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.

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.

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.

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.

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.

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. 

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.

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.

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. 

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.

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.

 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.
 

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.

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 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.

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

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

A declassified 1962 document shows that the Kennedy Administration considered “Operation Northwoods,” a plan to fabricate a terror attack and blame it on the Cuban government in order to legitimize an invasion of Cuba. The Northwoods plan was rejected by President Kennedy. This tactic of faking an attack for political purposes is called a “false flag” attack. Modern conspiracy theorists use Operation Northwoods as evidence that the American government fakes terror attacks in the 21st century, considering attacks such as the September 11, 2001 attacks and the 2018 Parkland shooting to be “false flag” events. I engage with the Operation Northwoods document, detailing its contents and implications. I then analyze the impact of the document in the conspiracy fringe, looking at its reference in various new media spaces, such as the online conspiracy editorial InfoWars and the alt-right social media platform Gab. I find that the power of the Northwoods document is often overestimated and exaggerated on online spaces and that the conspiracy theorists use motivated reasoning to further their belief in conspiracy.  Online spaces allow for the spread of false conspiracy narratives by enabling people with fringe beliefs to connect with each other more effectively. The wide propagation of Northwoods as evidence that major contemporary tragedies are fraudulent is a supreme example of dangerous information which can be spread unchecked online.

Robotics combines machining and artificial intelligence to create real world humanoid models for task automation and industrial applications. We have designed an in-house robot prototype having microprocessor controlled motion. The robot has lasers for eyes and has a position sensor with camera attached. We designed the gear box, track assembly and robot parts and have written software to control the motion of the robot. The robot is good model for Roomba like vacuum cleaner. We create random walls using Monte Carlo simulations and used vector directed motion to control its motion for avoiding these random walls that the robot encounters to simulate real world experience. We have also studied robotic arm kinematics, using matrix algebra and trigonometry to help design a robot arm that we can rotate or translate to any point in three -dimensional space. We study both forward and reverse kinematics and have written software for the arm motion. Our studies provide an elegant educational platform for studies of robot motion along with simulating real-world experience.

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

The use of magnetic nano-knots and Brunnian links for data storage and communications, makes understanding the geometric and network topology of knots and links very important. Recent reports suggest that DNA and other halogen networks self-assemble into exotic Borromean ring molecular topologies. Borromean rings form a Brunnian link with three rings linked in such a way that no two alone are connected. Only when all the three rings come together does the linkage occur. Borromean links form the current logo of the International Mathematical Union and they display strength in unity. Understanding knots, links and their networking is central to our understanding of DNA, protein folding, polymers and other soft materials. We have used a 3D printer to print and design a Borromean Math puzzle. The puzzle falls apart when a link is pulled out and is an excellent learning tool for studying Borromean link topologies. We use mathematical methods using parametric equations to study Borromean rings and trefoil knots. We wrote computer visualization code using SAGE to display trefoil knots and complex Borromean links for distorted circular, elliptical and other geometries. The SIEFERT surface of Borromean links are sketched using SeifertView and provide an aesthetic 3D view of the rings which can be oriented on a plane. The Seifert surface of a knot is a knot invariant; it is the characteristic of the knot with the knot as a boundary. The adjacency matrix and topological connectivity of the links are studied using vector directed graph models. A computer program is written to unravel the complex linking and intriguing connectivity properties of the trefoil knot and Borromean networks.

Current data storage elements have reached their threshold capabilities due to extensive data and limiting size requirements. Digital storage in DNA has aroused considerable interest as the next generation miniaturized high capacity storage device. Deoxyribonucleic acid (DNA) forms the genetic blueprint of life and is the primary carrier of genetic information in living cells and organisms. Data storage in DNA involves encoding of digital binary data into synthesized DNA strands. Here, we employ calculus-based methods to provide a comparative study of data storage capacities of conventional CD ROM and DNA. We use parametric equations to model the spiral structure in CD ROM and double helix of DNA and employ calculus-based methods to study the arc length, curvature and topological properties of DNA. The data storage densities for binary, base 3 and base 4 in DNA are estimated. The calculated data storage densities are found to be in good agreement with reported estimates. Recent studies demonstrate that magnetic nano-knots can be used for data storage. The topological properties of DNA including twists, links and knots thus provide additional attributes which may in future be used for data storage.

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

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

The associations between toxic stress, adversity, and mental health are widely documented in public health, medicine, and social science research. Much of this work stems from the findings of the CDC-Kaiser Permanente Adverse Childhood Experiences (ACE) Study from the late 1990s. The results of this study showed that individuals who experienced significant childhood adversities and traumas were at a higher risk for depression and suicide attempts, health risk behaviors, and adult diseases such as cancer and heart disease (Felitti et al., 1998). This research has been invaluable in improving the health of populations who have faced such severe stress, but it is somewhat limited in that it does not acknowledge other aspects of health, such as immune function and frequency of acute illnesses. It also does not take into account adversity that occurs after childhood and adolescence. Recent studies demonstrate that toxic stress and adversity in different stages of the life-span can have negative effects on immune function. This indicates a need for more emphasis on the immune impacts of adversity in future health interventions and research, as well as a need for integration of trauma-informed practice into clinical settings. Although more research is needed to thoroughly establish the causal pathway between adversity and immune dysfunction, the studies discussed in this review demonstrate a strong correlation between these variables, thus providing justification for these interventions.

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

Due to antibacterial resistance and the high recurrence of urinary tract infections (UTIs), studies have shifted to focus on anti-adhesive therapies as alternative to antibiotics. Often treated with antibiotics, UTIs are caused by uropathogenic Escherichia coli (UPEC). The bacterial adhesin, FimH, found on the terminal end of fimbria, hair like structures expressed on the perimeter of UPEC, is the main etiological factor of UTI prevalence and recurrence. FimH increases the virulence factor of E. coli by mediating the initial binding of the bacteria to glycosylated cells in the urinary tract. FimH has two domains. The lectin domain (LD) recognizes and binds the terminal mannose on glycosylated cells lining the urinary tract, whereas the pilin domain acts as an anchor to the fimbria. Previous studies have shown that α-methyl-mannose (αMM) competitively inhibits glycoproteins, such as horseradish peroxidase (HRP), from the FimH active site. We hypothesize that αMM can non-competitively inhibit HRP through a novel mechanism of inhibition. To determine the mechanism of inhibition of HRP in the presence of αMM, we are using Enzyme Linked Immunosorbent Assays to measure the dissociation of HRP in the presence and absence of αMM, after the FimH-HRP complex has formed. We expect to see an increase in the dissociation of HRP in the presence of αMM. HRP in this case, will act as a model to the glycosylated cells lining the urinary tract. This study aims to assist in the design of innovative anti-adhesive therapies that inhibit binding of FimH once bound to glycosylated cells lining the urinary tract.

Modern cells discriminate among the amino acids chosen to be included in protein synthesis: some, like leucine, serine, glycine, and alanine appear in most proteins across most cells, whereas other amino acids, like (g)-aminobutyric acid and aminoisobutyric acid do not appear. This raises the question of how selectivity among amino acids arose – does the selectivity rely on modern protein machinery or could it have arisen in the first protocells of the Early Earth? For example, could certain amino acids have, by some mechanism, associated more strongly with protocell membranes, increasing their chances of being integrated into the first peptide chains? To test this hypothesis, our group assembles rudimentary protocells from molecules that would have been present on the early-Earth: decanoic acid (a fatty acid), sodium mono-phosphate, salt, and water. Vesicles of the decanoic acid spontaneously form. We then add different amino acids to the solutions and measure their turbidity to determine whether each amino acid causes the number of lamellae in the vesicles to increase or decrease. Increased lamellarity correlates with a sturdier vesicle. If certain amino acids increase lamellarity of protocells, that could serve as a method of selection for certain amino acids rather than others. Our results are that particular amino acids (most notably serine, glycine, and alanine) do in fact increase the lamellarity of fatty acid vesicles significantly, whereas other, less common, amino acids do not. We are currently exploring the plausibility of a mechanism for this occurrence involving ease of rotation around the alpha carbon of the amino acids, and we are investigating other ways in which interactions between amino acids and fatty acid membranes might be manifested, for example by a shift in the solution’s critical vesicle concentration. Our results will fit into the overarching goal of understanding peptide formation and protocell stability in order to gain insight into the origins of life on Earth.

Long non-coding (lnc)RNAs have multiple biological functions, including recruitment of kinases to regulate signaling pathways involved in tumorigenesis and other human diseases. Of particular interest is the proposed interaction between Long Intergenic Noncoding RNA for Kinase Activation (LINK-A) and the membrane component phosphatidylinositol-3,4,5-triphosphate (PIP₃). The proposed interaction between PIP₃-LINK-A would be the first example of a direct interaction between a non-coding RNA and phospholipid. I investigated the proposed interaction between LINK-A and PIP₃ using Nuclear Magnetic Resonance (NMR) spectroscopy. Multiple NMR-based experiments were performed to assess the degree of binding on the basis of line-width broadening of NMR spectra. Wild-type and mutated RNA constructs were titrated into a 100 uM solution of PIP₃, but the NMR data showed no evidence of line-width broadening, indicating that no direct interaction occurs between wild-type or mutated RNA constructs. Presumably, the reported cellular interaction is not direct and might require an additional mediating factor. I determined the 3D structure of the LINK-A RNA hairpin, required to recruit PIP₃, using biophysical molecular modeling and NMR data. My results provide a biophysical foundation to elucidate the functional role of LINK-A in PIP₃ recruitment and kinase activation.

Within the domains of graphic and video game design, there is often need for tools to quickly develop convincingly realistic models of plants. A common tool applied to this problem is L-systems, a kind of rewriting system that can be used to define rules for iteratively transforming plant models to increasingly fine detail. However, the connection between L-systems and the graphics they generate can sometimes be unintuitive. To enable more intuitive development of plant models, we propose a method for generating models of branching structures from simple specifications of a few given iterations of the model. Our approach involves encoding plant models as bracketed L-systems and applying SMT (Satisfiability Modulo Theory) solvers to solve a form of the inverse L-system problem. Iterations of growth in the form of simple vector graphics are compiled to formal constraints for an L-system that can indefinitely generate further growth iterations. The satisfactory system is then found using an SMT solver. This technique allows for branching structures to be conveniently developed by providing meaningful specifications.

Trigger-action platforms enable end-users to program their smart homes using simple conditional rules of the form: if condition then action. Although these rules are easy to program, subtleties in their interpretation can cause users to make errors that have consequences ranging from incorrect and undesired functionality to security and privacy violations. Based on prior work, we enumerate a set of nine error classes that users can make, and we empirically study the relationship between these classes and the interface design of eight commercially available trigger-action platforms. Particularly, we examine whether each interface prevents (e.g., via good design) or allows each class of error. Based on this analysis, we develop a framework to classify errors and extract insights that lay a foundation for the design of future trigger-action programming interfaces where certain classes of errors can be mitigated by technical means or by alerting the user to the possibility of an error. For instance, we identify that an analysis of a dataset of functionally-similar trigger-action rules could be used to predict whether certain types of error patterns are about to occur. We believe that this work is a first step towards trigger-action interface designs that significantly mitigate user error.

What does it take to burst the “bubble” of white privilege...what are the moves? Awaking to one’s complicity as a white person who benefits from racist systems of unearned privileges that mark a white supremacy culture can be a difficult experience. This research is the result of one person’s willingness to enter the transformative journey of following the auto-ethnographic process of dissolving and reconstituting their understanding of a white-self through the lens of indigenous scholarship and growing relationships with people of color whose voices and stories told of a reality that was unlike her own. In choosing to resist resisting the fear that is bound up in entering conversations about white privilege and racism, and holding space in an uncomfortable process, the researcher turned to her 89.7% predominately white community of Bainbridge Island, Washington to examine the culture of relationships between communities of color and those who identify as white. She asks the question “can, and if so, where, when and how are white identities transformed from positions of White Fragility and white supremacy into identities and relationships with people of color, of solidarity, allyship, accompliceship and race-traitorship in denouncing white privilege in order to create a culture that is equitable and inclusive for all people? Centering the methodology of relationships as sites of knowledge, the researcher engaged in cultivating cross-racial friendships with community members who were actively working in spaces of racial equity, inclusion, and social justice. In documenting the intersection of their lives and stories, valuable knowledge was gained in the accounts of privilege, fragility, oppression, hope, despair, joy, adversity, and triumph that is embodied in their collective experiences. This research contributes to the ongoing discovery and scholarship of the ways in which white identities move through the stages of transformation in relationship with communities of color.

Black womxn in the United States have a long-standing history of creating community-based support networks and utilizing strategies of resilience to thrive in an oppressive society. Black feminist scholars have formulated useful frameworks such as “transformative work” and “intersectionality” to help contextualize long-standing practices of resistance, resilience, and transformation. As a medical anthropology student, the aim of my project is to understand how Black womxn in Seattle make sense of and advocate for the health, well-being, and safety of their communities. In order to answer this question, I collaborated with a diverse network of Black womxn who are initiating conversations about health and social justice in their churches, workplaces, and advocacy groups. Mount Zion Baptist Church, a predominantly African American church in Seattle, functioned as a community center for a network of Black womxn actively working to advance health equity. To learn about the ways that Black womxn in Seattle express, communicate, and act on their personal and political views regarding health, I engaged in participant observation at health-centered church events, advocacy meetings, marches, and health equity committee gatherings. Furthermore, I conducted structured and unstructured interviews to understand how Black womxn in Seattle perceive societal conditions and rely on support networks to radically better their lives. Through the experience of listening to Black womxn’s life history narratives, I learned about the vital role that solidarity, collaboration, and faith have in creating positive social change. My ethnographic research process has enlightened me to the importance of listening to and learning from the lived experiences of Black womxn who consistently work to transform their own health and the health of their communities.

Millions of people across the United States struggle with disordered eating. For the proportion of those who have been clinically diagnosed with “eating disorders”, many will continue to fall in and out of the grasps of their illness - even after the privilege of receiving comprehensive treatment and therapeutics. The issue of “chronic relapse” amongst individuals who have attended inpatient, partial hospitalization, and/or intensive outpatient care for disordered eating necessitates a thorough questioning of “treatment”, “illness”, and “recovery”. Despite so many years under the “medical gaze” of research in medicine and psychology, as well as in sociology and feminist scholarship, little has been done to make space for the voices of those affected. Therefore, the intent of this project is to strip away hegemonic discourses on disordered eating, and radically listen to those who have traditionally been silenced, isolated, and reduced to statistics in other literature. Drawing from subaltern and feminist theory, I seek to illuminate the lived and embodied experiences of women who have attended and returned to clinical treatment for disordered eating on multiple occasions. A phenomenological, (auto-)ethnographic approach is adopted to explore the liminal period between their treatment cycles. Having personally returned to treatment for disordered eating numerous times, I will use reflections from my own experience to inform my engagement and collaboration with other women who have embarked on a similar journey towards healing to produce a collection of narratives. Deeply listening to these individuals and juxtaposing their narratives may shed light on the ways they resist, negotiate, and perform relationship and identity in the sphere of “recovery”. Contextualizing healing trajectories in this way has implications for a new lens through which “relapse” and “recovery” are discussed, and could reveal what may be missed in the realm of current therapeutics for disordered eating.

Dravet syndrome (DS) is a severe form of childhood epilepsy caused by a mutation in the SCN1A gene, which encodes the NaV1.1 voltage-gated Na+ channel. This channel is present in most GABAergic neurons, the main inhibitory neurons in the brain. Reduced activity of the channel in DS leads to loss of inhibitory activity in the brain; this, in turn, leads to seizures and developmental deficits. Through previous research using the mouse model of DS, the de la Iglesia lab has demonstrated that DS also affects circadian rhythms, which are the endogenous biological rhythms synchronized to the 24 hour day. These symptoms are likely caused by the loss of NaV1.1 in a sleep regulatory center called the suprachiasmatic nucleus (SCN), a set of cells which functions as the ‘master clock’ of the circadian system of mammals. However, the de la Iglesia lab found that selective deletion of the SCN1A gene from the SCN fails to replicate the abnormal circadian phenotype. We believe that these mutant mice are phenotypically normal either because there is a compensatory increase in the expression of another sodium channel, NaV1.3, or because the targeting strategy does not reach all cells within the SCN. To test the first hypothesis we employed in-situ hybridization to visualize the expression of the genes that code for NaV1.1 and NaV1.3 channels in either SCN-specific knock outs or their wild type littermates. My results will help explain the phenotype seen in the SCN-specific SCN1A mutants and determine whether developmental compensatory mechanisms are important in the SCN of DS mice.

Most organisms show a roughly 24-h cycle in their physiological and behavioral processes, called circadian rhythms, generated endogenously through the ~24h cyclic expression of genes known as clock genes. Clock gene expression oscillates in the master circadian clock of mammals – the suprachiasmatic nucleus (SCN) - and nearly every cell of the body. Typically, circadian clocks and the rhythms they sustain are ‘entrained’ by the 24-h light-dark (LD) cycle. Our lab has found that fear can also behave as an entraining factor. We observed that when mice or rats need to leave a safe nesting area to access a foraging area, they forage and feed during the dark phase of the LD cycle. If the foraging area is rendered dangerous with random uncued footshocks during the active dark phase, the animals’ foraging and feeding activity shifts to the light phase. My goal is to understand the neural circuits and molecular processes involved in fear entrainment. I have analyzed the expression of clock genes in animals exposed to nighttime fear and control animals exposed to daytime fear; this allowed me to assess the circadian rhythm of expression of clock genes of interest (Per1 and Bmal1) in the SCN and amygdala, and I found that the amygdala entrains to fear but the SCN does not. I have also performed trials with brain-specific-knockout mice and found that nocturnal fear entrainment requires an intact molecular clock. My current experiments use a more specific knockout strategy of viral injections into the brain to determine whether a functioning circadian oscillator in the basolateral amygdala (BLA) or the SCN is needed for nocturnal fear entrainment. These experiments serve to unmask the molecular mechanism of fear entrainment and could also help understand the mechanisms linking fear and anxiety disorders to problems with circadian rhythms and sleep.

