Phoenix, Arizona – as well as ten open-ended interviews with community organizers, government officials, and lawyers involved with the projects’ resistance movements in some way. Through this process, I found that two main factors determine the success of a resistance movement: organization (the timing and coordination of the resistance) and opportunity (the local and federal context and framing of the project and resistance). Through the interviews and in-depth analysis of formal government documents and news articles, I conclude that while aspects of a group’s organizational capacity were important to the outcome, the political opportunity available to them – specifically the attitudes and priorities of the current federal administration – was most critical to the success of a movement. While this leaves several questions for the future of environmental justice resistance, I end with a series of suggestions for how government officials and grassroots organizers might approach the issue with the current federal administration.

The basal ganglia, evolutionarily old subcortical brain structures, are not commonly considered to be part of the 'language network' despite mounting evidence of their involvement. The current experiment explores two existing hypothesised roles for the basal ganglia in language, based on their known neurocomputations. These hypotheses characterize basal ganglia function as "control" - (prioritization of competing, stable-valued responses), or as "anticipitory" - (ongoing semantical organization based upon syntactic rules). The current experiment aims to adjudicate between these hypotheses by investigating the role of the basal ganglia using an individual differences approach. We utilize two neuroimaging paradigms targeting these hypotheses via lexical-semantic selection under uncertainty and sentence comprehension under varying syntactic complexities, completed by the same subjects. By correlating the neural responses to these tasks with individual differences in vocabulary and working memory capacity, we will explore the predictions made by two hypotheses. Specifically, if the basal ganglia nuclei are involved in controlling compteting linguistic responses, we expect to see greater levels of activation in the left caudate head when subjects are prompted with ambiguous lexical-semantic word choices, as well as 'spillover' activation in the right caudate nucleus negatively correlated with vocabulary percentile and accuracy; if the basal ganglia nuclei are involved in anticipating meaning via syntactic cues, we anticipate higher levels of activation in the left caudate with more syntactically complex sentences in lower-working-memory-capacity readers.

With reduced operating hours and additional pressures, there is a rising importance in the development of an accurate surgical simulation. In order to improve the effectiveness of surgical simulations, there must be an accurate model of the human body that can be used for practice. Although cadaver and animal models are imperative to the training of future and current surgeons, there is a rising ethical interest paving the way towards alternative solutions. My undergraduate research at the Center for Research in Education and Simulation Technologies (CREST) aims to develop an accurate model for adipose tissue in the greater and lesser omentum. We have developed four prototype recipes for simulated adipose tissue using chemically-modified polydimethylsiloxane (PDMS) composites. In order to evaluate how the prototypes compare to in-vivo and in-situ adipose tissues, we have collected quantitative data through uniaxial tensile, coefficient of friction, and puncture testing in addition to qualitative data collected through conducting surveys of physicians. By utilizing this collection of both quantitative and qualitative data, we have developed an accurate synthetic adipose tissue model.

Magnetic fields (MFs) and cosmic rays (CRs) are decidely important aspects of galactic disk and halo evolution, however, their precise roles are not yet completely understood. While there are many simulations studying galactic evolution, few have deeply explored the exact impact of CRs and MFs in the evolutionary process. The current goal of our research is to learn more about how CRs and MFs contribute to the evolutionary process by looking at how MFs grow and change in the circumgalactic medium (CGM) under the influences of CRs. Using a suite of simulated, isolated disk galaxies, we investigated the role of CRs in MF growth and galaxy evolution by comparing different galactic models, each possessing slightly varied CR physics. We present the role of CR transport on the geometry, strength, and growth rate of MFs in these simulated galactic halos.

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.

Reported human tissue properties and behaviors vary significantly across studies based on the characterization protocols utilized. My undergraduate research at the Center for Research in Education and Simulation Technologies (CREST) aims to address the gap between practitioners in the hospital by developing high-fidelity materials for medical simulation through data analytics. This will allow more accurate research in the field as well as better access to material properties and data. Raw uniaxial and puncture human tissue data is analyzed through MATLAB scripts to quantify human tissue behaviors. The processed data is restructured and transferred into bulk storage databases using Azure SQL servers and SQL databases, enabling cloud access. By utilizing Azure SQL databases, Tableau is used to visualize and manipulate targeted data. The human tissue property database bridges the gap between engineering and medicine. This database will be used to create the next generation of finite element models of the human body to help build virtual reality simulators.

Measurement in Psychology usually assumes continuous dimensions. Correspondingly, theoretical constructs are typically conceptualized as dimensions, meaning that observations differ in degree. However, theoretical constructs may also be categorical, i.e., rather than differing by degree, differing qualitatively. Different construct operationalization’s may lead to different scientific conclusions. Self esteem has long been of interest in Psychology. It has been conceptualized in various different ways, but always dimensional. Some self-esteem measures (for example, the The Rosenberg Self Esteem scale) seek to measure globally how much one values themselves as a person, without focusing on specific domains. On the other hand, other self-esteem measures (for example, the State self esteem scale) focus on perceived capabilities in specific domains, such as performance, social, and appearance. In the National Survey of Youth, participants rated themselves in specific areas, and then again as they would like to be. Using these data, we examined how different operationalization’s of self-esteem are associated with a few psychologically interesting outcomes such as drug use and crime. Specifically, we compared continuous and categorical representations of self-esteem. By examining the assumption of continuous latent variables, we shed light on how scientific conclusions differ based on construct operationalization.
 

African Americans may be at increased risk of developing Alzheimer's disease. Decreased social engagement and depression are related; changes in older adult levels of social engagement are associated with dementia. The Sharing History through Active Reminiscence and Photo-Imagery (SHARP) study aims to improve cognitive health among cognitively normal and mildly cognitively impaired older African Americans by employing a culturally celebratory framework integrating walking and community-based social reminiscence. In triads, African Americans aged >55 (n=40) walked 3x/week for 6-months in 2016 and 2017 while engaging in image-prompted conversational reminiscence about neighborhood history. Walks took place in Portland, Oregon’s historically Black neighborhoods. Baseline and end-study surveys had seventeen close-ended questions about physical and mental health and health behaviors. SPSS analytical software will aid in analysis. Focus groups discussed the impact of the program’s culturally celebratory approach on physical activity and mental health. Qualitative data will be thematically coded. Preliminary data highlights self-reported health-related outcomes which include increased activity throughout the day on days that walks occurred, rekindled friendships, increased impromptu social engagement, and heightened sense of community connectedness as a result of increased social engagement and place-based group reminiscence. Participants feel that the program’s social aspect, rather than physical activity, is the primary driver for sustained engagement. Structured socializing and the focus on neighborhood history contributes to improved self-reported mental health, important for sustained cognitive health. Finding innovative, culturally meaningful ways for older adults to be socially engaged may improve mental and cognitive health outcomes.

