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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Visual art is one of the compelling factors in changing society and culture, and many visual artists--from primitive to modern times—have left their impact on the world. Art is thought of as a system or method of communication that goes beyond language and has the capacity to fully capture a moment in time or an individual’s experiences, emotions, desires, and more (Schellekens 44). For the artists themselves, discovering their reasonings, motives, and influences becomes a critical component in creating more meaningful artwork and understanding themselves. The purpose of this research is to investigate, learn, and predict the factors that are influencing my own personal body of artwork. The methodology of this research is divided into three steps: 1. Research and Identify, 2. Narrow Down & Categorize, and 3. Analyze & Conclude. Through an immersive, month long, experience at the New York Academy’s Summer Residency Program, data was collected and recorded. A list of the potential factors was created before attending the residency that consisted of a list of contemporary artists, old masters, techniques, and many more. After the residency, a comparison was drawn between the data. In order to have more tangible and quantifiable data to analyze from, each factor will follow a system of ranking. The results of this research is critical to developing a new artistic perspective and direction for my body of work.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

We previously observed that turmeric could be used to manipulate gut motility in a microbiome-dependent-bile acid-mediated manner via the enteric nervous system (ENS). Bile acids comprise a class of metabolites synthesized by the host and modified by gut microbes. Bacterial bile salt hydrolases (BSH) are responsible for deconjugation, the first step in bile acid metabolism for generation of secondary bile acids. We hypothesized that homeostatic ENS signaling is dependent upon gut bacterial bile acid metabolism. To test this hypothesis, we colonized wild-type gnotobiotic mice with different defined consortia varying in BSH activity and subjected them to a two-week low-fat diet ± turmeric. As a control, one treatment group remained germ-free. mRNA isolated from small intestine and colon was subjected to gene expression profiling returning counts of 68 target genes, including ENS-specific genes, and 7 housekeeping controls. A machine learning algorithm was deployed to identify genes whose expressions were most impactful in discriminating between treatment groups. Glp2r and VIP were highly discriminatory with respect to BSH activity. Enteric neurons express Glp2r, activate the mTORC1 pathway in response to GLP-2, and modulate intestinal epithelial cell growth. We found that Glp2r expression was significantly greater in mice harboring consortia with BSH activity than in germ-free mice. GLP-2 induces VIP neurotransmission from enteric neurons. Indeed, VIP expression is correlated with Glp2r expression. These data suggest that gut bacterial bile acid metabolism regulates homeostatic ENS signaling, with implications for gut motility and colorectal carcinogenesis.

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

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

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

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

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

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

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

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

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

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

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

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

The delivery of cell and drug-based chemotherapeutics to tumors have presented major challenges in effective cancer treatment. Opportunities to improve current small molecule drug delivery systems exist by increasing overall delivery specificity and decreasing harmful off-target effects. Towards this, we have recently developed a chemical framework for creating user-programmable hydrogels that undergo programmed degradation in response to multiple environmental cues following Boolean logic. Exploiting this methodology, user-specified combinations of environmental inputs (e.g., tumor-presented enzymes, reducing conditions) yield material breakdown and accompanying therapeutic release. To translate these materials for chemotherapeutic delivery in vivo, we established strategies to formulate these stimuli-sensitive materials into nanogels that circulate in the bloodstream before acting on the desired target site. We developed techniques to formulate gels on the 50-250 nanometers size scale, one which should enable circulation in the blood and uptake within tumors based on the enhanced permeability and retention effect. Different ultrasonication conditions allowed us to tune nanogel, size and dispersity. This system is scalable, translational, and simple to recreate. In the future, these materials can effectively hone and selectively deploy small molecule chemotherapeutics to tumors in patients.

Pre-hospital patient protocols standardize medical procedures for EMTs and increase the quality of care for patients. In Washington state, these protocols vary by county and often contain a section for psychiatric emergencies with variant restraint protocols. The immediate use of restraints in these situations can be seen as dismissive to the patient and can lead to agitation and violence. Verbal de-escalation can enhance provider-patient relations and decrease likelihood of restraints, seclusion, and hospital admissions.  The goal of this project was to explore restraint and de-escalation methods used in WA state county-level EMS pre-hospital patient protocols. To complete the project, a codebook was created with binary variables with definitions that determined whether the procedures listed in the protocol satisfied the definition. Using the codebook, each protocol was independently coded by 2 people and disagreements were reviewed by a third person. Finally, we created descriptive statistics from the restraint protocols and stratified based on rurality. Of the 39 counties in WA state, 77% of counties mentioned verbal de-escalation methods in their pre-hospital patient protocol. The de-escalation method with the highest proportion in all counties recommended reassuring the patient that the providers care for them (28%). The second highest proportion in all counties was to mention the use of de-escalation methods without explicit instructions (23%). Counties that do not have specific instructions and just mention the use of de-escalation methods can be confusing if the provider does not have de-escalation training or has not trained recently. These findings highlight the need for future research concerning the adherence of EMTs to these protocols and to see the what the outcomes are of the different protocols. More research can be done through contacting individual EMS agencies to see if internal protocols exist outside of county protocols.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

High rates of forest conversion and fragmentation have placed many endemic species in the rainforests of Sri Lanka under threat. Ceratophora is an endemic and endangered/critically endangered genus of lizards containing five species, and C. aspera has the widest distribution spanning four forest regions, making it an ideal candidate species for broader conservation management projects. The goal of this project is to study the phylogeography of C. aspera across its range in the forests of southwest Sri Lanka to assess the genetic variability of the remaining populations across two lowland areas, the submontane zone (Sabaragamuwa Hills), and the montane forest zone (Central Hills). Analyses of genetic data are important for understanding the relationships between geography and genetics and to determine where populations are connected and fragmented. During the 2018 and 2019 field seasons, tail clippings were collected from wild lizards. In the University of Washington's Biology Department, DNA sequencing of mitochondrial DNA (ND4 gene) was used to measure genetic diversity within and among populations, and to estimate phylogenetic relationships. Genetic diversity is highest (6%) between the population from Hiyare (lowlands) and the Sabaragamuwa Hills (submontane zone). There is also strong evidence for highland and lowland groups. Populations from Hiyare, Sinharaja and Gilimale show no intra-population variation. Sri Lanka has pledged to reforest 200,000 ha of degraded forest to create forest landscapes under the Bonn Challenge, and to increase forest cover to 30% unde the Paris Climate Agreement. Phylogeographic profiles of endemic species, such as C. aspera, are critical for forest restoration strategies as they identify priority areas for reforestation and inform connectivity strategies based on the need to maintain metapopulation structure and genetic diversity. 

Automatic scales are designed to weigh and count animals when they step on or cross the device. This means that high quantities of data may be collected when researchers cannot be present, with minimal interference to study subjects. However, remote and automated data collection requires verification of the quality of data before analyses. We use automatic scales in Punta Tombo, Argentina to weigh Magellanic penguins (Spheniscus magellanicus). Our scales record the time that each penguin crosses, and if certain conditions are met, they record a weight. We verified our data by comparing counts from automated scales with counts from a video recording of penguins crossing the scales. Over twenty hours of video footage were made during a 17-day period where penguins were recorded crossing automatic scales in the morning, midday, and evening on different days. We then counted the number of times a penguin was present in the video and not recorded by the scale. We expect that the proportion of penguins missed will be higher in the morning and evening when more penguins cross the scales, and lower around midday when fewer penguins cross the scales. The scales are designed to record weights when one penguin is present. When several penguins are on the scale or cross rapidly, the scale does not record a weight and may not record the correct number of penguins. Preliminary results support our prediction, with 75% and 78% of birds crossing the scales recorded during the morning and evening respectively, and nearly 100% of birds crossing the scales recorded at midday. By comparing the counts and the times between the scale and the video recording, we can determine how many penguins are missed, count the total number of penguins crossing the scales, and identify when most penguin crossings occur.

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

My guiding question is, “how we can I use storytelling to empower the stories and experiences of the black community in the Central Area that has been displaced through gentrification?” Redlining has historically made it harder for people of color to obtain a mortgage or buy a property in certain neighborhoods, and it continues to exist as gentrification. As tech companies like Microsoft, Amazon, and Airbnb among others continue to expand their presence in the greater Seattle area, rent prices have risen and property owners have started building expensive apartments and living complexes for the influx of workers with a high income. This expansion has displaced people of color who have historically lived in the Central Area. Currently there are stories of resilience in communities that have been displaced by gentrification, but they are often not showcased in the public eye and media outlets. I want to focus on the use of radical storytelling as an act of defiance against erasure, and the role of tech companies in the greater Seattle area in displacing communities. Inspired by the interactive digital stories like “Trump Wants a Border Wall. See What’s In Place Already” in the New York Times or “Microsoft By the Numbers” on Microsoft Story Labs, I hope to create a visual digital story about the ways and means of gentrification, and I hope this story can be used to educate the public about the mechanisms of gentrification and where communities move. By conducting interviews with activists and community members in the Central Area and highlighting their perspective through direct quotes and testimonials, I hope to educate everyone about the strength of communities in the Central Area. My goal is to create a project that focuses on empowering people of color and their stories through community activation.

Scholarship on American Buddhism has, from its beginnings, struggled with defining “who” and “what” makes an American Buddhist. American Buddhism has thus been split off into two branches: one “ethnic,” which is defined as being practiced by Buddhist immigrants and their descendants, the other “convert,” which makes up Americans of all races and ethnicities who decide to convert to Buddhism. However, temples like the Tacoma Buddhist Temple, a Jodo Shinshu temple located in downtown Tacoma, is one of these many communities with varied membership that falls outside of the two-branch model and is thus why scholars have disputed the model for its inability to fully describe American Buddhists. The dualism of these the two terms create a divide within the American Buddhist community and also racializes the two categories since the term “ethnic Buddhist” is highly associated with the Asian community. As a result, the two terms fail to recognize many of those who fall outside the model, such as non-Asian Buddhists whose parents were convert Buddhists themselves and Asian Buddhists who grew up in a non-Buddhist household and chose to convert to Buddhism later on in their lives. The terms also have a tendency to polarize communities, making it seem as if “ethnic” communities and “convert” communities and thus “ethnic” and “convert” Buddhists have little interaction. The Tacoma Buddhist temple, however, is a community of not only “ethnic” and “convert” Buddhists practicing Buddhism side by side, but also those who the model fails to recognize. Therefore, through the research gathered at the Tacoma Buddhist Temple, it becomes evident that the two-branch model fails to capture the diversity of American Buddhism.