Detection of uncomplicated mild traumatic brain injury (mTBI) is difficult because there are no visible brain lesions that are often associated with more severe forms of TBI. New biomarkers would allow doctors to more sensitively screen for mTBI using neuroimaging methods. One promising biomarker technology is resting-state functional connectivity, which is brain activity measured at rest using functional magnetic resonance imaging. One particularly salient resting-state network is the Default Mode Network (DMN). Our research focused on identifying differences in resting-state functional connectivity between individuals diagnosed with mTBI and healthy controls. We examined mTBI in 254 U.S. military personnel deployed to a combat theatre in the Middle East from 2010-2013. Each subject underwent initial magnetic resonance imaging and screening for TBI following medical evacuation to Landstuhl Regional Medical Center (LRMC), the primary triage center for all evacuated combat casualties, up to 30 days post-injury. We used four distinct groups for our analysis; Blast/Non-Blast (n=79, 44) TBI, and Blast/Non-Blast Control (n=35, 96) while covarying for age and gender. We hypothesized that resting-state networks will be disrupted in TBI and blast populations when compared to controls. We used two different methodologies; the first was a seed-based analysis examining group differences in the correlations from the Posterior Cingulate Cortex (PCC, a key hub within the DMN) to the whole brain. The second analysis used the Yeo Seven Network parcellation to compute correlations between all seven networks to the DMN. We were unable to distinguish any group from controls, suggesting that early differences in functional connectivity are not a robust biomarker of injury.

Microglia, the immune cells of the central nervous system, are long lived. In mice, microglia have an average lifespan of 15.5 months. When microglia are experimentally depleted from the mouse brain, microglia populations quickly return to steady state levels. The mechanisms of this observed repopulation are unclear. More importantly, the mechanisms of microglia replenishment in the healthy brain are not well understood. The literature supports two competing hypotheses. One is that microglia proliferate simply by dividing. Another possibility is that pools of microglia progenitor cells within the central nervous system divide and differentiate into microglia. I hypothesize that microglia proliferate primarily through the differentiation of progenitor cells. Available data to date suggest CD133 as a potential marker for microglia progenitor cells. In order to study these putative progenitor populations, I used a genetic reporter mouse line in which administration of tamoxifen induces TdTomato expression specifically in CD133-expressing cells. TdTomato, a red fluorescent protein, allows these cells to be visualized under a fluorescence microscope. Importantly, all the progeny of these cells also express TdTomato, allowing us to determine whether CD133 cells generate new microglia over time. After tamoxifen treatment at the age of 10 weeks, mice were sacrificed at three and nine months of age. Brains were fixed, sectioned, and labeled with antibodies to a microglia specific protein and to TdTomato. Daughter microglia that differentiated from CD133-expressing cells express both markers. Using a fluorescence microscope, I identified several microglia daughter cells of CD133-expressing cells. This suggests that microglia populations replenish in the healthy brain at least in part through the division of CD133-expressing cells. We can apply this new knowledge about how new microglia are generated in the healthy mouse brain to further our understanding of how microglia population dynamics are affected in both health and disease.

Neurological diseases like stroke, paralysis and spinal cord injuries are some of the leading causes of disability and death across the world. Current medical treatments are not effective, and there is a world-wide effort to investigate new ways to restore function in the central nervous system. A treatment option that is gaining momentum is the use of brain-computer interfaces (BCIs), which has the potential to treat neurological diseases through reading and analyzing signals from the brain and sending electrical impulses to disease-affected areas. A significant obstacle that BCI implementation faces is biocompatibility, the ability for invasive devices to coexist with living tissues. Current BCIs are metal-based interfaces; their conductive properties allow them to efficiently record and send electrical brain signals. However, the human body elicits a foreign body reaction (FBR)- an immune reaction- in response to the “foreign” metal material. As a result, a capsule of scar tissue forms around the site of implantation, which mitigates the efficiency and longevity of BCIs. Hydrogels are an exciting organic material that have the potential to reduce FBRs and create biocompatible BCIs because of their elasticity, pliable material properties, and complex network structures. My project focuses on using poly(hydroxyethyl)methacrylate (pHEMA) as the base material of BCIs due to its ability to be accepted by the brain tissue after implantation. While pHEMA is biocompatible, it can not be used as a BCI in its current form because it is not conductive (not able to send and receive electrical signals in the brain). As a result, the gel is copolymerized with the conductive monomer 3,4-ethylenedioxythiophene (EDOT). This research project balances the conductivity and biocompatibility of the pHEMA-EDOT matrix to produce a new breed of long-lasting, efficient BCIs.

Fetal Alcohol Spectrum Disorders (FASD) encompass medical conditions resulting from prenatal alcohol exposure (PAE), including brain-based central nervous system deficits and physical impairments. Previously, FASD conditions that did not meet Fetal Alcohol Syndrome (FAS) diagnostic criteria were diagnosed as having Fetal Alcohol Effects (FAE). Beginning in 1974, Ann Streissguth, Ph.D. and colleagues at UW led multiple studies on FAS and FAE. The primary investigation was conducted from 1992 to 1996 among over 400 diagnosed individuals age three to 51 years old, with the purpose of examining types and magnitudes of secondary disabilities, i.e., problems not present at birth but occurring across the lifespan as a consequence of PAE. In a study recently funded by NIH, UW researchers are recruiting prior study participants to ascertain current physical health, mental health, and functional status. During online searches for former subjects, researchers discovered that many with FAS or FAE were deceased. Among 438 diagnosed subjects, 23 (5.25%) were deceased (mean age at death 36.8 years), compared to one of 60 (1.67%) control subjects (age 35 years). Death certificates have been obtained for 18 individuals. Causes of death among the diagnosed included physical health conditions: heart-related (27.8%), cancer (16.7%), kidney-related (5.6%), liver-related (5.6%), diabetes (5.6%); and conditions related to mental health: alcohol and/or drug abuse (16.7%), accidents (11.1%), suicide (5.6%), and violence (5.6%). Cause of death for the control was cancer. These data indicate a three-fold greater proportion of deaths among FAS/FAE diagnosed individuals compared to controls in this study population. Death certificate information suggests a high proportion of FAS/FAE deaths were related to physical and mental health conditions known to be associated with PAE. Our findings speak to the importance of preventing PAE, early diagnosis among the exposed, and medical and social interventions to reduce risk factors associated with FASD.

My research project involves the AP-3 (adaptor protein) complex, which plays a key role in membrane trafficking cells. Within all eukaryotic cells, there are membrane-bound sections of the cell that interact with each other in various ways to drive the cell's function. Vesicles mediate the transport of proteins and lipids among cellular organelles. These vesicles are created in various ways by proteins throughout the cell that form a "coat" around the vesicle as it travels to its destination. AP-3 is a protein complex that mediates vesicular transport from the Golgi apparatus to the lysosome. The current aim of my project is to analyze evolutionarily conserved features of the AP-3 complex by mutating subunits of the complex and observing resultant phenotypes in our model organism, Saccharomyces cerevisiae (baker’s yeast). In doing so, we utilize a gene reporter system called GNSI to analyze AP-3 function in different genetic strains. This reporter system is mainly analyzed through a colorimetric assay (chemical test to determine components), using qualitative observations of the intensity of colored halos around yeast colonies on a gel plate. We also use fluorescence microscopy by using signals from the Green Fluorescent Protein (GFP) to determine whether AP-3 was successful in trafficking to the lysosomal vacuole. So far, our results have shown that targeted truncations of proteins within the AP-3 subunit Apl6 yielded loss of function in trafficking. We are continuing our analyses by focusing on other proteins within AP-3. These basic studies will further our understanding of membrane trafficking and may provide insight into diseases linked to AP-3 function, including HIV-1 particle assembly and human genetic disorders.

Drepanosauromorpha is an extinct group of reptiles known from the Middle to Late Triassic (237–212 MA). The clade currently includes seven genera (Avicranium, Dolabrosaurus, Drepanosaurus, Hypuronector, Kyrgzsaurus, Megalancosaurus, and Vallesaurus) that are known from fossils collected in Europe (Italy, UK), North America (Arizona, New Mexico, New Jersey), and Asia (Kyrgyzstan). The first described drepanosauromorph, Drepanosaurus unguicaudatus, was based on a flattened holotype preserving most of a complete skeleton. Subsequently described drepanosauromorphs display the following diagnostic features: the length of the chevrons (ventral spines below the tail vertebrae) is substantially longer than corresponding tail neural spines, the cervical (neck) vertebrae are heterocoelous (saddle-shaped articular surface), the cervical ribs are absent as distinct ossifications, and the chevrons are fused to their respective centra. In recent years, both three-dimensionally preserved partial skeletons and isolated material of drepanosauromorphs have been found across both Europe and North America. These discoveries have helped shape our understanding of the biology and diversity of drepanosauromorphs. However, comparing isolated, three dimensionally preserved specimens to the more complete, yet two dimensionally preserved articulated specimens is difficult due to differences in preservation. Here, we describe a new drepanosauromorph species from the Chinle Formation in Petrified Forest National Park, Arizona based on the left second manual ungual (claw) . Some of the characteristics that distinguish this claw from those of most drepanosauromorphs is its size. It differs significantly from all known Drepanosaurus specimens (like the Italian holotype and the Hayden Quarry Drepanosaurus) because of the ventral placement of the cotyle (articulation surface), the height of the claw, the lack of compression along the pre-axial/post-axial plane, and a furrow along the midline. This new taxon not only highlights unsuspected morphological variation within Drepanosauromorpha, but also helps sheds light on the evolutionary history of smaller-bodied reptiles within Late Triassic ecosystems.

Electroencephalograms (EEGs) are commonly used for measuring electrical activity in the brain for neuroscience research. In order to better control experimental studies animals can be anesthetized, however there is minimal research done on how the anesthetics may actually change the response the brain has to stimuli. Two commonly used anesthetics are isoflurane and dexmedetomidine. It is currently hypothesized that isoflurane produces a slow wave brain state similar to sleep and dexmedetomidine produces a persistent active brain state similar to an awake animal. This study aims to determine the differences in activation from visual and focused ultrasound stimulation through intra-cranial EEG monitoring in mice. Studies were conducted with a surgery to implant intracranial electrodes in A1, S1, and V1 on both sides of the brain under 3% isoflurane. Isoflurane was then reduced to 1.5% and a recording of the brain was taken for 10 minutes. This was followed by a light stimulus in the right eye with an LED. Focused ultrasound was aimed in V1 left. After the isoflurane trials were completed, the mice were injected with dexmedetomidine and the previously mentioned trials of base line, light, and focused ultrasound were performed again for every animal. Analysis included examining the EEG traces of individual events, averages of 10 events in one animal, and averages of 60 events in an animal. Continuous wave transformation plots were also produced to determine the frequency contribution in the evoked response. Preliminary results show that there is increased activation in V1 left under each anesthesia with some activity appearing in A1 left, however this may be a result of the proximity of the areas. Further research is needed in order to determine the similarities between the brain states and fully awake animals and animals that are in a natural sleep state.

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

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

Through the use of virtual and augmented reality technology, we want to record clinical interactions within the respective environments on acute stroke patients to help us design more acceptable gaming technologies for a wide range of ages and backgrounds in future studies. With the combined efforts of the computer science and electrical engineering team, we were able to produce two games; "Dolphin Days" for the augmented reality environment and "Apollo" for the virtual reality environment. "Apollo" will be available for play during the duration of the symposium. The purpose of exposing patients to these environments is to promote neuroplasticity in the recovery process. Neuroplasticity is when the brain can reform or grow new nerve endings to reconnect with the affected areas in order to accomplish a function. Clinically, our experience has been that patient motivation is key to obtaining good clinical outcomes. Stroke rehabilitation therapies can often be tedious and difficult to maintain interest in. These types of interventions, by incorporating the desired exercises into a motivating and game-like environment, could potentially address this issue. Additionally, these systems offer the potential advantage of not requiring the immediate presence of a skilled occupational and physical therapist. Cost and insurance limitations often mean patients get a limited number of skilled therapy sessions. Therapists skilled in the rehabilitation of stroke are often less available in rural regions and patients often struggle to travel to therapy appointments. All of these factors limit the patient’s overall access to skilled therapeutic interventions. Our results found the overall patient census enjoying the environments while also having them engaged with the technologies. We believe using these technologies would further motivate patients undergoing stroke therapy to continue participation and ultimately reach a state where the patient feels confident physically and mentally to resume their daily tasks pre-stroke.

Domoic acid (DA), a common marine neurotoxin found in marine organisms such as shellfish and finfish, is gaining public attention with increasing outbreaks in the USA, Australia, China, and some countries in Europe. Most DA outbreaks are observed along coastal regions, increasing the risk of exposure by seafood consumption. However, little is known about the effects of low level prenatal exposure of DA. To address this growing public health issue, we administered behavioral and cognitive tests on 27 Macaca fascicularis infants prenatally exposed to 0, 0.075, and 0.15 mg/kg/day of DA. Their cognitive capacities were analyzed based on their speed of learning new tests using the Wisconsin General Testing Apparatus (WGTA). The WGTA requires testers to present stimuli to the infant and, depending on the response, reward the infant for a correct response. I was one of several testers that worked with the infants during testing sessions 5 days per week. I also worked with the investigators and data analysis team to analyze the results of the WGTA tests. Results from early cognitive tests of object and spatial discrimination did not indicate a statistically significant detrimental effect of DA on these basic learning tasks. This suggests that DA does not have an impact on basic discrimination learning in the early stages of life (< 1 year). However, due to the potential for delayed toxicity of DA, more complex learning and memory tests are being administered as the infants mature. The results of this study will provide insights into future research and influence policies being implemented regarding seafood consumption and food safety.

Transcranial magnetic stimulation (TMS) of the visual cortex can induce phosphenes - highly transient, generally formless lighted areas at the periphery of the visual field - of stimulated test subjects while they look at a small visual target. Non-diagnostic ultrasound, applied to the visual cortex, can also induce phosphenes, studied while test subjects had their eyes closed during stimulation. Here, we sought to study potential visual alteration of a visual target during application of diagnostic ultrasound to the anatomical location where TMS induced phosphenes in the periphery of that visual target. First we used TMS, guided by anatomical landmarks, to stimulate the visual cortex and generate phosphenes in the periphery of a visual target. Next, we applied diagnostic ultrasound over 21 trials for 15 seconds per trial to a test subject while they looked at a white cross with a beginning baseline and a mix of random sham and treatment diagnostic ultrasound exposures. 10/11 test subjects observed TMS-induced phosphenes. Diagnostic ultrasound stimulation of the visual cortex induced visual effects in 7/10 test subjects, with no effects in 3/10 test subjects. The likelihood of the 7/10 test subjects to observe a visual effect increased as the experiment progressed, increasingly so as ultrasound exposure increased. Diagnostic ultrasound, delivered transcranially to healthy test subjects, altered the perception of a visual target and generated a lasting effect on their visual perception. This observation of a prolonged effect on visual cortex is consistent with recent work on stimulation by diagnostic ultrasound of the human motor cortex as well as earlier work on stimulation of the human amygdala. These results suggest diagnostic ultrasound may one-day find rapid application to humans for a variety of purposes, and also raises questions about the advisability of applying diagnostic ultrasound to the human brain without medical justification.

Chronic stress induces the release of neuropeptides including dynorphin, which activates kappa opioid receptors (KOR) to encode the dysphoric components of the stress response. Dynorphin/KOR actions on dopamine neurons have been shown to underlie aversive learning, and it is hypothesized that potentiation of cocaine reward following stress is likely to occur through similar neural mechanisms. In this study, we investigate the neural substrates underlying stress-mediated enhancement of cocaine reward. First, we verified the reliability of a KOR (KT2) antibody. Immunostaining specificity was verified using KOR-Cre mice which express Cre-recombinase in KOR-containing neurons. By combining cell-specific targeting using Cre-dependent viral expression of fluorophores and immunohistochemistry staining, we confirmed the specificity of anti-KT2 to KOR containing neurons. Using this antibody and an anti-tyrosine hydroxylase antibody, we examined the co-localization of KOR and dopamine in the ventral tegmental area (VTA). Immunohistochemical analyses showed that KORs were expressed in a majority of dopamine neurons in the medial and lateral VTA. Furthermore, we investigated dynorphin-KOR circuitry in the mouse brain. Dynorphin-containing neurons projecting from the prefrontal cortex (PFC) and dorsal raphe nucleus (DRN) to the VTA were identified by injection of a retrograde virus (CAV2-DIO-ZsGreen) into the VTA of prodynorphin-Cre mice. In a separate cohort, an excitatory opsin (Channelrhodopsin2) was injected into the DRN of pDyn-Cre mice with an optic fiber implant. The DRN region was then optically stimulated and resulting KOR phosphorylation was measured in the VTA thereby verifying dynorphin-releasing projections from the DRN to the VTA. This projection was further investigated by examining the effect of DRN dynorphin on stress-induced potentiation of cocaine conditioned place preference (CPP). We found that deletion of dynorphin from the DRN, but not PFC, blocked stress induced enhancement of cocaine CPP. In conclusion, this experiment demonstrates a functional dynorphin/KOR circuit from the DRN to the VTA that mediates stress-induced increases in drug reward.

In 2009, the Department of Veterans Affairs (VA) integrated Store-and-Forward Teledermatology (SFT) to increase the dermatology care to patients with limited access. With this, patients are evaluated by their primary care provider (PCP) and referred to SFT for dermatology conditions. A technician on site takes images of the condition and send records to tele-dermatologist at a reading hub to evaluate and provide a differential diagnosis, treatment, and follow up. When skin biopsies are requested, Clinical Pathological Correlation (CPC) consultations are also requested. Dermatopathology reports are not standardized well and often require interpretation in context of other clinical information, including history, imaging, and microbiology studies to diagnose. Follow up imaging after an interval of treatment may be requested to confirm the diagnosis. The purpose of this quality improvement study is to assess adherence of PCPs to follow ups, determine whether failure to use means degraded clinical outcomes and interventions to improve outcomes. We conducted a retrospective review of 224 conditions addressed by teledermatology during the month of April 2018, on Veterans in the Pacific Northwest Network (VISN 20) where recommendations for either CPCs, re-imaging, or both were requested. We searched electronic medical records that requested follow-ups and determined a.) whether it occurred (if not, why); b.) timing it occurred; c.) affectability of treatment plans based on follow up findings; and d.) whether conditions were by intervention. Of 224 conditions reviewed, 161 requested CPC consultation, 63 requested reimaging, and 2 requested both. For CPC consultations, 90.06% patients had a re-consult, through CPC process or FTF and 9.4% of cases were lost in care. For reimaging consults, 73% of cases had reimaging or FTF re-consult while 27% of cases were lost in care. Data from this project will be used to improve follow up and quality of care Veterans receive through SFT.