Metal catalysts exhibit greater catalytic activity as nanoparticles rather than bulk-like particles. Metal oxide supports can promote the activity and stability of metal catalysts due to the strong metal-support interaction, which can change the electronic properties and structure of metal nanoparticles. Metal-on-oxide-support systems are important for fundamental research and applications in heterogeneous catalysis. Nickel-based catalysts are widely used in industrial purposes such as carbon monoxide oxidation for industrial exhaust cleaning. However, nickel can rapidly deactivate due to solid carbonaceous material (coke) formation and nanoparticle coalescence (sintering) on the surface during a catalytic reaction. Metal oxide supports, such as ceria (CeO₂), improve metal catalytic performance by preventing coke formation and sintering, and in particular, ceria has a high oxygen storage and release capacity during catalytic reactions. Here, the adsorption energies, growth morphology, and charge transfer of adsorbed nickel on stoichiometric ceria (CeO₂(111)) and reduced ceria (CeO_1.8(111)) thin films at 300 K and 100 K are studied using single-crystal adsorption calorimetry (SCAC) in ultra-high vacuum (UHV) and surface sensitive techniques such as low-energy He⁺ ion scattering spectroscopy (LEIS), X-ray photoelectron spectroscopy (XPS), and low energy electron diffraction (LEED). The initial heat of adsorption of nickel atoms on stoichiometric ceria was ~45 kJ/mol greater at 300 K than at 100 K and ~65 kJ/mol greater than reduced ceria at 300 K. The calorimetry results indicate that nickel prefers step edges over terraces and binds stronger to stoichiometric ceria than reduced ceria due to nickel's oxophilicity. LEIS growth mode measurements indicate that nickel grows as 3D nanoparticles. XPS charge transfer experiments show that adsorbed nickel transfers electron charge to ceria below a coverage of 2 monolayers. These results encourage additional study of the adsorption energetics of other group 8 transition metals on ceria supports.

The life history traits of parasites are dependent on the host environment and host immune response. Heligmosomoides bakeri, is an intestinal nematode parasite that infects laboratory mice (Mus musculus). This investigation used rapamycin, an immunosuppressant drug, in the diet of the host. Rapamycin is currently being considered as an over the counter drug to extend life expectancy. The purpose of this experiment was to determine if inhibition of the host immune system by rapamycin had a significant effect on parasite life history traits during a secondary infection. Mice were fed either a rapamycin diet or control diet for two months. Mice were then infected with H. bakeri, drug cleared of the primary infection, then re-infected with a secondary H. bakeri infection. Starting eight days after the secondary infection fecal egg counts were done daily to determine worm reproduction in vivo. Eighteen days after the secondary infection the mice were euthanized and worms were removed, sexed and counted. Length of ten female and ten male worms from each mouse was then measured, and 10 females were cultured to measure ex vivo reproduction. After 24 hours of incubation in culture media, egg output and worm motility (an index of viability) were measured. For this experiment I was involved in recording the worm length and was responsible for performing the ex vivo egg count and motility measurements. Results will provide important information about potential over-the-counter use of rapamycin in humans to slow biological aging and how changes in immune function may affect susceptibility to parasite infection.

Obesity is associated with 2-3-fold increased risk of hypertensive disorders of pregnancy and 3-4-fold increased risk of gestational diabetes compared to a normal weight cohort. While obesity is a leading attributable risk factor for hypertension and diabetes during pregnancy, approximately 70%-80% of women identified as obese, based on a BMI, will not experience either disease process, suggesting limited predictability of BMI alone. The purpose of our MEDPREG study is a pilot and feasibility study with the objective to properly differentiate and accurately identify women at risk for metabolic dysfunction in pregnancy. To do this, we are evaluating two physiological processes- a central one that regulates body weight and a peripheral one that evaluates the role of body composition. The first process, known as MBH gliosis, focuses on the presence of inflammation in the mediobasalregion of the hypothalamus which regulates energy homeostasis and influences body weight. The second process measures abdominal fat, specifically visceral and subcutaneous fat, that plays a role in metabolic dysfunction. We are recruiting and enrolling normal (n=5), overweight (n=5), and obese (n=5) women in the first trimester based on first trimester BMI. In the pre and postpartum analysis, we are analyzing the association hypothalamic gliosis/intraabdominal fat and our primary outcome- a composite of hypertensive disorders of pregnancy, glucose intolerance or abnormal fetal growth. We are doing this through methods such as ultrasound fat depth, bioimpedance analysis (BIA), and laboratory data to possibly identify more approachable biomarkers that are accurately reflective of visceral adiposity. Our future directions include 1) assessing the effect of maternal gliosis and visceral fat distribution on the fetus and neonate and 2) to ultimately create a multivariable prediction model that could accurately screen and identify women at risk for metabolic syndrome in pregnancy.

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.

