In the age of the internet, literature is consumed in unprecedented ways. Modern social movements often call upon those of the past through key quotes and references to influential literary works. Quotes can go viral, seen outside of their context by thousands of people and become associated with these movements or rediscovered by new communities. For instance, key figures in post-WWII literature such as author and civil rights activist James Baldwin have had their words re-immortalized within the context of contemporary movements such as Black Lives Matter. Baldwin’s era of literature was one of marked social change and evolution within the literary world that parallels our society today, making it significant to understand how quotes from this period can reappear and spread across social media. To analyze the reception of post-war literature on Twitter, we utilized a dataset of over 40 million tweets quoting or referencing James Baldwin, as well as similar datasets quoting four other influential authors of the time including David Foster Wallace and Kurt Vonnegut. We focused on the patterns of text reuse (i.e., the repetition of known quotes) in tweets from 2006-2023, examining key moments of reception and exploring the context of virality for key quotes. During this context-finding process, we also developed a novel method for conducting self-identified user demographic analysis. We implemented clustering algorithms on both tweets and user bios, supplemented the resulting clusters with manual merging processes, and experimented with various visualization strategies. Our results yielded clear quote usage patterns for certain demographic groups, demonstrating the efficacy of the novel demographic extraction method. These methods can be expanded for further demographic-focused social media research and help us understand how cultural movements evolve today.

The Sensors, Energy, and Automation Lab (SEAL) aims to gamify undergraduate research by instituting a leaderboard, awarding points for tasks, assigning ranks for accomplishments and published papers, and framing research directions as Quests. Individuals receive a character sheet with a health bar, while groups compete against one another in Racetrack- a software for team challenges. Gamification in educational settings is well-studied: gamifying learning can boost students’ motivation, retention, and challenge appraisal. However, research indicates that the efficacy of gamification varies dramatically, particularly personality traits like extraversion, which correlate more positively with success in software with leaderboards. Significant gaps exist in gamification literature; existing research primarily studies gamification in classrooms, not workplaces or research environments. Further, the studies fail to incorporate modern approaches to psychology. The socio-psychological model suggests personalities and behaviors differ depending on the environment, meaning people may exhibit different personality traits in gamified environments. Moreover, gamer motivation, a personality test tailored to predicting player personality with strong correlations to the Big Five (psychological scale for key personality traits), has yet to be tested in gamification studies. By accounting for contemporary psychological theory, SEAL aims to rigorously test the hypothesis that gamification is an effective structure in lab organizations through multi-year longitudinal study on a scale never seen in gamification literature. SEAL’s large cohort and gamified structure offer a perfect platform to analyze the role of demographic and personality type in gamification outcomes. Our preliminary results explored collected qualitative and quantitative data on demographics, gamer motivation personality, and perceptions of the SEAL system by anonymously surveying 81 associates. Our longitudinal study contributes to the growing literature on gamification; a solution potentially improving productivity in research ecosystems.

Soil-transmitted helminths impact over 1.5 billion people worldwide, disproportionately affecting school-aged children and pregnant women. Hosts issue a “weep and sweep” Type II immune response to expel helminth parasites from the intestines. Ruptured epithelial cells secrete the cytokine interleukin (IL)-33, which recruits innate lymphoid type 2 cells (ILCs)2 and CD4+ T-helper type 2 (Th2) cells. ILC2s release IL-13, encouraging stem cell differentiation into tuft and goblet cells to facilitate tissue repair and worm expulsion. Anemia is prevalent in helminth-rich environments because of elevated rates of malaria and malnutrition. Despite correlations between anemia and helminth infection, the impact of anemia on the Type II immune response in the small intestines remains unknown. Using N. brasiliensis (Nb), a bloodsucking hookworm-like parasite, I observed that one week post infection, iron-deficient (ID) mice were less capable of expelling worms compared to iron-sufficient (IS) mice. Through tuft cell immunofluorescence staining in the small intestine, I observed comparable hyperplasia in IS and ID-Nb infected mice but noticed differences in cell localization: ID-Nb infected mice had decreased numbers of tuft cells in the crypts compared to IS-Nb mice. This suggests that ID Nb-infected mice could be experiencing decreased migration/proliferation of tuft cells, compared to their IS-infected counterparts. Using EdU, a synthetic nucleotide tag that labels newly synthesized DNA, we can understand cellular proliferation patterns in IS vs. ID Nb mice. Co-staining for tuft cells permits us to merge events and track unique vs. universal trends in cell behavior, including cells’ migration patterns. I hypothesize that ID-Nb mice will have decreased cellular proliferation and migration compared to IS-Nb mice, ultimately impacting worm burden. These findings offer insights into the mechanism behind negative outcomes in anemic hosts, and could contribute to dietary intervention or therapies targeting the epithelium to alleviate burdens of helminth infection.

