Malaysia is a multiracial/ multiethnic country that is rich with many traditional performing arts such as Wayang Kulit and Main Puteri. However, the number of artists practising these traditions is in decline and they are at risk of extinction according to several Malaysian news outlets. This project is dedicated to understanding the challenges faced by these artists and the strategies they use to overcome obstacles to preserve their art form. Tintoy Chuo, a puppeteer of Malay traditional shadow puppet theatre Wayang Kulit, has become my case study in examining Malaysian artists. Through interviews and analyzing Chuo’s online presence, I found some of his challenges include: (1) federal and state funding structures that favour STEM more than the arts; (2) the Malaysian state’s view on arts as tourism; and (3) state government bans on this art form because it is deemed unIslamic. Some of the strategies that Chuo uses to counter these issues are: (1) blending the traditional element with popular culture references, for example, Star Wars; and (2) seeking international recognition of his work through interviews that are published in magazines and aired on news networks. I compare Chuo’s methodology to the transformation Zapin, a Malay traditional dance, underwent in the 1960s when it was blended with Western ballroom dances as documented by Mohd Anis Md Nor. I reveal similarities between the two processes, including: funding, audience, recognition, methodology, inspiration and community. I argue that the concept of “preservation” used in the context of art-making is problematic, and discuss how framing this methodology in terms of “sustainability” can be a model for other artists hoping to see their art form survive into the next generation.

Only recently has mainstream American theatre celebrated minority representation on the stage. Small percentages of ethnically diverse actors perform in American theatre due to character-casting limitations and white male playwrights which dominate theatrical history and limit the representation of our diverse and multicultural world. By adapting the Hebrew Book of Ruth to stage, I hope to contribute a female voice and provide opportunities for women of ethnic, cultural, and socio-economic diversity on the stage. Like Shakespeare’s plays, this adaptation will be written in verse; however, "Pilgrims Far from Home" mimics the style of Hebrew and Ottoman poetry to pay homage to the story’s origins and contribute to the diversity of voices outside of the western poetic style. This story emphasizes female relationships and how our sisterhood can unify people of different walks of life. "Pilgrims Far from Home" brings this ancient religious text into the 21st century by addressing contemporary issues such as otherness, particularly in light of refugee crises. My project aims to contribute to the diversity of contemporary American theatre by using a well-known and multi-cultural story to address and ease the suffering relationships between peoples in our present-day society.

The questions of equality, decolonization, and anti-imperialism have rarely been so acutely felt as they are today, in a period of rising global fascism, repression, and radical social movements. Looking back to the 1950’s and 1960’s, we see another such turning point in world history. Analyzing the historical documents from global revolutionary movements, Marxist-Leninist and Maoist theory, and locally-situated knowledge, this project examines how a future that had diverged in the 1950’s towards a communist world could have manifested for the both the international community and the Pacific northwest through the medium of a fictional newspaper published in Seattle. Ultimately, this project hopes to examine and critique our current moment of potential change, show the interpretive and political power of creative fiction, and stir interest in historical materialist analyses of similar moments of world history.

The Toba Batak sub-ethnic group in Indonesia is known for their weaving of the traditional textile ulos. At the same time that they uphold ancient Batak traditions of textile weaving, the Toba Batak people are at the nexus of a growing textile industry on national and international scales. As Western interests further influence Indonesia's economy, Indonesian concerns about the production of ulos become more and more urgent to address. The concern that ulos will be replaced by modern, Western styles of clothing and production gives rise to a more pressing fear that weaving traditions will fade from cultural awareness entirely.

In my presentation, I share the uniquely Indonesian strategies utilized by the Toba Batak people to conserve their cultural knowledge and traditional weaving practices. These strategies keep in mind the shifting trends in the textile industry in order to keep ulos relevant, yet are still respectful of Batak tradition. Primary methods of my research include interviews with traditional weavers, with weavers who supervised modern machine looms, the local non-weaving Toba Batak population, Batak culture experts, and Batak culture conservationists. Secondary research includes the work of Sandra Niessen, who has conducted large scale studies on Batak ulos and culture, and news sources such as The Jakarta Post.

Green burial focuses on the interment of the body of a dead person in a fashion that supports decomposition so that the body can be naturally recycled. Green burial has grown exponentially within the past ten years and are now offered by hundreds of providers across the U.S., making it an increasingly popular alternative to conventional funerary customs, such as casket burial and cremation. While recent research has explored the conditions under which the green burial industry has become normalized and competitive, and the types of predictors of green burial support, we know little about the experience of participants and the characteristics of green burial ritual. To what extent have funeral participants internalized the industry’s goals of conservation and fostering an emotional bond with nature? Do green burial rites reinforce community among the living as with conventional funeral rites? Or does the ritual appeal mostly to participants sympathetic to environmentalism? To answer these questions, I conducted ethnographic interviews with green burial workers and participants and observations of green burial rituals. The results of my study furthered our understanding of the green burial as a growing social movement and new meaning making enterprise and revealed how supporters derived distinctive meaning within green burial.

The United States’ major American sports leagues, the NBA, NFL, MLB, and NHL, are turning to franchise expansion to increase their presence in the economic and media markets along the West Coast, including the NHL’s expansion to Las Vegas for the 2017 season and future expansion to Seattle for 2021. However, expansion franchises are very difficult to get off the ground since they require new ownership and management structures, buy-in from the local fan base, and are often subject to much higher scrutiny during their first few years than other franchises. Currently, no universal metric exists to determine whether or not an expansion franchises was successful, and it’s becoming increasingly more difficult to convince leagues to expand when they are unable to evaluate the likelihood of success for potential candidate cities. This research analyzed four major factors I identified that contribute to overall success for a team in any sport: financial prosperity, quality of national media coverage, public and local governmental support, and in-game accolades. Using these metrics as a starting point, I created an index that scored prior expansion franchises using a variety of indicators to quantify their overall success. Additionally, I applied this index to select cities currently under consideration for an expansion franchise to serve as a predictor of their potential success. Going forward, the use of this index as a predictive metric will allow leagues to make more informed decisions about the success of future candidates for expansion.

Homelessness is traumatic. Without shelter, people become more vulnerable to physical, emotional, and psychological harm. For unhoused people, traumatization often manifests in behaviors and vulnerabilities that are incredibly difficult, sometimes dangerous, for service providers to manage. At this time, many social services have acknowledged the importance of trauma informed care, hereafter referred to as TIC, a framework that takes into account the impact of past trauma and the resulting coping mechanisms adopted. My research, an independent study with the Law, Societies, and Justice and Disability Studies programs, aims to understand TIC’s potential to effectively manage the behaviors and address the needs of traumatized clients. Through interviews with service providers caring for young adults experiencing homelessness, I argue that young adult homeless service providers are currently unable to fully address the needs of their clients with histories of traumatization due to a combination of individual, structural, and systemic barriers. As a means to address this, I am in the process of creating a trauma-informed safety and accountability program at ROOTS Young Adult Shelter. The program is informed by interagency interviews and will address trauma, manage behaviors, and support direct service staff in homelessness services through a combination of restorative justice, support group, and individual support models. The efficacy of this program will be researched in relation to safety, accountability, and recidivism. This research has the potential to be widely applicable within social services, particularly shelters. It takes extensive research on the impact of trauma and TIC and applies into an expansive program that providers can use to address the behavioral needs of their clients. Further, it provides qualitative and quantitative research on the implementation of TIC in shelter spaces.

Over the last decade Seattle has seen the most dramatic population growth of any large American city. The accompanying rapid change in urban form of the city has been called staggering by longtime Seattle natives, causing a state of worry not unlike the feeling of solastalgia, a neologism that describes a form of mental or existential distress caused by environmental change. Longtime citizens can be forgiven for feeling as though their home has been irreparably changed in a way that doesn’t name them as a benefactor. But what has the effect of this rapid change had on the homeless community? Can a stable and strong sense of place have positive influences on the day to day lives of the homeless individuals? Can we facilitate a stronger sense of place as part of our response to the homelessness crisis in Seattle? My study examines the link between sense of place and stability in homeless individuals through interviews with individuals from within the homeless community, hearing perspectives from tiny house villages, tent cities, and the streets of Seattle. Through these conversations I demonstrate the impact that sense of place has on social stability, especially in times of rapid change to the urban environment, and how sense of place differs depending on the method of temporary shelter. The resulting study builds a better understanding of the intersectionality of the existential effects of placelessness in the homeless population, the differences between being homeless in a variety of spaces, and the meaning and significance of place making to people without a place.

Benefits of nature on children’s health and development are becoming increasingly recognized across the globe. Norway is revered for putting this research into practice, centering nature in early childhood education and setting precedents for ways in which preschools and kindergartens can get their children moving beyond the traditional classroom and up into the trees, down into the mud, and everything in between. Norway has taken a progressive stance on multicultural learning as well. The Norwegian Framework Plan for the Content and Tasks of Kindergartens defines education as an inclusive cultural arena to promote respect for the diversities of all children. I explored this intersection as a landscape architecture student. How might nature itself be important to children’s development and expression of cultural values? In what ways was learning facilitated differently outdoors vs indoors, and what implications might that have for the design of outdoor learning environments? Over the course of three weeks in Trondheim, Norway, I visited three barnehage (preschools) and conducted interviews on the connections between the landscape and the Framework Plan’s goal of inclusion. I found that outdoor environments could be less culturally coded than indoor classrooms, creating an unfamiliarity conducive to curiosity. This curiosity, coupled with undefined materials found in nature or man made objects placed outside of typical contexts, encouraged children to use play to design, communicate, and participate in imaginary worlds together, rather than having to rely on language or common frames of reference. Consequently, some Norwegian educators saw nature as a critical component of promoting children’s inclusion, tolerance, respect, and understanding of the diversities among one another, a revelation frequently overlooked in the U.S. More broadly, my findings point to that missed opportunity, where educational goals for children are similar but neglect serious consideration of the landscape as part of the approach.

Seabirds are often used as markers of ecosystem health due to their heavy dependence on the base of the food chain. The Alcidae family consists of small, diving birds who feed exclusively within the water column and rely on the sea year-round. Because of this, many view alcids as the only “true” seabirds. A research apprenticeship at UW’s Friday Harbor Laboratories on the pelagic ecosystem, Pelagic Ecosystem Function, has observed all seabirds since 2004, with consistent data since 2013. Alcids have been largely ignored in previous Pelagic Ecosystem Function studies, as the Common Murre (Uria aalge) artificially inflates the alcid family data due to their high abundance within the San Juan Channel. Upon removal of this species, it is found that non-Common Murre alcids are declining at a higher rate than any other seabird family within the channel, with a near-linear decline since 2013. In order to investigate the leading drivers of population decline, variables regarding food availability and habitat were collected in the form of chlorophyll, photosynthetically active radiation, and sea surface temperature. Compelling correlations were found between non-Common Murre alcid density and photosynthetically active radiation, as well as between chlorophyll and sea surface temperature. The data presented here is important not only for the mitigation of local ecosystem degradation, but also due to the consistency with global trends of seabird populations.

Urban stormwater runoff transports thousands of potentially toxic chemicals, metabolites, and degradation products to fish habitats. While certain contaminants, including metals and petroleum-derived compounds (e.g., polycyclic aromatic hydrocarbons) are known to adversely affect fish health, many others are unidentified and/or uncharacterized. Despite this uncertainty, green stormwater mitigation methods such as bioretention, the filtering of stormwater through a medium such as sand and compost, have recently been shown to be highly effective in terms of both reducing pollutants and improving water quality for the health of fish. However, the scope of this research to date has been limited to a small number of engineered media types. Here we used the embryonic zebrafish (Danio rerio) model to evaluate the impacts of urban arterial runoff, before and after filtration through several novel types of bioretention media. Measured toxicity indicators included eye and pericardial area, body length, and the expression of the biomarker gene cytochrome p450-1A (cyp1a). Untreated runoff from multiple storms was consistently toxic to zebrafish embryos. Conversely, each of the morphological and molecular health indicators was positively influenced by bioretention treatment. Our results indicate that bioretention compositions beyond the sand-compost mixture used in Washington State are promising in terms of reducing or eliminating near-term (i.e., acute) toxicity to fish. This expands the potential toolbox for site-specific pollution removal using green infrastructure methodologies.

Along the shoreline of Possession Sound, located in the southern basin of the Salish Sea are 10 outflows of combined sewage systems. Combined sewage systems collect rainwater, untreated domestic sewage, and industrial wastewater within a single sewer line. When heavy rainfall occurs, these systems overflow and are directed into designated combined sewage outflows (CSOs), which then empty into the estuary, releasing E. coli (Escherichia coli) directly into the estuarine ecosystem. These CSOs, along with other factors, change the pH of the waters within the basin. Preliminary analysis of primary literature suggests a relationship exists between pH and E. coli growth. The pH change affects the enzyme growth within E. coli. As river discharge fluctuates, so does the amount of outflow from the CSOs which then cascades into pH changes at the site closer to the CSOs. The guidelines and regulations in place today allow for significant volumes of sanitary waste to be overflowed into marine systems. When river discharge increases, the overall pH within the Sound decreases. It was hypothesized that when there is a large amount of rainfall that leads to heavy river discharge and low pH, there will be more Escherichia coli growth at all of the sites throughout the Sound. Ocean Research College Academy students collected bacterial sample data at 12 stations in Possession Sound from 2009 to 2019. All data were recorded with distance from a CSO. A Niskin bottle was deployed at the surface and halocline with a YSI 650 testing pH. Samples were tested for bacterial count and compared with other samples taken after heavy rainfalls. Further research will define the trends in river discharge, pH and E.coli for Possession Sound.

As anthropogenic climate change progresses it is drastically altering the health of watersheds globally. In efforts to mitigate changes to marine ecosystems, many studies are using physical and chemical measurements to inform plans and create legislation. The impacts of climate change on local ecological communities are harder to track and take longer to show themselves which is why it is vital that we develop accurate techniques for measuring this kind of change quickly. This project, completed as part of Puget Sound Foraminifera Research Project at the Burke Museum, uses calcareous benthic foraminifera recovered and identified from sediment samples collected by the Washington State Department of Ecology between 2017 and 2018. Benthic foraminifera are marine protists that live on or within sediment and form shells of calcium carbonate or agglutinated sand grains. Foraminifera used in this project were stained with Rose Bengal to ascertain whether they were alive at the time of collection and grouped according to World Registry of Marine Species protocol. Stained and unstained individuals were counted to create living and dead assemblages. The goal of this study is to determine the validity of using total assemblages that include both living and dead foraminifera as a proxy for quantifying the living assemblages in Puget Sound. This is important because previous research has found discordance between living and total assemblages of molluscs, pteropods and ostracods in embayments heavily impacted by anthropogenic activity. This study includes 5 embayments in Puget Sound. Results from Bellingham Bay and Sinclair Inlet suggest that the validity of using total assemblages as a proxy for living assemblages may vary across different areas of Puget Sound; while the total assemblage and living assemblage matched in Bellingham Bay, Sinclair Inlet has been found to have significantly different total and living assemblages.

Eelgrass beds in central Salish Sea are critical components of healthy ecosystems that are vulnerable to anthropogenic impacts. This study utilized two locations in Possession Sound to monitor water chemistry within and near two different eelgrass beds; one unmapped, and one established. The study compared these two locations and investigated the impact of location on water chemistry within the bed. Data-sharing and collaboration with the Samish Indian Nation Department of Natural Resources’ work on eelgrass beds in Fidalgo Bay provided a broader scope into regional differences within the central Salish Sea. This study was conducted by Ocean Research College Academy (ORCA) students at eelgrass beds in Possession Sound located near Mukilteo and Hat Island. The study ran from October 2019 to spring 2020, and utilized background data from past studies to inform studies at the bed near Mukilteo. Data were collected using a combination cast of a camera collecting visual data and a CastAway CTD, which collected vertical profiles of salinity and temperature at recorded geographic coordinates. Data were collected during a free drift across the eelgrass bed. An EXO Sonde was temporarily installed in the bed to collect chlorophyll and turbidity data in a longitudinal manner. The study primarily explored how location impacts the water chemistry eelgrass beds in central Salish Sea both within the bed and within a region. Research going forward could study remote beds more comprehensively using technology previously tested such as drones and SONAR, as well as a longer-term collaboration between the Samish DNR and ORCA.

Neural tube defects (NTDs) impact 3000 pregnancies a year in the US and are caused by both genetic and environmental factors. NTDs arise from errors in neural progenitor signaling, migration, proliferation, and differentiation during embryonic development. Spina bifida (SB), a prevalent NTD, can reduce the functioning of neural pathways responsible for pain and motor function in the lower body. A recent study discovered a novel variant of the receptor GPR161 present in screened infants with SB, but absent in all screened infants without. GPR161 is a G protein-coupled receptor localized in the primary cilia known to participate in the regulation of the pathways of key stem cell differentiation ligands, sonic hedgehog (Shh) and Wnt. Our study seeks to investigate the molecular mechanisms which connect the novel GPR161 variant p.Trp202Gly to neural tube defects using an in vitro model of neural stem cell differentiation. GPR161 variant and knock-out (K/O) lines are generated using CRISPR Cas9 technology in induced pluripotent stem cells (iPSCs). iPSCs are then guided through neural differentiation and harvested for analysis at multiple key stages of neural progenitor development. Markers of neural differentiation, SB, and downstream GPR161 factors are analyzed using western blot, RT-qPCR, immunostaining, and RNAseq. We expect to see a change in Shh activity in the variant line compared to the WT.

Substance abuse leads to alterations in cognition that affects processes such as impulse control and valuation. Decreased impulse control and aberrant valuation are responsible for continued drug seeking and are thought to be escalated by external stress stimuli. Stress leads to release of an endogenous opioid neuropeptide called dynorphin which binds to the Kappa Opioid Receptor (KOR). Upon KOR binding, dynorphin induces a protein signaling cascade that also promotes drug seeking behavior. In this study, we investigated the dynorphin/KOR system in the medial prefrontal cortex (mPFC) due to its critical role in cognition. We examined the properties of dynorphin release in the mPFC of C57BL/6 mice in response to different external stressors to determine if this nucleus is a potential therapeutic target for stress-induced drug seeking behaviors. Using a pharmacological approach, we first showed that systemic administration of U50,488, a KOR agonist, leads to KOR activation in the mPFC. U50,488 administration also disrupted cognition by impairing performance in a working memory behavioral task. We next tested whether different stress modalities stimulated mPFC dynorphin release and disrupted cognitive performance. Surprisingly, repeated forced swim stress did not cause dynorphin release in the mPFC and did not disrupt cognitive performance although it did activate dynorphin release in the Dorsal Raphe nucleus, as expected. In contrast, different stressors, including repeated foot shock and precipitated morphine withdrawal did effectively lead to KOR activation in the mPFC. This indicates that dynorphin release in the mPFC is dependent on the type of behavioral stress. Future experiments will utilize an in-vivo dynorphin sensor, kLight, to detect dynorphin release in real-time in response to these stressors. Exploration of the differences in dynorphin/KOR system functioning in response to different stress modalities is important for establishing how this system may be targeted to alleviate stress-induced drug seeking behaviors.

Alzheimer's disease (AD) is the most common cause of dementia, a general term for memory loss and other cognitive abilities. Although this disease has been a major research focus since the 1980s, the pathological mechanisms are still not well understood, and therapeutic interventions have been ineffective. The most definitive method for classifying AD is through identifying accumulations of toxic amyloid-beta (Aβ) and tau proteins in post-mortem brain tissue. Dr. Su-in Lee’s lab has developed a machine learning method that integrates the pathological protein phenotypes with gene expression levels in the same brain tissue. They have highlighted 25 genes with expression level changes that correlate with the tau and Aβ protein aggregation phenotypes. For this proposal, I have integrated these human neuropathology-based phenotypes with the genetic power of Caenorhabditis elegans (C. elegans) to directly test the impact of these candidate genes on the cellular pathology. Previously, all C. elegans tau models had neuronal specific expression. However, neurons are resistant to RNAi. Therefore, I generated a novel transgenic C. elegans tau AD model that has been codon-optimized to express tau in body wall muscles instead of neurons. I measured the animal’s health with age in a series of phenotypic assays: egg-laying, growth, movement, paralysis, and lifespan analysis. This line exhibits premature paralysis and decreased crawling speeds, providing an easy to score phenotype. This new model allows for high-throughput RNAi screening to test the identified 25 genes’ effects on worm health by utilizing the automated worm-movement technology developed in the Matt Kaeberlein lab that can simultaneously determine the rate of paralysis of thousands of worms. The results of my genetic screening will lead to a better understanding of the human genes that are dysregulated in human AD brains, provide a basis for genetically-dissecting the pathways influencing tau toxicity, and suggest new therapeutic targets.

Alzheimer’s Disease (AD) is a neurodegenerative disorder characterized by the formation of senile plaques and neurofibrillary tangles through the accumulation of toxic amyloid-beta and Tau protein. There is growing recognition that extracellular vesicles (EVs) can package and transport toxic peptides associated with neurodegenerative disorders – such as AD – to other cells in the brain. Researchers in the Kaeberlein lab have designed methods to isolate these type of vesicles from C. elegans nematodes, a popular invertebrate genetic model. However, current nematode EV purification methods do not permit the following of EV signals from specific tissues when they are under AD proteotoxic-stress. I have generated a transgenic C. elegans AD model that has muscle specific expression of the pathogenic human Tau protein. The protein coding sequence was designed to use optimized codons to ensure high expression of the transgene. I have also generated transgenic nematode lines that express versions of known transmembrane proteins with small affinity tags in a tissue specific manner. The small affinity tags on the proteins make it possible to specifically pull down the EVs from designated tissues through standard immunohistochemistry techniques. The abundance of tissue-specific EV protein and RNA cargos from transgenic lines with or without human Tau have then been quantified using LC-MS-MS and RNAseq analyses, and parsed and condensed into a MySQL database via a C# program. The database allows for simple searching through large amounts of MS data, making data analysis more efficient and effective. Thus the methodology and tools I develop in this project could become a promising new approach for identifying novel therapeutic gene targets and biomarkers of AD stress.

Dopamine (DA) neurons found in the ventral tegmental area (VTA) are associated with reward feedback, and dysfunction in DA circuitry is associated with disorders such as Parkinson’s, schizophrenia, bipolar, and addiction to drugs. To adequately treat these diseases, we must have a more complete understanding of how dopamine contributes to emotional processes. This research project addresses this issue by investigating neuropeptide regulation of dopamine neurons in the VTA. The bed nucleus of the stria terminalis (BNST) is a brain region that expresses many neuropeptide genes and sends strong projections to the VTA. We utilized Cre driver lines to isolate neurons that produce the peptides Neurotensin, Neurokinin B, and Corticotropin Releasing Factor. We injected a virus into the BNST that induces the expression of a light activated ion channel and allows us to stimulate axon terminals in the VTA. I then conducted behavioral experiments to assess the effects of activating these peptidergic inputs. Dopamine-dependent behaviors relating to pleasure, reward, and anxiety were measured through the behavioral tests of Real Time Place Preference, operant conditioning, and Open Field respectively. Most likely due to low expression, my behavioral analyses did not yield statistically significant results. Moving forward, it may be necessary to increase viral titer for wider expression. In the future, I intend to use CRISPR/Cas9 technology to isolate neuropeptide function from fast neurotransmitter release in these circuits. This research, by producing findings that help explain how neuropeptides modulate DA neurons, has the potential to generate advances for the understanding and treatment of dopamine-related psychiatric disorders.

With cardiovascular disease as the leading cause of death worldwide, there is a need for improved wearable monitoring tools for assessing the health of the cardiovascular system. Photoplethysmography (PPG) is a continuous, non-invasive measurement that encodes a multitude of informative vital signs, including heart rate, heart rate variability, respiratory rate, cardiac output, and arterial stiffness. Although existing PPG sensing technologies record from the finger or wrist, the face presents a promising and underutilized location for wearable pulse sensing. This work presents a novel wearable PPG sensing system that records at multiple wavelengths and facial locations. As a proof-of-concept, we seek to evaluate a potential application of our system incorporated in a surgical face mask for use in intra-operative hemodynamic monitoring. By collecting data with our system alongside ground truth cardiovascular vital signs, we can build and test non-invasive inference algorithms. After validating our system’s heart rate detection accuracy with a standard error of 2.84 beats per minute, we now proceed to test our device’s ability to infer additional cardiovascular parameters. In addition to showing promise for novel non-invasive, continuous surgical monitoring, this work has broader implications for wearable health applications based on face-worn form factors such as glasses, helmets, and headsets.

Blood pressure (BP) serves as the primary indicator of a patient’s cardiovascular health. Today, cuff-based BP monitors are the gold standard for routine blood pressure monitoring. However, they are prone to inaccuracies and cannot provide continuous readings. Continuously monitoring BP would allow patients to observe their BP fluctuations from eating, medicine intake, and exercise, thus empowering individuals diagnosed with hypertension to make better-informed health decisions. This motivates the need for a non-invasive, continuous blood pressure monitor. Prior studies have already shown the potential for pulse transit time (PTT), which is the time for a pulse wave to travel between two arterial sites, to be used for non-invasively measuring BP. In this work, I hope to improve upon this technique. To do this, I focus on testing and improving the pulse detection accuracy of a system incorporating an optical sensor array in a surgical eye protection face mask. By getting a better resolution of the pulse waves, I believe the estimate of BP will be more accurate and, in turn, provide a valuable dataset to further investigate the relationship between PTT and BP.

The dystrophin protein protects cardiac and skeletal muscle from damage during normal contraction and relaxation by acting as a shock absorber in the cell. Mutations in the dystrophin gene lead to Duchenne muscular dystrophy (DMD), an X-linked recessive disease. Boys suffering from the disease become ventilator dependent at a young age and usually succumb to cardiac failure in their thirties. Other symptoms of DMD include muscle wasting, cardiomyopathy and respiratory failure. Currently there is no cure for DMD and while gene therapy has shown great promise, it still needs to be complemented with additional therapeutic interventions in order to fully address the symptoms of DMD. Previous work by our lab identified several drugs that blocked a certain type of calcium channel in cardiac muscle and protected the cells from damage following injury by correcting calcium movement into and out of the cell during muscle contraction. In this study, the leading drugs will be tested further using a cross-platform approach. The drugs will initially be tested in cardiac and skeletal muscle differentiated from healthy and DMD patient-derived induced pluripotent stem cells (iPSCs). The top three drugs that restore normal contraction and relaxation kinetics in vitro will then be tested in the DMDmdx rat. This novel, small animal model has a similar progression of DMD symptoms to human patients. The rats will be fed the drugs in their chow. Skeletal and cardiac muscle performance will be evaluated to determine whether correcting muscle contraction kinetics ameliorates the symptoms of DMD. Furthermore, we will show whether the same drug is equally effective in treating both cardiac and skeletal muscle. The cross-platform approach may help to better predict drug efficacy, leading to a reduced rate of failure in clinical trials. Moreover, this approach may serve as a benchmark for drug discovery in other neuromuscular diseases.

Blood flow in microcirculation is a significant physiological parameter that reflects the adaptive response of organs to disease, trauma, and cancer. Although ultrasound Doppler imaging was previously unable to assess blood flow in the microvasculature (< 0.5 cm/sec), the introduction of microbubble contrast agents has removed this limitation. However, blood flow of the entire vascular tree is mixed together during imaging. We present a method that segments and visualizes the entire vascular tree, including capillary blood flow, larger sub-spatially resolved vasculature and larger vasculature (>50 µm). In this work, we present an approach that decomposes nonlinear Doppler acquisitions into different groups of velocity projections. We demonstrated the ability to segment these different levels of vasculature in a rat spinal cord injury model where the varying rates of low velocity microbubble decorrelations captured by our high frame rate acquisitions enable us to quantify microvascular blood flow. This approach overcomes limitations encountered in conventional imaging methods by removing tissue signal before Doppler processing by combining high-frame rate plane wave imaging, microbubble nonlinear pulse sequences, and Doppler segmentation of blood flow. Singular value decomposition was used to segment the nonlinear Doppler signal. Our results successfully illustrate the segmentation of lower velocity sub-resolution microvascular flow and higher velocity flow in larger vessels in a rat spinal cord injury model. We isolated low and mid-velocity flow in sub-resolution vasculature (<20 µm). We observed different spatial distribution and bolus kinetics between low- mid- and higher velocity Doppler projections. We are assessing the utility of these different blood flow features for the management of spinal cord injury and other applications (e.g. oncological).

Induced pluripotent stem cells (iPSC) have a high potential, for they can be differentiated into any cell type for regenerative medicine, drug discovery, developmental biology, and disease modeling. However, iPSC’s and their differentiated progeny display an undesired variability in their shape, contractile properties, growth rates, etc. Identifying subsets of phenotypes in iPSCs and their differentiated progeny will allow us to optimize tissue models for research. Here, we generated a rainbow reporter line in iPSCs that can track individual cells as they clonally expand and differentiate while providing phenotypic information. Knocking in four copies of a cassette containing three distinct fluorescent proteins allowed the expression of up to eighteen different colors. However, not all colors were present in equal proportion, increasing the probability that distinct lineages could have the same color. To achieve an equal color distribution, colored cells were isolated by sparsely plating a culture of mixed colored cells. After a week of expansion, individual colonies were picked and imaged under a spinning disk microscope to determine the color of the colony and whether it was single lineage or mixed. Viable cell lines were isolated and frozen in stock. These cells will be examined for markers of cell proliferation, pluripotency, apoptosis and quantitative RNA expression analysis to confirm that the color barcoded iPSCs act the same as non-engineered iPSCs. To date, we were able to create eight color barcoded iPSC lines for further experimentation, increasing the concentration limit of colored cells in non-colored cells by five-fold. The next step will engineer 3D tissues by growing iPSC-derived cardiac cells in a mold to simulate in vivo tissue development. Colored coded cells will allow us to track how the initial location/physical stresses/phenotype of an iPSC-derived cardiac cell in an engineered tissue determines its tissue layer and cell type.

Over the past fifty years or so, scientists have successfully isolated microorganisms, known as endophytes, from inside nearly every region of the plant, including the roots, stems, and leaves. Some of these microorganisms have the ability to fix atmospheric nitrogen, and have even been shown to confer an array of additional benefits to their plant hosts, ranging from fungal pathogen resistance to increased stress tolerance, and more. Recently, many scientists conducting endophyte research have observed their endophytes losing their plant-enhancing activity after extended periods of isolation from their original plant hosts. This makes the plant-enhancing effects of the isolated endophytes impossible to study, and more importantly points to a crucial need for a better understanding of plant-endophyte communication mechanisms. Because reactivation of several endophytes was observed after introducing native plant extract back into the isolated endophytes’ medium, we have embarked on a journey to determine what in the plant medium causes these inactive endophytes to regain their plant-enhancing abilities. To do this, we have first determined the level (transcriptional, translational, or post-translational) at which nitrogen-fixation, a crucial symbiotic activity, is regulated by the presence of plant extract in one of our endophytes. We then designed and built a reporter plasmid to track the expression of key nitrogen-fixing genes, and will next fractionate the native plant extract and use this reporter plasmid to monitor the effects of different plant fractions. This will hopefully lead to key insights into the potential plant signal that initiates many symbiotic endophyte activities. The exploration of the plant-endophyte symbiotic signaling system has the potential to impact the fields of agriculture, forestry, and environmental sciences worldwide.

Our goal is to predictively engineer bio/nanomaterial hybrid systems with targeted functionality in a wide range of practical, technical, and medical applications. The open literature provides datasets of the functional properties of crystals, aqueous chemicals, and biological macromolecules, but the design of hybrid systems necessitates the modeling of all of these molecular species in a single common framework. Molecular graph convolutional networks and other deep learning methods are capable to train on datasets from multiple disciplines simultaneously, but in order to build these networks, a far-reaching data infrastructure is needed. We have created this infrastructure for three data sets: The Immune Epitope Database (IEDB) of MHC-I binding peptides, the Quantum-Machine.org QM9 dataset (QM9), and results extracted from the Materials Project. The IEDB provides binding affinities between biological macromolecules (peptide sequences in association with multiple MHC-I alleles); QM9 consists of 140,000 small organic molecules encoded as SMILES strings and 17 associated properties (including thermodynamic, energetic, geometric, and electronic information). The Materials Project dataset provides band gaps and formation energies for 70,000 crystal structures. We present a standardized train/test split and machine-learning-ready import interface for each of these datasets, as well as early results on co- and cross-training of deep neural networks across multiple datasets. The framework is expandable to new datasets and provides a strong foundation for ongoing efforts to build universal molecular encoding neural networks.

People living in rural Northern Tanzania are highly dependent on their natural environment for their health and livelihood. Consequently, they are a vulnerable population with regard to the potential negative effects of climate change. In this study, a semi-structured interview questionnaire was used to interview inhabitants of the Laja, Getamock and Kaza Roho villages, and measure their perception of the effect of climate change on their livelihood, health, and gender roles in the Manyara and Arusha regions of rural Tanzania. A total of 226 interviewees were asked about their perceptions of rainfall patterns, natural resource availability, disease rates, gender roles, and birth control use. The majority of respondents perceived a decrease in the frequency of rainfall and an increase in the frequency of drought. Moreover, 89% of the respondents were determined to be pastoralists or farmers that are directly affected by reduced precipitation, which decreases natural resource availability and crop yield, and increases rates of disease in humans and livestock. Respondents also reported shifts in gender roles to accommodate the rise of health, natural resource, and financial burdens stemming from climate change; for example, men are increasingly responsible for gathering drinking water because sources nearby villages have dried up and only men can drive motorbikes and ox carts now required to travel such long distances. Lastly, it was found that contraception usage has increased in younger, more educated groups in conjunction with a decreased number of desired children. Because family planning are associated with girls achieving higher levels of education and economic growth, improved family planning presents a potential solution to the financial hardship imposed by climate change. Considering the challenge of mitigating the inimical effects of climate change to developed nations, solutions to these problems are critically important to vulnerable groups that are highly dependent on natural resources for their health and livelihood.

