Atypical sensory behaviors have only recently been included as an explicit symptom of DSM-5 Autism Spectrum Disorder (ASD), despite a considerable history of anecdotal evidence. As a result, sensory behaviors are not well characterized in ASD research. In the current study, we aim to fill a gap in the literature by specifically investigating auditory processing in 143 children with ASD and/or a likely gene disrupting mutation (LGDM) associated with ASD. Participants’ parents completed the Sensory Profile Caregiver Questionnaire about their child and psychiatric symptoms were assessed via a comprehensive evaluation with a licensed clinical psychologist. We hypothesized that responses on the Sensory Profile would reflect either hypo- or hyper-sensitivity to auditory stimuli. We predicted that extreme hypo- or hyper-auditory responses would reflect separate deficits, rather than a continuum of auditory sensitivity. We also predicted that we would see unique auditory response profiles associated with LGDMs in particular gene groups. Our results will be discussed with regard to current theories and information about sensory abnormalities in children with ASD. The results and findings from this study could be used to help lay a foundation regarding sensory markers and auditory processing deficiencies in children with ASD, a topic that is fairly new and has not been thoroughly investigated.

Wood is one of Earth's truly renewable resources. There has been much study into the improvement of timber’s sustainability and long term usage. While we have improved sustainability to a degree by improving forest ecology and studying species relationships, there are still issues that need to be addressed. One issue I focused on was non-merchantable forest residues from forest harvesting, or slash. During a timber harvest, a tree is felled, has its branches removed, and is cut to a mill standard. The resulting log is the merchantable portion of a tree, and is shipped to a mill. What is non-merchantable, and gets left on the site is branches, leaves, and parts of the stem that were removed to meet the mill’s standards. This leftover biomass is then piled, and often burned, to clear the site for replanting. Burning slash piles results in large quantities of smoke emissions, which if not planned correctly, can pose health risks to citizens in nearby cities. If not burned, slash piles can aid forest ecology by providing large woody debris for habitat and keeping nutrients at the site. While leaving slash on site may seem ideal, slash can pose a severe fire risk and decreases the aesthetic of the forest. For this project, I measured slash piles from a recent harvest at the University of Washington’s Pack Forest. Using a volume calculator created by the University of Washington, I found the total biomass in the piles. That volume was then used to calculate the amount of carbon, and other components in the slash piles. Better knowledge and understanding of these slash piles is important, as it allows for us to compare alternatives to pile and burn or leaving on site for habitat, such as removing slash and using it for biofuels.

Chemosensation is a key component of navigation and communication for aquatic invertebrates. The posterior tentacles of nudibranchs are called rhinophores and are their primary olfactory organs. We videoed and measured active water currents driven by cilia around the clavus of rhinophores using dyes and neutrally-buoyant glass beads to observe speed and patterns of flow. The speed of particle flow toward the rhinophore averaged between 0.1 and 1.0 mm/s across five species, and particles were apparently pulled in viscous laminar flow toward the rhinophore from up to 3-5 mm away. For the lamellate rhinophores found in dorid species, fluid is split into medial and lateral lamellae at the midline of each rhinophore and moved anterior to posterior through the lamellae. These rhinophores can rotate around their vertical axis to pull in water from the left or right. In other dendronotid species, fluid is pulled downward into the cup-shaped clavus of the vertically-oriented rhinophore and released in all directions at the base of the clavus before the stalk. In a burrowing arminid fluid moves distally to proximally parallel to the ridges of the conical rhinophore. Scanning electron microscopy showed densely-ciliated areas on the unexposed surfaces of the rhinophores which facilitates fluid movement through the leaflets of the clavus. Exposed surfaces had small patches of presumably-sensory cilia as found on all skin. We hypothesize that these currents minimize the boundary layer thickness and thus decrease the response latency of olfactory receptors to changes in odor density, and also increase the volume of water sampled per time. Some species show little or no current flow and a comparative study will help us determine the adaptive function of sniffing.

Ion Mobility Mass Spectrometry (IMMS) has become an important tool for separating small molecules such as peptides, glycans, and petroleum molecules. Ion Mobility is most often performed in He, N₂ or air. There is a great interest in using alternative drift gases to increase selectivity of ion mobility separations, specifically for complex mixtures like petroleum. In this study we measured arrival time distributions (ATD) of a set of double bond equivalents (DBE) in four different gases (He, N_2, CO₂, Ar) which span a range of masses and polarizabilities. Quinoline, isoquinoline, and their DBE were chosen because they are aromatic compounds that are easily protonated due to the presence of nitrogen and are similar to molecules found in petroleum. The measured ATDs were plotted as a function of reciprocal drift voltage; the resulting slope is inversely proportional to mobility. Using the mobility and the Mason-Schamp equation, we determined the collision cross section of each molecule with each drift gas. We also investigated the relationship between the dipole moment of an ion and its collision cross section. In general, collision cross sections increase with drift gas size and polarizability. Additionally some of the DBE were better separated with larger, more polarizable drift gases (N₂ and CO₂). We have shown that IMMS can be used with different gases to improve separation between ions of similar size and shape. This method can be used in future investigations of petroleum mixtures to potentially identify a wider range of molecules.

The lateral habenula (LHb) is a structure in the epithalamus that encodes aversive states and accumulating evidence indicates that the LHb exhibits hyperactivity during depressive-like states. Previously, we have shown that inhibition of the LHb using Gi-coupled designer receptors exclusively activated by designer drugs (DREADDS; hM4Di) can produce antidepressant effects. The LHb is known to project to several midbrain nuclei, including the ventral tegmental area (VTA), the rostral medial tegmental nucleus (RMTG) and the dorsal raphe nucleus (DRN). In this study, we seek to determine which lateral habenula output pathway may give rise to the previously observed antidepressant effect in rats. We are separately testing inhibition of the three output pathways of the LHb to the VTA, RMTG and DRN, using intersectional expression of a floxed hM4Di-DREADD in LHb neurons that project exclusively to these target regions. Using stereotaxic surgery, an AAV viral vector containing floxed-hM4Di is infused into the lateral habenula of a rat, while CAV2-CRE is injected into the respective target region. CAV2-CRE travels retrograde up the axons of neurons and produces the CRE-enzyme, allowing DREADD expression to be restricted to neurons that project from the LHb to each respective target region. After a recovery period, rats are either administered Clozapine-N-Oxide (CNO), which activates the DREADDS, or a control vehicle, and then undergo the modified forced swim test (FST), which is a validated behavioral measure of antidepressant effects in rats. High escape behavior in the FST indicates anti-depressant effects. After experimental testing, the rats are sacrificed and their brains examined histologically to confirm expression of the DREADDs within each pathway. By identifying which LHb pathways confer an antidepressant effect, this research could lead to future treatments of depression that act directly on those pathways.

Campylobacter jejuni infection is the most frequent diarrhea causing bacterial infection in the United States (CDC, 2014). C. jejuni can be present in many different warm blooded species without causing diarrhea (Griffiths and Park, 1990). The ability to infect a host and severity of infection are a direct result of the presence of virulence genes in the bacteria. In previous studies virulence genes from C. jejuni were identified and were tested using PCR and gel electrophoreses (Laprade et al., 2016). In this study C. jejuni was isolated from crows in the Seattle metro area. As crows move to and from a roost during the day it is important to know what possible risk to human health they can pose through their fecal droppings. The isolates obtained from the fecal droppings were tested for the motility gene flaA; the colonization genes dnaJ, racR, ciaB, and pldA; and the antibiotic resistance gene tetO using the method created by Laprade et al. Twenty-three fecal isolates were tested; 100% tested positive for flaA; 100% tested positive for dnaJ; 60.87% tested positive for racR; 43.48% tested positive for tetO; 91.30% tested positive for ciaB, and 13.04% tested positive for pldA. Presence of other virulence genes such as toxin genes from the cdtABC gene cluster need to be determined. My preliminary results indicate that crows in the Seattle metro area that carry C. jejuni may carry a virulent or pathogenic form of the bacteria.

The beta-amyloid (Aβ) peptide, implicated in Alzheimer’s Disease, forms toxic aggregates known as oligomers that cause brain degeneration. This aggregation process can be inhibited by designed peptides that have a novel structure, known as the alpha-sheet. This structure is similar to a beta-sheet except that the carbonyls all point in one direction and the amine groups in the other, generating a molecular dipole moment. The Daggett group hypothesizes that at some point, Aβ undergoes a conformational change that gives it this alpha-sheet character and the resulting molecular dipole causes Aβ monomers to be attracted to each other and form oligomers. There is also evidence to suggest from simulation that this structure occurs in many other amyloid-related diseases. As such, designed peptide inhibitors from the Daggett group all target this structure. One of the control designs, AP3, aggregates much more rapidly than Aβ does under acidic conditions. My project involves using AP3 to probe the reasons for Aβ toxicity as well as its aggregation mechanism – both of which are not understood. The residues involved in the turn sequence of AP3, which is hairpin peptide, are of particular interest due to their propensity to display β-sheet character. After synthesizing these “turn sequence” peptides, I found that the presence of these turn sequence peptides can increase the speed of AP3 aggregation, which is an analogue to the seeding of amyloids. I am characterizing these turn sequence peptides using circular dichroism to observe their secondary structure. In addition, I along with other undergraduates in the lab have optimized ELISA to quantify the interactions between our designed peptides and another peptide of interest. The behaviors of these turn sequence peptides as shown by characterization and various assays prove enlightening in understanding the pathology of amyloidogenic diseases.

Video games are seldom used for environmental science education, despite the variety of compelling lessons that they could be used to teach. We designed, built and tested a video game about the effects of climate change on a charismatic local animal, the pika. Native to North America and Asia, pikas are sensitive to changes in climate because they are covered with thick fur and get heat stroke even under modest temperatures (77 °F). Pikas have to gather food throughout the summer, enough for them to make it through the long winter in their burrows. When temperatures warm, pikas do not have as much time to forage for food during their day. We decided to take these ideas and turn it into the major mechanics of a game that we developed. The resulting project, Life of Pika, is a runner game in which players need to collect flowers to survive while managing their temperature to avoid overheating. We have taken inspiration from other runner games such as Frogger, Crossy Road, and Sonic the Hedgehog, but this game is unique in that player vulnerability centers around their temperature bar, rather than around avoiding obstacles. The game is divided into seven levels to represent the pika’s seven year lifespan. As one advances from level to level we make the game progressively harder by increasing the rate at which the player’s temperature increases to simulate increasing global temperatures. Developed with industry-standard software for implementation in classroom and museum settings, we aim to promote empathy in the player about the pikas’ struggle against climate change. We hope that players will become more thoughtful about their impact on the world and its inhabitants.

The cause of Western Europe’s mild climate has been under discussion for many years. Among the general public, heat transport by warm ocean currents is often given as an explanation. A prominent scientific study, Seager et al 2002, instead claimed that roughly fifty percent of the wintertime temperature difference across the North Atlantic is caused by the eastward atmospheric transport of heat released by the ocean that was absorbed and stored in the summer; another roughly fifty percent is caused by the stationary waves of the atmospheric flow; and that ocean heat transport only contributes a small magnitude of warming across the basin. Seager states that, “the next step of inclusion of a fully interactive mixed layer is unlikely to change the main results presented here”. We test whether the transport of heat northward by the Atlantic Meridional Overturning Circulation (AMOC) and its ensuing release into the mid-latitude westerlies is indeed a small contributor to Western Europe’s mild climate using simulations with two different fully coupled climate models. A model simulation where the Rocky Mountains were eliminated is used to test the effect of stationary waves on heat transport. Another simulation where the ocean heat flux of the Northern Hemisphere and the Southern Hemisphere is eliminated through symmetrization is used to test the effect of heat transport northward by the AMOC. In this simulation, land topography—such as the Rocky Mountains—was kept intact. In these simulations we examine temperature variations over Western Europe and the reasons for the changes using energy budget decompositions. An understanding of these climate system controls allows for an understanding of what controls future changes in climate.

Cytosolic pH is sustained by the movement of protons out of the cytosol. The vacuolar ATPase (V-ATPase) is a conserved protein complex that localizes to the membrane of organelles and transfers protons from the cytosol into the organelle lumen. The V-ATPase couples the energy of ATP hydrolysis to transport protons. Proper pH homeostasis is important for many organelles such as endosomes, lysosomes, and secretory vesicles. In Saccharomyces cerevisiae, the Pma1 protein localizes to the plasma membrane and pumps protons out of the cell, helping to maintain cellular pH homeostasis. In Saccharomyces cerevisiae, we have found that loss of activity of the V-ATPase results in a growth arrest at low temperature. We generated 66 yeast V-ATPase mutant strains that are able to suppress the low temperature induced growth arrest. In complementation tests of these mutants, our results suggest that all of the mutants belong in the same complementation group. We have performed whole genome sequencing on one strain and analysis of the whole genome sequencing data has identified a single putative mutation. We are validating that the identified mutation is causative for the phenotypic suppression, and performing targeted sequencing of the candidate gene in the other suppressor strains.

Cells can be thought of as aqueous solutions of proteins enclosed within a lipid membrane. A surprising and exciting discovery in the past decade is that several proteins inside of cells aggregate to form separate liquid droplets. This discovery has potential medical applications because the types of proteins that undergo aggregation are associated with prion diseases. In the lab, researchers use a specific type of alcohol (1,6-hexanediol) to disrupt droplets in protein solutions. However, it is unknown whether hexanediol disrupts lipid membranes at the same concentration that it is used to disrupt liquid droplets. If so, then hexanediol cannot be used in cell systems. By probing the effects of 1,6 hexanediol on model lipid membrane physical properties, this study will determine the suitability of 1,6 hexanediol for in vivo studies of liquid droplets.

Approximately 300,000 cases of appendicitis are diagnosed in the United States on a yearly basis. Appendicitis is the condition in which the appendix, located in the right lower quadrant (RLQ) of the abdomen, becomes inflamed usually due to a bacterial infection. A common symptom of appendicitis is when RLQ pain is sustained over time. We, the Surgical Outcomes Research Center (SORCE), hypothesize that antibiotics for intra-abdominal infections recommended by the Infectious Diseases Society of America and American Surgical Association are just as effective as appendectomies for treatment. This project will illustrate to both clinicians and patients that they will have more options when treating appendicitis. The Comparing Outcomes of Drugs and Appendectomy (CODA) clinical trial aims to investigate appendicitis treatment options and understand if antibiotics are just as good as appendectomies (the current standard of care) from the patients' and clinicians' perspectives. Previous studies in Europe suggest the usage of antibiotics is a viable option when treating appendicitis. Patients consenting to the CODA trial are randomized to determine which treatment they receive, either the surgical appendectomy or the antibiotic medication. If the patient wishes to not be randomized, they can opt-into an observational or electronic medical record cohort in which they choose their treatment option. We are currently still in the data collection stage as we continue to monitor and assess patient reported and clinical outcomes for two-years following initial presentation. This research is important because patient reported outcomes gained from the trial will educate patients about their treatment options, therefore patients can decide the treatment best suited for them. In addition, the same results may demonstrate to current healthcare professionals that appendicitis may be treated though other methods, namely antibiotics, which if successful, will revolutionize current perspectives on how appendicitis is treated in the United States.

The accumulation of pathological tau protein in the brain neurons occurs in many neurodegenerative diseases. Alzheimer’s disease and related dementia disorders are the most common diseases with pathological tau. In order to identify potential therapeutics for Alzheimer’s disease and related disorders, I screened the National Institute of Health’s Clinical Compound Library for modifiers of the disease associated phenotype seen in tau transgenic Caenorhabditis elegans (C. elegans). The compound library consists of drugs with a history of use in humans that we can assess for other potential uses, a process known as drug repurposing. Observing C. elegans disease models for specific drug effects may ultimately lead to identifying ways to alter or prevent accumulation of tau aggregates in the brain. Populations of tau-expressing C. elegans were cultured on nematode growth media (NGM) in the presence of a single library compound and assessed for modification of disease phenotype at day one of adulthood; roughly 3 days after eggs are placed on the media. I specifically looked for improvement or deterioration of coordination as well as the speed of growth, number of offspring, mortality, and general health and size of the population as compared to control populations without drug. I then evaluated the data and selected the best compounds for further analysis on the basis of each compounds dose responsiveness. Drugs generally have optimal effect at a specific dosage, so by observing a range of concentrations of the drug I can determine the best concentration for study. Once this has been completed, I will analyze the hits more closely and follow up with further experimentation including quantitative analysis of C. elegans behavioral response, and tau protein biochemistry. We hope that this work may be able to identify potential therapeutics able to ameliorate symptoms in dementia patients with pathological tau.

Sodium-yttrium-fluoride (NaYF₄) upconverting nanocrystals are currently being investigated for their applications in bioimaging, color displays, solar cells, and photocatalysis. Recently, Yb³⁺-doped-NaYF₄ nanoparticles have been predicted to also be a promising host material for laser refrigeration applications. However, to date, the laser-refrigeration of β-NaYF₄ single-crystals has not been reported due to challenges in bulk Czochralski crystal growth. We have demonstrated laser refrigeration of hydrothermally synthesized β-NaYF₄ nanowires for the first time. With a low cost, scalable hydrothermal synthesis process, we can prepare different sizes, morphologies, and phases of NaYF₄ nanoparticles by tuning the initial reagent concentration, synthesis time, and temperature. In the future, our results can be used to synthesize the optimal NaYF₄ nanowires for localized optoelectronic device cooling and physiological laser refrigeration.

Chronic kidney disease currently has no cure but continues to plague our population, demanding new effective strategies to treat kidney disease through the study of biochemical mechanisms of fibrosis. Kidney fibrosis begins with the loss of function of parenchymal cells that leads to excessive scarring in the kidney due to excessive extracellular matrix formation. Several studies in both human and experimental mice models have shown that increased oxidative stress plays a critical role in renal fibrosis due to the generation of reactive oxygen species. However, the mechanisms by which oxidative stress promotes kidney injury or fibrosis remains unclear. PRX2 is an antioxidant enzyme that normally protects the cell against oxidative stress by the reduction of hydrogen peroxide and oxidized proteins. Normally, an increase in oxidative stress has shown to increase an inflammatory response, potentially leading to fibrosis. Unfortunately, the exact mechanisms by which this occurs is unclear. In contrast to its role as an antioxidant, recent studies suggest that PRX2 may be an important mediator of the proinflammatory response as a direct result of oxidant stress. Based on these studies and our preliminary data, the Okamura Lab currently hypothesizes that the loss of PRX2 leads to a significant decrease in renal fibrosis by attenuating the inflammatory response. Our preliminary data suggests that PRX2 is expressed in tubular epithelial cells in normal kidneys and expression decreases with progressive injury by unilateral ureteral obstruction (UUO). Despite the decrease in PRX2 during UUO, PRX2-deficient mice had a significant reduction in fibrosis with a significant decrease in the proinflammatory cytokine TNF-alpha. Methods to further study the mechanism of PRX2 include western blotting, immunostaining, and quantitative PCR. As this study continues, the information on PRX2 will be a valuable asset to developing antioxidant treatment therapies to find a cure for chronic kidney disease.

In individuals diagnosed with Autism Spectrum Disorder (ASD), social motivation often undergoes atypical development, with individuals reporting less pleasure from friendships and collaborative engagements. Because the severity of ASD can differ depending on various genetic and environmental factors, non-diagnosed individuals may exhibit traits similar to milder variants of those of ASD known as Broad Autism Phenotype (BAP) traits. These traits are found to be of high heritability in autism families. The goal of this study is to examine social motivation in individuals with ASD and their family members. First, we will analyze social motivation in children with ASD compared to children with neurotypical (NT) development (age- and sex-matched). Second, compare BAP traits of parents of children with ASD compared to parents of children with NT. Third, we compare the relationship between social motivation in children with ASD and BAP traits in parents. Children with ASD (n = 64) and with neurotypical development (n = 64) participated in this study. To measure ASD traits, the parents of the children filled out the Social Responsiveness Scale (SRS) questionnaire for both their child (SRS-2) and their significant other (if applicable; SRS-Adult), as well as a Broad Autism Phenotype Questionnaire (BAPQ) for themselves. We expect that: (1) children with ASD will exhibit more autism traits and lower social motivation than children with NT; (2) parents of children with ASD will exhibit more autism traits and lower social motivation than parents of children with NT; and (3) there will be a significant positive correlation between children with ASD and parents’ report of autism symptoms. Understanding the relationship between BAP traits in parents and ASD symptoms in children allows us to further understand the neurological diversity of ASD; Specifically, how ASD characteristics and traits may co-occur in both individuals diagnosed with the disorder and unaffected family members.

Nucella lamellosa is a common low-intertidal snail in the Pacific Northwest. Unlike its Atlantic Congener N. lapillus, there are no recent thorough studies or data available on the morphology of N. lamellosa in the Salish Sea. Nucella plays an important structuring role in the intertidal ecosystem by preying on barnacles, algae and other bivalves. Moreover, Nucella does not have planktonic larva, the young hatch directly into juveniles instead. This unique life history characteristic contributes to a greater likelihood of reproductive isolation between populations. Understanding the morphological variations and environmental influences between populations is crucial for conservation management. Nucella lamallosa from up to six locations in the Salish Sea will be individually photographed on the front and back side and the images analyzed as part of the research done with the NOAA Northwest Fisheries Science Center. In Spring 2017, further analyses will be conducted on morphological variations among potential populations. Morphological shape differences will be assessed using three contemporary multivariate approaches as well as color pattern differences. The three multivariate approaches will be Principle Component Analysis, Thin Plate Spline, and Momocs. Shell features such as color, banding, shell thickness will be categorized according to locations to evaluate this source of variability in Salish Sea. Results from the three analyses will be compared and distinguishable populations will be displayed on a map as an outcome

There is a high demand in the medical research community for a high-throughput drug-screening assay to quickly and effectively identify particular osteoactive compounds of interest to make strides in osteoporosis and other bone disease research. A compound is considered osteoactive if it affects the biological processes that constitute bone formation. The goal of the following research is to develop a viable assay that can detect osteogenic compounds in less than four weeks using post-embryonic zebrafish that addresses the time-intensive nature of using alternative animal models for preliminary drug screening. Thus far, we have proved that a double fluorochrome staining technique is a viable method for tracking mineral apposition rate of zebrafish centra under the influence of a certain compound over a time period. Mineral apposition rate (MAR) is a parameter used to characterize bone formation by measuring activity of osteoblasts. Fluorescent imaging and analysis of mineralization aids in quantification of drug effects. Due to the high degree of variability in developmental stages in post-embryonic zebrafish, we are currently developing methods to stage fish in order to eliminate phenotypic variability. Once this and other challenges are addressed, an opportunity for quick breakthroughs in drug discovery pertaining to bone formation will be possible with this time-efficient screening assay.

Enlightenment, transcendence, mystical experience, and spirituality, these are all common descriptors of supernatural experiences that cannot yet be explained scientifically. Recently, the theories of the neural mechanisms behind spirituality have drastically evolved and in the past century, modern advances in science has allowed mankind to describe the natural world more objectively and empirically. Many college-educated individuals no longer believe in the mystic stories given by religious holy scripture. Even with this shifting in perspectives, the human brain cannot always distinguish between external real experiences and internally induced spiritual experiences. Many people use spirituality as a resource in finding meaning and hope in the world yet there is still much to understand about the neural mechanisms encompassing these feelings. Through a literature review, we discuss in detail the neurological mechanisms behind supernatural experiences and spirituality associated with common human emotion pathways. Comparing past research to more recent research we illustrate how the hypotheses behind spirituality have changed through time and note whether spiritual feeling utilizes a known emotional pathway or a completely novel pathway. The objective is to increase the awareness of the physiological mechanism of spiritual experience related to common human emotions and provide a deeper understanding of how this natural phenomenon occurs accessible at a relatively basic level of understanding.

Academic publications in medicine share important clinical information and increase name recognition and name branding. This study was done to evaluate disparities in numbers and types of publications for women in the field of urology. Work is ongoing but to date, 9 issues from 2001 from the Journal of Urology were looked at. Articles were reviewed and type of paper was listed, along with the first and last author from each, and authors’ gender. A total of 817 papers were looked at including papers involving clinical research, lab/science research, case reports, editorials, review articles, and letters to editors. There were a total of 1492 authors (as some papers only had one author), in which there were a total of 63 female authors listed as the first author and 39 female authors as the last given author, giving a total of 102 female authors. There were 6 papers in which both the first and last primary authors were female. In all, this gives 6.84% of papers written by a primary author who is female and all remaining papers written by men. To date, research has shown that men are more likely to author primary research in high impact journals then women, which represents an opportunity in post graduate medical training programs.

Efforts to combat the obesity epidemic have given rise to consumer trends toward healthier food options, such as organic foods, which consumers perceive to be healthier than conventional foods. Research suggests low-level cognitive involvement predisposes individuals to the health halo effect—the favorable effects of organic labels on health beliefs and positive food evaluations. Despite recent efforts toward healthy food choices, an inner conflict exists when the essential desire to eat tasty foods contradicts the desire to eat healthy, also known as the unhealthy equals tasty intuition (UTI). This research assesses the health halo effect of organic labels using the Implicit Association Test (IAT), adapted from Greenwald and colleagues. We predict that 1) The health halo will significantly increase implicit evaluations of organic labelled foods as compared to non-organic foods and 2) The health halo effect will be significantly mediated by level of deliberative processing as measured by frequency of reading nutrition labels, frequency of purchasing organic foods, level of health consciousness, and level of compensatory health beliefs. Research on consumer food product purchase intentions suggests taste as the dominant driver in decision making; therefore, our predicted results propose foods considered nutrient-rich and calorie-poor and labeled organic are shielded by the health halo effect. Consumers low in health consciousness and deliberative processing will base food decision making on organic labels because their belief in the UTI is diminished by the health halo effect. A clear consequence of this is the continued consumption of high-density foods, only now consumers believe they are making healthy food decisions under the assumption that high-density foods labeled organic are healthy.

Increasing atmospheric CO2 has lead to increased uptake of CO2 by oceans causing ocean acidification. Ocean acidification is the long-term reduction of pH that can have negative effects on marine organisms, especially young calcifying organisms. In Puget Sound, ocean acidification has already caused large-scale oyster larval mortality, negatively affecting a significant contributor to the Pacific Northwest economy. The native eelgrass in Puget Sound, Zostera marina, may be a local mitigation strategy for ocean acidification. Marine plants take up CO2 through photosynthesis to create biomass increasing the pH of the water. In this study, water samples were collected from several depths within the water column above eelgrass beds and surrounding mudflats in Padilla Bay. Water samples were analyzed for pH, total alkalinity, dissolved oxygen, dissolved inorganic carbon, and chlorophyll A. Eelgrass shoots and density were measured for leaf area index and the Padilla Bay National Estuary Research Reserve weather stations were used to calculate solar irradiance to estimate the photosynthetic activity of the eelgrass beds. Results suggest that eelgrass beds, in addition to providing critical habitat, may also help locally mitigate ocean acidification beyond the area of the eelgrass beds. Future research analyzing the input and output of carbon in eelgrass beds will be critical to developing large-scale carbon and pH models in marine environments.