Overdoses induced by fentanyl-laced cocaine are skyrocketing today. Meanwhile, in 2017, cocaine was reported as the fourth most prevalent substance used on college campuses. Even more alarming, research shows a modest decline in young people’s disapproval and perceived harmfulness of experimental cocaine use. Favorable depictions of cocaine use in the media contributes to these trends today: the entertainment industry continues to advertise cocaine as a drug of privilege, partying, and success. Conversely, studies investigating Adderall use found college students view cocaine use negatively. Students harshly judged their peers who exposed themselves to cocaine’s hazardous nature and high risks. This contradictory evidence makes it difficult to judge how problematic college students’ views on experimental cocaine use may be. This study aims at sorting this puzzle. The project tests the hypotheses that students think one-time use results in more benefits than risks to the individual. To assess this hypothesis, I use a web-based survey adapted from the so-called “prototype-willingness model” (PWM). The PWM is built on the idea that young people share very clear social images of risky behaviors. The favorability of these images is positively correlated with willingness to engage in risky behavior. Willingness, rather than planned intent, is the primary factor responsible for engaging in risky behaviors if presented with the opportunity. I examine the social image of experimental cocaine use and its favorability in order to predict willingness to use. Predicting how a college student may react when given the opportunity to use is crucial for future prevention planning, as cocaine use is a more pressing issue than ever.

Team leaders occasionally find themselves managing teams that have a member set on under-performing in the social group, or "social loafing." Many team leaders have difficulty managing this social loafer effectively. In our research, we focus on helping leaders identify social loafers on their team. Our goal is to create guidelines and strategies on how to work with social loafers after they have been identified. We use communication transcripts and performance data, gathered by social behavioral researchers, that conducted a hidden profile experimental simulation with rotating leadership and hidden social loafers amongst project members. This was done over time, as project requirements escalated. By applying recurrence quantification analysis, we gathered metrics on the development of communication patterns across time in terms of: being recurrent, deterministic, and chaotic. Statistical modeling was used with the intention of revealing the types of relationships between the ability to identify social loafers and project success. By providing a way to quantify the properties of dynamic systems, recurrence analysis offers group researchers a new approach for empirically studying group dynamics. Rather than presuming that such systems are linear, researchers can use recurrence analysis to assess the degree to which a system is stable, predictable, and complex. This work will provide value to researchers in demonstrating the application of the recurrence analysis method, and will help team leaders by exemplifying how they can manage tough situations where social loafers exist on a team.

Since the 1920s, plea bargaining in the United States criminal justice system has become status quo. Today, over 95% of federal cases have resulted in plea bargains and never been tried in court. The power of the prosecutor within the legal system has also increased substantially over the last century leading many scholars to believe that the proliferation of plea bargaining is a direct result of heightened prosecutorial power. Prior literature has addressed the increased power of the prosecutor and the need for reform if plea bargaining rates are to change, but has not yet provided an empirical observation as to whether prosecutorial reform makes a significant impact in plea bargaining. In this paper I theorize that the prosecutor’s discretion over exculpatory evidence plays an integral part in states’ reliance on plea bargaining and that states that attempt to reign in prosecutorial power experience reduced rates of pleas. To test this theory systematically, I have run a multivariate analysis at the county-level to compare rates of plea bargaining across states that have reformed prosecutorial discretion and states that have not. If states with a model rule suppressing prosecutorial power show a statistically significant difference in plea rates, criminal justice reform advocates should turn their attention to prosecutorial reform.

For this project, I examine why the majority of white women voted for Trump in the 2016 election, a fact that came as a shock to many observers. However, with few exceptions, white women have been shown to support conservative candidates in presidential elections since the 1950s. Yet, Donald Trump’s election can be considered unique as he was still able to gain most white women’s support despite his displays of various behaviors that could be regarded as overtly sexist. In this research design, I analyze white female voters using data from a 2016 Pilot Study by the American National Election Survey and hypothesize that racial resentment and internalized sexism are the primary factors that drove white women to support Donald Trump, controlling for partisanship, economic anxiety and other factors that might influence vote choice. I employ linear regression models using R programming software to examine a relationship between 2016 vote choice, racial resentment and internalized sexism systematically. In doing so, my analysis takes an intersectional approach, where both race and gender dynamics are useful in providing an explanation for white women’s support for Trump.

One of the most common questions that scholars of democratic theory address is how to best allocate and balance power across the different structures within a government. Historically, many theorists and philosophers have postulated that structures with separation of power are more effective at resisting tyrannical rule. Though researchers have established the effects of an imbalance of power between two branches of government, no study has attempted to systematically account for the relative balance of power among all three branches working in tandem or develop empirical metrics to this end. In this study, I theorize that designing separate branches of government that are equally strong strengthens conflicts across institutions, which ultimately leads to more robust protections against tyranny. I evaluate this model quantitatively by developing and introducing a new measure, the Separate Powers Index (SPI). My SPI assesses the balance of power between the three branches of government as postulated in a sample of 130 of the world’s constitutions. Using multivariate regression methods, I compare the SPI with a cross-national index of free expression in a cross-sectional analysis during the year 2008, I can systematically examine whether there is a relationship between structural provisions of institutions that distribute power and their outcomes to protect their citizens. In addition to providing a novel measure of tripartite power balance in national constitutions, the result of this study has a large impact on all scholars of constitutionalism and civil liberties.

Scholars recognize that politicians’ perceptions of their electability influence their home style, or the way in which they present themselves to their constituents. Marginality, or the proportion of a politician’s co-partisans in the electorate, is common indicator of electability. However, marginality fails to capture how polarization of the electorate augments politicians’ vulnerability. This study introduces a new indicator of electability that captures statewide polarization in the electorate. Building off the finding that more marginal Senators emphasize support for appropriations to build non-partisan support, I expect that Senators in more polarized states will emphasize their support for appropriations after controlling for marginality. Appropriations credit-claiming builds non-partisan support without alienating more partisan voters. I employ multilevel linear regression analysis to examine the relationship between state-level partisan polarization and topic expression in Senate press releases systematically. A positive relationship between partisan polarization and appropriations credit-claiming may reveal a mechanism by which polarization paradoxically minimizes the partisan content of Senators’ home styles.

Although legislative partisanship has traditionally been studied through measures like floor votes or debates, scholars have found that social media also provides a conducive environment for negative and positive displays of party politics. This project codes Tweets from both Washington and Texas State legislators in 2017 as either “partisan” or “neutral” in order to create a proportion for each category and correspondingly identify the extent to which these legislators participate in partisan behavior online. Then, these proportions are compared with an individual legislator’s roll call votes, markers of their general level of polarization, in order to view whether or not they are behaving in a more partisan manner online than their votes would indicate. My paper posits that the unique conditions of social media cause legislators to behave differently, resulting in a comprehensive increase in legislator partisanship. This research holds importance in future studies by shedding light on how social media is used by those in our state governments, especially as it pertains to their party posturing online.

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

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

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

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

Mapping is a powerful tool to visualize space and data. However, working with historical data and maps is problematic as spaces change across time. Given this, the scope of this research is to create visual maps using GIS software that accurately represents the Baghdad-Basrah region of the Ottoman Empire in the late nineteenth century. Our key research question is: how can cholera data from primary sources in the nineteenth century be visualized through mapping? We gathered the data for this research from the diaries of Joseph Svoboda, a resident of the region who traveled frequently up and down the river system and recorded information about numbers of deaths and quarantines from cholera in the cities he passed. The method we used for mapping the data includes a comprehensive reading of the diaries currently being transcribed to assess which information is important for mapping purposes, including the location and time period of the event in question. We mapped the data using Geographic Information Systems (GIS), a software that is used to analyze and represent data through maps, to geocode locations and include cities and other features as they appeared in the nineteenth century. Anticipated results include an interactive choropleth and dot maps that are accurate to the specific time period and show deaths from cholera in specific locations over time. One key implication for further work would be a standardized way to map disease data from primary sources and to increase the number of individuals who use data visualization with historical data. Additionally, our mapped data can be used for other types of GIS analysis that may be of interest to those studying the history of cholera or historic epidemics.

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

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

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

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

The Lyman-alpha power spectrum has previously been used to constrain the Universe’s initial conditions and particle constituents (such as the amount and mass of the dark matter) and the temperature of intergalactic gas (which constrains reionization processes). To further improve these constraints, we use another Lyman series transition (Lyman-beta). The Lyman-beta absorption cross-section is lower than that of Lyman-alpha so it probes the intergalactic medium at higher densities where Lyman-alpha features are saturated. Therefore, the Lyman-beta forest allows for a better measurement of the slope of the temperature-density relation, allowing additional constraints on reionization and the subsequent thermal evolution. In this work, we present an analysis of the Lyman-beta power spectrum using the VLT/XSHOOTER XQ-100 Legacy Survey.

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

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

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

Diabetes and cardiovascular disease play a significant role in disease and mortality in the US, especially among underrepresented groups. Lack of physical activity and unhealthy eating can lead to cardiovascular disease (CVD), diabetes, and other adverse health outcomes. This project will utilize community based participatory research to develop a wellness program from American Indians in San Diego County. This will be done through conducting focus groups, and interviews with community members and through conducting surveys on health and wellness. Further, a wellness program will be developed from community feedback. We expect to observe an increase of physical activity, better diet, and higher knowledge about healthy behaviors with the program.

Wildfires play a major role in the structure and composition of landscapes and the general ecology of the Pacific Northwest. The Klamath-Siskiyou eco-region in northern California and southern Oregon has been experiencing an increase in the frequency, scale, and intensity of wildfires in recent years. Understanding the effects of wildfires on small mammal communities is an important, yet understudied, aspect of the response of wildlife to wildfires. In 2014, two wildfires burned areas on and adjacent to a long-term study area of wildlife. We will investigate the effects of these wildfires on the occupancy of small mammals such as Neotoma fuscipes, Glaucomys sabrinus, and Tamiasciuris douglasii, using occupancy analyses of data collected during fall field seasons using track plate stations. The longitudinal data set that we have includes years of data before the fires occurred, allowing us to disentangle any effects of the wildfires from any naturally occurring variation. This research is important in determining what lasting effects these increases in wildfire frequency are going to have on predator-prey dynamics.

Many adults with Autism experience sensory processing sensitivities as a part of their diagnosis. Research shows that 94.4% of adults with Autism report co-occurring sensory abnormalities. These sensitivities can create accessibility challenges for the autistic community, especially for autistic individuals with hypersensitivities. This study will explore how these sensory sensitivities are experienced as barriers to accessing public spaces and the impact that limited access has on quality of life experienced by autistic adults. The author will develop a self-report survey to assess the frequency, diversity, and intensity of these barriers and create a publication which will include the photographs and narratives of the participants experiences of sensory dysregulation as a barrier. The survey and the publication will be reviewed through the process Community-Based Participatory Research (CBPR). Data will be obtained through using photovoice, narratives, and surveys highlighting the subjective experiences that hypersensitive autistic adults encounter in their everyday lives in the public sphere. We anticipate that multiple barriers to access will be reported by participants though we recognize these may differ in form, place, and intensity. The outcome of the proposed study will be used to center the voices of the self-advocating autism community about the barriers they experience daily and to promote policy change to create more sensory friendly public spaces.