Circadian clocks have evolved as a powerful adaptation in response to daily environmental changes, allowing optimally timed sleep-wake cycles. The solar light-dark (LD) cycle is the dominant zeitgeber (time-giver) for entrainment (synchronization) of sleep and wake to external cues. While our lab has found that humans sleep less and later the days prior to the full moon phase where moonlight is available in the early night, moonlight was found to be an unreliable cue in determining lunar modulation of sleep for the light-polluted city population. Thus, my project investigates whether lunar cycling on activity patterns remains present without photic moonlight exposure using a diurnal non-human primate model: captive titi monkeys (Plecturocebus). The California National Primate Research Center collected titi monkey data (n=16) between 2022 to 2024 using AX3 from Axivity, a wearable data log that measures acceleration to monitor physical activity. I am using the statistical software R to derive activity onset and sleep onset/offset as phase markers of activity. Additionally, I am fitting different cosine models to a 30/15-day period, respectively lunar and semilunar, to analyze the periodic data for activity across the lunar month. We expect to see phase markers of activity oscillate with the monthly lunar phase, showing how the lunar cycle influences circadian rhythms in diurnal non-human primates, even in the absence of moonlight. This study may reveal a novel finding on lunar rhythms on activity patterns and could incur interest on how endogenous processes have adapted to the lunar cycle. Further molecular work could elucidate the neural mechanism behind lunar modulation of sleep and provide insights on improved treatment of dysregulated sleep.

Intimate partner violence (IPV) is a widespread problem across the U.S. that typically begins in adolescence which can cause severe struggles for the impacted individuals. IPV can be mitigated through some preventative factors, such as education and understanding of IPV. The purpose of this study is to evaluate rejection sensitivity (RS)-- the tendency to strongly react to rejection, including the dismissal or refusal of ideas, people, or offers-- as a mediator between comprehensive sexuality education (CSE) and IPV. I designed this study to use a cross-sectional online survey to measure levels of RS, themes of CSE from middle and high school education, and levels of IPV that individuals have experienced. It includes a representative sample based on Unites States census data of 340 participants who range from 18-25 years and have had a romantic relationship lasting at least two months. The data is analyzed through a mediation model, with RS as the mediator, as well as testing the direct effects of CSE on IPV using R Statistical Software. Analysis models the three pathways: path a-- CSE to RS, path b-- RS to IPV, path C-- direct effects of CSE on IPV (CSE to IPV). I anticipate that RS will act as a mediator between CSE and IPV such that higher levels of CSE will be associated with lower IPV levels through the mediation of RS. Additionally, I hypothesize there will be a direct effect of CSE on IPV. This study aims to improve the understanding of potential preventative factors of IPV as well as inform future interventions, such as CSE. Keywords: intimate partner violence, rejection sensitivity, comprehensive sexuality education