Spontaneous electrical activity in the mouse neocortex has been extensively studied. Two main types of activity are observed: synchronous waves and asynchronous single cell activity. This synchronous activity has been believed to be unique to the developing brain. This research project investigated whether the phenomenon is as much a property of sleep as it is development. Synchronous waves exhibit remarkably similar dynamics to the up-down oscillations of slow wave sleep. Conversely, asynchronous single cell activity is very similar in form to the "persistent up" or wakeful brain state. Thus, the two types of spontaneous activity generally observed in the mouse neocortex may actually be a sign of overall brain state, with asynchronous single cell activity dominating during states of wakefulness and synchronous waves taking over during sleep states. Calcium imaging of slices of neonatal mouse cortex has revealed that application of curare, an acetylcholine antagonist, decreases asynchronous single cell activity and induces synchronous waves. As blocking acetylcholine puts the brain in a state associated with sleep, we hypothesize that the neurotransmitter may be involved in keeping the brain awake. Further experiments were conducted on the effect of curare on synchronous waves. According to our hypothesis, it should increase their frequency and/or propagation. The same experiments were performed with other acetylcholine antagonists, such as mecamylamine, to ensure the observed effect is not unique to curare as a drug. We also conducted experiments with acetylcholine agonists as well to see if they have the opposite effect. These synchronous waves are known to be involved in several developmental neural processes, and this research project may reveal they are a property of sleep, and could serve as precursors to adult slow-wave sleep.

Lake Washington is a freshwater ecosystem, which is characterized by a dynamic turnover of methane, an important greenhouse gas, serving as both a major source and a major sink. In this environment, methanotrophs are a key aerobic microbial group that oxidizes methane preventing its release into the atmosphere, thereby acting as a natural filter. Consequently, methanotrophs have been studied intensively in this environment. However, the data from different approaches have not always agreed with each other. In particular, DNA stable isotope probing (DNA-SIP) with 13-C-methane suggested that the genus Methylobacter species might be the dominant active type in laboratory setups approximating natural conditions. In contrast, pure culture experiments with other methanotrophs, including Methylobacter demonstrated the genus Methylomonas to display robust growth and the highest competitiveness. This suggested that there must be biotic and/or abiotic factors that act differently in pure culture and setups approximating natural conditions. In this study, we established synthetic communities to test the effect of Rare Earth Elements (REEs) and microbial diversity as explaining variables on the competitiveness of the dominant methanotrophs. We focused on Lanthanum as a representative of REEs because of its increasing importance in methanotrophy. Quantitative PCR and spectrophotometry were used to determine growth of cultures and individual abundances of methanotrophs. Over a time span of 4 weeks synthetic communities resulted in variable dynamics whereas two species synthetic communities clearly showed Methylomonas to be the stronger competitor compared to Methylobacter in the presence of Lanthanum. The distinct effects of Lanthanum are still being investigated, yet these results suggest that both biotic and abiotic factors determine the species interactions of this environmentally important group of bacteria. Future studies will aim to further disentangle the contribution of these factors to better understand the functioning of an important microbially driven biogeochemical process.

The lateral habenula (LHb) in the brain is an important regulator of midbrain dopaminergic systems that are known to be involved in the reinforcing properties of cocaine. We have previously determined that activation of LHb neurons using Designer Receptors Exclusively Activated by Designer Drug (DREADD) technology decreases cocaine-induced locomotor activity, cocaine self-administration and relapse in rats. To determine whether these effects were due to an increase in anxiety, here, we examined the effect of activation of LHb neurons using the Gq-coupled DREADD (hM3Dq) on anxiety-like behavior in an open-field test. Male Long-Evans rats underwent survival surgery and were injected with hM3Dq bilaterally into the LHb. They then participated in an open field test where their behaviors were observed and recorded. Before the test, the rats were injected with 1 or 3 mg/kg i.p. clozapine-N-oxide, which is the inert ligand that activates DREADD receptors. Twenty minutes elapsed before the test was performed. During the experiment, the amount of movement and location of the rat in the open field was assessed, with no movement and amount of time spent against the periphery of the field, indicating anxiety-like behaviors. I hypothesized that activating the LHb via DREADD viruses would result in subsequent anxiety-like behavior observations.

It has long been known that certain species possess the capacity to regenerate bony appendages following amputation through a process called epimorphic regeneration. For instance, zebrafish possess the ability to regenerate their tail fin bones when amputated. Early regeneration involves the formation of a blastema, similar to the blastema that mediates limb regeneration in salamanders. After the blastema forms, the bone regeneration process resembles the bone developmental process in humans. Thus, a better understanding of epimorphic regeneration holds promise to enhance our understanding of regenerative biology, allow for medical advances in bone tissue engineering, and increase understanding of the skeletal developmental processes. A challenge in understanding the regeneration process is the inability to immobilize fish to generate time lapsed images of various stages of regeneration. Typical methods for anesthesia in zebrafish only enable 10-20 minutes of sedation. Several studies (including those by our lab) have developed specialized methods to do long-term imaging with the use of tricaine methanesulfonate and benzocaine. However, both anesthetics are sodium channel inhibitors, which inhibit the regeneration process itself. In order to circumvent this problem, we designed a chamber for anesthesia-free imaging with a restraint system, and a removable glass-bottom window to facilitate imaging. The chamber is coupled to peristaltic pumps so water can flow in and out. The fish is secured and unanaesthetized, thereby bypassing the issue of lack of regeneration due to the anesthesia. In pilot studies we have found that the zebrafish quickly acclimate to the chamber, suggesting that the zebrafish can remain in the chamber for several hours. Our studies indicate that this anesthesia-free, long-term imaging chamber may allow us to see details of dynamic processes that unfold over a period of 24 hours, which currently can only be seen through snapshots of short-term imaging.

Newborns and children are at a much higher risk to adverse drug reactions, which is a significant public health problem. This is partially due to the lack of knowledge of the ontogeny of drug-metabolizing enzymes (DMEs). There are two types of DMEs, known as Phase-I and Phase -II DMEs. Phase I DMEs catalyze oxidation, reduction and hydrolysis reactions. Cytochrome P450s (CYPs) are a superfamily of Phase I oxidative enzymes responsible for the metabolism of a wide spectrum of drugs. Phase-II DMEs are responsible for various conjugation reactions including UDP glucuronidation, sulfonation and glutathione conjugation. Gut microbiome is known to regulate xenobiotic metabolism in adult mouse liver, but little is known of its potential involvement in the ontogeny of DMEs. The goal of this study was to determine the developmental regulation of Phase I and Phase II DMEs using germ free (GF) mice as a model. We bred both control and GF mice under the same housing conditions, and collected livers from male mice at the following ages: Days 1, 5, 10, 15, 25, 60, and 120. We isolated total RNAs and determined the RNA concentration using a Nanodrop spectrophotometer. We also determined the RNA integrity using gel electrophoresis by visualizing the 28S and 18S ribosomal RNA subunits. Using RT-qPCR we quantified the mRNAs of major DMEs and evaluated differences between control and GF mice using T-Test. As compared to age-matched control mice, the mRNAs of the xenobiotic-metabolizing Cyp3a11 was down-regulated in livers of GF mice at multiple ages including Days 10, 60, 120. Conversely, the expression of the lipid-metabolizing enzyme Cyp4a14 was up-regulated at the following ages: Days 5, 15, 60, and 120 in GF mice. In conclusion, our data suggest that the ontogeny of some DMEs is profoundly modified by lack of gut microbiota.

The Neotropics contain about 100,000 seed plant species, amounting to ca. 37% of the world’s species. The Olmstead lab is currently investigating Bignoniaceae, a plant family comprised of 82 genera and ca. 827 species distributed primarily in the Neotropics. There are 8 recognized clades in Bignoniaceae. One clade, Tecomeae, include 12 genera and approximately 55 species, with species distributed in North and South America, Southeast and Central Asia, and Australia. To create a phylogeny for Tecomeae, I gathered all available sequence data and DNA for species in the tribe from both the Olmstead lab and GenBank. Then, DNA from samples of additional species were extracted using the DNeasy Plant Mini Kits. Three different regions of DNA were sequenced, including two chloroplast regions (ndhF and rpl32-trnL) and one nuclear region (ITS). I amplified these regions via Polymerase Chain Reaction and sequenced the DNA using an ABI genetic analyzer in the UW Biology Department Center for Comparative Genomics. Sequences for all species were edited and aligned using Geneious. Phylogenetic analyses were performed in both Maximum Likelihood and Bayesian frameworks using RAxML and MrBayes. Creating a phylogeny for the Tecomeae is a crucial step toward deciphering the evolutionary history of Bignoniaceae. The overarching goal of our research is to not only create a phylogeny for Tecomeae, but for all 827 species within the Bignoniaceae family. Having a phylogenetic tree for Tecomeae allows us to identify when important divergences occurred, giving us an improved picture of how Bignoniaceae diversified and, ultimately, a better understanding of Neotropical diversification as a whole.

The Planetary Instrument for X-ray Lithochemistry (PIXL) is a micro-focus x-ray fluorescence spectrometer designed for use by the Mars 2020 rover. X-ray fluorescence is the emission of secondary, or fluorescent, x-rays from a material that has been excited via bombardment of high energy x-ray or gamma radiation. The secondary x-rays emitted by the material have spectral lines characteristic of the elements in the sample. PIXL looks for elemental and spatial signatures of past life. Moreover, its spectroscopic data collection is often affected by target surface tilt. Attenuation of the x-ray beam, i.e. a decrease in beam intensity, increases if the target is tilted away from the detector, and decreases if the target is tilted toward the detector. Attenuation is caused by absorption or deflection of photons from the x-ray beam, and decreases the accuracy of relative chemical abundance measurements. PIXL is programmed to account for these effects, and produce quantitative results identical to those of non-tilted surfaces, however, the accuracy to which it does this is unknown. We tested the model on two standard materials, of known composition, and compared those data to real spectra taken by the instrument at various tilt angles. The results were somewhat inconclusive, as errors were large in elements with relatively low chemical abundance and low signal-to-noise. The code will now need to be refined, and the experiments run again, changing the model until it has reached a desired level of accuracy.

Enteric diseases, or diseases of the gastrointestinal (GI) tract, remain one of the most prevalent killers of children in sub-Saharan Africa. The most practical way to prevent such diseases is through vaccination, but antigens for enteric diseases need to be delivered directly to the GI tract to be most efficient, making vaccination difficult. Recent studies by the von Adrian group at Harvard University have found that certain kinds of white blood cells are reprogrammed to home to the GI tract when they encounter retinoic acid, commonly referred to as vitamin A. The King group at the University of Washington is working to develop a vaccine using recently developed protein cages, which can transport all-trans retinoic acid (ATRA) and enteric antigens. The first step to developing this vaccine is to create a hyper-stable base protein for the cage, to allow the protein to be engineered into a protein cage. To do this, I created 23 different versions of Cellular Retinoic Acid Binding Protein I (CRABP-I) each with a different combination of 5 mutations. These mutations were identified using the PROSS server from the Weissman Institute which uses Rosetta to identify mutations which will stabilize a given protein. These constructs were then tested for stability at increasing temperatures. The construct that resisted denaturing at the highest temperature was selected, and I further mutated the protein to help it bind ATRA. This protein will be assembled into a cage combining ATRA and a model antigen, and sent with several other controls for testing in mice. We hope that our protein cage vaccine will generate increased immune responses in mice against enteric diseases.

Bull kelp, Nereocystis luetkeana, is a dominant kelp forest species in the Salish Sea and plays an important role in the marine coastal ecosystem. The biogenic structure formed by N. luetkeana provides habitat for marine mammals, crustaceans, echinoderms, mollusks, fish, and other algae and increases the productivity of the ecosystem. Throughout its lifecycle N. luetkeana faces a variety of biotic stressors that impact its distribution and abundance. These stressor include competition, availability of sori, the reproductive organ of kelp, and herbivory. The relative impacts of availability of sori and competition on the abundance of N. luetkeana were explored through a subtidal experiment that examined how clearing and seeding impacted N. luetkeana settlement and growth. 40 subtidal plots were placed off of Point Caution, San Juan Island, at approximately 20 feet during a medium low tide. A treatment was then applied to each plot. 10 were seeded with ripe sori, 10 were cleared of vegetation, 10 were both cleared and seeded, and 10 were left undisturbed as a control. The site was monitored via SCUBA over the next 6 months and new recruits of N. luetkeana were recorded. Data suggest that competition between macroalga is the limiting factor in kelp settlement. Once the macroalga survives settlement it still faces other stressors, such as herbivory. Feeding trials with two species of kelp crabs, Pugettia gracilis and Pugettia producta, tested feeding electivity on N. luetkeana using a choice no choice method. Results suggest a preference in both species for juvenile stipe over juvenile blade, and sori over non-reproductive mature blade. P. producta also elected to eat mature blade over mature stipe. Identification of challenges faced by N. luetkeana has the potential to allow for more informed preservation and restoration of kelp beds in the Salish Sea and in other areas.

People have an instinctive understanding of what it means for an object to be three-dimensional: it has height, width, and length. There is similar familiarity with two-dimensional shapes like squares and triangles, as well as one-dimensional shapes such as lines. The dimensions of some objects, on the other hand, cannot be understood in this familiar way. Take, for example, a set of points in the xy-plane that do not form a straight line or any familiar shape from geometry. One way to measure the dimension of these objects is to calculate the Hausdorff dimension of the set of underlying points. Intuitively, the Hausdorff dimension is a measure of how many small boxes it would take to cover an object. Our research aimed to calculate the Hausdorff dimensions of more complicated curves, such as those arising from Brownian motion, which is a probabilistic model for a randomly moving particle. In particular, we set out to corroborate known results about the Hausdorff dimensions of Brownian motion and the Brownian frontier. Further, we wanted to strengthen unsolved conjectures regarding the Hausdorff dimension of the Brownian earthworm model, which is a model of mass redistribution on the d-dimensional integer lattice introduced by Professor Krzysztof Burdzy. We attempted to develop answers to these problems by simulating Brownian motion in two dimensions and performing statistical analysis on our results. Our model correctly calculated the known dimensions and was in line with Professor Burdzy’s previous conjecture regarding the Brownian earthworm. It is our goal that this research will ultimately contribute to a greater understanding of the earthworm model.

Paper has been utilized for centuries by humans for writing, printing, and packaging. It has properties of being flexible, biocompatible, and biodegradable which make it a valuable low cost and environmentally friendly alternative to petrochemical-based materials for applications in robotics, electronics, and microfluidics. In particular, electrically conductive materials, which possess the merits of minimal weight and good processing ability, can be integrated into the manufacturing process of structural parts, allowing the implementation of a sensor function. By mixing multi-walled carbon nanotubes (MWCNTs), sheets of hexagonally packed carbon atoms rolled into concentric seamless cylinders, with insulating cellulose fibers, we were able to produce a conductive paper that retains its strength and exhibits sensitive resistive changes when exposed to water and humidity. The fabrication process was based on traditional papermaking methods and included the refining of unbleached softwood Kraft fibers, the suspension of cellulosic fibers in MWCNT–cationic polymer mixtures, and the filtration, pressing, and drying of the resulting pulp to prepare handsheets with grammage of 60 g/m^₂. The as-prepared MWCNT–cellulose composite papers were analyzed by electron microscopy and their water sensing abilities were examined. Results showed that, unlike most common petrochemical-based materials that are not sensitive to polar water molecules, the relative electrical resistance of the paper composites significantly increased under water and returned almost to their initial level of resistance after drying, with very fast and reproducible signals over multiple immersion/drying cycles. Future large-scale production of the paper is planned to explore industry-feasible methods.

My work is concerning polymer nanofoams, a thermoplastic material processed to have an interconnected porous structure with nanometer sized channels. These materials have applications in fluid filtration, medical devices, insulators, catalysts, and templates. While many techniques exist to create such structures, the material discussed here is made by the solid-state foaming process. This is a simple technique in which CO2 blowing agent is dissolved into the polymer in the solid state, and then heated to the glass transition to initiate cell nucleation and expand the polymer. I am in charge of the whole samples foaming process. Besides that, I analyze these samples under SEM (Scanning Electron Microscope) cooperating with my mentor. These expanded polyetherimide (PEI) by foaming process has been shown to have an interconnected porous structure with channels on the order of 50-100 nm. Dye permeation tests conducted by me confirm that the nanostructure will allow fluids to flow through. However, no work has been done to quantitatively characterize this material and obtain its permeability. Krause et. al has done basic experiments where nitrogen and helium gas was flowed through the cross-section of a PEI membrane, but no material property was derived from these experimental results. In my research, a material property known as permeability is computed by experimental data in conjunction with a fluid flow model derived by my mentor. Additionally, the diffusivity of gasses through the nanostructure is also computed and correlated to the permeability. Finally, the relationships between a processing parameter (foaming temperature) and porosity, permeability, and diffusivity are established.

The patterning of skin appendages, such as hair, feathers, teeth, and scales, is crucial for a vertebrate’s ability to survive in their environment. For example, an increased density of eccrine sweat glands in humans has a large impact on our capability to maintain our body temperature. While some key developmental genes have been identified, little is known about the molecular mechanisms involved in skin appendage patterning. All skin appendages evolved from a single ancestor, and although they have different morphologies they share many developmental mechanisms. Zebrafish scales are simple skin appendages made of dentin-like extracellular matrix that form a partially overlapping pattern resembling roof tiles. While mouse and chick-models of skin appendage development require examination of fixed specimens, we can conduct conditional genetic manipulations while imaging the entire skin through scale patterning in live animals. Therefore, zebrafish scales are an ideal system to gain insight into mechanisms underlying skin appendage patterning. We manipulated conserved cell-cell signaling pathways and assayed scale patterning. The zebrafish genome harbors multiple Fgf receptors that are partially redundant, and removing one of them results in fewer, larger scales, while inhibition of all Fgf receptors completely abolishes scale development. This suggests that Fgf signaling, likely through multiple Fgf receptors, plays a role in scale initiation and patterning. Experimentally increasing Fgf signaling results in smaller and more numerous scales, likely due to delayed squamation, indicating that both Fgf and the timing of scale development ultimately determines density. This also implies that a specific level of Fgf signaling may be necessary for scales to form correctly. Inhibition of the Wnt signaling pathway also results in failed scale development. In summary, these results suggest that skin appendage density is dependent upon the timing of their development, and is controlled by a mechanism involving multiple signaling pathways.

Serotonin is a key player in the regulation of anxiety, fear, and stress. While acute stress is associated with increased activity in serotonergic neurons, chronic stress is characterized by the transition to decreased serotonergic neuron activity, the desensitization of serotonin autoreceptors, and the development of maladaptive emotional behaviors. We hypothesize that chronic stress causes dysregulation of serotonergic neuron excitability, and that these adaptations affect emotional responses to future exposure to stressful and hedonic stimuli. The goal of this study is to determine if alterations to serotonergic neuron excitability can alter the effects of stress on subsequent emotional behavior. We predict that reducing or intensifying the excitability of serotoninergic neurons will decrease and increase maladaptive behavioral responses to chronic stress, respectively. We expose experimental groups of wild type and transgenic mice expressing either excitatory or inhibitory DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) to chronic stress. The mice undergo 5 consecutive days of social defeat stress, during which they receive injections of saline or clozapine-N-oxide (the ligand for DREADDs). Following chronic exposure to stress, behavioral responses are measured through sucrose preference, social interaction, and immobility during forced swim tests. Mice expressing inhibitory DREADDs are anticipated to exhibit greater hedonic responses (increased sucrose preference), improved sociability, and decreased immobility during forced swim, compared to wild-type mice. Mice expressing excitatory DREADDS are anticipated to show decreased sucrose preference, decreased sociability, and increased mobility during forced swim. By altering the activity of serotonergic neurons, we can potentially modify the emotional and behavioral effects of stress. This study could provide new insight into the role of the serotonergic system in behavioral responses to chronic stress, and yield new therapeutic targets for conditions such as depression and post-traumatic stress disorder.

Less than 3% of therapeutics can cross the blood-brain barrier, and the lack of penetration of therapeutics into the brain is the most cited failure for neurological clinical trials. In order to assess the efficacy of developing therapeutics which have the potential to address these issues, we are working towards establishing a high-throughput organotypic ex vivo brain slice model. We are specifically interested in developing a model that allows us to study and characterize the brain in the presence of glutamate excitotoxicity. Glutamate excitotoxicity is cell death due to an excess of the excitatory neurotransmitter glutamate, and is a common disease hallmark in neurological injury. The slice model we developed consists of cultured newborn rat brain slices to simulate an in vivo brain environment. However, in slice form, we have the ability to systematically study key pathophysiological variables, such as exposure to various excitotoxins that induce glutamate excitotoxicity. We use quantitative assessments of cytotoxicity (cell death) through cellular staining and imaging, as well as assays for lactate dehydrogenase (LDH), an enzyme released from the cytoplasm during cell death. We have established percent cytotoxicity profiles for both healthy untreated and maximum death control brain slices, and developed a protocol for testing excitotoxins to simulate glutamate excitotoxicity. With this slice platform, we will be able to compare the efficacy of potential therapeutics based on the decreases in rates of cell death they produce in brain slices with induced glutamate excitotoxicity. This research represents a promising platform to assay behavior, mechanism, and efficacy of therapeutics in development for the treatment of neurological disorders associated with glutamate excitotoxicity.

In fruit flies (Drosophila melanogaster), grooming is an innate behavior comprised of sequential movements of particular legs over specific regions of the body. However, we know little about the neural circuits that control the locations, durations, or behavioral transitions of grooming. We sought to identify neurons in the central nervous system that control these aspects. To investigate this, we used optogenetics, which involves expressing light sensitive ion channels in defined neurons, allowing us to activate them with red light. We then recorded videos of the flies as we stimulated them with red (625nm) light for various durations (0.5, 1, 5 seconds). Finally, we manually annotated the videos by assigning binary tags to specific behaviors and aggregated the results to see trends across flies. We were able to identify neurons in the brain that influenced head grooming, neurons in the ventral nerve cord that influenced hind leg grooming as well as additional neurons that influenced other behaviors. Identifying these neurons opens up new opportunities to dissect neural circuits controlling grooming behaviors and, in the future, to understand how these circuits interact to control sequential behaviors.

Store-and-Forward Teledermatology is used as a system for increasing access to dermatology care for patients in the Veterans Health Administration (VA). Where dermatologists are not available, primary care clinics partner with teledermatology to help patients access high-quality, timely healthcare. Rather than being seen face-to-face by a dermatologist, patients’ skin lesions are imaged and sent asynchronously to a teledermatology reader (a dermatologist) in another location. Many types of skin conditions can be diagnosed through this system, including melanoma, a dangerous form of skin cancer. While this health system has demonstrated good diagnostic sensitivity for melanoma, little is known about its positive predictive value (PPV), also called precision. PPV is the proportion of melanoma diagnoses that are confirmed by pathology to be truly melanoma. Pathology diagnosis is considered the ‘gold standard’ for diagnosing dermatological conditions. Because the threat of melanoma is taken very seriously, low PPV leads to more unnecessary biopsy procedures and pathology consultations- actions that strain VA health system resources. This quality improvement study investigated the PPV of all teledermatology readers in the Seattle VA program from February 2015 – January 2016. Chart reviews (n=552) were completed and data were analyzed to determine an overall PPV rating, to find individual provider PPV ratings, and to identify factors correlated with high PPV. We hope to use this analysis for two primary quality improvement actions. First, we aim to develop PPV standards for teledermatology providers to meet. Secondly, we aim to identify what steps could be taken to maximize teledermatology reader PPV. Policy changes could be applied to help minimize waste in our teledermatology program.

In Kenyan HIV-1 infected children, it is likely that exposure to household indoor air pollution (HAP) increases susceptibility to respiratory illness, cancer, growth failure, and compromised cognitive abilities. Kenyan families usually live in one-room houses and use wood or charcoal cook stoves indoors. Smoke from burning of wood and charcoal contains large quantities of polycyclic aromatic hydrocarbons (PAHs) which are among the many components of incomplete combustion. Many PAHs are carcinogens that undergo metabolism and are excreted in urine. In order to assess children’s exposure to wood and charcoal smoke, single spot urine samples were collected from 100 subjects: 50 recently diagnosed HIV-1 infected children, age-matched healthy HIV uninfected children, and their mothers. Urine samples were hydrolyzed by treatment with glucuronidase enzyme and cleaned up with solid phase extraction. High-performance liquid chromatography with fluorescence detection was used to analyze the samples for PAH metabolites. We anticipate that urinary hydroxyl PAH metabolite concentrations will be high in these cohorts of HIV-1 infected and healthy children reflecting the exposure to HAP by use of wood and charcoal for cooking. Findings of this research will help to understand the pathogenesis of cancer and respiratory diseases in HIV-1 infected children, healthy children, and their mothers.

The purpose of this study is to effectively measure and estimate the health impact of common sources of artificial lighting that humans are exposed to at night. To compare the impact of many different types and intensities of artificial light, we have developed an approach for analyzing the profiles of these light sources that evaluates them in terms of the full moon and the way in which the melanopsin photoreceptors in the human eye respond to a full moon. Melanopsin photoreceptors play a key role in regulating circadian rhythms and biological timing in all systems of the body. At an evolutionary scale, natural moonlight is what humans are adapted to, and by comparing full moon exposure (FME) to artificial light source exposure in the context of how much is absorbed by melanopsin photoreceptors, we can understand how unnatural different devices and light sources are at night and compare their relative impact on circadian rhythms and sleep health. The results of this study show that many common electronic devices easily exceed 5X a full moon exposure and can reach as high as 100X. Ambient lighting in the home, from light sources ranging from incandescent to LED deliver well over 100 full moons of exposure at recommended ambient lighting conditions. The implication of these results is that most devices and light sources disrupt normal sleep rhythm in some way and could lead to a variety of health concerns if not properly managed. Individuals can use this data to adjust their light exposure at night, to make adjustments to urban lighting in cities, and to inform architects and designers to light residential spaces in a way that minimizes health risk.

The Ocean Research College Academy (ORCA), a running start program in partnership with Everett Community College has been conducting research in the Possession Sound since 2004. Those carrying out this investigation added to ORCA’s longitudinal data set in 2016 and 2017. Possession Sound is part of the north Whidbey Basin of the Puget Sound and is bordered by Snohomish County to the east and Whidbey Island to the west. Dissolved oxygen (DO) is an important factor in the survival of many aquatic species, and the loss of these species due to a lack of dissolved oxygen can disrupt the lives of other predatory animals and negatively affect marine industries. As DO levels fall below 4 mg/L, waters become hypoxic which can be fatal to marine life. This study investigates the effect of temperature on DO levels in the Possession Sound from a single site location (referred to as Deep) during 2015 and 2016. Water samples were collected from a depth of about 20 meters by deploying a Niskin sampling bottle. Then DO and temperature were measured with a YSI-85 handheld instrument. Results show that DO levels are lower in waters with warmer temperature. For instance, a DO level of 7.7 mg/L was observed at 11oC, while a DO level of 4.78 mg/L was surveyed at 12.16oC. These results are attributed to water molecules being less dense in colder water, allowing for more volume to be occupied by dissolved oxygen. This suggests that warmer temperatures in Possession Sound may not be suitable for sustaining diverse and healthy marine life. Since this research only investigated dissolved oxygen at 20 meters deep, it would be of interest to investigate DO levels of surface waters in order to probe the effect of photosynthesis on DO in the future.