 The United States’ participation in “othering” is nothing new. Government policies for centuries, including executive orders, have long targeted minority populations living in or seeking refuge within the U.S. These populations are often the scapegoats in politically turbulent times and are treated as such in order to not deal with greater issues. During World War II, Japanese Americans—including citizens and legal residents—were sent to internment camps not knowing when they would return home. This was the “solution” to war hysteria post-Pearl Harbor. Similarly, current immigrants from non-European populations are targeted by ICE and taken away from their families with no promise of return. Although the rationale is complex, this rhetoric often revolves around jobs and criminality despite any significant statistical back-up. My presentation seeks to compare these two situations: what is currently happening with Latin American and Southeast Asian immigrants in the U.S. to the incarceration of Japanese Americans during WWII. These families, whether nearly 80 years ago or today, have and are being systematically stripped of their livelihood and humanity for the sake of political scapegoating. Through intensive archival research—including collecting historical photographs, first-person accounts, and government propaganda of and against those incarcerated in the Japanese Internment Camps and current U.S. detention centers—, I examine the similarities in these families’ plights, the situations’ causes, and their inevitable long-term impacts. Through this analysis, I seek to interrogate the broader structure of U.S. immigration policies and our place in these events as global citizens. It is only through such analysis that we can began to understand the cyclical nature of rhetoric and trauma and have a chance to stop it.

The focus of this study is to examine the motivation behind organizing conservative and counter-conservative events and the meaning students attribute to their involvement. Furthermore, the study also addresses the extent to which such coordination is related to group influence. In other words, how do participant relations within and outside of their organization shape their decision to organize political events on campus? This study explores how students understand and interpret their actions. Data for this study will be collected by conducting structured interviews with 10 participants (n = 10). The intended population is college students from a Southern California college campus. Half the participants will identify or have identified with a conservative campus organization while the other half with a counter-conservative organization at the time of a campus political event. Convenience and snowball sampling will be used to recruit participants. This methodology follows what sociologist Max Weber (1914) referred to as,“Sociology is a science concerning itself with the interpretive understanding of social action and thereby with a causal explanation of its course and consequences.” An interpretive understanding of the meaning and drive behind the formation of these political events is crucial to developing an explanation for what triggers social action. By studying the dynamics by which the group members interact and interpret one another, we can understand the role of in-group cohesion and out-group bias in politically-related communication. My study aims to contribute to the following 1) increase our knowledge of the motivations and meanings college students place on organizing events with controversial speakers, as well as protesting them, 2) how students weigh the consequences of their actions, especially as it relates to social relations (stigma or approval), campus climate, safety and property damage, and economic costs (e.g. security, police, taxes).

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

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

Many genes are associated with microcephaly, a condition characterized by a small head size. Through exome-sequencing, we identified de novo missense mutations in an actin polymerization gene, ARPC4, in four individuals with microcephaly, mild developmental delay, and mild intellectual disability. ARPC4 is involved in actin filament formation. Actin is an essential component of the cell’s cytoskeleton that gives the cell its structure and aids in cell movement and division. The goal of this research project is to understand the molecular mechanisms that lead to the disease phenotype observed in these patients. I began by using CADD, a measurement used to predict the deleteriousness of single nucleotide variants. The mutations identified in the patients were located in highly conserved loci, indicating they might be pathogenic. To provide further evidence of the pathogenicity of the ARPC4 variants, we were interested in determining the functional effect these variants have on actin polymerization – specifically, the role of ARPC4 in this mechanism. I established fibroblast cell lines from two patients with the same ARPC4 mutation. I performed immunofluorescence staining for actin to quantify the amount of actin present in the patients and control cell lines. Preliminary data from this experiment suggests that there is greater abundance of actin filaments in the control sample compared to the patients’ cells. To observe the effect of decreased actin abundance on cell migration, I executed a scratch migration assay. The results from this study elucidate the impact of ARPC4 in actin polymerization, and establish actin deficiency as a clinically recognizable cause of microcephaly.

Human T-Cell Leukemia Virus type 1 (HTLV-I), a retrovirus that currently 10 to 20 million people are infected with, has been shown to be associated with the Adult T-cell Leukemia (ATLL) and HTLV-associated myelopathy-tropical spastic paraparesis (HAM/TSP). 1 After an extended period of time, 3-5% of those infected with HTLV-1 will develop ATLL or HAM/TSP. The viral Tax protein is thought to have involvement in the development of these diseases. The Tax protein inhibits telomerase and topoisomerase-I which in turn inhibits the process of DNA repair. Tax prevents apoptosis and does not allow cells to enter the G0 phase of mitosis. The oncogenic properties of Tax are correlated to the interaction of Tax with host cellular proteins which are strongly influenced by the large amount of Tax protein made from the integrated provirus. We are using viral promoter magnetic pull-downs to investigate HTLV viral-host interactions involving minimal -306bp viral promoter containing vCRE enhancer sites and Tax-recruited host proteins. Experiments have used electrophoresis to determine whether or not the magnetic beads bind the promoter DNA. Absolute quantitation is necessary for consistency and reproducibility in analysis of proteins suspected of recruitment to the promoter.

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

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

The nucleus is the information center of the cell, acting as a hub for DNA storage, regulation, and replication. Therefore, transport of molecules into and out of the nucleus is vital for proper biological functioning. This transport is tightly regulated via the nuclear membrane, and a collection of proteins called nuclear pore proteins that interact with molecular signals. These signals allow molecules that cannot passively diffuse through the nuclear membrane (typically greater than 60 kD) to be shuttled into or out of the nucleus via a variety of pathways. Like all biological pathways, this process can be disrupted and lead to phenotypic abnormalities. Our lab identified two siblings with biallelic variants in NUP188, a known nuclear pore protein; we identified four additional cases in three families through collaborators. Clinical features include brain abnormalities with thin corpus callosum, progressive microcephaly, severely delayed myelination; congenital cataracts; mild dysmorphic features; and hypoventilation leading to death in infancy. In order to better understand our patients’ phenotype, we are investigating nuclear import pathways as a potential mechanism of disease. Using green fluorescent protein (GFP), we can directly visualize protein localization in living cells, without the use of additional stains such as immunohistochemistry. Based on size restriction of the nuclear pore, we used a vector construct with three repeats of GFP and our nuclear localization signal (NLS). Specifically, we are investigating four main NLS pathways: Importin α+β (SV40 NLS), Kap β2 (hnRNP NLS), Importin β (CREB NLS), and no NLS. We have been able to successfully create a viral vector for each NLS. Next steps include optimizing expression in patient cell lines. This approach will allow us to quantify and visualize discrepancies between patient and control localization patterns, leading to better understanding of causes of patient phenotype and potential novel therapies.

The ability to derive information through automated scanning of personal documents has significant economic and societal value, stemming from applications in surveillance and digital forensics, e-commerce, tailored advertising, recommender systems, human resource management, mental health care, and more. Giving applications access to one’s personal text messages and e-mails can easily lead to (un)intentional privacy violations. We have developed and implemented cryptographic protocols to scan personal documents in a privacy-preserving manner, using techniques from Machine Learning (ML) and Secure Multiparty Computation (SMC). In a typical scenario of interest for our research, there are two parties, nick-named Alice and Bob. Bob has a trained ML model that can automatically classify texts like e-mails, for instance inferring whether the author is depressed, suicidal, a terrorist threat, or whether the e-mail is a spam message. Our SMC based protocols allow for the classification of a personal text written by Alice with Bob’s ML model in such a way that Bob does not learn anything about Alice’s text (other than the class label resulting from the classification) and Alice does not learn anything about Bob’s model. We demo the cryptographic protocols in an application for privacy-preserving detection of hate speech against women and immigrants in text messages, built on top of the SMC framework Lynx developed at UW. In this use case, Bob has a boosted decision tree model that flags texts as hateful based on the occurrence of particular words. We show that Bob can label Alice’s texts as hateful or not without learning which words occur in Alice’s texts, and Alice does not learn which words are in Bob’s hate speech lexicon, no how these words are used in the classification process.

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

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

Augmented reality (AR) for the consumer market is gaining momentum and public attention. Besides smartphone platforms, early-stage head-mounted displays such as the Microsoft HoloLens are now publicly available. Many compelling uses of these AR technologies are multi-user: for instance, in-person collaborative tools, multiplayer gaming, and telepresence. Although multi-user AR technologies enable new forms of interaction, they also raise new security and privacy challenges, not only from untrusted applications but also from other users’ malicious or unthinking behavior. It is imperative that these challenges be addressed while the technology is still new and highly malleable. In this work, I explore emerging challenges in securing multi-user AR content sharing from user-to-user threats. I argue that supporting secure and private AR content sharing when users can augment each other’s reality requires careful consideration of AR’s tight integration with the physical world. I systematize design goals for security and functionality that an AR content sharing module should support, and I design and prototype an application-level module for the HoloLens that meets these goals. By evaluating my module against representative application case studies, I show that it meets desired security and functionality goals flexibly across a range of use cases. I further demonstrate that applications’ content sharing needs can be achieved in relatively few lines of code and with low performance overhead. I am currently converting my research prototype into an open-source toolkit so that developers can address these challenges in practice. This work opens up directions for future research on supporting developers in effectively addressing these issues in practice, including making recommendations on how these underlying paradigms should manifest in user interface design. By building foundations for secure multi-user AR content sharing, my work takes steps toward allowing AR to securely reach its full potential.

Maternal Health is an important topic, especially in developing countries, because of the significant inequality in access to healthcare in places such as the Ivory Coast (West Africa). This presentation presents a one-month research conducted in the Ivory Coast, with the aim of analyzing how sociocultural, political, and historical factors affect maternal health i.e. quality and access to care. To conduct this research the history of the country dating from its independence to his present day were assessed. Secondly, sociocultural factors such as one’s culture norms were also covered by talking to hospital staff and local women about their experiences. Additionally, the political state of the country such as the civil wars that it has endured were discussed. All the data for this project were gathered using ethnographic field research methods such as site visits and key informant interviews with two politicians, two physicians and locals. In order to provide a comparative analysis, the research was conducted in two distinct locations, Korhogo and Abidjan which have differing economic status and government help. Interviews were audio recorded, transcribed, and analyzed to look for common themes around barriers to maternal health. Site visit notes were transcribed and analyzed, and pictures were documented for further descriptive analysis. Key themes from analysis include high healthcare costs and culture barriers as negative impacts on maternal health. The study revealed that when treating a patient, it is important to take into consideration their culture norms and it will also be beneficial to have free care for pregnant women which will in turn hopefully encourage them to seek care. We hope to conduct further research, which allows governments and people to recognize that community health is crucial in healthcare and that breaking the inequitably cycle in access to healthcare is essential.

With the global refugee crisis, resettlement agencies do important work to insure successful refugee resettlement. Previous research suggests that some refugee families struggle with segmented assimilation, which is when a child assimilates faster than their parents, disassociating from their culture of origin, creating conflict with their parents. Building on this research, this qualitative ethnographic study investigated segmented assimilation concern among families through semi-structured interviewing. Refugee families and childcare providers for refugee children were interviewed to understand the needs of families in managing segmented assimilation and to gain insight from childcare providers serving those families. While it was hypothesized that families would be concerned about segmented assimilation, the recently arrived families in this study were not experiencing segmented assimilation. This is due to a lack of resources which maintains daily stresses of supporting themselves. The resettlement agency in the city where interviews were conducted solely provided housing and employment placement services, meaning that refugees had no resources for civic engagement, education, community building, and other necessary programs. While families are now physically safe, in terms of not being in a war zone or crowded refugee camp, their lives are still extremely strained, in part due to the lack of adjustment resources. Many families work long hours simply to have enough money to live in their apartment and feed their children. The lack of resources given to resettlement agencies, especially in the recent years under the Trump administration, have profound impacts on the lives of hundreds of refugees that are being resettled, and the thousands more that have not been allowed into the United States due to restrictions under the Trump administration. After refugees move to America, it takes time for them to establish their lives in their host country, and the lack of resources allocated to refugee resettlement impedes this process.