Oceanic biogeochemical pathways, and particularly nitrogen, play a large role in global carbon cycling. Oxygen Deficient Zones (ODZs) such as the Eastern Tropical North Pacific (ETNP) have microbes that use distinct metabolic pathways for energy and nutrients in the absence of oxygen. These ODZ pathways shape the global inventory of nutrients and are thought to be responsible for around half of marine bioavailable nitrogen losses. While some of these pathways such as canonical denitrification and the more recently discovered anaerobic ammonia oxidation have been studied, there are also other potentially significant pathways. Trimethylamine N-oxide (TMAO), a small nitrogen-containing organic molecule with pathways that connect into other nitrogen cycle pathways, was seen to be diminished to nonexistence in ODZs which suggested it was being utilized. While studied in other environments, microbial utilization of TMAO in ODZs has not been significantly studied. We mapped metagenome reads collected from the ETNP ODZ onto a phylogenetic tree annotated with genes for TMAO degradation found outside the ODZ. We were able to confirm the presence of genes for TMAO degradation pathways and identified a range of organisms involved. We also examined the distribution of these genes and organisms across the different depths we sampled from to create a more complete picture of nitrogen cycling in ODZs.

Sea ice plays a significant role in the global climate, but the details of summer melt processes remain poorly resolved. Sustained low-wind events over the Arctic Ocean have been observed to correspond to high salinity and temperature stratification in sea-ice leads, consequently increasing lateral melt rates during summer. Such an effect is currently unaccounted for in leading climate models, and appropriate parameterization could potentially reduce error in projections. We used a wind reanalysis dataset produced by the National Center for Environmental Prediction (NCEP) and the National Center for Atmospheric Research (NCAR) to study wind patterns in the Arctic. We focused on daily variation in oceanic regions at latitudes above 65 degrees during Summer (May 1 - September 30) over 2010-2019. An index of low-wind events was extracted from the reanalysis data and these events were classified according to length of event and geographical extent. Our results suggest that low wind events are frequent throughout the summer, but are not equally distributed spatially across the basin. Low-wind events were compared to other climate data, including sea-ice extent, on a spatial and temporal basis. Our results were compared to climate model output and differences were examined. We propose a basic parameterization of the effect of low-wind events on sea ice melt, and suggest further collection of observational data to improve physical representation in climate models.

In order to perceive attack by herbivores and pathogens and subsequently mount appropriate defensive regimes, plants rely on a variety of protein receptors that recognize and initiate responses to damage, pathogen, and herbivory associated molecular patterns (DAMPs, PAMPs, and HAMPs, respectively). Although DAMPs and PAMPs have been studied extensively, the first HAMP-receptor pair was only recently discovered. The inceptin receptor (INR) discovered in cowpeas (Vigna unguiculata) binds to inceptin, a small peptide and potent HAMP found in the oral secretions of Lepidopteran caterpillars, promptly eliciting an immune response leading to enhanced resistance against herbivory. In order to further characterize the structure and function of INR, I am developing a fluorescent reporter for use in Nicotiana benthamiana, a model organism that normally lacks INR. Expression of the fluorescent protein mScarlet will be driven by putative promoters of genes found to be upregulated in response to inceptin binding to heterologously expressed INR in N. benthamiana. Transfer of this reporter system into N. benthamiana via Agrobacterium-mediated transformation will allow fluorescence to act as a reporter of INR function by generating quantifiable fluorescence in the presence of inceptin binding functional INR. By simultaneously transforming wild-type N. benthamiana plants with the reporter and mutagenized variants of INR, key domains and residues for the recognition of inceptin by INR and subsequent activation of plant defense will be elucidated. This will identify key structural and functional aspects of INR that will inform engineering practices for enhancing crop resistance to herbivory.

Sex determination is a crucial process in many organisms and there are many ways in which it is regulated, including through genetic and environmental mechanisms. Despite its popularity as a model for development and disease research, the precise mechanisms of zebrafish (Danio rerio) sex determination remain uncertain. Zebrafish lack the typical heteromorphic sex chromosomes present in many other species, and no specific chromosome or gene that determine sex has been conclusively identified. In a preliminary experiment, a genetic analysis found sex was associated with inheritance of single nucleotide polymorphisms (SNPs) from various regions of the genome. To test the reproducibility of this observation, we used PCR and Sanger sequencing to identify SNPs in candidate causal regions. We tested these to obtain genotypes of individual zebrafish. These fish are being crossed to assess whether significant deviations from genotype ratios are found in males and females, which would suggest that loci linked to these SNPs are in fact involved in sex determination. This work attempts to further elucidate the genetic contribution to sex determination in zebrafish.

Pain and unpleasant stimuli carry a negative hedonic valence, indicating an intrinsic aversiveness useful for avoiding harm. There are instances, however, of unpleasant stimuli carrying positive valence – such as the pleasure from spicy food, suggesting that pain and aversion can be decoupled. The Dhaka lab has discovered a small molecule Analgesic Screen 1 (AS1) which reverses the valence of a number of nociceptive and other aversive stimuli, whereby animals prefer normally aversive stimuli. Behavioral studies with zebrafish indicate that AS1 induces preference for noxious heat, painful chemical (AITC) and normally aversive dark environments. As positive valence or reward is often mediated by the neurotransmitter dopamine, we tested for the affects of dopamine antagonism on AS1-evoked behavior and found that the effects of AS1 are reversed by a D1 dopamine receptor antagonist. We currently propose that AS1 potentiates activity in the dopamine reward system in the presence of nociceptive and other aversive stimuli via D1R activation, thereby creating “pleasure from pain.” Understanding these pathways and the mechanisms underlying AS1 action, could provide a path forward for the development of novel therapeutics to treat debilitating pain disorders.

Natural proteins often assemble into various complex geometric structures based on their interactions with each other. The King Lab at the University of Washington's Institute for Protein Design uses the way these proteins behave to develop computational models that enable the design of novel self-assembling protein cages, or nanoparticles. The designed particles are capable of holding and transporting molecules or displaying antigens on their surface, making them effective vaccine candidates. My project involves recovering the solubility of one of these protein cages known as T33_dn2. T33_dn2 is a tetrahedral protein cage comprised of four copies each of two trimeric components known as T33_dn2A and T33_dn2B. While both components can be expressed individually through E.coli before being assembled in vitro, they can also be expressed bicistronically and assemble in vivo. Currently, the use of T33_dn2 as a vaccine scaffold is limited because T33_dn2B is insoluble, and only seems to be stabilized in solution when associating with T33_dn2A. When expressed bicistronically, however, the cage has an extremely low yield. For a protein to be developed into a vaccine, it must be soluble. To recover the solubility and yield of T33_dn2B, I am testing ten plasmid variants of bicistronic T33_dn2. The “original” plasmid consists of one gene coding for a high-expressing cleavable SUMO protein attached to T33_dn2A and another coding for T33_dn2B. The additional nine variants have single point mutations at specific locations on the T33_dn2A gene intended to affect binding strength. After expression, introducing wildtype T33_dn2A in vitro will allow for the formation of T33_dn2. I will be presenting the results of these expression, purification, and assembly tests.

Humans are incapable of regenerating a majority of their major tissues following traumatic injury. Tadpoles from the frog species Xenopus tropicalis have the ability to regenerate lost spinal cord, vasculature, muscle, and cartilage within a few days following injury. The regulatory mechanisms of gene expression necessary for regeneration have not yet been well defined. My primary interest is in understanding the relationship between stress signaling and gene expression during regeneration. The lab has shown that the stress responsive transcription factor Hypoxia Inducible Factor 1α (Hif1α) is necessary for the expression of Wnt target genes, one of the primary signaling processes necessary for regeneration. While we have found that Hif1α is necessary for Wnt target gene expression, we do not know the epistatic relationship between Hif1α and Wnt. In order to test this relationship, I utilized the drug IWR to antagonize Wnt and found that tadpoles treated with IWR have reduced tail regeneration 72 hours post amputation (hpa). I then supplemented these tadpoles with DMOG to stabilize Hif1α and found that DMOG is sufficient to rescue tail regeneration, suggesting that Hif1α is downstream of Wnt. In order to determine if Hif1α is sufficient for Wnt target gene expression, I extracted RNA from regenerating tails 24 hPa and used quantitative PCR (qPCR) to determine relative gene expression. I also utilized in situ hybridization to see if expression of these genes is restricted to regenerating tissues. As Wnt is a known regulator of neural and muscle development, I investigated how inhibiting Hif1α would impact complex tissue regeneration and found that Hif1α is necessary for regeneration of axons and muscle specifically. By determining the epistatic relationship between Hif1α and Wnt through the analysis of specific gene expression, we continue to improve our understanding of how regenerative organisms convert stress signals to cell fate signals.

There is a high prevalence of depression in the United States, and the impairment from depression and the impact it has on an individual’s functioning can also be severe. Thus, it is vital to examine the different causes of depression. In this study, I am investigating the effect a sense of belonging has on depressive symptoms by administering questionnaires to participants from the Midlife in the United States (MIDUS) study and participants from the University of Washington. MIDUS is a national longitudinal study of different aspects of health and well-being. I am also investigating the moderating effect a strong ethnic identity, specifically ethnic identity for individuals of Asian descent, has on the relationship between a sense of belonging and depression through questionnaires that will be completed by participants from the University of Washington. I am predicting that individuals, both from MIDUS and the University of Washington sample, who have a higher sense of belonging will have a lower level of depressive symptoms. Additionally, I am predicting that participants who have a lower sense of belonging but a strong sense of ethnic identity will have a lower level of depressive symptoms. Regardless of the results, the findings of this study will aid in our understanding of the role of sense of belonging for individuals with depression, and will also shed light on the importance of ethnic identity for minority ethnic groups.

3% of children live with Amblyopia (‘lazy-eye’), a visual disorder where acuity in one eye is poor even with glasses on. Amblyopia includes (1) reduced sensitivity in the amblyopic eye, and (2) interocular suppression, whereby the good eye suppresses the amblyopic eye. Our goal was to develop a method to efficiently characterize both mechanisms. Participants viewed a Gabor stimulus modulating between 0-100% contrast over time through a stereoscope, that presented a different image to each eye. Participants reported perceived contrast over time using a joystick. On each trial, the initial 14 s consisted of binocularly identical gratings modulating at 1/7 Hz, followed by 48 s where the gratings modulated at 1/8 Hz in one eye, and 1/6 Hz in the other. Separately, we measured visual acuity, stereoacuity, contrast sensitivity, the interocular suppression ratio. This method was highly efficient: only 30 min of data were needed to estimate monocular sensitivity and interocular suppression. Another advantage of this approach is that the stimulus is relatively naturalistic – the images in the two eyes are the same, except for the difference in contrast. This is important due to the nature of its binocularity and naturalistic conditions, as this will be the first of its kind - allowing clinicians a better way to assess those with amblyopia. 

The phenomenon of cognitive dissonance is described as the psychological process an individual undergoes when making a decision that involves conflicting beliefs or information. Understandings come mainly from both a biological perspective and a cognitive-behavioral perspective. Studying decision-making at an individual’s cognitive level has applications for the study of complex social processes such as political group action, modern digital communication, and religion. Understanding the phenomenon of cognitive dissonance is important to furthering our understanding of how people both obtain, retain, and replace ideologies. This literature review discusses the long-standing theories of cognitive-dissonance and then goes further to list and contrast criticisms of these paradigms as well as new data gathered on this topic. While the model of cognitive consistency, which is defined as an inherent human motivation to reduce inconsistent beliefs and ideas, is still widely accepted and used in psychology, there are now several challenges to this construct, mainly over the conception of consonance and dissonance and the subsequent processes that follow. These criticisms include the perspective that current methods over-measure processes of cognition that manifest in action, the perspective that people look outward to socially verified opinions and paradigms more than previously accounted for in current and past research, and that the choice process for decision preference is active during or already concluded by the time that subjects are self-aware of any conscious decision-making process. Methods are widely varied in this field and include fMRI, PET, behavior studies involving decision-related attitudes, and specific group case studies that include ethnography. Further research remains to be done regarding cognitive dissonance in both psycho-cultural and neurological contexts, as well as a reexamination of past literature on the topic within cognitive psychology.

Anxiety symptoms are common in children with attention deficit hyperactivity disorder (ADHD). It is unknown whether the neurobiological origins of comorbid anxiety and ADHD symptoms are shared or distinct. The current study addressed this using an event related electrophysiological potential (ERP) component, the error-related negativity (ERN), which occurs after an individual makes a task error. ERN amplitude has opposite associations with ADHD and anxiety symptoms: it is weaker in association with increased ADHD, but greater in association with increased anxiety. We tested whether 1) anxiety symptoms and ADHD have separate neurobiological origins, indicated by greater anxiety being associated with increased ERN in children with ADHD or 2) anxiety and ADHD symptoms share an origin, as evidenced by no effect of anxiety on ERN in children with ADHD. The current study investigated the association between ERN amplitude and anxiety levels in a sample of 7- to 11-year-olds with ADHD (n = 98) and without (controls; n = 26). Participants completed two ERP tasks of varying difficulty. ERP data were segmented around incorrect task responses, and mean ERN amplitude was extracted. Data on child anxiety and ADHD symptoms was collected via parent report. Linear regression analysis was used to estimate the associations among ERN amplitude, severity of anxiety, and ADHD symptoms. Preliminary results (n = 73) indicated that ADHD symptom severity was associated with smaller ERN amplitude (r =.31, p =.007), but anxiety symptoms were not associated with ERN in the ADHD group. Preliminary results indicated that the ERN is not a marker of anxiety in children with ADHD to the same degree it is in controls. This is consistent with shared neurobiological etiology for ADHD and anxiety symptoms in children, which has clinical implications for conceptualization and treatment of anxiety symptoms in childhood ADHD.

Assumptions about gender and sexuality in the health care system often manifest as structural barriers to accessibility. Stakeholders, such as healthcare program managers, executive directors, practitioners, and other staff members, inform the organization’s structure, which guides providers on the service provision they provide to their LGBTQ+ patients. Thus, understanding health care staff perceptions on how current policies and programs contribute to the health care environment for the LGBTQ+ community will assist efforts for equitable service provision. Semi-structured interviews were conducted on staff from 6 health care organizations. Open-ended questions focused on their perspectives on current practices and policies, organizational areas of growth, as well as barriers, for equitable care. The purpose of the study is to discuss LGBTQ+ health within their organization to elicit staff perceptions on values and perspectives that address LGBTQ+ health disparities. Interviews were transcribed and inductive thematic analysis was done to find common benefits, viewpoints, and areas of improvements. Themes such as lack of knowledge, cultural biases, historical discrimination, and collaborative leadership, emerged. The findings of this study show gaps in delivering coordinated, patient-centered care for LGBTQ+ patients. This suggests greater importance for organizational education and training, particularly related to how historical oppression impacts bias in their setting. The overall implications of the study illustrate the relationship between the themes and organizational impact on service provision, which impacts the accessibility, safety, and quality health care environment for LGBTQ+ patients. This is crucial to giving context and describing the systematic impact on an individuals’ access to and quality of health care for the possible use in future studies.

The world’s largest high-energy particle accelerator, the Large Hadron Collider, relies on sub-millisecond processing performed on massive amounts of data coming out of its particle detection system, which is due for a major upgrade in 2024. The old particle detection chips will be upgraded to RD53B chips with faster data transmission, allowing for more complicated data processing. The readout systems that interact with the particle detection chips, YARR and FELIX, need to be tested with the RD53B chips and debugged before the system is put in place. The goal of our research is to create an emulator of the RD53B chip that can produce dynamically generated pseudo-realistic data at the same rates that would be seen in the Large Hadron Collider without the need for heavy radiation. This will allow for readout software to be fully functional and debugged before the actual RD53B chips are fabricated and placed into the Large Hadron Collider. We are using Field-Programmable Gate Arrays (FPGAs) to mimic the hardware inside the real RD53B chips. In place of RD53B’s analog sensors, we have substituted digital logic that generates pseudo-realistic data because FPGAs cannot emulate analog hardware. The alpha version of the RD53B emulator with basic communication and pre-programmed data was completed in February. Recently, the beta version of the emulator with dynamically generated data was completed, and we have been testing communication between the emulator and FELIX. With the beta version of the RD53B emulator tested and verified by us, the developers of YARR and FELIX will use our hardware to help verify that their systems will provide accurate readouts from the real RD53B chips. The next steps for the RD53B emulator include a hardware data decompression accelerator, as well as any additional features requested by the YARR and FELIX teams.

Filtering the data produced by the Large Hadron Collider (LHC) is computationally challenging due to the sheer quantity of the data, on the scale of hundreds of terabytes per second. In the coming years, data production for the LHC is projected to increase by a factor of 15 with the high luminosity upgrade. Machine learning algorithms could provide pattern recognition capable of filtering data produced by the LHC. Specialized hardware could increase the throughput to match the data rates required by the LHC. We analyzed several cloud-based specialized hardware solutions including Amazon Web Service FPGAs, Microsoft’s Brainwave Service, Google’s TPU, and NVIDIA GPUs to compare the performance of each of them for particle physics application. The networks accelerated were trained on a variety of data including: Top vs QCD quark classification, Hadron calorimeter data, and electron energy regression. These experiments demonstrate the feasibility of machine learning algorithms in high throughput required situations such as high energy particle physics.

Chronic respiratory infections and diseases are the third leading cause of death globally. The Frevert lab studies the protein versican (Vcan), an extracellular matrix proteoglycan, whose expression is highly upregulated during lung injury and inflammation. However, it is unclear whether this upregulation is an anti-inflammatory or a pro-inflammatory response. We are testing the hypothesis that the cellular source of Vcan determines its inflammatory actions; versican from myeloid cells is anti-inflammatory but versican from stromal cells is pro-inflammatory. Vcan deletion in our cells of interest can test this hypothesis. To do this we have generated Vcan^fl/fl genetically engineered mice, which allow for conditional removal of functional versican with Cre Recombinase. Cre excises versican’s exon 4, recombining exons 3-5 and creating a premature stop codon. This produces a truncated non-functional form of versican. The goal of this research project is the development of cell-specific protocols for in vitro deletion of versican in both myeloid cells (bone marrow-derived macrophages) and stromal cells (lung explant fibroblasts). These protocols will allow for further evaluation of versican’s role in the inflammatory response when different cell types are confronted by a bacterial or viral agonist. So far, I’ve been investigating the dose response and time course for exposure of macrophages to Cre to optimize its efficiency and have been able to demonstrate by qPCR that intact versican decreases and non-functional versican increases. The inflammatory response is quantified through qPCR analysis of the fold increase of Ifn-b compared to the house-keeping gene MRPL32. Ifn-b is a cytokine released by the innate immune system in response to viral pathogens. Next, I will investigate the conditions necessary for efficient Cre deletion of Vcan in fibroblasts. These experiments allow us to investigate the effects of Vcan made by different cell types furthering our understanding Vcan’s function during injury and inflammation.

Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of wound and hospital-acquired infections. Glycopeptides (e.g. vancomycin), lipopeptides (e.g. daptomycin), and lipoglycopeptides (e.g. dalbavancin) are three classes of cell-wall/cell-membrane targeting antimicrobials effective for treating MRSA. Since in S. aureus cell wall synthesis and lipid synthesis are metabolically closely connected, response to cell-wall/cell-membrane targeting antimicrobials is likely to be mediated by lipid synthesis. Indeed, our lab previously demonstrated that the overall lipid abundance decreased in the dalbavancin-resistant S7-D2 strain (vancomycin-intermediate), isolated by in vitro exposure of a clinical MRSA isolate S7 strain (vancomycin-susceptible) to multi-stage escalated concentrations of dalbavancin. Here we examined a lipid synthesis inhibitor, AFN-1252, to determine its potential synergistic effects with vancomycin, daptomycin or dalbavancin, using the S7 and S7-D2 strains. Broth microtiter MIC measurements and static time-kill experiments were performed to evaluate potential synergy. We found that, through the MIC measurements, the pellet sizes in the wells seemed to be reduced when S7 and S7-D2 were treated with AFN-1252 at half the MIC in the presence of vancomycin. Hence, a static time-kill at 2xMIC of AFN-1252 and/or vancomycin was performed to interrogate the growth difference. S7-D2, but not S7, showed increased killing with the combination, suggesting that killing by vancomycin could be aided by AFN-1252 in vancomycin-intermediate strains. The killing by the combination in S7-D2 also approached the level of killing by vancomycin alone in S7, suggesting mechanistically membrane lipid remodeling might have happened that counteracted the slower killing in the vancomycin-intermediate strain. Our preliminary results so far suggest that lipid synthesis inhibitors might be able to enhance the MRSA treatment effects of vancomycin. In future studies, we will evaluate the potential lipid profile changes using comprehensive lipidomics analysis, and further screen and evaluate other lipid synthesis inhibitors and their potential synergistic effects with vancomycin, daptomycin or dalbavancin.

X chromosome aneuploidy refers to an atypical number of X chromosomes, differing from two X chromosomes in females, or one X and one Y chromosome in males. Unusual numbers of chromosomes arise from errors in cell division that result in too many or too few chromosomes in a cell, with X aneuploidy reported to occur in around 1 in 1000 births depending on the disorder. X chromosome aneuploidy disorders, such as Klinefelter (47, XXY), Triple X (47, XXX) and Turner (45, XO) syndromes are associated with developmental abnormalities, including cognitive and cardiovascular defects. Our goal is to generate isogenic induced Pluripotency Stem Cells (iPSCs) with different numbers of X chromosomes from patients with X aneuploidy, and subsequently differentiate them into relevant cell types to identify genes affected by aneuploidy. Our lab has previously generated isogenic XXY and XY iPSCs from patients with Klinefelter’s Syndrome by removing the extra inactive X chromosome (Xi). My project is to establish and characterize isogenic lines from mosaic XXY/XY patients, who have a mixture of cell karyotypes. Specifically, I am screening iPSC clones derived from mosaic patients for expression of XIST, a gene expressed only from the Xi, by RT-PCR to determine presence or absence of the Xi. Isogenic control XY iPSC lines derived from the same patient serve as a control to XXY cells, lessening potential for confounding variables due to differences between individuals. Next, I will screen clones with different genotypes for integration of reprogramming vectors by genomic DNA-PCR. Integration-free isogenic XXY and XY clones will be differentiated into cardiomyocytes, neural progenitor cells, and cortical organoids, cell types that are associated with the adverse effects of X aneuploidy. By doing so, we hope to gain insight into gene expression and epigenetic changes associated with X aneuploidy phenotypes in a controlled genetic environment.
 

Osteoporosis is the leading cause of decreased bone density in elderly patients, putting them at increased risk of insufficiency fractures. Surgical fixation of these fractures faces high rates of failure in part due to the difficulties in achieving secure fixation of hardware in weakened bones. This has become an increasingly prominent issue in recent years due to the notable increase in sacral insufficiency fractures. This project studies the distribution of bone density across the cortical and trabecular bone of the sacrum in order to highlight areas of variable bone density for better surgical planning of screw placement. We hypothesized that there would be significant differences in local cortical and trabecular bone density associated with age and sex. CT scans of the abdomen/pelvis were obtained for 50 patients without fractures. The sacral bones were segmented and manually edited to produce a 3D model of the sacrum. Bone density values were then determined for the full bone from calibrated CT data. This allowed us to create a linear model including age and sex as a predictor of bone density at each of the surface and internal points. A heat map of the bone models was created using a color scale in order to visualize the cortical and trabecular bone mineral density. A trajectory following the typical path of fixation screws in the S1 and S2 segments were manually identified on these bone models and density values across this were estimated. We were able to locate regions of the sacrum where bone mineral density was significantly associated with age as well as sex. This data can be used to identify areas to avoid or target during the surgical planning of screw fixation to improve screw purchase. Further cadaveric biomechanical investigations are suggested to explore this concept. 

 An estimated 50% of patients scheduled to undergo surgical correction of their adult spinal deformity (ASD) are preoperatively managed with chronic opioid therapy. In recent years, preoperative opioid use has been correlated with increased morbidity and mortality following major abdominal, orthopaedic, and spine surgery. Despite high prevalence of chronic opioid consumption in ASD population, limited data is available to guide preoperative opoid tapering to improve postoperatve outcomes. First attempt to identify a morphine equianalgesic (MEA) dose threshold for patients undergoing spine procedures was described in Neurosurgery by Wick and co-workers. After calculating MEA values for 1020 cervical and lumbar spine surgical patients, the group reported MEA dose threshold beyond which patients are less likely to achieve the minimum clinically important difference (MCID). In patients undering a Complex Spine Surgical procedure, we hypothesize that an increased preoperative opioid dose may have a threshold beyond which patients are more likely to suffer from an adverse event. A trained data abstractor will collect data for the analysis during the retrospective chart review. In addition to data collection, abstractor will calculate morphine equivalent dose (MED) values for each patient meeting the inclusion criteria. Statistical analysis will be performed to evaluate association between MED values and postoperative outcomes. Parametic and non-parametic tests will be used as necessary, inclusing but not limited to t-tests for Equality of Means, Fishcer exact test, Chi-square, Independent Samples Mann-Whitney U Test, and logisitic regression. All data will be reported in aggregate. Reporting a defined opioid theshold for ASD patients may aid in developing a standardized tapering protocol aimed at improving postoperative outcomes. 

The 2019 Novel Coronavirus (COVID-19) pandemic has necessitated the implementation of various infectious disease control measures, including the closure of non-essential businesses, social distancing, and the virtualization of schools and universities. As final year nursing students at the University of Washington (UW) adjust to virtual learning and social distancing, certain students working in healthcare may also face the threat of contracting the virus. Little is known about the psychological implications of the COVID-19 pandemic on this population, and there is a need to fill this knowledge gap. This study first aims to capture the perceived stress levels of final year nursing students at the UW amid the COVID-19 pandemic. It secondly aims to explore associations between perceived stress and factors such as COVID-19 testing history, living situation, and healthcare work history. We administered an online survey to final year UW nursing students that inquires about their COVID-19 testing history, living situation, and healthcare work history since March 1, 2020. The survey also includes the 10-item Perceived Stress Scale, which questions students’ feelings and thoughts over the past month. We will analyze the data for associations between scores on the Perceived Stress Scale and students’ testing history, living situation, and work history. Overall, we expect to find moderate to high perceived stress levels among nursing students. We also anticipate that several factors may be associated with higher stress levels among nursing students, including having a history of COVID-19 testing, living with more individuals, and working more hours in healthcare positions. The results of this study may indicate a need for increased psychosocial support in final year nursing students at the UW, as they complete the nursing program and join the nursing workforce to help combat the COVID-19 pandemic.

Fall prevention in hospitals and long-term care facilities in the community setting depends on staff being trained in best practices. However, little is known about the cost, availability, and accuracy of online trainings on fall prevention for nursing staff. The type of education given can be outdated, incorrect or unnecessary depending on what organization that the nursing staff belongs to. The purpose of this research is to identify and evaluate existing online fall prevention training programs and provide the findings to the Washington State Department of Health (DOH) for them to present options to provider organizations as part of the State’s Fall Prevention Strategic Plan. Materials evaluated were previously used for staff education in hospitals and long-term facilities. The criteria for evaluating the websites and educational learning resources (ELRs) were: authority, objectivity, authenticity, reliability, timeliness, relevance and efficiency. Cost was also considered in the evaluation as a factor. Following the evaluation, ELRs were classified by two independent reviewers as either highly recommended, recommended, partially recommended or not recommended for use. From our initial findings, we identified two ELRs that are highly recommended for use, two that were recommended, and three that were partially recommended out of 24 ELRs. After finalizing our results, we will randomly select modules to be evaluated by a group of University of Washington Nursing students for verification of our assessment in reliability and validity of the ratings. We will disseminate findings and recommendations to WA DOH Older Adult Fall Prevention Program and clinical partners through a webinar. This should improve training provided to health providers of care to older adults in hospitals and long-term care facilities. This evaluation method can also be applied to other ELRs to improve the quality of these offerings and assist providers in choosing the best available programs.

Public health nurses and leaders who work for small, rural health departments (LHDs) face unique challenges that prevent the effective use of data to understand and address health equities. Among these is limited access to high-quality training in data utilization. In response, Solutions in Health Analytics for Rural Equity across the Northwest (SHARE-NW) is developing an online learning hub that contains accessible training modules for LHD leaders and practitioners to use and interpret data easier. The purpose of this study is to determine gaps in the quality of the trainings available to rural LHD practitioners in six top health priority areas: obesity, diabetes, tobacco, mental/behavioral health, violence and injury, and oral health, in order to improve population-level health equity. To date, approximately 30 training modules have been evaluated using 25 items from the Quality Standards for Training Design and Delivery tool by the Public Health Learning Network, and approximately 50 webinars have been evaluated using a set of 6 criteria. Next we will identify the patterns of gaps across the evaluation criteria and top health priority areas. Once patterns are identified, we will conduct semi-structured interviews with public health practitioners to assist in the interpretation of identified patterns. Preliminary findings suggest a lack of training activities that assist LHD leaders and practitioners to learn about data utilization in several to health priority areas. By identifying the patterns of gaps in available trainings, we aim to help busy, low-resourced rural LHDs utilize the highest quality trainings to improve their ability to interpret data and address health disparities.

Premature infants are commonly born with an inability to feed properly from their mother’s breast, and enteral (tube) feeding is often too stressful on the still-growing body of a premature infant. A recent intervention called Oropharyngeal Colostrum (OPC) administration aims to safely and effectively strengthen the infant’s digestive and immune system, shortening the time to safe enteral feeding. Colostrum, the milk produced right after delivery, is exceptionally high in antibodies and proteins necessary for an infant’s development, and contains an even higher concentration of protective bodies after delivery of a susceptible premature newborn. With OPC administration, colostrum is swabbed on the infant’s cheek or tongue in small amounts on a regular schedule. When the colostrum comes in contact with the tissue in the mouth, the antibodies are taken in and boost the baby’s immune system, heightening resistance to common infections suffered by premature infants, especially in the gastrointestinal region. In 2018, the Lactation Program of the Hospital de la Madre y el Niño (HMN) in Formosa, Argentina began administering OPC to all infants admitted to the Neonatal Intensive Care Unit who were born <35 weeks gestational age and whose mothers consented to the procedure. This research will examine average time to enteral feeding among 400 premature infants administered OPC between 2018-2019. Differences are examined in average time to enteral feeding by gestational age, sex, Apgar score, birth weight, and colostrum administration. The data will be used to determine what characteristics in premature infants cause the most obstacles to enteral feeding. Results will be compared to other studies of time to enteral feeding with and without OPC administration. Results will be shared with the HMN administrators to inform them of the efficacy of the program.

The modern human longitudinal arch is a structural adaptation to bipedal locomotion, rigid enough to be a propulsive lever but flexible enough to stabilize a large body mass over a relatively small base of support. Early hominins appear to have a low or absent longitudinal arch—a condition equivalent to human pes planus. The morphology of the calcaneocuboid joint (CCJ) has been suggested to play a critical role in the stability of the longitudinal arch, but the relationship between articular shape and arch height has yet to be tested empirically. This study examines the covariation of the shape of the CCJ with arch height, via calcaneal inclination angle (CIA). Eleven calcaneal measurements and CIA were measured on weight-bearing radiographs of 103 patients from an urban US trauma center. An equation to predict CIA was determined using stepwise regression analysis using Böehler’s angle, plantar and distal angles of the calcaneal tuber, anterior angle, and the angle of inclination of the posterior talar facet (all p’s<0.01, R2=0.67). Landmark data were obtained from 3D surface scans of the CCJ of 24 calcanei from lower limbs amputated due to infection or acute ischemia. Individuals with bony pathology were excluded from analysis. Data were analyzed in R using Procrustes ANOVA with principal components analysis to explore patterns of variation within the sample. No significant associations were found between CCJ shape and CIA (p=0.51, R2=0.03, F=0.91). Consequently, calcaneocuboid joint shape may not be a useful for interpreting the longitudinal arch morphology of fossil hominin pedal remains.

An estimated 20.6 million people live with Human Immunodeficiency Virus (HIV) in Eastern and Southern Africa. In 2012, the World Health Organization (WHO) announced Option B+ which adopts a single, universal regiment to both treat HIV-infected pregnant women and prevent mother-to-child transmission of HIV. Unlike other HIV treatment options, Option B+ is a lifelong provision of antiretroviral therapy (ART) for all HIV-positive pregnant women regardless of their immune status or viral load. However, I hypothesize that the implementation of prolonged HIV treatment (Option B+) may pose a substantial financial burden for women in very resource poor settings, which could ultimately decrease ART adherence--resulting in no change or even an increase in maternal transmission. This research will examine how economically accessible Option B+ is for expecting mothers in different populations across Eastern and Southern Africa. I am statistically evaluating the cost of ART in relation to household income, living expenses, and cost of childcare at the national level. Future research will use this data to examine maternal transmission risk in relation to economic accessibility, and identify how conceptual frameworks of HIV healthcare are implemented in varied resource settings.