Cannabis is a widely used drug, however the impact of cannabis use in HIV-infected individuals is unknown. While current antiretroviral treatments (ART) can successfully suppress viral burden in HIV-infected individuals, treatment alone does not always completely restore health. We aimed to assess how cannabis may affect HIV pathogenesis to better inform how to advise HIV-infected patients. Previous studies in animal models have demonstrated anti-inflammatory effects of cannabis, and thus we aim to assess the immunological implications associated with cannabis use in HIV-infected individuals. This retrospective study assessed peripheral immune cell frequency and phenotype in HIV-infected individuals (n=185) that either frequently use cannabis (n=57) or do not use any drugs of abuse (n=128). Expression of protein markers associated with cell activation (HLA-DR+ CD38+), proliferation (Ki-67+), and exhaustion (PD-1+) was assessed via flow cytometry and differences between groups were analyzed using Mann-Whitney T-tests. No statistical differences in CD4+ and CD8+ T-cell population frequencies were found between cannabis users and non-users, nor did we find differences in plasma biomarkers of inflammation or microbial translocation. Cannabis users were stratified into lower, middle, and upper quartiles of cannabis metabolite concentration (11-nor-carboxy-THC), as measured by mass spectrometry. Comparing high-use cannabis users, defined as above the 75th percentile (>251.8nM), to non-users indicated statistically significantly lower frequencies of activated CD4+ and CD8+ T-cell (HLA-DR+ CD38+ expression; p=0.0307 and p=0.0454, respectively) and CD4+ and CD8+ T-cell exhaustion (PD-1+ expression; p=0.0184 and p=0.0254, respectively.) These data suggest that cannabis use in HIV-infected individuals does not increase markers of HIV pathogenesis, but may actually reduce activation and exhaustion of T cells. Thus, further studies to determine how cannabis impacts systemic and tissue inflammation and disease progression in HIV-infected individuals are warranted.

Protoporphyrin IX (PpIX) is a red fluorescent metabolic by-product of oral bacteria and serves as an indicator of early and late stage caries. PpIX has a strong absorption band centered at 405 nm and exhibits an emission range from 615 to 710 nm. Spectroscopic and imaging devices targeted at PpIX require a fluorescent standard for calibrating their detection sensitivity. However, PpIX lacks photostability and an alternate molecule is needed to represent the excitation and emission fluorescence characteristics of PpIX. Evaluation of instrument performance over time is especially important for long range clinical studies examining changes in fluorescence in response to disease therapies. The scanning fiber endoscope (SFE) is an optical imaging system currently used in clinical dental research to quantitatively monitor the fluorescence of PpIX. Water based solutions of PpIX are unstable and led us to develop a dye-in-polymer standard that offers photostability, portability, and uniform fluorescence. Organic europium complexes model the fluorescence spectrum of PpIX closely, with a similar red emission range from 615 to 710 nm. Preliminary photobleaching experiments using a 405 nm laser illuminating a europium dye embedded in a polyurethane polymer demonstrated that it offers significantly better photostability than PpIX, exhibiting a 3-4% drop in europium fluorescence after one hour of continuous laser excitation. Under similar laser illumination conditions another PpIX phantom molecule, octaethylporphyrin (OEP), suffered a >20% drop in fluorescence after only 3 minutes of excitation. The photodegradation curve over time for europium was evaluated using the same 405 nm laser and LED excitation sources used for measuring the pH dependence of PpIX fluorescence in oral biofilms. Dye-in-polymer europium materials were also exposed to elevated temperatures in addition to laser illumination to further assess their suitability as fluorescence standards.

Zooplankton live throughout the water column and what they ingest gets passed to marine life in the higher trophic levels and can ultimately be consumed by humans. Microplastics, 5 mm in diameter or smaller, can contain and absorb high concentrations of toxins and have been consumed by zooplankton in laboratory studies. This research examines whether zooplankton are eating microplastics in Puget Sound. Zooplankton samples were collected from two locations on the east side of Whidbey Island, at an approximate depth of 180-200 meters, and preserved in formalin to prevent further ingestion or regurgitation of microplastics. Samples were then processed according to the National Oceanic and Atmospheric Administration’s methods for the analysis of microplastics in the marine environment. The zooplankton and other organic materials were dissolved and the remaining inorganic components were weighed and examined using light microscopy. The most abundant plankton collected were various species of amphipods, chaetognaths, copepods, and shrimp. Microplastic fibers were observed after completion of the chemical digestion. These results suggest that zooplankton are consuming microplastics in situ and provide evidence of the introduction of microplastics into the marine water column.

Autism Spectrum Disorder (ASD) is a developmental disorder in which individuals experience significant problems with social skills, behavior, and communication. It is less clear if there are systematic impairments in executive function (EF), a set of mental processes that include working memory, mental flexibility, response inhibition, and planning/organizational skills. The prevalence of ASD is 1 in 68 children, with the diagnosis 4.5 times more prevalent among boys than girls. Impairment in EF may differ between genders with ASD, although previous findings suggest the magnitude and direction of the effect vary by age and EF subscale. For example, girls outperformed boys in multitasking and planning, adolescent girls compared to boys have been found to have poorer response inhibition, and adult males compared to females had better working memory and mental flexibility. The aim of this study was to further explore EF in individuals with ASD or neurotypical (NT) development, specifically comparing genders, age, and IQ and their role in the variability seen in EF. 50 boys and 50 girls age 8 to 17 years, with and without an ASD diagnosis, participated in this study. Parents completed the Behavior Rating Inventory of Executive Function (BRIEF) an 86-item questionnaire with 8 subscales. EF was compared between group (ASD/NT), sex (male/female), and IQ. We expect that ASD subjects will express greater deficits in EF when compared to NT subjects. Additionally, we expect that differences in EF will be present between boys and girls, but that the direction of these differences will vary by subscales. Lastly, we expect that a greater IQ will correlate to fewer EF deficits. This study will contribute to a greater understanding of the cognitive differences across genders that occur in ASD.

The purpose of this project is to demonstrate using bacterial comunities in a reactor to detoxify and decolor wastewater that is discharged from textile factories. Currently available methods include chemical and physical treatment, which are expensive. Four specific bacteria that have these abilities were previously isolated. These were used in an experimental design that incorporated three major components: Anaerobic reactors, aerobic reactors, and toxicity tests. The anaerobic reactors were designed to cycle synthetic textile wastewater, decoloring the discharge before flushing and repeating. This was done both with and without biomedia. Data was collected in order to determine the growth kinetics of the different bacteria. Preliminary results suggest that repeated filling and flushing of media with bacteria successfully decolors wastewater and growth kinetics for the bacteria can be modeled. The decolored ‘flushed’ media was then run through a second aerated reactor for detoxification. In this step, COD (chemical oxygen demand) tests were run in order to determine and model growth and chemical degradation. The third and final component was phytotoxicity tests. These tests were run by sampling media throughout both reactors’ cycle. The results of these phytotoxicity tests will determine whether or not detoxification has successfully occurred. In conclusion, this study suggests that these bacteria are promising for both detoxification and decoloration of textile factory wastewater and that, moving forward, a two reactor system should be considered for scaling up.

The new field of gravitational wave astronomy has the potential to answer leading questions in astrophysics. With the latest technology of LIGO (Laser Interferometer Gravitational wave Observatory) and contributions from over 1000 scientists from around the world, we have made the first detection of a merger of two black holes which occurred more than one billion light years from Earth. The first few black hole mergers that have been observed by LIGO imply a merger rate in the Universe that is higher than expected. It can be estimated that there is an upper limit of three black hole mergers per hour somewhere in the Universe. If the black holes are significantly far away they will not be able to give a strong enough signal to see through the background noise. It's like trying to hear someone whisper from across the room at a busy restaurant. However, many distant mergers could produce a combined background signal like the static between radio stations. Currently, LIGO utilizes a Bayesian wavelet decomposition to match strong nearby signals to a template in the database, but a frequentist method to search for a stochastic background signal. Our research is a novel approach, using an adapted version of the Bayesian algorithm to extract the background signal emitted by these black hole mergers. The goal of this research is to find patterns in the stochastic background signal of the O1 and O2 observation runs of LIGO and from these create templates for future data analysis of gravitational waves. The more that is known about gravitational waves, the more we are able to learn about the nature of gravity and therefore the Universe itself.

Polio is on the cusp of worldwide eradication but remains endemic in Afghanistan and Pakistan. Nigeria’s endemic status is being reconsidered because poliovirus was found in circulation after two years being polio-free. The Global Polio Eradication Initiative has implemented an environmental surveillance program to detect poliovirus (PV) in environmental samples such as sewage. Systematic environmental sampling provides supplemental data to disease-based clinical surveillance data. However, traditional PV detection methods from environmental samples, cell culture and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), are time consuming and expensive. Development of a screening test has potential to streamline environmental surveillance of PV. Reverse transcriptase recombinase polymerase amplification (RT-RPA) is an isothermal molecular amplification technique with potential as a screening test. In this technique virus particles are lysed to release RNA, which is converted to cDNA and amplified using recombinase enzymes. Amplified PV cDNA can then be detected through lateral flow detection. Collaborators at PATH have developed a RT-RPA protocol that has shown promise in rapid PV detection in stool samples. The aim of this research is to adapt PATH’s clinical PV RT-RPA protocol for use with environmental concentrates and to determine the limit of detection. Concentrates will be obtained by filtering raw sewage from a Seattle wastewater treatment plant. Results of the RT-RPA test and subsequent visualization on lateral flow detection strip will be compared to cell culture and RT-qPCR. We anticipate that RT-RPA will show a similar limit of detection when compared to traditional methods and will be suitable as a rapid screening test for environmental concentrates. Future work will include determining the specificity of RT-RPA. Rapid PV detection with RT-RPA may streamline environmental surveillance methods, improve outbreak detection, and provide data for certification of polio-free status and global eradication.

DNA stores genetic instructions that are required to program cell activities. Therefore, it is important for DNA to replicate in order to provide a copy of genetic material to daughter cells during mitosis or meiosis. Origin recognition complex (ORC) is a six-subunit assemblage that promotes the initiation of DNA replication. ORC proteins bind in all eukaryotes to a specific sequence found within an origin of replication to assemble and bring together other key initiation factors. Although the ORC proteins themselves are highly conserved throughout evolution, dramatic changes in the origin DNA sequence motif have been observed across species. These changes are most likely accompanied by changes in one or more subunits within the ORC complex. The aim of this project is to understand how changes in the ORC’s binding preferences across species are determined by changes in ORC protein sequences, specifically within the yeast phylogeny. Using genetic engineering approaches, I will introduce foreign ORC alleles into knockout strains of Sacchoromyces cerevisiae which we have generated. Previous data generated by members of our lab and others show how ARS (autonomous replication sequence) Consensus Sequences (ACS, the binding site for ORC) differ across the yeast species. The data indicate that Lachancea kluyveri and Lachancea waltii have intermediate levels of ACS differentiation from Sacchoromyces cerevisiae, so I am introducing alleles from these species as a starting point. Differences in the cell growth rate, size, and fitness will be observed within haploid strains of Sacchoromyces cerevisiae containing the foreign ORC protein in order to determine which ORC subunit(s) is/are responsible for binding preferences for different ACS sequences within the yeast phylogeny. This research can provide a fundamental understanding of evolution of the genome sequence and the proteins that bind it.

Airborne and satellite remote-sensing surveys of Antarctica have revealed over 400 subglacial lakes beneath the ice sheet. These lakes are one component of a subglacial hydrology network that also includes drainage channels, swamps, and estuaries. The influence of this subglacial hydrology network on ice-sheet dynamics is unclear. Water under ice sheets can reduce friction at the ice-sheet base, and thereby increase ice velocity. Alternatively, partitioning of water into lakes or channels, can also limit the area lubricated by water, and thereby decrease ice velocity. Ice-penetrating radar can map the presence of subglacial water due to the differing electrical properties of an ice/water vs. ice/sediment (or rock) interface at the ice sheet bed. The radar surveys also map constant time (isochronal) layers within the ice sheet that are formed due to chemical (and thus also electrical) differences in the snow deposited at the ice-sheet surface, which is eventually compressed into ice. Burial by subsequent snowfall and ice flow deforms these layers, which were originally surface parallel. Thus mapping these layers reveals the internal stress state and flow history of the ice. Here we report on the internal architecture of the ice sheet in the vicinity of Subglacial Lake Whillans, West Antarctica, as imaged by ice-penetrating radar. In the 2010-2011 austral summer, 500 line kilometers of ice-penetrating radar data were collected over Subglacial Lake Whillans in support of subglacial lake access drilling. In radar profiles (2-dimensional cross sections through the ice), we trace isochronal, internal layers imaged by the radar. Compared to nearby grounded areas, layers in the ice over the lake are highly deformed, suggesting ice-flow disruption over the lake. This interpretation is consistent with the active nature of the lake, which fills and drains every few years, causing changes in friction at the ice-sheet base, and thus non-steady ice flow.

For more than three decades, the innovation of cochlear implants (CI) has improved the lives of patients who have trouble hearing sounds. Using the technology of signal processing, the device can provide electric sound to patients at various frequencies. One thing cochlear implant patients have trouble with is the ability to perceive music. Cochlear implants can provide good speech performance but lack the ability to encode music in a better way. Our research is designed to provide the ability for patients to enjoy music through its three facets: rhythm, pitch, and timbre. The purpose of our study is to investigate pitch coding in cochlear implants which is important for music and speech and the quality of life for CI patients. The ultimate goal of our research is to improve sound-processing in deaf or hard-hearing patients all over the world. We will have determined how to deliver the best acoustic simulations of cochlear implants to study pitch coding and identify the ideal combination of carrier type frequency, channel and envelope that will deliver optimal music perception of any sound entering the cochlear implant. Features will be extracted from the simulated sounds to investigate spectral and temporal coding in cochlear implants. This will help in finding new ways of processing music and speech in cochlear implants for the benefit of its users.

The increasing costs of diagnostic healthcare have necessitated development of hardware independent non-invasive Point of Care (POC) testing systems. In this work, we analyze a cloud-based platform hosted POC application, which is directed towards smart monitoring of anemia-like pallor. Although anemia prevalence rates in global populations vary between 10-60% in various demographic groups, smart monitoring systems have not yet been developed for screening and tracking the treatment of patients for anemia. Our POC diagnostic application focuses on detecting the presence of anemia through pallor site images of the tongue and eyes. The application consists of a front-end which is hosted on the Microsoft Azure cloud computing platform, and a back-end image processing algorithm. The front-end consists of a graphical user interface, designed to guide patients to upload images of their eye and tongue pallor site regions. From here, the back-end collects these images and performs a series of image processing techniques to assess the degrees of anemia indicative pallor, returning test results immediately. Such a system provides affordable, accessible, and immediate results in a non-invasive manner. We observe low time-complexity of the cloud hosted front-end that is independent of the machine hosted back-end. Thus, Azure-based POC diagnostic applications, encourage quick diagnostics to improve the resourcefulness of follow-up care.

Parkinson’s disease (PD) is a progressive, neurodegenerative disease with a global and national prevalence of four million people and one million people affected respectively. Though PD can be clinically characterized by dyskinesia, resting tremors and rigidity, it remains largely idiopathic biochemically. PD patients can be pathologically characterized post-mortem however, by the presence of Lewy bodies in the Substantia Nigra pars compacta (SNpc) of the ventral midbrain. While the major protein constituent of Lewy bodies is known to be α-Synuclein (α-Syn), the pathogenesis of α-Syn fibrillation in the SNpc remains elusive. One mitochondrial chaperone protein, mortalin, is thought to play a part in PD pathogenesis for its anti-apoptotic effects, role in stress responses, and through its regulation of transcription factor p53. We previously found mortalin to be down-regulated in the corpus striatum of manganese (Mn) miners, as well as primary murine glial cells. In the study at hand, we evaluated the connection between mortalin and p53 and the resultant effect on α-Syn oligomerization in astroglia with Mn-induced neurotoxicity. Using primary astrocyte cultures, western blot analysis, immunofluorescence and confocal microscopy, we evaluated this possible connection and its implications for α-Synucleinopathy. Within Mn-induced neurotoxic conditions, we saw decreases in total p53 of cortical and striatal mortalin knock-down astrocytes and increases in the density of cytosolic oligomeric α-Syn of these cells. Notably, we found that overexpressing mortalin under the same conditions decreased the density of oligomeric α-Syn dose-dependently. Taken together, these data suggest that the interaction of mortalin with p53 could have a role in α-Syn up-regulation, resulting in oligomerization within Mn-induced neurotoxicity. Further study is necessary to elucidate mortalin’s role in α-Synucleinopathy and Lewy Body pathology more precisely, but this work illuminates an important protein-protein interaction and provides implications for understanding PD pathogenesis and for developing therapies against α-Syn fibrillation in Parkinsonian diseases.
 

Detecting gravitational waves from the merging of supermassive black hole binaries (SMBH) in the centers of galaxies is the focus of intense interest among many in the astrophysics community. I am interested in collaborating with other scientists and students to locate and catalogue undiscovered pulsars with data collected by the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) radio telescopes (Green Bank Telescope and Arecibo) and employing data reduction techniques using the pulsar searching program PRESTO. I am also contributing to the data collection of known pulsar signals with remote observing sessions. Pulsars are neutron stars that have dense rotating magnetic fields that transmit electromagnetic radiation in the form of radio waves. The pulsars that have spin rates of once per one thousandth of a second, known as millisecond pulsars (MSP), are of particular interest as their spin periods are highly regular. The goal in finding new pulsars is to establish a Pulsar Timing Array (PTA) in which the signals have a timing precision on the scale of 200 nanoseconds for decades. The Pulsar Timing Array consists of 30 millisecond pulsars dispersed throughout the galaxy acting as a system of galactic clocks. This could allow for the monitoring of gravitational waves that exhibit frequencies in the sub nanosecond ranges, allowing these waves to be detected by analyzing the unique properties in their signals. As we add to the NANOGrav observations we become capable of studying the evolution of galaxy formation. Support from the National Science Foundation (NSF) Physics Frontier Center (PFC) makes this research possible.

The leading cause of mortality in the developing world is infectious disease. Because such diseases are often treatable, the expanded use of accurate and rapid diagnostic devices plays an important role in reducing the burden of these illnesses. Point-of-care (POC) diagnostic devices can be inexpensive, which expands use in low resource settings, and rapid, which expands options for immediate patient care and treatment. The Yager lab designs low-cost, rapid and easy-to-use POC diagnostic devices based on paper microfluidics. These devices perform sample preparation, nucleic acid amplification and visual result detection in sequential, automated steps. As with lateral flow tests (LFTs), these devices have generally employed colorimetric detection, but this method increases test duration compared to fluorescence detection, which can give results in real time. Additionally, we hypothesize that fluorescence detection could provide a semi-quantitative evaluation of pathogen load via competitive thresholding. When a second DNA species is introduced, competition for reagents can generate different chemical sensitivities by varying the concentration of the secondary species. The competitive threshold, which we aim to calibrate by this method, is the point at which a known concentration of competitive targets amplifies in preference to the pathogenic target. We first performed amplification reactions in aqueous solutions with the number of copies of the pathogenic target and the competitor varied across five orders of magnitude. We visualized this calibration matrix as a surface plot, which we used to establish an accurate, order-of-magnitude competitive threshold that did not hinder pathogenic target amplification. Implementation of this method in paper-based amplification reactions will lead to shorter test times and, possibly, semi-quantitative detection in a new family of optics-enabled POC diagnostic devices.

Helicobacter pylori is a gastric bacterial pathogen that infects 50% of the world’s population. H. pylori’s helical shape is presumed to help it drill through the mucus lining of the stomach and arrive at the surface layer of gastric epithelial cells, its preferred niche. The bacteria then use a type IV secretion system to deliver toxins to the gastric epithelial cells. Once infected, the gastric epithelial cells initiate an immune response via numerous receptors resulting in a signaling cascade that leads to activation of pro-inflammatory genes including a cytokine called interleukin 8 (IL-8). Gastric epithelial cells secrete IL-8 in an attempt to recruit immune cells to fight the bacterial infection. However, this immune response seldom results in clearance of the infection. This is because H. pylori controls the host’s immune response through a set of virulence factors that are responsible for invoking and maintaining a pro-inflammatory response. Inducing inflammation allows H. pylori to thrive, however, too much inflammation will result in a clearance of the infection. My goal is to understand which H. pylori genes are responsible for modulating the immune response in gastric epithelial cells. To find these genes, I am screening a mutant library that targets virtually all non-essential genes (approximately 1000 out of 1500) in the H. pylori genome. I co-culture individual H. pylori mutants with gastric epithelial cells and assay their response to the bacterial infection. Using enzyme-linked immunosorbent assay (ELISA), I can quantify the amount of IL-8 gastric epithelial cells secreted into the supernatant. By determining which mutant bacteria in our library induce more or less IL-8 secretion in gastric epithelial cells, I can identify bacterial pathways that are important for modulating the host immune response. This approach may potentially uncover bacterial factors that can be targeted therapeutically.

Many court cases in the United States are resolved through plea bargaining. A plea bargain is an agreement between the prosecutor and the defense for a reduced sentence in exchange for a guilty plea from the defendant. This study hypothesized that a) strength of evidence, b) client acknowledgment of their substance use problem, and c) substance use rehabilitative history would predict attorney recommendations for taking a plea bargain. Participants were recruited through the Washington State Bar Association and included 491 active and retired attorneys. Each received an informed consent and one of eight counterbalanced vignettes. In this 2x2x2 between subject’s design, a potential client was described and the possibility of conviction was manipulated based on strength of evidence, defendant’s acknowledgement of a substance use problem, and prior history of substance abuse treatment. 91 participants had completed surveys and identified as Public Defender (51%), Private Defender (34%) and both (15%). This study found a significant interaction η2 = .08, F(1,85) = 8.12, p < .01 and three significant main effects that indicate defense attorneys consider all of the aforementioned variables when making recommendations that clients accept a plea of diversion to treatment. They placed greatest importance on clients’ rehabilitative histories η2 =.48, F(1,85) = 77.47, p = .00, followed by acknowledgements of substance use problems η2 = .26, F(1,85) = 30.24, p = .00, and then strength of evidence η2 = .19, F(1,85) = 19.52, p = .00. A possible limitation, though anonymous, the self-report nature may have been impacted by participant’s social desirability. This study had a strong counterbalance design, which eliminated the potentially confounding impact of order effects. Future research would benefit from investigating differences factors that may be significant to prosecutors offering a plea and moderating or mediating factors involved in this decision-making process.

Swarm robotics consists of multiple robotic systems that interact with each other within a set environment. Inspiration for swarm robotics comes from behaviors observed in biological systems, namely insect colonies, that migrate collectively. Robots in a swarm are decentralized and behave independently, but their movements are based on that of their surrounding neighbors, thus collective movement is reliant on sensing and modification of each robot. Different algorithms are available for different types of swarms, but the overarching idea of decentralization and simplistic independent behavior persists. The collaborative effort between these robots is critical when performing a task in an efficient and timely manner. However, methods of attaining advanced swarm robotic behavior is limited to expensive laboratory manufacturing. To address this limitation, this work focuses on developing a process for creating low-cost, three-dimensionally printed robots with swarm intelligence. The design of the robotic swarm consists of wheeled robots equipped with sensor electronics, such as proximity and accelerometer sensors, and computer software applications for robot control. Currently, the main application is for tabletop uses such as having the robots work together to form shapes and move small objects. Future applications include human-robot interaction, such as utilizing the robots to provide assistance for the physically disabled. Thus, the main contribution of this work is a manufacturing process for low-cost, three-dimensionally printed swarm robots.

Many inherited diseases are attributed to monogenic mutations; however, some human disorders and conditions are genetically complex, requiring mutations at multiple loci. One of the research goals at the Waterston Lab is to identify genetic interactions that could affect developmental pathways related to human disease. Using the small nematode, Caenorhabditis elegans, as a model organism, we have developed a high-throughput approach to look for interactions. RNAi bacteria were grown separately for knockdown of forty different transcription factor (TF) genes on pooled populations composed of 38 mutated and fully sequenced strains of C. elegans from the Million Mutation Project (MMP). After growth for several generations, the abundance of strains in each condition was compared by targeting strain-specific single nucleotide variants with Molecular Inversion Probes and sequencing on an Illumina MiSeq system. From ~115,000 possible screened genetic interactions, we identified a number of candidate interactions and focused our efforts on a positive interaction between the strain VC20424 and the TF gene B0261.1. While most strains had poor growth on the B0261.1 RNAi, VC20424 had a much higher abundance. We confirmed this candidate interaction by re-testing VC20424 alone and against a control strain on B0261.1 RNAi. We then genetically mapped the VC20424 interaction to a region on chromosome X. In this region we identified a deletion in C25A11.2 which shows similar expression patterns as B0261.1, suggesting a good interaction candidate. We will test additional MMP strains that share the same allele of C25A11.2 on B0261.1 RNAi to look for a similar interaction. We also plan to use CRISPR/Cas-9 to induce the mutation into a control strain and look for conferred resistance to B0261.1, which would further validate our results. Broadly, studying the nature of genetic interactions and potential roles of transcription factors may contribute to the elucidation of human development and complex disease.

Methods to isolate and analyze single biomolecules have enabled the exploration of enzyme dynamics at incredible resolution and have revealed phenomena that cannot be observed with traditional bulk assays. For proteins like DNA helicases and polymerases, such a detailed understanding is essential to study genetic pathways like excision repair and the regulation of homologous recombination. Single molecule experiments also allow new biotechnology to be developed, such as DNA sequencers or gene editors. Despite these single molecule advances, conflicting results have been reported about biomechanical properties of UvrD helicase, including the number of nucleotides that UvrD moves per reaction step. UvrD is of particular interest given its highly conserved structure across species and its many roles in regulatory genetic processes, making it an ideal target for antibacterial drug development. We analyze UvrD using a new single-molecule technique called Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT), developed at the UW nanopore lab, which has unprecedented spacial and temporal sensitivity. In SPRNT, a membrane protein pore MspA is embedded in a phospholipid bilayer, forming an electrical connection between two salt solutions. A voltage applied across the pore causes ion current to flow through. It also draws negatively charged DNA bound to UvrD into the pore. UvrD is too large to fit through MspA, and comes to rest on the rim, arresting the DNA’s motion. Different DNA nucleotides in the pore modulate the ion current. As UvrD walks along the DNA, it draws the DNA out of the pore and changes the ion current. Therefore, the durations of ion-current states are kinetic measurements of UvrD. With SPRNT we directly measure the sizes and durations of single steps taken by UvrD along DNA, which cannot be seen with any other single molecule technique and enable us to shed new light on an important enzyme.

The link between climate and range distributions is a key area of study for ecologists interested in predicting how species will respond to anthropogenic climate change. However, most studies only focus on abiotic factors (like climate), and ignore biotic determinants of species performance. In this study, I seek to understand how competition influences the success of a common conifer species in the Pacific Northwest. Specifically, I ask whether interspecific responses to competition lead to a predictable competitive hierarchy across different locations or whether competitive hierarchies vary. To address this question, tree cores from six focal conifer species, Abies amabilis, Tsuga heterophylla, Tsuga mertensiana, Thuja plicata, Pseudotsuga menziesii, and Callitropsis nootkatensis were collected from 18 stands of varying elevation and climatic conditions within Mt. Rainier National Park, with 20 individual trees cored per species and stand. Annual tree growth was used as a proxy for performance as growth is known to be sensitive to competition and results can be extrapolated to overall population performance. The competitive neighborhood of each cored tree was determined by identifying all individuals within a 10-meter radius by species, and quantifying the distance of competitors to focal individuals as well as their size. Growth rates for each individual tree within the stand were compared to the sum of the basal area of neighbors around that tree, using analysis of variance to determine the relationship between the two variables. These relationships were then compared across species to see which species were competitively superior, and then compared across stands to determine whether competitive hierarchies varied. The importance of this study is to identify which species are more sensitive to competition which would expand our knowledge on the biotic factors that may limit their ability to shift their range.