Pottery is ubiquitous across all levels of civilization, with distinct styles and patterns that can be used to give insight into the nation from which it was crafted. Looking deeper than what the eye can see, the mineral and chemical components can also reveal origins by mapping the components of the pottery piece to likely locations of where that mineral or element is commonly found. Ceramics may have many layers of interest, including the glaze, the slip, and the main body, that can be studied with minimal invasion and destruction of the artifact. Holistic analysis and characterization of these historical pieces requires a multidisciplinary perspective, incorporating fields such as materials science, history, and archaeology. The methods involved in this experiment include x-ray fluorescence (XRF) and scanning electron microscopy (SEM) in order to determine chemical composition and microstructure, respectively, of artifacts (circa 8000 BCE to 1250 CE) found in modern-day Iran. However, not all artifacts are made in the area they are found, hence the need to establish provenance. Preliminary XRF data shows certain samples may contain seashells, owing to their calcium components. This suggests that provenance could in fact be from Iran because Iran is not landlocked. In this we see that provenance is established in part by determining the composition of the artifact and where those materials most likely came from. In attempting to trace the origins of these particular artifacts, a protocol is also developed for mapping other samples and ensuring repeatability while doing so.

 Developmental and epileptic encephalopathies (DEEs) are an early-onset form of epilepsy characterized by intractable seizures and severe cognitive and developmental impairment. While most genetic variants that cause DEE reside in the coding regions of genes, splice-site variants can also be pathogenic. Splice-site variants are changes in the DNA close to, or on, the exon-intron boundary, which can cause aberrant splicing, resulting in exon exclusion or intron inclusion within spliced mRNA, generating a protein that is non-functional, partially functional, or aberrantly expressed. Aberrant splicing can have pathogenic consequences, but predicting which variants near splice-sites will have an effect on splicing is difficult. I am studying three potential splice-site variants in three genes associated with DEE: SYNGAP1, SCN1B, and WWOX. I used RNA extracted from fibroblasts from three DEE patients, each with one of these variants, to confirm whether the splice-site variants cause aberrant splicing and what the predicted consequences of this aberrant splicing is on the protein. I have been able to discover the effects of the variants on splicing in WWOX and SYNGAP1. In SYNGAP1, a synonymous variant at the exon-intron junction caused an exon 4 deletion, resulting in a severely truncated protein (SYNGAP1:p.Glu120Alafs*20). In WWOX, a duplication which included exon 5 resulted in a transcript with the inclusion of two copies of exon 5, leading to a frameshift mutation and predicted truncated protein (WWOX:p.His173Glyfs*13). We are still investigating the effects of the intronic variant in SCN1B, which appears to decrease expression of the gene. We are using nonsense-mediated decay inhibitors in order to better understand the mechanism through which this decreased expression occurs. This research could potentially improve the care of these patients by providing genetic evidence of the causes of DEE, which can be the basis for advancing better treatments.

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

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

Developmental and Epileptic Encephalopathies (DEEs) are a group of severe epilepsy disorders in children and infants characterized by prominent EEG (electroencephalography) abnormalities that disrupt brain function leading to cognitive decline. Identifying genetic causes of DEE is a key step to help researchers develop and personalize medical treatments for affected patients. Approximately 5% of DEE cases are caused by a copy number variation (CNV), where a region of DNA involving a disease gene has been duplicated or deleted. Historically, this type of mutation has been difficult to detect using sequence data. To address this, I have written a multi-step algorithm that analyzes smMIP (single molecule molecular inversion probe) targeted DNA resequencing data for known DEE genes to identify CNVs in patients’ DNA that are potentially disease causing. I have run this algorithm on the large collection of smMIP data for 1158 DEE patients available in the Mefford Lab and identified several potential CNVs. Among these, three CNVs ranging in size from 250,000-2,790,000 base pairs, each involving a DEE gene - GNB1, GRIA2, and UHRF1BP1L - were validated by a second method, array CGH, the current gold standard for CNV validation. To date, the validation rate of high-confidence CNV candidates is 50% or higher. Currently I am expanding the algorithm’s functionality to include the ability to selectively search for single-exon CNVs, which are as small as 500 base pairs, are more challenging to detect, have largely been missed by all CNV detection methods, but could still be pathogenic. To do this, I am leveraging the power of intersecting duplicate smMIP datasets to improve the sensitivity of single-exon CNV detection. As any disruption of a pathogenic DEE gene could be disease causing, inclusion of these smaller CNVs will increase our ability to solve DEE cases and improve patient care.

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

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

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

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

The focus of this research is on Spanish heritage language (HL) and second language (L2) learners. An HL learner is a student who comes from a house where Spanish is spoken, but still; needs Spanish classes to master certain aspects of his/her first language. Sometimes English is also spoken at home: e.g., one parent speaks Spanish and the other English, or the student speaks Spanish with his/her parents but English with his/her siblings. On the other hand, an L2 learner is a student who is learning Spanish in a classroom setting. His/her first language may be English or any language other than Spanish. Between these two groups of students, there are important differences when it comes to learning Spanish, for example, L2 students are more knowledgeable about Spanish grammar rules and academic vocabulary. On the other hand, HL students have more fluency and much more knowledge about the culture. The focus of this research is on how the interaction between an HL and an L2 learner in a classroom impacts learning for both students. My role in this research is to transcribe the audio-recorded conversations between two L2 students and to compare these conversations with those between the same L2 students and an HL learner. I will analyze how the students collaborate and how they work to find the solution to any challenge they face that is associated with vocabulary, grammar or orthography. I hypothesize that pairing an L2 and an HL student will generate more interaction since each student offers different sources of knowledge. Pairing an L2 student with an HL student creates a diversity of ideas that I expect to increase learning. This analysis will help us to better understand how to create a more efficient learning environment, for both HL and L2 students, within mixed classrooms.

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

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

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

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

Sarcopenia, or age-related of loss of muscle mass and function, is associated with a decline in quality of life for elderly populations and few effective treatment options. Sarcopenia is linked to mitochondrial dysfunction and elevated mitochondrial oxidant production. We are investigating the role of mitochondrial oxidative stress in sarcopenia using a mitochondrial targeted therapeutic and a mouse model of accelerated sarcopenia. SS-31 is a mitochondrial targeted peptide that associates with cardiolipin, decreases oxidant production, and increases ATP production. Superoxide dismutase 1 knockout (SOD1KO) mice lack superoxide dismutase 1 (an enzyme that converts the oxidant superoxide into hydrogen peroxide and molecular oxygen) resulting in an accelerated sarcopenia phenotype. We are testing whether treatment with SS-31 preserves muscle function in the SOD1KO mice. We hypothesize that improving mitochondrial function with SS-31 treatment will delay the decline in muscle function in the SOD1KO mice. To test this, we are administering SS-31 to SOD1KO mice through surgically-inserted osmotic pumps for 8 weeks between 3 and 5 months of age (the published timeframe for the onset of skeletal muscle decline in SOD1KO mice) and performing in vivo muscle function measurements of the gastrocnemius before pump insertion and monthly after pump insertion for 3 months. We compare muscle functional measurements with histological and biochemical analyses of mouse tissue samples upon euthanasia and determine skeletal muscle fiber type, metabolite and protein concentrations, and muscle fiber respiration and oxidant production. We expect SOD1KO mice with SS-31 to have a lower rate of decline in muscle force production and increased fatigue resistance over time, higher max ATP production, and decreased oxidative stress. The effect of SS-31 on muscle function, mitochondrial quality, and redox homeostasis has exciting potential as a translational therapeutic treatment for human sarcopenia.

Exposure to particulate matter (PM) is associated with adverse health effects including asthma, cardiopulmonary diseases, and lung cancer. These adverse health effects are responsible for the premature death of 7 million people worldwide each year. To reduce the consequences of air pollution, real-time individual exposure data is essential for health risk assessment and tailored intervention strategies. Portability and cost are significant barriers for consistent and personalized tracking. Unfortunately, the only accurate data regarding levels and types of air pollutants come from static monitoring stations that do not allow personalized analysis. Aero-Spec was developed to provide real-time analysis of air quality particles while also delivering a compact and low-cost approach. It is a wearable exposure monitor that combines real-time measurements of PM using an optical particle sizer (OPS). The OPS sensor allows for individual particle sizing and error reduction associated with the particles’ optical properties. Personal PM exposure data is provided to the user through a smartphone application such that intervention actions could be triggered given the detection of poor air quality. For personalized analysis, indoor localization is used over the global positioning system (GPS) for a more accurate and localized diagnosis. Aero-Spec utilizes this network technology to track the wearable sensors and report back localized air particle data. In conclusion, using a portable and low-cost approach to real-time air particle analysis, Aero-Spec delivers an effective and personalized solution for air quality monitoring. Recently, in a movement to monitor their employees’ exposure to particle data in real-time, Boeing has collaborated with the Sensors, Energy, and Automation Laboratory (SEAL) for further research.

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

In Zea mays (maize), MEDIATOR OF PARAMUTATION 1 (MOP1) is involved in paramutation and epigenetic regulation of gene expression. MOP1 in an RNA-dependent RNA polymerase that functions as part of the RNA-directed DNA methylation (RdDM) pathway, by producing double-stranded RNA molecules that are further processed into small interfering RNAs (siRNAs). These siRNAs are able to trigger DNA methylation which can decrease or silence gene expression. The MOP1-FLAG transgene was created by overexpressing the mop1 gene with the FLAG epitope tag. As a consequence of using agrobacterium-mediated transformation, the chromosomal location of the MOP1-FLAG transgene is unknown. To identify the sequences flanking the transgene, we used an adapter ligation-mediated PCR and cloning technique, as described by O’Malley. To do so, we first digested the MOP1-FLAG DNA with restriction enzymes designed to cut the DNA in specific locations along the genome. We then ligated adapters onto the DNA fragments. Through PCR using gene-specific and adapter-specific primers, we were then able to amplify the fragments that contain MOP1-FLAG and the surrounding genomic sequence, clone and then sequence them. We used the recovered flanking sequence to BLAST search the maize genome in order to identify the maize chromosome that the MOP1-FLAG transgene is on. Chromosomal mapping of the MOP1-FLAG transgene is useful to distinguish between the endogenous mop1 gene in ongoing complementation and chromatin immunoprecipitation (ChIP) experiments.