Seasonal and weather change on humans have countless effects on mood, sleep, and diet. Seasonal affective disorder, also known as SAD, is a seasonally linked mood and behavior disorder that typically lasts for four months, starting in the autumn. Similar to depression, SAD involves symptoms of lowered mood, energy loss, fatigue and some atypical symptoms such as hypersomnia, and increased appetite and eating. SAD may have a genetic factor related to serotonin metabolism and melatonin secretion, and rates of autumn-winter SAD may increase with latitude because of the increased seasonal differences in daylight hours. Due to genetic variations among certain ethnic groups, SAD may also disproportionately affect populations who are genetically from southern climates but were raised in northern climates. Yet it is not known how prevalent SAD symptoms were historically in populations adapted to northern climates, and what cultural traditions, if any, these cultures may have evolved in response to SAD. To answer this question, I have conducted a systematic search of ethnographies available through the Human Relations Area Files (HRAF) database. The HRAF databases have indexed and coded ethnographic knowledge across over 400 cultures. I examine the prevalence and traditions of SAD in the indexed ethnographies, and apply these insights to current migrant populations in northern latitudes that may experience SAD.

The Pondaung Formation of central Myanmar consists of fluvial and alluvial sedimentary rocks deposited during the Middle Eocene, 40 million years ago. The formation has yielded fossils of some of the earliest anthropoid primates, coeval with the first primate dispersal from Asia to Africa. Previous sedimentological and paleobotanical studies have shown that the Pondaung Formation was deposited in a landscape of open-forested seasonal wetlands with isolated riparian and monsoonal deciduous forests. However, the spread of these forests and locations of primate habitats within this mosaic landscape remains unclear. This project aims to provide a more precise reconstruction of the landscape at primate-bearing fossil sites using isotopic data gathered from paleosols as proxies for vegetation and climate during its deposition. We propose to use carbon isotope data collected from soil organic matter to produce estimates of precipitation. They are combined with the carbon isotopic composition of pedogenic carbonates to give direct estimates of soil productivity and vegetation cover. Together, these data allow us to decipher the landscape at the fossil sites, providing context for the evolution and dispersal of these primates. Our preliminary results agree with previous studies of the region, showing that the landscape was forested and flooded for considerable periods of time, experiencing strong seasonality in precipitation.

The landscape of southwest Montana is dominated by topography and adjacent sedimentary basins that resulted from deformation associated with the Sevier and Laramide orogenies140-50 million years ago and ~70-40 million years ago, respectively. Stark changes in drainage and deposition from Permian to Miocene (300 to 5 million years ago) have been described from uplifted sedimentary sequences. Despite numerous studies, the precise timing of eastward propagation of the Sevier fold‐thrust belt and its impact on drainage, as well as the timing of sedimentary basin partitioning into smaller intra-basins remain unclear. For this project, I worked under the guidance of Dr. Licht and Megan Mueller to collect field samples in Montana, isolate zircon grains for analysis and synthesize the results. Here we present geochronological and petrographic data that explain the timing of changes in drainage patterns, and place constraints on the chronology of orogenic development from Permian through Miocene sedimentary rocks exposed near Dillon, southwest Montana. The techniques used in this study are zircon geochronology and sandstone petrography. Zircon geochronology determines the age of zircon minerals found in sediment and offers insights into the ages of the sediment source areas. Sandstone petrography is used to classify the mineralogy of grains in sandstones and allow us to determine potential sediment sources. Understanding the evolution of drainages and changes in sediment transportation is critical to reconstruct the complex tectonic history of this region and aid in uncovering the chronology of Sevier and Laramide deformation.

The uplift of the Cascade Range in Washington had a dramatic impact on regional ecosystems and global climate by creating continent-scale rain shadow effects, enhancing regional aridity, and providing an anchor to the North American ice-sheet during glacial ages. Despite their importance, however, the chronology of the Cascades uplift remains poorly understood, with proposed ages for the uplift ranging from Eocene (~40 million years ago) to Pliocene (~4 million years ago). Before the onset of uplift, rivers would have drained westwards across Washington State; the uplift would have disrupted these river systems and separated river drainages on both sides of the mountain range. The goal of this study is to determine when uplift began by determining when this drainage disruption occurred. To do so, we propose to compare the sedimentary provenance of geological units of various ages on both sides of the mountains. Our methods include U-Pb dating of detrital zircons and sedimentary petrography of sandstones. Sediment samples on the west side of the Cascade Mountains have previously been analyzed for these two methods on an earlier research project. We will focus here on new results from multiple samples from the east side of the Cascade Mountains, and compare them with samples from the west side to propose a time window for the onset of uplift.

Tabletop Role-Playing Games (TTRPGs) are an increasingly popular group activity known both for their collaborative nature and creative demands. Despite the growing popularity, TTRPGs have yet to escape their reputation as a medium for social outcasts to construct escapist power fantasies. The intent of my research is to show that these “power-fantasies,” can actually become a valuable way to explore political and personal identity. I constructed a TTRPG called Blank Spaces, designed for exploring identity, and played with 6 different groups for 22 hours. After each session, I interviewed the players and used recordings of these sessions to qualitatively analyze player experiences. Players were often surprised that they had unwittingly performed meaningful self-criticism and world-criticism, all while simply enjoying a game. This has demonstrated that TTRPGs can be incredibly powerful self-exploration, critisim, and development tools.

La Llorona's ghostly figure has haunted the pages of Chicanx literature for years as the monstrous woman. While her story shifts forms depending on the cultural context, the essentials remain: she was a woman, wronged by the father of her children, who now wanders the rivers at night wailing for the two children she drowned in anger, grief, or desperation. She has often been considered a monstrous figure whose function has been to regulate female identity. However, authors like Gloria Anzaldúa and Sandra Cisneros have sought to reclaim this ghostly visage from the grasp of patriarchal structures that condemn la Llorona's actions. Anzaldúa's poem "My Black Angelos" and Sandra Cisneros' short story "Woman Hollering Creek" revise la Llorona to acknowledge the female agency she represents. While critics have focused on feminine agency in these works, the function of the monstrous has been overlooked. The monstrous usually refers to something feared or uncanny with women and people of color's bodies representing cultural fears, but in these cases the monstrous is reimagined as a tool for agency. Through the lens of monster theory, and drawing on the theories of Jeffrey Cohen, Cristina Santos, and Luce Irigaray, this paper argues that Anzaldua's and Cisneros' representations of la Llorona develop feminine agency and community just as other critics have mentioned, but they also complicate monster theory by resituating the subjectivity to account for the postive monster of la Llorona. Through this, monster theory's dependence on a self/other dichotomy falls away and, with it, la Llorona's position as only a monster to be feared. Instead, these representations of la Llorona invite Chicanx women into the community of the monstrous, where Cisneros and Anzaldúa transform it from an androcentric space of "othering" and oppression to one of belonging and power. 

British women participated in public political work at a higher rate than ever before during the 1906 United Kingdom general election campaign. Working as fundraisers, door-to-door canvassers, and even orators, women were particularly active in debating the campaign's central economic question: should Britain uphold the free trade policies it had maintained since the 1840s, or should it follow its economic rivals, Germany and the United States, in strengthening tariff protections? Dorothy M. Hunter (1881-1977) rose to prominence during this period as a compelling public speaker who worked on behalf of the Liberal Party and its free trade agenda. Her career serves as a fascinating case study for understanding how some British women established their credibility in traditionally male spheres at the beginning of the twentieth century; nevertheless, historians of the Edwardian era have largely overlooked her work. Based on an analysis of the collection of Hunter's documents held at the Surrey History Centre in Woking, England, this paper argues that Hunter built her authority as an activist in the public sphere upon the conventional understanding of women's power over the private sphere. Following the rhetorical tradition established by Victorian philanthropists, Hunter increased the scope of her influence by extending the definition of "the household" and "domestic duty" to encompass public life and civic virtue. This strategy is present throughout her work from 1900 to 1914, from emotionally persuasive didactic literature written early in her career to economic arguments presented in public meeting halls at the height of her fame.

The late nineteenth and early twentieth centuries saw a profusion of archaeological discoveries in Egypt which led to the period being dubbed the 'Golden Age' of Egyptology. While much of this archeological activity is tremendously important and well-known, less known yet equally significant are the personal histories of those present in Egypt during this time. The letters of Helen Winlock, wife of the Director of the Metropolitan Museum of Art's Egyptian Expedition, provide an intimate window into daily life and thought in the context of early twentieth century excavations. From bugs in the food and exploding furniture, to racially prejudiced observations of the locals and the difficulty of finding formula for a newborn child in the desert, each of Helen's many letters sheds light on the quotidian and mundane aspects of life in this often-sensationalized period. Her writings demonstrate the intersectiosn of race, gender, and colonial power in this time and place, as Helen's comments about herself, other women, and other peoples around her demonstrate the complicated politics of knowledge in this 'Golden Age' created and maintained. As a research intern in the Emma B. Andrews Diary Project, I have transcribed dozens of Helen Winlock's letters. Working from scans of the original handwritten letters, my role in transcribing these letters is a foundational first step in the process of creating digital editions of these documents, which will include versions encoded in XML, following Text Encoding Initiative (TEI) guidelines. This will facilitate the investigation of the archive using computational methodologies. Our team includes faculty, students and librarians from multiple departments across the University of Washington. This interdisciplinary and collaborative digital humanities project seeks to make a wide range of unpublished or inaccessible primary sources from the period freely available to scholars in an online format. 

This project examines what legal writings from ancient Rome reveal about the political ideology, social values, and power dynamics in Roman history. I focus on these concepts through analyzing selections from two sets of speeches given by Cicero, a politician, loyal proponent of the Roman Republic, and philosopher educated in both Latin and Greek. Additionally, I explore the scholarship on Roman legal history to provide supplementary cultural context. The sociopolitical climate of the late Roman Republic was tumultuous. Near the beginning of Cicero’s political career, he gave a set of orations, In Catalinam, to the Senate that accused Catiline of conspiring against the consuls. Much later, Cicero tried to keep the Republic alive after Caesar’s assassination and accused Mark Antony of being disloyal to Caesar by wanting to create an empire. This urge to defend the Republic prompted Cicero to write his Philippicae to attack Mark Antony. These orations ultimately resulted in Cicero’s death, as Mark Antony wanted, and the Republic ended. My research compares Cicero’s In Catilinam 1, 2, and 4 and Philippicae 4, 5, and 14: both sets involve murder plots, denunciations of powerful men, and the senatus consultum ultimum decree for Republican emergency. Specifically, I analyze how Cicero uses oratory to convince the Senate to declare Catiline and Mark Antony as public enemies. This process reveals elements of Roman sociopolitical culture, such as values, threats, and legal procedures, and follows these differences in this short, but crucial, time period in Roman legal and governmental history. Furthermore, it demonstrates the complexity between the government and the conflicting political ideologies during the late Roman Republic. Thus, through detailed analysis of these selected passages and their wider contexts, I explore how the Catilinarian and Philippic orations use references from Rome’s earlier history to adapt to, and reflect, their particular moments.

Astrology, the prediction of events from the movements of stars and planets, has grown from Mesopotamian omen-literature to the astrology of Hellenistic and Roman periods, and strangely enough it has endured even into the modern day. In this project, by drawing on scholarly analyses of the intellectual and religious context of astrology (Barton) and the worldviews of the non-elite (Toner) I examine how astrology was interwoven into the political, intellectual and social framework of the ancient world; and how the authority of astrologers was both supported and challenged by the polyvalence of their discipline, as well as their ability to connect to individual consultees. As for ancient sources, the Astronomica of Marcus Manilius, composed as a didactic poem in the early first century CE, shows how astrology was understood and used by the elite. It considers astrology in a broad theoretical context, encompassing a wide array of astrological concepts. He also illustrates the historical period in which he writes, under the new Principate of Augustus, by using astrology to legitimate Augustus's self-made status as princeps. On the other hand, other works such as that of Dorotheus of Sidon concern the more practical side of astrology. He is less concerned with theory and more with specific horoscopes, and better depicts the sorts of questions and concerns clients of a variety of social status would have had. Finally, skepticism toward astrology in antiquity is best rendered in Cicero's On Divination and Sextus Empiricus's Against Professors. These critiques and others, however, were directed less at astrological theory and more at its practitioners. By coming to understand how ancient peoples viewed astrology as both an intellectual discipline and a practical tool, we can better understand their cultural conception of the universe and in the process provide a useful comparison to similar institutions today.

As the 2020 presidential election is fast approaching, per our democratic process, Americans will soon be held responsible to fulfill, arguably, their most important political right. Elections are thought of by many as both a mechanism of accountability and a measurement of performance. Although fair elections are a necessity to uphold democracy, it is essential to recognize that this belief is a misconception. The result of a political election is predominantly decided by the culmination of individual voters making decisions based upon their backgrounds, experiences, and beliefs. To examine this notion further, it is our goal to address the question: How does obtaining a college education affect political voting patterns? To accomplish this task, we have obtained data from the American National Election Survey (ANES). The data includes over 50,000 survey responses, ranging in years from 1948 to 2016, covering topics that include, but are not limited to, wealth, background, beliefs, ethnicity, age, gender, and socio-economic status. With this data, we have performed a regression analysis that is weighted and uses the Taylor Series adjustments to compute design-consistent standard errors. Through our research, it can be seen that the trends reveal a widening gap between educational attainment and party affiliation. Furthermore, those with higher education hold more leftward leaning beliefs, and in turn, are more likely vote Democrat when compared to those with less education. Lastly, the trends over-time reveal a dramatic shift; as, non-college-educated Americans used to primarily be Democrat, while college-educated Americans were mostly Republican. We feel that this no longer holds. This research has implications to demonstrate the importance, or lack of importance, of higher education in terms of the effect and influence it has on real life decisions, which in our case is voting patterns for presidential elections.

In this project, I seek to examine the relationship between economic development and Russian influence in the post-Soviet states of Romania and Bulgaria. While scholars have studied the individual paths that these recently formed states have taken since the Soviet Union collapsed in 1991, there has been little inspection of how these nations regard the now Russian Federation. My work studies this relationship at a closer level. Specifically, I examine data on economic development at the district level (standardized by NUTS 3) in these countries and vote share for pro-Russian parties. I run a multivariate regression to examine the effect that level of development has on citizens’ willingness to accept Russian influence in their country, controlling for other relevant factors. I hypothesize that as the amount of development increases, the level of vote share for pro-Russian parties will consequently decrease. This hypothesis is grounded in the well documented positive effect that development has on democracy. In this case, a nation such as Russia, who touts anti-democratic ideals, would be looked upon less favorably by a district that is relatively more developed. Thus, I expect to see an inverse relationship between my variables. This analysis will inform research on the interactions between nations in Eastern Europe and Western Asia, areas of growing importance in this world, and allow us to examine the path forward for other post-Soviet states.

This project seeks to explore the effect of spending on state-level ballot initiative campaigns on voter turnout. Past research into the area of voter turnout has revealed evidence of relationships between campaign spending, voter turnout, and vote outcomes. Differentials in spending by competing campaigns has been demonstrated to have clear effects on vote outcomes in a variety of electoral contexts, and aggregate spending has been shown to affect levels of voter turnout as well. However, no work has in the past sought to look exclusively at the role of spending allocated to ballot initiatives in its ability to affect turnout. I anticipate higher levels of spending by pro and opposition groups correlating to higher overall voter turnout. In addition, I expect spending by opposition groups to have the greatest impact, as these groups are able to allocate funds mainly to media ads which seek to influence voter behavior through psychological aspects like fear. Using publicly disclosed data on ballot initiative spending tied to election year, the relationship between spending and voter turnout for the previous six biannual elections in four states with active ballot measure processes is investigated. Types of election, changes in voter partisanship, voter registration, and quantities and policy areas of ballot measures considered are controlled for to establish a baseline for voter turnout. The influence of campaign spending on turnout is sought after to help bridge-the-gap in relationships between spending and vote outcome, and turnout and vote outcome.

In 2010 alone, National Institutes of Health (NIH) spent $10.7 Billion (one-third of funds) on clinical trials research while pharmaceutical companies spent $32.5 Billion (70% of overall). However, we know little about the choices in co-funding and the impact generated by the co-funded projects. Every funding agency is targeted towards solving specific problems, but how inter-locked are these problems and how interconnected are the agencies? As an initial effort towards this, we explore the structure of a co-funding network, where a funding agency represents a node and an edge signifies co-funding of a project. Our core data on clinical trials includes all papers that cite and receive citations by the Cochrane Database of Systemic Reviews, a prominent journal that reviews clinical studies. From these papers, we find communities of co-funders that are guided by similar funding objectives and the primary region of operation. Next, to quantify success in funding, we use a g-index type metric that considers the average citations received by the top g most cited papers, which also indicates efficiency in funding by an agency. We find that as a funder, seeking multiple, direct connections with various dis-connected funders is more productive rather than being part of a densely inter-connected network of co-funders. This type of local network structure likely reduces redundancy in information sharing and enables efficient exchange of resources, ideas, and money. While this is not a causal relationship, we theorize that, co-funding strategies, when carefully mediated can allow a funder to achieve higher social capital which then leads to higher research success for clinical investment.

The link between protein sequence and structure is not always apparent. The dogma is that sequence determines structure, but it is not clear how very different sequences can give rise to the same structure. Here, we employ high temperature molecular dynamics unfolding simulations to probe the pathways and specific interactions that direct the folding and unfolding of the SH3 domain, a family of small proteins consisting of two β-sheets arranged to form a barrel. SH3 domain proteins are involved in various functions including protein binding, cell signaling, and nucleic acid modification. The SH3 metafold consists of 753 proteins with the same structure but varied sequence and function. To investigate the relationship between sequence and structure, we selected 17 SH3 proteins with an average pairwise sequence identity of only 27%. Six unfolding simulations were performed for each protein and unfolding transition states were determined, revealing two unfolding/folding pathways. Transition states were also expressed as mathematical graphs of contacts between chemical groups, and three positions in the transition state structure were consistently more connected to the rest of the graph than other nearby positions. These positions represent a folding hub connecting different portions of the structure in the transition state. Analysis of the multiple sequence alignment and covariation also highlighted positions with high conservation due to packing constraints and long-range contacts. This study demonstrates that the SH3 domain can fold through two distinct pathways, but certain folding/unfolding characteristics are conserved independent of sequence and unfolding pathway. By identifying similar interactions, we demonstrate how different sequences can have the same influence on folding pathway and final structure.

Cannabinoids, the main constituents of Cannabis, are a class of highly abused compounds of which, Δ-9-tetrahydrocannabinol (THC) is the primary psychoactive molecule. Despite the wide use of THC, its metabolism in humans is still in need of greater understanding. THC is metabolized to 11-OH-THC and sequentially to 11-COOH-THC by cytochrome P450 enzymes (CYPs) 2C9 and 2C19. 11-COOH-THC is then further conjugated to form 11-COOH-THC-glucuronide by UDP-glucuronosyltransferases (UGTs) 1A1 and 1A3. THC and its subsequent metabolites have been shown to bind to liver-type fatty acid binding protein (FABP1). FABPs are intracellular lipid binding proteins (iLBPs) that regulate the homeostasis of their endogenous ligands by solubilizing these hydrophobic compounds in the cytosol. Knockout of FABP1 in mouse hepatocytes was shown to decrease the formation and clearance of 11-OH-THC while the metabolism of 11-COOH-THC appeared to be unaffected. The goal of the current investigation is to translate these results into the human liver. Previously, our lab expressed and purified human FABPs to test their effect on THC metabolism in incubation assays with human liver microsomes (HLMs) and recombinant enzymes. After initiating the THC reaction with the CYP cofactor, NADPH, the 11-OH-THC product was extracted and quantified using LC-MS/MS. We found that both FABP and albumin changed the metabolic rate of THC in an enzyme specific manner. Because 11-OH-THC formation was altered in the presence of FABPs compared to the HSA control, we extend this method to continue our investigation with 11-COOH-THC metabolism. Considering that UGTs are on the luminal rather than the cytosolic side of the endoplasmic reticulum and that 11-COOH-THC has greater water solubility, we expect to observe enzyme and substrate specific effects of FABP. 11-COOH-THC and 11-COOH-THC-glucuronide are biological markers of THC metabolism so understanding this metabolic pathway is important for developing better methods of characterizing THC use in humans.

Lymphatic malformations (LM) are congenital vascular malformations resulting from dysregulated growth of lymphatic vessels. LM can cause difficulty in breathing, swallowing, or eating, and in rare cases, infection or death. LM are associated with postzygotic somatic mutations in PIK3CA, which encodes for the catalytic subunit of PI3K and regulates cell growth and proliferation. Three hotspot mutations cause the majority of LM: p.E545K, p.E542K, and p.H1047R. These mutations occur at very low level in the affected tissue; usually at <10% variant allele fraction (VAF) which makes diagnosis challenging. We hypothesize that variant allele fraction (VAF) differs throughout the vascular malformation and will correlate with location in the lesion. We used droplet digital polymerase chain reaction to detect PIK3CA mutations in 8 LM subjects with 95 samples including lesion, muscle, skin, and fat. We then mapped the VAF to magnetic resonance imaging to assess genetic heterogeneity by sample location. Globally, no sample had a VAF greater than 10% indicating that assaying multiple samples does not increase the observed VAF compared to other studies where one sample was assayed. Within patients, VAF varies within the lesion, ranging from undetectable to 10%. Non-lesion tissue, including skin, and most muscle samples, had no mutation detected. All four fat samples and two muscle samples were positive for mutation with VAF <2%. We did not identify any correlations between VAF level and location within the lesion. Though we didn’t identify a correlation between VAF and location in our data, these findings will be used for further analysis including understanding how cell type composition within the samples correlates with VAF. Our goal is that this dataset will help us explore the development of LM and eventually provide information useful for the advancement of targeted therapies for future pediatric patients.

The quality of contraceptive counseling has been shown to influence contraceptive use. Minorities and women of lower socio-economic status (SES) report that the contraceptive counseling they received as being lower quality than white, or higher SES women. Additionally, while contraceptive counseling is usually provided through verbal interactions with the clinician, evidence shows patients value the use of visual aids, such as videos, as part of the visit. The extent to which minorities or lower SES patients are satisfied with a contraception counseling video when compared to white or higher SES women is unknown. This project compares satisfaction ratings of a hormonal intrauterine device (IUD) counseling video of minority and lower SES women to white and higher SES women. To date, 93 English-speaking women ages 18+ from family planning clinics in Chicago, Seattle and Los Angeles have been counseled by their clinician and had chosen to receive a hormonal IUD watched a 6-minute counseling video the day they received their IUD. The video showed racially/ethnically diverse clinicians who provided factual information about the IUD, and either white or Asian IUD users who described their personal experiences with the IUD. After watching the video, participants completed a satisfaction survey containing 8 categorical and 2 open ended questions. We will compare the satisfaction scores of the Likert Scale questions and use thematic analysis for the open-ended questions to determine whether attributes of the video differed along demographic lines. Of the 93 women who watched the video, 55% were white, and 45% were African American, Asian, Hispanic, Native American, or multiracial. Approximately 55% had a less than a college degree, while almost 40% reported a yearly income of $25,000 or less. Further analysis may show that certain aspects of the video are perceived differently depending on the demographics of the participants.

 Hoarseness is a common symptom of multiple laryngeal diseases such as inflammation, paralysis, neurologic disease, or laryngeal cancer. Many patients with these diseases are not diagnosed with the correct underlying cause of the hoarseness early enough. Therefore, healthcare providers need better methods to screen for and evaluate different types of hoarseness. Currently, a combination of tools are used to evaluate voice disorders in specialty clinics such as patient history, perceptual voice evaluation, and laryngoscopy. We want to better understand how providers with different medical backgrounds evaluate patients with voice complaints. We are most interested in seeing how history, perceptual voice evaluation, and laryngoscopy impact decision-making and diagnosis. In addition, our group has developed a machine learning algorithm that analyzes voice to detect the presence or absence of a laryngeal mass. We want to see if this algorithm could be clinically useful for generalist providers. To address these questions, a group of clinician evaluators including general practitioners, otolaryngologists, and speech language pathologists, will be recruited remotely. Subjects will be asked to complete an electronic questionnaire with patient case scenarios, asking them to evaluate hoarse voice samples and laryngoscopy exams, with and without case history. For perceptual voice sample evaluations, clinician performance will be compared to the algorithm’s classification of whether a hoarse voice is from someone with a laryngeal mass. From there we will see if clinician detection of laryngeal masses from voice could be improved with this algorithm. If the algorithm has better performance than clinicians, then it may be clinically useful as a screening tool in the future. Our results will help us understand how evaluations for hoarseness are done and can be improved.

In 2018, tuberculosis (TB) was the leading cause of death by a single infectious disease, causing 10 million new cases and 1.5 million deaths. Upon Mycobacterium tuberculosis (Mtb) infection most people develop non-transmissible latent TB, and some develop active TB disease. Healthy hosts have a 5-15% lifetime risk of progressing from latent to active TB, and prior studies have demonstrated that a type I interferon-stimulated gene (ISG) signature can predict progression to active disease. Type I interferon (IFN) and ISG expression is induced by DNA-sensing pathways and has anti-viral functions. However, the innate immune mechanisms and genetics controlling type I IFN responses following Mtb infection are not well understood. We hypothesize that genetically regulated higher type 1 IFN responses are associated with lower anti-microbial responses and higher Mtb replication in macrophages, as well as increased risk of TB disease. To test this hypothesis, blood was collected from 40 healthy donors. Donors were genotyped using Illumina MEGA^EX SNP Array. Monocytes were isolated, differentiated into monocyte-derived macrophages (MDMs), and stimulated with 3 ligands (supercoiled plasmid DNA, cyclic guanosine monophosphate–adenosine monophosphate, and sheared calf thymus DNA) to activate DNA-sensing pathways and induce a type I IFN response. RNA was isolated at 4 and 24 hours. Interferon-beta (IFN-β) and interleukin-6 (IL-6) gene expression were quantified using Real-Time PCR. Donors had highly variable IFN-β induction upon ligand stimulation. Donors’ genotypes will be linked to these in vitro phenotypes to identify expression quantitative trait loci (eQTLs) that regulate IFN-β expression. We will assess if these functional polymorphisms in genes of interest are associated with TB disease using patient samples from a Brazilian cohort. The results of this investigation will identify novel pathways that control TB progression that can inform vaccine development and host-directed therapeutic approaches.

yEvo (“yeast evolution lab”) provides experimental evolution teaching modules to high school classrooms to bring genuine research experiences to students. Our goal is to show students how evolution can be applied to solve biological problems by asking them to carry out their own evolution experiments. Recently, we developed an experiment where students evolve yeast in wood hydrolysate media, which comes from lumber waste and contains plant sugars that yeast can convert to biofuel. Wood hydrolysate is a stressful condition for yeasts, as it contains acetic acid and harsh phenolic compounds, therefore yeast struggle to grow in this media. Mutations that yeast acquire while evolving in this media could be used to engineer a better biofuel-producing yeast. Students at Foster High (Tukwila, WA) evolved yeast in this media for seven weeks with transfers to fresh media every week. We retrieved the student’s evolved yeast and they showed striking new characteristics. We then used whole genome sequencing to identify underlying mutations. Some yeasts developed ring-like growths above the wood hydrolysate media and whole genome sequencing of two of these clones revealed mutations in regulators of cell-cell adhesion. Other yeasts reached very high population densities but whole genome sequencing revealed no novel mutations. I then utilized DNA staining and flow cytometry to check the DNA content of these evolved yeasts to see if changes in ploidy caused their new characteristics. The results showed that these yeast effectively became diploid, which has been shown by other labs to increase fitness in sugar-rich environments. yEvo is currently designing future experiments to further expand upon these interesting new results so that we can further understand mechanisms of adaptation to wood hydrolysate.

Of the estimated 38 million HIV infections globally, approximately 1-2 million are people living with HIV-2 (PLHIV-2). Infection with HIV-2, which is endemic in West Africa, is characterized by lower viral loads (VL) and slower disease progression to AIDS than HIV-1. However, many PLHIV-2 eventually progress to AIDS and death if left untreated. Antiretroviral therapy (ART) for HIV-2 is complicated by fewer effective drugs and significant challenges in drug resistance testing to identify appropriate therapy. This study aims to validate a novel method of HIV-2 drug resistance testing using nucleic acid from dried blood spots (DBS). One hundred and fifty DBS have been collected as part of two clinical studies of ART for HIV-2 in Senegal. HIV viral nucleic acid (DNA/RNA) is extracted and the regions encoding protease (PR) and reverse transcriptase (RT), which are the most common drug targets, are amplified by PCR, then sequenced. Sequence data are examined for evidence of drug resistance-associated mutations. To date, we have tested 115 samples with a median viral load of 84 (range: 0-24,000) and obtained drug resistance data from 43 (37.3%). Testing was most commonly successful from samples with higher viral loads; samples with viral loads >250 copies/ml were successful 75.7% of the time. We observed several drug resistance mutations, including PR V47A (5 patients), I50V (3 patients), and L90M (2 patients), and RT K65R (4 patients), Q151M (2 patients), and M184V (10 patients). Eight patients had no known resistance mutations. Once DBS testing is complete, we will select a subset of sequences to compare to genotypic resistance testing from corresponding plasma samples to evaluate the sensitivity of DBS-based testing vs. standard methods. DBS-based resistance testing has the potential to revolutionize ART for HIV-2 by allowing faster, easier, and cheaper assessment of drug resistance to optimize second-line therapy for HIV-2-infected patients.

Embodiments of additive manufacturing that utilize hydrogels as building materials have recently received much attention for their ability to construct biological systems in vitro. These embodiments, often referred to as 3D bioprinters, build up layers of cell-laden hydrogel by rasterizing two dimensional patterns of material deposited in a layer-by-layer fashion; the most common mechanisms of pattern deposition include extrusion, where a shear-thinning gel is forced through a thin nozzle, and light-induced polymerization, where a laser polymerizes material from a vat of liquid hydrogel precursor solution. These methods of material deposition work well for hydrogels which are designed and optimized for their respective deposition method, however, many unique and useful designer hydrogels cannot be printed using conventional 3D bioprinters. Herein, we describe a novel method for layer-by-layer fabrication of hydrogel structures using open microfluidic patterning. For each layer of a printed hydrogel structure, a hydrophilic track or “rail” is manually placed parallel to and several hundred micrometers above the previously patterned layer. Hydrogel precursor solution is then introduced between the underlying layer and the rail, and flows along the rail via capillary action. The cross-sectional geometry of the rail constrains fluid flow to the space directly under the rail, meaning that the pattern of each layer of hydrogel is defined by the pattern of the rail corresponding to that layer. We show that this methodology can be used to fabricate relatively large (1 cm^3) structures of agarose gel, as well as cell laden structures of collagen and a novel peptide-based synthetic hydrogel. Finally, we show that the patterning rail can constrain fluid flow via differential surface chemistry, opening up the possibility for an automated 3D printer and advancing the commercial viability of the method.

Native mass spectrometry (MS) experiments provide direct mass measurements of intact proteins and protein complexes. Protein samples for native MS are prepared in solutions that mimic physiological conditions, which maintain a protein’s native folded state before entering the gas phase of the mass spectrometer. Ammonium acetate solution is typically used due to its volatility and relevant ionic strength. However, protein purification protocols typically require inorganic salts and detergents to maintain protein stability. Native MS experiments can be hindered or made uninterpretable by those salts and detergents. Furthermore, the presence of protein modifications or multiple proteins can make native mass spectra difficult to interpret. Anion exchange chromatography (AEX) is well suited for the requirements of native MS, as it can simultaneously desalt, remove non-ionic detergents, and separate proteins or proteoforms directly into an ammonium acetate solution. This project seeks to develop a comprehensive method for desalting, removing non-ionic detergents, and separating proteins through an ammonium acetate-based anion exchange chromatography method. Preliminary experiments in egg whites, a complex matrix with a high sodium concentration, showed separation and four distinct proteins using an AEX pH gradient from pH 10 100 mM ammonium acetate to pH 4 100 mM ammonium acetate. Native MS analysis showed low interference from sodium or other contaminants and the various modified forms of those proteins were identified. Refinement of this preparation technique can result in the improvement and efficiency of native MS analysis of proteins.

Mutations in Complex I (NADH:Ubiquinone Oxidoreductase) of the mitochondrial electron transport chain have been reported in up to 30% of pediatric mitochondrial diseases (MDs) and affect 1 in 5000 live births. One of such pathologies, Leigh Syndrome, is often fatal in the first three years of life and has no known cure. Knock-out (KO) of Ndufs4 in mice recapitulates several aspects of the disease, including lethargy, encephalopathy and retarded growth. Acarbose delays the onset of neurological symptoms and prolongs the lifespan of both Ndufs4−/− mice and heterogeneous wild type mice. Acarbose is a type 2 diabetes drug that inhibits alpha glucosidases, resulting in delayed absorption of complex carbohydrates and increased activity of the intestinal flora, including increased levels of short-chain fatty acids (SCFAs) and other fermentation products. No formal study has been conducted to determine whether increased SCFA concentration mediates the effects of acarbose on longevity and MD suppression. Our goal is to elucidate the mechanistic basis of acarbose. We hypothesize that acarbose delays MD progression in Nduf4-/- mice by increasing circulating levels of SCFAs. Thus, SCFAs supplementation should recapitulate the effects of acarbose. We will feed chow containing tributyrin to control and mutant mice from weaning until humane endpoint. We will measure body weight, observe the incidence of forelimb clasping behavior (a widely tested neurological symptom), and record percent survival daily. We expect to observe a delay in clasping behavior and prolonged survival in acarbose-treated KO mice compared to that of untreated KO mice, and that these effects are recapitulated more pronouncedly with higher tributyrin doses. SCFAs are promising therapeutics because they are natural metabolites that are inexpensive and can be manufactured into easy consumable pills. A successful outcome of this study will help progress therapies for patients with MDs and for anti-aging purposes.