Quantum dots (QDs), fluorescent semiconductor nanocrystals, can be used as a biomarker and diagnostic tool because of their unique optical and electrical properties, including high luminescence, resistance to photobleaching, and broad excitation and emission spectrums. But in order to use QDs as biomedical imaging devices, particularly in sensitive organs such as the developing brain, toxicity must be adequately characterized. Little is known about the toxic effect of QDs on the brain, especially on the neonatal brain. QDs consist of a metal core, typically cadmium selenide, and a shell to protect the core. Cadmium is known to be highly toxic to many of the body’s systems, including the central nervous system. However, expanding the shell and attaching functional biomolecules prevents cadmium release and changes the characteristics of the particles. In our study, several surface ligands were tested at variable concentrations and periods of exposure to measure the toxic potential of QDs on an ex vivo organotypic brain slice model. Three methods of characterization were used: a lactate dehydrogenase (LDH) assay, a propidium iodide stain, and a fluoro-jade C stain. The cellular stains were evaluated using confocal microscopy. Results showed that toxicity is a function of QD exposure time, surface chemistry, and concentration. Several QD conjugations displayed minimal or no toxic effect after 24 h of exposure. The results of this study will be useful in identifying a QD conjugate as nontoxic in a biological setting. QDs can then be tailored to site and cell-specific uptake in the brain, thereby improving the selectivity of current imaging techniques and providing a powerful diagnostic with regards to diseased cell fate.

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by decline predominantly in episodic memory. Previous research has demonstrated that individuals with AD suffer from depression at higher rates than healthy individuals. Predicting depression levels in individuals with AD may be important for mental health care preparation as the disease progresses. To predict depression levels, I trained a generalized additive model (GAM) regression algorithm to predict scores on the Geriatric Depression Scale (GDS) using diffusion tensor imaging (DTI) data of fraction anisotropy (FA) means in 15 different regions of interest (ROIs). The GAM regression algorithm is a non-parametric expansion of the linear regression model. Data were gathered from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). This data set includes 150 subjects with DTI and GDS scores at the 6-month visit for individuals with AD, early mild cognitive impairment (EMCI), late mild cognitive impairment (LMCI) and healthy controls. A k-fold cross-validation method was used to split data into testing and training data. After training and testing the data on a GAM regression algorithm, we attempted to predict depression scores from contemporaneous FA data. The accuracy of this algorithm was assessed by calculating the mean-squared error (MSE) of the testing data. The MSE measured how well the GAM regression model formed from the training data fits the testing data. We evaluated sensitivity, specificity and area under the receiver operator curve for depression prediction as a binary outcome. The purpose of this project was largely to gain experience with machine learning. Fitting a predictive model could inform our understanding of how white matter microstructure might relate to depression in AD.

 Many genetic mutations have little effect on phenotype. One hypothesis to explain this phenomenon is that strong genetic modifiers buffer genetic and environmental variation. Chromatin remodeling proteins are candidate genetic modifiers because they regulate the transcription of many genes, provide greater robustness to environmental changes, and cause pleiotropic genetic diseases when mutated in humans. To test the hypothesis that chromatin remodeling proteins buffer genetic variation, we will comprehensively assess how deletion of one of three chromatin remodeling proteins (Chd1, Hda1, and Cyc8) alters the phenotypic effect of variants of the transcription factor Ste12. Ste12 is a crucial component of the yeast mating pathway, as it activates the transcription of cell-type-specific genes needed for mating. A mutational scanning experiment of the STE12 gene done in the Fields lab yielded data on the effect on mating of thousands of mutations of STE12. These data provide a baseline for similar scans in strains with a chromatin remodeler deletion. First, we constructed double mutants by deleting each chromatin remodeler gene along with a STE12 deletion. We analyzed the growth rate of each double mutant. The chd1Δ ste12Δ and hda1Δ ste12Δ strains showed healthy growth, but the cyc8Δ ste12Δ strain grew poorly and was flocculent. We then assessed the mating ability of chd1Δ ste12Δ and hda1Δ ste12Δ strains containing the wild type STE12 gene, and found that they could mate sufficiently to continue with the deep mutational scan. We transformed both double mutant strains with a library of plasmids encoding the same Ste12 variants as previously studied, and will calculate a mating score of each variant in the two double deletion backgrounds. If the chromatin remodeler deletion alters the effect on mating of a large number of variants, this result would indicate the importance of chromatin remodeling in phenotypic robustness.

The world’s reliance on plastic is a contemporary dependence as its malleable function, low production cost, and increasing abundance has been universally favored over all other products. Created with the intention of short-term and one-time use, the global production of plastic reached 299 million tonnes in 2013, with 10-20 million tonnes ending up in the oceans annually. This study explores the contribution of microplastics to the marine environment from river systems, and quantifies the microplastic load within the stream as it passes from rural to urban environments. Microplastics are separated into two categories based on how they are formed; primary and secondary. Primary microplastics are manufactured, generally as resin pellets, which are melted down to form anything from shampoo bottles to water bottles. Secondary microplastics form from the breakdown of macroplastics after extended exposure to UV radiation and/or weathering. The sampled river is fed by a remote, glacially fed lake in the Cascadia Mountain Range, flowing into the upper Skykomish River, the Snohomish River, and eventually to the Puget Sound. Samples were collected by towing a 335 µ mesh manta trawl and analyzed, after a wet peroxide oxidation and density separation, to quantify the concentration of microplastics present in the stream. From the samples processed thus far, and the data from another study conducted on the same river system, a correlation has been found between the amount of plastics in the stream and the populations of the towns the stream passes through. This correlation implies that the growing quantity of microplastics within the stream, as it flows from rural to urban environments, is supplied through anthropogenic influences. Following this study, microplastic pollution can no longer be thought of as a coastal and marine issue, but rather a problem that starts much further inland. 

Nemerteans are a phylum of soft-bodied coelomate protostomes worms with specialized organ, the proboscis, that is used for prey capture and are known as voracious ambush predators on other marine worms and crustaceans. Several neurotoxins have been extracted from nemertean tissues, including tetrodotoxin (TTX), a paralytic neurotoxin, suggesting a potential role in both prey capture and predator deterrence. TTX is used by a variety of marine animals for defense and is produced by a symbiotic bacterium, Vibrio alginolyticus. Past research has demonstrated the presence of TTX on the epidermis and lining of the intestine in several local species of nemerteans. This research examines the bacterial community of local nemertean species and attempts to identify the presence of Vibrio spp. through DNA barcoding.The process with which we analyzed the worms was to rub them onto highly selective agar media that selects for Vibrio species of bacteria. Then we tried to use PCR in order to amplify the barcoding gene 16S so that we could compare it to other species in the database.

Glioblastoma multiforme (GBM) is the most common malignant adult primary brain tumor, accounting for 70% of malignant brain tumor diagnosis. However, regardless of therapy – surgery, radiation, and anticancer drug therapy – virtually all GBM patients eventually succumb to the progressive disease within 12 – 15 months of diagnosis. This is indicative of the proliferation and differentiation of neural stem cells into various cell types in the tumor which is thought to be a main contributing factor of malignant tumor resistance to standard treatments. This project aims to address this therapeutic challenge by identifying and testing potential new therapeutic regiments that leverage the underlying genetics of glioblastoma to improve treated response. We propose that certain genetic modifications (i.e. modifications in IDH1 or MGMT) can be made in glioma stem cells such that when a gene loses or gains a function, it will increase sensitivity of cells to a combination of therapies that is greater in magnitude than a single drug by itself. Towards this, we have generated whole exome sequencing data that will guide us in building a genetically-defined glioblastoma cell line and allow us to identify potential new therapeutic combinations predicted to have high specificity for GBM cells. Implementation of these predicted synthetic lethal combinations in a co-culture system will determine if the predictions are tumor, genotype, and treatment-specific. Results of this project will help us better understand therapeutic vulnerability and its determinants, and test specific combination therapeutic regiments that could be applied to improve the treated outcome of patients with this deadly disease.

Plastic pollution in the marine environment is an increasing concern leading to the need for more studies. Microplastics (0.3-5 mm in size) are the most concerning because they cannot be easily spotted, last the longest, and are easily ingested by marine organisms and make their way through the food chain. These microplastics are generated by many industries from cosmetics to laundry, to traffic erosion of tires. This study examines the distribution of microplastics found on Seattle beaches and on beaches to the north and south of the city. I collected sediment from three 1 m² quadrants on each beach of my 10 sample sites using the Beach Sampling Protocol from the Port Townsend Marine Science Center to ensure comparison of data with other studies. Samples were taken directly below the wrack line left by the previous high tide. In the lab, after a subsample was weighed out, density separation and wet peroxide oxidation were performed, in addition to other standardized analyzes. My results show the levels of microplastics and changes in concentration of microplastics found in sediments close to Seattle and at greater distance on the beaches. As the beaches erode, these microplastics are transported into Puget Sound and the larger Pacific Ocean. It is important that marine plastics are studied so that preventative measures can be put in place to limit microplastic pollution, in addition to having a baseline study for future research. 

Recreational outdoor winter activities on national forest lands are enjoyed by hikers, skiers, snowshoes, and snowmobilers. These activities come with the risk of being caught in an avalanche. It’s the number one cause of death on forest lands in the United States. Recreationalists are highly encouraged to wear avalanche transceivers. These devices transmit a beacon to be used in locating someone caught in an avalanche. Avalanche survival greatly decreases beyond 15 minutes because of asphyxiation and trauma. Professional Search & Rescue (SAR) teams can rarely arrive within this time limit, but locating a victim after an event is necessary. We will design a portable avalanche beacon detection device that can be attached to an Unmanned Aerial System (UAS or Drone) and can be carried by a SAR team into the field to locate victims. The SAR team can designate a search area via a user interface. The UAS will search this area for the victim’s avalanche transceiver frequency (457 kHz). The sensor attached to a UAS will determine signal location. This location information will be sent back to the rescue team. UAS application increases the safety of the SAR team given additional rescuers are not put in a high-risk avalanche path where another avalanche could occur. Our sensor presents challenges in integrating the payload into a UAS embedded system and user interface while maintaining realistic power and flight capabilities. Our initial customer is Seattle Mountain Rescue, a non-profit organization, so our product must be as cost-effective as possible. In the future, we hope the technology can be used on smaller, more portable UAS’s by all outdoor recreationalists such that at the time of accident they can immediately locate their friends, significantly increasing their chance of survival.

Parasites can be very influential in various aspects of aquatic health, conservation, industry, and environmental management. They can affect the size and marketability of fish, compromise wildlife conservation, and pose risks to public health. However, despite their ubiquity and significance, how human impacts on the environment affect their distribution is largely unknown. This study investigated this by creating a historical timeline for the abundance of Philometra spp. blood worms in Puget Sound, WA. In this study, I used preserved specimens of English sole from the Burke Museum Ichthyology Collection to document the presence of the parasite and make comparisons of fish caught in different regions and oceanographic regimes within the Sound. I used this data to investigate how Philometra spp. abundance tracks with implementation of restrictions on English sole exploitation. I also obtained live samples of English sole in order to compare the historical timeline with contemporary data. This timeline ultimately provides insight into the mechanisms of how oceanographic features, fishing, and fishing cessation affected the distribution and abundance of Philometra spp. in English sole. Change in parasite abundance through time is relevant to the conservation of fish species, as well as determining fishing regulations and policies that in turn affect the economy and public health, making this area of study one of great value and worthy of further pursuit. 

Point-of-care diagnostics are needed to improve the detection of pathogens like the Zika virus. The Zika virus can be transmitted by mosquitoes, or by the exchange of blood or other bodily fluids. The implications of the virus in pregnant women and their children are still largely unknown. So monitoring, and if possible, preventing the spread of the disease is critical. Paper-based diagnostic assays enable complex assays in settings without laboratory assets. Today, sample preparation for molecular testing requires training and expensive machinery. The Yager lab recently created a fully automated multi-material paper-based system that can extract DNA from urine, but had not yet developed an automated system for blood targets. My initial work centered on adapting the paper-based system to enable diluted blood processing. Our updated design successfully flowed ~1.6 mL diluted blood sample through the paper in ~20 minutes. By passing large volumes through the system, low-concentration DNA can be extracted from the sample, removing assay inhibitors at the same time. This work continues the study of fundamentals of fluid movement through porous networks in the Yager lab, enabling a foundation for DNA sample preparation necessary for blood diagnostics. These advances will help detect the Zika virus in blood samples outside the laboratory, contributing to the monitoring and prevention of the disease.

Universal sport analytics was made possible with the emergence of different technology in the past two decades. With existing statistical software and data recording, the performance of players can be quantified by organizations that are seeking to obtain a more scientific analysis of player performance. Specifically, more statistics are made to eliminate biases and better summarize a player’s contribution to their team. Major League Baseball and its drafting rules place themselves above other professional sports for analytics because players do not have to sign up for the draft, draft picks and players cannot be traded during the draft, and the lengthiness of its draft. Although individual organizations make efforts to pick suitable selections in the draft, the performance of baseball players is more difficult to predict at the professional level when compared to other sports. Despite the publication of MoneyBall, a book by Michael Lewis about methods to make quantifiable player signings, other research on player selection is often sensitive and discoveries are rarely published due to organizations fearing they will give away their competitive edge in the process. For this specific research project, data was gathered through web-scraping Baseball-Reference, a widely used online database for baseball analytics. By using analytical statistics and accounting for other factors, statistical analysis was done on different categories of players. This research identified differences between the predictability of success for pitchers and position players, and observed the impact of age or level of education of the player that is drafted. This study demonstrates how the different characteristics of these players reflect on the predictability of their accumulated value throughout their career. Preliminary results show pitchers’ performance as more predictable, perhaps due to the physicality prowess of pitching. This research suggests further work to produce better indicators for prospective players at the Major League level.

In collaboration with Booz Allen Hamilton (BAH), our Entrepreneurial Design capstone project addresses the challenge of providing continuous operation to an underwater remotely operated underwater vehicle (ROV), utilizing wind power. The main goal of this project is to study the feasibility of powering ROVs with renewably generated power. The project consists of system integration of wind turbine, generator, battery and control system with a buoy platform which will be connected to an underwater ROV through a tether. Our team’s role is to (1) Identify generator and battery options to connect to the wind turbine prototype provided by BAH. (2) Determine power storage requirements for an 8 hour operation of the ROV. (3) Develop and build prototype power management system to use harvested wind energy to support the battery. (4) Develop softwares packages that collect data on turbine and battery performance, and power consumption during operation. Our current research has been focusing on determining desired power requirements, designing individual subsystems circuits, and selecting off-the-shelf components accordingly. The project will be able to produce a on-buoy wind power system prototype that delivers 200 W average output power to the underwater ROV. This ROV will be at least at a 100 ft of depth along with a 5 V and a 9 V output rail for micro-controllers that enable control system packages to monitor power consumption and give data for onshore analysis. Our research has potential implications for improving access to the underwater domain for a prolonged period of time, including low-cost maritime sensing and deployment applications and military training and simulation applications.

Contrary to common belief, all vertebrate brains are capable of adult neurogenesis, or the birth of new neurons in the adult brain. Few brains show as an extreme ability to generate and add new neurons as that of the songbird. Songbirds exhibit rapid changes in the rate of neurogenesis, survival of mature neurons, and as a result, total volume of brain regions that contribute to the development and production of song. For example, the songbird Gambel’s white-crowned sparrow (Zonotrichia leucophrys gambelli) is capable of adding more than 68,000 neurons to a region of the brain responsible for song production called HVC, all within four days of transition to breeding conditions. Along with this addition in new neurons, these sparrows also increase song production and song quality. To identify the dynamics between neurogenesis and the addition of new HVC neurons during rapid seasonal growth, we labeled dividing neural stem cells and their progeny, and quantified the incorporation of these progeny into HVC. Throughout the course of the experiment, we recorded individual bird’s song and analyzed the spectral features and stereotypy of whole songs. Ultimately, we aim to correlate improvements in song quality and rate with the cellular changes occurring HVC and the neural stem cell niche during seasonal rapid growth. Such correlations will provide a model for tracking the behavioral progress of the plastic neural circuit as well as for identifying and testing molecular and physiological mechanisms underlying neuronal birth, maturation, and survival.

Uridine diphosphate glucuronosyltransferase 1A4 (UGT1A4) is a phase II drug metabolizing enzyme that plays an important role in the conjugation of various xenobiotics and endogenous compounds. In the context of vitamin D metabolism, conjugation of 25-hydroxyvitamin D3 (25(OH)D3), the main circulating form of vitamin D, may function as a pathway to help facilitate the enterohepatic circulation of vitamin D. Allele variants of the UGT1A4 gene are reported to contribute to inter-individual differences in enzyme activity, with the UGT1A4*3 variant gene product exhibiting increased glucuronidation activity. Previous work in our lab evaluated the polymorphic glucuronidation of vitamin D using human liver microsomes isolated from liver samples that were procured by St. Jude Children’s Research Hospital and University of Washington. The study found that carriers of the UGT1A4*3 allele showed increased 25(OH)D3 glucuronidation activity. While the samples used in this previous work was limited to a smaller subset of livers with the UGT1A4*3 genotype, we sought to further our investigation to include gene expression data obtained through RNA-Seq analysis and UGT1A4 protein quantification in LC-MS data. In addition, the current analysis was expanded to include a significantly greater portion of both the St. Jude and UW liver banks. From this study, we hope to gain greater insight into the impact that the *3 allele may have on the RNA and protein expression of UGT1A4. In addition, by assessing the relationship between UGT1A4*3 genotype and 25(OH)D3 glucuronidation, we may develop a better understanding of factors that may contribute to the variability in the biliary excretion and/or plasma levels of vitamin D glucuronides.

While autonomy values are central to individualistic cultures (e.g. USA/Canada), it can conflict with the family values internalized by individuals from collectivistic cultures (e.g. East Asia). Due to this incompatibility, individuals exposed to both cultures (e.g. Asian-Americans) may be conflicted regarding which path to follow. For instance, does one major in Art because it is one’s personal passion, or Accounting because of the stability it would provide family? To investigate the potential conflict stemming from dual expectations, we presented 120 European-Americans and 117 Asian-Americans with scenarios of different major life decisions, in which personal interest directly conflicts with family interest. For each scenario, participants imagined making the autonomous decision (e.g. major in Art), and the family decision (e.g. major in Accounting), and reported their anticipated distress in making each decision. Results showed that Asian-Americans experienced distress regardless of their decision because upholding one cultural value unavoidably came at the expense of the other. For Asian-Americans, the conflict they experienced occurred in terms of moral distress (e.g. feeling like a bad person) rather than just emotional distress (e.g. feeling angry). In contrast, European-Americans, who are less likely to face such dual expectations, showed distress more clearly in one direction (e.g. giving up autonomy). Finally, greater moral conflict was explained by specific cultural values, such as self-expectations to provide for family in the future. Together, these findings provide important insight into the bicultural experience, and the potential challenges associated with holding dual values. These findings may help explain the greater psychological distress reported among second-generation Asian-Americans. Based on this study, further inquiry can investigate potential solutions for alleviating such conflict, such as focusing on moral concerns, or identifying alternatives that may satisfy both autonomy and family assistance needs.

Plants respond to abiotic factors in natural settings in order to regulate physical responses at the most appropriate timing. The timing of flowering affects seed and/or fruit production in many agriculturally relevant plants, so understanding its mechanism is essential for addressing agricultural needs as climate changes. To address this aim, we have used Arabidopsis thaliana as a model plant to understand the molecular mechanism of seasonal flowering. It has been shown that the expression of FLOWERING LOCUS T (FT), which encodes florigen, peaks in the evening under long-day lab conditions (16 hours light, 8 hours dark, 22°C) and promotes flowering in a day-length specific manner. However, our lab found that FT also peaks in the morning under outside long-day conditions over the summer solstice in Seattle (16 hours light, 8 hours dark, highest average temperature 21°C). This double-peak of FT can be re-created by changing the light quality and temperature settings of long-day lab conditions. In addition, we found that a mutant of PHYTOCHROME A (PHYA), which encodes a red/far-red light photoreceptor in plants, lacks FT expression in a morning-specific manner, suggesting that PHYA is involved in regulating morning expression of FT. In order to understand the molecular mechanism of PHYA-mediated FT regulation, we are in the process of identifying transcription factors and other molecules that work with PHYA to induce FT expression. We have successfully cloned various transcription factors that are reported to act in the flowering regulatory pathway and are in the process of testing protein-protein interaction against PHYA by yeast-two-hybrid methods. Identifying the components that act in the PHYA-FT pathway will allow us to further understand how light affects flowering regulation.

In the small animal clinical veterinary setting, the pet owner can play a key role in encouraging or discouraging the use of safety practices to prevent physical injury towards veterinary personnel. The factors that influence pet owners' perceptions of these safety practices, however, are not well understood. In order to better understand their role in the injury pathway, we set out to conduct a study of current pet owners utilizing qualitative methods. Pet owners who have accessed veterinary services at least once in the 12 months prior to the study's inception were invited to participate in focus group discussions regarding their perception of safety practices aimed at reducing physical injury to veterinary personnel in the veterinary clinic setting. Three qualitative focus groups of small animal pet owners were conducted in Seattle, WA during the month of November 2016. Each focus group consisted of 4-10 participants and lasted approximately 60 minutes. Questions asked during the focus group covered information relating to veterinary worker behavior and practices, clinic enviornment, animal behavior, and human behavior and practices. The results of the interviews suggest that veterinary personnel-client communication plays a key role in the delivery of veterinary services. This overarching theme was found to influence how pet owners chose their veterinarian, as well as influenced their perceptions of the treatment areas, safety practices, and clinic policies. For instance, the lack of communication between veterinary personnel and clients resulted in negative perceptions of treatment areas and of the veterinary personnel themselves. Thus, personnel must work to improve communication with their clients in order to improve safety outcomes as well as the overall experience for the pet owner. 

Currently, the only two treatments available to people with chronic kidney disease are organ transplants and dialysis. With such a high demand for kidneys, regenerative medicine is needed to create new therapies. Human pluripotent stem cells (hPSCs) can be used to generate immunocompatible tissues on-demand, which can be used to study human disease processes or potentially transplanted back into the original patient as a tissue replacement therapy. New protocols allow the differentiation of pluripotent stem cells into small, kidney-like organoids that contain the major proximal structures of the nephron, the functional subunit of the kidney. These organoids include podocytes, proximal tubules, distal tubules, and endothelial cells, but they lack a collecting duct system, a crucial component of the kidney. To address this need, we have developed a protocol to differentiate hPSCs into ureteric bud (UB) cells, which are the precursors of collecting duct cells. Undifferentiated hPSCs were treated with a growth factor, glial cell line-derived neurotropic factor (GDNF), that signals the outgrowth of the UB in the human kidney, and a differentiation factor, CHIR 99021, at different concentrations. Immunofluorescence was used to characterize the resulting cells, which were stained with Dolichos biflorus agglutinin (DBA), a collecting duct marker, DAPI, a DNA marker, and GATA 4, a transcription factor that is important for kidney development. We found that both DBA and GATA 4 were co-expressed together in isolated patches of cells under one of the conditions tested. This staining pattern suggested that these were UB cells. This is the first time UB cells have been differentiated from hPSCs. The development of this differentiation protocol will lead to the growth of the collecting duct system in the kidney organoids, which will optimize them for kidney disease modeling, high-throughput drug screening, and regenerative medicine approaches to reduce the need for kidney transplants.

The phytoplankton assemblage around the Olympic region is well described, but due to the various hydrologic and oceanographic features that affect water conditions, little is known about the phytoplankton assemblage in the Chehalis River Basin. This research seeks to provide an outline of common species of different locations, the environments in which they were found, and the obstacles that block their movement. To do this, sampling sites around the basin that would cover various different geographic features of the Chehalis River Basin were selected, along with the phytoplankton sample, salinity and temperature were taken, and wind direction and strength were taken to determine if an upwelling or downwelling phase could be predicted. When back at the lab, toxin and chlorophyll samples were filtered for future analysis and saved. Microscopy was performed to identify species, if a harmful algal bloom species was identified, a whole water cell count was performed. Species that were found ranged from freshwater to marine; however, frequently species that are marine were found in low salinity environments. These results can be used to identify locations of interest in further studies and could be used to identify areas that may be useful for shellfish harvesting.

Muscular dystrophy affects millions of people across the globe; the disease leads to the progressive degeneration of skeletal and cardiac muscle tissues. The goal of this project is to identify a pharmacological treatment for muscular dystrophy in zebrafish. The disorder results from a mutation in the DMD gene, which encodes the instructions for producing the dystrophin protein. Dystrophin both protects and strengthens muscle fibers. Because of their genetic similarity to humans and the relative ease of introducing genetic mutations, we used zebrafish as a model. The lab utilizes a method that renders the dystrophin-encoding gene non-functional, eliminating the dystrophin protein in zebrafish larvae and producing a DMD zebrafish mutant strain. Without the protective effects of dystrophin, these zebrafish develop a severe form of muscular dystrophy. Previous results indicated that Trichostatin A (TSA), a selective inhibitor of some histone deactylase enzymes, is an effective treatment for salvaging deteriorating muscle fibers in mutant larvae. TSA disrupts the removal of acetyl groups and thus alters gene expression. We hypothesized that we could use the mutant DMD zebrafish to identify additional new pharmacological interventions. Upon testing new drugs, we looked for fish exhibiting less muscle deterioration than mutant DMD zebrafish with no drug treatment. After zebrafish larvae from fish carrying the DMD mutation were treated with novel drugs or control media, we performed genotyping on the larvae to identify the DMD homozygous mutants. Once animals were genotyped, we scored the animals for muscle defects using microscopy. We predicted that effective drug treatments for zebrafish DMD would show improved muscle in the larvae when compared to the untreated control DMD larvae. This research may provide a foundation for drug therapy and treatment possibilities in humans with muscular dystrophy. 

We are UW Smart USB Charger Team supervised by Plugable Technology and a UW EE faculty mentor. The main objective of this project is to design and implement a Smart USB charger that has five USB ports. It is called “smart” because the charger will be able to charge the higher priority phones at almost full rate before moving on to lower priority phones. With that function, this USB charger will fully charge several phones much faster than traditional USB chargers having only a 5V 3A power supply. However, there is no such five ports USB charger in the current electronic device market, so we see the important implications of solving this problem. What our team will have done by the day of our Symposium presentation is to implement the priority charge behavior module using C language and an Arduino Mega Board which has a microcontroller inside. The challenges of the task are that the actual charging behavior of different devices is often unpredictable or sometimes disappointing and the devices themselves decide how much current to draw and manufacturers have not settled on a single standard. Therefore, our module should be able to select the best charging mechanism for each of different devices while supporting priority charge. To do this, it requires us to test our module with as many different devices as possible and to collect data for future references. The other goal is to make the product as low-cost as possible: We will use lowest-cost microcontroller with sufficient I/Os to control all ports and lowest-cost external components for port power control. Finally, if more time is allowed, we will try to design and implement a PCB.