Tumor cell survival and recurrence remain a leading cause of death among cancer patients, and it is likely that the residual tumor cells that form the secondary tumor have distinct phenotypes from the primary tumor. The transcription factor NRF2 is thought to play a role in tumorigenesis, metabolic reprogramming, and recurrence in breast cancer. Emerging evidence suggests that NRF2 also intersects with the circadian rhythm, the 24-hour oscillatory clock present in all cells. My project investigates how NRF2 interacts with circadian rhythm genes, and how this interaction affects cancer cell growth. Mouse cell lines NMuMG, EMT6, 66Cl4, and 4T1 were cultured, treated with dexamethasone for synchronization of cellular clock, and harvested over three days. Cell pellets were collected every eight hours after synchronization, for a total of seven timepoints across 48 hours. I performed RNA extraction, cDNA synthesis, and RT-qPCR to analyze gene expression of  NRF2 (Nfe2l2), NRF2 target genes (Nqo1, Slc7a11, G6pdx, Gpx2, Txn1), and circadian rhythm genes (Bmal1, Clock, Per2, Cry1, Per1, Nr1d1) at each timepoint. 66Cl4 cells were further used to perform a CRISPR knockout screen for NRF2 target genes, to investigate which genes are essential for tumor cell viability. I cultured and infected cells with Cas-9 enzyme and sgRNA corresponding to 30 NRF2 targets using lentivirus, then allowed them to proliferate to 14 population doublings over the course of the screen. After the screen had completed, cells were sent for genomic sequencing to identify hit genes. Though these experiments are ongoing, we aim to identify 4-5 hit genes through the screen to direct future research on how NRF2 promotes tumor cell survival and proliferation. My data on NRF2 and circadian clock will also shed light on the intricate role of NRF2 in the cell, and open the door for new therapeutic targets.

Formalization is the process of translating human-written mathematical proofs into a form that can be verified by a computer. A popular tool for this is Lean, a proof assistant that represents proofs as code. However, the process of formalizing proofs in Lean can be slow and time-consuming. Our research explores so-called "autoformalization" strategies, which aim to automate the generation of Lean proofs. We propose a tree-based search framework to formalize mathematical theorems in Lean using Language Models. This approach explores potential proof steps as branches in a tree, using AI models to suggest "tactics" at each node. This has the benefit of avoiding hallucinations by rigorously checking that AI suggestion represent valid Lean code. We employ both Large Language Models such as Claude Sonnet 3.5 and specialized fine-tuned Small Language Models such as Lean-Dojo. We use Pantograph to interact with Lean, leveraging its native support of Monte Carlo tree search. We assemble a small set of simple and medium-difficulty mathematical theorems to benchmark against, called nanoF2F. Additionally, we benchmark our system on the well-established miniF2F benchmark created by OpenAI.

Over the years, the relationship between universities and corporations have become more and more intertwined through research and building funding, student opportunities, and company influence on administrators and faculty. My research explores the connections between the University of Washington (UW) and Boeing, a large transnational weapons manufacturer, and the impacts these connections have on research, education, and students' future career prospects. In this project, I ask: how are student’s educational experiences and career opportunities impacted by the university’s close connection to the Boeing company? I am focusing on a potential student to Boeing pipeline–a process for where students are primed to work at Boeing through their educational experiences at UW. I address this question through a variety of methods and sources, including a comprehensive analysis of all publicly available information on UW websites, including individual websites run by UW research labs, interviews with engineering students, Public Records requests, and a review of relevant Critical University Studies literature. My findings indicate that there is significant evidence towards the existence of a student-to-Boeing pipeline at UW. Boeing has given an extensive amount of money to the university, placed employees/affiliates in professorships, and is vastly overrepresented in internship and capstone opportunities available to students through the University of Washington. Furthermore, my research found a correlation between departments with a high amount of funding from Boeing with higher rates of student employment at Boeing after graduation. I argue that the student-to-Boeing pipeline has fundamentally changed the education of UW Engineering students to better fit Boeing’s needs, and it upholds the military-industrial complex. This project contributes to broader debates in critical university studies about the mission of public universities in providing students an unbiased education and universities' role in combating the climate crisis.