With our rapidly changing climate, plant communities are predicted to experience more variable conditions. Climate change predicts that there will be longer periods of drought followed by heavy rainfall at unpredictable intervals. With this, plants may experience selective pressures to combat the stress that come with these variable conditions, which ultimately may influence plant evolution. Phenotypic plasticity and epigenetic modification are two factors we believe may strongly influence the adaptative ability of plants. I predict that these variable conditions will promote phenotypic plasticity and epigenetic “memory” (where plants’ stressful experience can be inherited from parent to offspring), and potentially help offspring plants cope with the same abiotic stress. We have implemented an experimental design mimicking the predicted variable conditions of climate change. For two generations, we exposed plants to either drought or non-drought conditions. Then in the third generation, we took seeds from parents that experienced those conditions and exposed them to either drought, non-drought, or variable watering in a cross-replicated design. I hypothesize that there is inherited epigenetic memory, and that the different treatment groups will pass memory that will benefits plants if the offspring was exposed to the same condition its parent experienced.

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

Food contamination outbreaks have become increasingly prevalent in the United States. Food processing companies often do not have sufficient resources to accurately monitor pathogenic bacteria and biofilms on their food preparation surfaces. Unfortunately, consumers assume that the food is safe because it is packaged and ‘screened’ but invisible bacterial contamination may be present. This creates an opportunity to improve methods for detecting pathogenic bacteria in food handling and processing environments. BioVizia provides an alternative solution for detecting pathogenic bacteria on food processing surfaces that is efficient yet effective. We have developed a device that uses an LED to excite a fluorescent dye. Fluorescein is an FDA approved dye that exhibits pH dependent spectral properties. When viable pathogenic bacteria metabolize sugar, they produce acidic byproducts. Therefore an optical system using fluorescein as a pH disclosing agent may provide sufficient sensitivity for detecting bacterial contamination. Our optical system records the fluorescein emission spectra which contains two overlapping, pH dependent spectral features. The fractional amount of the two contributing bands are calculated using a spectral unmixing algorithm. A calibration with standardized pH buffers yields a linear relationship between pH and the fractional amount of each band. This noncontact optical pH measurement method has been successfully employed in an in vivo dental study to measure the pH drop produced by dental plaque following a sucrose rinse. We seek to demonstrate that BioVizia can make the detection of pathogenic bacteria and biofilms on food preparation surfaces fast and quantitative.

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

The damascene process is an additive manufacturing technique commonly used in the nanofabrication industry to produce semiconductor devices. This process utilizes deposition and patterning of successive layers to produce interconnected copper patterns separated by interlayer dielectric. The goal of this project was to implement the damascene process to develop and refine methods at the Washington Nanofabrication Facility (WNF) for manufacturing multi-layer devices. For our purposes, we constructed an integrated passive device (IPD) that contains capacitors, resistors, and inductors. We utilized basic nanofabrication tools in our damascene process including deposition, photolithography, etching, electroplating, metrology, and polishing tools. In fabricating this method at the WNF, our main objective was to produce a highly repeatable device with structural integrity. The main challenges accompanied with this involved generating a successful etch on all three layers of the IPD and optimizing polishing conditions. Cross sections of the final product were analyzed in order to demonstrate that the layout expected from the process was achieved. The procedure we developed can be applied to future multi-layer damascene processes at the WNF. Multi-layer devices are significant in the semiconductor industry as they allow for high packing density and an increased variety of circuit configurations in a compact device.

The Zea mays (maize) crop is essential to global agriculture and food security, and is also vital to the US economy. Like many crop plants, maize is often subjected to extreme environmental stresses, such as drought, extreme cold and high salinity, that negatively impact crop yield. Therefore, it is important to characterize the molecular (epigenetic) changes that occur to a gene under environmental stress conditions in order to manipulate these responses to improve crop yield under stress. We are interested in characterizing the epigenetic regulation of stress-responsive transcription factors under normal (control) and abiotic stress (drought) conditions in maize seedlings. Using bisulfite conversion of genomic DNA, we previously identified that the Zea mays basic transcription factor 3 (ZmBTF3) gene displays some variations in methylation patterns in parts of the gene promoter between the two treatments. To confirm these results, we used an alternative method: a methylation sensitive restriction digest technique, which uses methylation sensitive restriction enzymes (MSREs) that cut DNA molecules at precise locations and are sensitive to DNA methylation. Our results show some treatment (control vs. drought) and restriction enzyme (sequence/context) specific methylation patterns. Using these two independent techniques, we identify stress-responsive epigenetic variations (DNA methylation) in the promoter region of the ZmBTF3 gene, previously uncharacterized in maize. Ongoing research includes (i) characterizing the sequence contexts of these methylation patterns between the two treatments, (ii) determining if the observed DNA methylation changes correlate with transcription of the ZmBTF3 gene, and (iii) characterizing the drought response phenotype in maize plants with a mutation in the ZmBTF3 gene. This study will help us gain a better understanding of how the BTF3 gene in maize is regulated through epigenetic modifications.

Atomic Layer Deposition (ALD) is a process whereby thin films of a material, ranging from dielectric materials to metals, are deposited onto a substrate. ALD reactions operate using two vapor phase chemical precursors that react with the substrate material sequentially one at a time, slowly forming the thin film. Because of the sequential nature of ALD, the process is self-limiting and offers exceptional control of thin film thicknesses, film composition, and high conformity on high aspect ratio features, such as trenches and sidewalls, making ALD an extremely useful process for the fabrication of semiconductor devices. The purpose of this project was to develop processes and refine process parameters for thin film deposition using an industry grade ALD machine. Thin films were deposited onto silicon substrates with etched features. The films were then examined and characterized using ellipsometry and sidewall conformity was measured using a scanning electron microscope.  This data was used to refine processes and parameters that were then employed by research staff and industry users in the fabrication of semicondctor devices.  Overall, this data can be employed by the semiconductor industry to better understand this process and utilize it to manufactor silicon devies with  greater uniformity and efficiency.

 RNA-directed DNA methylation (RdDM) is an epigenetic pathway that induces transcriptional gene silencing through DNA methylation of target genes. The Zea mays (maize) RMR1 protein has an important role in the RdDM pathway as it functions to assist the process of making double stranded RNAs, required for progression of the pathway. Abscisic acid (ABA) is a plant hormone that accumulates under abiotic stress, and can inhibit seed germination. We determine if the RMR1 protein is involved in epigenetic regulation under abiotic stress by measuring maize phenotype and identifying transcriptional changes in ABA treated (vs. control) rmr1-1 mutants. To determine the effect of the rmr1-1 mutation on maize phenotype, we are measuring shoot length, primary root length and additional roots in maize germinating seeds from a segregating family. The genotype of the individual seeds is determined by amplifying the region of the rmr1 gene that includes the point mutation (C to T) that is on the 4th exon of the gene, followed by Sanger sequencing. The genotype is then associated with the measured phenotype. We are also interested in determining if ABA-induced transcriptional factors are differently expressed in rmr1 mutant compared to wildtype under ABA, and this will be measured by quantitative reverse transcription and PRC(qRT-PCR). This research is in progress and results will be presented. Maize and other crop plants are often negatively affected by abiotic stress, therefore, understanding how epigenetic pathways are involved in these responses is important to agricultural productivity.

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

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

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

Water is the substance that exists everywhere in our lives ranging from drinking water to the blood in the body. It is well known that there are 3 phases of water: gas, liquid and solid. Yet, in Dr. Gerald Pollack’s lab, we conduct researches on the Exclusion Zone (EZ) water, which we term as the ‘Fourth Phase of Water.’ Dr. Pollack’s lab centers largely on the identification of EZ water and many applications in nature and technology. Among the natural applications, since EZ water fills out cells, and they cannot function without enough EZ water, the lab emphasizes on the role of EZ water in human health, including cell biology. Dr. Pollack’s lab conducts the research that is uncovering the nature’s hidden secret and the tremendous potential of EZ water to be applied to different bioengineering products. I am currently conducting a project on how Wi-Fi impacts EZ water as an external source of disturbances. Humans are exposed to Wi-Fi signals constantly in our everyday lives. As human body cells are filled with EZ water, we predict the Wi-Fi signals could alter our bodily functions through changes in EZ water properties such as amount of EZ water. As EZ water can be built around hydrophilic substances, Nafion tube, hydrophilic tube is used to build EZ water, and then I can measure the amount of EZ water by measuring the length of EZ water built around the tube in 2D picture. For this project, we compare the difference in the amount of EZ water built with and without presence of Wi-Fi. We currently have preliminary results that Wi-Fi decreases amount of EZ water. As a further step in the future, I hope to research on different bioengineering fields to reduce the effect of Wi-Fi on EZ water for further health care.

This work describes an inexpensive and accurate gesture control implementation designed for an industrial setting. Sensing hand movements and being able to remotely operate devices without use of a tangible control can be useful, particularly in manufacturing applications where other methods of communication may not be available. One gesture recognition method is to use a camera or set of cameras to capture the motions of the user. However, this method imposes line-of-sight workspace constraints and is sensitive to environmental factors, such as consistent lighting conditions. My approach is to use an instrumented glove that detects the amount of bend in specific joints and sends those positions to a central processor that is programmed to recognize control gestures. Similar glove controllers are available but are either not well suited to an industrial setting because the sensors are vulnerable to metal dust and debris, or are not accurate enough to identify commands quickly and consistently. My version has custom sensors exactly fitted to this application and aims to have all sensors sealed and self contained to protect against contamination. This system is able to capture high resolution movement from the wearer and either save that data for machine training or send it immediately to be acted on. Going forward, onboard capabilities such as local gesture recognition will be added, as well as allowing the user to add custom gestures suited to their particular application.

Despite possessing only one photopigment in its retina, a feature which should render an animal colorblind, the octopus, like other cephalopods, possesses an unrivaled capacity to camouflage itself with its surroundings. A recent theory suggests that cephalopods discriminate color in their environment through exaggerated chromatic aberrations, or the focusing of different wavelenths of light at different points behind a lens, caused by morphological changes in the eye. By monitoring the blurring of different wavelengths of light upon the retina from the visual field in response to the shape of the pupil, a cephalopod can still perceive color with only one photopigment. We test this theory using conditioning to a two-toned visual stimulus and its two differently-colored halves, to look at whether strobing between the two differently colored stimuli evokes the same response as that paired to the combined stimulus or one of its halves. Evoking the response of the combined stimulus would suggest that they can see the two differently colored halves simultaneously, and that a morphological change is not needed to see two different wavelengths of light. This would present a model for color perception with one photopigment that could be explored in various other vertebrates and invertebrates previously thought to be colorblind.

Despite their sophisticated visual system, convergent and comparable in complexity to that of vertebrates, Octopus rubescens is largely nocturnal and forages mostly at night. Without visual information, their primary means of gathering information from the environment is through the sophisticated chemotactile sensory system within their arms. Octopuses blinded from lesions to their optic nerves have been observed relying on chemotactile perception of their environment with their arms fully extended to maximize their sensory range. Such behavioral profiles optimizing the acquisition of one sensory modality in the absence of another would be critical for navigating and monitoring changes within their environment. Our intention is to characterize how Octopus rubescens modifies its chemotactile range after an acclimation period of either light or darkness, simulating a natural 24 hour light cycle, and then a rapid change to the opposite lighting condition. Using 3d tracking cameras we will be able to quantify the change in the range of arm extension and overall posture that accompanies locomotion during light and dark conditions.