Tuberculosis is a major infectious disease with approximately 2 billion people infected worldwide. With the emergence of multi-drug resistant tuberculosis (MDR-Tb), efforts to develop efficient treatments with fewer cytotoxic effects are currently under investigation. Dual host and pathogen directed therapeutics hold promise towards more effective treatments against tuberculosis (Tb) through mechanisms that enhance bacterial clearance and reduce tissue damage and immunopathology. We investigate RGFP966, a drug that modulates the host's immune defenses and directly reduces Mtb growth (a histone deacetylase 3 (HDAC3) inhibitor). The aim of my project is to characterize the effect of RGFP966 on Mtb growth. My hypothesis is that the antimicrobial effects of RGFP966 are specific to Mycobacterial species, and the bacterial target of RGFP966 is required for its survival. Within the experiential growth period, I treated Mycobacterium avium and M. Smegmatis in 7H9 broth with a range of RGFP966 concentrations (0.5 uM, 5 uM, and 50 uM) and incubated in culture tubes and 96-well plates for 3-7 days. Within designated time intervals, I analyzed levels of dose dependent inhibition using optical density, luminometry, and fluorometry methods. Current results through optical density and luminometry demonstrate that RGFP966 controls M. Avium growth in 7H9 broth with an MIC50 of approximately 5 uM. Fluorometry and optical density results indivate no restriction of M. smegmatis growth. Comparing these results to previous findings in our laboratory, where RGFP966 lacked effects against common gram-positive and gram-negative bacteria, indicates possible specificity of the antimicrobial effects of RGFP966 to Mycobacterial species. We will further examine the effects of RGFP966 against mycobacterial growth. A comprehensie understanding of its pathogen directed effects combined with its host directed effects hold promise as an adjunctive therapeutic against Tb infection. 

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.

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.

Age related immune decline may play a role in susceptibility to parasitic helminth infections among the octogenarian population. Few studies have examined very old age on susceptibility to helminth infections in people. Effects of age on host susceptibility using mouse models also has not been thoroughly studied for older ages of laboratory mice (Mus musculus), such as beyond about one year. In this study, the intestinal nematode (Heligmosomoides bakeri), a model for hookworm infection in humans, was used to infect 1-year-old and 2-year-old Swiss Webster mice. At 40 days post-infection, worms were removed and worm survival, sex ratio, ex vivo egg output, and worm length (as an index of growth) were measured and analyzed. I expect to find an increase in worm survival, ex-vivo egg output, and worm length in older mice. These results will be valuable because they will model the helminths capacity to proliferate in older hosts in comparison to younger hosts during a human hookworm infection.

Washington State Forest Practice Rules require wider riparian buffer zones adjacent to streams that support fish versus those that do not. Consequently, verification of fish presence in streams is an important pre-timber harvest requirement of landowners. These determinations are made by professional biologists using single pass electrofishing protocols prescribed in state policy. The protocol stipulates that fish are presumed absent if no fish are found after sampling 1,320 feet beyond the last detected fish. What confidence should be placed in this level of effort? To better characterize the confidence in last fish detections, we implement a Bayesian hierarchical model, using distance to first fish as a measure of sampling effort, to estimate the distribution required to find fish using single pass electrofishing methods. We use the model output to determine the distribution of 99th percentile distances for first fish detections given fish are present in the stream. Further, the distribution of 99th percentile distances can be used to establish confidence in the boundary between fish presence and absence for single pass electrofishing surveys. Other percentile distances could be selected by policy makers to describe desired confidence levels. The model was developed using distances to first fish detections collected on 108 randomly selected streams from western Washington. Ancillary data included the length of the first detected fish, wetted and active channel widths, and stream gradients.

The growing opioid use epidemic in the United States affects all aspects of the population, including pregnant women. The fetus may have chronic exposure to opioids from the pregnant woman’s substance use or from addiction treatment with legally prescribed opioids such as methadone or buprenorphine. These fetuses are likely to go through withdrawal after birth when the supply of opioids from placental transfer is removed. This withdrawal is called neonatal abstinence syndrome (NAS) and often leads to prolonged hospitalization to treat the symptoms of withdrawal, including irritability, feeding intolerance and poor sleep. Studies have found that the mothers of these infants often feel judged by the nurses caring for their infants and they are unable to build a trusting therapeutic relationship due to stigma. Nursing curricula have limited content on substance use disorder; this leaves nursing students and future nurses unprepared to care for childbearing families affected by opioid use disorder. The purpose of the study is to explore the knowledge, attitudes, and beliefs of undergraduate nursing students about opioid use disorder in pregnancy and NAS. We will conduct an anonymous online survey to explore students’ perceptions of caring for mothers and infants affected by NAS. We will also examine student characteristics (demographics, personal or professional exposure to substance use) that may predict stigmatizing attitudes. Findings will inform development of educational materials and programs that can better prepare future nurses to care for this population. These educational tools may address stigma towards opioid use disorder, best practices in caring for infants with NAS, and promoting mothers’ engagement in the care for their infants while hospitalized.

The engineering of cells to be capable of detecting and responding to multiple input signals has major applications in the area of diagnostics, cancer therapy and biological computation. Current biological signal processing methods rely on single input single output computations. This proves ineffective when detecting and responding to multiple inputs such as determining a pathology based on combinations of different microscopic cues. The aim is to build non-linear computation in S.cerevisiae (baker yeast). A well-known example of nonlinear computation is neural networks, a complex framework of parallel computations talking together to come to a common output signal. The goal is to build several yeast strains that work together to perform these parallel computations. Each individual strain would process multiple inputs and release a singular output signal to another yeast strain. Combining many strains together would create a complex decision tree capable of higher-order computation. With this goal in mind, we decided to edit the native alpha-factor pathway within the yeast cells. Alpha-factor, a signaling molecule involved in yeast mating, is secreted by yeast and detected with surface protein STE2 (a protein in the GPCR family). We also inserted, a non-native version of STE2 from C.albicans yeast cells. This allowed our engineered strains to detect two different alpha-factor inputs (S. cerevisiae alpha-factor and C.albicans alpha-factor). When detected both alpha-factors trigger the pFUS1-yeGFP pathway causing the yeast cells to fluoresce. We investigated how different concentrations of STE2 and C.A.STE2 on the cell surface influenced the output fluorescents of the yeast strain. Mathematical models were used to interpret the data and predict signal response. These models can be used to design and predict more complex networks.

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. 

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.

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.

Music, like language, is considered a human universal. However, like language, individuals learn particular genres of music based on their cultural exposure. Recent behavioral and neuroimaging research on music cognition has shown that individuals can more easily process and remember music that is culturally familiar to them than music that is culturally novel. The goal of this research is to investigate whether individual differences in the ability to learn novel musical structures (or music aptitude) relates to individual differences in the ability to learn new languages, or language aptitude. Our study includes 5 minute eyes-closed resting-state electroencephalography (EEG), language aptitude tests (LLAMA D&F) of phonological awareness (tests participants’ memory of a series of words in a foreign language) and grammatical inferencing (ability to extract underlying rules), and a music learning test in which participants learn a form of foreign music. We predict that phonological awareness will positively correlate with overall memory for foreign music, as it relates to the ability to remember sequences of sounds. In contrast, we predict that grammatical inferencing will positively correlate with the extent to which individuals learn to distinguish between different types of foreign music through statistical learning. This study provides evidence of the connection of individual differences in foreign music comprehension to individual differences in second language acquisition at both a behavioral and neurological level.