Despite our society’s growing awareness that transgender people exist, transgender children remain an understudied group that falls victim to huge amount of misunderstanding in both the scientific community and the public sphere. While academic literature is decidedly mixed on how to best support children who express a cross-sex gender identity, a growing number of parents have begun to support their children in social transitioning, a process that allows the child to live as their identified gender in all social contexts. The objective of this study was to understand the impact of social transition on children’s mental health using structured interviews with the parents of socially transitioned transgender children. We focused on parent’s report of how transgender children’s mental health (child’s mood, anxiety symptoms, and externalizing behaviors) changes over time. We recruited 60 parents of transgender children whose child socially transitioned between the age of 3 and 12. To maximize representation and generalizability, we then stratified them into subgroups by age at social transition (3-5; 6-8; 9-12); gender (girls; boys); and race (white; non-white). The interview was structured around three moments in the child’s life: the first sign of gender non-conforming behaviors from the parent’s perspective, the parent’s first realization that the behaviors might signify something more deeply about the child’s stable identity, and the age at which the child socially transitioned. The interviewer asked the same set of questions regarding the child’s mental health condition at the first sign, at first realization, during the year before transitioning, and during the year after (if applicable). Two coders then coded the wellbeing of each child in each of the mental health domains at each time point. Findings of the study will have implications for the developments of research and clinical work as how to best support transgender children regarding their social transition.

Hydrogen fuel is a non-polluting, sustainable energy source that is a very attractive alternative to fossil fuels. The most efficient way to produce it is to split water with a semiconductor photocatalyst (a semiconductor photocatalyst is a catalyst that uses visible light, mostly sunlight, to work). A team in China has shown that Cadmium Sulfide nanocrystals effectively split water to produce hydrogen fuel, meaning that semiconductor photocatalysts in nanocrystal form are a very good means of producing hydrogen fuel. There are still several problems with the team’s results, however. For example, nanocrystals agglomerate, which means they stick together in unusable clumps, very easily. Additionally, many people are uncomfortable using cadmium sulfide because other cadmium compounds are carcinogenic. Instead of storing crystals in a way that allows them to stick together, we have suspended the crystals in the holes of a porous fiber. To put crystals in the fiber matrix, we soaked the fiber in a solution of a soluble semiconductor photocatalyst. Once the semiconductor saturated the fiber, the crystals began to precipitate.The crystals were now stored in a way that separated them from one another. The goal of this research is to find a photocatalyst that is both more effective and more positively viewed than cadmium sulfide. In this project, we have explained the advantages and disadvantages of several semiconductor photocatalylsts that we believe to be the most viable options to find the most effective compound that can use visible light to produce elemental hydrogen from water. The commercial production of hydrogen fuel using this method would be much more effective than current methods, and would be very inexpensive, because the fiber we use is nothing more than pulp from Alder tree -- which is available commercially at a very low price.

Youth with T1D, although encouraged to exercise as part of their treatment plan, are not implementing recommendations to adjust insulin around exercise. Little is known as to whether insulin delivery method impacts these behaviors. Our aim was to compare behaviors surrounding exercise between youth on insulin pump therapy and those on insulin injections, specifically focusing on evening behaviors after exercise. We recruited 50 youth aged 10-18 years with T1D who completed the Type 1 Diabetes Report of Exercise Practices Survey (T1D-REPS), a questionnaire designed to assess specific practices around insulin management, nutrient intake, and glucose monitoring. 30 were on insulin pump therapy and 20 on injection therapy. We measured frequency of glucose checks and hemoglobin A1C (HbA1c). HbA1c measures average blood glucose level over the preceding 3 months. Higher HbA1c indicates worse blood glucose levels. Pump users were more likely to be male (73%), had lower HbA1c (8.5% ±1.3 v. 9.8% ±2.7, p<.05), and reported more glucose checks per day (5.1±3.0 v. 3.2±1.9, p<.05). Pump users were less likely to check their blood glucose prior to exercise (37% of pump users reported often or always checking v. 60% of non-pump users; p=.07). Pump users were also less likely to adjust insulin for bedtime snacks following exercise (8% of pump users v. 31% of non-pump users, p<.05).  Overall, pump users reported less glucose monitoring before exercise and were less likely to implement interventions to prevent overnight hypoglycemia, though they displayed more frequent monitoring around exercise. Understanding populations at risk for glycemic excursions around exercise will allow for the development of intervention strategies to improve adherence to these recommendations.

This project focuses on adding unique telemetry and communication capability to one of the largest and fastest growing areas in the Washington State aerospace industry: Unmanned Aerial Systems (UAS). These systems have the potential to revolutionize a wide variety of commercial applications such as precision agriculture, disaster management, mapping, and ecological/biological monitoring and represents a $13.6 billion civilian market. One of the main challenges for UAS integration is to provide reliable and effective guarantees for safe operation that in turn requires high-performance and flexible control/navigation of the aircraft and reliable transmission modes from air to a ground control station or operator. For example, a typical commercially available UAV will have 3 distinct sensor-processing-radio chains, one each for onboard camera, one for data telemetry (navigation and strategic command) and one for primary command & control data. This effort fundamentally seeks to mature ongoing work at UW and will allow for greater communication bandwidth, enhanced flexibility, and levels of control between the UAS and GCS and achieve the required situational awareness as mandated for UAS operations. The outcome of this project will be a modular, encapsulated radio system that can be used to combine the myriad data links between a UAS and the GCS into a single, robust, and reconfigurable link. The link quality will be tested using a bladeRF software defined radio paired with a student built, Pixhawk based octocopter. Several flights tests will be conducted by students using custom built software which will measure the strength of the UAV based link in various environments. This project encapsulates the construction of the octocopter, the build of the software defined radio system, and flight testing. A publicly accessible link quality database will be populated with fight test data in order to encourage further development of software defined based communication links.

Plant phenology studies have shown that flowers are blooming earlier now than they did several decades ago. These shifts in bloom time are attributed to warming temperatures, earlier snowmelt, and other climatic factors related to temperature. One underutilized data source for phenology studies is herbarium specimens, which are plants that are collected, often during bloom, and preserved for the purpose of studying species traits and distributions. Since collection date and location is recorded, herbarium specimens can be used to study the relationship between climate change and long-term shifts in the timing of phenological stages such as flowering and fruiting. My goals for this study were to determine 1) What is the relationship between changes in climate over the past century and changes in bloom time? and 2) Do shifts in the timing of phenological stages in herbarium specimens match shifts reported by field studies? My study species is glacier lily (Erythronium grandiflorum), a subalpine plant native to the Pacific Northwest that is known from field studies to be sensitive to climate change because it blooms immediately after snowmelt. Specimen data from Pacific Northwest herbaria was accessed using the Consortium of Pacific Northwest Herbaria’s database. When not listed, phenological stages were classified using specimen images and geographic coordinates were determined using GEOLocate and descriptions of specimen collection locations. Historical climate information was gathered by entering specimen geographic coordinates and elevations into ClimateWNA, a spatial climate model. I hypothesized that warmer spring temperatures and less snowfall would result in earlier bloom times. I also expected that my results would support shifts in bloom times reported by field studies. My findings contribute to the collective understanding of the historical effects of climate change, which assists predictions and management strategies concerning the future effects of climate change on plant species and communities.

1.25 million Americans are living with Type 1 Diabetes (T1D), with the associated annual healthcare costs $14 billion.
T1D is characterized by an insufficient quantity of insulin, a hormone that enables people to get energy from food.
It occurs when the body’s immune system attacks and destroys the insulin-producing cells in the pancreas, called beta cells.
The cause for this is not entirely understood, but it is believed that both genetic factors and environmental triggers are involved.
Measurement of natural cleavage product of insulin, C-peptide, provides a reliable way to quantify beta cell function and production of insulin.
C-peptide levels are lower than healthy people at diagnosis of T1D, and typically decline further thereafter.
However, there are distinct groups of subjects where this phenomenon does not occur or occurs very slowly, and this is associated with a reduced likelihood of complications later in life.
To identify predictors of rapid vs slow C-peptide decline, our team has developed an aggregate rule-based T1D risk model.
The first phase of this model operates by predicting whether T1D patients’ C-peptide levels have fallen below detectable levels or not.
A rule is a quantifiable range for a list of biomarkers.
To satisfy a rule, traits fall in certain measurement ranges of the corresponding risk indicators resulting in the T1D patient risk to increase or decrease.
Since our model is derived from available cross-sectional RNA-seq data of whole blood samples from T1D patients, our goal is not only to improve prediction performance but also clinical significance for T1D researchers that can be drawn from the model.
In the future, we will apply these rules to a different dataset to confirm our findings.
By creating a clinical index for T1D, researchers and other medical practitioners can assess patient’s current disease state with a simple blood test.

Viziometrics is an image search engine and classifier created by researchers at the University of Washington eScience Institute. Its purpose is to further the communication of scientific results through increased access to visual information as well as study the relationship the use of visual information and between scientific impact. Currently the search and classification are performed on 8 million images from PubMed Central, a major research database for scholarly works in the life sciences and biomedical fields. As a part of continuous efforts to improve the Viziometrics platform, we are working on a feature that automatically identifies a ‘central figure’ in a scientific publication. We have defined the central figure as either the visualization that encapsulates key aspects of a scientific publication, or that which best represents the research findings. In order to improve the underlying central figure search algorithm we are conducting a study that answers the question: which image, if any, do authors themselves identify as a “central figure” within a given publication? The research presented here is based on a survey of authors, whose email contacts can be found in the PubMed database. Based on the survey data, we are looking for common features characterizing papers for which authors were able to find ‘central figures’, as well as those for which authors could not make a decision. We are using this data to increase the accuracy of the Viziometrics algorithm. As more data sets are added to the Viziometrics platform, we hope to encourage scientists to find new ways to collaborate and communicate across disciplines.

Led by students in the Jackson School of International Studies, this task force proposes a course of action that the United States, under the new presidential administration, should pursue to address the salient maritime security concerns in East Asia. The task force developed a comprehensive research report that not only analyzes the breadth and scope of East Asian maritime security concerns, but also recommends the appropriate course of action the United States should take to preserve both its own interests and the greater security of the region. This report makes direct policy recommendations within the framework of the prevailing issues that dominate both traditional and non-traditional concerns in East Asia, particularly security concerns including Sea Lanes of Communication (SLOCS), the increased militarization of the region, and the rise of conflicts in the South and East China Sea. In addition, competing interpretations of international law and claimant perspectives in the South China Sea are also assessed. The report also analyzes the nontraditional security concerns such as resource scarcity (i.e., hydrocarbons and fisheries), competition and depletion, climate change and environmentalism (and the lack of a comprehensive international policy thereof), as well as piracy and human trafficking. The report completes its analysis through exhaustive review of primary and secondary sources that include think-tank and Department of Defense reports, Congressional hearings, joint governmental statements, interviews with foreign policy experts, tribunal decisions on international law, news sources and periodicals, and academic journals. The report recommends that the United States develop a course of action that balances destabilizing forces in the region and encourages cooperation. To achieve that end, the report recommends ratifying the UN Convention on the Law of the Seas, developing a clear environmental policy towards the South China Sea, and strengthening multilateral ties with Japan, India, and ASEAN.

Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts longer than 200 nucleotides. Recent studies have recognized lncRNAs as crucial regulators of transcription, mRNA processing and protein activity. However, little is known regarding the pharmacological regulation of lncRNAs in liver, which is an important organ for xenobiotic biotransformation. The goal of this study was to investigate the correlation between lncRNAs and the constitutive androstane receptor (CAR/Nr1i3), which is a liver-enriched xenobiotic-sensing nuclear receptor that plays an important role in xenobiotic biotransformation and intermediary metabolism. Three genotypes of mice, namely wild-type (WT), CAR-null and humanized CAR-transgenic (hCAR-TG) mice at 5- or 60-days of age were administered a species-appropriate CAR ligand (TCPOBOP for mCAR, and CITCO for hCAR) or vehicle once daily for 4-days, and livers were removed on the 5th day. The lncRNA gene expression was determined using RNA-Seq (n=3 per group, Cuffdiff, FDR-BH<0.05). At Day 5 neonatal age, mCAR activation altered more lncRNAs than hCAR activation (877 vs. 234). Interestingly, only 87 lncRNAs were co-regulated by both mCAR and hCAR, whereas 790 were only regulated by mCAR, and 147 were only regulated by hCAR. At Day 60, mCAR activation also altered more lncRNAs than hCAR activation. Among the differentially regulated lncRNAs, 126 lncRNAs were co-regulated, 1110 and 87 were uniquely altered by mCAR and hCAR respectively. The results also showed the significance of age in the expression levels of lnRNAs. For example, mCAR activation produced more changes in lncRNA expression at Day 60 than at Day 5; however, his pattern was not observed in hCAR-TG mice. This study highlights the age and the species differences of the lncRNA regulation in liver following pharmacological activation of CAR. The differentially regulated lncRNAs may serve as novel biomarkers or therapeutic targets for human diseases such as metabolic syndrome and drug-induced liver injuries.

Over the past few years, marijuana use has been on the rise in colleges, with 5.7% of college students saying that they smoke marijuana daily or almost daily according to a study done by the University of Michigan. Although this shows that daily marijuana use has increased, it does not explore the relationship between living situations and how much marijuana college students smoke. The purpose of this exploratory study is to examine living situations, specifically college students who live in fraternity/sorority housing, in residence halls, or in off-campus apartments/townhouses, and marijuana use among college students during a year. It is hypothesized that students who live in fraternity/sorority houses will have smoked more marijuana than students who live in apartments/townhouses and residence halls, respectively. The sample is comprised of three groups who attend four-year universities: 25 participants were Greek members, 634 participants lived in off-campus housing, and 121 participants lived in residence halls. Study participants were Washington State emerging adults (18-25) who completed the current measures as part of a larger assessment in 2016. A chi-squared test was conducted and it was seen that 44% of the Greek members, 15.77% of off-campus housing members, and 4.96% of residence hall members smoked marijuana at least 2-3 times per month. Preliminary findings support the hypothesis, showing that Greek members smoked the most out of all three groups and further analysis will be done to show whether these findings are significant.

Sorsby Fundus Dystrophy (SFD) is a rare autosomal-dominant macular dystrophy that causes central vision loss in early adulthood due to mutations in the TIMP3 gene, yet its pathogenesis remains unclear. SFD is clinically similar to age-related macular degeneration (AMD), the leading cause of vision loss in older persons in the United States. Preliminary data revealed structural and functional differences between retinal pigment epithelial (RPE) cells differentiated from SFD patient-derived induced pluripotent stem cells (iPSC) and control iPSC-derived RPE cells. In contrast to control iPSC-derived RPE, SFD RPE does not accumulate any detectable extracellular matrix (ECM) and demonstrates a 40-fold increase in the level of intracellular hydroxyproline, a collagen degradation product whose increased expression adversely impacts SFD RPE metabolism and increases its susceptibility to oxidative damage. We wanted to determine whether differential protein expression between SFD and control RPE cells could elucidate the mechanisms behind these changes. A shotgun proteomics approach using isobaric Tag for Relative and Absolute Quantification (iTRAQ) identified peptide sequences present in these cells, and proteins were identified based on these sequences. Proteins with a twofold increase or decrease between cell types were noted, which included glutathione-s-transferases, gamma-glutamyl transferase 5, and chitinase-3-like 1. I am confirming these results through Western Blot and will analyze them by protein network analysis to determine their relevance to the disease model based on previously obtained metabolic data. The results from this experiment will help reveal the mechanisms behind SFD pathogenesis and potentially identify targets for disease treatment.

Quadrature amplitude modulation (QAM) is a form of modulation in which two signals, differing in phase by 90 degrees, are modulated and summed together in order to create a final output wave. QAM is often utilized in radio communication systems to transmit data. The objective of this project is to develop a 16-QAM communications system on an X310 Universal Software Radio Peripheral (USRP). This system would provide a high data rate communication line for the usage of space-ground links. The applications of such a waveform would allow for massive transmissions of data such as ultra-high-definition video or fast internet. The development of the product will begin with developing a simulation of the system using GNU Radio. After the simulation has been successfully developed, work will be begin to implement the design onto the X310 device. This will be accomplished by using GNU Radio or a hardware description language (HDL) such as Verilog. Testing will take place in order to ensure that data is being properly communicated between the motherboard and daughterboard. It is our hope that our communications system will improve the communication between space and ground centers.

Cancer stem cells (CSCs) are small populations found within tumors and appear to be more resistant to anti-cancer treatments. Although evidence supports that CSCs play a major role in initiation and in the clinical outcome of cancers, the roles of breast CSCs in metastasis and invasiveness are not fully understood. Moreover, the association of the invasiveness of breast CSCs with genomic variations is unclear. The overall goal of this study is to investigate the migration abilities and genomic expression changes in breast CSCs. Human breast CSCs and immortalized/non-tumorigenic cells were derived from the same parental breast normal stem cells. To recapitulate tumor microenvironment, the cells were cultured on nanotopography-defined extracellular matrix (ECM)-mimetic platforms. We have employed a live cell imaging microscopy to measure migration at the single cell level as an indicator of invasiveness in breast tumorigenic and immortalized cells. Our preliminary results indicate that breast CSCs migrate significantly faster than immortalized cells on ECM mimics. Interestingly, we only find this difference under ECM-mimetic culture conditions, but not under flat control surfaces lacking ECM structures. This suggests that the invasive abilities of breast CSCs are lost when they are cultured in vitro on flat control surfaces without ECM structures. We will perform RNA sequencing to identify differences between the transcriptomes of breast CSCs and immortalized cells, and between cells cultured on ECM-mimics and substrates without ECM-mimics. The current study will characterize transcriptome profiling in breast CSCs and identify the genes that are differentially expressed between breast CSCs and immortalized cells. This will have implications in classifying molecular subtypes of breast cancers and in identifying potential therapeutic targets to regulate specific gene expressions for the inhibition of breast CSC invasiveness.

As our planet warms, it becomes increasingly important to study the impacts on biotic systems’ structure and function.  While there is consensus amongst the scientific community that changing climate will affect species’ ranges and distributions, there is a dearth of data on the intricacies of how such changes specifically alter the interactions among species. Notably, few studies simultaneously consider the effects of climate and competition on (current/existing) species performance, which is particularly important for generating a body of knowledge that relates climate change to shifts in species distributions.  This study seeks to investigate how competitive interactions vary across climate gradients for several conifer species common in the PNW and abundant in Mt. Rainier Park. Specifically, I am examining whether neighborhood effects on annual tree growth vary across elevational and climatic gradients. To accomplish this, tree cores were collected from Abies amabilis, Tsuga heterophylla, Tsuga mertensiana, Thuja plicata, Psuedosuga menziesii, and Callitropsis nootkatensis at 18 stands in Mt. Rainier Park, covering a large range of elevation (and thus climate). Additionally, the neighborhood of all cored trees, including the distance between cored trees and their neighbors, the species identity and diameter of neighbors was collected. Core samples were cross-dated by stand to ensure proper assignment of year of growth to each tree ring, and subsequently core and neighborhood data were analyzed using statistical models (multiple regressions) to extract relationship between competition, growth rates, elevational and climate variables. This is an ongoing project, whose growing body of data will be useful in predicting the way climate shifts may affect competition and thus growth of tree species in the PNW.

PEDOT:PSS-based organic electrochemical transistor (OECT) has been widely used for various sensing applications such as glucose, antigen, DNA, and pH sensing thanks to the much lower working voltages, typically less than 1 V, and known biocompatibility of a PEDOT:PSS. OECT comprises three electrodes (source, drain, and gate), a PEDOT:PSS channel between source and drain, and electrolyte solution of analytes. Electric current flows through the conductive PEDOT:PSS channel. However, upon the application of a positive gate voltage, cations from the electrolyte are injected into the channel, decreasing a conductivity of the PEDOT:PSS. Hence, electric current decreases as a gate voltage becomes more positive. In general, OECT is implemented by submerging a separate gate electrode in an electrolyte solution, thereby, making this only suitable for a laboratory environment. However, reports dealing with the impact of in-plane gate electrode on the OECT performance are relatively scarce. The proposed double-in-plane gate electrode for OECTs possesses great potential for the development of highly integrated OECT where each transistor can be separately controlled from its own gate electrode. All electrodes (gate, source, and drain) were placed in the same plane. High conductivity PEDOT:PSS was used to create a channel between source and drain. A PBS (Phosphate-Buffered Saline) was used as an electrolyte and pH value was adjusted with a hydrochloric acid. A drop of electrolyte of pH 3, 4, 5 or, 7.4 was placed just over the channel and the gate electrode. Compared to the transistor with a single gate, the double-gate transistor exhibited much higher transconductance of 35 mS. This means that the double-gate transistor can modulate larger current at the same gate voltage. Such a high transconductance with in-plane architecture will allow the development of portable OECT arrays for various chemical/biological sensing applications. 

For a nanoparticle to become a pharmaceutical transport device, it must have shelf life stability and avoid aggregation. Spontaneous aggregate formation, or particle sedimentation, can render a therapeutic nanoparticle ineffective and potentially harmful as a pharmaceutical. Using a biologically safe material that provides steric stabilization (i.e Pluronic F127) may slow or eliminate aggregation, improving shelf life and potential for pharmaceutical use. The use of a surfactant coating instead of a chemically conjugated method will improve ease of nanoparticle formulation. To determine aggregation kinetics, various surfactant-coated nanoparticles (SCNP) have been compared in a number of medias, including standard measuring media (10mM NaCl), known aggregate media (30:70 methanol:water solution by volume), as well as in complex media such as artificial cerebral spinal fluid (aCSF) and high ion concentration media like phosphate buffered saline (PBS). These SCNP’s have been compared to stock carboxylated-polystyrene nanoparticles, as well as polyethylene glycol-coated polystyrene nanoparticles. Characterizing SCNP behavior can have significant implications for nanoparticle design for drug delivery.

Gender differences exist in science, technology, engineering, and mathematics (STEM) fields, as women are underrepresented in some STEM fields than others and continue to face discrimination even in fields in which women are better represented (Cheryan, 2016). Will using different American ideologies help to explain gender disparities in interest in STEM fields in the U.S.? This study examined this question by exploring differences in expressing interest in engineering careers between men and women. Specifically, we designed a study to investigate whether women are deterred from engineering when advised to “follow their passions.” Eighty undergraduate students completed a questionnaire, in which they are asked how interested they would be in pursuing a career in engineering based on listening to the advice to follow their passions or based on following the advice to do what is practical. We hypothesized that women will report less interest in engineering career when asked to base their decision on the advice of following their passions versus when asked to base their decision on the advice of doing what is practical; the difference for men will be weaker. This study explores how popular American ideologies may contribute to gender gaps in STEM.

Influenza is a prolific and hazardous virus, affecting even those in the population who have been previously infected or vaccinated. The innate immune system serves as a key first line of defense against this pathogen, with the signaling components, called interferons, driving the production of a potent cellular antiviral response. Studies have indicated that viral populations replete in defective virus particles, virions with a deletion in a portion of their genome, are less efficient at blocking the antiviral response, as shown by increased interferon in the host. Our project seeks to explore this phenomenon of RNA deletions leading to increased interferon expression in host cells by testing the hypothesis that deletions in the three polymerase genes of influenza alone are sufficient to cause an increase in the interferon response. To begin answering this question, an interferon reporter system was used to analyze the viral genome of interferon positive cells, and deletions within various lengths of the PB1, PB2, and PA polymerase genes were found to be enriched. I then created pure populations of influenza with these empirically derived gene deletions in PB1 while my mentor, Dr. Alistair Russell, created pure PB2 deletion populations, which were grown on cell lines expressing functional PB1 and PB2 proteins respectively. When used to infect unmodified cell lines, it was found that pure populations of both PB1 and PB2 defective influenza were sufficient to induce the host interferon response. In the future, I will create PA expressing cell lines and influenza with deletions in PA to analyze the effect of PA deletions within the influenza genome on the host interferon response, and it is hoped that these results can be used to explore a mechanism for how influenza occasionally fails to escape the innate immune response.

The recent refugee crisis has shown an unprecedented increase in people seeking asylum in European countries over the last five years. This sudden change in population creates potential challenges for water and wastewater utilities in providing services. These challenges may include interagency coordination and assessing network capacities. As such, it's important to understand how utility employees prioritize their responses to an unexpected population influx. Identifying these patterns in response will be useful for utility providers to accurately predict demand and efficiently plan systems for municipalities. There is a lack of literature regarding utility involvement in urban emergency response, ergo an exploratory analysis was conducted to document water and wastewater utilities’ responses to disaster migrations. The project goals are twofold: identify areas of response from German utilities involved with coordinating emergency housing for displaced persons, and compare those results to a hypothetical utility disaster response survey conducted in the United States in 2016. Ten ethnographic interviews with German water and wastewater utility employees were recorded during summer 2016. Four significant areas of response have been identified through qualitative analysis of the interviews: Coordination, New Infrastructure, Technical Capacity, and Financial Capacity. Based on relative frequency, Coordination was predominant in the German interviews while Technical Capacity was prevalent in the US. This suggests the utility employees may have different perspectives and priorities between the two countries. Understanding these patterns provide a clear representation of utility employees’ primary priorities and concerns in the event of rapid population increase.

Accurate quantification of DNA replication errors is difficult to measure since mutations are exceedingly rare. Recent attempts have relied on Next Generation Sequencing however, they are limited by its high error rate, with 5 x 10^-5 as their lowest detected mutation rate. Duplex Sequencing is an error correction method that reduces sequencing error through barcoding strands with unique identifiers and comparing the complementary strands, to achieve error rates as low as 10^-7. Our assay starts with a cloned single-stranded m13mp18 phage DNA with a base accuracy of 10^-7 as a template for replication. After annealing a forward primer we have our test polymerase extend the complementary strand and then we excise and isolate an 850 base pair region to undergo Duplex Sequencing. Through the improved baseline error rate of Duplex Sequencing, we hope to assay high fidelity polymerases, such as human polymerase delta. Accurately measuring the in vitro mutation rate and mutational profile of human polymerases is important in establishing the role of DNA polymerase generated misincorporations in somatic mutagenesis and human cancers. Furthermore, we have the potential to define a mutator signature that indicates the misincorporation of nucleotides in cancer by a specific DNA polymerase.

Dacarbazine (DTIC) is a chemotherapeutic drug, which targets cells at the time of cell division by damaging the DNA or RNA, thus interrupting cell duplication and division. DTIC is a DNA-methylating agent and is commonly used with adriamycin, bleomycin, and vincristine to fight certain types of cancer such as malignant melanoma and Hodgkin’s Lymphoma. Hormones and enzymes change during pregnancy, which affects the efficacy and toxicity of drugs in the body. With this study, we better understand how Dacarbazine is metabolized during pregnancy as compared to the non-pregnant state. Two pregnant patients with Hodgkin’s Lymphoma were recruited for our study. The first was a 31-year-old who presented with enlarged supraclavicular nodes at 10 weeks gestation and the second subject was a 34-year-old who sought medical attention for enlarged cervical nodes at 15 weeks gestation. Dacarbazine relies on the P450 enzyme CYP1A2 as the primary pathway for DTIC metabolism. It has been reported in the literature that CYP1A2 activity during pregnancy is significantly reduced. As a result, the concentrations of DTIC, an inactive pro-drug, are higher and its active metabolites, MTIC, HMMTIC, and AIC, are lower during pregnancy compared to postpartum. Since DTIC is inactive and the lower enzyme activity leads to lower concentrations of the active metabolites, the lower CYP1A2 activity potentially decreases the efficacy of DTIC during pregnancy. Although the women in this study had lower concentrations of the active metabolites of dacarbazine during pregnancy, both patients still successfully achieved remission of their lymphomas. This research will help us better prescribe chemotherapeutic drugs that interact with P450 enzyme CYP1A2 to pregnant women who have certain types of cancer. Personally, I analyzed the specimen results to determine drug concentrations in the blood and excretion along with other PK parameters and wrote a manuscript describing the results.