The Moses Prairie Project is an effort to restore and enhance culturally important plant species on the Quinault Indian Nation Reservation through the traditional land management practice of controlled burns. Moses Prairie was selected because it was the only wetland fully owned by the tribe, unlike the other various prairies that are on allotted acreage. The prairie is a fen which makes it a biodiversity hotspot that supports both plant and game species if managed well and is not encroached by the surrounding temperate rainforest. In September of 2015, the prairie was burned for the first time in 150 years. I witnessed the complex difficulties and successes that come with collaboration across different agencies, cultures, and peoples. It brought up questions of what it meant for conservationists to do a cultural resource restoration project for tribes on the Olympic Peninsula, in the Pacific Northwest, and the rest of the United States and beyond. There are more contexts that bring to light why this project conserving both culture and the environment. I analyzed the data from the vegetation monitoring project on Moses Prairie, researched Quinault natural and cultural histories, looked at the kind of laws and systemic barriers that for tribes doing natural resource management, suggested future considerations such as climate change, and made recomendations on how to do more holistic and interdisciplinary natural resource management and ecological restoration. The goal of this report is to analyze the way restoration on reservations is shaped by the historical climates and natural events, tribal culture and resource management, and the past and present colonization and capitalization of the landscape. The aim is for scientists in my position to consider the many influences of the way a landscape is formed and the considerations we must keep in mind going forward with climate change and the continual erasure of the tribes. I also hope to provide a resource for the tribe to be able to reference either for their own knowledge or for people they hire or work with.

Oral swab analysis (OSA) is a possible alternative sample type for tuberculosis diagnostics. It has been observed that tongue swabs contain greater amounts of Mycobacterium tuberculosis DNA than cheek swabs (p<0.0001) from tuberculosis patients. After determining that oral microbiota follows this same pattern, several factors including time-of-day swabbed and health status were analyzed to understand factors affecting the amount of bacteria on the tongue. This project aims to optimize the oral swab sampling methods in order to facilitate more sensitive diagnostic tests, using universal bacterial 16s rDNA as a proxy for Mtb DNA. Previously tested samples from South Africa were further analyzed to investigate amount of oral microbiota by day collected, HIV status, health status, and other demographic factors. To evaluate whether collecting multiple swabs per sample yielded more universal bacterial DNA, tongue swabs were taken from healthy volunteers in Seattle. Each subject provided a 1-swab sample and a 3-swab sample, which was then extracted and analyzed by a previously optimized universal bacterial PCR. Additionally, tongue scrapers are being assessed as an alternative to oral swabs. Swabs collected early in the morning had more bacterial DNA than swabs collected later (p<0.03). 3-swab samples yielded an average of 2-fold greater amounts of bacterial DNA than 1-swab samples. Bacterial biomass correlated with M. tuberculosis signal in most comparisons. Bacterial biomass may serve as a useful proxy when developing better oral swab sampling strategies for TB diagnosis.

The transfer of carbon in and out of ecosystems is a complex process that is affected by many factors. The largest factor in carbon transfers is the photosynthesis and respiration rates of plants, which sequester and release carbon dioxide. Additionally, processes like soil leaching, sediment burial in lakes, downstream transport and even forest fires and animal migrations have an effect on the movement of carbon throughout ecosystems. In this study we ask the question: “How do physical and climatic conditions influence the concentration of carbon in small streams in the Pacific Northwest?” Our study site includes sixteen watersheds with areas that range from 500-2,500 acres in the northeastern portion of the Olympic National Forest. Using a GIS framework, we compiled satellite and LiDAR datasets of soil type, rainfall, slope, tree age and aspect and summarized these data for each of the sixteen watersheds. Our goal is to better understand which physical factors have the most influence on carbon transport in streams. By comparing our watershed-specific data to measurements of dissolved organic carbon and water quality characteristics in the streams, we identify correlations that can inform on the potential controls on carbon export in the rain-dominated catchments on the Olympic Peninsula.

Long non-coding RNAs (ncRNAs) play a significant role in transcriptional regulation; therefore, mutations in their sequences can lead to human disease. An example is provided by the promoter associated non-coding RNA (paRNA) that, when bound with Argonaut 1 (Ago1) and a miRNA, plays a key role in coordinating gene silencing of the tumor suppressor CDH1 in epithelial cells. The paRNA expression can be implicated with cancer. This is due to a single nucleotide polymorphism (SNP) at positions -160(C/A) relative to the CDH1 promoter. The -160(A) isoform favors a unique secondary structure of the paRNA, distinct from more common -160(C), which favors over-suppression of CDH1 and leads to increased cancer risk. To better understand how the -160(A) isoform mechanistically drives increased suppression of CDH1, our lab is applying NMR-based methods to determine the 3D structure of the paRNA. However, the T7 RNA polymerase used to synthesize RNA is prone to producing heterogeneous products in longer RNAs such as this one. Having exact lengths of the transcript is important for improving signal-to-noise and peak sharpness in NMR spectra, which is critical for 3D structure determination. To overcome this problem, I designed a pUC19 plasmid containing the paRNA -160(A) sequence with a downstream self-cleaving hepatitis delta virus (HDV) ribozyme. Following transcription, the HDV ribozyme undergoes self-cleavage, producing homogenous ends at the 3’ end of the paRNA. My results show that HDV incorporation produces a single species of RNA with no 3’ overhang and improves NMR spectra quality. This cloning tool is easily adaptable to other large RNAs, facilitating data collection for other large RNAs used in our lab. Ultimately, our ability to predict the 3D structure of this paRNA could someday lead to its use as a potential drug target.

Methylmercury (MeHg) is a bioaccumulative neurotoxin, dangerous to human health even at trace levels. In inundated soils, MeHg is formed from inorganic mercury by mercury-methylating microorganisms; a process termed methylation. Demethylation, by contrast, converts MeHg into less-dangerous inorganic mercury, and also occurs via microbial activity throughout the aquatic soil profile. Rice grains can be contaminated with MeHg when grown in soils where methylation rates are high; human exposure to MeHg is thus a serious public health concern in places where rice cultivation, high rates of consumption, and soil mercury (Hg) contamination overlap. Our research aims to better understand the soil conditions that favor demethylation over methylation – this information can then be used to reduce rice grain contamination through agricultural practices or rice breeding programs. Specifically, our research focuses on the role of oxygenation and carbon root exudates on the net MeHg accumulation throughout the soil profile. Rice plants grow in flooded, oxygen-free (anoxic) soils, but their roots can leak oxygen (making the rice rhizosphere oxygenated in varying degrees), as well as carbon root exudates. Our project simulated both fully oxic and transiently-oxic (transition) zones, with two different levels of root exudates; we use isotopic tracers to assess respective methylation and demethylation rates in all four treatments in both the vegetated (rhizosphere) and non-vegetated (bulk) soil. Carbon root exudates have been collected from hydroponically-grown rice variety M-206, and can be applied to different soil zones via tubules. Oxygenation of the soil can be measured with mm-scale optode imagery, which allows delicate testing of various oxygen-introduction designs. My role in this interdisciplinary project has been to develop, scale-up, automate, and verify the accuracy and dependability of root-oxygenation and root-exudate introduction systems to be used in upcoming experiments.

Alzheimer’s disease (AD) is a neurodegenerative illness affecting millions of individuals in the United States and represents the leading cause of dementia worldwide. AD is pathologically defined by abnormal accumulation of interneuronal plaques composed of amyloid beta protein and intraneuronal tangles composed of tau protein. The focus of our current research involves understanding how tau protein homeostasis is restored using the model organism C. elegans. One process by which protein homeostasis is modulated is through the endoplasmic reticulum unfolded protein response (UPRER), which is composed of three signaling branches. Initially, the UPRER acts to restore normal protein folding, but if restoration is impossible, it triggers apoptosis. Our lab became interested in this signaling pathway after we identified the UPRER master transcription factor XBP-1s as a modifier of tau pathology (tauopathy). Specifically, XBP-1s overexpression protects against tauopathy in our C. elegans model. Previous RNA sequencing (RNAseq) analysis identified several downstream target genes upregulated with XBP-1s overexpression in our pathological tau C. elegans model. To follow up, I am working on understanding the molecular basis of XBP-1s-mediated tauopathy suppression by generating C. elegans models containing target genes of interest. Assessment of the effect on tauopathy phenotypes includes behavioral analysis by performing a liquid thrashing assay and tau protein analysis via the Western blot technique. Using the microinjection technique, I have generated a transgenic C. elegans model overexpressing hsp-4, an upregulated XBP-1s target gene identified by RNAseq that potentially modulates tauopathy. We are currently determining whether overexpression of hsp-4 can ameliorate tauopathy similar to XBP-1s overexpression. Gaining further information about the role of these XBP-1s target genes in tauopathy using the model organism C. elegans is valuable for future translational studies in mammals, along with being integral to research for neuroprotective therapies for neurodegenerative diseases such as AD.

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

 Esophageal adenocarcinoma (EAC) has received considerable attention recently due to a three-fold increase in occurrence affecting 20,000 people each year in the US with <20% patients surviving 5 years past diagnosis. Thus, there is an urgent need to advance our understanding of EAC’s molecular pathology and to use this understanding in improving our ability to prevent and manage EAC. Gene mutations and epigenetic alterations drive the formation of a pre-malignant condition called Barretts’ esophagus (BE), which can then progress to EAC. Epigenetic modifications of numerous genes, in the form of DNA hypermethylation with subsequent gene silencing, have been demonstrated to occur frequently in BE and have been postulated as a driving force for EAC formation. In prior studies, we discovered a novel methylated gene, TUSC1, with silenced expression in primary EAC tissue samples and cancer cell lines (Yu et al., Gut 2018). This study aims to investigate the biological consequence of TUSC1 loss in EAC cell lines by utilizing CRISPR-Cas9 gene editing technology. We hypothesize that TUSC1 is a novel tumor suppressor gene in EAC. To test this hypothesis, we will be generating TUSC1 knock-out (KO) EAC cells by introducing TUSC1-silencing guide-RNA into EAC cell culture. We will be assessing the extent of TUSC1 KO at the gene expression and protein level by conducting quantitative real-time PCR and Western blotting, comparing the KO cells to the control cells. We will also use PCR-based sequencing to verify the DNA alteration introduced by CRISPR in single-cell colonies. Successful completion of these experiments will lead to the next stage of phenotypic assays, in which we will investigate whether loss of TUSC1 in EAC cells would promote oncogenic behaviors of cancer cells. The proposed studies would demonstrate the biological function of TUSC1 in EAC and illustrate the molecular mechanisms of DNA-methylation driving EAC tumorigenesis.

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

 Many veterans live in rural areas with limited access to traditional face-to-face (FTF) dermatological services. This barrier to care can result in worse health outcomes. Store-and-Forward Teledermatology (SFT) is a program that aims to address this disparity by providing veterans with increased access to dermatological care. Instead of seeing a dermatologist in person, veterans with suspicious lesions first see a primary care physician (PCP) who then arranges for pictures of the lesions to be taken. These pictures are electronically sent to a dermatologist who reviews them remotely and then suggests a plan of care for the patient. SFT allows veterans to both avoid potentially long wait times at in-person dermatology offices and address lesions that may have gone untreated. This study focused on the timeline of care for the treatment of melanoma. Because of its lethality, it is important to diagnose and treat melanoma as quickly as possible. In this study we compared the timeline to treatment – from when the lesion was first discovered to the date of its surgical excision – in groups receiving standard FTF dermatological care and SFT care. Using chart data from patients within the VISN 20 network, we retrospectively gathered the dates of discovery, biopsy, and excision in patients. From there, we calculated the mean days from discovery to biopsy and biopsy to excision in both groups. Upon comparing these timelines to each other we found that the overall timeline for SFT was approximately 12 days longer than that for FTF. We identified sections of the SFT process that may be responsible for the delay as potential quality improvement points in the future.

A protein's function is dependent on its structure, which is made up of amino acids. Proline, (an amino acid) is known to cause the kinks and turns in protein structures. However, little is known about the influence of pH on the isomeric preference of proline-attached dipeptides. For this experiment, the isomeric preference of methionine-proline was measured in 10% solutions for pH levels of 7 and 11, the pH of the human body falls between the range of 6 and 9. At pH 11, NMR-90 spectra showed that the cis- isometric form was preferred at a rate of 14% more than the trans- isometric form, measured by the alpha hydrogen. At neutral pH of 7 trans- isomers are preferred 36% more than the cis- form measured by the alpha hydrogen and 73% more measured by the delta hydrogen. In conclusion, this experiment supports the hypothesis that proline-attached dipeptides’ isomerization is pH dependent and is more likely to be in cis- form when in high pH in comparison to a neutral pH. The purpose of this experiment is to determine if pH levels can change the structure of a protien, with further research exploring if the change of structure changes the function. This is important to determine if medications containing amino acids can have an optimal or range of pH.

Manipulating airflow over aerodynamic surfaces with plasma, compressed air jets and textured surfaces has become an area of intense aeronautical research and international competition in the last few years. Electrohydrodynamic (EHD) thrusters or plasma actuators have been demonstrated as remarkable devices for separation control and lift enhancement. The application of EHD thrusters to an aerial vehicle can drastically reduce the power consumption, weight and response time of mechanical controls. The focus of the present work is to determine the performance of a full-scale aircraft wing with an integrated corona discharge driven EHD thruster numerically. The numerical model is carried out by coupling the interactions between fluid mechanics and electrostatics. The study has been conducted on an augmented NACA 0012 airfoil with trailing edge flaps at a Reynolds number of 160,000 (10m/s). The EHD induced jet delays separation while lengthening and flattening the separation region. Preliminary results show that the actuator has increased the moment on the airfoil by 50% which helps in better maneuverability. The numerical results are compared with the experimental wind tunnel results. These findings can favor a strong design of a new generation energy-efficient aircrafts

Parkinson’s Disease (PD) is a neurodegenerative movement disorder characterized by muscular rigidity, slow movement of the limbs and resting tremor. The onset and progression of PD is attributed to the combined effect of environmental and genetic risk factors, with several specific disease-causing genes having been identified. PD onset is determined by the loss of more than 80% of dopamine-synthesizing neurons from the substantia nigra as well as formation of α-synuclein protein aggregates, called Lewy Bodies. Recent research has identified several potential pathogenic variants in the LRP10 gene on chromosome 14, suggesting that LRP10 may be a novel PD causative gene. It has been shown that the LRP10 protein is implicated in vesicular transport and that it may regulate α-synuclein aggregation, intracellular trafficking, and cell-to-cell transmission. The goal of my project was to analyze the association between LRP10 and PD by sequencing the regions on LRP10 that harbor these variants described in other families and check for co-segregation in the relatives of mutation carriers. DNA samples from 188 PD familial patients were sequenced. LRP10 regions of interest that were examined included exons 1-7 (protein coding regions) and intron 5 (a non-protein coding region). These LRP10 regions in patient DNA were amplified by polymerase chain reaction and sequenced subsequently using Sanger Sequencing. Relatives of LRP10 mutation carriers were then analyzed for co-segregation between the variant and PD. It was expected that certain LRP10 variants would be found to segregate with the disease in inheritance or increase the likelihood of its onset. The molecular function of both the normal and mutated LRP10 protein are still largely unknown and future research into their mechanisms will provide valuable insight into their specific role in Lewy Body formation and dopaminergic neuronal loss.

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

Epithelial-mesenchymal transition (EMT) refers to a biologic process that allows a polarized epithelial cell, which normally functions in the basement membrane of a cell, to undergo biochemical changes that makes it express as a mesenchymal cell phenotype. This mesenchymal phenotype allows the cell to have enhanced migratory capacity, invasiveness, elevated resistance to apoptosis, and increased production of extracellular matrix (ECM) elements. The process of EMT is considered completed once the underlying basement membrane breaks down, and the mesenchymal cell becomes migratory. Another component that proves EMT is the loss of e-cadherin. E-cadherin refers to cell-to-cell adhesion and the degradation of e-cadherin levels are a hallmark of EMT happening. There are three distinct types of EMTs; I will be focusing on type II EMT. Type II EMTs are associated with inflammation/wound repair but usually stops once inflammation subsides. However, in the context of organ fibrosis, type II EMTs can continue to over-respond to a persisting inflammation and can lead to organ death. In my experiment, I hypothesize that in HEK 293 human cells, SNAP -Δ1-91 alpha-1D adrenergic receptors undergo type II EMT. SNAP -Δ1-91 alpha-1D adrenergic receptors are a truncation of the extracellular portion of the receptor. Certain receptors undergo this truncation to increase its expression. It is shown that in SNAP – Full Length alpha-1D adrenergic receptors  (wild type receptors) do not undergo EMT. I will be able to observe the process of type II EMT through imaging the breakdown of the cell membrane in SNAP- Δ1-91 alpha-1D adrenergic receptors and the measuring of e-cadherin levels. The purpose of this research would be to potentially influence future therapeutic interventions that target wild type receptors to induce would repair. 

Computer vision models are used to help analyze biomedical images for diagnosis and treatment through looking for differences between images by a comparison to a template image. For instance, optical coherence tomography (OCT) is used to diagnose and treat retinal issues. When looking at the brain, injury, cellular uptake and characteristic features vary across regions, therefore images are often segmented into established brain regions to determine how the brain is impacted in a particular study. Current models fail to work in segmenting brain regions because each brain has variation in local microstructure, making it difficult to compare one brain to another. Furthermore, when brains are sliced, the exact location within the brain can be difficult to pinpoint, particularly in regard to depth, because the regions vary slice to slice. Therefore, my research addresses the increasing need for a method of analysis to align and compare images from brain regions across slices from a single brain, and from brain to brain. Using scikit-image analysis tools, I extracted information from cell images and videos of nanoparticles obtained in brain slices and determined trends within various regions. My program extracted cell density, shape, and death, then analyzed the uptake of nanoparticles to determine where a small segment of an image is most likely located within the brain. Iterating over the entire image generated a rough map of the regions within the brain which is refined using mapping descriptions detailed in literature. This research resulted in a systematic program that uses image analysis tools to extract features of defined brain regions. This program allows for quick, accurate and consistent analysis of regional differences of cellular features, nanoparticle distribution, toxicity, and other important measures.