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.

The global network of nature reserves are intended to be refuges for wildlife species around the world. However, nature reserves are experiencing increasing amounts of human visitation each year, and it is critical to investigate how this influx in disturbance is influencing the space use, abundance, and richness of wildlife species in those reserves. We used camera trap data collected at La Selva Biological Station in Costa Rica, to understand how the presence of humans and other environmental factors are influencing the presence and distribution of various wildlife species. We deployed 9 cameras, in three blocks, on 9 different trails and accumulated 208 active camera nights in 2018. A total of 9,692 photos were obtained of 17 different animal species. We hypothesize that the occupancy rate of species will be primarily influenced by human presence on trails within the reserve. The most commonly detected species were Collared Peccaries (Pecari tajacu) with 0.837 average detections per day, Central American Agoutis (Dasyprocta punctata) with 0.409 average detections per day, and Great Curassows (Crax rubra) with 0.173 average detections per day across all camera sites. Collared Peccaries had a 72% diel activity overlap with humans, Central American Agoutis had a 66% overlap, and Great Curassows had a 78% overlap. I will use the package “unmarked” in the program R to determine the influence of humans on species occupancy and richness. These results will help inform managers at La Selva Biological Station on how to best limit the impacts of human visitation on wildlife species.

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.

Ankle range of motion (ROM) is frequently measured in clinical settings for the purpose of diagnosing and treating foot and ankle pathologies. Gastrocnemius equinus (GE), a condition in which isolated gastrocnemius contracture inhibits ankle ROM, contributing to foot pain in otherwise neurologically healthy individuals. Controversy surrounds the definition of GE, however, and the reliability of goniometer-based measurements of dorsiflexion—and consequently identification of gastrocnemius contracture—is untested. This study examines the reliability of using a goniometer to measure ankle dorsiflexion. Two observers (KR and CG) measured ankle dorsiflexion in 14 neurologically healthy individuals (6M/8F; ages 20-56 years; 6 participants measured by both observers) with the knee in fully-extended and flexed positions. Three measurements were taken for each position with the goniometer fulcrum on the lateral malleolus; stationary and moving arms aligned with the fibular head and fifth metatarsal, respectively. Inter- and intra-observer reliability was assessed using Cronbach’s alpha. Intra-observer Cronbach’s alpha was 0.230 (CG) and 0.533 (KR) for dorsiflexion with the knee extended, and 0.805 (CG) and -0.350 (KR) for dorsiflexion with the knee flexed. Inter-observer Cronbach’s alpha was 0.656 for extension and -0.245 for flexion. Little correlation exists within or between observers for goniometer-based ankle dorsiflexion measurements in either a flexed-knee or extended-knee position. The clinically-accepted practice of using a goniometer to determine ankle ROM, and consequently to diagnose and treat GE, may be unreliable and needs further evaluation.

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.

ovine Leukemia Virus (BLV) is a disease that affects US beef herds and large-scale dairy herds. A recent studied found correlations to the presence of BLV particles and human breast cancers. Although no actual retroviral insertion (zoonosis) was found in tissue samples, this raises concerns about BLV consumption in from infected dairy samples. To investigate this phenomenon, the prevalence of BLV from raw dairy milk samples will be analyzed. Western blotting will be used to look for the major reactionary viral glycoproteins, gp51 and gp24. Controls were designed for blotting to subclone the coding region of gp51 or gp24 into bacterial expression vectors from a plasmid containing the entire bovine viral genome. Subcloning and quality assays were confirmed first by restriction digestions, PCR then also will be sent for sequencing. The expressed glycoproteins along with infected cell culture samples will then be used in blotting procedures as positive controls while analyzing raw milk samples collected from farms.

In the last 30 years temperature has risen 0.6°C per decade in high latitude regions, twice as fast as the global average. This extreme warming is causing perennially frozen ground (permafrost) to thaw, thereby changing subsurface hydrology and exposing previously stored, deep millenial-aged soils to microbial activity. These changes are stimulating greater organic matter mineralization and emissions of potent greenhouse gases (GHG), carbon dioxide and methane (CO₂ and CH₄). The magnitude of soil carbon mobilization is poorly contained, in part because it is unclear what fraction of GHGs are emitted to the atmosphere directly, versus released to above ground aquatic networks. To better define the role of streams in the changing arctic carbon cycle, we explored headwater stream carbon chemistry in 10 individual catchments situated in a remote and understudied subarctic landscape of interior Alaska. We found an unexpected, positive relationship between CO₂ and CH₄ across streams, with concentrations peaking in the summer for CO₂, and fall for CH₄, suggesting stream emissions peaked when soil active layers were deepest and permafrost carbon layers were most hydrologically engaged. The positive relationship between surface water temperatures and the concentration of each gas reflected these strong seasonal shifts in stream GHG content. Organic carbon content in stream water was also linked to CO₂ but not CH₄, indicating potential differences in sources and sinks of each GHG that are currently being explored with ongoing stable isotope analyses. Taken together, our findings show that closer-than-expected coupling of CO₂ and CH₄ may make some streams much greater emissions hot-spots than others, and that accounting for seasonality is critical for understanding the greenhouse gas budget of individual streams. 