Duplex Sequencing (DS) is a Next-Generation Sequencing technology employing double strand molecular tagging to reduce technical errors.The high accuracy of DS enables the resolution of low frequency mutations in nuclear and mitochondrial DNA (mtDNA). We are interested in using DS to analyze mtDNA mutations in ulcerative colitis (UC), an inflammatory bowel disease that predisposes to colorectal cancer. Tumor progression in UC is related to mitochondrial dysfunction. By sequencing mtDNA mutations in colonic biopsies from UC patients, we aim to elucidate the role of these mutations in tumorigenesis. A critical limitation, however, is the high number of low frequency mtDNA mutations present in these biopsies and the lack of appropriate computational methods to process large amounts of information generated by DS. The goal of this study was to develop computational methods to enable the extraction of mtDNA mutation information from DS data. DS identifies the reads corresponding to each strand of DNA by grouping them by their unique tags, making single-strand consensus sequences (SSCSs), which are then paired to form duplex consensus sequences (DCS). SSCS reads remove technical errors, but contain errors caused by DNA damage. The first computational method that we developed compared sequencing information from SSCS and DCS reads to assess the level and type of DNA damage in each sample. Other computational methods consisted of a program to classify mutations according to their sequence context, and a script that calculates mutation types and frequencies inside and outside the D-loop region as well as in all mtDNA genes and allows comparison of these parameters in large batches of samples. These tools will enable the processing of mtDNA DS information in a fast and high-throughput way, leading to assessment of the range of different types of mtDNA mutations in the progression of ulcerative colitis and colorectal cancer.

I have been developing and executing a research project since early July, regarding the community-based response to gaps in the Indian justice system that fail to protect women from sexual violence. Dynamics of gender, caste, class, and religion have propelled violence against women in India. The goal of this project is to connect with and learn from community-based organizations that serve women who have survived sexual and relationship violence. My underlying research question that I hope to answer is: “How do agencies serving Indian women who survive sexual violence resist cultural and legal norms and provide safe, brave spaces of survival?” This project includes an examination of the difference in India’s global “outward” versus the internal “inward” facing commitment to women’s rights. My research project involves a multi-phase approach; from literature research to self-funding a trip to India to interview three non-profit and non-governmental agencies and understand their perception of the gaps of the moral and legal system, and their methods to protect and empower women. I am in the process of transcribing and translating these interviews to frame a project and showcase the material and knowledge I obtained. I engage in thematic content analysis of my qualitative data to surface patterns of experience described at agencies that support Indian women. My preliminary analysis suggests that Indian agencies have developed and adopt creative and empowering methods for supporting women. Insights into their strategies for resistance may be useful for other agencies in India as well as US-based agencies. I also hope that with this project, those who wish to help support sexual survivors in need all over the world can use these developed practices and insights as a foundational point to consider while they design support mechanisms for women.

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutation in either of the genes PKD1 or PKD2. This disease has been the focus of ongoing research due to its high prevalence and lack of curative treatments. How does ADPKD develop? To understand cyst formation in ADPKD, we are utilizing the murine model PKD1 p.R3277C (RC). Human dominant expression of the APKD phenotype is not similarly found in mice; null mutations of PKD1 or PKD2 are embryonic lethal, and the cystic phenotype of mice is observed only in conditional deletion mutants. However, the RC murine model recapitulates the late onset cystic growth of human ADPKD. The morphology of the pre-cystic kidney was characterized by formalin-fixed paraffin embedded (FFPE) sectioning in combination with H & E staining performed on RC homozygous mutant and control kidneys at post-natal time points of p20 (days), p40, p60, and p80. In the future, RNA from RC mutant and wild-type kidneys at p20 will be collected and sequenced. RNA sequencing will be utilized to determine pre-cystic expression changes between affected and unaffected phenotypes. Although less advanced, cyst formation has been shown to occur as early as p20. Because of this, the earlier time point of p10 was also assessed. By investigating these time-points we aim to identify the earliest differences that we hypothesize are more likely to be causal for cyst formation, versus changes that are a secondary consequence of PKD pathology.

Underbites are when the lower jaw protrudes further than the upper jaw and can lead to respiratory and feeding complications. One method currently used to correct underbites is the reverse pull facemask which puts tensile strain on the nasofrontal suture to promote growth of the upper jaw. The reverse pull facemask has major shortcomings such as a long duration of the treatment (12-18 months 16-18 hours a day), and is aesthetically unappealing. An alternative treatment that may produce faster results is to use an oscillatory cyclic load on the nasofrontal suture to increase the growth rate of the upper jaw to correct the underbite in less time than the reverse pull facemask. However to know how effective this method is for underbite correction it is vital to understand how the cyclic treatment changes the nasofrontal suture. My question is how the cyclic load changes the suture gap and growth rate (Mineral Apposition Rate MAR) of the nasofrontal suture in farm pigs. To measure the effectiveness of this treatment, the nasofrontal suture was extracted from farm pigs after they had been treated with the cyclic load for 30 minutes for 5 days. The sutures were then embedded, sectioned and examined under a fluorescent microscope to measure the MAR and suture gap for the control, and cyclic treated pigs. The control pigs had a suture gap range of 157-179 µm (n=5) and a MAR range of 7.75-15.25 µm/day (n=4). The cyclic loaded pigs had a suture gap range of 326-383 µm (n=2) and a MAR range of 29.9-33.2 µm/day (n=2). These data suggest that our cyclic treatment increases the suture gap and MAR of the nasofrontal suture. However, more data will need to be collected to validate our preliminary findings.

In this method comparison, research was performed to determine if the polyspecific anti-human globulin (AHG) reagent from Immucor® was significantly better than the currently used Bio-Rad. Direct antiglobulin test (DAT) experiments were performed on 11 subject samples with strengths of strong positive, weakly positive, and negative. After reviewing the results obtained, it was observed that the currently used Bio-Rad polyspecific AHG reagent produced stronger results with regards to samples that were weakly positive when compared to Immucor®. Results that were 1+ or higher indicate that the two reagents express relatively consistent results, with Bio-Rad presenting stronger agglutination when compared with Immucor®. A comparison between using 1 drop vs 2 drops of Immucor®(Norcross, GA) polyspecific AHG was also performed to determine if there was a significant difference in results, as the package insert from Immucor® mentioned that 1 or 2 drops may be used, with 2 drops having the risk of diminishing results. The results after testing suggest that there is most likely no significant difference between the numbers of drops used.

Working memory is a cognitive skill that allows temporary storage and manipulation of information. It is an important skill as previous studies have shown relations between working memory and various cognitive abilities, such as reading comprehension and speech perception. So far, evidence have suggested that working memory can be enhanced with training. One of the training experiences that has been extensively researched is early music training. Most studies have shown that music training experience has a positive correlation with working memory while other studies has shown no difference in working memory capacity for musicians and non-musicians. For this study, our aim is to further delve into this controversial topic and seek more information and data to find out whether early music training could enhance working memory. We recruited a group of musicians (N=20) and non-musicians (N=20) and compared working memory capacities between the two groups with two tasks: Memory Updating and Operation Span, targeting slightly different aspects of working memory. We hypothesized that those who had early music training would have higher scores on both tasks. Data analysis has been completed and the initial results from the data shows that there is no significant difference in working memory capacity between musicians and non-musicians. Currently, further analysis of data is still ongoing to help understand the results we observed. We will be discussing the similarities and differences of the tasks compared to previously published studies and how our results contribute to this field. 

Repeated dopamine release through sustained amphetamine usage promotes long-term plasticity changes within the striatum that contributes to drug-related behaviors. Although addiction has been linked to dopamine release in the striatum, there exists other neurotransmitters whose function is less known. In the past, we have shown that after repeated amphetamine exposure, acetylcholine is also involved in mediating long-lasting plasticity changes in the dorsal part of the striatum which is linked to habit formation. However, it remains unclear whether this mechanism also plays a significant role in the ventral striatum, a crucial structure in reinforcement and reward processing. To address this question, we used mice in which acetylcholine production in the ventral striatum, specifically in the nucleus accumbens (NAc Core), can be abolished by genetic inactivation of choline acetyltransferase (ChAT) using an adeno-associated virus encoding Cre recombinase (NAc Core ChAT-KO mice). These mice were tested for a drug-related behavior called locomotor sensitization, a phenomenon where locomotor activity is progressively increased through repeated amphetamine injections. The procedure consisted of 2 days of saline injections followed by 5 days of amphetamine treatment and a 10-day break to induce withdrawal before an amphetamine challenge. Each day, locomotor activity (ambulations) was measured for 90 minutes by recording successive infrared beam-breaks in activity chambers. We observed a significant main effect of time and a significant time x genotype interaction effect where NAc Core ChAT-KO mice were less active than their sham controls on the fifth day of amphetamine treatment. We found no significant differences in locomotor activity during the withdrawal treatment between sham and NAc Core ChAT-KO mice. These results indicate reduced acetylcholine levels attenuated the extent of locomotor sensitization, suggesting that acetylcholine in the ventral striatum is involved in mediating long-term behavior adaptations following amphetamine treatment.

The use of graphene in nanoscale systems serves many applications not only in solar cells but also in biomaterials because of the combined optical, electrical, and structural properties. Conventional methods including chemical vapor deposition and electrospraying to produce a layer of graphene on nanostructures is costly. Reduction of graphene oxide using chemical reagents presents an easier and cheaper alternative while maintaining the unique properties of graphene. But these methods are typically solution-based and further steps must be taken to coat reduced graphene oxide onto nanostructured surfaces. Dopamine chemistry was applied in a simple simultaneous approach of self-polymerization to reduce graphene oxide while creating an adhesive to incorporate a heterogeneous coating of polydopamine and reduced graphene oxide on a nanostructure. Use of various concentrations of graphene oxide demonstrated control over the sample's surface conductivity profile. Surface analysis characterizations confirmed the presence of the coating through X-ray photoelectron spectroscopy (XPS) while the electrical properties were determined using conductive atomic force microscopy (cAFM). The overall topographical morphology will be confirmed with atomic force microscopy (AFM). A potential application of the proposed device serves to provide functionally and structurally mature human pluripotent stem-cell derived cardiomyocytes (hPSC-CMs) for use in research and clinical drug trials.

There has been expanding research into Resistive Random Access Memory (ReRAM) in order to replace conventional flash memory due to its lower programming voltage and faster read/write speed. In a ReRAM device, information is stored in a varying resistor whose resistance value can stay longer without an external power supply, hence making this as a good nonvolatile memory device. The resistance value can be changed by applying set/reset voltages and read by applying very small voltages. Furthermore, a ReRAM can be highly dense by implementing a cross-point array structure to store information. Recently, there has been great interest in a multilevel ReRAM in which one memory cell can have many different resistance states. This means that one memory cell can store more than one bit of digital information, i.e., ones and zeros; hence, enabling high density and miniaturization memory cell implementation. The ReRAM device that we have fabricated has a three-layered structure. The bottom electrode is a 150 nm layer of Indium-Tin- Oxide (ITO) and a 10 nm thick active layer molybdenum oxide was deposited by thermal evaporation. Finally, the top electrode of Ag (150nm) was deposited through a shadow mask by thermal evaporation. Current-Voltage (I-V) curve was measured by applying voltage between top and bottom electrode. The voltage was incremented from -2 to 2 Volts with 5 mV steps. A compliance current, or limiting current, was set to avoid breakdown due to the large current flow. The device exhibited 4 different resistance states by sweeping the device with different compliance current (10µA, 1mA, 10mA, and 100mA). Once the resistance states were set to a new value, original resistance values would not be restored. The irreversible characteristic of this device makes it suitable for many applications that need Write-Once-Read-Many (WORM) memory technology such as BIOS for computer and portable electronics.

Each year bee specialists report detection of larger numbers of bee colonies suffering from colony collapse disorder. One of the suggested causes is the increasing use of neonicotinoid pesticides in farming agriculture. To study the effects these pesticides have on the environment, it is necessary to establish a method to quantify the amount of imidacloprid in an environmental sample. Previously, we found that off-line C-18 cartridges were suitable for enriching imidacloprid from complex matrices and for preparing samples for analysis in GC-MS (gas chromatography-mass spectrometry). Our previous work primarily focused on achieving a reliable calibration curve by enhancing signal-to-noise in the GC-MS. To further evaluate our findings, a spiked environmental sample was subjected to C-18 extraction and analyzed. This method resulted in a limit of detection as low as 160 micromolar, which is similar to the 120 to 320 micromolar range for limits of detection achieved by other research groups using more complex extractions. This is important to the future study of imidacloprid because it allows us to progress towards the analysis of environmentally relevant concentrations of imidacloprid in soil, plant and honey samples.

A glomerulus is a structure in the kidneys that filters the blood in the first step of urine production. Focal segmental glomerulosclerosis (FSGS) is a condition where the glomeruli in the kidneys lose podocytes (epithelial cells lining the blood capillaries), severely limiting their ability to filter blood and leading to potentially fatal kidney diseases such as chronic kidney disease (CKD). One way that the body responds is through mesenchymal-to-epithelial transformation (MET), where mesenchymal juxtaglomerular (JG) cells, identifiable by renin expression, migrate into the glomeruli to replace lost podocytes. My project assesses the role of WT-1, a gene linked to the differentiation of cells in the kidney, in MET of cells of renin lineage (CoRL) in FSGS. WT-1 knockout and wild-type mice were used, and FSGS was induced by injecting anti-glomeruli IgG. Some of the mice were treated with the drug Enalapril each day after FSGS was induced, which has been shown to increase the number of CoRL. Baseline tissue was collected via a kidney biopsy one week before FSGS was induced, and a kidney necropsy was carried out 28 days after FSGS was induced. I then stained kidney sections for mesenchymal and epithelial markers using indirect fluorescent immunohistochemistry. From visual analyses of the stained kidney sections, we observed that in wild-type kidneys with FSGS, mesenchymal marker expression in CoRL generally decreased and epithelial marker expression in CoRL generally increased relative to baseline biopsies. Moreover, expression of all markers in WT-1 knockout kidneys with FSGS remained similar to baseline expression. We concluded that WT-1 is necessary for MET of CoRL in FSGS. These results highlight the importance of considering WT-1 in podocyte regeneration in experimental FSGS, bringing us one step closer to effectively treating the 5400+ people diagnosed with this disease each year.

The environment plays a large role in shaping someone’s future, especially their academic achievement. Children who have access to necessary resources, such as books, quality schools and teachers, have been shown to perform better in many subjects. In this study, we examined the associations between Socioeconomic Status (SES) and academic success in college-aged students. Also, we examined the choices that a student makes, such as amount of time spent in the workplace, and the format of classes taken (i.e., online, hybrid, face-to-face), and how they predict students’ academic success. SES was assessed by parent education and household income. We predicted that students who have a high SES will perform better academically than those who have a lower SES. Students who work full time will be more likely to take classes in an online format, to fit their work schedules. Conversely, students who work part time or not at all will take classes in the standard, face-to-face format. We predicted that students who work part time or not at all will perform better academically as they can dedicate more time and effort to their schooling than students who work full time. To answer our research questions, we examined college students who took a 30 minute online survey assessing SES, types of classes taken, how many hours worked in part-time and/or full-time jobs, and academic achievement (i.e., GPA). Implications of these results may inform colleges of the various needs of support based on types of classes taken to better students’ academic achievement. Future studies should examine additional measures of SES (e.g., Income-to-needs ratio) and how that impacts the associations between SES and academic achievement.

Alzheimer’s disease (AD) is the most prominent cause of dementia worldwide, affecting up to 5.3 million elderly Americans. AD pathology includes decreased neuronal count and synaptic connections, intracellular pathology and increased affinity for neurofibrillary tangles resulting in cognitive deterioration. The hippocampus is known to be particularly vulnerable and is an early structural biomarker of AD. Our aim is to investigate the longitudinal relationships between hippocampal volume and memory performance using neuroimaging data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The ADNI database contains biomarker, neuroimaging, cognitive, and behavioral data from hundreds of elderly individuals, divided into groups including normal/normal aging (CN), Alzheimer’s Disease (AD), Early Mild Cognitive Impairment (EMCI), and Late Mild Cognitive Impairment (LMCI). Cerebrospinal fluid biomarkers are a “gold standard” for detecting the presence of amyloid and tau pathology. Neuroimaging methods include amyloid PET tracers (i.e. F-18 florbetapir), which detects amyloid beta plaques and FDG-PET imaging which measures metabolic activity within the brain. Both techniques reflect neurodegeneration and synaptic dysfunction. Structural MRI imaging is used to assess neuroanatomy as a measure of brain atrophy and changes in neuronal density. Cognitive assessment data quantifies the extent of memory loss and general cognitive decline. Using the R programming language, we will conduct longitudinal analyses of neuroimaging analyses to examine the relationship between cognitive, structural and metabolic neuroimaging variables across different diagnostic groups over time. This initial investigation is preparation for learning longitudinal methods that will later be applied to physiological measures within the entire brain. Our hypothesis is that a decrease in hippocampal volume will be less correlated to decline in memory in CN than in other groups. If our hypothesis is correct, it suggests that compensatory mechanisms preserve cognition in early stages of AD, which we can explore using subsequent extended analyses of functional connectivity.

Autism spectrum disorder (ASD) is a complex developmental disorder that includes impairments in social interaction, communication skills and presence of repetitive behaviors. The CDC estimates that rates of autism are almost five times higher in boys than among girls. Implicit learning tasks have demonstrated that ASD children have atypical neural responses to social rewards, and it seemed to negatively impact their implicit learning relative to typically developing (TD) children. TD boys are also more likely to learn faster and benefit more from implicit learning than girls, but this has not been examined in ASD. This study investigated whether the presence of social and non-social feedback can impact implicit learning in children with ASD, and whether there is a difference between genders. Forty children with ASD and forty children with TD between the ages of 8 and 17 completed an implicit learning task involving classification of visual shapes and provided positive and negative Social (happy or sad faces) or Nonsocial (symbols) performance feedback. We hypothesized that TD children will have better accuracy and faster reaction times to stimuli associated with social feedback compared to ASD children. We also hypothesized that within the ASD group, ASD boys will show enhanced implicit learning to social feedback compared to girls. The results of this study will provide insight into gender difference in implicit learning in autism.

With dramatic increases in life expectancy over the past century, millions of people are living long enough to develop age-related neurodegenerative diseases often associated with cognitive decline and dementia. These neurodegenerative diseases are all proteinopathies, or diseases associated with misfolded proteins. Abeta and Tau protein aggregation is a key hallmark of Alzheimer’s disease (AD) while aggregated alpha-synuclein is a strong indicator of Parkinson’s disease (PD). This categorization is not definitive by any means because many patients with dementia exhibit multiple neuropathologies with combined Abeta, Tau, and alpha-synuclein aggregation. However, there has been almost no research studying the effects of the combined expression of multiple neurodegeneration-associated protein species. Therefore, we have developed the nematode C. elegans as a powerful genetic model for quantifying the functional consequences and mechanisms of action of interacting neurodegenerative-related proteins in vivo. To do this we have generated new transgenic worm lines with neuronal expression of different AD-related toxic proteins (both singularly and in combination) and developed new ways for assessing neuropathologies in these animals. We have generated worm lines with neuronal expression of the individual proteins as well as combined expression and seen that we can discriminate between the physiological effects of neuronal Abeta, Tau, and alpha-synuclein through our touch response and pharynx pumping assays we developed. Our escape response assay measures the number of reversals a worm completes upon stimulation by bending a piece of surgical thread over its pharynx. Our pharynx pumping assay measures the electrical activity as the worm feeds and allows us to extract precise measurements for pump frequency, amplitude, and duration. This proposed research is significant because it develops new neurodegenerative worm lines and uncovers new phenotypes that can be used to determine the physiological impact of individual and combined neurodegenerative toxic peptides.

The addition of cholesterol to pure phospholipid bilayers changes the structural properties of the composite membrane. A well-known example of this change is the condensing effect: the average thickness of the bilayer increases, and the average area per molecule decreases, upon addition of cholesterol. We study the spatial extent and variation of these structural changes. We use all-atom Molecular Dynamics computer simulations of mixed cholesterol/dipalmitoylphosphatidylcholine (DPPC) bilayers to quantify lipid structure in a spatially resolved manner. We use order parameters such as area per lipid, tail ordering, and head group tilt angle to measure the ordering potency of a single cholesterol molecule. One challenge when working on a molecular scale is to define a unique area for each lipid in the bilayer, which we have achieved using the Voronoi tesselations of the leaflets. We show that significant changes in phospholipid structure can be observed within the first two solvation shells of the sterol molecule. Our findings provide a simple and direct way to test the controversial Umbrella Model, describing phospholipid-cholesterol interactions and the structure of the bilayer, to improve and expand the theory.

Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs), dichlorodiphenyl trichloreothane (DDTs), polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecanes (HBCDs) are toxic nonpolar molecules that can cause damage to the reproductive, developmental, behavioral, and endocrine systems. These pollutants accumulate within the fatty tissues of important species in Puget Sound, including orca whales, salmon, herring, and plankton. This study measured the concentrations of two banned POPs, PCBs and PBDEs, and one currently used POP, HBCD, in plankton communities in Possession Sound. POP concentration in the water was measured in situ using a Chemcatcher deployment device to passively sample water at five locations across Possession Sound. Gas chromatography-mass spectrometry (GC-MS) was used to identify and quantify the POPs collected on the Chemcatcher filters and in the plankton samples. This two-pronged approach to sample both the water and plankton communities helps better define the relationship between POP concentrations in the water and those in the plankton community. This relationship is critical as plankton serve as the primary entry point for POPs into marine food webs. Additional research is needed to help determine the pathways that these pollutants travel between organisms.

Electric vehicles have gained attention in recent years as an environmentally friendly alternative for conventional, gasoline-fueled vehicles. While internal combustion engines power gasoline-fueled vehicles, electric vehicles use electric motors or batteries for propulsion. It is true that electric vehicles produce little to no tailpipe emissions and, overall, produce fewer pollutants than comparable gasoline-powered vehicles. However, when comparing the total environmental impact of electric vehicles to their gasoline counterparts, it is important to consider the associated impacts from the electricity grids from which they glean their power. In the United States, modes of electricity production vary by geographic location and include coal, natural gas, petroleum, nuclear, hydroelectric, and renewable sources. The purpose of this research has been to understand and quantify these environmental impacts and communicate them in an accessible manner to K-16 learners. To date, only the greenhouse gas emissions of electric vehicles have been quantified in such a way, providing equivalent miles to the gallon compared to gasoline vehicles by state. Our research efforts have taken this comparison one step further by capturing equivalent emissions of lead (Pb), land usage, and water usage of electric vehicles for every state in the U.S. While useful in and of itself, this information has been embedded in clickable maps, various multimedia, and exhibits for K-16 audiences using principles of exhibit design that allow a participant of any age to understand and absorb key principles surrounding electric vehicle usage in the United States. Effective exhibit interactives emphasize the engagement of all five senses through physical activity and stimulate visitors both intellectually and emotionally. Our exhibits and presentations have been carefully engineered to convey factual and intuitive information to K-16 students in an inviting, exploratory, and accessible manner.

Heart disease and other cardiac degenerative diseases account for 1 in 4 deaths in the United States. Current in vitro tissue models for cardiac disease modeling and potential drug testing lack dimensionality, scale, biomimetic behavior, and longevity. Manipulation of biophysical cues via biomaterial scaffolds in 3D bioprinting methods can alleviate these limitations as have been shown in 2D models. By mechanically inducing alignment in 3D tissue models, cells will respond to extracellular cues and form more organized structures similar to in vivo. This project focuses on implementing cardiac muscle cells into a mechanically aligned structure using a decellularized extracellular matrix (dECM) “bioink”. A BioBots extrusion based bioprinting system is utilized to manufacture cardiac cells laden in porcine left ventricle cardiac muscle dECM. We hypothesize that a polycaprolactone (PCL) post system design will induce cell alignment in a band-like tissue structure suspended in a Pluronic F-127 polymer bed along the axis of tension during tissue manufacturing. Induced bioink tension will enhance cardiac structure and function compared to current bioprinted models. This bioink composition and biomaterial process will provide cardiac cells with a better niche for development into a mature state that accurately mimics in vivo conditions. Bioprinted tissues will exhibit increased mechanical properties and structural organization with expression of contractile markers via uniaxial cell alignment upon bioink gelation in culture. This process is high throughput and provides a streamlined standard method for drug screening that more accurately tests possible side effects inside native heart tissue.

A recurring relationship between low socioeconomic status (SES) and poor health outcomes has been substantiated in recent research, both at individual and broader geographic levels. Research increasingly suggests that increased social spending and the expansion of the welfare state has the potential to address SES disparities in health. Yet, some studies have concluded that welfare expenditures merely correlate with child health outcomes, failing to significantly impact adult health disparities. This study examines the intersectional relationships between state-level SES, state social and healthcare policies, and state-level mental health status. The primary aims are to first verify the kind of relationship that exists between SES and mental health outcomes for state populations, and then to detect whether state policy can moderate this relationship. State-level SES, social welfare generosity, and mental health outcomes are mapped using Geographic Information Systems (GIS). It is expected that this study reveals state social welfare expenditures as having a weak moderating influence on the relationship between SES and mental health outcomes. These findings form the foundation for future research which will use a multilevel approach to understanding the various intersections between individual-level SES, state-level SES, individual-level health, and social welfare generosity.

Women are underrepresented in STEM (Sciences, Technology, Engineering and Math) fields in U.S. contexts. In this study, I investigate whether the prominence of the “follow your passion” ideology in choosing careers may be one factor that contributes to the gender discrepancy in STEM fields. Passion ideology is the idea that people choose their career mainly according to their idealistic personal interest. Previous research has shown that in terms of career preference, women tend to choose feminine stereotyped careers and are less interested in masculine stereotyped careers, and vice versa for men. STEM fields are masculine stereotyped. Therefore when U.S. society in general advocates for the priority of personal interest in career choice, we hypothesize that passion ideology mediates the relations between gender and interest in STEM fields, where women are less likely to develop interest in STEM. Considering passion ideology is less popular in Asian culture, in the current study, I primed Asian American women with either their American identity or Asian identity by using leading questions. Then I measured how interested participants are in engineering careers and art careers and how much participants agree that people should either follow their passions or be practical when choosing a career using a questionnaire. Following predictions are made: participants primed with American identity will be less interested in engineering careers than those primed with Asian identity, but not for art careers; participants primed with American identity will express stronger beliefs in the passion ideology than those primed with Asian identity; weaker interest in engineering careers when primed with their American identity will be mediated by stronger beliefs in the passion ideology. If these predictions stand, it suggests that, in U.S. context, these culture factors can partially explain the gender discrepancy in STEM fields.