Reinforcement Learning (RL) is a subcategory of machine learning, in which an agent (the decision maker) observes its environment and executes the best course of actions to maximize rewards. This is similar to teaching a pet to perform tricks using treats as positive reinforcement. Our research compares different RL methods on low-performance devices like a Raspberry Pi in real-time, real-world environments. RL has gained popularity recently with breakthroughs from DeepMind’s paper, Playing Atari with Deep Reinforcement Learning, where an agent learns to play Atari games from raw pixels and from DeepMind’s AlphaGo (DeepMind, https://deepmind.com/research/alphago) program that was the first computer program to beat a world champion Go player. RL projects like AlphaGo have utilized big data, powerful computing resources, and simulated environments that do not require real-time interaction to train the machine learning models. Our group compares the effectiveness of different RL methods on an accessible level of computing power on offline devices that an average consumer could acquire. The team constructs a physical environment for the robot to navigate, creates an OpenAI Gym environment that our agents will use to control the robot and get feedback from the environment. We train our agents using different RL methods to optimally navigate the environment and avoid collisions. We then compare the performance of the different methods in our physical real-time environment. Reinforcement Learning in small, offline devices could pave the way for a variety of devices that learn over time without being connected to a network. Imagine a small Mars rover that learns to navigate its environment efficiently over time.

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

Beginning in the 1880s, tens of thousands of impoverished Italians immigrated to Buenos Aires, Argentina to create a better life. Upon arrival, they found themselves freshly socially alienated. Hybridity theory helps us understand this phenomenon demonstrated through cocoliche, the contact language spoken by the new arrivals. The period of mass migration lasted until the 1930s when Italy’s political turmoil calmed and struggling economy began to recover. The combination of southern Italian culture and Argentina’s produced lasting cultural changes and a transitory dialect that I classify as a contact language. Hybridity theory, which hinges on representing the voices of the subaltern, allows a reinterpretation of power that helps us understand the migrants’ unusual position in history as low class, white Europeans whose migration to the Global South ended not only in social stigma and continued poverty but also the dialect-speaking, comical, Southern Italian character Cocoliche. Cocoliche as a language has been studied by linguists in both Italy and Latin American southern cone countries. Cocoliche as a character has been analyzed as an element of Argentine theater. But despite these focuses little research has been done on the social and economic statuses of the Europeans who uniquely migrated to the Southern Cone and how their dialect reveals the oxymoron of their identity- that they held simultaneous and contradictory positions as privileged and yet destitute people.

Students of the Ocean Research College Academy (ORCA), an early college program through Everett Community College, have monitored bacteria data near Everett, Washington where the Snohomish River meets the Possession Sound since 2004. Used as an indicator of fecal contamination, Escherichia coli (E. coli) are found in the intestinal tract of humans and other homeothermic animals. This study investigates the spatial and temporal trends of E. coli levels at three sites within the Possession Sound between 2014-2019 in order to better elucidate the ecosystem’s health and potentially negative anthropogenic influences. Variation in coliform levels were analyzed with regard to physical and chemical factors such as tidal stage, depth, the Snohomish River discharge, salinity, temperature, dissolved oxygen, pH, and point sources  including combined sewer outflows and storm drains. Water samples were collected with a Niskin bottle while a YSI 650 CTD or a YSI EXO Sonde was utilized to measure salinity, temperature, dissolved oxygen, and pH for each of the samples. ORCA students followed the Coliscan® Easygel® Protocol for inoculation, incubation and quantification. Data were reported as colonies of E. coli per 100 mL of water. Preliminary results show that E. coli levels have a seasonal correlation with river discharge, increasing in the fall, winter, and spring months when river discharge spikes. Coliform levels are higher at the halocline than at the surface or near-deep. Further sampling at additional upriver sites will demonstrate more sources of E. coli data. The results of this study will provide a foundation for understanding the fluctuations in the spatial and temporal trends of E. coli levels within the Possession Sound in order to better assess threats to the ecosystem health.

Eelgrass (Zostera marina) is an ecologically important species of marine angiosperm that inhabits sublittoral sediments in the northern hemisphere. Eelgrass beds provide critical food and habitat for many species of fish, invertebrates, and birds. Its root system has the capacity to interact with both the water column and sediment, making it uniquely poised to influence metal cycles within the ecosystem, including those affected by anthropogenic activity. Eelgrass, sediment, and water samples were collected from three sites in Possession Sound, a part of Puget Sound that borders the City of Everett and contains the Snohomish River Estuary. Samples were processed in the University of Washington Isotope Geochemistry Lab before being analyzed for trace metal concentrations using an ICP-MS. In addition, two-meter long sediment cores were taken from three sites in the Possession Sound and the bottom 5cm were analyzed, allowing the researcher to quantify the anthropogenic influence on metal concentrations within sediment. It was hypothesized that the roots, shoots and blades of the eelgrass would exhibit differing concentrations of heavy metals, and that sediment collected within eelgrass beds would contain higher concentrations of metals than sediment collected outside eelgrass beds. Additionally, samples from sites closer to human activity would contain higher concentrations of metals and a greater proportion of metals from anthropogenic sources. Preliminary results of the ongoing study show that concentrations of arsenic, copper, and zinc were higher in eelgrass blades than roots, and eelgrass tissue had higher metal concentrations than the surrounding sediment. These results suggest that eelgrass uptakes metals from its environment, accumulating as well as translocating them in its tissues. Additionally, study locations nearer to the mouth of the Snohomish River and human activity had higher concentrations of heavy metals overall in both sediment and eelgrass.

Insects use feedback from multiple sensory modalities to control their motor output. Hawkmoths are crepuscular insects that fly in low light conditions, hovering over flowers as they pollinate and feed from them. They use their long and flexible mouthpart, the proboscis, to explore flower surfaces and feed from a tiny nectary opening in these flowers. We asked how moths combine visual and mechanosensory feedback to find the nectary opening in flowers. To test the effect of light level on their efficiency in locating the nectary we combined 3D printing technology to generate artificial flowers, with micro-sensing technology that allowed us to detect the proboscis tip inside the nectary, and computer vision techniques to track the motion of hovering moths at two different light levels; 0.1 lux (moonlight) and 50 lux (dawn/dusk). Using a combination of low light videography and machine vision, we quantified how floral exploration changed between visits, and between the different light levels. We also measured the length of time moths took to find the flower nectary each visit. We found that moths took less time to find the nectary at lower (moonlight) levels compared to higher (dawn/dusk) levels. Hawkmoths are typically active in low light conditions, hence the higher light levels might be adversely affecting flight control. Moreover, preliminary reconstruction of their flight paths suggests that moths hovered over the flower in tighter trajectories under lower light conditions, as compared to the higher light conditions. These results suggest a decreased control over their flight motor output at higher light levels, resulting in reduced hover feeding. These behavioral differences have led us to a series of questions looking at the physiological effects of the different stimuli.

For many years, concerted efforts to combat malaria through the use of antimalarial drugs, bed nets, and other public health measures led to marked reductions in morbidity and mortality. Unfortunately, progress has stalled. Reductions in malaria have leveled off and even reversed in certain areas (WHO, 2017). As of 2016, there were 216 million cases and 445,000 deaths annually due to Plasmodium infections (WHO, 2017). To regain momentum and accelerate malaria eradication efforts, an effective and durable vaccine is needed. The Murphy Laboratory focuses on developing novel pre-erythrocytic (PE) malaria vaccines that can effectively stop the Plasmodium sporozoite (spz) before the clinically symptomatic blood stage begins. Identification and inclusion of multiple different protective Plasmodium antigens is thought to be crucial to developing a broad immune response and durable protection against this intracellular parasite. To test and define protective antigens, the Laboratory developed an “Acute Challenge” (AC) model in order to sensitively measure T-cell responses that are completely or partially protective. In this model, DNA vaccines encoding Plasmodium yoelii proteins are delivered by gene gun to induce CD8+ T-cell responses in BALB/c mice. At the peak of the immune response, we challenge the mice with luciferase-expressing P. yoelli sporozoites and measure the parasite burden and protection using IVIS imaging. A known protective epitope derived from P. yoelii circumsporozoite protein (CSP) induces a potent and protective response in this system. My project is to utilize the AC model to assess P. yoelli candidate antigens, of unknown protective potential, that are putatively exported or secreted from the parasite-containing vacuole into the host cell cytoplasm. Confirmed protective antigens will then be assessed for their localization and defined T-cell epitopes. The results will be used to create vaccines designed to maximize such responses and target the responding T-cells to the liver.

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

In cystic fibrosis (CF), a genetic defect in the CFTR anion channel compromises host defenses and causes chronic lung infections with organisms like Staphylococcus aureus. Our lab has been studying the effects of combining ivacaftor, a CFTR modulator which increases CFTR channel activity, with a period of intensive antibiotic treatment. We found that S. aureus lung infections generally persisted despite this aggressive treatment. However, most subjects undergoing treatment were found to be infected by different S. aureus strains one year after treatment than were present before treatment was initiated. Understanding the dynamics of strain switching provide new knowledge about the natural history of chronic CF infections, help define the effects of CFTR modulators and antibiotics, and inform new approaches that might produce infection eradication. We hypothesize that (1) strain switching is most likely to occur during the period of combined ivacaftor and antibiotic treatment, as sputum bacterial burdens were lowest during combined treatment; and that (2) strain switching is rare in the absence of combined treatment. To test this, we used a new population-based multilocus sequence typing (PopMLST) method we developed to perform strain-level genotyping on S. aureus. PopMLST uses PCR amplification and next generation sequencing of housekeeping genes from bacterial isolate pools cultured from sputum. Sequencing determines the number and relative abundance of unique sequence types present, and the data can be used to infer the number of strains present. This analysis was performed on samples obtained before treatment, during treatment with ivacaftor alone, and during combined treatment. We also examined a cohort of subjects receiving usual care. These data improve understanding of strain dynamics during CF infections and suggest new strategies to eliminate infection.

The Laser Interferometer Gravitational-Wave Observatories uses michelson-type interferometers that have two, 4-kilometer-long arms with suspended test masses (mirrors) at the ends of the arms. The test masses reflect high-power lasers to be combined at the output port of the two arms and create an interference pattern, which is sensitive to gravitational waves passing through the interferometer. For a stable interference pattern, the test masses must be oriented precisely; the low frequency orienting of the test masses is done using optical levers. The optical levers consist of optics that launch light from a diode laser to reflect off the test mass and hit a quadrant photodiode which measures the position of the light spot. However the measurement of this position has elevated amounts of noise at low frequencies, limiting the angular motion accuracy. The reduction of this noise by a factor of 10-100, would allow for a more accurate orienting of the cavity holding the test mass. One possibility is that the noise is due to mode fluctuations in the fiber optics connected to the launching telescope. To isolate this noise I recreated parts of the LIGO OPLEV setup with a level of electronic position noise well below the order of LIGO's current OPLEV noise at 0.1 Hz (10-9 meter per square root hertz level). To achieve noise at this level I have made a new low noise pre-amplifier, improved the physical stability of the setup, and analyzed data to identify the noise sources.With this reduced noise setup we plan to search for the source of LIGO's OPLEV low frequency noise and ultimately reduce noise in gravitational wave detection at low frequencies. Reduced noise will lead to more GW detections and new astrophysics, which will allow us to 'hear' the universe in a unique way.

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

Advanced oxidation treatment processes involve powerful and indiscriminate radical intermediates, including hydroxyl radicals (•OH) and sulfate radicals (SO4-•). Inefficiency in radical-driven treatment systems involves scavenging reactions where radicals react with non-target species in water and solids. Radical scavenging studies have been focused on soluble scavengers in the water and have not assessed radical scavenging by solids which are also present in oxidation treatment systems. The objective of this study was to quantify radical scavenging by solid surfaces. •OH were produced in iron (Fe)- and UV-activated hydrogen peroxide (Fe-AHP, UV-AHP) systems where the loss of rhodamine B (RhB) dye served as an indicator of •OH activity. The basis used to estimate the •OH surface scavenging rate constant (k≡S) were comparisons of treatment results between simple solids-free oxidation systems and more complex systems containing mineral solids. The solids-free system was based on Fe-AHP and UV-AHP reactions; the solids-amended systems were identical but contained different mineral species. Therefore, differences in the loss of RhB were attributed to •OH scavenging by the solid surfaces in the Fe-AHP and UV-AHP treatment systems. Alumina (Al₂O₃), silica (SiO₂), and montmorillonite (Al₂H₂O₁₂Si₄) (MMT) are solid minerals found in soil and aquifers. These minerals were used in this study to assess the solid surface scavenging rate constants. Preliminary results in the Fe-AHP system indicated that k≡S for silica (2.85×10⁶ 1/m²×s) was not statistically distinguishable from alumina (3.92×10⁶ 1/m²×s). k≡S values in the UV-AHP system for silica (4.50×10⁶ 1/m2×s) and alumina (7.45×106 1/m2×s) were greater than estimates in the Fe-AHP system and may be due to pH. k≡S,MMT (≤ 4.22×10⁵ 1/m²×s) was much less than k≡S for silica and alumina indicating k≡S is mineral-specific. A critical analysis suggests that radical scavenging by solid surfaces in aquifer systems is orders of magnitude greater than scavengers in the water.

Econometrics lacks an analytical framework for estimating and discussing the impact of intersectionality on economic outcomes of groups of marginalized people (e.g., women and people of color). As a result, a rich body of literature on intersectionality is left largely unused, leading to potentially misspecified regression models. In this paper, I outline an analytical framework for estimating and discussing the impact of intersectionality on economic outcomes, such as annual wage differentials between groups of marginalized and privileged people. I construct the analytical framework using principles of intersectionality theory, such as simultaneity and multiple jeopardy. I then use the framework to construct a multiple-linear regression model to investigate the following hypothesis: Do people with more marginalized identities earn less average annual wages than people with more privileged identities in the United States, all else equal? The results indicate that there is evidence to support the hypothesis, yet more in-depth investigations are necessary to better estimate the impact of marginalized and privileged identities on average annual wages.

Take Charge is a statewide family planning initiative that provides men and women in Washington State with free access to family planning services. As one of the most accessible family planning programs in the nation, Take Charge has expanded into school based clinics, allowing adolescents as young as thirteen to receive contraceptives without the knowledge of their parents. Success of family planning initiatives are typically measured by how much they reduce unintended pregnancies among their low income or minority populations, but the effect of these programs on economic indicators such as income and educational attainment are generally less well explored. Thus, the purpose of this research project is to determine the impact of having access to Take Charge on college completion for Hispanic women in Washington State. To address this question, individual level data from the Minnesota Population Center Current Population Survey were used to conduct a variety of difference-in-difference and triple difference tests to measure the effect of having access to Take Charge on college completion. The results depict that having access to this program starting at age 13 significantly increased the likelihood of completing college by 14-18% for Hispanic women. These findings imply that Take Charge can be used as a model program for other states that hope to reduce their number of unintended pregnancies and increase college completion among their low income and minority populations. 

Quantum confined nanomaterials have become an important field of study with many applications from color displays to low-energy alternative lighting sources. Discovered in the early 1980s, these semiconducting nanocrystals continue to draw attention; their unique properties differ from their bulk counterpart’s due to a quantum confinement effect rising from their small nanometer-scale size. Indium phosphide (InP), a group III-V semiconductor, is a promising nontoxic, environmentally innocuous material. The morphology of the synthesized InP nanocrystal is commonly a quantum dot quantum-confined in all three dimensions. However, the utility of the dot in biological imaging and display applications is hindered due to reabsorption resulting from overlap in its absorption and emission properties. This dims the light of an indicator and limits efficiency in catalysis. The subject of this investigation—InP quantum rods— offers a solution to this problem, as it is quantum confined in two dimensions and exhibits bulk semiconductor characteristics in the third, separating the absorptive and emissive features and improving the photoluminescent quantum yield. My procedure involves a hot-injection method. Currently, a magic sized cluster hot-injection synthesis in N-methyl pyrrolidone at 150 °C is known to afford InP rods (Dr. Friedfeld, UW Cossairt lab). I explore multiple experiment sets that manipulate the reaction length and temperature of the synthesis, cluster identity and concentration, and the identity of the aprotic polar solvent in which the reaction takes place. I characterize all material via UV-vis spectroscopy and imaged on a transmission electron microscope. The aim of the investigation is to learn why these rods form and what reaction conditions favor their formation. In understanding how to efficiently control the distribution of InP rods v. dots using chemical tools, the usefulness of nanocrystals in nanobiotechnology and clean energy science can be improved.

Crucial processes in clean energy research, such as the splitting of water into H₂ and O₂ and the reduction of CO₂, require multi-electron redox events throughout a catalytic cycle. Noble metals such as iridium and platinum prefer such events, while more abundant and consequently cheaper base metals prefer single-electron events. Redox-active ligands offer the potential of enabling noble metal behavior in base metals by combining a single-electron transformation at both the metal and the ligand to create an overall two-electron process. While redox non-innocent ligands are typically comprised of organic components, cobalt selenide clusters offer an attractive alternative given their wide variety of accessible oxidation states. Here, I present the synthesis of heteroleptic cobalt selenide clusters [cis-Co₆Se₈(PEt₃)₄(RNHP(C₆H₅)₂)₂ Et = ethyl, R = alkyl, aryl] containing ditopic aminophosphine ligands. The cluster was then metallated using copper(II) triflate and the product was fully characterized by multi-nuclear nuclear magnetic resonance, ultraviolet-visible, and infrared spectroscopies. Further analysis was performed using cyclic voltammetry and the solid-state structure has been solved via single-crystal X-ray crystallography. Upon spectroscopic analysis, it appears that copper(II) is reduced to copper(I) by the cluster. This result is encouraging, as using clusters as redox-active ligands would require facile electron transfer between the metal atom and the cluster core.

The Internet fundamentally altered what copyright means and how it functions in society. Now anyone who downloads music or uploads videos to YouTube is deeply implicated in the complex set of laws known as copyright. Despite this daily interaction, the public at large is unaware of or even apathetic towards the current copyright system. The question then is why is there a gap between public opinion and understanding of copyright and the copyright legislation itself? To answer this question this research investigates the copyright discourse across time as the internet and thus digital copyright expanded. To do this a discourse analysis was conducted surrounding three different pieces of proposed copyright legislation: The Digital Millennium Copyright Act (DMCA), the Stop Piracy Online Act (SOPA) and the EU Copyright Directive. The analysis included the bills themselves, congressional/parliamentary hearings, newspaper reporting, statements by supporters/opposition, and online discussion forums. These data were then coded to gauge what the public was informed of and how they were interpreting digital copyright legislation and the impact it would have. Preliminary findings indicate that public awareness of copyright and copyright violations has grown over time, as has concern and involvement by the public in copyright debates. These findings show that as the Internet became more ingrained in people’s day to day lives copyright or at least concern over copyright legislation and the impact it would have on the Internet also became more prevalent. Understanding this discourse and how various parties are interpreting copyright is important because in the digital age copyright is a fight over who gets to control, alter, create, and access content and information. In a world that relies on access to information, the importance of this decision should not be underestimated.