Fossil Fuels are associated with contemporary energy crises and climate change. The combustion of fossil fuels is leading to increased greenhouse gas emissions, which in turn have increased the overall earth’s temperatures and is predicted to grow at an alarming rate. Fuel cells are alternative, sustainable sources of energy that uses hydrogen (or hydrogen-rich fuel) and oxygen to generate electricity through electrochemical processes. I conducted a survey, focused on Bellevue College’s (BC) Chemistry Department, that indicated broad support for a simple hydrogen proton exchange membrane (PEM) fuel cell lab to be incorporated into the introductory chemistry curriculum. I will design a lab that will spark student interest in sustainability and expose students to real-world electrochemistry applications while addressing electrochemical, thermodynamic, transport phenomena, and clean energy concepts. The educational goals of this lab are to promote a deeper conceptual understanding of electrochemistry, to improve quantitative reasoning, and to improve explanations of observed scientific phenomena. I collaborated with BC’s Chemistry Department to determine learning outcomes and a systematic process to quantifiably assess fuel cell labs from other institutions. This information was used to design an effective lab and lesson plan surrounding fuel cells. Four fuel cell labs were evaluated: (1) A pre-constructed Hydrogen PEM Fuel Cell from Horizon Fuel Cell Technologies (2) A microbial fuel cell, (3) A fuel cell using platinum electrodes that is bathed in an acid solution (4) A fuel cell using graphite electrodes that is immersed in an acid solution. This research produced an economical and introspective laboratory experience that utilized basic laboratory equipment and materials. The results were presented in an engineering framework that details how aspects of the lab promote critical thinking and engagement, addresses learning objectives, and was cost-effective.

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

Sleep problems are prominent in adolescence and most commonly include short sleep duration, poor sleep quality, and insomnia symptoms. These problems are even more pronounced in youth with headache, with research finding that poor sleep contributes to increased headaches and disability. It is important to screen for insomnia in order to accurately diagnose and treat this disorder. However, there is currently no brief, adolescent-focused measure of insomnia that would allow for a high level of accuracy in screening and diagnosis that is relevant for youth with headache. A recently developed screening tool, the Adolescent Insomnia Questionnaire (AIQ), appears to be a valid measure of insomnia in adolescents with chronic pain, diagnosed sleep problems, and in the general community. This study aims to extend validation of the AIQ to children and adolescents with headache from clinical and community settings. 169 adolescents (ages 12-18) were enrolled and completed the AIQ and the Adolescent Sleep Wake Scale (ASWS), a measure of sleep quality, to determine the validity of the AIQ as an insomnia screening tool for youth with headache. Reliability, or internal consistency, of the items in the questionnaire was tested by computing Cronbach’s Alpha. The correlation between the AIQ and ASWS was high (0.736), indicating high validity of the AIQ as an insomnia screening tool for youth with headache. Cronbach’s Alpha was 0.892, which indicates high internal consistency of the AIQ. Based on these results, the AIQ appears to be a valid and reliable tool in the screening and diagnosis of insomnia in adolescents with chronic headache. Further research should continue to focus on insomnia screening within specific adolescent populations at high risk for insomnia, and the development of effective treatments tailored to these populations.

Through mapping the complexities of spatial inequality, I examined the geographic differences in economic and socio-cultural inequality across the state of Indiana. I grew up in Indianapolis, Indiana in an upper-middle class neighborhood that undoubtedly limited my ability to see inequality. Examining inequality in my home state provided me with a deeper understanding of the gap between rich and poor within the state, how Indiana fits into the growing wealth gap in the United States, and how income inequality further impacts access to education, housing, and healthcare. I collected data from the US Census Bureau for Indiana and Indianapolis, as well as the three richest and poorest cities in the state, St. John, Zionsville, Carmel, Gary, East Chicago, and Muncie. Across the state and the seven cities studied, I measured educational attainment, employment status, health insurance coverage, housing costs, and income in the past 12 months. In Indiana, less than 25% of the population over 25 has a Bachelor’s degree. Rates of health insurance coverage vary greatly across the cities studied, but are fairly consistent across racial lines within cities. Income distribution varies drastically across the state, and by race across the seven cities in this study; however, single mothers, regardless of their race or ethnicity, are far more likely to be impoverished compared to the average in each city. In the three richest cities, populations are almost entirely white, while populations in the three poorest cities are almost entirely African American. Economic differences are not the only indicator of inequality in Indiana; socio-cultural differences also underlie many aspects of poverty and inequality. Mapping how inequality varies in terms of race, gender, and location provided a stronger sense of how geography affects the distribution of wealth and resources, and who is impacted the most.

The ability to respond to physical stress can be useful in gauging resilience to aging. Vaccine inoculation is an immune stress that triggers an easily quantifiable antibody response. This study was designed to identify antibody response patterns to a clinically relevant pneumococcal vaccine in mice, in order to show an association with resistance to age-related decline. Twenty C57BL/6 and twenty CB6F1 male mice in age groups of 8, 16, 24, and 32 months were inoculated with one subcutaneous dose of pneumococcal capsular antigen in adjuvant. Serum was collected 16 days later, diluted 1 to 625, and immunoglobulin G antibody levels were measured by an enzyme-linked immunosorbent assay (ELISA) using 410/490 optical density. All data points were standardized against serum from non-vaccinated mice. There was a clear differentiation between high and low antibody responders in both mouse strains, within the range of antibody levels following inoculation. Interestingly, the high antibody response pattern seen in mice at 8 months of age was also seen in a robust manner in mice at ages 16, 24, and 32 months, as opposed to their low-responding counterparts which actually showed decreasing antibody response patterns in an age-dependent manner. In general, C57BL/6 mice had a more vigorous antibody response than CB6F1 mice. These observations suggest that age impacts the effectiveness of a pneumococcal vaccine in conferring an adaptive immune response, and that certain individual mice can robustly respond regardless of age. This high response pattern can thus be very valuable in determining if a robust antibody response is a resilience factor capable of predicting resistance to age-related decline. The concept is clinically relevant since pneumococcal vaccine, for example Prevnar-13, is routinely used to protect elderly populations, and sera can be readily available to test robustness of antibody responses in relation to aging related parameters.     

Prostate cancer, the second most common cancer in American men, has a relatively low fatality rate – only around 2% of men will actually die of the disease. Prostate cancer has many treatment options. Each of these treatments comes with varying and oftentimes severe symptoms, so choosing a treatment plan is often based on patient preference. Since treatment is based heavily on patient’s values, it is important that patients are well informed about various treatments and related side-effects. This study aims to reveal how a patient’s socioeconomic background influences their decision making processes, with particular focus on how they receive information related to prostate cancer treatments. We review articles and studies from the past 10 years to determine how they address ethics in prostate cancer decision-making. The three framework topics used are: 1) how healthcare providers influence the decision-making process with their ethics and values, 2) how the socioeconomic and cultural factors of a patient informs their decision-making in prostate cancer treatment, and 3) how patients receive information and whether that information is reliable and accurate. In this literature review we find that patients are presented treatment options differently based on their education levels, race, and socioeconomic background, which has potential ethical implications. As this review progresses, we expect to organize these studies to inform how to best provide information to patients of varying cultural backgrounds. We aim to clarify future areas of study towards arriving at ethical consensus in decision-making in prostate cancer. Since decision-making in prostate cancer is a cost-benefit analysis, usually a trade-off between quantity and quality of life, studying how to best involve patients of varying backgrounds in the decision-making process is crucial to treating the disease.

Women and people of color are underrepresented in classrooms as both instructors and students, as well as in the field of physics. A lack of diversity limits the ideas that evolve and creates disadvantages for systemically nondominant groups. The goal of this research is to understand how we can make students feel more empowered to change the culture in physics. Students in introductory, calculus-based physics classes from both a two-year college and a four-year university participated in a similar equity unit, which focused on increasing awareness of the systemic marginalization of women and people of color in physics. At the end of the unit students brainstormed how to raise awareness of, and then ultimately remove, this inequity. We analyzed and coded students’ responses using key words and phrases coinciding with similar ideas. The themes were tested for reliability by the authors who addressed discrepancies through discussion, after independently categorizing these responses. Students from both populations (two-year and four-year colleges) concluded that learning about their own bias and having intentional conversations about equity issues are both important steps in physics for changing societal structures. One theme unique to the two-year college setting was to develop coping strategies that combat inequities in physics. Future work will involve acquiring more data from different student populations and using that data to better support students in various physics learning contexts. By following students’ suggestions from the equity unit, we can take action to create an inclusive and diverse physics culture.

Wound healing in the elderly can be a serious health issue because of a delay in tissue repair and compromised immune response. In these circumstances successful treatment can be challenging. New drugs and preclinical animal models are needed to develop alternative treatment strategies. This study was designed to investigate the effectiveness of a novel mitochondrial specific peptide, designated as SS20, in enhancing wound healing in an aging mouse model using a novel and relatively noninvasive ear punch wound. Ten C57BL/6 female mice 26 months of age were ear punched through and through in the central area of both ears using a 2 mm dermal biopsy punch. C57BL/6 mice were chosen due to them being well defined aging models both genetically and physiologically, allowing us to compare aging parameters in the same background. Five mice were randomly selected for daily topical treatment directly on the wound with SS20 at 3mM concentration in a volume of 10 ul. Five mice were treated daily with topical saline in the same manner. Two individuals separately and independently measured diameter of the wounds in two directions (because the wounds were more elliptical than circular) on days 1, 7 and 14 when treatment was stopped. Wound surface areas were then calculated and average change over the 2 weeks was determined between mice with SS20 and saline. A significant decrease in surface area was seen in the left ears of mice treated with SS20 but not with saline as measured by both individuals. Interestingly there was no difference in change in surface area in the right ears of mice treated with SS20 or saline over the 14-day period, confirmed by both individual measurements. These observations suggest that SS20 can prevent a delay in wound healing in very old mice by targeting mitochondrial activity. Additional studies are needed, not only for SS20 effects, but also to investigate utility of the ear punch in aging mice as a model of age-related wound healing.

As the global burden of neurological diseases continues to grow each year, there exists a need for drug delivery vehicles that can overcome barriers specific to the brain. The heterogeneous brain extracellular matrix (ECM) is an understudied barrier to effective therapeutic delivery, particularly in the presence of disease states. We utilize a novel multiple particle tracking (MPT) approach to characterize microstructural changes in perineuronal nets (PNNs), a key structural mediator of plasticity, in the developing brain. Our overarching goal is to develop a combined approach of MPT, statistical analysis using Python-based software packages, immunohistochemistry (IHC), and mRNA expression profiles to monitor changes in PNN structure and function through development and in the presence of neuroinflammation and oxidative stress processes. For this, we cultured 300 μm-thick organotypic whole hemisphere (OWH) brain slices prepared from postnatal day 35 (P35) rats. We treated slices with 100 ng/mL lipopolysaccharide (LPS, induced-inflammation model) or 100mM glutamate (MSG, induced-excitotoxicity model) for 3 h, removed the toxin and fixed slices at 1 h, 6 h, and 24 h after toxin removal. Fixed slices were stained using Wisteria floribunda agglutinin (WFA) and PNN counts were quantified using the ImageJ software package. In LPS and MSG-treated slices, 100-nm particles were added to live slices stained with WFA and MPT was performed in WFA+ regions, followed by statistical analysis of individual nanoparticle trajectories. From the IHC imaging and PNN count quantification, we observed differences in the number and morphology of PNNs present in the MSG and LPS models when compared to healthy controls. Characterizing structural changes in PNNs in living tissue furthers our understanding of the impact of neuroinflammation and oxidative stress on neuronal plasticity, and the subsequent impact on progression of neuropsychiatric diseases.