The tongue base is a key structure in respiration and swallowing and morphological and functional adaptations to its volumetric changes are largely unknown. Thus, addressing this gap could enhance the understanding of breathing and swallowing disorders in the enlarged and reduced tongue base. Twelve Yucatan minipigs 8-to-9-month-old (half each sex) were analyzed. Six minipigs received a high-caloric chow pellet to reach a BMI>50 (enlargement group), while the others underwent surgical partial tongue base ablation (reduction group). Five weeks after surgery all minipigs were scanned using magnetic resonance imaging (MRI) synchronized with respiratory cycle gating. Mid-sagittal cross-sectional areas of the velopharyngeal and oropharyngeal airways, and retroglossal space during inspiration and expiration were quantified using ITK-SNAP. The volumes were also calculated using segmentation techniques. These measurements were compared between the enlargement and reduction groups in the inspiratory and expiratory cross-sectional areas to determine differences. Extrapolating from one minipig from the enlarged group observed larger mid-sagittal cross-sectional areas of the interested regions compared to the reduction group. The enlarged minipig observed greater differences in range and larger averages and medians for each cross-sectional volume. The enlargement group also had slower inspiratory and expiratory rates than the reduced group. Observations from one minipig from the reduced group were observed to have smaller cross-sectional areas, medians, and averages for all interested regions. Additionally, the reduced minipig had more frequent respiratory rates. The current analysis of the sagittal views from the obese enlarged tongue base versus the reduced tongue base minipigs revealed larger volumes within the enlarged group. This pattern currently suggests enlarged tongue base minipigs with larger cross-sectional volumes, but less inspiratory and expiratory rates. However, the reduced tongue base minipigs are anticipated to have smaller cross-sectional volumes and more frequent respiratory rates compared to the enlarged group.

The aim of this study was to examine the respiratory 3D deformational changes in the tongue base with normal weight and obesity in a minipig model. This study included 6 same-sex sibling pairs (3 pairs each sex) of Yucatan minipigs 8-to-9 months old. Of each pair, one minipig was normal weight with a BMI<35 and the other was fed a special diet reaching a BMI>50 (obese,). While under sedation, eight 2mm ultrasonic piezoelectric crystals with an extended skin button attached to the back were surgically implanted at the base of the tongue in a cubic-shaped arrangement. These crystals represented dorsoventral lengths, anteroposterior widths, and thicknesses. The 3D deformational changes of the tongue base were recorded during respiration using a Sonometric system together with synchronized electromyography and airflow recordings to identify respiratory phases. The amplitudes and durations of each dimensional change within the crystal-defined region concerning inspiration were calculated for 5- consecutive respiratory cycles per minipig. The total respiratory cycle duration was 1.87±0.38s in the normal-weight group and 3.2±1.01s in the obese group (p<0.05).  Similarly, the durations of the inspiratory phase in the normal and obese groups were 0.62±0.36s and 1.19±0.77s respectively (p<0.05). Deformational changes in the normal-weighted group included dorsoventral lengthening, anteroposterior ventral widening with dorsal shortening, and thickening in all dimensions. In contrast, the obese group showed dorsal lengthening with ventral shortening, widening in all dimensions, and anterior thickening with posterior shortening. Overall, larger dynamics were observed in the normal-weighted group compared to the obese group (p<0.05). These results demonstrate that obesity affects tongue base respiratory kinematics, with longer respiratory cycles and decreased deformational changes mainly ventrally and posteriorly. These findings enhance understanding of obesity's impact on the oropharyngeal function, with implications for breathing disorders.