Cells use a variety of mechanisms to regulate gene expression. One way cells control gene expression is by forming structures such as DNA loops to position genes in 3D space near regulators. My lab is developing tools to synthetically control 3D genome structure and assess the relationship between positioning and expression. Our strategy is to engineer DNA loops by fusing DNA binding domains to targeting domains that dimerize and bring the two sites together. To ensure the binding domains bind to each other to form a loop, we are developing an allosteric sensor of DNA binding where the dimerization motifs are only active when bound to DNA. Without this switch, the looping interaction would be outcompeted by free binding domains that are not attached to DNA. We used LOCKR, a bioactive protein switch comprised of a protein cage that switches to an ON-state in the presence of a key protein. These proteins are tethered to DNA using dCas9 as a programmable binding domain. I have tested different system parameters, including the length of the linker between dCas9 and the key protein, for increased activation of green fluorescent protein, a reporter gene that is expressed when the switch is activated. My data show that the switch is effective with a variety of linker lengths. I am also exploring other parameters for optimization, such as changing the relative orientation of the dCas9 complexes. Exploring these parameters is important because the switch might be sensitive to small changes in structure or orientation, and we want to identify the optimal arrangement of dCas9 and switch proteins for effective switch function. After this system is optimized, we will be able to direct our efforts toward looping DNA, which will allow us to address broad questions about the relationship between gene position and expression.

Quantum confined nanomaterials have become an important field of study with many applications from color displays to low-energy alternative lighting sources. Discovered in the early 1980s, these semiconducting nanocrystals continue to draw attention; their unique properties differ from their bulk counterpart’s due to a quantum confinement effect rising from their small nanometer-scale size. Indium phosphide (InP), a group III-V semiconductor, is a promising nontoxic, environmentally innocuous material. My research is currently focused on investigating the implications of destabilizing kinetic InP intermediates. I explore how creating small nuclei with the same zinc-blende structure as quantum dots (QDs) can potentially lead to unique shelling applications to increase photoluminescence (PL) and color purity. I have developed a synthesis employing a destabilizing additive to yield the small nuclei, which I then shell with zinc chalcogenides to produce luminescent core-shell QDs. I characterize all material via UV-vis and emission spectroscopy as well as powder X-ray diffraction. My goal is to optimize the shelling procedure to produce QDs suitable for use in the market, particularly as blue emitters with a narrow emission range and high PL quantum yield. In optimizing this process, I can contribute meaningfully to the nanocrystal field and the display industry by presenting a unique strategy for making small materials through careful control over crystal phases.

Over recent decades, scholars have noted declining trends in perceptions of legitimacy in high-income, democratic countries. Many theories offer competing explanations for this decline, including immigration, polarization, and neoliberalism, but scholars have yet to connect declining perceptions of legitimacy to stagnant wages. I argue that within the Group of 7 (G7) countries, wage stagnation triggers a crisis of legitimacy because ordinary citizens’ living standards worsen as wages remain low and the cost of living rises, resulting in the belief that their governments are unresponsive and illegitimate. I hypothesize that wage stagnation plays into a legitimacy crisis in domestic democratic institutions, because stagnant wages increase economic inequality and generate perceptions of an illegitimate government. To test this claim, I create a legitimacy index to compare trends in perceptions of legitimacy cross-nationally. I also run a multivariate regression test to assess the strength of the relationship between stagnant wages and government legitimacy, controlling for other relevant factors. This project may reveal that if a productive economy fails to benefit its people, there is the possibility of democratic decline.

The implications in the connection between the Fifth Amendment and Miranda warnings have been well explored in Miranda v Arizona, highlighting that understanding such rights are relevant during police interrogations. The standardization of administering Miranda warnings before police interrogation becomes a mechanism in which to legitimize the State as well as the system of justice, since doing so becomes a form of checking and balancing the power dynamic between State and individual. The question then becomes, is there an effective way to clearly communicate an individual’s protection under the Fifth Amendment through the Miranda warnings in cases where the individual in question may be inherently more vulnerable, such as a child or a person with intellectual disabilities. In 2016, King County implemented a different set of Miranda warnings catered to juvenile competency. It is also crucial to examine how police are trained to understand the difference in the language in which they are mandated to employ. In this research, I aim to find out what and how the different sets of language of Miranda warnings influence the police’s state of mind. I anticipate on obtaining qualitative data by interviewing the police and other legal actors. First, I will ask police to recall what they are thinking after I have given a word cue in a randomized order to see if they are able to give the same meaning in both the adult and youth version. This should yield a baseline towards how the police are thinking about language. Secondly, my questions will also pertain to the ways in which the police are trained to interact with juveniles. I expect to find from interviews that the component of training is what will change how police perceive juveniles differently, rather than administering the warning.

After Saudi Arabia announced its VISION2030 plan to reduce its oil dependence through economic diversification, a wide-scale crackdown on corruption was carried out. Following that was the imposition of the first tax policy in the Kingdom, a 5% value-added tax. These reforms strike a delicate balance; to develop infrastructure and new industries, particularly for an oil-dependent economy (ODE), the country must sustain high levels of foreign direct investment (FDI) among other sources of funding. Nonetheless, attracting FDI requires transparent and resilient fiscal institutions, and the presence of corruption negatively impacts FDI by conveying uncertainty and increasing costs of conducting business. ODEs may also seek to enhance non-resource taxation, providing another stable revenue stream. FDI enlarges the non-resource tax base by including new firms and increasing employment opportunities. By relying on FDI as an indicator of institutional quality, this paper tests the interaction of corruption and FDI and its impact on levels of non-oil tax revenue. I employ regression models to conduct a cross-national study of 17 ODEs, controlling for population, GDP per capita, government expenditure, oil sector ownership and oil price. I expect to find that higher levels of corruption lead to lower levels of FDI, which in turn decreases non-oil tax revenue collection. Additionally, I will use a Fiscal Reliance Measure (Haber and Menaldo, 2011) to test the same interaction’s effect on the ratio of hydrocarbon and oil revenue to total government revenue as a second proxy for economic diversification. This research contributes to the growing field of oil-dependence and economic diversification in two ways: it rejects the presence of a “resource curse” and examines the relationship between corruption and non-resource tax revenue by studying institutional state structures, and it explores the causal mechanism running from FDI to tax revenue, whereas previous literature has tested the inverse relationship.

One of the Ultracold Atoms Group’s themes is to study the interaction between trapped ultracold atom mixtures. Certain experiments, such as the study of spin-dependent Feshbach resonance, requires us to select one specific nuclear spin state of the atom from the mixture. This process is achieved by the optical Stern-Gerlach technique, where we use the laser to produce the magnetic field gradient. However, this technique requires us to use the imaging path with relatively poor imaging quality due to, for example, vibrations of the optics. When we normalize these atom images, these vibrations introduce misalignment between images and thus unwanted noises. Hence my project is focused on stabilizing the imaging process by a software implementation of imaging alignment scheme. The code I developed can be seen as the analog to the inner product of two vectors, which characterizes the extent of misalignment between two vectors. This scheme has increased the efficiency of the experimental procedure and at least doubled the signal-to-noise ratio. Its easy implementation provides another route to reduce noises in the data of similar experiments. 

This study investigates the ways in which parents consider and rate their child’s temperament in relation to the ways in which their child interacts with them during play. Participants were typically developing children (TD, n = 26) ages 2-5, children with autism spectrum disorder (ASD, n = 25) ages 2-12, and children with fetal alcohol spectrum disorder (FASD, n = 18) ages 4-9. Attentional focusing was assessed with a parent-report child temperament questionnaire; child’s age determined which Rothbart Childhood Temperament Questionnaire was given (for example, the Children’s Behavior Questionnaire for ages 3-7). Play sessions were unscripted, free play time between the parent and child with a consistent set of toys (M = 14.4 minutes, SD = 2.8). The number of child attention switches (to a different toy, person, or object) was coded from video. Preliminary results indicate that parents rated TD children as more attentive in comparison to children with ASD and FASD based on the attentional focusing score from the Child Temperament Questionnaire (p< .001). There were fewer attention switches during the play sessions by TD children in comparison to children with ASD and FASD (p<.05). There is no significant difference in either of these measures between children with ASD and FASD. There is also no correlation between parent-reported attentional focusing scores and the observed number of attention switches. These results suggest that TD children demonstrate more attentiveness in both parent-reported and examiner-rated measures. Children with ASD and FASD were not distinguishable from each other based on parent report or direct observation of attention. Overall, attention should be considered as a contributor in a child’s interactions with their environment, relationships to others, and further growth and development.

The International Panel on Climate Change report of Global Warming of 1.5°C (October 2018) strongly recommends unprecedented scale of systems transitions to ensure little to no overshoot of global warming of 1.5°C. In the interest of examining educational efforts towards this reality, this qualitative study is designed to understand how the field of early childhood education is adapting to living with climate change and preparing early learners for their future under the guiding principle of the required systematic change that must be met to mitigate the effects of the human ecological footprint on the environment. This qualitative study features a cross-cultural comparison of early childhood professionals’ ideas about the role that early childhood teachers play in helping children learn foundational ideas about climate change. Three participants from Washington state and 4 participants from Trondheim, Norway were interviewed and the content of the interviews was analyzed and coded for themes. Participants all had early learning teaching experience, but their roles varied from State policymaking, teacher educators, and early learning educators. Participants described barriers in supporting early learners’ understanding of, relationship with, and caring for the environment and how the field of early education can be intentional in supporting these goals. Participants identified lack of educator knowledge, lack of access to nature, family emphasis on spending time in nature, the risk of scaring children, emphasis on academic readiness, and cultural emphasis on environment as the main barriers to effectively preparing early learners for their complex future. All the participants felt children were capable of understanding topics related to sustainable practices, cause-effect, and co-existing with the other life on this planet. The next steps of this work is to determine how to best prepare early educators in supporting the goals identified by participants through professional development or teacher preparatory programs.

Aphasia is a language impairment that is often acquired due to left hemisphere stroke. Although current treatment for aphasia is successful, it is often limited to what is explicitly trained during treatment. That is, when conducting a single-word treatment protocol, persons with aphasia tend to only improve on naming the words given during treatment and show little to no improvement on untrained words. This study is focused on identifying what conditions improve naming untrained words after receiving aphasia treatment. For 8 individuals with aphasia, we assessed change in naming 120 pictures after undergoing a repetition priming task for 30 of those words. For a given “trained” word, its corresponding picture, printed name, and spoken name were presented to the participant four times, followed by an opportunity for the participant to verbally produce the name. For pre- and post- test naming, we implemented a standard coding method to ensure specific and consistent scoring, where responses were only scored correct if the participant verbally produced the entire picture name. We found that all participants improved in naming the 30 trained words. However, our results were mixed regarding improvement on naming the untrained words. Critically, we noticed two participants whose responses were not always verbal productions of the word, but rather spelled words (in one case verbally and in the other case through writing). This led us to question whether these coding parameters allow us to accurately identify if an individual is benefiting from treatment. We argue that incremental gains in productions (e.g., through spelling) also provide evidence of improved access to words. We focus this presentation on how alternative coding schemes for these two participants might change our interpretation of their outcomes, and discuss how future research should consider more inclusive scoring methods.

Racial microaggressions are subtle manifestations of racial bias. Though they are subtle, they cause tremendous psychological strain for minoritized populations. Prior research from our lab has found four main types of microaggressions: intergroup anxiety, color blindness, objectifying, and negative stereotypes. Intergroup anxiety refers to nervousness about interracial communication, such as being perceived as racist, and often manifests into avoidance of such interactions. Color blindness is the denial of racial identity, saying “I don’t see color” for example, while objectifying is being preoccupied by differences, such as fixating on a Black woman’s hair. Lastly, negative stereotypes are predetermined racial judgements based on known labels like “welfare queen.” In the research study, we sought to understand whether women of color experienced these or other microaggressions while seeking services following domestic violence. A focus group was conducted with advocates, people who provide emotional support and resources for domestic violence survivors, to gather information about their clients’ experiences. From advocate responses, we identified themes that fell into one of our four microaggression categories. In addition, we uncovered a fifth form of microaggression, and found that many survivors reported macroaggressions. This research could inform future training strategies for service providers, and help domestic violence survivors access services without encountering microaggressive racial bias.

Sexual harassment engenders post-traumatic stress disorder, anxiety, and depression in targets, and disproportionally affects women (vs. men) in the United States. Critically, many harassment cases in the U.S go underreported. For instance, only 25% of women formally report instances of harassment to their employer and less than 20% of women describe sexually harassing behavior at work as “sexual harassment.” The current project explores whether women’s self-perceptions of gender-prototypicality impacts the reporting of sexual harassment. Specifically, it explores whether the extent to which a woman views herself as prototypically feminine promotes the reporting of harassment after it occurs. To begin to explore this hypothesis, we first test whether women can be primed to feel prototypically feminine (vs. masculine; Study 1). Second, we describe our experimental methodology, and predicted results, for testing whether feelings of sexual harassment can be engendered in women in the laboratory. Implications for the reporting and reduction of sexual harassment are discussed, along with theoretical and empirical extensions related women’s individual differences.

The lack of intimacy has long been known to contribute significantly to our mental health and psychosocial adjustment. Empirical research has substantiated strong connections between the fear of intimacy and other mental health problems such as depression. One could expect that the fear of intimacy poses as an obstacle to forming intimate relationships. The lack of such intimate relationships causes the individual to feel lonely and precedes a negative cognition as seen in depressed patients. Many other psychotherapy patients, too, experience intimacy deficits. Not much research has delineated the mechanisms underlying fear of intimacy. Specifically, when we say that we fear intimacy, what do we really mean? In this exploratory research, we are investigating how dyads with different levels of intimacy can possibly interact with each other to derive a certain level of connectedness within the relationship. For example, it is possible that both individuals with high fear of intimacy can still connect well with each other and form a close relationship. What then, in this scenario, is causing the relationship to work? For individuals with different levels of fear of intimacy (i.e., one high, one low), what should we expect to see in terms of connectedness within the dyadic relationship? In this research, we investigate these issues in a sample of 35 dyads (people in ongoing relationships, including friendships, family, and romantic partners) who were recruited for a larger intervention study to improve relationships. We attempt to integrate our findings with what is known from social psychology about relational functioning to explain the interaction of different levels of fear of intimacy within the dyadic relationship. This research advocates the importance of early screening of individuals' fear of intimacy and raising awareness for those at risk of difficult dyadic relationships.

Ever since they first appeared during the Late Cretaceous, members of the palm family (Arecaceae) have been ubiquitous in the fossil record. Traditionally, palms have been considered a key indicator of warm climates. In addition to leaf macrofossils, fruit, and pollen, palm phytoliths have gained utility as paleoecological indicators. Phytoliths are microscopic silica bodies accumulated in the tissues of many plants. Different plant taxa have unique phytolith morphologies, making them useful diagnostic tools. However, palm phytoliths currently lack diagnostic resolution below the family level, limiting our ability to fully utilize these powerful tools. The goal of our project was to increase this resolution by analyzing the morphology of phytoliths from across the entire Arecaceae family in more detail than has been possible before. We used confocal microscopy to take sharp, high-resolution images of palm phytoliths. Using these images, we took several key measurements, to which we applied multivariate ordination methods. Our analysis allowed us to test how well we can differentiate palm subclades within Arecaceae based on phytolith morphology. Ultimately, we hope to use this information to determine when and where specific clades of palms appeared in the fossil record, increasing our understanding of the evolution of the palm family. This will also allow us to describe past environments in more detail based on palm phytoliths, including estimating more specific climate parameter ranges, and characterizing particular biomes and habitats.

The spread of grasslands 26-22 million years ago has been linked to global climate changes in the late Oligocene to early Miocene. The pattern of vegetation change was established analyzing assemblages of microscopic plant silica (phytoliths) extracted from sediment samples from the Central Great Plains of North America. It is often presumed that as open-habitat grasses became abundant, vegetation structure concurrently transitioned from closed forests to open landscapes. However, recent work in the Cenozoic of Patagonia has pointed to a decoupling of grass dominance and habitat openness, each independently driven by climatic conditions. We set out to test if a similar decoupling occurred in the Central Great Plains by means of an a-taxonomic phytolith proxy using phytoliths produced in non-grass epidermal cells. Work in modern plants and soil assemblages has shown that the size and degree of undulation in these phytoliths (quantified by, respectively, Phytolith Area, PA, and the Phytolith Undulation Index, PUI) is correlated with the amount of light in the environment, reflecting habitat openness (measured as Leaf Area Index, LAI). We measure the PA and PUI of phytolith samples from Nebraska, dating 35 to 17 Ma, to reconstruct the regional LAI over time and place time constraints on the opening of habitats. By comparing this timeline to that of the rise to dominance of grasses, we hope to better understand changing vegetation and linked climatic conditions in Cenozoic North America.

Chondricthyes such as sharks, skates, rays, and chimeras share the slow maturation and low fecundity traits, thus making them susceptible to overexploitation. To ensure the survival of these vulnerable species it is necessary to protect the habitat important to their recruitment. The purpose of the present study was to determine the sediment preference of juvenile Beringraja binoculata to gain evidence as to where their nursery grounds may be located in the Salish Sea. To do this we conducted one-hour filming trials of three four-month old skates in a tank sectioned off into four different sediment size classes. Skate 1 died one-third of the way through the trials so was removed from statistical analysis. However, we found that Skate 2 and 3 preferred to bury and rest in the smallest sediment size of 0.125-0.3 mm grain size with p-values of 0.00126 and 0.0814 respectively. This is consistent with literature on different species of skates around the world. Ongoing research would be valuable to determining the reason behind this preference and to use the information to locate the Salish Sea nurseries.

Microplastics (plastic < 5mm) has become a prominent research topic over the last 15 years. Microplastic research papers are published around the world, using a variety of organisms, environments, and interactions as study systems. Findings from these papers suggest that microplastics have negative effects, like behavior disruption and cell death, on marine organisms. This research project uses scientometrics to analyze if trends in regional plastic policies are correlated with marine microplastic research papers. Utilizing spatial analysis, we compared the rate and spread of microplastic research and plastic policies across the globe to identify a statistical relationship between them. We then further explored this relationship by determining if the distribution of study systems in a region’s research affected the quantities of policies in that region. We used the Web of Sciences database to obtain data on microplastics papers from 2006 to 2018. Our data has revealed that specific species are being used in research more than others and that there are large concentrations of microplastics papers in areas like Europe and China. Countries with large amounts of plastic research also have the most plastic policies. The results of this project help decipher how marine microplastics research can have an impact on plastic policy.

Microplastic (plastic < 5mm) pollution is increasing at an exponential rate in marine environments, leading to increased contamination of marine organisms. Previously, it was thought that the majority of microplastics were found in surface waters due to their positive buoyancy; however, recent studies show pollution exists throughout the water column. Mussels, suspension feeding bivalves, can be catalysts to the spread of microplastic pollution to different trophic levels through filtration, ingestion, and egestion of microplastics. Mussels are prominent benthic-pelagic coupling organisms in marine ecosystems, moving particles and nutrients between habitats through different types of biodeposits. Mussels produce feces and pseudofeces, where feces is the digested biodeposit and the pseudofeces are the rejected materials. Accumulation of microplastics in their biodeposits may interfere with this coupling by altering sinking rates, giving other organisms more opportunity to feed on deposits and promote the spread of microplastics through the food chain.The purpose of our project is to test how different types of microplastics affect sinking rates of mussel biodeposits. Our hypothesis is that mussels filter microplastic particles differently.The more readily ingested microplastic will lower the sinking rate of the feces more drastically. In our experiment we fed mussels either polystyrene or polyethylene microspheres along with algae, collected their biodeposits, and measured sinking rate. Further, we quantified microplastic and algae found in each type of biodeposit. The selectivity of mussels toward a particular microplastic was determined by the amount of a microplastic present in the feces vs the pseudofeces. The results from this study can help us understand the impact of microplastic pollution and how mussels play a major role in the spread of microplastics. They may also provide insight into which types of microplastic are more readily spread, potentially providing information on how to distribute microplastic waste.

Early home life and classroom environments are crucial to lifelong success. Family structure, opportunities for learning, and socioeconomic status (SES) influence experiences within the home. Further, SES impacts the resources that a student has access to, which can shape academic support and learning opportunities. Factors such as family climate, caregiver occupation and education, and parenting style have been shown to influence academic self-regulation and achievement. Literature has also pointed to the importance of relationships with peers and teachers on academic and social success. Few studies have examined how both of these environments impact student life into adulthood and litte research has explored social success in terms of feelings within interpersonal relationships and self-efficacy. The goal of the present study was to retrospectively explore experiences in the home and school environments throughout formative, developmental years and success later in life. Participants (n = 149) were asked about their family structure, SES, home learning environment (HLE), experiences in three separate academic eras, academic success, feelings in relationships, and self-efficacy. This study fills a paucity in the discussion of academic success by exploring a new measurement tool: the academic ladder, which examines a student's own perception of their achievement in relation to their classmates. Results confirm the impact of early experiences in the home and at school on later academic and social success. Interestingly, caregiver factors do not significantly impact students' interpersonal success as much as relationships with teachers and peers. Results also show that SES does not have an effect on opportunities for learning in the home; however, caregiver educational attainment affects those opportunities. Both HLE and caregiver variables have an effect on self-perceived academic success. Continuing to examine how educational experiences and environmental factors impact students' well-being will help develop intervention programs that best prepare youth to succeed throughout life.

Animals in the natural world rely on sensory information in order to make quick decisions to stay safe. Sometimes a stimulus is paired to a predictable outcome, allowing the animal to make the appropriate response when encountering that stimulus later. However, it seems unlikely that individuals would have to learn, de novo, those stimuli which might signal danger during the first learning opportunity. Laboratory studies of animal fear, however, have largely been done using Pavlovian Fear Conditioning; generating fear by pairing a tone or other benign stimulus with an aversive one—typically a painful footshock. This is problematic. An owl does not hoot three times before it strikes, allowing the prey to form a conditioned response. To explore this innate behavior, we developed a novel, naturalistic approach to fear conditioning that uses a pseudo-predator paired with physical pain to induce fear responses. In this experiment, I trained male and female Long-Evans rats to forage for food pellets in an open space. After training, a fake owl plunged towards the foraging rats while a shock was delivered through subcutaneously implanted wires. Certain groups were presented with a tone or light to pair with the owl and shock, while others received no other predictive stimuli. Additionally, to test the effects of environmental context on their behavior, animals were tested in two chambers that differed in size, lighting, shape, etc. Even after changing foraging contexts, some rats that were never conditioned to fear the tone fled upon its presentation. The visual cue also induced a fear response in rats that were never previously conditioned to fear the light stimulus, but only fled when the shock was presented with the owl. Experiments performed under naturalistic conditions utilizing animals’ innate behaviors will better aid in our understanding of how the brain makes decisions in complex environments

When a child is diagnosed with pediatric cancer, it puts a strain on the whole family, including the marital relationship. However, there is little consensus as to the factors that predict marital adjustment. This proposal examines the relationship between parental emotional styles and marital adjustment in the first year following a pediatric cancer diagnosis. I propose that poorer marital adjustment as well as declines in marital adjustment over the first year of treatment will be predicted by 1) emotion-dismissing philosophies in both men and women and 2) a mismatch in couples' emotion philosophies. These findings would provide insight into the factors that may put the marital dyad at risk, which could inform clinical interventions to better support the families after diagnosis.

I began this project last year as an honors student in the Psychology Department Honors program and under supervision of Dr. Lynn Fainsilber Katz and clinical graduate student, Laina Keim. I independenty discovered a gap in the literature, developed my hypothesis, performed an extensive literature review and wrote a proposal for this this honors thesis. I became a trained and reliable coder for the internationally recognized coding system that is being utilized in this study. This year I have focused on coding our data with our lab team, data analysis with Laina, and now I am writing up results. 

Chronic myeloid leukemia is among myeloproliferative neoplasms that cause an increase of myeloid cells. All CML cases have a reciprocal translocation causing the novel fusion BCR-ABL gene causing the disease. BCR-ABL protein is a drug target and BCR-ABL mRNA is a diagnostic target. The polymerase chain reaction (PCR) is a technique used to diagnose and monitor treatment response in CML. Tyrosine kinase inhibitors (TKIs) have raised the survival rate of CML patients from an average lifespan of 6 years to a normal lifespan. However, monitoring and diagnosing CML patients requires expensive equipment and technical expertise. Medical testing and therapy of CML in lower to middle income countries is difficult, because drugs are expensive and access to sophistical equipment rare. However, when the disease is confirmed by testing, a non-profit organization (the Max Foundation) can provide TKIs free for life through partnerships with pharmaceutical companies. Dried blood spots (DBS) can potential stabilize nucleic acid for long periods of time. This approach has facilitated retrieval of the genetic material on the DBS that can be used to analyze more genetic analysis related to CML response and progression and has reduced transportation costs. In this study, we isolated DNA & RNA from DBS, quantified the genetic material, performed quality control, and carried out DNA & RNA sequencing-based on gene mutation assays. Tapestation and qPCR were performed to check the quality of the genetic material. DNA samples showed a higher DNA integrity number with an average of 7.7. However, the RNA samples demonstrated a lower RNA integrity number with an average of 1.8. The DNA samples had excellent quality whereas the RNA samples had poor quality but were acceptable enough to carry on with our study. These results will help us determine if genetic material on DBS can be used for more genetic analysis.

Rhabdomyosarcoma (RMS) is a devastating pediatric soft tissue cancer. Currently, the standard treatment regimen for RMS patients remains relatively unchanged. Conventional treatment of RMS includes a combination of chemotherapy, radiation, and surgical tumor resection. Unfortunately, with the heterogeneity of cancer between patients, these therapies are not always effective and can cause undesired health issues for the patient due to their non-specific effects. Targeted drug therapy can help patients live more normal lives. The angiotensin II receptor type 1 (AGTR1) and 2 (AGTR2) are potential targeted therapy targets that can inhibit RMS cancer growth and cause less side effects compared to conventional therapies. AGTR1/2 are the main effectors in the renin angiotensin system regulating cardiovascular health. While there are Federal Drug Administration (FDA) drugs blocking these receptors to treat high blood pressure (Irbesartan), AGTR1 and AGTR2 have yet to be investigated for their role in RMS. Tumor propagating cells (TPC), which function as tumor stem cells in RMS, are proposed to drive tumor metastasis and relapse through a process called self-renewal. Preliminary disruption of AGTR1 and AGTR2 in the two major subtypes of RMS (embryonal and alveolar) with the CRISPR/Cas9 gene editing system resulted in decreased tumor cell growth and self-renewal capabilities. RMS cell lines treated with Irbesartan also decreased in viability compared to untreated cells. Based on our preliminary results, I propose that AGTR1/2 plays a role in regulating RMS cell growth and self-renewal. Further functional characterization of AGTR1/2 and investigation of the cellular mechanism by which AGTR1/2 regulates RMS tumor cell growth and self-renewal can provide a strong rationale for prioritizing AGTR1/2 as targets for drug therapies to slow the progression of RMS without greatly compromising more of the patient's health.

Fanconi Anemia (FA) is a recessively inherited genetic disorder resulting from a loss-of-function mutation in any of the 23 genes that comprise the Fanconi (FANC) gene family. FA is characterized by congenital abnormalities, bone marrow failure, and a predisposition to hematologic and solid cancers. The elevated risk of cancer in FA is largely limited to the squamous mucosa lining of the oropharynx, esophagus and vulva, and is not ameliorated by successful prior bone marrow transplantation. Apart from surgery, effective treatment of these cancers is limited by patient hypersensitivity to standard-of-care therapies that include ionizing radiation and DNA cross-linking drugs. The pathogenesis of FA-derived cancers is still not well understood. As a result, we are developing a “Fanconi Anemia Cancer Cell Line Resource” to provide preclinical models for research on FA-derived head and neck squamous cell carcinoma. The resource will include genomically well-defined, isogenic HNSCC cell line pairs (FA-patient/complemented cells) from patients with FA and isogenic cell line trios (wild-type/FANCA-deficient/FANCA-complemented cells) from control sporadic HNSCC cells. FANCA-deficient control cells were generated by targeted Cas9-mediated deletions in both FANCA alleles. Complementation of the resulting FANCA-deficient cells and patient cells was accomplished by targeted FANC- transgene insertion at a chromosome 4 ‘safe harbor site’. The molecular and cellular phenotype of the clonally-derived knockout and knockout/complemented cell lines was verified by PCR analyses; by Western blot and Multiple Reaction Monitoring (MRM) mass spectrometry analysis of FANCA and FANCD₂ protein expression/modification ± DNA damage; and by cell survival as a function of mitomycin-C (MMC) dose. The FA-HNSCC and sporadic HNSCC cell lines will be available for investigators via the FARF- sponsored Fanconi Anemia Cancer Cell Line Repository. We anticipate this versatile resource will be valuable in the development of novel treatment and faciliate in improving our understanding of FA cancers.
 

Nicotine is the addictive substance found in various tobacco products. CYP2A13 is an enzyme localized in the lungs, metabolizes tobacco-specific nitrosamine carcinogens that contribute to lung cancer. Therefore, pinpointing CYP2A13 inhibitors is an approach to lower tobacco-based lung cancer risk. Cinnamaldehyde is a common flavoring agent in the fluids of electronic nicotine vaping devices. Cinnamaldehyde was found to be a potent inhibitor of CYP2A6, another enzyme that metabolizes nicotine. Because CYP2A13 and CYP2A6 exhibit overlap in substrate/inhibitor selectivity, the goal here was to evaluate the inhibition of CYP2A13 by cinnamaldehyde. A time-dependent inhibition coumarin assay was performed to determine the kinetic parameters for cinnamaldehyde in recombinant CYP2A13. Primary incubations contained cinnamaldehyde, CYP2A13 Supersomes, and potassium phosphate buffer. Incubations were initiated with NADPH. Secondary incubations contained coumarin, NADPH, and potassium phosphate buffer. At selected time points, an aliquot of the primary incubation mixture was transferred to the secondary incubation tubes, which were terminated with trichloroacetic acid after heating at 37°C for 5.5 minutes. A linearity study was conducted to determine the appropriate termination time. CYP2A13 activity was measured by the detection of hydroxycoumarin using high-performance liquid chromatography (HPLC) and a fluorescence detector. Hydroxycoumarin formation decreased with time and inhibitor concentrations. Maximal inhibition following an 18-minute incubation was 38.3 ± 1.6 and 4.0 ± 0.6%. The maximal rate of inhibition was 0.109 per minute. The results provide evidence that cinnamaldehyde is a time-dependent inhibitor of CYP2A13. Furthermore, cinnamaldehyde appears to be a more potent inhibitor of CYP2A13 than CYP2A6, based on the maximal rate of inhibition. The results imply that cinnamaldehyde could interfere with the bioactivation of nitrosamine lung carcinogens. Additional kinetic studies are needed to confirm the results of this study and to evaluate the safety and toxicity profiles of cinnamaldehyde in complex physiological models.

Liver cancer is the world's second most deadly malignancy with a five-year survival rate of just 18%. Hepatocellular Carcinoma (HCC) accounts for most of the cases and its incidence is projected to rise to one million deaths per year by 2030. Unfortunately, HCC is extremely difficult to treat because several molecular pathways that promote drug resistance are upregulated in tumors, the most important of these being the epithelial-to-mesenchymal transition (EMT). Under physiological conditions the EMT regulates embryonic development, wound healing and tissue repair. However, cancer cells can hijack EMT signaling pathways to acquire a metastatic and drug resistant phenotype. Therefore, cell signaling enzymes that promote the cancer cell EMT are an attractive target for pharmacological intervention. Recently, we discovered that 71 protein kinases are highly enriched in mesenchymal HCC cells. To determine if these signaling enzymes are bona fide drivers of the EMT and drug resistance, we generated kinase RNAi knockout cell lines, quantified differences in EMT marker mRNA expression by qPCR, determined EMT pathway activation using quantitative proteomics, and tested differences in drug sensitivity. Here we demonstrate that inhibition of several of the 71 candidate EMT kinases reverses the phenotypic transition and sensitizes drug resistant HCC cells to chemotherapy. We conclude that these kinases could present attractive targets for the development of novel drugs that block cancer metastasis and overcome therapy resistance.

Embryonal rhabdomyosarcoma (ERMS) is a common pediatric cancer that has poor prognosis for patients with relapsed disease. ERMS typically harbors mutations in one of 3 RAS proteins. Mutations in NRAS, a member of the RAS family, have been shown to be a driver for many different cancers, including ERMS. The Chen lab previously demonstrated that genetic disruption of the NRAS gene by the CRISPR/Cas9 technique successfully reduced ERMS tumor growth in a human xenograft mouse model. However, these mice also experienced disease relapse. I was able to confirm successful targeting of at least one copy of NRAS in ERMS cells. I have subsequently isolated clones of ERMS cells that continued to grow despite the presence of NRAS gene disruption. In my investigation of candidate genes and pathways that might be responsible for driving continued ERMS tumor cell growth, I saw an increase in the level of YAP1 being produced in NRAS-targeted ERMS cells when compared to the control cells. Based on my preliminary findings, once NRAS is successfully disrupted in ERMS cells, tumor relapse is then driven instead by YAP1. This study could provide novel insight into the mechanisms underlying cancer relapse in response to NRAS targeting and promise alternative treatment plans for ERMS patients.