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

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

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

Every year 26,000 pounds of human waste left by Mt. Everest climbers is disposed in pits near Gorak Shep (elevation 16,942ft.), a village close to Everest Base Camp in Nepal. The Mount Everest Biogas Project (MEBP) is working to build an anaerobic digester (AD) adapted to the extreme conditions of Mount Everest to treat this waste. All project materials must be carried by foot, including the biologic seed for starting the reactors. Thus, identification of a near-by seed is a critical step in the project’s success. Archaeal microbial community from five anaerobic digesters in Nepal were profiled. House-hold digesters and a mid-sized municipal digester in Katmandu were compared. The goal was to determine if methanogenic populations critical for establishing anaerobic digestion were similar among the potential seeds. Between 65,511 and 94,602 archaeal sequences were recovered from each sample. The sequences clustered into 580 operational taxonomic units (OTU). Species richness and Shannon-Weaver diversity indices ranged from 238-320 and 2.38-3.03, respectively. Significantly lower proportions of Methanosaeta, an important genus of acetoclastic methanogens, were detected in the municipal AD sample than in household AD samples (31% and 43%, respectively; t-test p=0.05). Conversely, the other known genus of acetoclastic methanogens, Methanosarcina, represented < 0.2% in all samples. Methanogen populations (phylum Euryarchaeota) dominated all samples (73 to 97%). However, household AD samples contained a significantly higher proportion (21% versus 3%, t-test p=0.007) of poorly characterized archaeal phylum with unknown function in anaerobic digesters. Principle Component Analysis (PCA) revealed that 2 of 3 household AD were similar. Thus, while all systems contained the Methanosaeta and other methanogenic species desired for startup of the MEBP AD, continued study of anaerobic digester is needed to understand how microbial communities evolve in response to the extreme temperatures of Mount Everest to assess the prolonged sustainability of the system.

Tin-doped indium oxide (ITO) is a n-type semiconducting material that have been widely used in solar cells, smart windows, and transistors. This material conducts electricity due to excess free charge carriers which charge-compensate the tin dopants. We are working to develop new chemical treatment methods to build optoelectronic devices from ITO nanocrystals. Colloidal nanocrystals are well-suited for solution-processing and low-temperature deposition techniques. These routes can be ideal for fabrication of thin-film electronics, especially on flexible substrates; however, increasing electronic communication between nanocrystals require post-deposition treatments. Few low-temperature methods to create conductive films from oxide nanocrystals have yet been reported. We seek to increase the conductivity of ITO nanocrystal films with ligand-exchange procedures to decrease the distance between each nanocrystal, then chemically crosslinking them. We synthesized ITO nanocrystals, then resuspended in solvents at high concentrations for film deposition. We first modify the surface of our nanocrystals by replacing the native long nonpolar ligands with short polar ligands. The modified crystals were deposited by spin-coating onto glass substrates and a variety of solvents/conditions were tested to optimize uniformity and thickness. Four-point probe measurements resulted in sheet resistance (R_s) ranging from 1 MΩ/square (ligand exchanged nanocrystals) to 2 TΩ/square (untreated nanocrystals). Profilometer measurements probed film thickness that can be used to calculate our films' bulk resistivity. Next, we used zinc and aluminum compounds as chemical solders to build bridges between nanocrystals to increase the material’s conductivity. R_s drops to ~0.15 MΩ/square with aluminum bridges and ~0.10 MΩ/square with zinc bridges. We plan on using other undoped metal oxides with this same scheme and apply them to thin-film field effect transistors (FET) to investigate how these treatments improve FET performance. We are also working on using similar techniques with SnO₂ nanocrystal films for application as electron-transport layers in perovskite solar cells.

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

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that results in progressive degeneration of upper and lower motor neurons, leading to muscle weakness, paralysis and death. Currently, ALS affects 15,000 Americans in the U.S., who have an average life expectancy of three to five years at the time of diagnosis. There are only two FDA-approved medications for ALS treatment, which minimally slow but do not reverse the progression of the disease. Understanding the genetic causes of ALS can help us to identify more effective treatments, therefore we seek to identify pathogenic variants and investigate how they contribute to the death of motor neurons. We previously showed that a tandem repeat in an intron of the gene WD-repeat-containing protein 7 (WDR7) may be involved in ALS. To better characterize this repeat, we PCR-amplified the repeat region and quantified repeat size in 500 ALS samples, including those from sporadic cases and those with known pathogenic variants. These repeat sizes were compared to approximately 500 Parkinson disease samples, 100 Primary Lateral Sclerosis samples, and 500 control samples from the Coriell Cell Repository, to verify whether expansion of this repeat was specific to ALS. Furthermore, to determine if repeat blocks were enhanced in certain subsets of patients, the lengths of the intronic repeats in genomes of ALS patients were profiled and compared with de-identified phenotypic information. To resolve the exact sequence of repeat in ALS samples, a subset of patient DNA samples and controls were sequenced using single molecule real-time (SMRT) sequencing. Together, these findings help us gain insight into the disease and guide us to develop a better treatment.

Cranial elaboration, in the form of domes, horns, and bony bosses, has evolved multiple times in vertebrate history, including in non-mammalian synapsids, the extinct ancestors of mammals. The lack of similarly thickened skulls in living animals has meant that very little can be inferred about how these features developed or why they evolved. Here we use comparative bone histology to describe the microanatomy of Oudenodon, a 255-million-year-old synapsid with distinctive nasal bosses. We compared thin-sections from the thickened portions of Oudenodon to the non-thickened skull of its relative, Diictodon, in order to better understand how cranial elaboration developed in synapsids. We took thin sections from the thick nasal bosses as well as non-thickened regions of Oudenodon to capture changes in tissue microstructure. Then, we compared these thin-sections to similar regions of the skull in Diictodon, which lacks cranial elaboration. In the bone tissue of both Oudenodon and Diictodon, we observed a cancellous, spongey interior sandwiched between two layers of compact cortical bone. This pattern of bone is typical in many modern skulls but the thickness of the cancellous region in Oudenodon is strikingly thicker, even in regions away from the boss. We hypothesize that increased cranial thickness in Oudenodon is due to this middle expansion of spongey, cancellous tissue. As a result of the increased bone thickness, sutures in Oudenodon are deep, wide, and convoluted when compared to the relatively simple interdigitated sutures in Diictodon. These and other histologic comparisons with distantly related taxa allow us to interpret the growth and construction of cranial elaboration in synapsids, adding to our understanding of how these thickened skulls evolved. Future work can also explore the possible soft tissue covering of these bosses and domes, which may have been used for intraspecific display or combat. 

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

Skeletal reduction is a common feature among deep-sea fishes that have diversified from shallow-water relatives, such as snailfishes. These skeletal reductions may be an adaptation to environmental conditions of high pressures, low temperatures, declining luminosity and limited food availability. Snailfishes (family Liparidae) are found across a large bathymetric range (0 – >8,000 m), with intertidal ancestors giving rise to a large clade of deep-sea species. We used microcomputed tomography (micro-CT) to estimate average bone mineral density and examine jaw, pectoral girdle, and neurocranium morphology. Our results suggest at least three mechanisms of skeletal reduction: (1) reduction of bone size, (2) reduction of bone density, and (3) loss of skeletal elements. First, using phylogenetic generalized least squares (PGLS) analysis, we found that the change in cranial dimensions with depth was not uniform. While the size of the maxilla, dentary, and pectoral girdle decreased with greater depth, length of the upper premaxilla and the neurocranium did not vary with collection depth. Second, average density of the lower jaw decreased with increasing depth. Lastly, the ventral suction disc has been lost multiple times within the deep-sea lineage. While all three methods are seen in snailfishes, other groups may use some or all of these mechanisms to different extents. Some mechanisms of skeletal reduction may be more advantageous than others. The extent to which a structure is retained in deep-dwelling fishes may indicate its functional importance. Variable skeletal reduction in the family Liparidae provides insights into the physiological adaptations that allow fishes to survive in deep-water environments. We conclude that some skeletal elements are maintained at the expense of others as fishes balance the functional demands of life in the deep sea.

Extracorporeal membrane oxygenation (ECMO) is used to maintain adequate blood-gas exchange in patients experiencing cardiac or cardiopulmonary failure. Close therapeutic drug monitoring of anticoagulants is required to prevent thrombosis within the ECMO circuit or in vivo bleeding from mucosal membranes. The goal of this research was to implement a laboratory developed test for bivalirudin quantification based on plasma diluted thrombin time (dTT). The assay was run on the Diagnostica Stago STA compact. Two calibrations were performed each with R2=0.99. The analytical measurement range was 0.0 to 2.9 ug/mL with a limit of detection of 0.1 ug/mL. Clotting times strongly correlated with the current standard of measurement. Although further testing must be performed, using this calibrated plasma diluted thrombin time assay would improve efforts for safe therapeutic drug monitoring of bivalirudin.

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

The equivalence principle maintains that all mass is equally affected by gravity and is fundamental to our understanding of gravitational physics. Torsion balance experiments at the University of Washington have tested the equivalence principle at the 10^-13 level. Torsion balances are susceptible to systematic uncertainty caused by changing gravitational gradients formed in the environment, e.g. rainfall saturation in nearby hills. If changing gravitational gradients could be continuously monitored, then the full torsion balance sensitivity (differential accelerations below 10^-15m/s²) could be reached. The goal of this project is to measure and correct for gravitational gradients. Simultaneously monitoring gravity gradients and testing the equivalence principle requires the construction of a concentric torsional gradiometer. Such an instrument has never been built before, requiring unique geometrical design constraints. Several functional prototypes have been constructed along with a complimentary data acquisition system. Improved equivalence principle limits will further constrain the unification of gravity with the standard model of particle physics.

Dandy Walker malformation (DWM) is the most common human cerebellar malformation, affecting 1 in every 3000 live births. DWM is an imaging diagnosis that is characterized by three features: cerebellar vermis hypoplasia, an enlarged posterior fossa, and an enlarged fourth ventricle. Although recent advances in neuroimaging have improved diagnosis of DWM, virtually nothing is known about the cellular and histological defects that lead to DWM. One major reason is that little human specific data is available describing the histology of normal and abnormal human fetal cerebellar development. Currently, there is limited published fetal pathology of DWM. There is no comparative analysis available and most studies are confounded by lack of molecular confirmations of diagnoses. We have carried out the first comprehensive histo-pathological analysis of human DWM. Such histo-pathological analysis, that I specifically was responsible for completing, included measuring the length and cell density of certain regions of the developing cerebellum in the 36 DWM cases, such as the external granule layer and the rhombic lip. Our results indicate a significant reduction in size and area of neuronal progenitor zones in the developing human cerebellum. We also observe aberrations in the developmental trajectories of specific cell types like Purkinje cells, and progenitor zones like the rhombic lip. Through our analysis of the human fetal DW cerebellum, we begin to directly address the developmental pathology of human DWM beyond that of the mouse models that share similar pathology. We believe our studies will fundamentally improve our view and understanding of the biology of the human cerebellar development and give us insights on the developmental pathogenesis of DWM.