Plants take up silica over the course of their lives along with other essential nutrients in the water that they absorb through their roots. The silica becomes deposited within their tissues in the form of solid bodies (phytoliths); when the plant dies and decays, phytoliths are left in the soil where they can fossilize. Fossil phytoliths preserve the original morphology of plant cells and can be used to reconstruct past vegetation. The Middle Miocene Climatic Optimum (MMCO) was a major global warming event that happened ~17-14.5 million years ago. Researcher have reconstructed the climate of the Santa Cruz Formation in Patagonia, Argentina during this period as warmer and drier. While we would expect the vegetation to become more open (i.e., grassy or shrubby versus forested), phytoliths from the Santa Cruz Formation tell a different story; in particular grass phytoliths (and therefore grass abundance) seem to decrease through time, but also become smaller. Some researchers have noticed that grasses tend to respond to reduced water availability with reduced cell size. Therefore, we hypothesize that the reduced size of grass phytoliths observed in the Santa Cruz Formation during the MMCO is due to increasing aridity. However, because this trend of decreasing cell size was only noticed by qualitative observation, we need to quantitatively assess significant changes in cell size. To do so, I studied and imaged grass phytoliths under a microscope, categorized them by subfamily/tribe based on their shape, and measured their size. I then statistically compared the phytoliths from younger and older strata to test whether there was a change in size through time. This work will be used to predict how our current global warming event may impact plant life based on the trends of the past.

Recent studies like the Coupled Model Intercomparison Project Phase 5, or CMIP5, have sought to quantify how atmospheric variables will change due to climate change. Even from decades of rigorous study, it is still uncertain how cloud feedbacks will respond to a warming climate. However, it is possible to try and minimize this uncertainty in part by examining deep convection, and specifically anvil clouds, in the Tropical Pacific. Anvil clouds are not simulated well by the current generation of climate models, but by studying both large scale motions and small scale, local cloud structural evolution, Professor Hartmann and I seek in this study to determine the underlying mechanisms of the differences in vertical cloud structure in the Eastern and Western Pacific. I use the ERA-Interim, CloudSat, Calipso, and CMIP5 datasets in addition to climate model output from the Community Earth System Model (CESM) to analyze differences in cloud structure and model output. This is important work, because reducing uncertainty in an era of global warming can mean better advanced warning systems and more informed, ethical policy decisions moving forward.

The northern circumpolar landscape holds nearly twice as much carbon as the atmosphere, mostly as organic matter in perennially frozen (permafrost) circumpolar soils. Climatic warming may cause increased greenhouse gas emissions from arctic landscapes linked to thawing and mobilization of stored permafrost carbon. The role of circumpolar lakes in such climate-carbon feedbacks may be important, since lakes cover a disproportionately large fraction of the northern landscape, and emit carbon dioxide (CO2) and methane (CH4) to the atmosphere due to inputs of land-derived organic material. Yet northern lake carbon emissions are poorly characterized due to factors including limited sampling access and restricted sampling during prolonged inclement weather (winter and shoulder seasons). Here, we set out to define the environmental features most related to greenhouse gas build up in thirteen interior Alaskan lakes during winter ice cover, thereby providing information to better model lake emissions and identify hotspots across the regional landscape. We found that lakes with elevated CO2 tended to have elevated CH4 (with one exception), and that these patterns were predicted throughout the study region by variables that characterized the surrounding landscape, lake morphometry, and chemical properties of the lake. Shallow lakes at low elevation had the greatest concentrations of both gases, and also had the greatest quantities of organic matter readily available to fuel greenhouse gas production. Methane was mostly restricted to hypoxic conditions; whereas CO2 was found in both oxic and hypoxic conditions inversely proportional to oxygen. Given the limited information available for northern lakes during winter, this survey provides key information to advance our understanding of the patterns and factors related to winter greenhouse gas buildup in lakes, currently a major unknown in arctic carbon research.

Suspended sediment in the bottom boundary layer impacts both ecosystems and geomorphology. High concentrations of suspended sediment affect light attenuation, harming benthic plants, and sediment resuspension and transport can affect the distribution and size of sediment on the seafloor. The purpose of this project was to determine the variations and controls on suspended sediment in the Elwha River nearshore region and to find relationships between bed shear velocity and suspended sediment concentration. The 2011 Elwha River dam removal released a large pulse of sediment, giving us the opportunity to study a coastal environment with fine sediment deposits, and varying hydrodynamic conditions. Data collection measured near-bed turbidity and wave conditions, and sediment grab samples were collected to characterize bed conditions. Harmonic tidal analysis was used to predict tidal current velocity. Over the sampling period, on the east side of the river mouth, currents ranging from ~0 to 100 cm/s and wave heights up to 1.0 m were sufficient to resuspend sediment. Suspended sediment concentrations generally ranged from 1.5 to 25 mg/L. In Freshwater Bay, currents ranging from ~0 to 31 cm/s and wave heights up to 0.86 m were not sufficient to resuspend sediment. Instead, fine sediment settled out of the water column, resulting in near-bed sediment concentrations generally ranging from 1 mg/L to 101 mg/L. These findings show how variable the processes controlling sediment in suspension can be in a tidal environment with complex morphology.

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.

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. 

Located in the Whidbey Basin of the northern reaches of Puget Sound, Possession Sound contains the Snohomish River estuary, encompassing a river system that is the third largest contributor of freshwater to the Puget Sound. Myself, and several of my fellow students have had the opportunity to collaborate with the University of Washington, the Washington State Department of Ecology, and a local environmental consultant -- Gravity Marine. Utilizing data collected by permanently moored Sea-Bird CTD probes, during research cruises, and by the United States Geological Survey (USGS), my research partner and I have created a model to facilitate an investigation of how both tides and the discharge of freshwater from the Snohomish River influence the water quality of Possession Sound. To better understand the complex patterns of the water entering Possession Sound from the Snohomish River, we analyzed the relationship between a continuous stream of water quality data (temperature, salinity and turbidity) from a Sea-Bird CTD probe at the mouth of the Snohomish River and continuous discharge data gathered by the USGS at a station 12 miles up the river. The distance between these two sites results in a delay between when river discharge data is recorded up river and when it influences the water quality at the river mouth. From the analysis of these two locations and with guidance from ourcollaborators as well as outside professionals, we used the statistical analysis language R to create a model that predicts the travel time of water from the USGS stream gage to Possession Sound. This model can be applied when considering the effect on the estuary of important factors from the river, such as nutrient loading; influxes of cold water, which promotes upwelling; and the river’s contribution of heavy metals and other pollutants.