The stimulation of the genioglossus muscle may prevent upper airway collapse in breathing disorders such as obstructive sleep apnea (OSA). Thus, the present study was to analyze the 3D-changes of the tongue base by electric stimulation of genioglossal muscle in relation to volumetric alterations of the tongue base in minipigs. Twenty 8-to-9-month-old Yucatan minipigs were used. Of them, 8 were controls, and 12 were experimental. Each experimental same-sex sibling pair was randomly assigned: 1. Normal-weight having surgical tongue base volumetric reduction. 2. Enlargement having significant obesity, BMI>50. All minipigs received surgical implantation of eight 2mm ultrasonic crystals in a cubic-shaped array in the tongue base. The distance change between each crystal pair indicated dimensional deformations for lengths, widths, and thicknesses responding to the stimulation. Increased distances indicated elongations while decreased indicated shortenings. Stimulations to the left genioglossal muscle were ramping up in range of 10-40V to reach the maximal amplitudes (tetany). Stimulation of the genioglossus muscle in controls induced left lengthening, anterior thickening and overall widening along with posterior thinning and right shortening. In contrast, the reduction group showed thickening and widening with left lengthening and minor right shortening. Elongations in the reduction group were larger than those in the control group (p<0.05). The enlargement group showed decreased dorso-ventral lengths compared to those of the control and reduction groups (p<0.05), along with antero-posterior thickening and widening. Stimulation of the genioglossus muscle induces distinctive deformational patterns between the normal and volumetric-altered tongue bases. For instance, shortening in length in the enlarged tongue due to obesity may suggest retraction of the tongue base inducing narrowing of the oropharyngeal airway. These results may contribute to understanding kinematic adaptations in the respiratory dynamics in relation to the volumetric alterations of the tongue base, a current approach to treat moderate and severe OSA. 

As Cannabis use is becoming more widespread there is growing concern regarding the respiratory exposures of employees working in indoor cannabis processing facilities. Employees in these occupational settings are frequently exposed to volatile organic compounds (VOCs), particulate matter (PM), other respiratory irritants, and allergic sensitizers. These exposures are linked to work related illness and disease, such as occupational asthma. Notably, a fatality, in 2022, in a Cannabis worker due to occupational asthma highlights the urgent need for improved exposure controls. Cannabis processing workers experience prolonged and frequent exposure via inhalation with little knowledge on the respiratory hazards of this work. This study aims to evaluate the efficacy of a local exhaust ventilation (LEV) system to reduce exposure to airborne hazards during automated joint filling. Automated joint filling is a common process in Cannabis production facilities, using mechanized equipment pre-ground material is dispensed into pre-rolled cones. This method is preferred in the field as it increases both consistency and efficiency. Over a ~2-hour sampling period across eight batches of pre-rolled joints, we conducted gravimetric sampling for inhalable PM using two inhalable aerosol samplers (IOMs) positioned at the workbench and in the breathing zone. VOC exposure was assessed using thermal desorption tubes and photoionization detectors (PIDs), while continuous respirable PM concentrations were measured using a Nanozen DustCount monitor. Testing air concentration for PM and VOCs with and without the LEV mechanism is being conducted to determine its effectiveness at reducing exposure. We hypothesize that this may be an effective solution, as the LEV has controlled these agents significantly in other similar workplace settings. As this field grows due to recent state by state legalization of Cannabis, these findings hold great impact for workplace safety regulation and solutions. Additional research should be gathered on long-term exposure effects and preventive mechanisms.

Wildfires are capable of altering landscapes, devastating forests, and communities, and are increasing in frequency and intensity. However, the hazard extends well past the burn phase as burn scars are at high risk for the generation of debris flows and flooding in the days, weeks, and years after a fire. Conconully, WA, experienced severe post-fire debris flows and flooding in 2022 following the 2021 Muckamuck fire. Witnessing the effects of both the fire and the subsequent debris flow on my community motivated me to explore why these events occur, to investigate how they initiate, and help inform future warnings or mitigation strategies to increase resilience in the face of these hazards. Whether these floods and debris flows were initiated by shallow landslides, or storm runoff remains unknown, and could alter how post-fire hazard or evacuation warnings are issued. In this study, we employ geospatial analysis to identify areas affected by the fire and correlate these with the origins of the debris flows and flooding. Additionally, we use meteorological data and historical records of similar incidents over the past century, to identify thresholds for flooding initiation both before and after fires. By focusing on this topic, we hope to shed light on the long-term consequences of fires on communities and initiate a dialogue about the ongoing risks they face.