Hoarseness is a common symptom reported to generalist healthcare providers, with approximately 1% of the clinical population being affected by it each year. It can be caused by multiple etiologies, such as hoarseness due to a cold, acid reflux, or laryngeal cancer. Perceptual evaluation of the voice is inaccurate, and it is therefore difficult to differentiate between hoarseness requiring urgent referral for specialty evaluation (i.e. laryngeal cancer) versus a disorder that could be managed without specialty care (i.e. acute laryngitis). The current gold standard of diagnosis for hoarseness is laryngoscopy, an in-clinic endoscopy recording of the larynx performed by an otolaryngologist specialist. Our research team seeks to improve perceptual voice evaluation by developing and testing machine learning algorithms which analyze voice for underlying pathology, beginning with an algorithm which screens voice for laryngeal masses. We hypothesize that our algorithm will have greater than 80% sensitivity and specificity in the classification of voice samples from patients with laryngeal masses. To test this, we are developing a large, prospective database of voice samples from a laryngology clinic using a smartphone application. Subjects are adult patients presenting to the laryngology clinic, with and without voice disorders, who have had a recent laryngoscopy exam and no laryngeal surgery within the past three months. We are collecting patient history which could influence voice quality, such as age, gender, alcohol use, smoking history, and subject-perceived voice disorder impact. After collection of the voice sample and patient history, cases are classified into underlying pathologic categories. We see recruitment of a well-classified and prospective patient population with a range of voice disorders. This work could lead to improved screening of patients with hoarseness in underserved and primary care settings, and more appropriate and timelier specialist referrals and treatment.

Current estimates by the centers for disease control (CDC) suggests that roughly 1 in 59 children in the US are affected by Autism Spectrum disorder (ASD). Despite its high prevalence, our current understanding on the biological etiology of ASD is limited. However, an ASD associated gene, TAOK2, which encodes a serine/threonine protein kinase, has been found to mediate neurodevelopmental disorders like ASD. Mutations within TAOK2 are associated with atypical neural connectivity in different brain regions, abnormal synapse formation, reduced cortical layering, and increases in brain size. Though TAOK2 plays a crucial role in neuronal development through phosphorylation of its substrate proteins, catalyzing or inhibiting their activity to regulate cellular processes, substrates of TAOK2 have not been fully elucidated and several candidate substrates have yet to be explored. Through my research, I explore TAOK2's interaction with putative substrate HDAC6, a histone deacetylase enzyme that functions to mediate a variety of cellular processes such as protein degradation, transcription, and the ability to regulate α-tubulin to mediate microtubule dependent cell motility. HDAC6 has been identified as a putative substrate of TAOK2 through mass spectrometry. Here, I present my findings regarding TAOK2's regulation of HDAC6 deacetylase activity and the potential it has for expanding our understanding of the molecular mechanisms underlying ASD.

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders characterized by impairments in social interaction and repetitive behaviors. One of the most common mutations leading to ASD is 15q11-q13 duplication, a CNV mutation where extra copies of a chromosomal region are expressed. The major gene within this region is ube3a. My lab has generated a mice model with increased copies of this gene and demonstrated a novel deficit in phosphorylated-AKT, a key protein in the mTOR/AKT signaling pathway. Other mice models of autism have exhibited deficits in this pathway and have rescued behavioral deficits with a drug, rapamycin. Rapamycin is an inhibitor of a key protein of the mTOR/AKT pathway suggesting a similar behavioral rescue might be observed with ube3a transgenic autism model mice. Behavioral testing of 4 groups of 20 mice, wild type and ube3a transgenic mice treated with and without rapamycin, found that there were no baseline social deficits in ube3a transgenic mice not treated with rapamycin. This is not similar to previously published findings and could be due to a number of reasons. It can be difficult to get consistent results with mice behavioral testing. In order to assess if rapamycin had its intended effect in restoring deficit levels of phospho-AKT, protein levels will be assessed. Brain slices from the hippocampus of behaviorally tested mice will be analyzed by western blot, a method of identifying and measuring specific proteins. Successful rapamycin treatment would be observed as increased levels of phospho-AKT, similar to wild type mice. This would suggest that repeated mice behavioral testing is needed and therapeutic treatment of the mTOR/AKT signaling pathway could be a viable target for patients with 15q11-q13 duplication.

The maternal bond is an intimate attachment between a primary caregiver (PC) and their infant which provides the infant with security, facilitating physical, social, and emotional development. A sensitive and responsive environment, such as the presence of healthy maternal bonds, guides an infant’s neurodevelopment. Changes in mood and emotional state can alter the care a PC provides and cause difficulties in bonding with their infant, impacting the baby’s psychological and physical development. In infants, the mechanisms by which development may be impacted are unknown. Recently, research has shown early atypical attention to visual pop-out in autism spectrum disorders. Attention to visual pop-out describes our cognitive ability to quickly identify differing objects presented among similar looking ones. In this project, we investigated whether PC mental health affects attention to visual pop-out in infants. Participants included 50 infants who were assessed at 6 and 12 months of age. PCs completed the Beck Depression Inventory (BDI) and Beck Anxiety Inventory (BAI) at both timepoints. Infants watched a 4-minute visual pop-out paradigm, which included social (face) and non-social (shape) trials. We assessed responses to visual pop-outs and explored whether BDI and BAI scores correlated with visual pop-out performance at 6 and 12 months. We also investigated whether BDI and BAI scores influenced the development of attention to visual pop-out between 6 and 12 months. We hypothesized infants of primary caregivers who report more (a) depressive and (b) anxious symptoms will demonstrate weaker identification of the pop-out during social trials compared to their peers but be unaffected during nonsocial trials. This study will help deepen our understanding of the impact of maternal depression and anxiety on infant development and help health providers identify and support families.

As information processing machines approach the nanoscale level, DNA has emerged as a powerful tool in molecular engineering systems. The specificity and programmability of its hybridization interactions offer flexible and fine-tuned control over reacting species. Among the DNA computing techniques used today, strand displacement circuits are highly popular, with potential applications ranging from disease diagnostics to DNA-based artificial neural networks. The fundamental mechanism of these circuits is the hybridization of a single-stranded DNA input strand to a double-stranded complex which triggers the release of a prehybridized output strand. When released, this output can be detected and used to characterize circuit behavior. The output strands of strand displacement circuits are typically read out using fluorescence spectroscopy. However, due to spectral overlap of traditional reporters (e.g. FAM, TAMRA, Cy5), the number of outputs that can be detected in parallel is severely limited. To address this, we present the use of nanopore sensing technology as an alternative readout device that enables highly scalable, real-time detection and quantification of DNA strand displacement circuits. We demonstrate dynamic sensing of an operating circuit within the flow cell of a commercially-available high-throughput nanopore sensor array (Oxford Nanopore Technologies’ MinION device) and show that strand capture frequency can be correlated to concentration, allowing for direct quantification of desired circuit elements. To investigate this reporter strategy’s multiplexing potential, we present a collection of ten orthogonal circuit output sequences (barcodes) that can be classified at the single-molecule level from raw nanopore signal data using machine learning, with the potential to scale to larger barcode sets. We conclude that nanopore-based detection of strand displacement circuits holds key advantages over fluorescence-based methods for real-time, multiplexed circuit readout on an inexpensive, portable sensor device.

In the general population, adherence to a daily routine is linked with well-being.This appears to be the case to an equal if not greater extent among individuals with schizophrenia. Individuals with schizophrenia-spectrum disorders who consistently engage in activities that typically occur in a routine – e.g. employment, education, healthy sleep, social connections, and physical activity – enjoy an array of physical and mental health benefits. The study of adherence to routine has been limited by the use of retrospective scales, which are common in clinical research. These measures require respondents to provide estimates of the amount and frequency of behaviors over weeks or months. Such estimates are insufficiently granular to assess adherence to routine. The present study aims to examine the relationship between behavioral stability and symptoms in schizophrenia. Our team previously deployed a multi-modal mobile assessment system in a sample of individuals with schizophrenia for twelve months. In this study we revisit those data to develop models that quantify within-day adherence to routine among individuals with schizophrenia. We operationalize adherence to routine as defined in an individual’s behavioral stability, or the extent to which their behaviors detected by sensors stay stable from one day to the next during the study period. The present study has four main aims: whether (1) passively sensed behavioral stability can be quantified, (2) whether it is associated with symptoms and dysfunction in schizophrenia, (3) whether the addition of behavioral stability improves predictions of symptoms and dysfunction, and (4) whether this behavioral stability metric might be associated with future risk of poor outcomes.

 The internet has changed the norms for how we write and communicate. Many major technology companies communicate with their users in much more casual and conversational language than the formal written English taught in schools. For instance, contractions and sentence fragments are common, the word “like” often used in place of “such as”, and “info” often used instead of “information”. This casual writing style may help users view a company as more approachable, but they may also perceive the casualness as lacking professionality and trustworthiness. Trust and taking the right action are especially important in security-related interfaces, as a user’s security and privacy may be compromised if an interface fails to educate users on secure behaviors. Through an online quantitative study we will explore the effects that formality of language has in security-related prompts. These effects include: how a user understands a prompt, their perception of the prompt’s formality, and how likely they are to take the action the prompt suggests. We will also investigate how users perceive the formality of various major technology companies and whether these perceptions match how the companies actually communicate with users. As average-level formality is different for everyone, we will analyze our results across different demographics, such as education-level, age, and the country the person grew up in. Our goal is to measure the likelihood of a person to take an action based on the wording of a security prompt, the person’s sentiments towards the prompt, and whether these depend on the person’s demographics and the company with which they are interacting. Our work serves a practical purpose, that is, helping technology companies decide what tone they want to address users with to accomplish their goals. It also serves a more theoretical purpose, in furthering understanding in the intersection of human-computer interaction and security.

Circumbinary planets, those that orbit two stars, are a unique challenge for traditional ideas of planetary habitability. Due to orbital considerations and different stellar properties for the two host stars, these planets receive sunlight that continuously varies in time and as a function of wavelength. These changes could result in time-dependent changes to atmospheric composition and climate. Earlier theoretical studies of circumbinary planets indicate that there is likely a habitable zone where liquid water could exist on these planets, and that climate variations may not be extreme. However, these models did not take into account the effects of atmospheric photochemical reactions, which can alter planetary composition, including the abundance of greenhouse gases, and so also the climate as well. We have developed a new time-dependent coupled photochemical-climate model which allows for exploration of these effects. Here we describe the model, validate it against prior results, and present initial results on the impact of photochemistry in binary star systems.

This paper argues that a discourse of “commercial colonization” permeated the writings of early European explorers of the Pacific Northwest, which fundamentally shaped how colonizers understood the spaces and peoples with whom they interacted. In doing so, I have examined the writings of several late eighteenth century European and Creole American colonizers of the region, especially Juan Perez, James Cook, and Robert Gray. From this basis, I was able to explicate the content and function of the economic discourse in these colonial texts as well as the colonial process more broadly. The discourse of commercial colonization in this region emphasized reciprocity in all encounters yet consigned Indigenous peoples to inherently inferior status in relation to colonizers and was used to justify colonial violence. My work with these texts shows that when the idealized practice of European commerce was challenged, instead of revising their guiding ideals, colonizers relegated those who challenged their theories to subordination. I illuminate how Cook, Gray, and others portray relationships in transactional terms, motivated by profit above all else. Thus, this paper argues that the tensions in these colonial texts are examples of an emerging Capitalist worldview that links the European colonial project in the Pacific Northwest to modern theories of race, commodification, and exploration, allowing us to better understand the relationships between each

 Contemporary scholarship on the transition of immigrant churches from the language of their country of origin to the one of their new country has often focused on it as a process of concessions undertaken by a reluctant first-generation aiming to keep a partly assimilated third-generation in the church. This functionalist view of religion sees the church primarily as a transmitter of culture, and the immigrant church as a tool for ethnic preservation. By contrast, historians studying ethnic minority groups have warned against treating them as monoliths pursuing a single trajectory towards cultural accommodation. In line with this criticism, I study the Swedish-American church ‘’Swedish Evangelical Mission Covenant of America’’ and its transition from using Swedish to English in the 1920s. As with the ''Augustana Church'', which was the largest Swedish-American church in the U.S, The Covenant Church had its theological origins in Lutheran pietism. However, The Covenant came to develop differing views on the role of the church in relationship to Swedish culture, which was reflected in its openness towards the use of English and American theological concepts. My research draws on Swedish-American newspapers, the Nordic Museums collection of information on Scandinavian-American churches that I have assisted in digitalizing this quarter, and secondary literature to show that the Covenant’s adoption of English as its main language instead of Swedish was based on the denomination’s historical and theological background and its perceived duty to spread the gospel beyond the Swedish-American community. This case study illuminates the complex motivations that drive the process of cultural accommodation in immigrant groups, and offers a counternarrative to the portrayal of immigrant churches as helpless victims of assimilation, instead coming to the conclusion that the Covenant members actively and counsciously created a new form of ethnic identity.

There is a long-standing concern that in American society, historical roots, structural racism, and systems of power have perpetuated the spectrum of negative health outcomes in communities of color. As the status quo is maintained, policy and public opinion reflect the continual oppression of minority families. Through my research, I created a visual and multimedia project that will identify the relationship between public policy and the social determinants of health, and how these factors have affected different communities of color within Washington state and the national level. I conducted extensive library research, analyzed and interpreted data, and utilized GIS technologies to visualize the placement of different communities. This work includes identifying historical background information, past U.S. policies, and relevant literature. In this visual and multimedia project, I displayed four puzzle pieces representing different communities (Asian, Native American, Hispanic, and African Americans) on a map, and examined public policies implemented by European colonizers that racialized minorities in unique ways. This chronological project displayed contemporary policies in housing, economic, employment, education, and criminal justice. Overall, I looked at each group's distinct experience of racial health disparities and will use this platform for dialogue to emerge for students and community members on these topics to prioritize the needs, barriers and solutions to confront racism.

Design awareness is the practice of being cognizant of the steps one takes in the design process and how one moves through them. Design awareness can help designers make more informed choices and find the best pathway through their design processes. In a quarter-long seminar, students explored the concepts of design awareness and created prototypes for a design awareness tracking tool to help them stay aware of the design process while fully immersed in it. The goals of this research are to explore methods of teaching students design awareness and to determine the effectiveness of these methods at demonstrating concepts of design awareness and the tools that can help them stay aware. The seminar began with students keeping a journal as they engaged in a design project over the spring break. The students closely examined their own design processes while exploring other methodologies of design. The seminar culminated in student presentations of their sketched prototypes for an artifact designed to increase their personal design awareness. Students reflected on their experiences and were found to have new definitions and understandings of the design process and what it meant to them. Follow-up research explored one design awareness tracking tool and the development of a physical working prototype. The design awareness tracker could record a design process through the different design activities that were engaged in. Data from paper prototypes of the device demonstrated that using the device increased users awareness as engaged in the design process. Further work is being done to widen the scope of design awareness teachings to reach a broader audience.

While some high school students are able to make the transition to higher levels of education, if they so aspire, other students have great difficulty achieving the goal of higher education. This study broadly examines barriers to higher education for students who face challenges graduating from high school and continuing to higher education. For example, students who become truant, attend poorly funded schools, of color, and/or are court-involved face real challenges and barriers in the transition to college. This research explores a variety of sustainable education-driven interventions that have the potential to widen the pathway wherein these populations of young adults can find success in transitioning to a college or university setting. Through multiple interviews with community stakeholders (including governmental, non-governmental, for-profit, and non-profit agencies), I have explored and assessed interventions and programs that are making an impact. These include student to advisor ratios, being surrounded by diversity in leadership positions, family support, neighborhood environments, and additional outside of school influences that ultimately effects these students’ lives every day. Yet, for all these interventions and programs some students still fall through the cracks. There remains a significant lack of equity. This research contributes by drawing attention to the best programs and practices that successfully widen the path for young adults to achieve higher education.

The Indian education system, like many countries, focuses strongly on annual national exams. This results in an emphasis on rote learning, discourages student participation and engagement in lessons, and yields a lack of motivation to learn. Prioritization of rote learning is ubiquitous across India, but is especially detrimental for students from adverse backgrounds and resource-poor settings. Parikrma Humanity Foundation is a non-profit school in Bangalore India that serves students from “the poorest of poor” backgrounds. The school integrates a “360-degree” model that prioritizes student happiness, while emphasizing student and family health as central to learning. Despite these well-established values, students at Parikrma are not exempt from national exam requirements and are also subject to the implications of the heightened importance of exam results. We sought to understand whether key stakeholders perceived that exclusive focus on rote learning hinders development of social-emotional life skills. We conducted over 70 interviews with students, teachers, school faculty, and alumni and analyzed these qualitative results through a method of conceptualization. From this we developed a scale to determine the degree to which the absence of explicit instruction of psychosocial skills impacts overall well-being. Respondents overwhelmingly reported that the lack of material to develop psychosocial skills such as teamwork and active listening results in students with less established life skills and limits access to future opportunities. We aim to develop a curriculum that promotes psychosocial skills key to professional success and overall happiness to be integrated within the context of Parikrma by establishing a cross-aged peer mentorship program that encourages students accountability to each other and themselves. We seek to engage teachers and students through the administration of comprehensive surveys that empowers individuals to self- report the impact of the program in order to assess results.
 

As the Latinx student population continues to grow in public K-12 institutions, it is increasingly important to center this student group within educational research studies. Existing research shows that Latinx students face challenges that discourage them from continuing on to higher education, such as apathetic teaching, language barriers, and institutionalized cultural erosion. The bulk of such findings come from studies conducted in larger urban cities, thus excluding students from the many small farmworker communities that exist in rural agricultural areas such as those in eastern Washington. My research aims to include such populations in the educational discourse, using an asset-based model. Instead of asking students from these rural populations what went wrong for them, the current research project focuses on what went right for them in their paths to higher education. The present study asks the following question: What familial, social, and aspirational forms of cultural capital aid Latinx students in their transition from rural school districts to higher education institutions? To answer this question, I analyzed the retrospective accounts of first year Latinx students from small schools in central and eastern Washington state. Following the Grounded Theory approach, I used semi-structured interviews to collect data, which will later undergo transcription and analysis. I anticipate that results will highlight cultural resources such as community bonds, familial support, and encouragement as helpful resources in the pursuit for higher education. The findings of this research will aid rural secondary-school educators and staff to provide resources that support the educational attainment and success of Latinx students.

In cities throughout the developed world the dizzying rate of urbanization has led to a growing instability in housing fueled by a lack of affordability. A survey of 200 global cities by the Lincoln Institute of Land Policy revealed that 90% were considered unaffordable, based on the standard of a house price being more than three times the median income. This paper will analyze and compare factors impacting affordability in residential real estate markets in Singapore, Vancouver B.C., the Seattle-Bellevue-Tacoma MSA, and Copenhagen. Preliminary research indicates that the primary drivers leading to a lack of affordability are an insufficient supply to meet demand, geographic limitations, household costs rising faster than incomes, demographic impacts from population growth, ageing, and shifts in household composition. The financialization of housing has resulted in its commodification, a means of accumulating wealth and as the security for financial instruments traded on global markets, which has in turn decoupled housing from its primary connection to local markets. The primary intent of this project is to advocate for long term strategic policy changes to affect affordable housing solutions that address both the supply and demand side of housing markets, as well as advocating for a unified national housing policy that places housing as a human right.

Substantively engaging with local communities is critical to ensuring effective quarantine response and treatment to disease outbreaks. This engagement involves the integration of international-based aid with religious and government leaders to reach affected residents and treat disease while respecting local cultures. Significant gaps in community engagement by international humanitarian organizations were observed during the 2013-2016 West Africa Ebola epidemic. These shortcomings hampered trust in aid collaborators, impacted dissemination of disease information, and disrupted the daily lives and community frameworks of residents. Such issues continue to have relevance as the Kivu Ebola epidemic in the Democratic Republic of the Congo enters its third year. This research explores how humanitarian organizations operating in Kivu incorporate community engagement procedures into their work. Institutions such as the World Health Organization and Red Cross are qualitatively analyzed using an evaluation matrix designed to measure the scalability and implementation of community-based integration and participation. Indicators are drawn from official directives and policies. General patterns of cultural understanding and respect of local traditions are observed but vary across organizations. Applying similar collaborative procedures to future epidemics may aid organizational response in engaging affected populations.

Traumatic cervical spinal cord injury (SCI) results in a wide range of outcomes from partial paralysis to complete tetraplegia depending on the location of injury along the length of the cervical spinal cord. Importantly, there is a high density of motor neurons in the cervical region which are involved in important motor outputs such as breathing and hand function. The present study aims to minimize the secondary damage to the spinal cord after the primary insult, by addressing two substantial contributors to neuron death: first, surgical decompression is conducted to reduce local tissue swelling after injury, and second, administration of the metabolite oxaloacetate (OAA) to minimize excitotoxicity by stimulating glutamate transport away from injured neurons. We hypothesized that animals treated with decompression, OAA, or both, would have increased neuronal survival, general tissue sparing, and improved behavioral outcomes than those without treatment, and that combined treatment would be more effective than each individual treatment. We tested the treatments using a clinically relevant rat model for bilateral, moderately severe cervical spinal cord injury. Following treatments, we determined effectiveness by assessing animals’ forelimb function and quantifying motor neuron and white matter sparing in the injured tissue. Results consistent with the hypothesis would have meaningful impacts for future cervical SCI patients, as even a limited increase in tissue sparing in the cervical region have profound functional outcomes for patients’ independence and opportunities. Future studies will work to visualize parameters for segmental tissue at risk after acute injury in order to specify each patient’s treatment and maximize their opportunities for recovery.

Treatment of neurological disease has made little progress due to the inability of many therapeutics to access the brain environment. However, delivery vehicles like nanoparticles can allow therapeutics to overcome brain-specific biological barriers including the blood-brain barrier (BBB), the dense extracellular space (ECS), and cellular targeting. The ability of nanoparticles to overcome these barriers is influenced by surface properties which can be modified through the formulation process. One understudied parameter is the choice of surfactant, molecules which stabilize nanoparticle formation and likely form an interface between the nanoparticle and brain environment. First, we investigated the potential toxicity of several commonly used surfactants on brain cells and slices. We added surfactant solutions to mouse microglial cells (BV2) or cultured brain slices and assessed cell viability two days later with colorimetric assays. Our results showed that while surfactants cholic acid (CHA) and polysorbate 80 (P80) caused toxicity at high doses, they were nontoxic at the low doses involved with nanoparticle formulation. Other surfactants, including Pluronic® F127 (F127) and poly(vinyl alcohol) (PVA), were nontoxic throughout the tested dose range. Interestingly, although the F127 compound is nontoxic on its own, nanoparticles formulated with F127 reduced cell viability. This result was not observed with any other nanoparticle-surfactant combination. Confocal microscopy indicated higher intracellular accumulation of the nanoparticles formulated with F127 compared to all other formulations, suggesting that toxicity is mediated by nanoparticle internalization and surfactant choice. Finally, we used a live cell imaging technique to capture videos of the nanoparticle internalization process. Building off these results, ongoing experiments will evaluate several nanoparticle-surfactant formulations on their ability to accumulate within brain tissue after in vivo administration. Findings from this work will guide nanoparticle design for future clinical translation.

Millions of people have vision diseases that are not yet treatable, leading to blindness. Mouse models exist for some inherited retinal diseases, and thus have helped develop vision loss therapies. However, other common retinal diseases like glaucoma lack accurate mouse models. Human pluripotent stem cells (hPSCs) are a promising technology that provide a new way to model human retinal diseases. hPSCs can be induced to become layered, 3D mini-retinas called retinal organoids. Retinal organoids mirror early neurogenesis of the human retina, and thus can be used for modeling developmental disorders. However, we and other research groups have shown that as retinal organoids mature, they lose many features of the normal human retina. In particular, the neurons that are damaged during glaucoma, called retinal ganglion cells (RGCs), are not well preserved in organoids. As the organoid matures, the RGC layer becomes disorganized and RGCs migrate through the retina. RGCs are the projection neurons of the human retina, so their axons extend through the optic nerve and carry visual information to the brain. Unlike in human development, retinal organoids are grown in isolation from their brain targets. We wondered whether we could preserve RGC organization by providing organoid RGCs with synaptic targets. We investigated this hypothesis by combining the retinal organoids with their natural targets in the brain, the lateral geniculate nucleus and the superior colliculus. It is not yet known how to make these brain regions from hPSCs, so we used newborn mouse brain and combined the retinal organoids with these brain regions into structures called “assembloids.” We are now testing whether these assembloids preserve the RGC survival and laminar organization that retinal organoids lack. Promoting RGC survival and organization will allow organoids to become better in vitro models for glaucoma and improve the outcome for patients with vision loss.

Alzheimer’s Disease (AD) is a progressive, debilitating, neurodegenerative disorder where patients lose their ability to think and carry out tasks. This disease is characterized by aggregation of the β-amyloid (Aβ) peptide. Cannabidiol (CBD) and delta-9-tetrahydrocannabinol (THC) are derivatives of marijuana which have been shown to possess neuroprotective properties. Experimental work in this field, is limited in its scope when probing mechanisms driving the phenomenon of Aβ peptide aggregation. Molecular dynamics (MD) simulations have been used to understand the intra-peptide interactions and potential impact of cannabinoids. In order to understand the effects of cosolvent structure on the mechanism of amyloid aggregation, we used classical molecular dynamics simulations of Aβ derived switch-peptides in the presence of model cannabinoids (i.e. CBD and THC). Aβ peptides transform from functional peptides into beta-sheets and therefore impact function within the brain. We tracked beta-sheet formation as a function of time to understand if cannabinoids sterically inhibit interactions between and within peptides. Preliminary results indicate that CBD and THC demonstrate a trapping effect on aggregated peptides. The impact of synthetic cannabinoids are much less understood, prompting additional interest in investigating the interactions among these molecules.

Since Computed Tomography (CT) scans expose the patients to high x-ray radiation dose which may potentially induce lifetime risk of cancers, researchers have been finding ways to reduce the radiation dose while maintaining the high quality of reconstructed images. One approach to lower the total X-ray radiation dose is to reduce the number of projections acquired, which generated sparse-view CT image. However, when the number of view angles is too less to satisfy the Shannon/Nyquist sampling theorem, serious streaking artifacts will appear on the reconstructed images. In this work, we present two iterative reconstruction algorithms, which implement convolutional neural networks (CNN) in each iterative step, to help eliminate these defects. The first algorithm is LEARN, which uses a CNN in place of a regularization function while solving a least squares problem. The second algorithm is based on SART and the superiorization methodology (an iterative method for constrained optimization), where the CNN is used to perturb the solution between SART iterations. We use Tensorflow and the Pyro-NN library in Python to train on data obtained from The Cancer Imaging Archive’s QIN LUNG CT dataset, and compare the performance of these two frameworks from the perspectives of PSNR value (often used to exam the quality of an image), training loss, penalty term, and learning rate. Besides testing on different sparse-view imaging datasets, we also demonstrate the performance of the proposed networks in limited angle CT image, where some view angles are missing due to geometric constraints.

Immunological memory prevents reinfection by a pathogen. This protection is accomplished by memory T cells expressing T cell receptors (TCR) specific for previously encountered pathogen-derived peptides (antigens). Conventionally, memory T cells are thought to be inert during novel infections because there is no interaction between their TCRs with their specific antigens. Despite this, we and others have demonstrated that these T cells (here termed “bystanders”) can be activated by inflammatory signals alone and gain cytotoxic effector function in the absence of TCR-antigen interaction. This study aims to determine how inflammation regulates and attenuates bystander responses and how we can leverage these cells therapeutically. Using in vitro cell stimulations, we found that the inhibitory receptor, programmed cell death protein 1 (PD-1), is strongly upregulated by bystanders after exposure to certain inflammatory cytokines. This finding is unique because the current paradigm is that PD-1 expression is caused by TCR stimulation and PD-1 represents a target to manipulate bystander responses. Further, in mouse models of vaccination, we found that bystander-mediated killing can limit vaccine antigen. We believe that interfering with bystander T cell effector functionality could be targeted to improve antigen-specific vaccine responses. Through understanding the mechanisms that dictate bystander function, we may better modulate bystander T cells function during infection, vaccination, and cancer to improve patient outcomes.

Engineered solid binding peptides can be used as molecular tools for a variety of applications, with our focus lying on bio/nano interfaces. Peptide-solid interactions involve surface phenomena such as binding, surface diffusion, and self-organization on atomically flat solids. Each of these phenomena requires the knowledge of peptide folding patterns, which are difficult to study both experimentally and computationally. Molecular dynamics, MD, has been used to computationally model peptide/solid interactions, but without information regarding the energy landscape of peptide conformations, the challenge of predictive design remains. While several methods exist for finding the energy landscapes for single peptide systems, currently no approach is capable of handling multi-peptide/surface systems. Here we use dynamic mode decomposition, DMD, to efficiently explore the energy landscapes of such systems aiming to find accurate linear approximations for predictive design of peptides at bio/nano interfaces. We make use of extended, multiresolution DMD to allow for analysis of various datasets with identical timesteps while minimizing impacts of statistical noise. It is anticipated that some descriptions of conformation will be better suited to describe peptide conformation energy landscapes than others; based on this premise, we examined various descriptions of peptide conformations through DMD. These descriptions include interatomic distances, adjacencies and peptide backbone torsion angles, alongside wavelet, Hilbert, Fourier, and Laplace transformations of select datasets. Through such analyses, it is becoming possible to describe how peptide conformations in multi-peptide/surface systems evolve through the energy landscape and settle into energy minima corresponding to stable conformations. These conformations can then be corroborated to peptide self-assembly on the surface using scanning probe microscopy techniques with sub-A resolutions for the development of predictive design platforms for future applications in biosensors, bioelectronics, and logic devices. 

The long term goal of this project is to study and mathematically characterize how the mammalian (mainly Homo sapiens) brain creates and maintains meaningful neuronal connections and organizes into connectomes and cortexes, and to compare what we learn to an existing (patented and under development at GEMSEC) brain-like computational neural network. A key point in understanding the formation, organization and long-term existence of new brain neural networks is the fundamental relationship between the geometric entropy of the physical network embedding, and information entropy of the network adjacency, connectivity. To our knowledge, there is currently no study in the literature that focuses on understanding biological neural networks through the entropy of their connections. Here we pose the question whether entropy related learning rules emerge from biological network connections or are the driving force for these connections. We also ask whether such learning rules can be imposed on artificial neural networks for enhanced functionality. To find the information entropy analogue of the geometric entropy term from a network point of view, we need to define the information entropy of the neuronal adjacency matrix. We define the information entropy of the neuronal adjacency, with random numbers between 0 and 1 symbolizing strength of the connections, i.e., synaptic plasticity, as the Shannon’s entropy, i.e., information entropy, of the spectral distribution of the neuronal adjacency matrix. To aid us in this study, two public neuronal datasets have been found: the Janelia FlyEM research group’s Hemibrain, and the NeuralEnsemble simulated spike train data. We test the entropy of the inferred neuronal connections from these datasets toward achieving our goal of the mechanism of formation of neural connections and connectomes. This project is supported by the UW Computational Neuroscience Center, and the DMREF Program of NSF through the MGI platform under DMR# 1629071, 1848911, and 1922020.

 Spontaneous self-organization of solid-binding peptides on single-layer atomic materials offers enormous potential in employing these systems for technological and medical applications from biosensors to logic devices. Molecular self-organization of peptides depends highly on their sequences, which affect their conformational behavior under aqueous conditions. Traditional ways of computationally studying the effect of mutations on the conformation states involves dimension reduction on cosine and sine transformed torsion angles, often represented as Ramachandran plots. Although these studies successfully cluster conformation states, they fail to intuitively characterize the effect of the point mutation(s) directly, necessitating further data analysis. Here, we apply Hilbert Space-Filling-Curve, HSFC, on the torsion angles and demonstrate intuitive visualization for the effect of point mutations on secondary structure dynamics along a reaction coordinate. We perform molecular dynamics simulations on graphene using the graphite-binding dodecapeptide, WT-GrBP5. The 12-AA long peptide was selected by directed evolution using M13 based phage display. The WT-GrBP5 is known to self-organize on graphene under low-neutral pH at room temperature. A rationally designed charge-neutral mutant, M9-GrBP5, assembles at a broader range of pHs widening the range of practical implementations of the peptide. The HSFC shows that the mutated amino acids in M9 do not correlate with the reaction coordinate of pH change, unlike that of WT. Understanding the effect of amino acid φ-ψ pairs that contribute to the changes in the peptide’s conformational space, with changing conditions, will help in analyzing effects of point mutations. The effect of the peptide’s conformational behavior on their self-organization propensities on surfaces would lead to the design of sequences that form soft bio/nano interfaces with controlled molecular interactions towards strategies for practical applications. The research was supported by the DMREF Program at National Science Foundation (NSF) through the MGI platform (Materials Genome Initiative) under grant numbers DMR# 1629071, 1848911, and 1922020.