Archaeologists increasingly use three-dimensional modeling to analyze artifact attributes and document in situ relationships. Less attention has been paid to modeling’s potential in strengthening connections between descendant communities and their cultural heritage. In collaboration with the Grand Ronde Historic Preservation Office, we created three-dimensional models of excavation units and belongings associated with the Molalla Encampment, a late nineteenth and early twentieth century settlement area on the Grand Ronde Reservation in northwestern Oregon. This work proceeded in two steps. First, we established a modeling methodology applicable to a variety of excavation contexts and artifact types. This required defining proper artifact handling techniques and modeling procedures, including optimal camera settings and software workflow. Second, we used this methodology to capture hundreds of artifacts photos in order to build each model. Photogrammetry provides an alternative approach to heritage curation, allowing us to share interactive, three-dimensional models of historic belongings within the Grand Ronde community. This not only lends additional transparency to our research process, it can also initiate conversations with tribal members about the functions and meanings of belongings in historic reservation lifeways. Photogrammetry can thus play an important role in the development of community-based research practices.

Lecture demonstrations have a long history of use in science learning spaces. While extant research in STEM education show that demonstrations can be used to rouse student interest, some studies suggest that demonstrations have little to no effect on improving students’ understanding of the concepts taught in class. In chemistry, demonstrations are commonly used in lectures with the belief that student understanding of chemical concepts improves from observations of chemical phenomena. The purpose of this mixed methods study was to investigate students’ perceptions of lecture demonstrations and their usefulness in preparing for exams. To measure students’ perception of lecture demonstrations, a survey was administered to first year students (n <1500) in nine introductory chemistry classes over two quarters. Initial findings reveal that while students do in fact remember and enjoy lecture demonstrations, they found it difficult to apply demonstration concepts to problems on exams. Results also suggest a strong link between student engagement and exam performance. Overall this study highlights the importance of soliciting student feedback for improving and designing course materials and tools. Various strategies and implications for practice are also addressed.

A positron emission tomography scan (PET scan) can be used to map areas of potential cancer in the body. Cancer cells multiply at an incredibly fast rate, and in doing so, use a greater amount of glucose to fuel their high-energy needs compared to normal tissues. PET scans use radiolabeled fluorodeoxyglucose to quantify cellular metabolic activity, producing visual hotspots that are usually overlayed on computed tomography (CT) images and correlate to cancer sites (“PET/CT”). PET/CTs are often used to follow patients with acute myeloid leukemia (AML) after hematopoetic cell transplantation (HCT). In the lab’s database of over 300 consecutive patients whose AML relapsed after HCT, we found 15 patients who were followed with PET/CT because of extramedullary disease. These patients received a variety of treatments for their AML relapses, including induction chemotherapy, radiation, and/or hypomethylating therapy. We sought to assess if a negative post-treatment PET was helpful in predicting a cure. Through detailed chart review, we found PET scan negativitity is hard to achieve, a negative PET is not reassuring (50% still relapsed) and even a low SUV-positive PET is prognostic of disease progression. Moreover, if any extramedullary disease is present, systemic therapy prolongs life more than local radiation alone, but no treatments are likely to be curative.

The study of peptide self-assembly on solid surfaces has the potential to catalyze numerous nanotechnological advances such as biosensors and nanoelectronics. A comprehensive understanding of the factors that influence peptide binding to solids would allow for expansive integration of biomolecules and solid-state devices, and organic-inorganic interface bridging will permit greater information flow between biological systems and technological devices. The Genetically Engineered Materials Science (GEMSEC) lab has engineered peptides that are capable of binding to substrates such as graphene, monolayer molybdenum disulfide, and boron nitride nanosheets. Utilizing experimentally determined binding affinities of these binding peptides alongside a database of biochemical and physicochemical properties of amino acids, we have developed a method to computationally predict short amino acid sequences that preferentially bind to atomically flat surfaces. Matrix factorization and linear regression is used to train a model capable of predicting an experimentally observed peptide count number (observed during sequencing of eluate of phage display biopanning) from 8 Total Similarity Scores (TSS) that are calculated from 8 novel similarity matrices. This model is then used to predict the ranking of actual binding affinities of genetically engineered peptides to monolayer molybdenum disulfide from fluorescence microscopy experiments. The ability to predict solid binding by peptides will facilitate further research into peptide structure and functional properties upon adsorption. Ultimately, these methods will be implemented in a cohesive software platform using machine learning and signal processing tools to allow determination of sequence-property linkages and pattern recognition in a larger bioinformatics context, and allow for nanomedical and nanotechnological advances at the intersection of materials science, biology, and genetics. Supported by the NSF-DMREF program through the Materials Research Initiative.

Analysis of faunal remains provides crucial insight into the subsistence patterns of past groups. This is particularly important for the Grand Ronde community in northwestern Oregon, where past and present populations have balanced traditional practices and lifeways with imposed colonial assimilation pressures and economies. This research examines faunal remains found at the Molalla Encampment and Grand Ronde Agency Schoolhouse, two nineteenth and early twentieth century archaeological sites on the Grand Ronde Reservation. Our research focuses on documenting and analyzing faunal remain attributes such as degree of fragmentation, taxonomic presence, and bone modification at the two sites. In addition to comparative faunal analysis, our research takes a step further by looking into the implications of observed bone modifications. Aided by archival and primary sources, we reconstructed the taphonomic pathways of these remains, determining whether they have been altered by either humans or animals. For example, our analysis of cut marks revealed if meat was butchered commercially at the site, what meat cuts were consumed, and meat prices at Grande Ronde during the early 1900s. Comparing these data by site and stratigraphic level paints a better picture of life at Grand Ronde across space and time. This research provides insight into subsistence patterns within the Grand Ronde community and how they navigated the challenges and opportunities of life on the reservation.

Biological mineralization is the formation of minerals in hard tissues guided by proteins. Unique aspects of these minerals include the molecular control of hierarchical structure, intricate architectures, and multifunctional properties for inspiration in bionanotechnology and nanomedicine applications. Numerous biomineralization strategies have been developed in hard tissue regeneration therapies. However, there is currently no in-depth understanding of how proteins regulate the synthesis of these inorganics or the physiological formation of the minerals. The ability to control mineral formation for biomedical applications, therefore, is still limited to the use of a few mineral-directing proteins extracted from tissues. Biomineralization can also be controlled using short peptide domains derived from natural proteins known to have a regulatory role in mineralization. Our laboratory has designed peptides derived from amelogenin (ADPs), the key protein in tooth formation, using combinatorial selection and computational design, whose utility in rebuilding hydroxyapatite (HAp) mineral on tooth has been demonstrated in numerous case studies. The goal here is to understand the fundamental mechanisms of biomineralization guided by ADP5 and develop a methodology to form HAp with exclusive control of its growth kinetics and mineral crystallography. We designed mutants of ADP5 to investigate changes in mineralization kinetics, nucleation, and morphology. In the current study, we are establishing the conditions for ion-peptide interactions on the onset pH for mineral nucleation using calcium/phosphate and mutant ADPs. The goal is to gain insights into the correlation between sequence domains and biomineralization outcomes eventually facilitating greater control over the reaction and further optimize remineralization approach. The developed method has a high potential to develop non-invasive oral health care materials and methods by restoring mineral loss, the root cause of dental ailments and, eventually, help bring clinical and over-the-counter dental products into the market with preventive, restorative, therapeutic, and cosmetic characteristics. Sponsored by SoD Spencer Funds.

Major Depressive Disorder (MDD) has the largest life time prevalence (17%) of mood and anxiety-related disease. The prevalence of MDD is also 1.7 times greater in women than men. Chronic stress and anhedonia are the primary symptoms of depression, and decisions are affected. Our laboratory has shown that corticotropin releasing factor (CRF), the stress hormone, potentiates dopamine release in the core of the nucleus accumbens (NAc), suggesting a relationship between stress and reward processing. While it is known that an individual’s decision making is altered in a depressed state, the precise neurological pathway between stress and reward processing in the brain is unclear. To characterize this “stress-reward” pathway, I used a novel decision-making framework where a cohort of male and female mice performed an operant concurrent-choice task choosing between 0.1M sucrose solution or water. Mice were injected intracranially with α-CRF, a non-selective CRF antagonist, or vehicle in the NAc prior to performing the task. I measured task performance. I hypothesize that mice injected with α-CRF demonstrate less appetitive and reward-seeking behavior compared to the vehicle group, implicating a lower sucrose nosepoke percentage, sucrose choice percentage, and higher sucrose latency during the decision-making task. I also hypothesize that females have a greater reward sensitivity system than males, resulting in an augmented decline in appetitive and reward-seeking behavior compared to males. If these results indicate a significance in further elucidating the “stress-reward pathway” through the decision-making task, this can pave way for potential new treatments targeting this pathway for depression.

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

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

Anecdotal evidence suggests patients that undergo Targeted Muscle Reinnervation (TMR) surgery, an operation where nerves are implanted to muscle instead of cut and left between muscle, report less residual and phantom limb pain when compared to standard amputation patients. To our knowledge, this is the first study to investigate this claim. Based on the nature of the TMR procedure, it should facilitate higher pressure thresholds than a severed nerve from a standard amputation, resulting in less pain for the patient. The risk of neuromas, a collection of highly sensitive tissue that can develop on a damaged nerve, should also diminish. To evaluate the efficacy of TMR in relation to pain reduction, a populace upwards of 135 people (comprised of TMR amputees, standard amputees and a control cohort) will have their nerves stimulated using focused ultrasound, allowing the application of focal intense and transient pressure on the nerve and not on the surrounding tissue. In this study, diagnostic ultrasound imaging guided the application of intense focused ultrasound on intact and transected nerve endings in our test subjects. We increased the ultrasound intensity until we either elicited a sensation or reached the maximum output possible by our device. We anticipate TMR amputees to have a higher threshold for ultrasound-induced sensations than standard amputation test subjects, but a lower threshold than the control test subjects. Due to the limited availability of TMR amputees in the area, a definitive conclusion has not been made about the effect TMR has relative to the standard amputation. When analyzing results from standard amputees specifically, there are three subgroups that possess an intriguing feature that distinguish them from each other. This study can potentially influence the types of surgical techniques offered to future amputees if TMR operations do in fact reduce the amount of pain experienced by patients.

X-ray binaries consist of a star gravitationally bound to a compact object (white dwarf, neutron star, or stellar mass black hole). Matter from the star is pulled onto the compact object and accretes in a disk which emits high-energy X-rays. These objects have variability observable on human time-scales—days and weeks rather than millions of years—and provide insight into high-energy physics. In this project we analyzed the light curves of time-variable objects to identify candidate binary systems. We cross matched data from optical variability surveys such as ASAS-SN, ATLAS and ZTF with the ROSAT all-sky X-ray survey. We were able to confirm known cataclysmic variables (CVs) and active galactic nuclei, and also discovered new CVs. These methods will be useful in identifying these rare objects in LSST’s massive data set in a few years.

Whispering Gallery Mode (WGM) sensors have unprecedented sensitivity in the optical detection of label-free biomolecules. These sensors can detect surface adsorption and have been used to detect single molecule adsorption and interaction processes. By observing resonance shifts during molecular interactions, WGM sensors can characterize a molecule’s surface adsorption. The goal of this project is to develop a robust WGM dip sensor array controlled by a three-axis stage in order to perform high-throughput characterization of peptide binding and adsorption within a 96-well plate format. The peak of spectral absorbance is the WGM resonance, and as this changes with surface adsorption we measured a spectral shift. Using this spectral shift in combination with the known concentration of our peptide species, we determined binding kinetics. The WGM sensor was used to characterize different peptide sequences to further understand the effects of peptide mutations on binding kinetics. A single microsphere resonator was used as proof of principle and will eventually be adapted to an array of eight WGM microsphere resonators to generate large amounts of data. This high throughput approach will provide the much needed large amount of quality data that is necessary for the development and adaptation of machine learning and applied statistical analysis algorithms toward the eventual development of artificial intelligence platforms in material science. The project is supported by NSF-DMREF through the Materials Genome Initiative.

During HIV infection, CD8+T-cells are crucial for the control of viral replication. Increased CD8+T-cell polyfunctionality, which is the ability for one cell to perform more than one function within the immune response, was associated with improved clinical outcomes, is now the focus of experimental curative therapies for HIV. One therapy that showed promise is a Conserved Elements DNA (CE) vaccine, which is designed to prime the immune system with essential regions of the virus, thereby eliciting polyfunctionality and circumventing escape mutants. A novel immunotherapeutic combinatorial approach was investigated for the ability to reduce or eliminate viral burden in Simian Human Immunodeficiency Virus (SHIV) infected macaques receiving antiretroviral drug therapy. We evaluated effects of this regimen on CD8+T-cell polyfunctionality and its correlation to viral control after analytical antiretroviral treatment interruption (ATI). Our combinatorial immunotherapy regimen uses the CE vaccine to target highly conserved viral sequences, latency reversal agent GS986, exhaustion reversal agent anti-PD-1, and CCR5 gene editing to delete the co-receptor for viral entry in CD4+T-cells. Analysis of CD8+T-cell polyfunctionality was performed using intracellular cytokine staining and flow cytometry to measure the frequency of CD8+T-cells secreting one or more of the following effector functions: TNFα, IFNγ, IL-2, and both CD107a and Granzyme B. Polyfunctionality induced by the combinatorial regimen was algorithmically quantified and compared to a control group receiving no interventions and a group receiving CE vaccine and CCR5 gene editing alone. Our analysis showed neither significant differences in polyfunctionality between treated and control groups, nor any changes in polyfunctionality within the subset of CD8 targeting conserved regions of the virus. However, we observed diverse viral control post-ATI among all animals, and additional experiments are in progress to determine if CD8 polyfunctionality played a role in improved viral control post-ATI.

Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent neurodevelopmental disorders to date, affecting 5-7% of school-age children. Characterized by inattention, impulsivity, and hyperactivity, those diagnosed with ADHD often have difficulty in navigating multiple tasks, sustaining attention, and inhibiting impulses. Although prior research suggests increased attention to sensory stimuli enhances task performance temporarily when the stimuli are task-related, little is known about the effect of irrelevant stimuli on task performance. The current study evaluates whether irrelevant stimuli decreases response accuracy and speed during computer tasks among children with ADHD. Children between the ages of seven and eleven, with (n=50) and without (n=30) ADHD, are recruited to participate in comprehensive neurocognitive phenotyping, including completion of two computer games varying in difficulty (i.e. easy and hard versions). The tasks involve ignoring irrelevant visual stimuli that are presented alternatively with task-related visual stimuli. Irrelevant stimuli consist of three stimulus types, including standard (60%; white bracket-shaped image), deviant (20%; white bracket in opposite orientation to standards), and novel (20%; white line drawings of animals and vehicles). The current study hypothesizes that compared to non-ADHD children, children with ADHD will have lower accuracy and slower reaction times in response to task stimuli that immediately follow novel irrelevant stimuli, as compared to standard irrelevant stimuli. Preliminary results (n = 23) support this hypothesis through a variance analysis, indicating children with ADHD show worse accuracy following novel, i.e. more distracting, stimuli than standard stimuli compared to typical, non-ADHD children, F(1, 19) = 5.028, p = .037. Through this study, we will gain a greater understanding of children’s needs of attention maintenance. Implications of this study include reduction in classroom distractions could improve task-related accuracy and processing speed among children with ADHD.

Mitochondrial dysfunction, characterized by decreased efficiency of the Electron Transport Chain (ETC) and loss of structural integrity, is linked to cellular senescence, an irreversible end to the cell-division cycle that contributes to aging. Minimizing senescence through late age intervention may prevent aging tissue dysfunction. Systematic treatment of old mice with a tetrapeptide, SS-31 reduced mitochondrial dysfunction and senescence in kidneys. We hypothesized that a similar effect would occur in other organs, and with other mitochondrial targeting interventions. These interventions included the SS-31 tetrapeptide which interacts with mitochondrial cardiolipin to improve structure and function, and NMN (Nicotinamide Mononucleotide), which fuels the organelle for more efficient adenosine triphosphate generation through the ETC. We treated old mice at 24 months-of-age for 8 weeks with either SS-31, NMN, or both interventions combined. Control groups included young-untreated mice at 4 months-of-age and old-untreated mice sacrificed with the treatment groups at 26 months-of-age. By comparing tissues, including heart, kidney, liver, skeletal muscle, skin and brain, within individual mice, we were able to account for differing rates of aging between mice. To determine the relative levels of senescence and treatment response in each tissue, we used Immunohistochemistry to quantify known senescence markers p16 and HMGB1, and quantitative-PCR to measure p16 mRNA transcript levels. As expected, preliminary results from p16 staining showed higher overall senescence burden in old as compared to young mice. The staining patterns also revealed senescence susceptible cells, with majority of p16 positivity in liver satellite cells, glomeruli and tubules of kidney, fibrocytes of heart and myocytes of skeletal muscle. Overall, the kidney and liver had more p16 positive senescent cells than did heart and muscle. These tissues are currently under analysis to determine whether intervention treatments can reduce cellular senescence.

Black bears are the most abundant bear in North America and Washington, but present knowledge is dominated by telemetry studies on home range size or vegetation class preference. Camera trapping data indicating black bear presence were used to build an occupancy model for the two study sites in Washington, one in Okanogan county and one in the northeast. The camera traps are intended for a predator-prey study focused on wolves, cougars, and ungulates, but detected a large number of black bears, suggesting the importance of black bears in these ecosystems. Black bear distribution may be driven by land-use patterns including variables such as elevation, vegetation and habitat type, approximate percent canopy cover, slope, aspect, and land management type. The constructed single season occupancy models of black bear presence can be used to better understand habitat selection by black bears in different regions of the state. This study seeks to fill in gaps of knowledge about black bears in Washington and provides a framework for future occupancy studies on black bear habitat use.