This research project explores relationships between queer activist organizations and the business community in Portland, Oregon, during the early 1990s. By examining the fight against Ballot Measure 9, which would have curtailed LGBT rights in Oregon if it had passed, this paper shows how queer activism was shaped and developed during the late 20th century, by both internal and external concerns. As they led the charge against Ballot Measure 9, queer organizations in Portland actively sought to engage businesses for their monetary support and tacit endorsement of LGBT rights. By comparing and contrasting the experiences of one queer organization that was developed specifically for this fight and one that had long-standing grassroots ties, this paper illuminates the scope and variety of queer-business connections. My focus on the opposition movement to Measure 9, composed of queer organizations and their business allies, also demonstrates the critical nature of these alliances to the political success of queer organizations, starting in the 1990s, with an impact reaching well beyond the specific context of this specific ballot measure. This project, centered around extensive archival research that was supported by Pacific Lutheran University’s Benson Summer Research Fellowship, offers a new layer of understanding to American queer activism during this period, with implications that still shape current-day affairs in both the U.S. queer community and the U.S. business community.

Essentialist beliefs about gender modality, which conceptualize being transgender as an inherent and unchanging aspect of an individual, stand in contrast to perspectives that emphasize the social construction and fluidity of gender identity. These contrasting beliefs about the transgender identity are meaningful, as they shape the attitudes and behaviors among and towards trans individuals, who historically and currently face discrimination. To understand how trans people make sense of both cisgender and transgender individuals’ beliefs about the trans identity, I am conducting 12 semi-structured interviews with University of Washington students ages 18-25 who identify as transgender and/or non-binary. I analyze how specific assumptions, expectations, and cognitive worldview perspectives impact experiences and identity formation through a double consciousness perspective, a concept that has adapted from the writings of W.E.B. Du Bois about the impacts of racism. Double consciousness is an instinctive social awareness to uphold two identities, one that is “true” to oneself, and one that is constructed to conform in accordance to societal expectations in an act of self-protection. This can lead to feelings of inauthenticity and loneliness in a society that has rigid expectations for how gender should be represented. Therefore, certain assumptions and essentialist explanations about the social category of transgender, may motivate trans people to hold an additional social awareness to anticipate how cis people will react to their identities under the cis gaze. My data provides insight into the forces behind trans prejudice and offers transphobia mitigation recommendations, while centering transgender and non-binary voices in the research. Additionally, this research provides theoretical contributions, important for understanding the processes motivating essentialism and double consciousness. I conclude with directions and suggestions for future research.

The Molecular Case Network (MCN) connects biology and chemistry educators and fosters collaboration to create narratives that enhance interdisciplinary teaching and learning while providing support for their professional development. This research presents a case study of 10 MCN participants who were interviewed about their experiences creating interdisciplinary educational case studies to implement in their courses. These lessons aid the teaching of the content material and technology in a real-world context. These educators are considered expert participants and bring diverse perspectives and experience, allowing them to contribute unique ideas and create multifaceted case studies. Our objectives are to articulate the definition of molecular storytelling through the instructors’ perspective, gauge the instructors' confidence in the interdisciplinary teaching of biochemistry, and examine their self-efficacy in implementing the molecular case study with technology. We used a thematic analysis when looking at the interviews to identify common sentiments and refine them into themes to better understand the relationship between the participants' experiences. Through analysis of the interviews with the participants, we found major themes about the usefulness of technology and the importance of a strong leader in building confidence in both the technology and the writing of the case studies. We explore each unique narrative to find what motivates, excites, frustrates, and ultimately leads to the success of each instructor. By exploring these areas, we aim to provide insights that can help improve education in the relevant scientific disciplines. By understanding the factors that influence the success of these educators we hope to inform the MCN to help strengthen and expand their success long term.