The United States of America is one of the most culturally, ethnically, and racially diverse countries in the world. Much of the previous research heavily investigates the relationship among higher education classroom and multicultural education to promote better multicultural education practice that accounts for every student in the U. S. classrooms. Over my research, I recognized there is a limited amount of studies that looks into this topic, which is the connections between early childhood education and multicultural education. Early childhood educators need to respond to this issue because being open-minded and receptive is crucial for young children since children begin to acknowledge differences and identities very early. To account for this lack of research, I analyzed multiple global studies focusing on this field to explore how early childhood teachers could better use multicultural education practice in their classroom so they could help young children to become more accepting and understanding of multiple cultures. In order to examine the results from the studies, I also conducted an in-depth group interview with the classroom teachers at After School Program of Chinese Information and Service Center. I used conclusions drawn from their experience gained while working with students from multicultural backgrounds. In the result, all the studies I found and interviews I collected agreed that teachers could use multicultural education practices including care and attention to each students’ identity and cultural background, open discussion about race and culture, reading with regular or picture books to extend students’ thinking, and building relationships with parents to positively influence the students in the most efficient way in order to help children to become more accepting and understanding of multiple cultures.

A seed’s successful growth into a seedling depends on it finding a suitable site for germination. This may be limited by the parent’s ability to distribute seeds over a large area (dispersal), or by the seed’s ability to grow in given environmental conditions (microsite characteristics). This study attempts to answer the question: how is tree germination limited by dispersal and by the soil moisture of germination sites? A forest in a 25.6 hectare plot located in the Gifford Pinchot National Forest is the subject of this study. This forest is dominated by Tsuga heterophylla and Pseudotsuga menziesii, but also includes Thuja plicata, Abies amabilis, and Acer macrophyllum. Past surveys on trees, seeds, and seedlings within the plot have been conducted since 2014. Specifically, the species, size, and location of all trees are known. Forty paired seed traps and seedling quadrats throughout the plot provide data on seed and seedling densities by species, as well as soil moisture readings. The role of dispersal in germination success will be assessed by comparing the number of germinants within each seedling quadrat to the abundance of nearby parent trees. Soil moisture’s role will be determined by comparing germination rates (calculated by seedling densities divided by seed densities) to soil moisture in seedling quadrats. Results will be separated for each species. The species composition of these communities may prove to be determined largely by differences in dispersal and moisture requirements between species. For example: we expect to find a high dispersal capacity for Tsuga heterophylla, which would explain its dominance in the stand. We also predict that most species will fail to germinate in areas of low moisture. This might suggest serious implications for how these trees will respond to the warmer and drier conditions expected to accompany anthropogenic climate change in the Pacific Northwest.

Since the 20th century, the concentration of atmospheric carbon dioxide has increased dramatically, inducing several environmental issues. Our research seeks to reduce this excess carbon dioxide in our atmosphere by using a chemical method to capture and utilize carbon dioxide. In our research, we have developed a bimetallic complex coordinated by a multidentate carbene-phosphine ligand. We hypothesize that the carbon dioxide molecule will be cooperatively reduced by the two metal centers. Using nuclear magnetic resonance and crystallography techniques we have been able to analyze our complex's molecular structure. So far, we have concluded that this complex successfully reduces a molecule with a shape and stability similar to that of carbon dioxide. Moving forward in our research, this bimetallic complex should behave similarly with the bonds of carbon dioxide and thus represents a potential method of reducing the amounts of carbon dioxide in our atmosphere. 

Extracellular vesicles (ECVs) are small vesicles secreted into the extracellular space to transfer proteins, lipids, and genetic material throughout the organism. Although ECV signaling is thought to be a conserved cell-signaling modality, seen by all cells from bacteria to human, very little is known how this signaling occurs in a living multicellular organism. I used the simple genetic worm model organism C. elegans to conduct genetic screens to understand the mechanisms by which ECVs are formed and secreted in a living animal. In addition, I generated worm lines with fluorescent ECV markers allowing myself and others to monitor ECV signaling in an intact organism. C. elegans uses the ECV machinery to secrete extracellular vesicles that are needed to form alae – two rows of three “racing stripes” that run down the lateral sides of the worm. This clear phenotype allows me to perform a reverse genetics screen using RNAi (RNA interference) to identify the key molecular components for proper signaling. In my first screen, I selected 20 genes that my mass-spectrometry experiments indicated were on ECVs. I found that several of them also prevented proper alae formation, indicating they are key for proper ECV signaling. I then screened all 21 members of the C. elegans tetraspanin family, an ECV-associated transmembrane protein family that is implicated in loading, secretion and cell targeting of the vesicles. Then I generated transgenic lines with artificially introduced DNA that produce fluorescent versions of the genes that are key for ECV secretion. This research is significant because it will uncover new genes necessary for ECV secretion in C. elegans and will find markers that will monitor ECV trafficking in vivo. This results of this will open up the study of ECV signaling in a powerful model system, allowing us to identify physiologically relevant signaling pathways that utilize this communication modality.

Spontaneous waves of electrical activity occur in many brain regions during early development and are critically important for many aspects of brain development. These waves are initiated primarily in the hippocampus and the piriform cortex and propagate throughout the neocortex during the first postnatal week. Most studies of spontaneous activity have utilized brain slice preparations and thus the properties of these waves in vivo are almost completely unknown. We are using calcium imaging in GCaMP transgenic mice to measure wave activity through the intact skull, which is transparent in neonatal animals. We have been able to measure cortical responses to somatosensory stimuli, and have detected widely propagating spontaneous waves similar to those seen in brain slices. We are now determining the developmental time course of spontaneous waves of activity and asking how they interact with responses to sensory stimuli. Preliminary results have shown a greater distance of wave propagation during sleep, implicating wave activity in the emergence of adult sleep-wake cycles. These experiments will determine, for the first time, the properties of spontaneous waves of activity in vivo, providing information about how sensory-driven and spontaneous activity cooperate to shape brain development

Prime numbers are fascinating objects in mathematics, fundamental to number theory and cryptography in particular. A primality test takes an integer as input and outputs whether that number is prime or composite. Most practical applications require primality tests to be efficient. Today, the largest known prime number has over twenty million digits. Proving that a number of this size is prime can be computationally expensive. Most tests are probabilistic and do not guarantee that any given prime number is in fact prime. Other tests fail to filter pseudo-primes, like Carmichael Numbers, that are in fact composite integers. In 2002, Agrawal, Kayal, and Saxena published the first deterministic primality test that also runs in polynomial time relative to the binary representation of the input. Although their algorithm represents an important breakthrough in the field of computational number theory, it is seldom used in practice. Our objective was to determine why this idealized algorithm is not practical enough compared to other primality tests. We have re-created the algorithm and optimized our initial naïve implementation by studying each step to achieve optimal complexity using Fermat’s Little Theorem, modular arithmetic, and the Fast Fourier Transform for multiplicative efficiency. To confirm that probabilistic methods are still preferred, we compared execution times and accuracy of other tests to our own results.

In the past few years, cholera has caused many outbreaks of disease. Many studies have been done on its transmission pathways and its effect on non-pregnant patients. This literature review focused on the application of research to discover the preferred recommendations for pregnant women in an outbreak of cholera. This project explored research in academic journals and other professional publications with keywords such as “cholera and pregnancy” and “cholera transmission.” We explored existing transmission pathways of cholera, as well as current recommendations for these specific cases. Such recommendations would be to prevent maternal illness and death, as well as diminishing the risk of fetal demise. It was found that cholera is present in biofilms and endemic in certain regions. Its contamination can be prevented through sewage, chlorination of water, and proper food preparation. This review used the disciplinary lenses of microbiology, clinical medicine, epidemiology, and public health. The information concerning cholera in pregnancy is conflicting regarding fetal demise pertaining to first or third trimester outcomes. However, there is overwhelming evidence pointing to the recommendation to vaccinate in the circumstances of an epidemic. Literature suggests that women who are pregnant are not at a higher risk of getting infected with cholera, however given a change in immune response, the fetus is at a higher mortality risk due to the mother’s emesis and dehydration. This review will suggest implementation in regards to vaccination and treatment options.

Zebrafish are widely used for the regenerative capacity of their fins and its application to human bone growth and remodeling. The purpose of this experiment is to investigate the role of neurotransmitter systems in the process of fin regeneration and their impacts on de-differentiation of bone cells proximal to the amputation plane. Neuronal signaling is vital to all processes in the human body, however a link between specific neurotransmitter systems and the formation of bone has yet to be fully determined. From our past experiments we have identified a link between botulinum toxin (BTx), a common neurotoxin that inhibits the acetylcholine neurotransmitter system, and Nicotinamide adenine dinucleotide (NADH) levels in the fin during regeneration. NADH levels are indicative of cellular metabolism and are increased in cells that are actively differentiating into mature osteocytes. From this finding we have expanded our study to two neurotransmitter systems, the cholinergic, which focuses on acetylcholine, and the adrenergic, which focuses on epinephrine. From large ligand libraries we formed a ranking of compounds based on their application to bone and prior use in vivo. The four initial compounds utilized were propranolol, galantamine, ICI 118 551, and hemicholinium. Zebrafish were subjected to fin amputations followed by seven days of dosing. Following this procedure, the levels of NADH, green fluorescent protein (GFP), and bone mineralization were analyzed using fluorescent microscopy. GFP is a protein used as a reporter of gene expression. Each condition showed a variation in at least one of these criteria. Three conditions showed an initial increase in NADH, similar to the results of BTx. These results suggest that the relationship between neurotransmitter signaling and regeneration may be composed of many complex interactions between signaling molecules and pathways, and we will continue to investigate this as the experiment progresses into the remaining neurotransmitter systems.

Zinc is essential for the regulation of many biological processes in all known species. However aquatic species, especially invertebrates, are relatively sensitive to zinc toxicity compared to most terrestrial organisms. As oceans warm due to climate change, zinc previously trapped in ocean sediment will be released into the water column, exposing sensitive benthic and coastal species to elevated, potentially harmful zinc levels. Our study focuses on the impacts of elevated zinc on the calcium uptake of the pacific oyster. Previous research has shown that zinc can mimic other ions, disrupting calcium uptake in the gills. This is thought to be due to their similar size and charge, and could be especially harmful to shellfish and other organisms which use calcium to form their calcium carbonate (CaCO₃) shell. In our study, sixty-four oysters were randomly distributed into four tanks of varying elevated zinc concentrations. Following a 72 hour exposure period, the oysters were dissected and the gills were analyzed using Flame Atomic Absorbance Spectroscopy (FAAS) for calcium concentrations. The uptake of calcium through the gills of the oyster is expected to decrease as the concentration of zinc exposure increases. These results contribute to the growing body of knowledge concerning the interplay between zinc and calcium ions in aquatic organisms. Additional research is needed to characterize this effect on a wider variety of marine organisms, especially those in areas with significant run-off from urban or industrial localities.

The goal of this research is the generation of induced pluripotent stem (iPS) cells and derived kidney organoids from urinary cells. iPS cells are somatic cells reprogrammed to an undifferentiated state, making them an exciting advancement in regenerative medicine as they could model an in-vitro progression of many disorders and show great promise for replacing or repairing tissue damaged due to disease or injury. To generate new kidney tissues, adult somatic cells were isolated from a patient’s urine sample. This method of sample collection is advantageous over the traditional skin biopsy because it does not require a physician and is easier for the patient to supply. This protocol was further optimized to accommodate remotely collected urine samples, showing the ability to isolate somatic cells from patients located across the globe. We successfully isolated somatic cells with various morphologies, ranging from epithelial to mesenchymal-like cells, from 25 different patients. By introducing into these cells RNA encoding four specific transcription factors, a safer alternative to introducing DNA as it eliminates the risk of inserting a mutation into the patient’s genome, we successfully reprogrammed urinary cells of an international patient with autosomal recessive polycystic kidney disease into iPS cells. These iPS cells were further differentiated into kidney organoids, which have the capacity to become a powerful tool in improving current therapies for kidney disease as an in-vitro model. Thus, for the first time, we have generated patient-specific kidney tissue from a urine sample. This will increase our understanding of the disease and improve current methods for the screening of investigational therapeutics. The ability to create new kidney tissues in the lab also raises the possibility of transplanting these tissues back into their original patients, where they could potentially function without the need for immunosuppression.

Aggregation of alpha-synuclein is known to be a critical step in the development of Parkinson’s disease and Dementia with Lewy bodies . Dementia with Lewy bodies and Parkinson’s disease are both chronic, neurodegenerative diseases that affect motor movements and cognitive development. The aggregation of alpha-synuclein induces neurotoxicity, which contributes to disruptive synaptic behavior which results in the neurodegenerative disease. Misfolded protein structures are a result of the accumulation of aggregated aSyn  that form fibrils. Recent studies have found that plant extracts from plants with longer lives have inhibitors that could decrease fibrillation of alpha-synuclein. Previous research from our lab included screening of extracts from different plants. We found that some of the plant extracts that contain molecules smaller than 3kDA had anti-aggregation activity. Acer Saccharum extracts had results that showed a similar inhibitory effect. In the present study, we used this extract to treat brain tissue of Dementia with Lewy bodies and a healthy control on tissue slides. Treatments included testing with Phosphate Buffered Saline as a control as well as using multiple concentrations of the Acer Saccharum extract. We applied Thioflavin T Fluorescence assay to quantify and analyze the relative amount of alpha-synuclein to the experimental conditions. Based on previous research, we expect the fluorescence intensity to be lower for tissue treated with the extract, especially for the higher concentration. Elucidating the inhibitory effect the plant extract has on fibrillation of aSyn can potentially lead to pharmacological developments for future therapies for Parkinson’s disease and Dementia with Lewy bodies Disease patients.

The axons in the nervous system are collectively referred to as white matter. White matter forms intricate fiber connections among the brain’s grey matter (neurons). These connections change with development, learning, and disease, and therefore are of interest to several medical researchers. Tract-Based Spatial Statistics (TBSS) is an analysis technique which is used to analyze white matter integrity. Currently, this is the best existing method to align and analyze white matter. However, we are creating and evaluating an improved method to more accurately measure changes to integrity. Diffusion Tensor Imaging (DTI) Voxel Based Morphometry (DTIVBM) is a technique that we are developing which allows us to compare white matter statistics by using nonlinear registration to align the DTI image to a structural image and then a standard template. We are comparing several variations of DTIVBM with the established method of TBSS. We are using four different datasets, three of which contain adult brains ranging from ages 18-35, and one containing preteen/teen brains ranging from ages 11-15. One of the datasets also contains a mixture of normal brains and brains affected by neurodegenerative disease. Each subject has two separate brain images taken within a month’s gap. By running both the DTIVBM scripts and TBSS scripts on these brain images, we will be able to determine which method is more reliable, as measured using an Intra-Class Correlation (ICC) statistic. We are currently in the process of gathering the results, but we expect to see that DTIVBM will have higher reliability on most datasets than TBSS over a wider range of white matter. If this is true, we would have demonstrated a potentially better method to analyze white matter changes through aging and development, which will require fewer people and allow us to see changes in more of the brain.

With concern about global warming rising, assessing how increases in temperature impact plant performance is crucial in understanding how plant communities may alter. Genetic diversity, local adaptation to climate, and gene flow may interact with the direct effects of climate to determine how plants fare in a warmer world (e.g. through range shifts and shifts in phenology), but these interactions are poorly understood. Studying local adaptation is crucial for predicting how local populations will fare with warming, as a high degree of local adaptation may cause populations at the range center to be negatively influenced by warming. Conversely, populations in newly climatically unsuitable habitats may be able to cope with warming by adaption. This study measures how the climate of different elevations affects population growth of the high-elevation plant mountain monkeyflower, Mimulus tilingii, at Mt. Rainier National Park. Utilizing data from the past two years, we will parameterize matrix population models to explore how climate influences fitness and population growth rates of different populations, thereby assessing how local adaptation contributes to population dynamics (and potentially, the impacts of climate change). Matrix models will also allow us to determine how local adaptation affects particular life stages, which climatic factors drive local adaptation, and how genetic diversity promotes local adaptation. Previous results show that plants growing in different environments (high vs. low elevation) did not significantly differ in reproductive success whereas different genotypes (crossed between 2 elevations vs. 1 elevation) did, suggesting genetic diversity is an important primary driver of fitness. We predict that vital rates will be greater for populations grown in their native range (high elevation) with genotypes matched to their environment (within 1 elevation). Through these analyses, our understanding of population response due to warming will help us make better ecological inferences of what to expect in the future.

A breakthrough in the field of physics was made when LIGO (Laser Interferometer Gravitational Wave Observatory) detected the first gravitational wave in September 2015. This discovery now proved Albert Einstein's general theory of relativity. LIGO was built to be extremely sensitive so that it can detect tiny gravitational waves originating from the far reaches of the universe. However, this also means that it can detect a multitude of other signals coming from non-astronomical sources. LIGO uses a Bayesian wavelet model algorithm called BayesWave to look for gravitational wave signals in the data gathered by LIGO. BayesWave also has the capability to search for and characterize non-gravitational wave signals called "glitches." The ability to identify glitches is important in order to rule them out as possible gravitational waves. Although very successful so far, the use of BayesWave to classify glitches is a relatively new endeavor, so it is still possible to improve its abilities to do so. The goal of this project is to develop improved input parameters for BayesWave that would allow the program to find more glitches. By using a test data set with manually injected glitches, improvements to the command line (the user inputs that tell the program how to run the data) can be easily seen and measured. Studying gravitational waves opens up a brand new gateway into better understanding the universe in which we live.

Prior research has demonstrated that there is a relationship between sleep and academic performance, yet few studies have assessed the role of stress on these variables. It was hypothesized that stress would act as a mediator between sleep and academic performance. Seventy-six undergraduate students made up the preliminary sample from a public university in Washington. Participants completed an online survey which asked demographic questions, including self-reported GPA. Additionally, students completed the Perceived Stress Scale and the Pittsburgh Sleep Quality Index. The preliminary regression analysis indicated a nonsignificant effect of sleep on GPA, R² = .03, F(1, 74) = 2.13, p = .15. The effect of stress on this relationship was also a nonsignificant effect, R² = .01, F(1, 73) = .84, p = .36. However, a power analysis indicated a minimum of 107 participants is necessary to reach beta of .95, alpha = .05, with an effect size of F² =.15, the number of predictors at 1 for level A and 2 for level B. Correlations show predicted, but nonsignificant, relationships between GPA and sleep (r = -.17, p = .07) and GPA and stress (r = .01, p = .45), with a moderate correlation between stress and sleep (r = .47, p < .01). The current sample is underpowered, making it difficult to confidently draw conclusions. Participants will continue to be recruited but if power is met and results continue to be nonsignificant, it is probable that this is due to GPA failing to have a normal distribution for each level of the independent variable. The lack of heterogeneity in GPA would then raise concern. If the necessary sample size is met and results are significant, this is likely due to poor sleep increasing student’s susceptibility to high levels of stress, which consequently leads to a decline in GPA. 

 The North Creek watershed in Bothell contains elevated levels of fecal coliforms, including Escherichia coli. This research is primarily concerned with the characterization of the E. coli present in the North Creek watershed and the determinination of the sources of contamination. Contamination in these waters may increase the risk of infection due to contact. The North Creek Wetlands is a roosting destination for nearly 10,000 crows so, they may be major contributors to the contamination. E. coli isolates from water and feces have been obtained from the North Creek Wetlands where genotyping methods are employed to screen for extraintestinal pathogenic strains and intestinal pathogenic strains. The extraintestinal pathogenic strains are determined through the presence or absence of certain virulence genes. Some of these virulence genes include genes that encode for invasins, adhesins, toxins, and siderophores. The intestinal pathogenic strains are determined by the presence of Shiga toxin genes and the intimin adherence gene, eae. E. coli isolates obtained during June and July of 2016 tested positive for multiple extraintestinal pathogenic genes with 33% for TraT, 22.2% for PAI, 11.1% for iutA, 22.2% fyuA, 25.0% for KpsmtII, 2.8% for sfa/foc, and 13.9% for papEF. Further virulence testing with more recent isolates are currently in process. None have tested positive as intestinal pathogenic strains. Additionally, amplified iutA PCR products from a few isolates have been sequenced and used in a BLAST search through NCBI to determine their source. The ones which had successful sequencing primarily point towards an avian origin but more source tracking methods will be utilized to make the source determination more precise and reliable. In future studies the complexities of the North Creek ecosystem should be explored as well as the interconnectedness of environemental, microbiological, and human factors that affect the risk of infection. 

Many in vitro and in vivo approaches (e.g. overexpression or depletion) have established that proteins’ expression levels can affect the cellular response to stresses and stimulus. Here, I describe an approach to examine the lowest protein amount necessary for a physiologic cellular response. My studies are focusing on Fanconi Anemia (FA), a heritable human genetic disease characterized by cellular and developmental abnormalities, including congenital abnormality, bone marrow failure, and an increased risk of malignancy. The FA pathway responds to inhibition of DNA replication due to DNA damage, particularly interstrand cross-links such as mitomycin-C (MMC). Mutations in the FANCA gene, however, can disrupt this pathway and cause cellular defects. The specific goal of this research is to investigate how much functional FANCA (wildtype FANCA) is required to suppress these cellular defects. To modulate FANCA protein amount, we are currently developing vectors with variable strength promoters that allow for graded expression (from 0-100%) of wildtype FANCA gene. These vectors will be integrated in a unique chromosomal location in corresponding FANCA-deficient isogenic cell line to generate a cellular library. The integrated transgene consists of two regions: a variable strength promoter and a common EGFP linked via a T2A self-cleaving sequence to the FANCA coding sequence. FANCA protein expression will, hence, be quantified using Western blot and using the co-translationally expressed fluorescent protein (EGFP). Lastly, the cellular library will be subjected to differing doses of MMC and promoter sequencing will be used to quantify promoter-specific survival (aka FANCA protein expression-specific survival) as a function of MMC dose. The findings from this study will enable FA-specific drug/therapeutic research by establishing the quantitative requirements for FANCA protein function in human cells.

Transporters are membrane proteins that modulate the absorption, disposition, and clearance of xenobiotics, and they are potentially involved in adverse drug reactions (ADRs). In the liver, which is the major organ for xenobiotic biotransformation, uptake transporters bring substrates into hepatocytes for further processing, whereas efflux transporters eliminate substrates out of the cell. In predicting pharmacokinetic effects, regulation of transporters may determine the availability of substrates to intracellular enzymes and affect the toxicological responses to xenobiotics. During development, profound changes occur in the expression of transporters, and understanding the age effect is crucial in predicting the efficacy and toxicity of therapeutic drugs for the pediatric population. Furthermore, age profoundly alters the gut microbiome, and this may alter certain microbial metabolites and modify the host response. Very little is known regarding the relationship between transporter regulation and gut microbiome during development. Therefore, the goal of this study was to determine the developmental regulation of transporters using germ-free (GF) mice as a model system. Both conventional (CV) and GF wild-type mice were bred under the same housing conditions, and livers were collected at the following seven ages: Day 1, 5, 10, 15, 25, 60, and 120 (n=5 per age per sex). RNA was isolated from the liver and the mRNA expression was determined using RT-qPCR. Significance was determined using a T-Test between age-matched CV and GF by sex. Our data show that expression levels of Abcg5 and Abcg8 are consistently higher in male GF than CV mice. For Abcg5, GF males at days 1, 60 and 120 and for Abcg8, GF males at days 1, 10, and 120 had significantly higher expression levels than CV mice. Our result suggests that liver transporters may in part be regulated in a microbiome- dependent manner.

Aging is a process which causes the deterioration of cellular function in organisms. In order to understand the mechanisms of aging and to begin to identify ways to extend healthy life expectancy, research in the Kaeberlein lab uses Saccharomyces cerevisiae, a species of yeast. The technique that our lab uses to quantitate lifespan in yeast is known as the replicative lifespan (RLS) assay. When a yeast cell divides, the original “mother” cell and the newly produced “daughter” cell can be differentiated based on size. Daughter cells are microdissected away from mother cells, the cell division is recorded, and this cycle repeats until the mother is no longer able to produce daughters. We have tested the effects on lifespan resulting from the manipulation of thousands of genes and numerous environmental conditions. This data can be analyzed to understand the process of aging in yeast cells. By studying the mechanisms of aging in unicellular yeast cells, we can transfer these findings to identify conserved factors in the aging process that are also present in multicellular organisms. The study of the basic biology of aging in yeast can yield insights into the aging process that may contribute to our understanding of aging in humans and help facilitate the development of therapies aimed at decreasing age-related diseases.

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition marked by deficits in social communication. According to DSM-V, these deficits are characterized by lack of coordination between verbal and nonverbal language. Studies have shown that typically developing (TD) children with siblings display greater pro-social behavior and language development by forming close peer relationships with each other. In this study, we use Electroencephalogram (EEG) to explore how the presence of a TD sibling affects the sibling with ASD’s language learning system. EEG is a technique used to measure electrical activity in the brain. The N400 is a negative going ERP component that occurs 300-500ms after an auditory stimulus. The N400 is sensitive to the context of the word and is more negative to unexpected words compared to expected words. In our study, 60 ASD individuals with a TD sibling (n=30) and without (n=30) between the age of 8 and 17 completed a two-part EEG task. During the “learning” phase, the individuals listened to a robot speak a nonsense-language which consisted of a string of non-parsed syllables that were systematically ordered so that 3 sets of 12 phonemes statistically co-occur at a higher rate to create 4 words (e.g., “Pa-bi-ku”). In the test phase, EEG was measured as the individuals were exposed to the same words that should have been implicitly learned in the previous phase, as well as non-words (e.g., “Ku-do-ra”). We expect that children with ASD who have TD siblings will show a smaller average amplitude N400 to the learned words compared to non-words, indicating language learning occurred during the task. We also hypothesize that the difference in amplitude between the two conditions will be greater for individuals with siblings. This will provide evidence that sibling relationships may have a positive impact on the individual with ASD’s language learning skills.

The Northwest Detention Center (NWDC) was built on Tacoma’s Commencement Bay-Nearshore Tideflats, a hazardous Superfund site containing arsenic, lead and other contaminates. A Superfund site is any land in the United States that has been contaminated by hazardous waste and identified by the Environmental Protection Agency (EPA) as a priority for cleanup because it poses grave risks to human health and/or the environment. While the area was only cleaned up to heavy industrial standards, the NWDC today is one of the largest immigration prisons in the country holding up to 1,575 people at any given time. Some people are held for many months or years, separated from their families and their lives, subjected to ill treatment, and forced to live on a Superfund site. How and why are immigrants fighting to stay in the US housed in an area that is not zoned for human housing? This study is a site genealogy using archival research, looking at environmental impact statements from the EPA, city land use permits, and other documents as well as in-depth interviews to map how this site came into being. Using critical race theory and abolition ecology, this paper explains how state actors subjected people of color to harm, in particular through their exclusion of the public comment and non-resident classification. It examines the planning and expansion of this facility, as well as the implications that neither state agencies nor community advocates can examine site conditions. Rather than signal a lack of a problem, this means that it is structurally impossible to know the depth of the problem. Study findings can inform advocacy work in how stakeholder communities are constituted and what role they can play in planning processes.

 A common class of problems is that of understanding the large-scale properties of a system defined by small-scale relationships. These problems arise in fields such as statistical mechanics. We have been considering such problems as they apply to graphs, mathematical structures that can be used to represent networks, by investigating the limiting behavior of finite approximations to infinite graphs. In particular, we have been studying the growth rate of the number of spanning trees on these finite graphs. This allows us to quantify the complexity of various infinite graphs. The Matrix-Tree Theorem gives a formula for the number of spanning trees on a finite graph using techniques from linear algebra. This allows us to numerically approximate growth rates. These calculations can help us see patterns and develop theoretical approaches for obtaining exact values, as well as test theoretical results. In the case of graphs with translational symmetry, we have used techniques from group theory, a powerful area of mathematics, to derive an elegant expression for the exact growth rate in terms of Mahler measure. This is an integral formula connected to dynamical systems and number theory, among other research areas.While these considerations on spanning trees are facilitated by the Matrix-Tree Theorem, there is no known formula for counting spanning forests, a structure consisting of one or multiple trees which is more natural in some ways. Our current research generalizes the questions on trees to various types of spanning forests. We have also been exploring different ways to consider how a graph grows. This work can be used to build on this active research area of determining properties of large-scale structures.