Art can be a healthy way to express emotions and bring healing to the hurting mind. Tapping into the creative mind and using art to express oneself can provide a calm that other methods may not. Mental health disorders and substance use disorders are giants that cannot be defeated by one method alone. The safest place to be for an individual suffering in silence is outside the mind in an inclusive, creative, empathetic, and healing environment. The LWTech Lion's Pride Healing Art club is intended to help individuals safely experience and express emotions while bonding and sharing a safe space with like-minded people. To understand the effect that the healing art club has on its participants, I am conducting in-depth interviews with key students and staff. I hypothesize that participation in the healing art club helps express themselves in a therapeutic way, foster feelings of belonging to the community, and contributes to their overall health. The data collected is a helpful start in encouraging college communities to adopt similar programs and to promote positive mental health on campus.

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

Bignoniaceae, also known as the trumpet creeper family, consists of 800 species of trees, shrubs, herbs, and lianas. Bignoniaceae diversity is highest in the Neotropics, but have a worldwide distribution in both tropical and temperate zones. Molecular phylogenetic studies recognize 8 major clades in the family. The goal of this work is to construct an updated Bignoniaceae phylogeny by gathering all available DNA sequence data in the family from previous studies, GenBank, and unpublished sources. I organized, gathered and selected genetic data that I used to create locus alignments for a concatenated matrix. Phylogenetic reconstruction of the concatenated data was done using Maximum Likelihood and Bayesian methods. With these results, we aim to better understand family-wide diversification patterns in the family. Previously recognized clades are supported, additional resolution among them is obtained, and major biogeographic events are reconstructed.

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

 Antibiotic resistance is a growing threat to public health. This resistance, coupled with a dearth of new antibiotics, makes the study and development of antibiotics of critical importance. Many antibiotics derive from microbial pathways that synthesize complex natural products, and engineering these pathways to produce new antibiotics is an exciting prospect. I aim to use such a strategy to produce variants of the klebsidin lasso peptide, known for its distinct lariat knot structure and its antibiotic activity. Klebsidin is produced by three biosynthetic enzymes that modify and export a ribosomally-synthesized precursor peptide. We have developed an assay that relies on cellular growth to (1) investigate how mutation influences the antibiotic activity and biosynthesis of klebsidin, and to (2) identify variants of klebsidin that overcome a known resistance mutation. When expressed in E. coli, klebsidin inhibits growth of its host cell. I expressed a library of approximately 10,000 klebsidin variants, each within a single cell, and used next-generation DNA sequencing to count the frequency of each variant before and after a growth selection. Functional klebsidin variants should decrease in frequency after selection, whereas null variants should increase in frequency. Using these sequencing data, I generated functional scores for a majority of single amino acid mutations within klebsidin, identifying positions that tolerate mutation and positions for which mutation abolishes bioactivity. To better understand these trends, I am performing mass spectrometry experiments to study the biosynthesis of key variants. In addition, we are interested in how mutagenesis of klebsidin can combat known resistance to lasso peptides. By performing the same growth selection in an E. coli strain resistant to wild type klebsidin, we hope to identify variants that overcome this resistance. Together, these studies will provide a framework for understanding lasso peptide engineering and identifying novel peptide-based antibiotics.

Embryonal rhabdomyosarcoma (ERMS) is a devastating pediatric cancer that affects soft tissue such as skeletal muscle and connective tissue. Currently, there is no effective treatment for patients with ERMS. Mutations in the gene PTPN11 are found to have cancer-promoting roles in leukemia, lung, and breast cancers, but its role in ERMS is virtually unknown. PTPN11 codes for the SHP-2 protein, which is a component of the RAS/MAPK (mitogen-activated protein kinase) signaling pathway. Abnormalities in this pathway are known to transform normal cells into cancer cells when certain proteins are upregulated. My central hypothesis is that PTPN11 promotes RMS tumor growth by allowing cells to proliferate and differentiate out of control. To test the hypothesis, I used CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas gene editing technology to disrupt PTPN11 gene function in two models. I designed constructs that express guide RNAs that target the PTPN11 locus in the zebrafish or human genome. If PTPN11 has a tumor-promoting role, I expect targeted disruption of zebrafish PTPN11, delivered via microinjection, to result in reduced RMS tumor formation and growth compared to zebrafish tumor with no PTPN11 gene disruption. In the human ERMS cell lines, I will use virus-mediated transfer to introduce the CRISPR DNA construct in vitro. My hypothesis will be supported if the cells harboring targeted disruption of PTPN11 have reduced growth and less self-renewal capacity compared to the control cells. My findings will elucidate the role of PTPN11 in RMS, which will allow further research into the potential therapeutic benefit of targeting PTPN11 in pre-clinical RMS models.

Through rapid industrialization and development, much of the Green River Valley landscape and townships from the earlier periods of settlement have been obscured. However, several historical cemeteries remain largely preserved. Cemeteries can have an equalizing power when it comes to representation of past populations, while preserving societal ideas of hierarchy. While cemeteries cannot tell the full history and lives of those interred, they do provide names, ages, and the placement of the individual in conversation with other deceased people. A cemetery is not a passive location in a town, but rather a place created with the ability to reflect societal values regarding death and social integration and spiritual significance for the living. My research focuses on what relationships can be rediscovered in the development of the Green River Valley’s townships, as these relationships may speak to the social organization of the Valley townships in development, the role death had in society, and how race, gender, religion or other factors were presented. These relationships will be investigated following three lines of inquiry: a) relationship among the dead in cemeteries, b) relationship between cemeteries and the living in modern and historical times, and c) relationship of the deceased’s identity and their position within the cemetery landscape.  Though each cemetery has been researched and written about separately, conducting a survey of several cemeteries in the region and analyzing them together will allow for a bigger picture of health discrepancies between men and women, white and non-white residents, and differences of land quality broadly associated with members of different social classes, building a more comprehensive history of the Green River Valley.

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

Our Lab, GEMSEC, uses molecular biology, bioinformatics, genome sciences, and engineering for de novo design of short amino acid sequences for various applications such as tooth remineralization strategies in dentistry, biosensing in cancer diagnostics, and bioelectronics in single-molecule detection. Designing and constructing peptides for a desired function begins with selecting the appropriate sequence of amino acids with the predictive conformation that affects the function. In this project we use latent-space representation (matrix factorization) in conjunction with a simple neural network to create a model that is able to predict peptide binding affinity to several alleles of MHC-I protein. Python was used to encode amino acids by creating data frames defining the functional groups within them, differing by n-terminus, intermediate, and c-terminus of each amino acid and their placement along the backbone of each structure. A tensor was created using the data frames describing each amino acid to encode the 9- and 10-length sequences of thousands of unique peptides from the Immune Epitope Database. Each chemical structure and peptide sequence can be described by k attributes, or latent features. Matrix factorization was used to discover the latent features and send this feature encoding to a neural network (NN) to determine binding affinity. The goal is to minimize the mean-squared-error by stochastic gradient descent in a supervised learning protocol. The two modules of matrix factorization and NN provide an optimum between interpretability and predictability simultaneously.The successful prediction of peptide binding affinity towards nanoscale targets provides novel opportunities for drug design towards targeted public health initiatives and in technology applications such as bio/nano hybrid devices. This research is supported by NSF/DMR-DMREF program under the Materials Genome Initiative.

Over the past 15 years, early college students of the Ocean Research College Academy (ORCA), which is offered through Everett Community College, have collected information about fecal coliform levels in Possession Sound. This research is comprehensive spatially and temporally, but does not include information about potentially dangerous antibiotic resistance. Carbapenem-resistant enterobacteriaceae (CRE) are a class of antibiotic-resistant gram-negative bacteria that are specifically resistant to Carbapenem-class antibiotics, which are often considered last-resort antibiotics. As such, CRE pose a major health risk and cases are often difficult to treat. This study will investigate the presence of CRE in Possession Sound at 5 public-access beaches. Samples will be collected using sterile containers and then cultured on selective media containing graduated levels of imipenem using MacConkey agar. Viable CRE colony-forming units will be tested using disc-diffusion for sensitivity against a panel that represented other common antibiotic treatments for enterobacteriaceae on Mueller-Hinton agar and species-identified using a API 20E kit. This study will provide a reference point for future researchers looking to investigate the presence of CRE organisms or other resistant bacteria in the Possession Sound.

How can we improve healthcare in under-served South East Asian Countries? One possibility is via mobile-health technology. Mobile-health or m-health is the practice of medical and public health supported by mobile and wireless devices. This literature review looks at over 20 years of the emergence of m-health and the prediction of future possibilities. The goal is to look at areas of improvement such as cost efficiency, adapting to the specific country’s infrastructure and integration of m-health in healthcare. In countries like Nepal, m-health has helped to eradicate diseases like malaria, improve neonatal health care and empower female health volunteers. It has also helped gather information such as statistics on usage and distribution of drugs, healthcare workers' interactions with patients and disease surveillance. With the rise of mobile users, healthcare facilities can create a structured international framework to regulate and increase the efficiency of m-health. This research will help facilitate conversations about the potential of m-health and where it needs to be improved so that it can play a pivotal role in healthcare of South East Asian countries.

Physiological and behavioral rhythms are controlled in mammals by a central circadian clock located in suprachiasmatic nuclei of the hypothalamus (SCN). This master clock has outputs to other organs and tissues crucial to keeping the organism properly synchronized. The SCN clock is synchronized by environmental cues, most importantly is the light-dark cycle (LD). Fearful stimuli (i.e. presence of predators) can also present cyclic variations. The de la Iglesia lab has recently shown that timed fearful stimuli during the night can switch the locomotor activity rhythms of mice to the light phase, overriding their natural nocturnal behavior. Interestingly, while the expression of the so-called “clock genes” (which sustain the circadian rhythms at the molecular level) remains unchanged in the SCN, it displays a complete inversion in the amygdala, the brain region that encodes fear. Currently, we aim to determine the pattern of expression of clock-genes in peripheral organs of mice subjected to cycling fear stimuli. Using qPCR, we will assess RNA expression of the clock genes bmal1, per1, and per2 in the adrenal gland, kidney, and liver to determine whether entrainment of activity by cyclic fear also impacts peripheral clocks at the molecular level. We hypothesize that the pattern of expression the clock genes in the liver and kidneys will be modified in mice subjected to nocturnal fear, due to altered feeding and drinking patterns. However, the adrenal gland is difficult to make predictions about the pattern of expression of the clock genes given the fact that preliminary data from our lab showed that cortisol shows two peaks in mice displaying diurnal activity after nocturnal cyclic fear exposure compared to the single peak displayed by nocturnally active mice. Thus, it is unclear if we will observe an inversion peak, much like the amygdala, or a peak similar to the LD cycle.

The three year-long civil war in Yemen between Houthi militia, made up of Yemen's Zaidi-Shia Muslim minority, and the Saudi-led coalition over the restoring of each of their respective powers to the Yemeni government has had irreversible impact on both Yemeni people and society. Thousands have died, either directly from bombing or indirectly due to blockades put in place by the opposing forces, and hundreds have gone missing or been forcibly disappeared. Soaring inflation, in combination with years of blockades and bombs, have had disastrous effects on the economy of Yemen. As part of a seminar on Human Rights through UW Bothell, I explored policymakers' response to the ongoing crisis. My research took place in two phases: first was gathering data regarding the war, where I found that current UN reports project that if bombing continues and a resolution between the opposing parties is not reached soon, over 14 million people will die of starvation. Step two was to make a policy recommendation on behalf of the U.S. as a result of this research. Scholars have engaged in long-standing debates over what U.S. response should be to the crisis. In my research, I argue that the United States, as an ally of Saudi Arabia, must act immediately to end support of the Saudi-led coalition in Yemen that is directly responsible for the deaths of thousands and for the dire humanitarian crisis of millions. No administration has gone to Congress to approve the involvement in Yemen's civil war, and thus, Congress must enact the War Powers Resolution of 1973 and end U.S. support of the Saudi-led coalition in Yemen. If the United States wants to be seen as a protector of human rights worldwide, we must stop aiding the blatant human rights abuses in Yemen.

Hydrogen is a non-polluting, sustainable energy alternative to fossil fuels. One method of generating hydrogen is by splitting water with sunlight and a semiconductor photocatalyst. In this study, determining the most viable semiconductor in terms of efficiency and safety for the environment is critical for making hydrogen energy available for commercial usage. When the catalyst absorbs UV light, water molecules in contact with the activated surface are split. Hydrogen is produced more rapidly when the photocatalytic crystals have a high surface area to volume ratio. Therefore, greater efficiency can be attained by reducing the size of the photocatalyst crystals. Nanometer-sized crystals can be synthesized within nanopores, thereby avoiding loss of surface area by agglomeration. Particular attention has been focused on placing the most efficient and cost-effective semiconductor inside a matrix of cellulose fibers and introducing doping, quantum dots, and other engineering strategies to improve the suitability of the photocatalyst. Selecting the most fitting photocatalyst candidate for large scale mass production of hydrogen is imperative for providing a viable source of renewable energy.

Self-efficacy has been shown to be associated with fewer problem behaviors in adolescence. However, the research investigating this association has been primarily based on self-report measurements of delinquency. The purpose of this study is to see if this association is maintained with a more objective measure of delinquency by examining juvenile offenders’ self-efficacy, and its predictive relationship with probation violations. Using self-report survey data of juvenile offenders’ self-efficacy along with probation violation data from Pierce County Juvenile Court, we conducted a statistical analysis of self-efficacy measurements and official probation violations. The self-reported self-efficacy measures address feelings in desire of academic and career success, prosocial behavior, and a reduction in the desire to express aggressive behaviors. If self-efficacy is shown to be a good predictor of fewer probation violations, further research can investigate determinants of high versus low self-efficacy, or how to improve self-efficacy, in order to promote probation adherence of juvenile offenders.

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

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by clinically recognized deficits in social communication, repetitive behaviors, and restricted interests. While the etiological underpinnings of ASD have yet to be determined, biological indicators of the disorder (e.g. biomarkers) hold promise as valuable diagnostic methods. Neurological biomarker initiatives are particularly essential in their potential to pinpoint the neural activity that gives rise to the disorder’s hallmarks. Resting state electroencephalography (EEG) studies suggest altered default signaling associated with ASD, with particular deviations in the power of the alpha frequency band. However, previous work has produced contradictory findings regarding the directionality of these abnormal power patterns, which motivate the need to better understand the implications of certain methodological decisions. In this study, we acquired EEG recordings during resting state paradigms in individuals with ASD and a neurotypical control group. We hypothesized that individuals with ASD would display reduced alpha activity, in comparison. We suspect that activity will be reduced, both when analyzed by peak power and average power over the entire frequency band.

Molecular interactions that occur between surface components of pathogens, termed adhesins, and complementary receptors presented on host cells are critical for establishment of infection. The adhesion-receptor binding event may trigger diverse signaling cascades in the host cell that result in activation of innate host defenses or the subversion of cellular processes facilitating bacterial colonization or invasion. Hence, microbial adhesins are important targets for the development of antimicrobial therapeutics and vaccines. One of the interests of the Sokurenko Lab at UW is understanding the structure and function of the ubiquitous Escherichia coli adhesin, FimH, and its potential as a vaccine candidate against urinary tract infections. FimH is expressed on top of filamentous hair-like appendages called type 1 fimbriae that confer bacterial binding to glycoproteins with terminally exposed mannose. In the laboratory, we use a variety of assays to study FimH-mediated bacterial adhesion and test different mannose-containing compounds and glycoproteins for optimal inhibition of FimH-mediated interactions. We also elicited a great number of FimH-specific monoclonal antibodies that are tested for their potency to inhibit binding properties of the FimH, and to understand the structural mechanisms of antibody-mediated inhibition. By generating and analyzing various FimH mutants, we seek to elucidate how the function of FimH protein can be efficiently regulated. The ultimate goal of these experiments is to gain knowledge on the optimal structure (conformation) of the FimH protein that can be used as an antigen for efficient induction of protective antibodies during immunization.

Women in the most underserved area of Seattle experience higher rates of pre-term birth, low birthweight rates, and cesarean section surgeries. The focus of this project is to see if female genital circumcision (FGC) correlates with the cause of these issues, but also if there are other factors that have an influence on high reproductive health disparities such as, racism, access to resources, and any other barriers of the community that are driving these issues. This project works with Somali immigrant and refugee residents in the south Seattle area because it is the most under-served, ethnically and economically diverse area. Somalia has the highest rate of women who have undergone the practice of FGM/C with a leading 98% of the female population between the ages of 15-49 years being circumcised. My project works collaboratively with the Mama AMAAN Project which seeks to test out a community-led, integrative services approach to improve perinatal health outcomes in this population. The goal of my project is to understand why these issues are consistently happening amongst women that come from similar backgrounds, more specific amongst East African women. While trying to reach the goal of this project, we seek to answer the following questions; What are the ways that FGC played a part in their perinatal experience and outcomes for Mom and infant? What is their perspective on the practices of FGC in Seattle as relates to themselves, their families, their community? To accomplish the goal of my research I plan on using qualitative methods by conducting written surveys, participant-observation during child birth education sessions. This project is significant because it assesses the reason for the high rates of reproductive health disparity that we are seeing amongst the women of the Somali community and how FGC is related to those problems, if at all.

Fatty Acid Binding Proteins (FABPs) are intracellular proteins that facilitate the transport of fatty acids and other lipophilic substances into the cell for various biological functions. For example, FABP5 is important for binding endocannabinoid anandamide (AEA) which helps regulate cognition, learning, and memory. Compounds such as tetrahydrocannabinol (THC), the psychoactive component of cannabis, competitively inhibit FABP5 and prevent catabolism of AEA in the cytosol by fatty acid amide hydrolase (FAAH). Because many drugs (like ibuprofen and progesterone) are also lipophilic and poorly water-soluble, we predict that FABP5 has a role in their metabolism. The goal of this investigation is to better understand how FABP binding may affect drug metabolism by determining the binding affinities of different drugs to FABP5 using a fluorescence displacement assay. We first validated an assay for screening drugs and determining drug-FABP5 binding. Both ANS and NBD-Stearate, molecular probes that generate a fluorescence signal upon binding, were evaluated. FABP5 was titrated with increasing concentrations of each probe and the resulting changes in fluorescence plotted a hyperbolic curve used to calculate Kd (dissociation constant). In these trials, NBD-Stearate was found to have high background fluorescence and low sensitivity to changes in fluorescence upon alternative ligand binding, so ANS was selected for further method development. We found that factors such as mixing and time to equilibrate affected the Kd, possibly from non-specific binding. The binding affinities for ANS were 1.177 ± 1.005 μM (Morrison equation fit average), and 4.744 ± 1.387 μM (One Site Specific average). The preliminary data showed that fluorescence decreased by 48.28% with the addition of arachidonic acid (positive control) which confirmed ANS as a suitable assay. By adding increasing concentrations of various drugs to competitively inhibit the binding of ANS, a decrease in fluorescence will be measured and used to calculate Ki (inhibitor binding affinity).