Preterm birth is a leading cause of neonatal morbidity and mortality, with intra-amniotic infection and inflammation being major contributors to early preterm labor (PTL). Despite ongoing research aimed at reducing inflammation in neonates, most studies have focused on post-delivery while few have been done prior to delivery. IL-1 is a central upstream mediator of inflammation in the amniotic cavity and the neonate. IL-1 is a key cytokine that is responsible for induction or propagation of the cytokine cascade responsible for PTL. Rytvela, an interleukin-1 receptor antagonist made up of seven D-amino acids, acts as a selective antagonist of IL-1 signaling, which could be used to act as a therapeutic approach to reduce inflammation and prevent PTL. The purpose of this experiment is to determine if interleukin-1 (IL-1) is a key molecular target for the development of antenatal therapeutics to prevent PTL and fetal injury. We hypothesize that Rytvela administered intravenously to the mother will cross the placenta and be detectable in the amniotic fluid and fetal plasma, suggesting that Rytvela could effectively block IL-1 signaling in the fetus and therefore reduce fetal inflammation. Maternal blood plasma samples were drawn at Day 1, 2, 6 and 10 post infusion. To confirm the transfer of Rytvela to the fetus, we used liquid chromatography-mass spectrometry (LC-MS) to detect the drug, looking at integration, peak identification, and backlog pressures to see if Rytvela is detectable in maternal plasma. Rytvela was detected and luminex plates were run to measure cytokine levels. After GBS infection, Il-1 beta and Il-23 concentrations increased. After Rytvela administration, the concentration of the pro-inflammatory cytokines decreased. Future directions will involve measuring cytokine levels at these time points and correlating them with Rytvela infusion to evaluate the drug’s impact on maternal-fetal inflammation

The Kodiak Archipelago in southern Alaska has a rich archaeological heritage that has fascinated archaeologists and local communities for decades. Despite the presence of many archaeological research projects, archaeobotanical remains found during excavation have yet to be analyzed. The archaeobotanical remains recovered from the Kodiak Archipelago have often gone overlooked by archaeologists who considered preservation too poor in the wet climate and focused instead on fauna from shell-midden sites or other cultural artifacts. The Tanginak Spring site on Sitkalidak Island in southeast Kodiak was excavated by University of Washington field schools between 1994 and 2003. It is considered one of the oldest identified sites on the archipelago, dating to 7500-6000 cal BP. Sediment samples taken during these excavations were retrieved, floated, sorted, and identified by the archaeobotany class at the University of Washington. This poster presents the initial results of the analysis of wood charcoal and other preserved plant remains from the site, providing evidence to develop new insights into plant use by Kodiak’s earliest settlers.

Pregnant women infected with influenza A virus (IAV) are at higher risk of morbidity, mortality, and poor fetal outcomes. However, the difference in the pathogenesis of IAV between pregnant women and non-pregnant women remains inadequately understood, primarily due to the lack of animal studies that use a translational model of infection. I hypothesized that higher IAV viral load and Type I interferon concentrations would be observed in the lungs and bronchoalveolar lavage of pregnant pig-tail macaques compared to non-pregnant macaques, and that correlating these metrics would yield different results across groups. We inoculated pregnant (n=11) and non-pregnant female (n=18) pig-tail macaques (Macaca nemestrina) with IAV H1N1 (A/California/07/2009) and euthanized them at 5 days post-inoculation, when we expected to observe peak lung pathology. We tested pulmonary function at baseline and study endpoint and conducted clinical assessments daily. I extracted RNA and performed quantitative polymerase chain reactions on the samples to calculate viral load. I also performed enzyme-linked immunosorbent assays to quantify concentrations of Type I interferons (IFN-α, IFN-β). Lastly, I analyzed pulmonary physiology data and clinical assessment scores as a reliable measure of disease severity. A bi-modal distribution of viral load was observed in the lungs of pregnant animals (high>9e5 copies/mg; low<2e4 copies/mg), which was not observed in non-pregnant animals.  When correlating viral load at 5 days post-inoculation with Type I IFN in the lung of the pregnant animals, I found a significant positive correlation between IFN-β and viral load in both the lungs (ρ=0.8, p=0.03) and BAL (ρ=0.9, p=0.02). These results suggest that despite a strong IFN-β response in the lung, a high viral load persisted in the pregnant animals. Next steps could explore whether the kinetics of the pulmonary innate immune response is delayed in pregnancy, which impairs viral clearance. 