Misinformation is a large component of social media. Sometimes, misinformation increases during times of uncertainty and panic, such as during crisis events. By collecting Twitter data from events such as the Boston Marathon Bombings, Paris Terror Attacks, and a WestJet Airlines Hijacking, it became apparent that thousands of individuals turn to social media as a real-time news source. First, data from public Twitter profiles was collected during major crisis events. After collecting the data, it was qualitatively coded based off a scheme pertaining to rumor acknowledgement. Next, individual Twitter users were contacted to participate in a semi-structured interview centered around their social media use habits. Through interviewing individuals who participated in the online conversation, data shows that there are emotional feelings related to online rumoring. This research aims to identify different ways misinformation is handled on Twitter and explore a new idea, "emotional proximity." Implications of this research include a deeper understanding of how information travels online during crisis events, and the emotional influence social media has on individuals during drastic times. 

This research examines the politicized conversation around officer-involved shootings. Drawing on a dataset of shooting-related tweets containing #blacklivesmatter, #bluelivesmatter or #alllivesmatter, we construct a network graph of Twitter users who participated in this conversation, utilizing a measure of shared audience to connect and cluster accounts into communities. We then employed mixed-methods, including visual and qualitative analysis, to explore the communities, influencers, and information flows of this discourse. Our findings identify and describe several distinct clusters of accounts—both left- and right-leaning clusters, including a cluster of alt-right media—and show how users within the latter cluster were significant in shaping the flow of discourse. We situate our findings within the broader context of competing political narratives leading up to the 2016 presidential election. This work provides insight into the underlying structure of politicized discourse on Twitter, and demonstrates the utility of a shared audience network relation for guiding interpretivist analysis of Twitter conversations.

Safety precautions are only effective when implemented properly. This is a major obstacle when using wearable devices to promote workplace health and safety. User compliance is a serious concern: Is the user using the device and is it worn as intended? Monitoring user compliance using electronic sensing systems faces limitations. The systems must be cost effective, small, and fit the form of the wearable device all while maintaining enough power to be beneficial. This research monitors compliance in the proper wear of safety eyeglasses within these limitations and constraints. Specifically, information on safety eyeglass orientation and location on the head is gathered continuously using a hall effect sensor mounted on the glasses themselves and a magnet mounted on the user’s ear. Tests on six different users (including both male and female adults) show that four different positions (on the bridge of the nose, on the tip of the nose, on the forehead, on the top of the head) of the glasses can be detected for each user and four different motions, all beginning in the proper ‘on’ position on the bridge of the nose, can also be detected. The overall error rate for data sets collected among six different users is less than 10% and error rates within any one user did not exceed 25%. Collecting both transient motion and steady-state position data minimizes error rates for understanding user compliance. These preliminary tests demonstrate the viability of using these safety glass monitoring systems for not only understanding where the glasses are at any point in time but also how they got there. This information is useful to not only capture non-compliance but also to understand behavior well enough to support effective measures to increase compliance (of wearing safety glasses when they are needed).

DNA replication is the process by which genetic information is duplicated and passed from cell to cell. The process of DNA replication occurs with the assistance of various enzymes, including DNA polymerases, which synthesize new DNA molecules using template DNA and deoxyribonucleotides (dNTPs). Faithful DNA replication is vital for population survival and protected by exonuclease domains on the major DNA polymerases, which proofread replication errors. A secondary error-correction pathway known as mismatch repair (MMR) also scans the genome for replication errors. Defects in proofreading and MMR lead to "mutator phenotypes" marked by elevated mutation rates and increased cellular mutation burden.  In microbial populations, mutators spontaneously emerge and can increase adaptation to new environments by fueling genetic diversity. However, at extreme mutation rates, the accumulation of harmful mutations can also drive extinction of mutators.  Some mutator cells survive this "error-induced extinction" (EEX) by acquiring antimutator mutations that suppress the mutator phenotype. We have identified Saccharomyces cerevisiae strains that suppress elevated mutation rates through a screen for mutants that survive EEX. Using these eex mutant strains, we are currently mapping the genetic changes responsible for the antimutator phenotypes. Changes in mutation rates in haploid spores derived from these eex suppressor strains are being tracked to identify antimutator segregants, which are then being subjected to whole genome sequencing. As mutator phenotypes are important drivers in cancer, our analyses may reveal novel pathways that influence cancer evolution.

Women only make up 26% of the Information Technology (IT) workforce. These low numbers are attributed to the multitude of structural and social barriers women face in IT, which organizations have attempted to address through significant investment in Diversity and Inclusion interventions. However, women’s participation in IT has been falling from 36% since 1991, even with the substantial growth of the field. Currently, 93% of IT companies have a Women's Affinity Group (WAG), yet no metric exists to assess the efficacy of these groups. Our research examines the characteristics, obstacles, and nature of participation for WAGs in IT through an interpretive, multi-level analysis, in-depth case study. By utilizing more inclusive frameworks of information science and feminist theories, focused on including perspectives of intersectional identities, we improve our theoretical understanding of how WAGs are designed and used. We also holistically approach our evaluation, discussing current efficacy with WAG participants, non-participants, and organizational leaders. From our results, we will create an instrument for companies to create, deploy, and evaluate their WAGs, increase access and equity for women in the industry, as well as improve sensitivity education within IT-related disciplines in industry and higher education.

With a changing climate, rising temperatures are predicted to increase frequency and severity of drought. Along with drought, there is a need to increase crop production and expanding agriculture into areas with poor quality soil is one solution. Approximately 78% of the Earth’s atmosphere consists of nitrogen; however, plants cannot use nitrogen that is available in the atmosphere, since it is in the form of dinitrogen gas. The current dominant nitrogen solution in agriculture is chemical nitrogen fertilizer, which can be harmful to aquatic ecosystems and pollute groundwater if used in large quantities. This project focuses on the uses of microbial endophytes in agriculture. Endophytes are bacteria and fungi that live within plants. Some strains of endophytes have been shown to increase drought stress tolerance and nitrogen availability. In Prof. Doty’s lab, we have tested how individual and a consortium of endophyte strains mediate drought stress alleviation in rice by subjecting the plants to a period of drought followed by a rehydration period. We anticipate the plants that were inoculated with endophytes to survive the drought period and recover during the rehydration phase. We have also tested one endophyte strain for nitrogen fixation in rice and tomato plants by inoculating the plants with the wild strain and nitrogen fixation mutant strain. These anticipated outcomes suggest that endophytes could potentially be a more sustainable solution for agricultural crops under drought and nutrient stress.

For 4,000 years, paper has served the purpose of recording information and in this work, it's uses are being expanded upon. Within the advancing field of flexible electronics and wearable devices, paper has recently been investigated as an environmentally friendly alternative to the traditional petrochemical-based polymeric materials. In this work, carbon nanotubes (CNTs) were employed as fillers to produce electrically conductive papers using a universal papermaking process. Lignin, an underutilized byproduct of the pulp and paper industry typically treated as a waste and burned for energy recovery, was utilized as a renewable surfactant to prepare aqueous dispersions of CNTs and softwood fibers, which served as precursors for the manufacturing of conductive paper (60 g/m²). CNTs were functionalized to increase the presence of hydroxyl groups and further improve the interfacial strength between CNTs and cellulose fibers through hydrogen bonding. The microstructure of the CNT–cellulose composite papers was analyzed by electron microscopy and Fourier transformed infrared spectroscopy. Both tensile strength and internal bonding of the papers greatly increased with CNT loadings as low as 2.5 wt%, and the volume resistivity was in the range of 1.5 kΩ.cm. The piezoresistive behavior of the composites revealed through examination that the relative resistance first increased linearly at low strains followed by an exponential growth at larger strains. When employed as a stress/strain sensor, the conductive papers exhibited higher sensitivity compared to conventional strain gauges. These novel CNT-cellulose composite papers have outstanding multifunctional properties that can revolutionize the way smart materials and electronic devices are manufactured and used.

Inflammation in the brain, called neuroinflammation, is typically considered a negative response following neuronal injury and damage. However, neuroinflammation can also play a beneficial role in the healthy adult brain. For example, one type of inflammatory cell, microglia, become polarized from the “inactive” surveying (or ramified) state following neuronal loss and promote the classic “negative” inflammatory response. Alternatively, in the healthy brain microglia elicit positive effects through neuronal and synapse pruning to maintain proper neuronal number and connections. To identify the dynamics of microglial responses between healthy and natural degenerative states, we employed the seasonal neuronal regression of avian motor pathways for song production in Gambel’s white crowned sparrow (Zonotrichia leucophrys gambelii). Neuronal number in the song control nucleus HVC (proper name) changes seasonally such that as male sparrows transition from nonbreeding to breeding conditions, HVC neuronal number increases by about 68,000 neurons. Useful for our study, an equal number of HVC neurons die through programed cell death as sparrows transition from breeding to nonbreeding conditions. Using this unique model of natural and rapid neurodegeneration, we quantified the number of ramified and activated microglia in HVC of birds maintained in breeding and nonbreeding conditions using immunohistochemistry. To identify microglial promotion of local neuroinflammation within HVC, we examined the number of ramified and activated microglia in HVC of birds treated with pro- and anti-inflammatory agents. Additionally, we identified and quantified a putative downstream effect of this local inflammation: reactive neurogenesis, or the birth of new neurons following neuronal loss. Our results indicate that microglia promote reactive neurogenesis through local inflammation, and suggest that discrete microglial activity could have therapeutic consequences for various neurological diseases.

In modern dentistry, the goal is to remineralize small lesions in the teeth, before there is a cavity. To monitor the healing process in teeth, infrared 3D optical imaging is being developed at the UW that does not have the safety risk of x-ray imaging. However, to calibrate this new prototype, teeth with natural lesions need to be imaged with x-ray to create a gold standard of lesion volume and density. This project will design, build, and test a fixture that will hold a tooth of various shapes, sizes, and orientations for microCT (computed tomography) scanning to obtain a high resolution 3-D image. X-Ray CT scanning can provide a high quality 3D image; however, it is harmful to use directly on humans due to large dose of radiation needed to form 3D images. This research and development project will use the new UW CT Scanning system in Moore Hall with highest 3D resolution of 2 microns. The fixture was designed by taking dimensions of the existing rotational plate of the CT Scanner, and the CAD design file is in the process of being 3D printed. The fixture must mitigate any effects from the CT scanner during operations (such as heating and vibration during scanning), and must be versatile so that it can hold different sizes of teeth at different orientations. The fixture design will be designed to also accept commercially available calibration specimens of known spatial and density values to ensure that image quality is being preserved.

Duchenne Muscular Dystrophy (DMD) is an X linked, recessive genetic disease caused by mutations in the dystrophin gene. The disease is characterized by progressive muscle degeneration. Dystrophic mice (mdx^4cv) are a DMD animal model. Here, we compared mdx^4cv and WT mice to quantitatively assess motor performance. We hypothesized that the mdx^4cv mice would show differences in gait compared to WT as a result of muscle weakening. To test our hypothesis, mice were assessed at 1.5, 3 and 6 months of age using the Noldus CatWalk XT system to analyze gait. The mice voluntarily moved across an enclosed walkway on a backlit glass plate. The prints were captured by a camera and later analyzed using the CatWalk software. Our results show that there are significant differences in gait between the WT and mdx^4cv mice. The mdx^4cv mice were slower to cross the runway than WT at 1.5 (mdx^4cv: 3.60.8s WT: 2.80.5s) and 3 months (mdx^4cv: 3.80.9s, WT 2.51.2s ). The distance between the front paws of the mdx^4cv mice were wider than WT at 1.5 months (mdx^4cv: 3.60.8cm WT: 2.80.5cm), 3 months (mdx^4cv: 3.80.9cm WT: 2.51.2cm) and 6 months (mdx^4cv: 1.50.2cm WT: 1.20.2cm). Print position is the distance between the position of the hind paw and the position of the previously placed front paw on the same side. In mdx^4cv mice the print position was larger than WT at 1.5 (mdx^4cv: 1.30.8cm WT: 0.40.2cm) and 3 months (mdx^4cv: 1.40.8cm WT: 0.50.4cm), indicating that the hind leg moved a shorter distance in a single stride. The gait analysis assay can be extended to assess gene therapy based treatments that our lab is currently developing. This will allow us to determine if the treatments are successfully able to mitigate the effects of DMD.

The objective of this study is to explore the television viewing behavior of preschool-aged children (24-59 months) with autism spectrum disorder (ASD). Data regarding television viewing behavior was constructed and collected via retrospective visual media diaries of television consumption reported by parents regarding duration, percentage focused, method of access, concurrent social interaction, and the presence of commercials. Comparisons will be made to a neurotypical control group along these dimensions in addition to between group comparisons made among participants in high and low severity ASD groups. I predict less variation in the content of programs consumed by children with ASD than their neurotypical counterparts (duration of a single program divided by total duration), in addition to a greater frequency of noncommercial television viewing. I anticipate that children with mild cases of ASD will demonstrate greater variation in the types of programs they watch, more frequent concurrent social initiation, more frequent viewing of live television versus recorded, and lesser focus on television programming. Lastly, repetitive behaviors have been found to be characteristic of ASD and are also considered, such that I expect to find a positive correlation between program variation among subjects in ASD groups and various aspects of repetitive behavior centered around limited interests and/or inflexibility of a routine. If correlations exist, I then further predict that parents will report these respective components of their child’s repetitive behavior as problematic.

Composed of 5HT cells, the serotonergic system influences mood, social behavior, sleep, memory, libido, pain perception, motor activity, and respiration, among other functions. Understanding the regulation of proper serotonergic development then becomes vital in the development of pharmaceuticals and treatment of individuals suffering from the symptoms of a dysfunctional serotonergic circuit. Using mice as a model organism for the human brain, previous research work has shown that propagating waves of spontaneous intracellular calcium activity (SA) are necessary in the development of the serotonergic system within the hindbrain. Blocking SA with the drug ketanserin has been shown to reduce the number of of 5HT cells during embryonic development. To elucidate the second messenger pathway activated by the ketanserin-sensitive response, we carefully characterized the 5HT receptors responsible for SA. This research project focuses on characterizing whether 5HT2A, 5HT2C, and/or 5HT3 receptors regulate SA within the hindbrain. By using [Ca2+] imaging techniques to monitor SA in real time, drugs selective for specific 5HT receptors were applied to both acutely isolated hindbrains and also through 24hour cultures in order to pinpoint the receptor(s) regulating SA. Results currently show that antagonists of the 5HT2A receptor, M100907 and 4F 4PP, inhibit SA. Meanwhile, antagonists of the 5HT2C receptor, N-desmethylclozapine and SB242084, appear to have no effect. In addition, an antagonist of the 5HT3 receptor, zacopride hydrochloride, appears to have no effect as well. Therefore, results currently suggest the proper functioning of the 5HT2A receptor is important in the regulation of SA, thus playing a vital role in the proper development of the serotonergic system. In future experiments, we will determine the second messenger pathway underlying this regulation.

Core needle biopsy (CNB) is used as a minimally invasive method to diagnose prostate and other cancers. However, this method still has limitations of getting non-diagnostic and inadequate CNBs due to sampling error. Thus extra CNBs are often taken and other time-consuming tests looking at surface cellularity such as histological evaluation on tissue smears are done to reduce probability of this error, which leads to needless pain and cost. Therefore, we propose to design a rapid-on-site evaluation system by imaging the outer surface of needle biopsy samples. This system generates a whole surface image of CNBs that contain cellularity information as a quicker and more informative adequacy testing of CNBs. This proposed project aims to develop cost-efficient imaging for obtaining sub-cellular and structural information from CNBs at the point-of-care. There are three phases: Design of System, Development Image Stitching Algorithm, and Integration, testing, and generating surface image. Phase I aims to determine the optimal optical imaging system and developing a staining protocol for CNBs. Phase II is developing an image stitching algorithm that takes in images from Phase I. Phase III will integrate I and II and generate a whole surface image of CNBs to provide morphological features for clinicians so that they can determine the adequacy of biopsy and needs for additional biopsies. The main criterion of this design is to perform evaluation within 20 minutes while still maintain intactness of specimen. If the design is successful a commercial device will speed the process by 10x (<2 minutes), while maximizing use of CNBs and reducing the number of biopsies taken to minimize suffering of patients. It may also accelerate diagnosis speed for prostate cancer. Importantly, this design can be applied to other types of cancer diagnosis, such as remote radiology clinics where a pathologist is typically not available.

The purpose of this research is to better understand the connections between dice and elections in voting theory. We explored the phenomenon of nontransitivity in dice and elections. In a set of 3 dice, labeled A, B, C, it is straightforward to designate sides such that, on average, A beats B, B beats C, and C beats A. Similarly, in an election of more than two candidates, where voters create a preference list for the set of candidates, it is simple to make nontransitive relationships in voter preference. Motivated by these situations, we aimed to find a correspondence between these two mathematical objects. Additionally, we defined the concept of an overall winner for a set of dice and an election, and explored the effects of nontransitivity in determining it. We used tournaments (from graph theory) as a tool to visualize the relationship structure among dice and elections. As a result of this work, we have shown that, from any dice set, an election can be constructed such that the dice possess the same winning-losing relationships. The converse is also true: given an election, a set of dice can be constructed with identical winning structure to the election. We defined the notion of a contest, which serves as a classification for both objects. Finally, we developed a triangular inequality for contests, and proved that dice and elections both satisfy this inequality.

This research project focuses on the study of the mitochondrial Cytochrome -c-Oxidase 1 gene (MT-CO1), in salmon species of the Pacific Northwest. The MT-CO1 gene encodes for a protein located in most eukaryotic cells called Cytochrome-c-Oxidase 1. This protein is located in mitochondria and plays an extremely important role in cellular metabolism. The MT-CO1 gene has become one of the standard sequences for a technique called DNA Barcoding. The idea of this technique is to compile MT-CO1 gene sequences in a database in which researchers can use computer software, such as Mega Software, to accurately identify species and analyze the subtle differences between them from a small tissue sample available. This allows taxonomists to accurately identify new species and track changes in a given population of organisms. In this project, we used the MT-CO1 Gene as a barcode to identify different samples of the salmon which were purchased from different local stores to find out whether they belong to the Pacific Northwest Salmon species. The laboratory techniques used in this research project included DNA extraction, polymerase chain reaction (PCR), gel electrophoresis, DNA imaging, gene sequencing and analysis. Our results indicated the expression of the identical MT-CO1 gene within the Northwest salmon species. Gel electrophoresis confirms the successful replication of 660 base pair MT-CO1 gene. Further analysis of the sequences indicates these salmon samples are of the species Oncorhynchus: nerka, tsawytscha, keta, and kisutch. This was confirmed using alignment search tools, such as blastn and MEGA6. The implication of this study is that DNA Barcoding using the MT-CO1 gene or other specific gene sequences can be used as a supplementary identification tool to track evolutionary changes, mis-labeled food products and identification of pathogen bacteria allowing the medical practitioners to accurately identify and treat the diseases caused by these agents.

Synaptic plasticity influences many functions in the body, some of which include the mechanisms of learning and memory. However, isolating these cells for further study is inefficient as grinding up a portion of the brain yields a mixture that includes synaptosomes, neuronal and glial contaminants, and free myelin as well as mitochondria. One way to sort synapses from the mixture is to use FACS (fluorescence-activated cell sorting). However, this method is limited as it is very time consuming. Instead, our lab is developing methods to sort specific synapses based on immunology cell-sorting techniques that can isolate activity-dependent synapse species from the assortment of synapse types in the brain. We have created TAG proteins that targets glutamate synapses, therefore potentially enabling us to utilize the more efficient MACS (Magnetic Cell Sorting) method that is proven to isolate cell types at higher rate. My project is to develop a method to ensure that the TAG RNA is translated only in specific neurons. I utilized Cre-lox recombination methods so that the TAG RNA is translated only when a CRE protein removes the lox-stop-lox gene. To do so, I used a plasmid with an AS-LSL-TAG insert previously made by the lab. I then used HEK 293 cells, each with a different condition to evaluate how well the CRE protein will be able to remove the LSL portion of the tag construct: one with untransfected cells (control), another with the CRE-RFP plasmids only, a third with only AS-LSL-TAG plasmids, and the last with both CRE-RFP and AS-LSL-TAG plasmids. If I achieve HEK 293 cells with the AS-LSL-TAG and the CRE-RFP that express the both the green fluorescence from the AS-LSL-TAG and the red fluorescence from CRE-RFP, I will then insert the LSL TAG construct into neurons and analyze the results by western blots and microscopy.

The presence of protein biomarkers in specific human tissues can be indicative of diseases such as Parkinson’s Disease (PD). One such protein, α-synuclein (α-syn) commonly exists in brain and blood and can be transmitted between different cell types in secreted membrane vesicles called exosomes. The blood levels of α-syn are very high, and α-syn originally from red blood cells (RBCs) could be transported in exosomes.  In order to study α-syn in RBC exosomes, we have collected α-syn-containing exosomes from RBCs by culturing fresh blood samples. However, RBCs degrade quickly, meaning that in the past, RBC exosomes could only be collected from fresh samples on the same day as collection. So the purpose of this work is to save time and resources from culturing exosomes by determining if they can be pulled down from previously frozen blood plasma. RBC derived exosomes could be targeted by the RBC membrane specific cell surface protein CD235a and using antibody coated superparamagnetic beads to pull down the desired exosome from samples. We hypothesize that the technique of immunoprecipitation is able to make a pure preparation of RBC exosomes which can be use for studying exosome α-syn from RBCs.

We proposed an approach for solving Mathematics optimization problems, which should be in the topic of numerical analysis results, to be more specific, unconstrained minimization problems with non-differentiable convex objective functions. They are usually solved by using the subgradient method, whose convergence is guaranteed if the optimal value of the objective function is known. In this work, we combine the subgradient method with the spectral step length, which does not require either exact or approximated estimates of the optimal value. Since subgradient methods are not descent methods, we add a nonmonotone globalization strategy to ensure sufficient progress is made. This work also presents numerical results on a set of non-differentiable test functions. These numerical results indicate that using the spectral step length furnishes significant improvement over other subgradient methods.

Preclinical screening and toxicity studies are crucial steps in the drug development processes to ensure safety of new compounds when exposed to patients during clinical tests. Cellular responses in blood vessels play an important role in drug screening in terms of permeability and control of blood flow. The structure of the smooth muscle cell layer is crucial to the function of vessels in terms of contractility, mechanical properties and extracellular matrix production. Through recapitulating native tissue properties, tissue-engineered vessel models provide insights to study cellular responses when exposed to different environments, such as drugs. Although much research has been done in the development of tissue-engineered blood vessels, limitations in current in vitro models are yet to be addressed. Existing models such as synthetic and autologous vessel grafts are limited by thrombosis, non-native cellular resonses and poor mechanical properties. Bioreactors or microfluidics device are limited in terms of the complexity of the model and the scale to mimic larger vessels. The project addresses the need for an in vitro tissue-engineered arterial vessel model that replicates in vivo functionalities of the vessel by developing a fabrication method to form smooth muscle cell tubes that is reproducible and functional. The project is divided into three phases: (1) Formation of three-dimensional smooth muscle cell tubes using a cell sheet rolling method, (2) Optimization of the rolling method and (3) Validation of model by contractility analysis. Ultimately, the success of this project allows formation of vessel graft with functionalities in terms of mechanical properties, compliance and contractility. Vascular grafts can be created by human or patient derived sources and serve as drug screening or disease modeling purposes.

Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) is the etiological agent of Kaposi’s Sarcoma (KS), a highly vascularized tumor predominantly made up of cells of endothelial origin. KSHV establishes a predominantly latent infection in endothelial cells in culture and in the KS tumor. KSHV latent infection alters cellular metabolism to improve the survival of the infected cells. These metabolic changes resemble a common alteration in cancer cells, termed the Warburg effect. This refers to an increase in glycolysis in the presence of oxygen and a decrease in oxidative phosphorylation. The mechanism of KSHV induction of the Warburg effect is currently unknown. Hypoxia-induced factors (HIFs) are likely candidates for KSHV induction of the Warburg effect as both HIF1α and 2α are induced by KSHV latent infection. To determine if HIF1α or 2α is required for the survival of KSHV infected endothelial cells, I constructed HIF1α or 2α knockouts using the CRISPR/Cas9 gene editing technique in a lentivirus vector. I expressed the endonuclease Cas9 and guide RNAs that lead Cas9 to cut at the HIF1α or 2α genomic sequences leading to genomic mutations in HIF1α and 2α respectively. To determine if HIF1α or 2α is required for the survival of latently infected endothelial cells, I infected the HIF1α and 2α knockout cells with KSHV and looked for cell death at 48 hours after infection. To evaluate if HIFs are required for KSHV induction of the Warburg effect, I will determine if one or both of the knockout cells produce less lactic acid and increase oxygen consumption at 48 hours post KSHV infection as compared to infection of wild type cells indicating the Warburg effect is not being induced by KSHV in the knockout cells. These results will aid in the future efforts to develop antiviral drugs by inhibiting viral latency.

For many, mathematics is just the language of numbers. But, what people forget is that the universe is made of numbers, thus mathematics is its language. That is why we used a mathematical approach to study the long-term behavior of a moving ball influenced by the Earth’s gravitational field. For our purpose, we experimentally defined gravitational billiards to be vertical billiards in which the earth gravitational field affects the billiards ball’s motion. We also assumed that the billiards boundary could be any mathematical function of our choice, and the experimental system was conservative. Once in motion, the billiards ball followed a two-dimensional projectile trajectory until collision with the boundary occurred. After that, the ball engaged in a new projectile trajectory. As a matter of fact, each trajectory between two points of ball-boundary collision could be considered as an isolated two-dimensional gravitational motion with its own set of conditions. We took advantage of that aspect to build different simulations in parabolic, circular, paraboloidal and spherical gravitational billiards. The long-term behavior of the ball under gravity in our different gravitational billiards presented some aspects that so far corroborated the physics behind our study.

The entirety of this research focuses on a cochlear implant test system. Cochlear is an implantable device which bypasses the middle and inner ear to directly stimulate the nerve system, in order to give patients hearing ability. Current implants are helpful for speech recognition, however, their performance decrease in recognizing pitch in music or speeches with background noises. This proposed test system has the hope to model after the conditions in which the cochlear implants is already implanted in a patient with cochlear impairment. The pitch test system is designed to simulate what a subject with a cochlear implant would hear. A set of sound through a series of filters programmed using MATLAB will be created to perform the simulations.Data will be collected from approximately 5 to 10 normal hearing subjects and 5 cochlear implant subjects. The testing system is intended to evaluate the subject's ability to recognize different controlled sound pitches. A standard deviation will be taken from the data collection versus the standard data to determine the validity of the result. As the outcome will determine the accuracy of the test system and for further construction of an improved system. The result from the tests for both groups will be graphed in MATLAB. The current pitch testing system has been tested on two normal hearing subjects. The subjects response to the test is consistent to what is expected in normal hearing subjects. Further studies will consist of more subjects, therefore, a larger data set will be accumulated allowing for more in depth data analysis and better understanding of cochlear implant patient’s pitch recognition.