In Possession Sound, a salt wedge estuary in the Whidbey Basin in Northwest Washington State, interactions between the saltwater of Puget Sound and the freshwater of the Snohomish River create a dynamic environment. Students from the Ocean Research College Academy deployed two Sea-Bird Conductivity-Temperature-Depth (CTD) probes within the estuary to monitor water chemistry in this complex system. A grant from the National Science Foundation supported eleven students to analyze water chemistry data from summer 2018 to increase their understanding of biogeochemical processes in the estuary and communicate their knowledge to the general public. Data from the month of May were analyzed to investigate the river’s influence on the temperature and salinity. Lower levels of salinity correlated with peaks in freshwater input as indicated by river discharge data. Salinity also correlated with tide height. To further investigate the spatial influence of the Snohomish River on Possession Sound, this study endeavored to manufacture a Fast Oceanographic Automated Measurement (FOAM) sampler in collaboration with Gravity Consulting. This device uptakes surface water and pumps it over an EXO 2 Sonde to measure surface water chemistry while traveling on a research vessel, associating data with GPS points, to track the freshwater plume. Salinity was used to examine the relationship between the spatial extent of the plume, river discharge, and tidal patterns, and temperature and pH was analyzed to explore the influence of the river. Lower salinity levels were used as indicators of higher freshwater influence. During periods of high river discharge, average salinity values will be lower and the freshwater influence will cover a larger area. During high tides, higher average salinity values are expected and there will be smaller areas of freshwater influence. It is hypothesized that areas of higher river influence will be warmer and more acidic than areas of increased saltwater influence.

Recent studies have shown just how important microbiomes are for individual health, population health, and environmental health. Unfortunately, these studies are often limited by the costs of meta-Genomics. Furthermore, meta-Genomic data itself is limiting by only providing information on population characteristics, but not the functional contributions of members within the population. Single cell transcriptomic sequencing aims to lessen the latter issue by providing information on the gene expression of each individual cell within a sample. Even so, current single cell sequencing technologies are costly and require specialized equipment. SPLiT-seq is a single cell transcriptomic technology developed by the Seelig lab at the University of Washington that uses split-pool ligation to create uniquely barcoded cDNA for each cell using every-day laboratory bench tools and techniques and costs only one cent per cell. Currently, SPLiT-seq is well-optimized for mammalian cells. However, using this method on bacteria requires its own set of optimized procedures given the morphological and biochemical differences between eukaryotes and prokaryotes. The aims of this project are to deal with these biological differences to increase the information obtained from messenger RNA and decrease the amount received from ribosomal RNA, as well as reduce the amount of cells that get the same cDNA barcodes. By optimizing this single-cell transcriptomic technique for bacteria, future studies involving microbial communities will be able to obtain more robust information on the individuals within those populations.

Genes encoding the RNA portion of the ribosome (rDNA) are present in essentially all eukaryotic genomes as tandem repeated arrays. In humans, rDNA copy number is highly variable and an undervalued potential source of genetic disease. Changes in rDNA copy number can occur through DNA breakage and repair as well as through errors in DNA replication. High transcriptional activity at the rDNA locus poses challenges for replication; all tested eukaryotes have evolved replication fork barriers (RFBs), ensuring that replication machinery does not collide with transcribing RNA polymerases. In yeast, the RFB is a specific sequence to which the protein Fob1 binds, blocking replication forks that converge with transcription. Mutants lacking Fob1 have greatly reduced variation in rDNA copy number. There are currently two models to explain how Fob1 binding to the RFB produces rDNA copy number instability. One model suggests that binding of Fob1 actively recruits DNA break and repair machinery which induces recombination between rDNA repeats. Another model proposes that the stalled replication fork at the RFB is inherently fragile, increasing the likelihood of breakage. To distinguish between these two models, I am generating yeast strains where Fob1 binds to the RFB but does not arrest forks. Using CRISPR/Cas9 gene editing technology, I am reversing the direction of the RFB in each of the 150 rDNA repeats in yeast to prevent replication fork stalling. By confirming the absence of replication fork stalling and determining whether rDNA instability has also been reduced, I can distinguish whether Fob1 binding to the RFB in the absence of fork blocking contributes to rDNA copy number changes. Clarifying involvement of the RFB in rDNA copy number changes will additionally provide insights into the connections between transcriptional activity, replication fork stalling and genome instability.
 

In order for multipotent stem cells to properly differentiate into specialized cells, specific genes must be expressed at a specific time and amount during development. Many of the factors that regulate expression have been identified; however, it remains unclear how they work together to control the timing and amplitude of gene expression. Non-coding DNA elements, known as enhancers, can increase the the likelihood of transcription of a gene by integrating signals in the cell to provide regulatory logic for gene regulation. To understand how enhancers tune gene expression timing and amplitude during development, our lab has generated a transgenic mouse in which each of the two copies of the T-cell identity gene, Bcl11b, have been tagged with distinguishable fluorescent reporters, providing a sensitive readout for gene activity at the single locus level. Bcl11b turns on during T-cell development, and its activation executes a developmental switch from a hematopoietic stem cell to a T-cell committed progenitor. There is a non-coding region far downstream of Bcl11b which harbors a cluster of putative enhancers. To interrogate the function of individual candidate enhancers, we use CRISPR/Cas9 targeting to generate specific genomic deletions in T cell progenitors. From our preliminary experiments, we have shown that cutting off the entire enhancer region completely inhibits the expression of Bcl11b entirely compared to when we cut out only an individual enhancer peak which only partially inhibits it. This is promising because it shows that we have found an enhancer that controls the probability of activation while not being necessary for the activation of Bcl11b. This work will reveal the cis-regulatory logic that underlies the control of a master lineage-specifying gene. This better understanding will help us identify new strategies to control the expression of master regulatory genes for cellular reprogramming.