Asymmetric cell division (ACD) is an integral process that multicellular organisms use to create cellular diversity. For instance, stem cells use ACD to form differentiating sibling cells while recreating the stem cell in order to maintain the stem cell pool. Defects in ACD can result in a variety of diseases ranging from neurodevelopmental disorders to cancer. Using Drosophila melanogaster neural stem cells (neuroblasts) as a model to study cellular asymmetries, we recently found that hydrostatic pressure is an important factor contributing to ACD. However, the mechanisms and proteins that regulate hydrostatic pressure are unknown. Based on our previous results, I hypothesized that Na+/H+ antiporters are involved in establishing hydrostatic pressure. To examine this hypothesis, I tested the function of four Na+/H+ channels in Drosophila using RNAi knock-down experiments and subsequent live cell imaging. This imaging allowed visualization of fluorescently tagged myosin and microtubules--two critical components of the cell division process. I found that knocking down each of the four antiporters results in a bent mitotic spindle, delayed division times, and centrosome abnormalities. I conclude that the four antiporters play a role during ACD in fly neural stem cells. To validate these results, I will use CRISPR/Cas9 gene editing to develop deletion mutants and EGFP-tagged versions of the four antiporters—two crucial steps in studying the regulation of Na+/H+ channels. Further in the future, I will use CRISPR/Cas9 to create optogenetically controllable Na+/H+ antiporters, such that I can use light to control hydrostatic pressure in Drosophila neuroblasts. I also plan on measuring the  intracellular pH using genetically edited Drosophila, as disruptions in pH could cause the described phenotypes. These studies will provide mechanistic and functional insight into how hydrostatic pressure contributes to successful ACD.

Asymmetric cell division (ACD), a process that generates daughter cells with different cell fates and sizes, is a fundamental mechanism for generating cellular diversity during development. We use Drosophila melanogaster neural stem cells, or neuroblasts, to study ACD. Neuroblasts provide an ideal model for ACD since they are intrinsically polarized and divide with physical as well as molecular asymmetry, resulting in a self-renewed stem cell and a smaller ganglion mother cell (GMC). Kinesins, plus-end-directed motor proteins, have previously been implicated in asymmetric cell division and spindle dynamics. However, the specific kinesins that influence ACD and the mechanism by which they do so remains unknown. Elucidating the function of kinesins in cell division will help establish a more holistic view of cell development. To learn the role that kinesins play in asymmetric cell division, we performed an RNAi knockdown-based live-cell imaging screen of most kinesins in Drosophila. We found that knocking down the Drosophila kinesin genes Klp3A, Klp10A, Klp59C, Klp67A, Klp68D, CG14535, cos, or ncd causes the mitotic spindle to bend during metaphase and anaphase. We hypothesize that this phenotype is due to the spindle being so large that it buckles under the pressure of the cell as it divides. We are currently investigating this hypothesis by imaging knockout mutants to confirm this phenotype and tagging each kinesin with GFP to study how these proteins are localized during typical ACD.

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

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

The level of plastid DNA (ptDNA) declines as plastids develop from colorless proplastids to green chloroplasts. The decline in ptDNA is associated with an increase in DNA damage resulting from oxidative stress and ultraviolet (UV) radiation. 8-oxoguanine (8-oxoG) is a lesion in ptDNA that results from the oxidation of guanine. Our lab previously found a reduced amount of ptDNA in light-grown plants compared to dark-grown plants, likely due to increased oxidative stress that increases ptDNA damage. Here, our objective is to quantify ptDNA damage by assessing 8-oxoG lesions during the greening of maize leaves. We hypothesize that as plastids mature, 8-oxoG lesions increase. Our experimental outline involves the quantification of 8-oxoG by the enzyme-linked immunosorbent assay (ELISA), as well as immunofluorescence microscopy using antibodies that target 8-oxoG. We are examining plastids isolated from light-grown and dark-grown stalk and leaf tissues. As 8-oxoG lesions are one of the markers of oxidative DNA damage, our results will be used to assess DNA damage during development of maize plants. This research will provide a better understanding of role of oxidative stress in plant development

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

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

Humans hear sound through two main pathways: air conduction (AC) and bone conduction (BC). The AC pathway is dominant under normal listening conditions, but conductive hearing loss (e.g. outer/middle ear diseases) impairs one’s ability to hear by AC. BC hearing aids can improve hearing under such conditions. To determine the presence of a conductive hearing loss, BC hearing thresholds must be compared to AC thresholds. For populations that cannot respond reliably to behavioral audiometric testing (e.g. infants, elderly, individuals with cognitive impairments), clinicians instead record sound-evoked brainstem activity through the auditory brainstem response (ABR) test. While AC ABR test results are clinically reliable, BC ABR test results suffer from electrical artefacts generated by the BC transducer and variable ABR waveform morphology. Therefore, determining the presence of a conductive hearing loss by comparing AC and BC ABRs is often unreliable. This study aimed to (1) reduce the severity of electrical artefacts present in the early BC ABR waveform (Wave I/II) by shielding bone-vibrating transducers (Radioear B81) with MuMETAL and (2) improve the quality of the ABR signal by using ‘chirp’ stimuli (ascending frequency sweep) to enhance the summating amplitude of auditory neural responses. Ongoing measurements leverage three transducer types in total (shielded and unshielded BC, earphone AC) and three stimulus types (chirps, constant-frequency tone bursts, and broadband “clicks”) to evaluate main and combinatorial effects of the transducer and stimulus on BC ABR data quality. Early indications show that shielding the BC transducer does not materially change its frequency response. Therefore, any observed changes in the BC ABR waveform can be attributed to electrical shielding and/or stimulus modifications per se and not to unintended changes in transducer acoustic output. Data will inform efforts to improve the clinical reliability and utility of BC ABR measures for detection and treatment of conductive hearing loss.

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

With the rise of social media numerous nationally publicized incidents of large groups of people harassing a private party over the internet have taken place. A review of current research points to several possible causes. One body of research suggests certain patterns in neural activity which could be encouraging individuals to harass total strangers online - a phenomena which may be partially to blame. These patterns may be anthropological artifacts evolved to protect humans in primitive tribal groups which provide neurological rewards for actors who punish detrimental behavior in bad actors. These reward structures are now manifesting in the online environment due to its unique low-risk nearly anonymous nature and/or lack of tangible repercussions that would normally inhibit this behavior. Other researchers suggest these attacks may be a form of virtue signaling to let peers know the harasser is not like the perceived bad actor. (e.g. harassing a perceived racist signals to others that one is not racist). The issue is so new there is no strong scientific agreement in the psychological community as to what is really taking place, or in some cases even what terminology applies. Research in this topic may lead to better understanding of human machine interaction, and cyber-psychology.

Electronic movement can be modeled using the Schrodinger equation. For many-electron systems, however, these equations are not algebraically solvable, which is why this research uses direct numerical integration of Schrodinger’s equation to model time dependent electronic characteristics of molecules. The choice of numerical integration scheme can drastically change the outcomes of the simulation – even causing qualitative changes in molecular behavior. First, an advanced numerical integration technique (4th order Magnus propagator) has been implemented in the ChronusQuantum software package. Next, the effects on molecular behavior of choosing this integration scheme over preexisting schemes are evaluated. The implemented integration algorithms can be used to model the elementary steps of chemical reactions, as well as analyzing the effects of light on electron movement. The research provides meaningful information about the impacts of different implementations of algorithms along with analyzing the simulated behavior of electrons.

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

The environment in which a molecule resides can drastically affect both its reactivity and its spectroscopic properties. These effects can be clearly seen in phenomena such as solvochromism or increased reactivity in a protein active site. The most accurate models that can capture these effects are purely quantum mechanical, but they also have a steep computational scaling cost that prohibits their use on large molecular systems. In order to circumvent this, less expensive models, such as molecular mechanics, can be used for the environment while maintaining the accurate model for the system of interest. In recent years, development of polarizable molecular mechanics has enhanced the accuracy of this technique for time-independent systems, but a gap still exists for time-dependent systems. In particular, the frequency dependence of polarizability has yet to be addressed. This research uses frequency dependent polarizabilities to parameterize a novel molecular mechanics scheme. Specifically, a machine learning model is trained to predict the best locations to place isotropic polarizabilities in order to recover the molecular, frequency-dependent polarizability.

In recent decades, increased nitrogen (N) pollution in coastal aquatic ecosystems caused by increasing agricultural and urban activities has led to extensive habitat degradation and loss, change in the structure of aquatic food webs, and higher frequency of hypoxia. Nitrogen is ubiquitous in the biosphere, entering coastal environments through multiple pathways including ground- and surface waters, plus atmospheric deposition. The fate of much of the N entering coastal environments is not well established. In particular, the magnitude of N consumed at coastal margins, versus exported to downstream estuaries is poorly constrained. It is widely recognized that inland wetlands are important N sinks, as they are sites of fixation of reduced N to inert dinitrogen gas, however the role of coastal wetlands as N sinks is more difficult to establish due to the dynamic nature of these tidal environments. Here, to better understand the role of coastal wetlands in the global N cycle, we established a high-resolution budget of nitrate (the most abundant form of reduced N) from 9/12/2017 to 10/12/2017 at First Mallard Slough within the Suisun Marsh complex, a brackish tidal marsh in the San Francisco Bay Estuary. We modelled nitrate concentrations at 15-minute intervals using a submersible ultraviolet nitrate analyzer (SUNA), and matched these estimates with simultaneous hydrodynamic measurements of water flux. Data were synthesized in Python to establish 15-minute resolution estimates of nitrate mass exchange, showing that the wetland exported a net total of 2.54 Mg of N as NO₃^2- over the complete measurement period, or 84.6 kg N per day. Contrary to other studies showing wetlands are important nitrate sinks, our result revealed that the Suisun Wetland complex was an important N exporter to the San Francisco Bay Estuary, at least over the period measured here. Longer-term observations are needed to confirm this pattern at a complete annual scale.

For many Somali refugees in Italy, the journey from Somalia to Italian land is fueled by an overwhelming desire to seek better opportunities in education, employment, health, and lifestyle. As a country previously known for its luxurious beach resorts and affectionately named “the nation of poets,” Somalia has since dramatically shifted to a land inflicted with ongoing violence, terror, and instability. In this research, we will be exposing how the legacy of Italian colonial power has led to numerous detrimental effects on both the people and the government in Somalia. Furthermore, we will be investigating the ongoing refugee crisis in Somalia, focusing specifically on political and colonial history. Using an ethnographic approach, our research project provides insight into the harsh realities that face Somali refugee immigrant populations in Italy. Over the course of six weeks in Rome, Italy, our team has engaged in qualitative research methods in which we collected personal testimonies from current Somali refugees living in Rome through observations, interviews, and daily interactions. The results of our research will uncover the role Italy has had on the ongoing humanitarian crisis affecting the Somali diaspora.

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