Self-assembling peptides show great promise as an effective bottom-up technique that can be used to integrate biology and nanoelectronics. Such peptides can form a long-range ordered structure on the surface of Single Layer Atomic Materials (SLAM), such as graphene and transition metal dichalcogenides (e.g. molybdenum disulfide) through a chiral recognition mechanism. As graphene is highly sensitive to the adsorption of molecules, it is an ideal building block for biosensors. However, controlling the self-assembly of biomolecules to attain functional structures remains an engineering challenge. One fundamental question is how does the van der Waals (vdW) interaction between the graphene sheet and the adsorbing peptide, and the resulting strain field, affect the peptide binding footprint and the formation of an ordered phase. To investigate the phenomenon, I used Atomistic Finite Element Modeling (AFEM) to simulate the strain fields that arise during physical adsorption of a peptide to the surface of a graphene sheet. I then compared data from the AFEM simulation to experimental data collected using Scanning Tunneling Microscopy (STM) to determine whether the strain patterns correlate with the experimentally observed chiral assembly directions. Establishing a correlation between adsorption induced strain and chiral recognition would provide a more robust hypothesis concerning the optimal conditions for the generation of long-range ordered biomolecular structures on SLAMs; and, by extension, a step towards the realization of peptide-based biosensors.

The ease of data retrieval, analysis, and distribution can accelerate the pace of scientific research. A difference in philosophies and methodologies in the manner of data-collection and storage leads to a lack of semantic-consistency in naming-conventions across disciplines. Previous studies have opened this discussion within various research disciplines, however there has yet to be a study accomplished within a Convergence Science Lab such ours, Genetically Engineered Materials Science and Engineering Center (GEMSEC). Well-defined naming-conventions, clear-cut data standards, and set programmatic interfaces are required to provide improved data access to researchers and the public. This consistency is necessary to create a robust database with the ability to query large amounts of related information. The key point is that integrating design (of variables, research questions, etc.) with traditional, empirical research approaches in the natural sciences will result in more robust data and clearer analysis. Here we discuss the need for standardized protocol and metadata standards for data-collection and storage. We began by creating a data analysis and storage pipeline for two computationally involved experiments, Molecular Dynamics (MD) and Next Generation Sequencing (NGS), within GEMSEC. A database schema storing metadata associated with raw, cleaned, and analyzed files was created. We found homogenous collections of metadata with inconsistencies, especially in peptide naming conventions, between experiments. The target-database includes those from other labs some of which may store unconventional file types, use other naming schemes for key variables such as sequences, and have different standards for what metadata is stored and what is computationally retrieved at a later time. This schema is formed via interviewing various other researchers, determining similarities and differences within metadata, and creating a standard for all to use based on this collected information.

Proteins are the workhorses in biology and their functions are affected by their amino acid domains in a modular fashion. When placed on solid surfaces, such as single layer graphene, certain short-sequence solid-binding peptides possess specific conformation propensities that aid in the self-organization into long range ordered peptide nanowires on atomically flat crystal lattices, such as single atomic layer solids. The self-assembly of nanowires on two-dimensional solids create electronic junctions through the biological doping of the underlying material and, e.g., by ordering the dipole moments. The utilization of these self-assembled nanowires with unique electrical capabilities may be a significant step towards the advancement of biologically compatible electronic devices such as biosensors. One of the key aspects of the design, namely the driving force for self-assembly of peptides on inorganic crystals, is currently unknown. To further understand the surface phenomena, our goal is to apply theoretical computational modeling to simulate the behavior of peptides and analyze how various conditions, such as temperature, pH, concentration and molecular conformations impact self-assembly. Peptides are computationally simple and only act based on local information such as the conformation of their immediate neighbors on a shared surface. Therefore, the self-assembly behavior can be simulated by fully distributed and asynchronous Markov chain algorithms, which have previously not been applied to peptide folding behavior interacting with a substrate. From these simulation algorithms, we determined the ideal physical conditions and the driving-forces for self-assembled peptide-based bioelectronic networks interfaced with single layer materials. Understanding how to better form these bioelectronic networks could constitute the critical foundation to advance bio-nanotechnology through the creation of biosensors or other biologically compatible electronic devices.

The MAJORANA experiment and its follow-on, the Large Enriched Germanium Experiment for Neutrinoless Double-Beta Decay (LEGEND), search for the creation of matter in the form of neutrinoless double-beta decay, a process that would demonstrate that neutrinos are their own antiparticle and that lepton number conservation may be violated, allowing a deeper understanding of the matter-antimatter imbalance in the universe. MJ60 is a germanium detector used to investigate the low-energy region of the MAJORANA DEMONSTRATOR data, as well as the waveforms produced from incident betas in comparison with gamma events. The latter of these is important for understanding the background of LEGEND: the detectors are submerged in liquid argon, in which beta decays of argon-39 and argon-42 contribute to the background of the extremely sensitive experiment. MJ60 was originally a prototype for the P-type point-contact detectors used in the MAJORANA DEMONSTRATOR. Our group is using this detector to measure mechanisms of energy loss near the detector surfaces by recording events from the nearly monoenergetic beta emissions of metastable krypton-83 (83Kr) at 18 and ~30 keV. Analysis of the waveforms produced from these events, which has been my primary task, will allow us to investigate whether betas incident on our detectors’ passivated surface exhibit markedly different charge collection than gammas, as has been hypothesized. If this expectation is upheld, we will be able to produce a method to identify these events based upon a calculated parameter from the recorded waveforms. Such a parameter will help inform future detector R&D efforts, and will also contribute to background rejection capabilities in MAJORANA and LEGEND.

The COHERENT experiment is endeavoring to detect Coherent Elastic Neutrino-Nucleus Scattering (CEνNS) in several nuclear targets using the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL). We search for very low energy (on the order of keV) coherent interactions between neutrinos and atomic nuclei using an array of particle detectors made of different scintillating materials. Neutrinos are fundamental particles under the Standard Model of particle physics that historically have not conformed to theoretical expectations. Understanding their interactions with other particles helps us potentially find other unexpected qualities of neutrinos and in that, discover new physics. At the UW component of the COHERENT team, I along with several other physics undergrads, have just finished characterizing over one-hundred NaI(Tl) crystals to contribute to a large array of detectors at ORNL where they will be illuminated by a strong, pulsed flux of neutrinos born from pions and muons generated in the SNS beam target. For each crystal, I used two characteristic radioactive sources (133Ba & 137Cs) to gather data on each crystal for characterization of their use at ORNL. Each crystal was run for 1.67 hours to find the optimal operating voltage (gain) and to explore the energy linearity of radiation detections at different points in each 7kg crystal (this allowed us to identify if the crystals had any cracks that would interfere with detections). In this talk, I intend to present the statistics on the measured crystal characteristics, including gains, energy resolution, scintillation uniformity as we prepare to ship the crystals to ORNL for installation in the array of other detectors capable of detecting the CEνNS phenomenon.

Our research project aims to find red supergiant stars (RSGs) among the starburst galaxy IC10. Using stellar evolutionary theory, estimates can be made about how many RSGs are expected, based upon analyzation of known facts such as size, age, and metal content. The research conducted will allow for a comparison between observational data to theoretical expectations. RSGs are massive stars with a supergiant luminosity class; they are the coolest of the supergiants and have spectral types of K and M; hence temperatures below 4,100 K. Typically, they can be up to a thousand times the radius of the sun, and are therefore highly luminous. We began our search for these stars in IC10 by collecting the Two Micron All-Sky Survey and United Kingdom Infrared Telescope (UKIRT) J and K photometry. We then transformed the colors to luminosity and temperature allowing us to create an HR Diagram and identify candidate RSGs. Our next step was to continue to refine our results in order to remove foreground stars that aren't in the IC10 galaxy. We cross-matched our IC10 photometry with data from the GAIA satellite to obtain a list of proper motions and parallax values of all potential RSG candidates. From this we plotted the proper motion values vs. parallax to visually select stars in IC10. Our resulting list brings us closer to identifying RSGs in the starburst galaxy IC10.

Retinal diseases tend to affect specific neuron subtypes, ranging from age-related macular degeneration, which is caused by the deterioration of photoreceptors near the central portion of the retina (macula), to glaucoma, in which abnormally high intraocular pressure leads to ganglion cell death. Unfortunately, adult mammals are not able to regenerate retinal neurons. However, zebrafish and other amphibians can completely regenerate their retinal neurons in many different models of damage, and restore retinal structure and visual function. The source of regeneration stems from the resident Müller glia cells, which normally provide neuronal support and span all three retinal layers. A critical gene for the initiation of transforming Müller glia into neurons was found to be Ascl1. This led our lab to hypothesize that the introduction and upregulation of Ascl1 in mammalian Müller glia might stimulate them to become retinal neurons after damage, as occurs in these other regenerating species. Indeed, after introducing Ascl1 into the Müller glia of mice, we found newly regenerated retinal interneurons (bipolar cells) that successfully integrated into the retinal circuitry and functionally responded to light stimulus. In addition to Ascl1, we have identified two other transcription factors, that when introduced in combination with Ascl1, stimulate the generation of two different retinal neurons (ganglion cells and amacrine cells). We are currently developing a model of glaucoma, damaging the ganglion cells with a neurotoxin, and then testing the visual acuity using Optomotry to determine whether regenerated ganglion cells will mediate a functional improvement. Ectopic expression of a proneural transcription factor to stimulate retinal regeneration provides a potential therapeutic intervention for treating blinding diseases, that even now, have few modest treatment options.

Bivavle Mollusks, such as mussels, are generally considered to be well-known bioengineers due to their ability to aggregate and reduce local flow conditions. They are impacted by changes in their microenvironment, such as alternations in seawater chemistry or water flow. As a result, there may be benefits such as lower energetic costs and risk of dislodgment in reduced flow. However, there may also be harmful effects such as minimal water exchange and less food availability. Furthermore, the chemical conditions within mussel bed aggregations can affect mussel survival rates due to changes in byssal thread production and overall attachment strength. At the UW Friday Harbor Laboratories, Summer 2019, we conducted laboratory experiments to quantify how mussels alter the chemistry of the interstitial spaces within their aggregations. Specifically, we placed aggregations of mussels (M. galloprovincialis) in a flume and measured the dissolved oxygen (DO) concentration within the aggregation, referred to as “in bed,” and compared it to the dissolved oxygen values upstream, referred to as “ambient.” The mussels were arranged to mimic the set up of an aquaculture rope. We found that the difference between ambient and in bed DO concentrations went up to 2.5 mg/L when flow was less than 5cm/s. This difference increased with temperature due to increased respiration. These findings indicate that flow and temperature mediate processes that determine the chemical microenvironment in a mussel bed. Furthermore, the conditions in these microscale environments may have important consequences for the survival of mussels and other species that rely on them for shelter.

Hydra vulgaris are some of the simplest animals with neurons. They only have two thin, near transparent layers of tissue: myo-endodermal and myo-ectodermal layers. Interspersed in each layer is a network of neurons known as the nerve net. All cells in the animal are constantly renewed, which allows Hydra to regenerate after being cut in pieces or dissociated into single cells, though how the nerve net regenerates has not been well studied. Each cell in the animal can be examined simultaneously due to the animals’ small size and simple, translucent body pattern. Hydra also exhibit stereotypical (regular and defined) behaviors. This makes Hydra great models for examining simple signaling pathways from which the complex pathways in vertebrates derive. The Hydra nerve net is composed of circuits that coordinate the behavior of the animal. The most obvious are the contractile burst (CB) and rhythmic potential (RP) circuits. I selectively blocked these circuits to understand how they drive behavior. It has been found that N-[1-(2-phenylethyl)-3-piperidinyl]-1-benzofuran-2-carboxamide (E9), affects Hydra behavior, appearing to block the CB circuit but leaving others, including the RP circuit, uninhibited (unpublished data, Woods Hole MA). I worked to understand the affinity and response rate of this molecule to Hydra by establishing a dose response curve for E9 on Hydra. To determine effective concentrations of E9, I imaged animals in serial concentrations ranging from 3uM-300uM. I then identified the response of neural circuit firing patterns to varying concentrations of E9 by applying this technique to animals that express GCaMP, a protein that fluoresces when bound to calcium, in neurons. I found that 30uM is the lowest concentration of E9 sufficient to block the CB circuit. This research provides a tool for studying the link between circuits and behavior, and allows us to characterize how behaviors depend on identified circuits.

Members of the genus Psychrobacter, within the class Gamma-proteobacteria, generally live in very cold marine habitats. These bacteria can be found in Arctic and Antarctic sea ice and sediments, in deep-sea environments, and in permafrost containing relic marine sediments (cryopeg). Each of these environments provides a different combination of temperature and salinity, with different strains of Psychrobacter spp. potentially adapted to grow at different rates depending on environmental source and in situ conditions. I am exploring the growth characteristics of two Psychrobacter spp., each isolated from a different extreme environment. Psychrobacter sp. nov. strain CB7C was isolated from cryopeg brine (originally at –6°C and 140 ppt), and Psychrobacter sp. nov. strain 7E was isolated from winter sea ice brine (originally at –12°C and 128 ppt). We incubated strain CB7C in duplicate at 57 different sets of temperature and salinity conditions, including 19 temperatures, ranging from –7 to 12°C, and salinities of 35, 75, and 120 ppt. The strain was grown in a complex medium, Marine Broth 2216 (at 50% organic strength), adjusted to desired salinity. At regular intervals during the incubations optical density was measured, with cell counts made at start and end. Calculated growth rates and cell yields for CB7C varied across the different temperatures for each salinity. At higher salinity, the temperature at which the bacteria showed maximal growth shifted downwards, a result consistent with in situ conditions (lower temperatures at higher salinities) but novel in microbiology. By conducting similar incubations with strain 7E I will be able to compare growth patterns of the two isolates across a wide set of temperatures and salinities and determine if results with CB7C are singular or represent a more common trait amongst Psychrobacter strains, helping to explain their prevalence under such extreme conditions.

The effectiveness of different catalysts during biofuel production was investigated to determine if a heterogeneous catalyst, eggshells, could perform as well as a traditional homogenous catalyst, Sodium Hydroxide. Eggshells add up to a significant amount of waste each year. If they were repurposed, that would not only get rid of that waste factor but also serve as an alternative to fossil fuels. The biodiesel was synthesized from sunflower oil. The amount of each catalyst was fixed at 2.25 grams and the yield of each fuel was documented. Fifty milliliters of the fuels produced were individually tested to measure their efficiency. The fuels were tested in a pop-can calorimeter. The pre-calculated combustion of ethanol in said calorimeter was used as a baseline for calculating relative efficiency. From there, we were able to determine the richness of the fuels produced by the two catalysts. The biodiesel catalyzed by Sodium Hydroxide produced 38.17 kilojoules per gram and the one catalyzed by Waste Egg shells produced 34.81 kilojoules per gram.

Mitosis results in two genetically identical daughter cells, each containing their own nucleus and set of replicated chromosomes from the original parent cell. Inaccurate chromosome segregation can result in severe consequences like cancer and developmental defects. During mitosis, the replicated chromosomes line up at the center of the cell in preparation to be pulled apart by microtubules. Microtubules are dynamic cytoskeletal components that provide the forces necessary to pull the chromosomes towards their respective daughter cells. The ends of the microtubules attach to the kinetochore, which is an assembly of protein complexes located on the chromosome. Accurate segregation of these chromosomes relies on the ability of the kinetochore to strongly bind chromosomes to microtubule ends. Ndc80 complex is an outer-kinetochore component that binds microtubule ends and is required for proper segregation. Emerging cellular data suggests that multiple Ndc80 complexes interact with one microtubule end. We seek to assemble a particle of multiple Ndc80 complexes in vitro, which may model the native kinetochore-microtubule interface more closely. We utilized a designed protein, HBRP, that forms a hexamer in solution and was modified to couple with and artificially oligomerize any protein of interest. We optimized the coupling rate and completion degree of three different variants of the HBRP protein with Ndc80 complex to ensure a complete hexamer particle assembly. Successful formation of this particle assembly will allow us to better understand the binding mechanism of the kinetochore to microtubule ends.

Computational protein design is an emerging field that takes advantage of first principles derived from biological protein-protein interactions and explores the protein space that nature has yet to evolve. The Baker Lab developed a software called Rosetta that enables researchers to explore this space and create brand new proteins more stable than those produced in biological systems via evolution. This software has been adapted to take advantage of a concept that exists everywhere in nature- symmetry. Using this concept, I am building higher-order protein assemblies including protein nanocages and three-dimensional protein crystals. Researchers at the Baker Lab have developed a hierarchical approach to engineer these highly symmetric, complex structures. This hierarchical approach involves combining protein building blocks with different symmetric topologies multiple times to facilitate higher-order symmetric assembly of a three-dimensional protein crystal. By breaking up crystal symmetries into their constituent building blocks, we can design these higher-order symmetries with greater accuracy and troubleshoot experimental difficulties by pin-pointing structural deviations along the way. Here, I will describe my experience using this approach to create a protein crystal from symmetric building blocks.

Nondestructive 3D pathology is poised to play a transformative role in biomedical research and precision medicine in the decades to come, helping to usher pathology into a digital 3D era. Recent improvements in high-throughput volumetric microscopy, including light-sheet microscopy, have made it feasible for large pre-clinical and clinical specimens to be imaged in toto within reasonable time frames [Glaser, et al., Nature BME, 2017; Glaser, et al., Nature Communications, 2019]. However, these imaging methods depend upon the quality and reproducibility with which fluorescent labeling and optical clearing of thick tissue specimens is performed. In particular, while high-quality volumetric datasets can be acquired with pain-staking optimization and iteration of manual tissue-preparation protocols, high-throughput imaging assays demand that these methods be highly consistent and require minimal labor. We developed a protocol for automated micro-controller-based labeling and clearing of clinical specimens in order to generate volumetric imaging datasets that consistently mimic the appearance of “gold-standard” H&E histology. Archived formalin-fixed paraffin-embedded (FFPE) tissue blocks are first de-paraffinized with a combination of heat and xylene removal of paraffin wax. Next, specimens are put in an acidic, ethanol and water solution so that an aqueous nuclear and eosin labeling step can be achieved. This otherwise labor-intensive, two-day procedure is a critical step for automation since manual processing can lead to variabilities that will affect downstream labeling and clearing performance. Finally, specimens are cleared with a non-toxic clearing agent for refractive index-matching and 3D microscopy. By using automated micro-controller-based buffer exchange hardware, we demonstrate the reliability of these low-cost and convenient methods for imaging a diverse range of tissues. These methods will facilitate pre-clinical and clinical studies with large numbers of tissue specimens, such as those needed to validate the benefits of 3D pathology for clinical decision support.

Back contact solar cells improve on the standard geometry by arranging both the positive and negative electrodes on the back of the device. This significantly improves efficiency by eliminating three critical challenges faced by typical solar cells: (1) shading of the active layer by top contacts, (2) the conflicting requirement for conductive yet transparent top contact materials, and (3) difficulty in printing metallic contacts onto the sensitive photoactive layer. Electrodeposition is a disruptive method that offers an alternative pathway for solution processing manufacturing, but is relatively unexplored as a method of fabricating perovskite back contact solar cells. This study focuses on achieving selective electrodeposition of high quality nanoscale electron and hole transport layers (tin and nickel oxides respectively) onto interdigitated silver collectors. In this investigation, a silver working electrode and a nickel or tin counter electrode against a silver/silver chloride reference electrode comprise a three-probe system in nickel nitrate and tin chloride electrolyte baths. The conductivity and carrier mobility of the electrodeposited transport layers are discussed as a function of salt and dopant molecule concentrations in the electrolyte bath. High carrier mobility layers are desirable for increased solar cell efficiency. The microstructure and thickness of the transport layer are discussed as a function of bath temperature, stirring speed, and the magnitude and duration of the supplied current density. The transport layers are characterized using optical profilometry and scanning electron microscopy. Diode devices are fabricated to characterize the electrical properties of the oxide layers. Based on these results, an optimal electrodeposition procedure is recommended for producing high quality nickel- and tin-based charge transport layers for application in back contact perovskite solar cells. Achieving this device geometry via electrodeposition enables the production of more efficient solar modules using high throughput manufacturing methods - bringing novel photovoltaic materials one step closer to widespread use.

During the 19th Century, the Tigris River in the Ottoman Empire province of Iraq was an essential conduit for trade and travel between the East and the West. European, Ottoman, and Persian steamships plied the river from Baghdad to Basra and back, transporting goods and passengers. At present, there exists no detailed digital historical map of this significant waterway. Our project began with the Joseph Mathia Svoboda diaries. Joseph Svoboda, a European resident of Baghdad, worked as a purser on British Lynch Company steamships running between Baghdad and Basra. For about 50 years, he kept diaries recording his journeys, stopping places, cargos, passengers, weather, and events on the river. Our research project began by creating a schematic map based on Joseph’s accounts listing a number of stops the steamers made going up and downstream. Our next step is to identify the locations of the steamers’ stopping places on the river. We are exploring two options: the first, referencing 18th and 19th century maps of the river found in online map collections such as the David Rumsey Map Collection and the Library of Congress. The second option is using ArcGIS, a geographic information system with an extensive map database, to identify the places Svoboda mentioned. We expect to develop the map, either by manually plugging in the names in an empty, historically accurate terrain map, or by using the historical map database from ArcGIS to set up an interactive map. The finished digitalized map will be the first of its kind. It will help our project’s other research move forward. For example, the developed map will offer a clear visualization of Svoboda’s journey that could help our transcription team as they work with new diaries. It will also build a more comprehensive guide for scholars who study the history, economy, and geography of the Tigris and Ottoman Iraq in the 19th Century.

This presentation discusses, through a series of historical case studies, how the issue of nuclear waste on indigenous lands is a reproductive justice issue. Drawing on bioethical theory, secondary historical and sociological analysis, and primary source accounts, the presentation demonstrates that the impacts of nuclear waste on indigenous lands and communities are the result of systemic racism against indigenous communities, and that those impacts, including high rates of miscarriage and reproductive cancers, remove bodily autonomy and reproductive choice. Negative health outcomes make communities unsafe places to raise children, and the potential for increased exposure to toxins through traditional cultural practices impacts a community’s ability to raise children with those cultural practices. This history and attention to nuclear waste as an issue of reproductive justice must be part of the conversation as energy and waste storage policies are developed to address climate change.

Humanity is on the verge of a biotechnological epoch. What this will entail is a union of opposites: biological humans merging with artificial machines. Unity of opposites, or non-duality, is a timeless theme, one that is not only found in the ancient teachings of Heraclitus or in Greek mythology, but also in that of the I-Ching, and the Tao Te Ching. The yin-yang symbol is one of the earliest visual depictions of this. Support for a unified theory of the universe is now being widely embraced; hence the shift from the old Standard Model of particle physics to the new Core Theory. Modern interpretation of what Laozi referred to as, Tao, suggests a process that is characteristic of a double torus, with a cuboctahedron at its heart. Such a synergic principle would not only be observable in the nature of matter, but also in that of the mind. It is of no coincidence that humanity is beginning to integrate with arguably its finest of achievements—tools. Synergic inquiry is the method by which this literature review will be conducted, so as to build the argument that all things are interdependently connected, distinguishable sub-systems of a larger system. This implies that the convergence of human and machine is simply the beginning of a brand new, distinguishable part in that whole. The study of synergetics, in its wider applications, proves to be an invaluable tool to understand the macrocosm and microcosm relationship, and it will no doubt contribute greatly to the symbiotic relationship between nanotechnology and molecular biology, as humanity seeks to build a better world.

Melanoma is the most aggressive type of skin cancer. It can quickly metastasize and usually develops drug resistance to standard treatments. Our lab is working on investigating the transcription factors (TF) responsible for drug resistance in melanoma to help create more effective drug treatments. Single cell RNA-seq and ATAC-seq (assay for transposase accessible chromatin) was used, with single-cell level resolution, to ascertain transcriptome and epigenome information, respectively. This data was analyzed using bioinformatic toolkits to predict the transcription factors that control drug resistance. These predictions were validated using CRISPR knockout cell lines and melanoma cells with a specific transcription factor removed. Analysis of single cell RNA-seq data of melanoma cells after 24 days of drug treatment, when the cells typically become drug resistant, reveal the co-existence of four distinct subpopulations. These four subpopulations can be categorized into two groups, drug sensitive (melanocytic and neural crest) and drug resistant (mesenchymal and novel). We also gathered single cell RNA-seq and ATAC-seq on a timeline with days 0, 3, 6, 13, 17, and 24 to monitor the trajectories cells undertake to obtain the drug-resistant state. Analysis of the timeline single cell RNA-seq mapped out this trajectory from drug sensitivity to drug resistance and associated changes in cellular phenotypes. We expect analysis of the timeline single cell ATAC-seq data will show similar results and through an integration of the two layers of information, more solid predictions can be made for the TFs driving the transition towards drug resistance. We expect the cells with these TFs knocked out to be unable to form drug resistant subpopulations, as they can no longer activate drug resistance. Discovery of such TFs would suggest additional or more effective treatments that could halt drug resistance and mitigate the effects of melanoma.

Long-term exposure to traffic-related air pollutants (TRAPs) has been associated with multiple adverse health effects. However, many TRAPs, such as ultrafine particles, are poorly measured and thus their association with health outcomes is difficult to characterize. Our objective is to identify geographic characteristics that distinguish diurnal trends in TRAP concentrations at monitoring sites in order to estimate spatial contrasts in long-term average concentrations. Mobile monitoring (driving to many locations with multiple instruments) permits us to measure many TRAPs at many locations, but these measurements have short durations and may not capture the pollutant’s underlying trends. Therefore, these measurements may not reflect a site’s true long-term average due to our inability to fully sample the diurnal trend of the pollutant. In order to quantify the role of diurnal trends on annual averages, we use hourly measurements of CO, NO₂, and PM2.5 from California Environmental Protection Agency’s (CalEPA) monitoring sites where the true long-term averages are known. Using Principal Component Analysis (PCA) to reduce the number of dimensions, we will regress the pollutant levels against the time of day, the physical covariates and their interaction terms. The geographical variables include, but are not limited to, distance to a highway, distance to bodies of water, Normalized Difference Vegetation Index (NDVI), and population density. We utilize Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) as our model selection criteria and we assess model performance via leave-one-out cross-validation. We identify the most influential geographic factors that are associated with two to three categories of similar diurnal trends for each pollutant. With these variables, we will be able to group Seattle monitoring sites and distinguish their diurnal trends. Appropriate adjustment for diurnal trends in our mobile measurements will permit us to estimate spatial contrasts more accurately.

Human immunodeficiency virus (HIV) infection is a significant global health issue, with approximately 75 million infections, and over 35 million deaths, since the beginning of the AIDS pandemic. The majority of these are attributable to HIV type 1 (HIV-1). A second form of HIV – HIV type 2 (HIV-2) – is endemic in West Africa and has spread to other areas with socioeconomic ties to the region. Historically, regimens for first-line treatment of HIV-2 have differed from those used in HIV-1-infected patients due to the intrinsic resistance of HIV-2 to nonnucleoside reverse transcriptase inhibitors. This distinction is coming to an end, as countries throughout West Africa are implementing a new WHO-recommended treatment regimen for first-line treatment of all HIV-infected patients, including those with HIV-2. The regimen, known as TLD, is comprised of the nucleoside reverse transcriptase inhibitors tenofovir and lamivudine and the integrase inhibitor, dolutegravir that has potent activity against both HIV-1 and HIV-2. Although treatment-emergent drug resistance has been well characterized for HIV-2 patients receiving tenofovir and lamivudine, there are few data regarding resistance mechanisms in patients receiving the third component of TLD, dolutegravir. The two objectives of my project are: (1) to construct a system for generating recombinant HIV-2 clones that encode and express integrase sequences from TLD-treated HIV-2 patients, and (2) to determine the in vitro susceptibility of viruses produced from the patient-derived clones to the integrase inhibitor dolutegravir. Specifically, I am engineering a plasmid vector into which patient-derived integrase sequences can be ligated for virus production and drug resistance testing in culture. The plasmid vector produced in this study will be used to characterize novel genetic pathways to dolutegravir resistance in HIV-2 and will help identify patients who are failing TLD treatment due to drug resistance. This information is crucial for improving treatment outcomes in HIV-2-infected individuals worldwide.

Human Immunodeficiency Virus (HIV) remains on the forefront of research due to the ongoing global epidemic. HIV is comprised of two genetically different types, HIV-1 and HIV-2. HIV-2 is inherently resistant to some classes of antiretroviral drugs, and many HIV-2 patients develop drug resistance to first-line and subsequent regimens. HIV-2 can further be divided into two distinct genetic groups: A and B. While both are endemic to West Africa, group A accounts for the majority of infections and remains the most studied of the two groups. In-depth knowledge of drug resistance in HIV-2 group B is lacking, as only a few patients with drug-resistant virus are described in the literature and there have been no systematic efforts to characterize the drug resistance patterns of HIV-2 group B isolates in cell culture. My project's goal is to build drug resistance mutations, documented in literature, for HIV-2 group A into a full-length HIV-2 group B infectious molecular clone. Those results are used to compare the relative drug resistance conferred by those mutations to the phenotypes observed for equivalent mutants of HIV-2 group A. More specifically, common drug resistance mutations are introduced into the pol gene of a group B clone, individual mutant clones are isolated, and these are used to transfect replication-competent cells for virus production and drug susceptibility testing. Inhibitors targeting the reverse transcriptase, protease and integrase targets of HIV-2 are evaluated. The resultant drug resistance profiles are then compared to those found in published datasets for HIV-2 group A to determine how HIV-2 group A and group B mutants differ in terms of the magnitude and/or scope of drug resistance. These data are essential for developing evidence-based treatment guidelines for HIV-2–infected patients that harbor drug-resistant group B strains.

 Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant pathogen responsible for ~1/3 of antimicrobial resistance-associated mortality in the USA. The glycopeptide, vancomycin, remains the primary treatment for invasive MRSA infections while lipopeptides (e.g. daptomycin) and lipoglycopeptides (e.g. dalbavancin) are common alternatives. All MRSA are resistant to beta-lactams (e.g. nafcillin) but synergistic antimicrobial activity between vancomycin or daptomycin and beta-lactams is commonly observed. Some investigators attribute this synergy to the “seesaw effect”, a phenomenon where the susceptibility to beta-lactams increases with declining vancomycin or daptomycin susceptibility. However, the association between synergy and the seesaw effect hasn’t been rigorously tested. The objective of this study was to determine whether the seesaw effect was necessary for synergy. We used standard time-kill methods to test for synergy between nafcillin and vancomycin, daptomycin or dalbavancin in a series of isogenic strains with reduced susceptibility to vancomycin, daptomycin, and dalbavancin. Two strains exhibited the seesaw effect (N315-VAN8, N315-D1) with nafcillin while 1 didn’t (N315-DAL0.5). All time-kills were performed using half the minimum inhibitory concentration(MIC) for each drug. Nafcillin concentrations were capped at peak physiological concentrations if the MIC was above this value and all experiments were performed in duplicate. Bacterial survival was counted at 0, 4, 8, and 24-hours. Synergy was defined as ≥2 log10 colony forming units per milliliter increase in bacterial killing of the combination compared to the most active single agent. All strains tested exhibited synergy between nafcillin and vancomycin, daptomycin, and dalbavancin, independent of the seesaw effect, suggesting that these two phenomena are distinct. This is important because the emergence of the seesaw effect cannot be detected clinically. This suggests that the seesaw effect is not a therapeutically relevant phenomenon. Further work is warranted to characterize strains that don’t exhibit beta-lactam synergy to identify which strains we should target with combination therapy.

Maternal microchimerism (MMc) is the transfer of maternal cells to the fetus across the placenta during pregnancy. MMc is found in both normal and abnormal pregnancies. The Harrington lab has previously shown that the amount of MMc increases with Plasmodium falciparum infections during pregnancies. In the same cohort, children with detectable levels of MMc were more likely to become infected with malaria but interestingly less likely to experience symptoms, suggesting that these maternal cells may regulate or educate the infant immune response against malaria. I aim to assess whether maternal cells selectively proliferate in the infant during the first infection with Plasmodium falciparum in order to mount an immune response by comparing the levels of MMc throughout three time points. To investigate the role of maternal cells in the infant immune response, I will test blood samples of infants exposed to placental malaria from three time points (a cord blood sample, a blood sample immediately preceding the infant’s first parasitemia, and a blood sample immediately following the infant’s first parasitemia) for the presence and amount of MMc. I hypothesize that MMc will be found in higher quantities in blood samples following an infant’s first infection with parasitemia, indicating that maternal cells help mount an immune response in the infant. Blood samples stored as dried blood spots (DBS) have been received from Ugandan field sites. First, the DNA was extracted from DBS samples. After comparison of class II HLA markers between a mom and her offspring, quantitative PCR (qPCR) will be used to target a unique, maternal HLA-class II marker in order to quantify MMc levels. The levels of MMc will be compared across the three time points. The results of my research have important implications for the current understanding of how MMc regulates the infant immune system.