During embryonic development, a dormancy-like state known as diapause arises during the transition from pre to post implantation. This state of suspended development is a reproductive strategy which favors newborn survival in mammals during nutritional deprivation or stress. Studies from the Ruohola-Baker lab found potential candidate regulators of diapause by establishing an in-vitro diapause model using pluripotent mouse embryonic stem cells (mESC). One of the genes is Activating Transcription Factor 5 (ATF5) which encodes a protein capable of survival-mediated functions such as maintaining mitochondrial activity during stress, modulating cell differentiation, preventing apoptosis and regulating cancer pathway. ATF5 has been known to transcriptionally target mTOR, a mechanistic target of rapamycin. Energy stress in the form of starvation and pharmacological inhibition of mTOR has shown to induce diapause-like state in mESCs in vitro. Our hypothesis is that upregulation of ATF5 under energy stress will reestablish diapause-like state in naïve mouse embryonic stem cells in vitro. We will test our hypothesis by loss-of-function and overexpression experiments. We test if ATF5 gene knockout using CRISPR-Cas9 prevents the mutant lines from entering diapause-like state from energy stress. Using western blots, we will quantify phospho-mTOR levels and its downstream targets in the ATF5 KO lines and compare them with the wildtype lines. For the overexpression of ATF5, we will make rescue lines for the ATF5 KO cells. We predict that overexpressed ATF5 in rescue lines will enter diapause-like state, and have reduced mTOR and its downstream target signals compared to KO lines. Our discoveries of ATF5 function in diapause can be useful in understanding how early-staged cancer stem cells enter a diapause-like state or quiescent state which enables them to escape chemotherapy detection. We can potentially contribute to the development of therapies to target ATF5 mechanism so that these undetected cancer stem cells can be detected.

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.

Hybrid vigor or heterosis describes superiority of a hybrid compared to its parents; however, the genetic mechanisms underlying this phenotype remain largely unresolved. One potential mechanism is loss of heterozygosity (LOH), a process where there is loss of one copy of a gene or surrounding chromosomal region. In our previous work, we evolved hybrids between two species of yeast, Saccharomyces cerevisiae and Saccharomyces uvarum - which differ in their temperature preference - by growing them in a chemostat at different temperatures in phosphate limited media for several hundred generations. We repeatedly observed LOH events in these hybrids in response to changes in temperature. Each LOH event incorporated the gene region encoding the Pho84 membrane bound inorganic phosphate transporter protein on chromosome 13, which is important when phosphate is limited in the environment. These repeated LOH events all affect fitness based on environmental temperature; however the events span various lengths with some as short as a few kilobases and others as large as 200 kilobases. Because they are different in length we also know that they include different numbers of genes. To investigate whether these varying LOH lengths may include other genes that affect hybrid fitness, we have used CRISPR/Cas9 to create double strand breaks at specific sites along the S. cerevisiae chromosome 13, resulting in DNA repair using the S. uvarum chromosome as a template and formation of LOH events of different lengths. Our aim is to create a pool of hybrids with varying LOH tracts and let them compete in a phosphate limited environment to assess the relationship between the different LOH regions and fitness. This will allow us to narrow down genes that may be responsible for temperature sensitivity or that contribute to higher hybrid fitness in organisms that are heterozygous or homozygous.

Different phenotypes of normal cells may influence genetic and epigenetic profiles and tumorigenicities of their transformed cells. The current study presents a comprehensive analysis of mutations in the whole mitochondrial genome for different immortalized (pre-neoplastic) cell types, which were derived from normal breast epithelial cells with two different phenotypes (stem vs non-stem). Duplex Sequencing, which shows the lowest error rates among currently available DNA sequencing methods, was applied to investigate rare and subclonal (low-frequency) mutations as well as homoplasmic (high-frequency) mutations. We found that the vast majority of mutations in the cells occur at low-frequency and are not detectable by conventional DNA sequencing methods. The most prevalent mutation types are C>T/G>A and A>G/T>C transitions. The overall frequencies of rare and subclonal mutations are significantly lower in stem cell-derived immortalized human breast epithelial cells (SV1) than in non-stem cell-derived immortalized human breast epithelial cells (SV22). The decreased mitochondrial mutagenesis of SV1 cells occurred mainly in the noncoding RNA region (rRNA and tRNA) of the mitochondrial genome. In addition, the predicted pathogenicity for rare and subclonal mutations in the tRNA region was significantly lower in SV1 cells than in SV22 cells. Our findings suggest that different phenotypes of normal cells lead to distinctive mitochondrial mutation profiles of immortalized cells. The identified mutation spectra and mutations specific to stem (versus non-stem)-derived immortalized cells have implications in characterizing heterogeneity of tumors and understanding the role of mitochondrial mutations in immortalization and transformation of human cells.

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.

Amyloid diseases are characterized by the aggregation and buildup of proteins in vital tissues and organs. Insoluble β-sheet amyloid fibrils were previously thought to be the major underlying cause of tissue degeneration and cell death. However, recent experimental evidence suggests that soluble oligomers, which form during protein aggregation and before polymerization into fibrils, are the principal cause of toxicity in mammalian cells. These toxic oligomeric protein assemblies are believed to share a common sequence-independent secondary protein backbone structure known as α-sheet. This project proposes the investigation of a synthetic peptide known as AP3 that is capable of forming toxic oligomers and β-sheet amyloid fibrils. This peptide was de novo designed with a completely randomized sequence which preserves the underlying chirality that produces α-sheet character leading to its exhibition of amyloidogenic properties under acidic conditions. Furthermore, AP3 aggregation was shown to be inhibited by three naturally occuring amyloid proteins implicated in their respective dieseases: Amyloid Beta (Alzheimer’s), IAPP (Type II Diabetes), and Transthyretin (Cardiac Amyloidosis). Analysis using dot-blot assays, soluble oligomer binding assays (SOBA), and BLITz assays will provide additional insight into the behavioral, binding, and kinetic properties of AP3. Upon further evaluation, we aim to demonstrate the ability of AP3 to serve as a synthetic model for naturally occuring amyloids and provide a better understanding of amyloidogenesis as well as the interactions between amyloidogenic species. This research will prove useful in the creation of more effective amyloid inhibitors and treatments for amyloid diseases.

While there is an abundance of computational tools for protein design, the vast majority of them focus on static structures. Data for the most probable rotamers of an amino acid are often obtained from mining its appearances across crystal structures, which do not take into account the native dynamics or conditions of a protein. Additionally, conformational secondary structure propensities are often derived from the frequency that an amino acid appears within a certain range of dihedral backbone angles in static structures. However, these data do not emulate realistic conditions, because proteins are dynamic and surrounded by solvent; thus, incorporation of dynamic data should improve the design process. Wrangler, our in-house software for peptide design, integrates dynamic data for both rotamers and secondary structure propensities. The data are obtained from molecular dynamics (MD) simulations in explicit water, taking into account interactions with surrounding solvent to better sample the most probable conformations. Several amyloid peptide aggregation inhibitors were designed using Wrangler’s scoring metrics to validate the software. These inhibitors were shown via MD simulations to better retain secondary structure than our current standards. Future work involves synthesizing the peptides in the wet lab to determine whether they experimentally perform better than our current inhibitors.