The DArk Matter In Charge-coupled devices (DAMIC) group at the University of Washington tests and packages charge-coupled devices (CCDs) that are used to detect dark matter. The CCD pixel array collects the free electrons that originate from collisions between silicon atoms and outside particles traveling through the CCD. The signal from these electrons is then measured and a two-dimensional image is produced, showing the interaction of the outside particles with the silicon atoms. In order to "see" a dark matter interaction, the CCDs have to be isolated from non-dark matter particles that may pass through. To do this, the experiment is operated 2 km underground and surrounded with lead blocks. However, these measures are in vain if there are radioactive particulates on the packaged CCDs. Radioactive isotopes decay and produce an array of particles, which are detected. One opportunity for particulate contamination is when the CCDs are exposed to the air in the DAMIC cleanroom. Therefore, the cleanliness of the cleanroom must be measured. This is done using a sampling procedure that has been standardized by the International Standards Organization (ISO). We used particle counters to count the number of airborne particulates and then analyzed the data using the ISO classification system. From this, we now know the cleanliness of the DAMIC cleanroom. Additionally, electron microscopy is being used to characterize the particulates that land on the CCDs during the wire-bonding process.

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

Tuberculosis (TB) remains a major international health concern and one of the top 10 causes of death worldwide, according to the World Health Organization. Previous clinical work in our lab demonstrated that oral swab analysis (OSA) can successfully diagnose tuberculosis by detecting Mycobacterium tuberculosis DNA in the mouths of infected patients. In order to strengthen OSA against traditional but more invasive methods, such as sputum sampling, improvements to DNA extraction and swab type must be investigated. I am comparing different degrees of automation with MolBio’s Trueprep, the AudioLyse, and ThermoFisher’s KingFisher against our previously validated manual Qiagen extraction protocol—with the comparison lying in sensitivity and efficiency. In order to increase the versatility and sensitivity of OSA, I am also investigating boil preparations and dissolvable swabs. Boil preparation of swabs is a relatively simple extraction procedure, and early results have demonstrated its comparability against the Qiagen extraction. Meanwhile, dissolvable swabs have a hypothetical 100% yield of sample material. I have successfully dissolved calcium alginate swabs from Puritan in acidic sodium citrate solutions, and Luna swabs were dissolved in chaotropic agents. DNA yields are compared to non-dissolvable, previously validated swabs.

Interferons are signal proteins released by cells in response to infections which induce neighboring cells to synthesize anti-viral genes like Mx2, which encodes the MxB protein. MxB was thought to only restrict lentiviruses but recent studies have shown that MxB also restricts herpesviruses. It is hypothesized that herpesvirus and MxB have co-evolved in an ‘arms race’ to compete against each other. This suggests that regions of MxB that are under positive selection may have interfaces for its anti-herpesvirus activity. In order to test this hypothesis, I plan to determine whether different homologs of MxB can restrict human herpesviruses. I created MxB inducible cell lines using MxB homologs from three different primates - humans, rhesus monkeys and owl monkeys. Subsequently, I infected these cells with the following GFP labeled viruses: herpes simplex virus 1 (HSV-1), Kaposi’s sarcoma-associated herpesvirus (KSHV), and human cytomegalovirus (HCMV). I assessed the effect of these MxB alleles on viral replication by measuring viral titer and viral protein production (including GFP). I expect that the MxB restriction of herpesviruses will be species-specific, with only human MxB showing meaningful reduction in human herpesvirus replication. These results will guide future research aiming to understand the physical interactions and mechanisms of suppression between MxB and herpesviruses.

To keep peace with increasing world energy demands, scientific research has shifted to devising sustainable energy alternatives. Unlike widely used fossil fuels, solar energy is carbon-free and globally abundant, and therefore a promising energy supplement to aid global efforts in reducing anthropogenic carbon footprint. My project sought to employ light-harvesting colloidal semiconductor nanoparticles, namely quantum dots (QDs), to drive the energy-intensive depolymerization of lignocellulosic biomass and to store solar energy in chemical bonds. Accounting for 40% of biomass’ energy content, lignin is one of few naturally existing polymers composed of valuable functionalized aromatic species and is the target substrate for the decomposition reaction. Recently, iridium-based catalysts have been used to cleave β-O-4 linkages (predominant C-O lignin linkers), however, iridium’s high cost and poor long-term stability hinder its utility in extensive production and application. In contrast, prior work from my research team has demonstrated that QD photocatalysts boast lower synthetic costs, higher turnover frequencies (up to 15x faster), lower catalyst loading (333x less catalyst), and various traits desirable for industrial reproduction over iridium. Beyond QDs, my studies also looked at the synthesis of anisotropic nanoparticle photocatalysts such as nanorods and nanotetrapods. QDs are quantum confined, meaning photoexcited, oppositely-charged electrons and holes (electrons’ counter charges) recombine quickly in all dimensions, which endows them with size-tunable semiconductor functionalities. Nanorods and tetrapods are quantum confined in the width but not along the length dimension, which delays the recombination of paired electrons and holes (excitons). This elongated exciton lifetime allows more time for substrates to interact with our nanomaterials which facilitates photocatalysis. As pioneers in studying photoredox-active nanomaterials, we were motivated to decipher how nanomaterial design dictates photocatalytic performance, which not only furthers the search for most efficient photocatalysts but advances contemporary research on effectively using solar energy to derive solutions to presently-unfeasible, energy-demanding reactions.

All-trans-retinoic acid (RA) serves an important role in maintaining tissue health, either deficient or excessive levels can lead to health issues. Aldehyde dehydrogenase 1A1 (ALDH1A1), is generally believed to be the main enzyme responsible for the conversion of retinaldehyde (RAL) to RA in the liver, requiring the cofactor nicotinamide adenine dinucleotide (NAD+). However, previous studies indicated that after WIN18,446, a potent inhibitor of ALDH1A enzymes, was administered to mice; liver RA concentrations were not significantly altered, and in vitro the RA formation in mouse liver was only inhibited by about 50% suggesting other enzymes except ALDH1A1 synthesis RA in mouse liver. Mouse aldehyde oxidase has previously been proposed to synthesize RA. Hence, in the current study we tested the hypothesis that aldehyde oxidase (AOX) also contributes to the formation of RA in human liver. Our data shows that purified human recombinant AOX catalyzes the oxidation of RAL to RA. The K_m (indicating substrate binding affinity to the enzyme) and k_cat (indicating maximum enzyme velocity) values were determined by enzyme kinetic assays as 1.4 μM and 3.5 min-1. In the absence of NAD+(AOX mediated activity), RA formation was observed in human liver S9 fractions (HLS9) and the RA formation rate was, on average, 60% lower than that measured in the presence of NAD+(n=4). In addition, hydralazine, a selective AOX inhibitor, inhibited about 55% of RA formation in HLS9 in the presence of NAD+ while combining hydralazine and WIN18,446, more than 85% of RA formation in HLS9 was inhibited when compared to the control. In conclusion, this data shows that AOX and ALDH1A1 each contribute about 50% of RA biosynthesis in human liver. This research helps us better understand the regulation of retinoid homeostasis in humans.

The #MeToo movement has sparked a national conversation about what constitutes sexual consent, and a series of debates have erupted over the actions of famous men like Brett Kavanaugh, Louis C.K., and Aziz Ansari. Popular hits like Robin Thicke’s song “Blurred Lines” have also come under fire for promoting sexual violence by celebrating confusion around sexual consent. At this moment, when norms and expectations around sexual interactions seem to be changing quickly, it is especially important that we have comprehensive and systematic data on how people define sexual consent and interpret ambiguous sexual experiences. Existing studies have shown characteristics of an individual matter when it comes how they conceptualize appropriateness. However, we still do not know to what extent these characteristics matter. This study addresses this gap by answering the question: How do people of varying groups define appropriate sexual behaviors and boundaries? A Q-Method study of over 200 people will reveal how individuals of different characteristics sort scenarios of various sexual interactions into categories ranging from “most appropriate” to “most inappropriate.” Q method is similar to a rank-order techinque and allows for representation or reconstruction of perspectives concerning any given topic of interest. In addition to providing insight about how different people make sense of sexual behaviors, this study shows how Q-sorts can provide a more detailed look at sexual norms than the survey and vignette studies currently used in the field.

We have built an air quality sensor to track smoke from wildfires at UW’s Manastash Ridge Observatory (MRO). The increasing number of wildfires over the last few years has raised concern that smoke may contaminate the telescope optics at MRO. Our goal is to measure the amount of smoke in the air at the site in real time. Our design consists of an Adafruit micro-controller connected to two dust sensors that connect to Wi-fi. We interviewed Edmund Seto, a professor at UW, since he has much more experience with building sensors. He suggested that we use multiple of the same device so that we could average the data or have a backup sensor if one were to stop working. Using Arduino code and Adafruit.io, we were able to code the micro-controller and connect the data to a Wifi-interface so we could watch the data come in. We are currently field testing the sensor in Seattle, but we expect to permanently install at the MRO this summer.

Atherosclerosis, the underlying cause of most heart attacks and strokes, results from lipid accumulation in cells of the artery wall. Gene therapy, delivered directly to the artery wall, has the potential to prevent and reverse atherosclerosis. However, lipid accumulates primarily in cells below the endothelium, which are difficult to reach with gene therapy vectors. Our goal is to remove lipid from these cells by delivering therapeutic microRNA (miR) that increases cholesterol export from the cells. We hypothesized that if we introduced a therapeutic gene expressing the miR to endothelial cells (cells along the artery lumen), the endothelial cells would release this miR (anti-miR-33a-5p) via extracellular vesicles (exosomes) that transport miR between neighboring cells. We also hypothesized that smooth muscle cells (SMC) and macrophages would take up the therapeutic miR-containing exosomes, leading to higher expression of a critical cholesterol export protein (ABCA1) and increased cholesterol export. To test this in vitro, we introduced a therapeutic gene encoding the miR into endothelial cells and used RT-qPCR to test if the miR was released into the endothelial cell culture medium (CM) via exosomes. After confirming the presence of the therapeutic miR in exosomes purified from CM, we treated SMC and macrophages by incubating the cells with the exosome-containing CM. After incubation, we measured ABCA1 protein expression and cholesterol export. Expression of ABCA1 protein increased by 1.6- and 2.2-fold in SMC and macrophages, respectively, while cholesterol export increased by 1.4- and 1.6-fold. We conclude that gene therapy delivered to endothelial cells can produce therapeutic miR that is transferred to neighboring artery wall cells via exosomes, and increases cholesterol export in these target cells. If also effective in vivo, our approach has potential for reducing the severity of atherosclerosis by delivering therapeutic miR to cells that are difficult to reach with gene therapy.

Social determinants of health (SDOH) are non-medical factors that contribute to a person’s health and well-being. The Centers for Medicare/Medicaid Services recently released a standardized 26-question survey designed to capture SDOH in the following 13 domains: living situation, food insecurity, transportation, utility help, personal safety, financial strain, employment, family and community support, education, physical activity, substance use, mental health, and disabilities. However, there is limited study using this survey tool in a safety-net institution. Harborview Medical Center (HMC) is the public hospital serving King County, WA and provides care to a wide variety of patients. This project was a prospective, observational study which aimed to investigate implementation of this survey tool and to measure relevant SDOH and other medical factors in this setting. My role included administering the survey to patients admitted to the HMC Hospital Medicine service from October to December, 2018. I collected data related to the duration of the survey and any challenges patients encountered responding to the survey, as well as review of patient charts for demographic information, medical system utilization, and medical history. In total, only 24 of 90 patients (27%) completed the survey. Major challenges included patient lack of interest, language barrier, ability to consent, and competing time demands. These results have implications for the generalizability of this tool and whether it comprehensively identifies SDOH needs.

Skin plays an important function as a highly innervated sensory organ. This sensory function is critical to organism survival, but the skin, and its axons, are easily damaged and need to be repaired to maintain homeostasis. Zebrafish are an excellent model to study tissue repair because they regenerate tissue efficiently and share conserved skin architecture with other vertebrates. A cell type shown in previous lab experiments to contribute to skin repair is a macrophage like cell, the Langerhans Cell. I hypothesize that if Langerhans Cells are not present within zebrafish epidermis then tissue repair will be incomplete or delayed. I investigated these cells using two different methods. First, I analyzed mutations that cause a loss of function in genes required for Langerhans Cell development. Second, I used the transgenic ablation technique to inducibly kill Langerhans Cells in the skin by addition of the antibiotic metronidazole. I imaged fluorescent Langerhans Cells in the zebrafish epidermis in both of these genetic scenarios to quantify the reduction in Langerhans Cells. Following the completion of these experiments, we expect to see that a lack of Langerhans Cells will induce slower or halted recovery from damage. In the loss of function method, I expect that various mutants will not have as many Langerhans Cells and that following induced ablation, Langerhans Cells will die out when the drug is introduced and slowly recover following metronidazole removal. The key implication of this is finding more about our own biology that can lead to faster healing. In theory, if Langerhans Cells have a major effect on this process then knowing more about our own skin can help us translate this understanding to our own healing process.

A national organization named 2-1-1 provides assistance to populations with basic needs, mainly informing and answering questions, and researching resources covering 50 states. Not only is the demand for information growing, but also the complexity of calls is increasing. For example, a person may need information on shelters, medical issues, legal assistance, debt management and other services. Consequently, calls are taking longer, and with limited resources, wait times are increasing and even critical calls are sometimes abandoned. Assigning more staff to a call center is not realistic under limited budgets. Hence, an efficient call center system must be designed. Our research seeks to address the efficiency of the WA 2-1-1 call center system, in Washington State. We hypothesize that the application of call prioritization and skill-based routing can reduce the holding-call time, and eliminate call abandonment for those with urgent needs. We will identify classifications of calls, and evaluate how automation can be used to navigate or direct callers to a correct resource and expedite the whole process. Appropriate classification of calls and prioritization may not only decrease the waiting time but also help training operators with an appropriate skill set. We will apply the concept of operations research to forecast seasonal demand using available data within Washington State, and will estimate the number and allocation of resources the organization should provide. The anticipated result of the research is a call center design that will decrease the number of abandoned calls, provide an immediate response to an urgent call, decrease waiting time, and assign calls to available operators to exploit the limited resources. The WA 2-1-1 call center is important to provide assistance to efficiently serve populations in need. Increasing the efficiency of call centers with limited resources will enable WA 2-1-1 to reach more people in need.

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

Growing concern regarding brain injury in football has encouraged research on head impact exposure (HIE), incidence of concussion, and strategies to reduce injury risk. Reducing HIE in games has presented challenges due to the physical nature of the sport. However, limiting the amount of full-contact in practice may present a means for both decreasing HIE and minimizing concussion risk. In the past few years, guidelines limiting contact have been proposed, including decreasing the intensity of contact (limiting "two-a-days"), decreasing the number of full-contact practices, and eliminating practice drills associated with greater contact (such as the "Oklahama drill"). A few states have even modified their existing concussion legislation to include provisions limiting contact. The goal of our study is to review the literature regarding limitations on contact as a means for improving safety in football and to evaluate whether evidence supports this approach as a means for mitigating risk. We have identified studies assessing the impact of limitations on contact for either reducing HIE or concussive risk in football. We have then categorized the resulting studies by level of evidence, and summarized our findings. We concluded that reduced contact should result in a decrease in HIE and thereby a decrease in injury rate. 

Indoleacetic acid(IAA) is a common and well understood auxin class phytohormone that promotes plant growth by increasing cell division and elongation. IAA has also been shown to increase infectious adhesion and filamentation in certain strains of Saccharomyces cerevisiae. Increased IAA production by the plant’s microbiome has been demonstrated to stimulate host and symbiont growth. The IAA production in multiple strains of S. cerevisiae from the USDA ARS library was quantified using the Salkowski colorimetric technique, then the highest IAA producing strains were treated onto corn to examine the effect on biomass growth. Preliminary results have shown greatly increased root mass and moderately increased shoot mass in treated corn. This symbiotic yeast treatment could have agricultural applications, increasing crop yields without increased application of fertilizer, pesticides, or other products that could have a negative ecologial impact or detrimental effects on the crop.

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

In a majority of low- and middle-income countries (LMICs), resources for mental health care are extremely limited. For children and adolescents especially, there is little to no mental health care available. In a recent large randomized controlled trial, an evidence-based treatment (EBT) was delivered in two LMICs, Kenya and Tanzania, using trained lay counselors in a task-shifting/sharing model. Over a 12-week span consisting of weekly group meetings, this EBT, trauma-focused cognitive behavioral therapy (TF-CBT), was delivered to orphaned children who had posttraumatic stress (PTS) and/or grief symptoms, along with their guardians. The effects sizes were large for child PTS/grief, but little is known about how to scale up and implement TF-CBT to benefit more children. The current study uses data from a large TF-CBT trial implemented in 10 schools and 10 communities in Kenya by existing staff who served as lay counselors (teachers in schools and community health volunteers [CHVs] in communities). After the delivery of the treatment, qualitative interviews were conducted with the lay counselors from 6 of 10 sites in each to better identify efficient implementation practices and policies (IPPs) that supported TF-CBT delivery. The goal of studying the IPPs is to identify those that support the effective adoption and fidelity of TF-CBT. This study pinpoints which IPPs are most critical for the different settings, sectors, and populations that this study encompasses. We analyzed the IPP resource provision to be able to compare the difference in resource allocation in urban versus rural settings in regards to transportation, materials, etc. This study allows us to gain a better understanding of the necessary implementation strategies to better tailor to the needs of communities to support evidence-based mental health care in specific sectors and settings in LMICs.