In recent years, numerous studies have investigated the transfer of rare cells between a mother and her fetus during pregnancy, a phenomenon known as microchimerism. Maternal microchimerism (MMc) refers to maternal cells transferred to the fetus, whereas fetal microchimerism (FMc) refers to fetal cells transferred to the mother. FMc is found in both normal and abnormal pregnancies, and in particular is increased in settings of placental dysfunction such as pre-eclampsia. Plasmodium falciparum infection during pregnancy may lead to sequestration of infected erythrocytes in the placenta, known as placental malaria, that results in a phenotype similar to pre-eclampsia. The Harrington lab previously found that the fetus acquires more MMc in the setting of placental malaria. My research project investigates the reciprocal transfer of FMc to the mother in this setting. I hypothesize that malaria infection during pregnancy is associated with an increased prevalence of FMc. To complete this project, high-quality genomic DNA was extracted from samples gathered from a cohort of women in Mali. These samples came from women both with and without malaria infection during their pregnancy. After collecting the DNA, HLA-typing between a mother and her offspring were compared to determine a unique marker of fetal DNA. I am currently using quantitative PCR to amplify fetal alleles in the background of the mother in order to quantify FMc. Lastly, I will compare the level of assessed FMc in malaria exposed and non-exposed women. The findings from this research project have the potential to contribute important information about the complex role of microchimerism in immune function.

Each year, nearly 6 million deaths worldwide are caused by lower respiratory tract infections, diarrhoeal diseases, and tuberculosis. These infectious diseases are leading causes of death worldwide. Currently, the pharmacological treatment of infection is encumbered by the presence of inaccessible intracellular pathogen reservoirs, and the need for prolonged treatment regimes. Drug delivery systems can be engineered to overcome these biological barriers for effective treatment by facilitating intracellular delivery and tailored release. Extended release of drugs alleviates the need for exhaustive treatment regimes and increases patient compliance. Furthermore, this can decrease treatment duration, reduce the cost of treatment, and improve access for disadvantaged populations. Our research utilizes modular polymeric prodrugs composed of molecular targeting agents, cleavable linkers, and antimicrobial drugs. This platform permits facile alteration of functional modalities, enabling custom tailored treatments for each disease setting. By utilizing tunable linkers, we can control the precise delivery mechanism and therefore direct the localized release of drugs. To characterize the controlled release of antimicrobial drugs from our polymeric prodrugs, we are designing high performance liquid chromatography (HPLC) and liquid chromatography mass spectrometry (LC-MS) assays. The developed assay will evaluate the release mechanism with stability and release studies. Furthermore, the robust methodology will enable the determination of the pharmacokinetics of the polymeric prodrug delivery system. The assay and results from this study will ultimately support the development of improved therapies.

The Toll-interacting protein (TOLLIP) is an adaptor protein involved in the signaling pathways of interleukin-1 (IL-1) and Toll-like receptors (TLRs) in innate immunity. Evidence in published literature suggests that TOLLIP acts as a negative regulator of IL-1 and TLR-mediated immune responses by inhibiting the activity of IL-1 receptor-associated kinase (IRAK1), a serine/threonine kinase in the IL-1 and TLR signaling pathway. Lipopolysaccharide (LPS) is a major component of the gram-negative bacteria cell wall that activates host immune response upon recognition by TLR4. We hypothesize that TOLLIP deficiency leads to impaired inhibition of the innate immune response, resulting in increased inflammation in LPS-induced lung injury. We treated wild type (WT) and TOLLIP knockout (KO) mice with LPS through intratracheal instillation and bronchial alveolar lavage fluid (BALF) was collected at 3 days post-injury. Lung inflammation was measured by BALF total white blood cell (WBC) count and cell differential, BALF total protein, and BALF cytokine levels. Contrary to our hypothesis, TOLLIP deficiency was associated with decreased inflammation in LPS-induced lung injury as demonstrated by lower polymorphonuclear (PMN) cell count and significantly lower levels of cytokines in KO mice. In future studies, we will examine the mechanisms by which TOLLIP positively regulates inflammation in the LPS model of lung injury.

In order for cells to generate copies of themselves they must undergo a highly complex process called mitosis. During mitosis, many enzymes called protein kinases work together to ensure both daughter cells inherit the correct number of chromosomes when the cell divides. Polo-like kinase 1 (Plk1) is a protein kinase that regulates several events during mitosis including centrosome maturation, spindle assembly, sister chromatid cohesion, and cytokinesis. Recently, the A-kinase anchoring protein Gravin (AKAP12) has been implicated in regulating Plk1 function at mitotic centrosomes. Specifically, loss of Gravin has been linked to defective protein signaling at centrosomes, chromosome misalignment, and increased incidence of micronuclei (small nuclei, an aberration often seen in cancer). However, while previous studies used shRNA-mediated knockdown to reduce Gravin levels in cells, it remains unclear how complete loss of this scaffold in human cells influences mitotic signaling events. To test this, our lab generated Gravin knockout U2OS (osteosarcoma) cells using CRISPR/Cas9 genome editing. First, I employed a combination of immunohistochemical staining and quantitative imaging tools to assess how Gravin loss affected chromosome alignment, micronuclei formation, and gamma tubulin accumulation at centrosomes. I found that loss of Gravin in U2OS and HeLa cells caused misaligned chromosomes and micronuclei. Additional experiments I conducted revealed that Gravin-depleted U2OS, HeLa, and MEF cells presented aberrant gamma tubulin accumulation at mitotic spindle poles. Next, a local drug-targeting approach was used to specifically inhibit Plk1 activity at mitotic spindle poles in U2OS cells. I determined that localized inhibition of Plk1 produced similar mitotic defects as observed in cells lacking Gravin. Collectively, these findings suggest that Gravin is required for coordinating proper Plk1 signaling at centrosomes during mitosis while the loss of this scaffold protein leads to mitotic defects. Future work will uncover downstream substrates of Gravin-anchored Plk1 that becomes dysregulated in cells lacking Gravin.

Throughout history, human-induced habitat loss, pollution, and hunting have pressured mammals to adapt to lifestyles that limit human interaction. When humans threaten wildlife, a fitness advantage is provided to animals who avoid human interaction. But what about in protected regions where these threats are limited? Cocha Cashu Biological Station, located in Manu National Park, is an example of one of these regions. While native communities continue to hunt within the research station, overall levels of hunting, deforestation, and pollution, are significantly lower than in the surrounding unprotected areas. Our research team chose to design a study in Cocha Cashu to analyze terrestrial mammal distribution in relation to human habitation in areas where human threats have historically been limited. Our hypothesis was that mammal abundance would increase with distance from human habitation. Our study design involved a northern and eastern transect with a near (N), medium-distanced (M), and far (F) trap location. Each trap location had both a sand and camera trap, and data was collected from the traps morning and night for four consecutive days. On the eastern transect, there was a positive linear relationship between distance from human habitation and number of mammals observed (N: 2 mammals, M: 4 mammals, F: 8 mammals). On the northern route, the highest number of mammals was observed at the medium-distanced location (N: 1 mammal, M: 7 mammals, F: 3 mammals). Overall, our data did not support our hypothesis that mammal abundance increases with distance from human habitation in protected areas. Our results do, however, provide a platform for further research on resource accessibility and its potentially larger influence on mammal distribution patterns than the influence of human habitation.

 Seed dispersal is a crucial phase of plant lifecycles. Effective dispersal is important to the ecosystem as a whole because it affects composition of the community, ecological succession, and response to climate change. Given the importance of seed dispersal, understanding the factors that contribute to the evolution of varied dispersal modes and promote convergence on specific dispersal strategies is particularly important to understanding grass ecology because it may allow us to understand the relationship between dispersal mode and habitat. In this study, we are interested in dispersal modes within the onion grasses (Melica), a small genus of perennial grasses, primarily distributed in temperate regions. The onion grasses are found in a wide variety of habitats and possess a remarkable diversity of seed dispersal strategies. These traits make them a useful case study for better understanding the factors that influence the evolution of dispersal strategies in grasses. We are testing the hypothesis that evolution in traits associated with seed dispersal is correlated with changes in habitat. In particular, we hypothesize that the evolution of wind dispersed seeds follows transitions into open habitats. Seed dispersal structures (diaspores) were collected from 46 grass species (35 Melica and 11 outgroup). To assess wind dispersal potential, we quantify falling velocity by filming seed descent at 1000 fps. Lower falling velocities are associated with higher wind dispersal potential. Diaspores were photographed and the images were used to measure surface roughness, which is associated with adhesive dispersal potential. These data, along with diaspore mass and plant height, were mapped onto the evolutionary tree of the onion grasses. We then ran tests of correlated evolution between seed dispersal traits and habitat type. Initial results indicate that convergence upon wind dispersal may be in part driven by convergence upon disturbed habitat types.

The Cretaceous-Paleogene boundary is one of the most well-studied mass extinction events in history. However, there are still many questions left about what was occurring in terrestrial ecosystems in the 10-15 million years prior to the event. One major question is if theropod dinosaurs were declining in diversity and ecological stability prior to the event, or if they all died off suddenly. This stability is partially interpreted in this project through a geometric morphometric approach comparing Judithian and Lancian theropod teeth. Geometric morphometrics quantitatively analyzes tooth shape based on points called landmarks, that are universal across theropod teeth so variance can be measured and compared. Teeth are digitally imaged and processed with the landmarks to compute and then interpret their shapes in specialized programs. The landmarks measured are based on established standard literature of mesial and distal points of the tooth, the apex, and the mesial and distal terminal denticle. If the finalized analysis of the remaining confirms theropod dinosaurs are shown to have consistent morphological disparity through this time, this will be an indication that this group of organisms were not declining and were settled in their niches prior to the K-Pg boundary. Given that theropods were a diverse group that occupied many niches, as well as being the top carnivores that would have curbed other taxonomic populations, studying their economic stability through the window of deep time lasting from the Judithian to the Lancian immediately before the K-Pg boundary is leading to an invaluable understanding of how this environment was changing during this time.

Today there are more than 5,000 species of extant mammals that are categorized into three major clades: placentals, marsupials, and monotremes. The deep evolutionary history of marsupials is poorly known due to a fragmentary fossil record. In particular, cranial fossils of the ancient relatives of marsupials (stem marsupials) are extremely rare. The few cranial elements of these taxa that have been found are fragmentary, crushed, or missing major elements. Recently, some more complete cranial fossils of stem marsupials have been discovered at the Late Cretaceous (75 million years ago) Egg Mountain fossil locality in northwestern Montana. My research will describe the morphology of a partial skull of a stem marsupial from Egg Mountain. This delicate skull is encased in a hard siltstone, making it difficult to mechanically remove without damage to the fossil. Instead, we used micro-computed tomography (µCT) to scan the specimen block. Then I used Avizo software to virtually remove the rock and expose the details of the encased fossil. From the resulting files, I will study and describe the cranial morphology in detail. Thus far, we have identified the stem marsupial as Alphadon halleyi. With further study, I hope to (1) expand upon current knowledge regarding the morphology of Alphadon halleyi, (2) make comparisons with other stem marsupials and extant marsupials, and (3) more broadly, incorporate our findings into a phylogenic analysis of early metatherians (the clade that includes stem marsupials and marsupials) that will further elucidate the evolutionary history of marsupials.

In the Ratner Lab, our research focuses on engineered biomaterials and surface coatings for improving biocompatibility of implantable medical devices and tissue engineering. Currently, the long-term performance of implantable medical devices is limited by the body’s foreign body reaction (FBR). The body reacts to foreign materials in an inflammatory manner and ultimately encapsulate the device with a dense, avascular scar layer. The Ratner Lab has developed multiple strategies to reduce scarring and improve vascularization, including precision-engineered porous materials. The lab has discovered that materials with uniform 40 μm pores seamlessly heal within the body in a vascularized fashion. Previous research has mostly focused on biostable synthetic materials which remain stable in the body over the duration of implantation. My research will explore the potential of gelatin, a biodegradable, bioderived material, as a precision-engineered porous scaffold to promote healing. IL-4 is a cytokine that directs the inflammatory response towards a healing response. My research will also incorporate IL-4 into the biodegradable porous material to further enhance healing. Our long-term scientific goal is to enable complete regeneration of tissue by first promoting healthy blood vessels growth throughout the porous structure, then allowing the material to completely disappear (biodegrade) to make room for rest of the tissue to heal.

Microneedles are an effective method for transdermal delivery of a variety of pharmaceutically active agents primarily because of their ability to puncture the stratum corneum. Tissue puncture using microneedles also has potential to improve drug delivery at mucosal sites such as the buccal mucosa, where topical dosing is limited by a thick epithelial layer and continuous salivary flow. However, the low tissue stiffness and wide variance in epithelial thickness present in the oral mucosa preclude direct translation of currently available transdermal microneedle application methods. Further studies of microneedle drug delivery in the oral mucosa require methods for complete and reproducible microneedle application. This project aims to address this need with a device that can apply microneedles to the buccal mucosa with reproducible penetration depth and force, metrics which are correlated with delivery efficiency. The device is designed to be tunable to accommodate microneedle arrays with various dimensions and mechanical properties. Physical parameters of the device are optimized in silico via finite element analysis simulation of tissue puncture with a microneedle array. A prototype of the device is then evaluated using a tissue phantom model to assess penetration depth and force. Performance of the lead candidate device is then validated in tissue explants. This project provides insights for future improvements to microneedle application in the oral mucosa.

Exhibiting high photoluminescence quantum yield, tunable surface functionalization and well-defined emission linewidths, colloidal semiconductor nanostructures are promising materials for a wide range of applications from lignocellulosic depolymerization to low power nonlinear optics. In past decades, synthesis of zero-dimensional (quantum dots) and one-dimensional (nanorods) systems has attracted much interest. In contrast, the potential of two-dimensional (nanoplatelets) and three-dimensional (nanotetrapods) structures remains to be tapped. As a consequence of their anisotropic morphology, the tunable emission frequency and linewidth of nanoplatelets and nanotetrapods renders them excellent candidates for single-photon emitters in devices such as hybrid photonic integrated circuits. Integrated photonics are devices that utilize light-matter coupling with embedded light-emitting media to achieve state-of-art engineering processes like ultralow threshold lasing and quantum many-body simulations. However, it remains a challenge to find suitable photoluminescent agents with outstanding desirable features. The subject of this research presents a solution to this problem—nanotetrapods and nanoplatelets used for coupling to the nanocavities in the integrated circuits. Owing to their tunable surface chemistry, nanotetrapods and nanoplatelets have the potential to be optimized for efficient processing with photonic cavities, with clear pathways for deterministic positioning. Moreover, the structures’ adjustable sizes and dimensions allow for maximization of single-photon behavior, including high quantum yield and narrow emission linewidth. Herein, I report the seeded-synthesis of several II-VI and III-V nanotetrapods and two approaches to growing nanoplatelets via a solution-phase decomposition procedure and the colloidal atomic layer deposition pathway. To understand both the spectral and structural properties of the nanostructures, I characterize the products by UV-vis and fluorescence spectroscopy as well as transmission electron microscopy. By exploring different routes to synthesizing the highly absorbing and emissive anisotropic colloidal nanostructures and investigating strategies for modifying the materials’ surface chemistry, it will be possible to achieve specialized spectral functionalities with these nanostructures.

Though renewed efforts in tuberculosis (TB) research have facilitated massive strides in treating Mycobacterium tuberculosis (Mtb), TB remains a global health problem with an estimated 10 million infections and 1.5 million deaths in 2018. The ability of the pathogen to sequester itself inside a granuloma, a mass of immune cells whose precise mechanism of regulation is unknown, prevents the simple study of Mtb pathogenesis and subsequent treatment discovery. Current in vivo models have been established to study TB infection using animal models or tissues, limiting biological relevance of human disease while current in vitro models lack components of the complex lung microenvironment during infection. We present the creation of a novel microscale infection model, which uses open and suspended microfluidic principles to enable spatial and temporal manipulation of cultures in suspended hydrogel plugs. Utilizing the ‘stacking’ feature of the device, we demonstrate the ability of a model granuloma consisting of M.bovis BCG (Mycobacterium bovis bacille Calmette-Guérin) and monocyte-derived macrophages to interact with a model vasculature layer consisting of endothelial cells. Analysis of soluble factors for proinflammatory cytokines and characterization of infection-dependent angiogenesis in the vasculature layer are used to verify crosstalk between cultures. In the future, we envision this model expanding to contain multiple immune cell types and to incorporate additional aspects of the lung anatomy to approach a more accurate pathophysiological model as a tool for other researchers’ studies.

There are an estimated 300 million people worldwide who are affected by asthma, a respiratory condition in which a person has inflammation and swelling in the airways. Asthma patients also experience increased vasodilation in their lungs, i.e. the widening of blood vessels, which causes increased blood flow and results in increased inflammation. The goal of this project is to create a device that makes free standing hydrogel rings, modelling the structure of blood vessels, offering a simple approach to better understand asthma and potential treatments. The device used to form the rings is 3D printed and can be printed in a range of sizes. The rings are composed of collagen I that has been seeded with smooth muscle cells. Once the hydrogel rings are cast, they can be transferred to a 96 well plate and be free standing of any rigid structures. The ability to be free standing allows us to measure the ring diameter and wall thickness, as well as measure any change in size when a vasodilator is added. Future steps to be taken with this project include optimizing the size for biological relevance, introduce endothelial cells to create multiple layers of cells that are involved in signaling for vasodilation, and increase the responsiveness that the rings have to constriction factors as well as dilators.

Scaffold proteins, which assemble enzymes and their substrates into multiprotein complexes, are critical for many cellular functions. By bringing enzymes and their substrates into close proximity, scaffold proteins are thought to enhance the rates of enzymatic reactions. For instance, Axin is a scaffold protein in the Wnt pathway that binds the transcription factor, ß-catenin and the kinase, GSK3ß. This tethering method is predicted to enhance the rate of ß-catenin phosphorylation. An outstanding question is whether a scaffold protein that binds to both GSK3ß and ß-catenin is sufficient to observe these effects or whether Axin has other structural properties that are not currently understood. Although there is no detailed structural information about Axin, it is predicted to be disordered. To address this gap, we have engineered a synthetic scaffold protein that can bind both GSK3ß and ß-catenin and contains a linker that is also presumed to be disordered. Previous work in the lab has reconstituted the reaction between Axin, ß-catenin and GSK3ß in vitro and found that Axin enhances the rate of ß-catenin phosphorylation. Using enzyme kinetics, I have compared the rate of ß-catenin phosphorylation of the engineered scaffold to that of Axin. Identifying the quantitative kinetic comparisons between the engineered scaffold protein with the natural scaffold protein could tell us more about what aspects of a tethering system make it effective at enhancing the rates of reactions. We are expecting to see similar tethering effects between the two scaffold proteins, as their linkers are both disordered and equivalent in length. 

Extracellular Vesicles (EVs) are group of cell-derived structures including exosomes, microvesicles, and apoptotic bodies, which have been found to play a key role in intercellular communication, through the biological cargo that these EVs can carry. Their ability to deliver proteins and nucleic acids from donor cells to their target cells has led to growing interest in the potential of EVs being used as biomarkers for disease. But, a comprehensive understanding of EVs behavior is lacking, especially in neuroscience, which may hinder the development for further application of the EVs. Thus, we are interested in investigating the effect of brain-derived EVs (bEVs) on brain cells, especially microglia, the brain’s primary resident immune cells. To do this, we first extracted the bEVs from the rat brain through ultracentrifugation and purified them through size exclusion chromatography (SEC). We then applied the bEVs to cultured mouse BV-2 microglial cells and incubated for 24 hours before performing quantitative reverse transcription PCR (RT-qPCR) on the treated BV-2 cells to explore any bEV induced inflammation response. Preliminary results have shown that bEVs play a role in inducing both pro and anti-inflammatory responses in microglial cells, both to varying degrees in the cytokine markers expressed after incubation for 24 hrs. Furthermore, to better understand the interaction between bEVs and microglial cells, we labeled bEVs with fluorescent nano-sized semiconductor quantum dots (QDs). Through fluorescent confocal microscopy and time-lapse imaging, we were able to explore the time-dependent interaction of bEVs and BV-2 cells at high resolution. Our study can provide insights into bEV behavior, which can be used to better understand their potential use as biomarkers for specific brain disease models. 

In trying to understand biology’s dynamic heterogeneity, scientists have sought to recapitulate the spatial complexity and temporal presentation in which proteins are naturally presented to cells. Currently, the most promising strategies in this regard exploit sequential ligation/cleavage reactions, each controlled in time and space using light so as to reversibly immobilize proteins within synthetic biomaterials. Though our lab has utilized these approaches to spatially control complex biological fates with micron-scale resolutions, previous methods suffer from complex syntheses, as well as requirements for specialized equipment and skillsets rarely available in bio-based laboratories. Improving upon these fundamental limitations, our group has developed a scalable system wherein proteins can be bound/released from hydrogels using light, without the need for such expertise/equipment, by being fully genetically encodable. In this approach, biology performs all the modifications necessary to photopattern protein binding to gels, as well as install the reactive species requisite for the protein’s photo-mediated release. We have accomplished this using a photoactivatable protein-peptide ligation reaction developed by our lab, wherein UV irradiation “activates” the protein to ligate specifically with the peptide tag. Additionally, we exploit co-translational chemoenzymatic modification strategies to install a functional handle for tethering the protein into polymeric hydrogels during protein expression. To the peptide tag, we append a photocleavable protein that cleaves when irradiated by visible light, fused to a protein of interest (POI) to be tethered to the hydrogel. Expressing these proteins in E. coli yields the first-ever fully genetically encodable system which can reversibly pattern proteins into hydrogels, by first shining UV light to tether POIs into biomaterials, then subsequently shining visible light to photocleave the protein and trigger POI release. Highlighting the system’s versatility, we demonstrate that the approach is compatible with fluorescent proteins and bioactive growth factors to direct 4D cell fate.

Brain extracellular matrix (ECM) structure mediates many aspects of neuronal function. When ECM structure becomes dysregulated in neurological disease, one resulting impact is impaired neuronal function. Therefore, probing changes in ECM structure could provide insights into disease mechanisms and expose potential therapeutic pathways. Previous work in our group determined that degrading neural ECM structures, including perineuronal nets (PNNs), leads to a significant increase in the diffusive ability of nanoparticles navigating the brain extracellular space. However, this diffusion-based analysis provides little insight into changes in PNN-specific morphology or structure; it only predicts whether or not they are present and the degree to which they may be altered from normal. With this project, we aim to quantify changes in PNN structure with high spatial resolution. PNNs are stained using a fluorescently labeled lectin (Wisteria floribunda agglutinin) and images are acquired via confocal microscopy. Using Python, a coding language, we developed an automated image processing workflow to characterize morphological and structural features associated with PNNs, including total number of branches, average branch length, average mesh size of the net, and the areal density of fluorescence. This approach was applied to brains that span a range of chronological ages, from 14 days old to adult. PNNs are known to increase in counts early on in life, so this age-based study served as a proof of concept for our methodology. This same approach can be applied to study the effect of various neurological diseases on PNN structure. Collectively, this work aims to enhance our understanding of neurological disease mechanisms and open new avenues of therapeutic intervention.

Water-swollen polymeric networks (i.e., hydrogels) provide a structural platform for the manipulation of chemical and mechanical signals that mimics the complex heterogeneous environment experienced by cells in vivo. Photoresponsive chemistries have been of particular interest to this end, as they allow for precise spatiotemporal control of physiochemical properties and, thus, cell behavior. Here, we present a novel protein-based network that will allow for the photo-mediated stiffening of genetically-encoded hydrogels. In this system, we exploit a biochemical technology recently pioneered by our lab in which two pairs of proteins undergo irreversible, covalent heterodimerization after photoactivation. Through the incorporation of an inert, unstructured polypeptide backbone, we have exploited the aforementioned reaction to induce gelation in response to light through the formation of four-arm protein crosslinks. Unlike previous synthetic polymer-based hydrogel systems, this system is entirely genetically encoded, which provides significant advantages in terms of cost, time, and production simplicity. As we intend to demonstrate through photorheometry, this reaction proceeds in a dose-dependent manner, providing step-wise control of both where and when gel stiffening occurs. Such 4D control of a gel’s mechanical properties can be used to influence cell migration, growth, and differentiation, and, thus, could have applications in tissue engineering. Furthermore, we anticipate our system could be utilized to model the stiffening of the extracellular matrix, which is commonly associated with pathologies such as cancer, fibrosis, and cardiovascular disease.

Adolescents with newly diagnosed T1D are at risk for poor physical and psychosocial outcomes. We explored associations between glycemic control (A1C) with diabetes-distress, resilience, and psychosocial comorbidities (e.g., depression) over the first five years of diagnosis. Adolescents, aged 10-17, with newly diagnosed T1D completed validated diabetes-distress and resilience scales one-year post-diagnosis. Psychosocial comorbidities and A1C were extracted from patient charts for 5-years from diagnosis, and A1C values were averaged per year. Regression analyses were used to investigate associations between resilience, diabetes-distress and psychosocial comorbidities with A1C. A1C was assessed annually up to five years post-diagnosis. At one-year post-diagnosis, N=60 adolescents (M=13.22±2.09 years) completed distress (M=27.97±7.01) and resilience scales (M=40.35±17.10). Average A1C at 1-year was 7.73± 1.57 and at 5-years was 8.78 ±1.92. 14% of the sample had at least one psychosocial comorbidity at diagnosis. Between years 1-5 post diagnosis, 28.6% of the sample had at least one comorbidity. The most common comorbidities were depression and anxiety. Diabetes-distress was associated with average A1C in the second year (F(1,29)=4.397, p=.045, R2=.132), third year, (F(1,27)=6.596, p=.016, R2=.196), fourth year, (F(1,24)=10.196, p=.004, R2=.298), and fifth year post-diagnosis (F(1,19)=10.665, p=.004, R2=.360). Resilience was associated with average A1C in the second year (F(1,29)=6.848, p=.014, R2=.191) and fifth years (F(1,19)=4.790, p=.041, R2=.201) post-diagnosis. Total psychosocial comorbidities at diagnosis was associated with average A1C in the second year (F(1,49)=2.209, p<.01), third year (F(1,45)=7.925, p<.01), and fifth year (F(1,28)=7.919, p<.01) post diagnosis. The first year of diagnosis for adolescents with T1D is crucial for detecting patients who are at a higher risk for developing poorer health outcomes. Adolescents who present with psychosocial comorbidities at diagnosis and report poor resilience and high distress one year later are at risk for subsequent poor glycemic control. 

Executive function (EF), a broad term for an individual’s higher-order cognitive abilities, has been shown to be an important factor in proper development of play in childhood. Children with autism spectrum disorder (ASD) have been noted to score significantly lower on tasks requiring EF and are often noted to engage in more simplistic levels of play compared to typically developing peers. We investigated within-group associations of average play level for children with ASD, as observed during parent-child play sessions, in relation to parent-reported EF scores, as measured by the Behavior Rating Inventory of Executive Function (BRIEF). Participants with ASD (n = 28, age = 3-11 years) and participants with typical development (n = 27, age = 2-7 years) engaged in a video-recorded, 15-minute unscripted parent-child play session. Blind coders determined the child’s level of play, ranging from object manipulations to pretend play, on a numeric scale of 1-13. The highest level of play was coded at each one-minute epoch of engagement using Behavior Observation Research Interactive Software. Participant’s play scores were averaged and analyzed with their BRIEF scores using Pearson’s correlations. Results indicated no significant correlation between average play level and the BRIEF working memory, planning, and inhibition subscales, with Pearson’s correlations ranging from less than .01 to 0.03 (p > 0.8). Likewise, for participants with typical development, there was no correlation between average play level and BRIEF global composite scores, with Pearson’s correlations less than 0.01 (p > 0.9). Our current analysis did not account for parental support of the child’s play, which may contribute to why parent-reported EF scores did not relate to child play level in these unscripted parent-child play sessions. Future directions include examining the relationship between EF and play in children with other developmental disabilities.

Sarcopenia, the age-related of loss of muscle mass and function, is associated with a decline in quality of life in the elderly and has few effective treatment options. Sarcopenia is linked to mitochondrial dysfunction and elevated mitochondrial oxidant production. We are investigating the role of elevated 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 in vivo. 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 hypothesize that improving mitochondrial function with SS-31 treatment will delay the decline in muscle function in the Sod1KO mice. To test this, we administered SS-31 to SOD1KO mice through surgically-inserted osmotic pumps for 8 weeks between 3 and 4 months of age, the published timeframe for the onset of skeletal muscle decline in SOD1KO mice. Muscle force generation and fatigue resistance was tested in vivo in the gastrocnemius before pump insertion and monthly after pump insertion for 4 months. At the end of the treatment we used histological and biochemical analyses of mouse tissue samples to determine skeletal muscle fiber type, metabolite and protein concentrations, and muscle fiber respiration and oxidant production. We expected 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.

Traumatic spinal cord injury (tSCI) often leads to a debilitating loss of sensory, motor, and autonomic function. Currently there are no treatment options available for patients with tSCI. Immediately following the initial trauma, microvessels in the spinal cord rupture, leading to hemorrhage within the spinal cord. Bleeding is a major contributor to a cascade of subsequent injuries, defined as secondary injury, such as swelling, inflammation, and oxidative stress, which results in the expansion of the initial injury. We hypothesize that enhancing blood clotting would limit secondary injury, and subsequently lead to better functional outcomes. To test this, we employed newly developed hemostatic nanoparticles (hNPs), which are designed to localize to the injury site and reduce bleeding in a contusion tSCI model in rodents. The hNPs or control nanoparticles were introduced intravenously within 3 minutes after the injury, and tomato lectin was injected at the end of the experiment to label all patent blood vessels. Clusters of hNPs were found within areas of hemorrhage and blood clot within the injury epicenter, and never seen co-labeled with tomato lectin, suggesting that hNPs were only within parenchyma in areas of active bleeding. Our unique ultrafast contrast enhanced ultrasound (CEUS) imaging was used to visualize hematoma size, local spinal blood perfusion and swelling in real-time. CEUS imaging data showed there was 50% reduction in hematoma size in hNPs treated animals compared to control. We also found significant reductions in hypoperfused volume (50%, p<0.05) as well as spinal cord swelling (30%, p<0.01) in hNPs treated animals compared to controls. Current studies are underway to 1) analyze real-time hemodynamic data obtained from ultrafast CEUS imaging, 2) evaluate chronic 3D blood flow imaging, and 3) quantify functional and histological outcomes from hNP treatment after tSCI.

Prostate cancer remains the second leading cause of cancer-related deaths of men in the US. Currently, the major challenge is to prevent the tumor cell from gaining the resistance to androgen deprivation therapy which almost inevitably leads to lethal castration-resistant prostate cancer. We are repositioning antiparasitic agents to develop a novel therapy to target androgen receptor (AR) mediated metastatic castration-resistant prostate cancer (mCRPC). Among them, bumped kinase inhibitor (BKI) 1553, which was originally designed to inhibit Toxoplasma calcium-dependent protein kinase 1, has shown to efficiently inhibit AR-dependent prostate cancer growth and AR signaling. Upon binding to its cognate ligand androgen, AR undergoes a conformational change to translocate from the cytoplasm into the nucleus to act as a transcriptional factor. The aim of my project is to identify the target site of BKI 1553 on AR transcription activation pathway. I examined the subcellular localization of AR by using biochemical subcellular fractionation and immunofluorescence assay. I also observed the phosphorylation status of AR via Western blot, and evaluated the level of AR signaling through a luciferase-based reporter assay and quantitative PCR assay of several AR target genes, including PSA, FKBP5, and Nkx3.1. The results of the study reveal the potential site of action of BKI-1553 in AR signaling. This study will provide a better understanding of the mechanism of BKI-1553 on prostate cancer and contribute to the development of a new therapy to mCRPC.

Cystic fibrosis (CF) is a genetic disorder affecting the lungs, and chronic polymicrobial lung infections are responsible for decreased life expectancy and poor quality of life of CF patients. Staphylococcus aureus (SA) is a microbe commonly found in the respiratory tract of CF patients, and this organism adapts within the lung environment to establish chronic infections. Among the most common bacterial adaptations is the emergence of mutants known as small colony variants (SCVs). There are multiple subtypes of SCVs that arise from mutations in different metabolic pathways. Recent studies have demonstrated that SCVs are prevalent in the CF respiratory tract, are more difficult to treat with antibiotics, and are associated with worse lung health. SCVs are very difficult to detect in clinical laboratories, thus complicating the selection of appropriate treatment by physicians to improve the health of CF patients. The goal of this study is to determine if SCVs can be more readily detected than with standard culture by using mass spectrometry to identify proteins that distinguish these variants from normal colony S. aureus. Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) will be used to identify proteins unique to specific SCV subtypes by separating those proteins using ionization and Tandem Mass Spectrometry. This analysis will generate isolate-specific spectra of peaks which will subsequently be compared to each other using Principal Coordinate Analysis (PCoA). We hypothesize this technique will identify differences between proteins produced by each SCV type, which can then be distinguished from normal colony S. aureus, allowing the rapid identification of these variants. As a result, we anticipate the detection of SCV’s will improve, which will help inform physicians to select appropriate treatments to target SCVs.

Climate change has the potential to significantly impact how outdoor work is conducted. With an increased prevalence of wildfires, exposure to smoke has been identified as an occupational hazard that needs more research. Washington State has experienced an increase in wildfires and wildfire smoke over the past decade, and the length of wildfire “season” has increased by more than 64% from the years of 1970 to 2003. Nearly half of all workers in Washington are estimated to have some outdoor work during their daily responsibilities. Workers who spend significant amounts of time outside during wildfire smoke events can be exposed to air pollutants in smoke that are associated with a higher rate of mortality, respiratory problems, and other detrimental health issues. This study collected existing public sector policies and analyzed the content for exposure reduction actions for their outdoor workers during wildfire smoke events. We also conducted key informant interviews to elucidate actions taken during a 2018 state-wide wildfire smoke event by supervisors and employees in a county organization that lacked a standard operating procedure or other risk reduction policy. Focus groups were used to understand challenges and barriers to utilize exposure reduction actions with outdoor public sector workers. Findings were translated into a policy template that can be implemented in jurisdictions throughout Washington. 