Since 1982, with the introduction of insulin as the first recombinant protein therapeutic, peptide and protein drugs have grown to encompass 10% of the pharmaceutical market and are the fastest expanding class of drugs. Advantages of using peptides over small-molecule drugs include high potency, selectivity, and capability to be engineered for a diverse range of targets, most commonly to disrupt or facilitate key protein-protein interactions (PPIs) in the human body for a therapeutic effect. To search for strong binders for a therapeutic target, combinatorial peptide libraries of up to billions of different sequences are synthesized and screened against promising targets. Due to the enormous library size, screening for high affinity binders often requires multiple rounds of enrichment in order to isolate the most potent molecules, a laborious and potentially bottlenecking step in developing protein drugs. Current approaches that have strategies for enrichment, such as phage display and yeast surface display, are limited to screening a library of binders against one target instead of multiple targets (library-on-library). This proposal describes the development of a peptide binder screen utilizing a simple workflow of repeated mating and sporulation of genetically engineered S. cerevisiae, or baker’s yeast. This technology improves the throughput of established screening methods through a library-on-library format that efficiently isolates high-affinity peptide binding interactions.

The Genetically Engineered Materials Science and Engineering Center (GEMSEC) labs revolve around designing and synthesizing genetically engineered peptides for inorganic materials (GEPIs). Experimentally characterizing GEPIs can be slow, and therefore a computational method that can predict functionalities would greatly accelerate the development of bio/inorganic interface design and implementations. The Pairwise Similarity Score is a proven predictor of relative binding affinity and has been used to predict GEPIs specific for quartz, gold, hydroxyapatite, and MoS2. In previous work, a similarity matrix was updated based on whether a peptide (Strong or Weak binding) had higher similarity to strong peptides and less similarity with weak peptides. Our method instead obtains the most ideal similarity matrix via stochastic gradient descent to best predict the relative binding affinities. The values in an amino-acid similarity matrix are randomly initialized and subsequently updated until convergence by minimizing the errors in binding affinity prediction. 5-fold cross-validation is used as a metric to evaluate performance on test data. We expect to observe higher predictability with this learned similarity matrix than using a literature matrix. This would compound work done by the high throughput screening, confirming count numbers observed during phage display are correlated with their actual binding affinity, while using a novel large dataset to test known successful predictive models. All in all, the work carried out in this project accelerates the development pace of bio-nano-devices of the future. The research is supported by NSF/DMR-DMREF program under the Materials Genome Initiative.

Our laboratory, GEMSEC, which operates at the intersections of biology-materials-informatics fields, is developing materials and methods to seamlessly bridge biology with solid-state devices towards establishing the foundations of future hybrid devices, e.g., bioelectronics, bionanosensors, and biomolecular fuel cells. Towards this goal, we use the smallest functional biomolecule, peptide, combined with the smallest functional solid in materials science, i.e., single atomic layer materials. Herein, we study the interactions of genetically designed peptides with surfaces of graphene, a semimetal. A phage display library-selected peptide, GrBP5, is a graphene-binding dodecapeptide that has a wide range of applications. Since peptides have short amino acid sequences, they are known to display intrinsically disordered structures in solution. Here we study the conformational propensities of the WT peptide and its rationally designed mutants under a variety of experimental conditions (pH, concentration, temperature, time, etc.) to understand their behavior on solid surfaces that includes surface phenomena from binding, surface diffusion, intermolecular interaction and self-organization. Molecular dynamics (MD) simulations of WT-GrBP5 and its mutants have been completed in water and on graphene for 200ns, 20,000 timeframes under different temperatures and pH values that range from 5 to 55 oC and 3.5 to 10.0, respectively. The analyses, including the RMSD maps and Ramachandran plots, show explicit folding propensities, stable and unstable structures, for a given sequence under a given set of experimental conditions. The computational modeling, backed up by experimental validations carried out under similar conditions, are leading to the design of novel peptide sequences with predictable behavior under desired environmental conditions. The fundamental understanding of the differences in conformational behavior of GrBP5 mutants are now extended to other solid-binding peptides that are specific to semiconductor and insulator single layer materials providing the much essential information for the design of hybrid devices of the future. The research supported by NSF/DMR-DMREF program.

The goal of this project is to encode peptides, i.e., short amino acid sequences, in terms of smaller molecular components such as their VSEPR (Valence Shell Electron Pair Repulsion) features for training interpretable models with reasonable predictability of functionality. This enables us to go beyond the limitations imposed by treating peptides as sequences of letters, thereby enabling a generalized encoding that works for lipids and other biomolecules that are of interest in a comparable scenario. Biological processes are rarely disjoint and often complicated which lends justification to our approach. Current methods for binding affinity prediction, such as one-hot encoding, where letter-based sequences are converted to a binary representation, do not take into account molecular level features. Combined with a neural network, such a simple encoding is better at predicting affinities of short peptides, e.g., 5-9 Amino acids long, but with an increase in length from 9 to 10, the predictability suffers an exponential drop. Several alternatives have been employed in literature, but they also suffer from the negative impact of distal effects. In the VSEPR approach, encoding peptides in terms of their component functional-group geometries enables us to encode the actual physical length, rather than the number of amino acids. This leads to an overlap between peptides of different length, thereby reducing the fall in predictability. In this encoding, we create 5 channeled matrices with each channel corresponding to ‘central-atom connectivity’, ‘bond-types’, ‘bond-lengths’, ‘bond-angles’ and ‘lone-pairs’ that is then fed through a Deep Residual-Neural-Network. The metrics used to evaluate the models are Pearson-Correlation, Spearman-Rank-Correlation-Coefficient, and Area-under-Receiver-Operating-Curve. With this technique, we were able to consistently predict binding affinities of peptides without an appreciable loss between 9 or 10 length peptides. This method would allow one to create length invariant encodings, not limited to just peptides, significantly improving the practicality of using such a model. The research is supported by NSF/DMR-DMREF program under Materials Genome Initiative.