Chronic postsurgical pain (CPSP) develops in 10-50% of pediatric patients after major surgery. Despite potentially severe health implications, little literature exists examining the epidemiology and mechanisms of pediatric CPSP. A barrier to progress in this area is that while definitions of CPSP exist in adults, definitions do not include impact of pain on health related quality of life, a critically important aspect of pain assessment. Consequently, the objective of this research study is to develop a clinically meaningful definition of pediatric CPSP that incorporates measures of pain intensity and quality of life, which can be standardized across clinical and research populations. The aims of the study were to (1) identify and extract common elements of current definitions used for CPSP in the existing literature, and (2) identify clinically meaningful cutpoints for CPSP based on pain and quality of life, through secondary data analysis of two clinical research studies examining pediatric post surgical pain. Literature search found that existing studies employed inconsistent definitions of CPSP, limiting our ability to develop a literature-based definition. Our dataset included 179 adolescents 10-18 years old undergoing surgery for spinal and chest wall deformities. Measures included pain intensity (Numerical Rating Scale), quality of life (PedsQL) and pain interference (Visual Analog Scale) at 4 and 12 months post-surgery. We conducted scatter plots to visually inspect the associations among pain and health outcomes. Cluster analyses of pain and health-related quality of life identified four unique cluster groups differing on level of pain and functional impairment. Next steps will include determining cutoffs for pain and quality of life based on these cluster groups, and validating the newly proposed definition in an independent sample of youth undergoing surgery. A consistent definition for CPSP which incorporates both pain intensity and functional impact of pain will help guide future research and treatment.

Organic solar cells (OSCs), particularly all-polymer solar cells, have risen as an exciting alternative to standard inorganic solar cells. Their low-cost synthesis, easily tunable properties, and solution-processable fabrication enable facile scale-up for high-throughput production. For commercial viability OSCs will need to have power conversion efficiency (PCE), which is determined by the material characteristics and energetic properties, comparable to their inorganic counterparts (>20%). The question this research aimed to address is: How do processing conditions govern the electronic properties of the photovoltaic layer? Two primary methods were used to evaluate the energy levels: Cyclic Voltammetry (CV) for the highest and lowest occupied molecular orbitals (HOMO/LUMO) and Ultraviolet-Visible Spectroscopy (UV-Vis) for the optical bandgap. A binary blend comprised of a polymer donor, known as PSEHTT, and a polymer acceptor, N2200, was used as a proxy model. Blends of compositions ranging from 0 to 100 weight % PSEHTT were coated on platinum wires for CV and glass substrates for UV-Vis measurements. The collected data behaved as expected, exhibiting a decreasing trend in HOMO level from -5.29 eV to -4.94 eV as the weight % PSEHTT increased. The evolution of the LUMO level with blend compositions was rather challenging to obtain due to possible photoexcitation in the blend leading to free charge available for continuous current extraction. To verify, the samples were isolated from light over the course of the CV measurements to prevent interference. This should result in more accurate LUMO level approximations which are expected to display a similar trend to the HOMO level. Elucidating the relationship between blend composition and blend electronic properties enables a precise and facile device optimization process for highly efficient OSCs.

Microbial communities are essential to numerous biological systems from aquatic and land ecosystems to the human gut. Our understanding of interactions among bacterial strains can help us understand how these communities form and function. Such interactions may depend on the species themselves but can also be sensitive to the abiotic environment. Harsh environments, where mortality is increased, can reverse the outcome of a competition between species. Simple models predict that increasing mortality favors faster growers, and past experiments repeatedly confirmed this prediction. In these pairwise competition experiments, slow growers excluded fast growers in low-mortality environments, but increasing mortality caused fast growers to dominate. A necessary condition for observing the reversal is that slow growers are good competitors in low-mortality, high-density environments. While this tradeoff between growth rate and competitive ability was common in well-characterized lab strains of bacteria, it was unclear if it might exist elsewhere. In this project, we tested for the existence of a growth/competition tradeoff in a natural community of bacteria collected from MIT’s Killian Court. Contrary to past results and some evidence from the literature, we found a weak positive correlation between competitive ability and growth rate, which does not support the idea of a tradeoff.

Hypoxic-ischemic encephalopathy (HIE) and inflammatory responses are commonly seen in premature infants which can lead to cognitive delay and behavioral problems. A novel rodent preterm brain injury model is being developed to simulate histological and behavioral changes seen in preterm brain injury. It was hypothesized that injured pups [(in-utero hypoxia-ischemia followed by post-natal inflammation with lipopolysaccharide (LPS) + hypoxia + hyperoxia] will have a significant late behavioral deficit compared to controls. The rodent model of preterm brain injury includes: intrauterine hypoxia at embryological day 18, with LPS administration on Postnatal (P) day 2 followed by hypoxia (8% oxygen) and hyperoxia (80% oxygen). In order to assess late behavioral effect of early neonatal injury, I conducted motor tests on rats. The motor testing included: gait analysis via CatWalk XT and Rotarod analysis. For the Rotarod analysis, I performed testing on both, the injured rats and controls, on P28 to test their locomotor ability. Gait analysis was performed on P35. The results will be tested for significant differences between the groups. Future research will be conducted by repeating this experiment to verify these results and clarify what aspects of late behavior are impacted most by this injury model.

G-protein coupled receptors (GPCRs) - characterized by seven transmembrane alpha helical domains - are the largest family of membrane proteins, constituting ~1% of the human genome. The α1D-adrenergic receptor (A1DAR) is a GPCR that regulates function of the cardiovascular, urinary, and central nervous systems. Dysfunction of this receptor can lead to various diseases including schizophrenia, benign prostate hypertrophy, hypertension, and PTSD. Prazosin, a non-specific α1-antagonist is the first line treatment for PTSD, however, chronic use has deleterious side effects including orthostatic hypotension and potentially fatal reflex tachycardia due to interactions with off-target related receptors. Thus, understanding how A1DARs are regulated will allow for the development of targeted therapeutics. To this end, the Hague Lab has previously discovered that A1DAR undergoes an endogenous cleavage of its extracellular N-terminal domain, affecting its membrane localization and response to agonist stimulation. Located within the N-terminal domain of A1DAR are two glycosylation sites at amino acids 65 and 82. Currently, how glycosylation of these sites regulates the cleavage event remains unknown. To characterize this phenomena, I used molecular cloning to mutate the glycosylation sites of A1DAR in the pSNAP vector for expression in Human Embryonic Kidney 293 (HEK293) cells. Near Infrared PAGE analysis revealed that glycosylation of both amino acids is required for cleavage and proper expression of A1DAR. Sucrose density gradient and dynamic mass redistribution further showed that glycosylation controls function and trafficking of A1DAR to the membrane. These results allow for the development of targeted medications specific to the N-terminal glycosylation sites of A1DAR, further reducing the potential side effects experienced by patients.

In this research, we looked at the possible use of an Air Breathing Pulsed Plasma Thruster (AB-PPT) for propelling an aircraft that could potentially act as an atmospheric satellite at atmospheric altitudes > 25 km. One of the advantages of operating at such altitudes is that the aircraft is not subject to highly variable weather conditions. An atmospheric satellite is an aircraft that can perpetually fly around the same area, and can be launched at significantly reduced cost when compared to conventional satellites while providing similar services such as communication and imaging. At the desired altitude, conventional blade-based propellers are too inefficient due to low background pressure, but it is still too low of an altitude for conventional space propulsion, prompting the use of AB-PPT. The AB-PPT is an adaptation of the conventional PPT which is a pulsed device that uses an electric discharge to ionize and expel the solid propellant such as PTFE at high speeds. For the AB-PPT, a large amount of voltage discharge generated across the two coaxial electrodes ionizes and expels the background air instead. In order to identify the most efficient AB-PPT design, three different configurations were tested using a pendulum-based thrust stand to measure the thrust efficiency, a Rogowski coil to measure the current per discharge, and high-speed video. One configuration has been identified, and we are currently investigating an alternative electric connection to further increase the amount of thrust per discharge. Future work includes plasma diagnostics of the AB-PPT such as Langmuir probe, and B-dot probe, in addition to the development of more robust electronics capable of delivering higher power, and the development of the final version of the AB-PPT for patenting purposes.

Sea ice, frozen ocean water, in the Arctic is declining due to climate change. This is getting more attention, since sea ice can substantially affect wildlife, ecosystems, and human society. Sea ice extent, a measure of the surface area of the ocean covered by sea ice, is used to monitor the environment. A good sea ice extent model can benefit not only studies of the Arctic but also the global economy, as many ships use the Arctic area as part of their route. There are various sea ice extent models in the science community that give good estimates of sea ice extent. However, there are instances where their predictions do not match observations. My research explores bias correction methods that help predictions to match observations and compares the performance of sea ice models after bias correction. In this analysis, I consider the performance of a sea ice model produced by the Geophysical Fluid Dynamics Laboratory using boxplots and rank histograms. This work helps show the value of bias correction. I will compare the performence of the models to identify in what month and in what location models predict well. This information will support improved prediction of the Arctic going forward. 

Legionella pneumophila is a gram-negative, intracellular pathogen that is the primary causative agent of Legionnaires disease. During infection, Legionella utilizes a type IV secretion system to colonize the alveolar macrophages of humans and causes a pneumonia-like disease. Despite this, Legionella cannot be transmitted from human to human, and thus infection of humans by Legionella is seen as an evolutionary dead end for the bacterium. However, it is known that Legionella uses the same mechanisms to colonize macrophages as their natural, amoeba hosts. As a result, we hypothesize that genetic innovation driven by Legionella-amoeba coevolution has resulted in an array of cellular effectors in the Legionella genome that are used to infect and modulate and array of hosts. In this study, we use a Legionella-amoeba system to study the coevolution between Legionella pneumophila, and an amoeba host, Dictyostelium discoideum. In particular, we focus on identifying, and functionally characterizing the evolutionary trajectory of a rapidly evolving T4SS effector gene, MavN. MavN is a transmembrane, iron chelating protein that is critical to infection for all species of Legionella. As a result, we use a comparative evolutionary approach to study the efficacy of various MavN effector orthologs from across the Legionella phylogeny. By doing this, we can begin to trace the evolutionary trajectory of MavN effector evolution and specify sequence specific regions of MavN that have evolved to be more successful during infections.

Malaria is a disease associated with a significant global burden of illness, including hundreds of thousands of deaths every year. Severe malaria is most often due to the Plasmodium Falciparum species of parasite, the pathogenesis of which involves avoidance of host detection through endothelial sequestration. This process allows infected erythrocytes (red blood cells) to adhere to the vessel wall and avoid filtration via the spleen. Severe cases of malaria are often also associated with endothelial activation and release of the adhesive glycoprotein, von Willebrand Factor (VWF). Preliminary data from our laboratory suggests that erythrocytes infected with P. Falciparum may be able to bind to VWF fibers formed under in vitro conditions, and we believe that VWF binding may prove to be a novel mechanism contributing to endothelial sequestration. This study was conducted in order to understand the interactions between plasmodium infected erythrocytes and VWF fibers formed following endothelial activation. Because of the high demand for technical replication for such a project, and the labor and time expenses associated with the lab’s commonly used microvessel system, modifications were made to the geometry and housing to characterize it for the high-throughput platform for the study of VWF’s role in the binding of infected erythrocytes to activated endothelium. By utilizing nanofabrication techniques and soft lithogaphy with Polydimethylsiloxane (PDMS), we have successfully completed design and manufacturing of the novel devices that have allowed an increase in speed and efficiency up to three times that of previous assemblies. In these newly fabricated devices, we saw consistent formation of robust VWF fibers upon activation and aim to continue their use to observe and quantify binding of plasmodium infected erythrocytes in VWF-rich regions within vessels.

Cellular growth and aging requires constant replication of the genome. The processes of genome replication and segregation must be carefully regulated to prevent DNA damage which can cause cell death or oncogenic transformation. Damage can arise from errors in cellular processes, as well as environmental factors such as UV radiation or chemical agents. In mammals, the protein Retinoblastoma (Rb) prevents cells from beginning the process of DNA replication for cell division if internal conditions are not suitable for replication. This function is disrupted in virtually all cancers, and mutations in Rb have been widely studied as a result. Whi5 is the functional analog to Rb in S. cerevisiae. Whi5 activity is modulated by phosphorylation at 4 different sites, triggering Whi5 export from the nucleus and allowing transcription of DNA replication genes. Previous research suggested Whi5 export initiates irreversible progression through cell division. However, using single-cell observation technology, we show that Whi5 can re-enter the nucleus prior to cellular division, arresting the cell cycle. Cells that undergo Whi5 re-entry events exhibit a longer average replicative life span, counted in number of divisions. Additionally, cells without a functional copy of Whi5 have a reduced replicative lifespan. Our results suggest Whi5 may play a role in arresting the cell cycle in response to DNA damage to prevent the cell from making fatal errors during replication and ensure healthy aging. To investigate the role of Whi5 in response to DNA damage, I am using CRISPR gene editing technology to modify the phosphorylation sites on the Whi5 gene, modulating Whi5 activity. The ability of modified Whi5 strains to recover from UV induced DNA damage and their relative replicative life spans will clarify the role of Whi5 in DNA damage response. Our results may help us better understand the interactions governing Rb dysfunction in cancer cells.

Dravet syndrome (DS) is a form of intractable epilepsy that manifests itself in infancy. It is comorbid with behaviors resembling autism, motor deficits, and premature death. Human infants with DS also experience both febrile and non-febrile seizures. Therefore, research into the mechanistic pathway of DS in mice may shed light on the alleviation of DS symptoms detrimental to the human quality of life, as well as help to identify avenues for gene therapy and further research. Symptoms of DS have been shown to recruit certain immunologic entities such as microglia, a type of glial cell. Glial cells, or non-neuronal brain cells, have traditionally been thought to merely play the supportive role of providing nutrients to neurons. However, recent studies have shown that glia play a more active role in stabilizing information processing, brain function, and maintaining brain homeostasis. Following microglial recruitment, another type of glia, astroglia, are activated. Astroglia form the blood-brain barrier and collaborate with microglia to produce neuroinflammation through gliosis. Gliosis has been shown to interfere with normal neural function, which is postulated to contribute to Dravet phenotypes. Thus, DS symptoms may produce either hypertrophic astroglia or increased distribution of astroglia, both of which interfere with the ability of inhibitory interneurons to adequately regulate neural excitation as a result of induced neuroinflammation. Investigation into the link between glia and Dravet syndrome is the core of this research and has revealed sex differences in the distribution and size of astroglia. In particular, immunohistochemical staining of brain tissue on Dravet females have shown greater astroglial concentrations in the DG relative to their male counterparts, when coupled with behavioral analysis and EEG readings. This difference has implications in Dravet syndrome research and treatment.

There is a critical lack of knowledge regarding the effects of human immunodeficiency virus (HIV) and zika virus (ZIKV) coinfection in respect to ZIKV pathogenesis, vertical transmission and current vaccine strategies. ZIKV has received global attention because of its clinical complications including congenital malformations during vertical transmission and Guillain-Barré syndrome, a neurocognitive disorder in adults. Recently, ZIKV outbreaks have occurred in tropical and subtropical regions endemic with HIV, therefore it is imperative to understand the impact HIV-ZIKV coinfection may have when moving forward with ZIKV vaccine design. Furthermore, in humans and non-human primates (NHPs) frequencies of blood monocytes increase during HIV and simian immunodeficiency virus (SIV) infection and monocytes are early targets of ZIKV infection. Therefore, we hypothesize that cells from HIV infected individuals have the capacity to harbor increased ZIKV replication and could lead to enhanced ZIKV viremia and pathogenesis. For this study, we use a NHP model to determine the impact of acute SIV infection on ZIKV pathogenesis. We determine ZIKV cellular targets in the blood and preliminary results show an increase in NHP blood monocyte within the first six weeks of SIV infection. We evaluate whether SIV infection increases the susceptibility of cells to ZIKV infection by isolating cells from SIV- and SIV+ animals, infecting them in vitro with ZIKV, and assessing viral replication by plaque assay. Our preliminary findings suggest that in vitro ZIKV replication may increase in cells from SIV+ NHP blood when compared to SIV- blood. Future studies will look at the impact of SIV infection on in vivo ZIKV replication and whether ZIKV replication is enhanced in cells from HIV-infected individuals.

Harmful radiation, such as UV photons from the sun, can damage DNA in a manner that results in cation-radical formation which leads to nucleobase loss and strand breakage. In the Frantisek Tureček research group, DNA cation-radicals were generated in the gas phase, isolated and subjected to incremental wavelengths between 210-700 nm with intent to observe their absorption action spectra that can be used to assign structures and intrinsic properties. The difficulty with these experiments is the ability to effectively communicate the experimental set-up of mass spectrometers, tunable lasers, and various other pieces of equipment in a supporting manner that delivers concise information to be understood regardless of prior knowledge in this specific field. I had the unique opportunity to take two-dimensional, over-simplified schematics and transform them into three-dimensional, professional and photorealistic images of our experimental arrangements using Siemens NX CAD modeling software.

The DNA damage checkpoint (DDC) is critical for survival as it responds to damage such as mutations or chromosomal rearrangement, and prohibits the cell cycle from proceeding through a failed replication. One of the many responses DDC activates is histone degradation. When wrapped around histone proteins, DNA is blocked from repair mechanisms. By reducing histone and nucleosome density, the cell increases DNA mobility and allows the DNA to be quickly repaired via homologous recombination. The cell does this by uncoupling histone transcription from the S-phase of the cell cycle, which is normally confined to this phase. When DDC is activated outside of S-phase, the cell can no longer produce histones to replace those it consumed and ensure proper chromatin packing after the DNA is repaired. According to published literature, uncoupling histone transcription from S-phase increases lifespan but should compromise the DNA damage response. However, it is largely unknown how this uncoupling affects the DNA damage response in different mutants. Our goal is to explore how this affects mutants with reduced DNA damage responses. Our mutants of interest are 1) rad52Δ, which reduces homologous recombination, and 2) lif1Δ, which reduces non-homologous end joining (NHEJ). Our protocol involves yeast (Saccharomyces cerevisiae) spotting and exposing yeast to different durations of high-intensity UV energy. We will compare colony sizes across different strains, dilution factors, and UV-exposure degrees. We expect to see strains with rad52 or lif1 deletion to have a lower growth rate compared to the wild type. Following this experiment, we will explore how altering histone transcription interacts with, and may enhance rad52 and lif1 in DNA repair. We hope to apply our findings to mammalian and human genes, and help to decrease the onset frequency of age-related diseases such as cancer due to genomic instability.