The growing field of disaster resilience research deals with the complex and essential question of how we can prepare for and recover from disruption. Food assistance organizations have the potential to play an essential role in supporting communities after disaster events, especially for low-income residents. The goal of this study is to explore the factors that contribute to the resilience of Seattle’s food assistance organizations. My research will address how these organizations maintain food availability, acceptability, accessibility and stability before, during and after a disaster. I will conduct key informant interviews with representatives from food-assistance organizations, in-person and over the phone. I will sample all food assistance organizations from the Seattle areas of Cedar Park/Meadowbrook, University District and the Duwamish Waterway (South Park, Delridge and High Point). These include food banks and food pantries, meal centers, government assistance programs and school meal programs. To contribute to qualitative trustworthiness, a summary of key points gleaned from the interviews will be sent to all participants after their interview and they will be asked to verify that it represents what they wished to convey. I will analyze the interviews by coding for and synthesizing common themes in the transcripts using Nvivo software. I hypothesize that many of the organizations will cite strategies for maintaining day-to-day food security for their clients with less specific focus on disaster preparedness. I also hypothesize that infrastructure, funding, and food donations will be barriers to resilience while community partnerships, staff and volunteers will be factors contributing to resilience. Results from this project may inform Seattle's disaster planning efforts. 

Kaposi's Sarcoma associated Herpesvirus (KSHV) is an oncogenic human herpesvirus and the etiological agent of Kaposi's Sarcoma (KS), a cancer that afflicts HIV-positive individuals worldwide and is endemic in sub-Saharan Africa. KS tumor cells, known as spindle cells, originate from latent KSHV infection of endothelial cells. We have previously used a phosphor-proteomics approach to identify changes in the phosphorylation state of proteins during KSHV infection. We identified Platelet/Endothelial Cell Adhesion Molecule-1 (PECAM-1) to be significantly phosphorylated during KSHV infection as compared to mock infected cells. PECAM-1 phosphorylation leads to a cascade of signaling that promotes cell adhesion, migration, and cell survival, however, the role PECAM-1 plays to aid KSHV infection is currently unknown. To determine whether PECAM-1 expression and phosphorylation is important for KS pathogenesis, I propose to assess differences in gene expression levels with RT-qPCR, validate phosphorylation levels in vitro via western blot, and generate CRISPR-lentiviral constructs to knock out PECAM-1 and express PECAM-1 isoform variants in endothelial cells. These experiments will paint a more complete picture of how PECAM-1 interacts with endothelial cellular processes during KSHV infection. Many rounds of RT-qPCR have been conducted to asses gene expression levels with highly variable results. This indicates that some uncontrolled factor in the cell culture process is affected PECAM-1 expression levels. I hypothesize that cell density is the cause behind this variability and plan to use western blotting to elucidate differences in PECAM-1 protein levels in low and highly confluent cells.

Although transcriptomes are highly tissue and cell type specific, curated gene set collections are not constructed or analyzed with recognition of this bias despite much of transcriptomic analysis depending on curated gene set collections. Prior work has recognized the potential for gene bias due to the variable nature of manually curating gene set collections, but coverage has yet to be characterized across all tissues and in all commonly used gene set collections. The goal of this study was to perform a comprehensive analysis of curated gene set collections from the data repository Molecular Signatures Database (MSigDB) based upon tissue specific expression. We analyzed KEGG, REACTOME, BIOCARTA, and Gene Ontology (GO) including Biological Processes, Cellular Components and Molecular Function gene set collections available on MSigDB. We curated lists of enriched and elevated genes as defined by Human Protein Atlas for 36 tissues. Analyses, visualization, and statistical analyses were performed using the R statistical programming language. We revealed that the MSigDB gene set collections differ among themselves in the fraction of tissue genes covered. GO Biological Processes has the highest gene coverage. BIOCARTA has the lowest gene coverage. Additionally, each collection differs among tissues in the fraction of genes covered. We also showed differential gene coverage among tissues even when collections are combined. Within elevated tissues, the liver has the highest and the fallopian tube has the lowest gene coverage. Within enriched tissues, the lymphoid has the highest and the testis has the lowest gene coverage. We created a database describing the presence or absence of tissue specific genes for each tissue with which researchers can elect the most appropriate gene set collection to use for analysis of a specific tissue. This increases the utility of our findings and creates a direct resource for researchers in the field.

Experimental evolution can determine genetic interactions during natural selection in complex systems. Using whole-genome sequencing of 95 parallel populations of haploid Saccharomyces cerevisiae experimentally evolved for 250 generations, we discovered a possible epistatic interaction between two sets of beneficial mutations. The first mutation is a transposable element (TE) insertion into the promoter of FLO1, giving rise to a cellular aggregation phenotype known as flocculation. The second set are putative loss of function mutations in genes encoding members of the SAGA-complex, which is thought to increase expression of genes proximal to TEs. We hypothesize that without the members of the SAGA-complex, the FLO1 gene will be unexpressed, abrogating the flocculation phenotype. We isolated three flocculant clones with TE insertions from different experimental populations and crossed them with three clones with the deletion in the SAGA-complex. Through meiosis, the yeast sporulated into four cells. The ratios of flocculant to wildtype haploid cells are used to determine an epistatic interaction. A 2:2 ratio suggests a non-epistatic interaction while a 1:3 flocculant to wildtype ratio suggests an epistatic interaction. The project is in the early stages but segregation ratios suggest the members of the SAGA-complex with deletion mutations do not hinder the expression of the FLO1 gene. Our alternate hypothesis is members of the SAGA-complex have no effect on the activation of TE insertions that promote the expression of the FLO1 gene. While the initial hypothesis might not hold, this experiment will give us a further understanding of genetic interactions during evolution.

CRISPRa is a tool that can be used for metabolic engineering and information processing. However, many of the mechanisms and design rules are unknown making it extremely difficult to engineer metabolic networks without trial-and-error. The aim of this study is to use a data-driven approach to better understand, engineer, and predict the behavior of CRISPRa. Data-driven techniques used were: modeling and machine learning to study kinetics and predict the behavior of CRISPRa, engineering a programmable light for a light-inducible CRISPRa system to make data collection less error prone and to generate more experimental conditions, and data scraping and management to visualize the theoretical best PAM sites to engineer gRNAs for maximum activation. (A PAM is a short DNA sequence that follows the DNA region targeted for cleavage by the CRISPR system). Two notable ODE models resulted from the fitting process: the first has 9 parameters and an R² score of 0.882. The second model has 13 parameters and an R² score of 0.912. A test set of data needs to be generated to evaluate the model performance. The light inducible system is still in development, but once completed could be used to generate more experimental conditions and data to test and train models. Then data visualization was used to choose gene sequences to learn more about PAM design rules. We have preliminary evidence showing moderate activation for 2 of 7 highest scoring genes. Data is still in the process of being analyzed.

The blood-brain barrier (BBB) is a layer of tight-junction endothelial cells that make up the capillaries in the brain and strictly regulate what molecules can pass from the blood into the brain. Many molecules, including insulin, cannot passively cross this barrier but require an active transport system at the surface of the BBB. Once in the brain, insulin plays a role in memory and cognition. Indeed, Alzheimer’s disease is characterized by decreased sensitivity to insulin, which could be explained by a malfunctioning insulin receptor (IR) or impaired transport at the BBB. However, before we can begin to investigate the IR under disease conditions, we must first understand its standard regulation and function in a healthy system. Specifically, we aim to determine what factors mediate the endocytosis of insulin into the endothelial cells of the BBB. To do this, we focused on clathrin and caveolin, two proteins involved in different endocytic pathways. We performed cardiac perfusions on mice, where we first administered a drug to inhibit either clathrin or caveolin, and then we perfused with radiolabeled insulin. Afterwards, brains were collected and dissected into regions. Radioactivity was measured in the hypothalamus, olfactory bulbs, and whole brain, and the data was graphed over time to determine if there were changes in insulin binding or transport rates. Our results help elucidate the molecular processes necessary for insulin transport and binding at the BBB, which can ultimately help us understand how IR uptake and insulin transport may go awry in Alzheimer’s disease.

Children have more exposure to screen media today than any other generation. In the U.S., rates of obesity in children have also tripled in 4 decades. A disruption in the brain called gliosis has been described to participate in obesity pathophysiology if it occurs in a brain region important for energy balance, called the mediobasal hypothalamus (MBH). The objective of this study is to explore possible relationships between MBH gliosis and parents’ reports on screen time their child engages in. This study will also look into variables that may mediate these relationships, such as body adiposity and impulsivity. I hypothesize that there will be a positive correlation between screen media use and MBH gliosis with obesity and the level of impulsivity being positively correlated to both gliosis and screen time. The methodology consists of data from participants (N = 192) in the NIH Adolescent Brain Cognitive Development study. The NIH Toolbox Flanker Inhibitory Control and Attention Test was used to measure child’s impulsivity, and the parents were given the Screen time report to measure the average daily screen media time of each child. Along with these measures, participant’s age, sex, race, BMI z-score, waist/height ratio, and T2-weighted MRI will be included. MBH gliosis will be measured by T2 MRI signal intensity (brightness) of the mean bilateral MBH/Amygdala signal ratio; Putamen/Amygdala will be used as control ratio. Participants were 51% female with an average age of 9.9±0.63 years. Within our sample, 57.3%, 19.3%, and 23.4% of subjects were considered healthy weight, overweight, and with obesity, respectively. Anthropometric and behavioral data recorded on average 11.2 months after the initial tests will be included to calculate changes over time. This research will help to further illuminate the relationships between screen time and obesity, and will potentially be helpful in proposing new treatments for children with obesity.

In the US, the number of children with obesity has reached a staggering 13.7 million. Though there are diets to assist weight loss, recent research suggests a neurobiological basis of obesity specifically related to the mediobasal hypothalamus (MBH), a critical brain structure involved in energy homeostasis, metabolism, and appetite. However, proliferation of hypothalamic gliosis, a cellular inflammatory response, disrupts the function and is shown, in rodents, as a key component in diet-induced obesity. Further conclusions reveal that highly caloric and high-fat diets, in rodents, can cause MBH gliosis. This project seeks to investigate the relationship between diet and hypothalamic gliosis in children, the latter assessed by magnetic resonance imaging (MRI). We expect children with an unhealthy diet to have an increased BMI z-score and greater evidence of MBH gliosis. Participants (N=192) were recruited as part of the longitudinal NIH Adolescent Brain Cognitive Development study. Anthropometric and demographic data were collected along with brain MRI T2-weighted images at the baseline visit. MBH gliosis was measured by using the signal ratio for T2 intensity of the mean bilateral MBH/Amygdala signal ratio; Putamen/Amygdala was used as control ratio. At the one year follow-up, the child’s habitual diet in the past year was assessed using a parent-report food frequency questionnaire. Higher total points represented a healthier overall diet. Additionally, follow-up anthropometric data was obtained to determine the child’s adiposity change over time. At baseline, mean age was 9.9±0.6 and 49% were males. Mean BMI z-score was 0.76±1.05, 19% were overweight and 23% with obesity. Preliminary results in a subset of participants (N=60) revealed a trend for an association between an unhealthy diet and evidence of MBH gliosis (t=1.59, P=0.117). By emphasizing the neurobiological basis of obesity, potential insights can inform targeted diet-related treatments of childhood obesity; thus, furthering the understanding of child obesity pathogenesis.

Biomechanical characterization of human tissue is of increasing importance as new technologies gain importance in modern medicine. Without haptical sensation, measurement of forces associated with surgical techniques will be the primary source of feedback in technology assisted procedures (eg. robotic surgery). An important biomechanical parameter is the suture pullout force (SPOF), the maximum safe force that could be applied to a suture before tearing the tissue.The aim of this study is to analyze suture pullout forces of the pancreatic duct. This data could be used for a wide range of applications and will be useful in understanding how biomechanical properties of the biliary tract change with age, sex, and BMI. Donated organs used in this study were tested within 72 hours of death. Cross sections of the pancreas were prepared and 4-0 sutures were looped through one side of the pancreatic duct wall. The pancreas was held in place while the suture was pulled in tension. The tensile force was measured continuously and the peak force before specimen failure was taken as the SPOF. 103 suture pullout tests were performed on pancreatic ducts from 14 donors. The overall SPOF is 2.87 N ± 1.36 N. The mean SPOF for females is 2.12 N and 3.03 N for males (p=0.019). The SPOF of pancreatic ducts from donors with BMI less than 26 averaged 3.22 N while SPOF for donors with BMI greater than 26 averaged 2.51 N (p=0.045). Donors older than 35 averaged 2.69 N while donors younger than 35 averaged 2.87 N (p=0.123). Preliminary results suggest male pancreatic ducts have a higher SPOF than female pancreatic ducts. As BMI increases, the pancreatic duct SPOF decreases. The effect of age is inconclusive at this time.

Flavin-containing monooxygenases (FMOs) have historically been studied as xenobiotic metabolizing enzymes, but emerging data are consistent with a role for FMOs affecting longevity and metabolism through action on one or more endogenous substrates. Caenorhabditis elegans flavin-containing monooxygenase-2 (fmo-2) is necessary for the effects of multiple major longevity interventions including dietary restriction, and its overexpression is sufficient to extend lifespan. Despite this longevity-promoting role, the mechanisms by which FMO-2 extends lifespan remain undefined. We sought to test the hypothesis that fmo-2 interacts with the sulfur amino acid pathway to extend lifespan by screening RNAi clones of sulfur amino acid pathway genes for lifespan effects on wild type, FMO-2 overexpressor, and fmo-2(ok2147) loss-of-function mutant worms. We found that the increase in longevity induced by the overexpression of FMO-2 requires glutathione reductase, and that fmo-2(ok2147) worms are sensitive to the healthspan-shortening effects of glutathione synthesis RNAi. Additionally, HPLC analysis revealed that fmo-2(ok2147) worms synthesize significantly less glutathione. Our results are consistent with a model in which FMO-2 oxidizes glutathione to stimulate normal glutathione synthesis. This research serves to extend our understanding of the function of FMOs and provides insight into a mechanism by which cells maintain the reducing environment necessary for many metabolic pathways. 

In humans, aging is a major risk factor for high-mortality diseases such as cancer, heart disease, and Alzheimer’s, all of which do not currently have cures. One hypothesis is that by treating the aging process underlying these maladies, the progression of the diseases will also be alleviated. It has been found that many of the aging processes in the single celled eukaryote, Saccharomyces cerevisiae are also conserved in multi-cellular eukaryotes such as humans. One characteristic of aging yeast is the accumulation of extra-chromosomal rDNA circles (ERCs). rDNA is a repetitive region of the genome that encodes for ribosomes: cellular machinery that produces proteins. ERCs are small pieces of rDNA that become excised from the chromosome during homologous recombination. It is commonly thought that ERCs are a consequence of aging and that they build up over time and lead to cell death. My project investigates if ERCs have an evolutionary function that has been selected for. It is known that older yeast cells survive better on non- optimal carbon sources, such as galactose, compared to young yeast cells. I hypothesize that ERCs aid aging yeast cells in surviving on non-optimal carbon sources as an evolutionary adaptation. Sir2 suppresses the creation of ERCs and I have controled the amount of ERCs that accumulate in the cells by using a strain of yeast with a Sir2 deletion alongside a strain with Sir2 overexpression. I grew these strains on either dextrose or galactose to see if varying Sir2 activity affects old cells ability to grow on non-optimal carbon sources. Then I passaged these strains over many generations on glucose or galactose to see if ERC accumulation is favored in non-optimal carbon environments. We will also be quantifying ERC copy number through gel electrophoresis and quantitative Southern blotting.

Aging is the single largest risk factor for many diseases, including Alzheimer’s disease (AD). Therefore, many of the molecular mechanisms that cause aging may also contribute to the onset and progression of aging-related diseases. Our approach to tackling the progression of AD takes a biology of aging standpoint, where screening compounds (FDA approved or naturopathic) that impact lifespan may help identify therapies for AD. This is a novel approach with the potential to accelerate clinical translation. This study uses a human Amyloid-beta (Aß) protein-expressing C. elegans strain that becomes progressively paralyzed with age. Utilizing a novel robotic imaging system (the WormBot), we show the impact these compounds have on AD progression through quantification of a delay in paralysis, then behavioral data and health metrics are collected by tracking worm motility over their entire lifespan. Three compounds have been identified to delay paralysis: Thioflavin T, alpha-lipoic acid and resveratrol, all of which we have shown to increase lifespan. We expect to see Thioflavin-T to have a strong influence on paralysis due to its disruption in Aß aggregation. Resveratrol and alpha-lipoic acid's inflence is expected to be associated with its impact on increasing lifespan. Both behavior and binary paralysis results under these three compounds exposure provide holistic insight into mechanisms of Aß toxicity and could lead to promising treatments that have the potential to increase the quality of life for Alzheimer’s disease patients.

Astrocytes are characteristic star-shaped glial cells, and they are the largest and most numerous nonneuronal cells in the brain. They are involved in cell signaling, providing nutrients to neurons, removing toxins, repair and anti-inflammation response in the brain. However, relatively little attention has been paid to this cell type compared to neurons in neurodegenerative conditions, such as age-related cognitive impairment and Alzheimer’s disease. The basic question is: what functional changes occur in astrocytes with increasing age that could relate to vulnerability to neurodegeneration. C57BL/6 mice in age cohorts of 8 months, 16 months, 24 months, and 32 months were tested in a radial water tread maze, a well-standardized measure of contextual learning and memory in the mice. Brain tissues were then collected and parasagitally sectioned and stained with GFAP (Glial Fibrillary Acidic Protein), an immuno-reactive marker for astrocytes. In general, 8-month old mice showed very little cognitive impariment while several 16-month old mice showed mild cognitive impairment, but 24 and 32-month old mice showed moderate to severe cognitive impairment. Concurrent with this increase in cognitive impairment was an increase in ImageJ pixel intensity of GFAP immunohistochemistry staining of astrocytes with increasing age. This preliminary observation suggests that astrocytes are predominantly present with increasing age and decreasing cognitive ability and provides the rationale for further investigations into what role these nonneuronal cells are playing in brain health.

The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) will conduct an all-sky survey and uses difference imaging to identify and classify variable sources. Galaxies with an actively accreting supermassive black hole at the center, or active galactic nuclei (AGN), can vary in brightness significantly. They are powerful tools for improving our understanding of high energy astrophysics. We present an analysis of a subset of high-probability AGN from the High Cadence Transient Survey (HiTS) data release, a precursor for LSST. By comparing difference imaging light curves generated by both HiTS and LSST software, we eliminate bad sources, crossmatch with other datasets, and identify previously unknown AGN. We use these comparisons to assess why some known AGN were not found in the HiTS data. We also make suggestions for how the LSST software can be used to maximize variable AGN science.

The Balkans have played a pivotal role in the competition between the West and the East. Great Power competition during the 19th Century created the conditions for ethno-nationalism that led to turmoil during the 20th Century. Following World War II, Josip Broz Tito, the first president of the Socialist Federal Republic of Yugoslavia, attempted to construct a united multi-ethnic state by suppressing nationalist impulses. This effort began to collapse immediately after Tito's death in 1980 and culminated in the breakup of the Yugoslav state and a series of bloody ethnic and religious conflicts from 1991 to 2001. These wars challenged the capacity of the international community to arrest the conflicts, and then to rebuild the peace. The region continues to suffer the effects of these conflicts despite decades of international efforts supporting reconciliation and the development of civil institutions designed to overcome division. A vicious circle constituted by the lack of economic development and continued use of divisive ethnonationalist politics has developed. This study argues that external economic and political aid efforts have been insufficient and that internal cultural changes are necessary before reconciliation, and economic and political development may proceed. This project's driving question is, "What specific values shifts and domestic efforts are necessary for the people of the Balkans to reconcile with the past and construct a brighter social, economic, and political future?" To explore this question and to identify potential solutions, this study assesses contemporary scholarship on Balkans reconciliation and economic development and incorporates local language and ethnographic resources. It concludes with a discussion of the following policy steps - democratic governance and unbiased media and education focused on rebuilding relations between different communities - and assesses whether or not these steps can be generalized to other societies either entering or experiencing post-conflict status.

Plants respond to environmental changes by changing their growth patterns. For plants to continue to grow throughout their lives, they are constantly undergoing cell fate determination—how the plant determines the specific fate of new cells they are generating. One example of this is the development of roots that emerge from the primary root, called lateral roots. The number and spacing of lateral roots determine the overall root structure, which determines how well the plant takes advantage of resources in its environment. Auxin is a plant hormone involved in many aspects of growth and development, including the regulation of lateral root production. Using data from an experiment where mRNAs were sequenced from single cells isolated from roots, the Nemhauser Lab identified specific genes that may be active during lateral root development. My research question is: are these genes targets of auxin signaling? To test this, I will use quantitative RT-PCR to measure expression of the candidate genes in wild type and in plants that are deficient in the auxin response pathway. Genes that are targets of auxin should show lower expression levels in the mutants relative to wild type. The more we understand about how cell fate determination occurs in lateral roots, the more we can understand the underlying mechanisms by which plants arrive at their final root structure. Our understanding can then guide engineering or breeding projects, allowing optimal root growth that could drastically increase plant survivability and yield.

More than 442 million people worldwide have been diagnosed with diabetes, many of which regulate their glucose levels using the pump/catheter system. However, just 2-3 days after the catheter is inserted into the body, the tissue clogs due to the foreign body reaction (FBR), an immune reaction elicited by the body in response to any foreign material injected in the body. At this point, the patient must remove the catheter and insert a new device into fresh skin elsewhere, resulting in excess scar tissue. Our project focuses on preventing the FBR by reducing its triggering event--protein attachment--so that insulin catheters can last longer (2-3 weeks) and can reduce fibrotic accumulation in patients. To combat the frequency of delivery site changes, we have designed a nonfouling zwitterionic polymeric brush coating for the surface of the catheter to reduce protein attachment. For the coating, zwitterionic sulfobetaine methacrylate (SBMA) was surface-polymerized onto the catheter using atom transfer radical polymerization (ATRP). SBMA has been shown to resist protein adsorption down to less than 1ng/cm². The ATRP initiator was plasma-deposited to robustly adhere to the unique geometry of the catheter. In this work, we used a full factorial design of experiment (DOE) to determine significant experimental factors to the polymerization protocol to maximize the amount of SBMA on the surface. The coating was characterized using x-ray photoelectron spectroscopy (XPS) to confirm the presence of SBMA and the radiolabeled protein adsorption assay to measure the amount of protein adsorbed to the coating. We plan to use the results of the DOE screening to further optimize the nonfouling coating and ultimately plan to test this coating on insulin-delivering catheters in a diabetic mouse model to observe sustained lowered blood sugar levels and histologically review the extent of the FBR through collagen accrual.

Cancers are broadly characterized by changes in cell metabolism. Tumor cells typically exhibit functional respiration and inhibition of electron transport chain can impair cancer cell proliferation. However, certain neuroendocrine cancers can arise from loss of function (LOF) mutations in succinate dehydrogenase (SDHx/complex II), which plays a key role in the TCA cycle and in mitochondrial respiration. SDH, which catalyzes the conversion of succinate to fumarate, comprises four subunits: A, B, C and D. LOF mutations in subunits B, C, and D can promote tumorigenesis and mutations in subunit B (SDHB) are particularly associated with malignant and metastatic neoplasms. Interestingly, SDHB impaired cells show an accompanied loss of activity in complex I, implying that unlike the majority of cancer cells, respiration is not essential and may even be antagonistic for SDHB mutant cancer cell proliferation. Indeed, preliminary experiments indicate that inhibition of complex I can restore proliferation to cells treated with an SDH/complex II inhibitor. However, the molecular mechanisms behind this phenomenon are not well understood. We aim to investigate the metabolic mechanisms by which dysfunctional respiration is essential for the proliferation of SDH impaired cells. We hypothesize that inhibition of respiration in these cells can prevent oxidation of NADH to NAD+ at complex I and alter the redox homeostasis in the mitochondria to support proliferation. Specifically, we will test to see if increasing the NADH/NAD+ ratio is the required function of complex I inhibition that rescues cell proliferation in SDH impaired cells. In addition, we will characterize the metabolic consequences of specific alterations SDH, complex I, and mitochondrial redox state. Results from this study should allow us to delineate the importance of metabolic alterations in SDH mutant cancer cells and potentially help identify metabolic vulnerabilities for treatment of SDH impaired cancers.

Taking advantages of advances in controlled drug delivery, modern medicine now has the ability to access and treat disease within many parts of the human body not previously possible. Where current medicine lacks, however, is the ability to treat complex disorders that require specific control over the timing, order, and sequential dosing of active therapeutics. To access these systems, we have attempted to create a library of light-sensitive compounds that will release protein therapeutics orthogonally in the presence of different wavelengths of tissue-penetrating light. These compounds are based on ruthenium polypyridyl linker complexes and can be structurally tuned to respond to visible and NIR light irradiation, leading to exchange of a ligand with water and rapid cleavage. We have modified the complexes with a reactive azide handle for site-specific incorporation into hydrogel biomaterials that can be transplanted to or formulated within specific bodily locations. Varying the ligands in the complex gives rise to different photocleavable crosslinkers that cleave in response to up to 715 nm light, well into the therapeutic window for in vivo applications. In this poster, I will describe the synthesis and characterization of one model Ru-based linker (RuPhen), including its photolysis, stability, and applications of the complex in the development of dynamic biomaterials.

Planning for water resources management (WRM) requires the best available predictions of streamflow. We want to provide actionable predictions that improve WRM as climate change alters streamflows. However, the computer models of these systems result in imperfect predictions despite our best efforts to match observations. These systematic errors reduce the usefulness of model outputs. To improve our ability to plan for WRM, we apply statistical correction techniques to model outputs so that they agree better with observations. The Columbia River Basin, a major river basin in the Northwestern United States, is heavily regulated for a large number of competing uses. In this project, we focus on the Yakima river basin in central Washington, a subbasin of the Columbia River, and use it as a case study for evaluating multiple statistical correction techniques. By comparing streamflow observations to simulations for the same periods we can develop statistical corrections. The application of these statistical corrections is often referred to as “post-processing”. Post-processing adjusts predictions based on previous knowledge of the region as well as the historical observations.These post-processing techniques can then be applied at locations and times without observations. As part of this project, we developed a toolkit for the evaluation of different post-processing techniques. We explore which measures and visualization techniques are adequate at describing key aspects of the streamflow simulations. Our toolkit builds on open source technologies that will allow researchers to reliably measure the statistical performance of these post-processing techniques. Evaluation is performed through exploring different statistical metrics and building a suite of summarizing plotting capabilities in a standalone, open source Python package.

Given that greater than 15% of the world’s population currently relies on snow melt for drinking water, hydrological modeling of landscapes subject to routine snowfall is becoming increasingly important. Up to 60% of snowfall in forested terrain is intercepted by the forest canopy. Therefore, tree interception parameters that quantify how much water or snow a tree collects during a precipitation event are critical for understanding temporal and spatial water fluxes, which most notably determine when and in what volume water is delivered to communities. This project is evaluating whether a new video processing technique can be used to reliably and accurately identify snow interception parameters for coniferous trees. In particular, this project seeks to learn whether the resonant frequency of swaying snow-loaded trees, as determined by processing time lapse videos, can be used to compute the mass of snow in a tree. Having shown that video processing can correctly infer the sway frequency of a tree, we are now deploying cameras on Snoqualmie Pass to observe tree sway events concurrent with snow loading events. To date, we have four cameras monitoring a tree and the snow levels around it. Pending further video data collection, we will begin applying the tree sway processing algorithm, which uses FFT processing to compute changes in tree sway frequency and corresponding changes in tree mass. If successful, this method may improve tree interception parameterization and therefore hydrological forecasting. 

Conjugated polymers (CPs) are used in a wide variety of organic electronics such as photovoltaics, organic thin-film transistors (OFET), and flexible displays because of the increased flexibility of polymer-based electronics. However, CPs often have significant downsides such as being prone to environmental degradation, lacking mechanical robustness, and being overall very expensive to create and use. To combat these limitations, CPs can be blended with lower-cost commodity engineering plastics (CEP), such as polystyrene, to create a blended composite that forms nanoscale structures of CP in a CEP matrix. To characterize the blends, we use small-angle neutron scattering (SANS) and wide-angle x-ray scattering (WAXS), which are techniques that provide information in the form of a scattering pattern. After data reduction and background removal, SANS data can then be modeled to extract information about the structures that develop from 1 nm – 1000 nm. We have decided to focus on using the sphere, fractal, and parallelepiped models since those geometries often form from self-assembled CPs. The scattering pattern from WAXS can be used to determine the preferential growth direction of CP self-assembly, either along the pi-pi stacking or lamellar directions. Through the combined use of these techniques, we are able to characterize structural dependence on the choice of solvent including both moderate and good solvents for the CPs. We also tested different side-chain lengths on the CP which will affect solubility and the ability to self-assemble. From these experiments, we found that a moderate solvent (such as toluene) will encourage nanofiber formation growth at lower concentrations of CP. Control over nanofiber formation could potentially lead to more favorable electrical performance for these materials. Conductivity and rheology tests will be conducted which will allow us to determine how much of an effect solvent choice has on the mechanical and conductive properties of these blends.

Altruism encompasses an ethical principle that places significance on promoting the welfare of someone else, even at a cost to one’s self. In classic studies, young children and nonhuman primates have offered objects or moved items to help others. However, it is unclear whether this is evidence of altruism, because there was low self-cost. A stronger test would be to investigate infants’ willingness to give others high-value objects, such as desirable food. In the new research, we examined whether 19-month-old infants help others by transferring fresh fruit to an adult. This work tested whether infants can act altruistically and the generality of this tendency across trials. Infants (N=96) were randomly assigned to a group, either the experimental group (experimenter accidentally dropped and reached for fruit) or the control group (experimenter intentionally discarded and looked at fruit). In both groups, the fruit started in the experimenter’s hand and landed out-of-reach for the experimenter. Infants’ helpfulness was shown by whether they gave fruit to the experimenter (i.e., banana, grape, blueberry, strawberry). We hypothesized infants would be more likely to help in the experimental than the control group given that past work has shown infants can perceive the goals of others (e.g., reaching for fruit). We analyzed how often infants’ transfer high-value fruit as predicted by group, type of fruit, and test trial. We found that more infants helped in the experimental than the control group; we found that infants helped on the first trial, showing that they readily recognized the experimenter’s need. Infants’ willingness to hand over high-value food suggested that their helping behavior is an early form of altruism. Future research of infant helping behavior could examine the effects of low- versus high-value items on patterns of giving.

Autism spectrum disorder (ASD) is a developmental disorder that causes challenges with speech and nonverbal communication, social interaction and repetitive behaviors. It is hypothesized that ASD is caused by a combination of genetic and environmental factors such that symptoms and behaviors present differently between individuals. Given variability in causes and symptoms of ASD, it is important to look at the effectiveness of treatments for individuals with specific genetic and behavioral profiles, including individuals with rare genetic mutations linked to ASD. Recommended treatments include biomedical, behavioral, speech, and occupational therapies, which can be expensive and time consuming for families. Speech-language therapies and other services can be provided through a school district or through private providers, but the effectiveness of these services for individuals with rare ASD-associated genetic mutations is currently unknown. The aim of this project is to compare satisfaction with school-based versus private speech-language therapy for individuals with mutations to DYRK1A or SCN2A, which are associated with ASD and language delay. In this study, participants included individuals with a disruptive mutation to either DYRK1A (n=28, ages 4-24 years) or to SCN2A (n=23, ages 3-21 years). Treatment history interviews will be analyzed to assess caregivers’ perceptions of treatment effectiveness. We hypothesize that there will be greater satisfaction with private speech-language therapy than with school-based services, as these services may allow for greater communication and coordination with parents. We also hypothesize that satisfaction with speech therapy will be highest in the DYRK1A group, as increased medical complications in SCN2A (e.g., severe seizures) may lead to reduced response to speech therapy. This study will contribute to better understanding of effective treatments and parents’ satisfaction with current services for individuals with rare genetic mutations associated with ASD, which may inform future treatment choices and recommendations.

Can parenting styles offset the effects of neighborhood disadvantage on child life-course trajectories? Much research indicates that children raised in an economically disadvantaged neighborhood face a greater risk of high school dropout or expulsion, low-wage employment, and incarceration. Yet not all youths raised in disadvantaged neighborhoods follow this trajectory, and success stories abound. This study examines how low-income parents’ childrearing strategies positively or negatively affect the life-course trajectories of at-risk youth. Using the Denver Youth Survey (DYS), a nationally representative, longitudinal sample of high risk youth, I intend to test whether parents’ childrearing strategies affect young adults’ academic accomplishment, income, job type, and criminal record. I hypothesize that positive parenting, defined as monitoring, control, and warmth towards the child, is associated with a reduced likelihood of youths experiencing impediments to socio-economic mobility. As an alternative hypothesis, I test whether impulsivity of the child mediates the association between parenting style and positive life-course outcomes. In doing so, I aim to contribute to the intersecting literature on life-course theory, child developmental psychology, and criminology, as well as provide evidence to aid the development of policy assisting at-risk youths overcome their disadvantaged circumstances.