Understanding the ecology of vegetation systems in Earth’s past in response to past warming events helps contextualize how they might respond to current climate events. Ecological succession is an ecosystem dynamic in which plant species with different life strategies replace each other as plants colonize a disturbed habitat. Reconstructing which successional stage a fossil plant represents is an important step in reconstructing this process in the past. However, fossil plants preserve a limited number of traits. Leaf vein density (LVD) is a trait that relates to maximum photosynthetic rates and can be measured from fossil leaves, but there is limited empirical evidence for how it varies across succession in temperate deciduous forests. To address this knowledge gap, our study measures LVD of modern plant communities across a successional gradient in western North Carolina. We hypothesize that plants in younger forests have greater access to sunlight due to a less established canopy and will therefore have higher LVD to support a higher photosynthetic rate. As succession progresses and the canopy closes, we hypothesize that LVD will decrease with reduced light availability. Samples were taken from five sites in western North Carolina that vary in how long forest re-growth occurred following clear-cut timber harvesting, 4, 21, 44, 94, and roughly 200 years. At each site, leaves were collected and sampled at a community scale and were chemically treated to create images that highlight the veins. We then used ImageJ to measure LVD. The community mean and variance of LVD across succession will be analyzed, using both unweighted and weighted approaches, to test our proposed hypothesis of decreasing LVD through succession. Preliminary results suggest a potential LVD decrease as hypothesized but driven more by understory species rather than dominant tree species. Future work will refine interpretations and consider implications for the fossil record.

The Miocene Climatic Optimum (MCO) (17-14 Ma) represents the most recent significant global warming event and provides valuable insights into the future of our planet with higher CO2 levels and warmer temperatures. The Mascall Formation in central Oregon contains a fossil plant assemblage that reflects the vegetation present during the height of the MCO. Despite over 50 years of research in this formation, there is still much to learn about the ancient plant community. For instance, a fossil specimen, consisting of several leaves, that was collected recently exhibits similar trait to bamboo, which represents a new fossil finding in this formation. This project seeks to confidently assign this specimen to the bamboo subfamily Bambusoideae. By analyzing morphological and vein architectural features of the leaves using various microscopic techniques and digital photography. In addition to studying the specimen itself we explore the fossil plant silica bodies (phytoliths) also present in the surrounding substrate to provide independent evidence that bamboo was present in the region. The phytoliths can then be compared to those of current Native American bamboo to find evidence for relatedness or if it was part of some other lineage of bamboo, whether extinct or still present in South America or Eastern Asia. If the specimen turns out to be bamboo, it would have implications for the climate and ecology of eastern Oregon during the MCO as bamboo was not assumed to have previously been present.  

Overdose deaths in the United States have rapidly increased in the past few years accounting for over 107,000 deaths in 2022 with more than half being attributed to the co-usage of opioids and stimulants. Despite the prevalence of polysubstance use, research has predominantly focused on single substance use, leaving a gap in knowledge regarding its neurological effects. Addiction-associated behaviors such as drug-seeking, drug-taking, and relapse vulnerability has been attributed dysregulation of the striatum. We recently found that polysubstance exposure to methamphetamine and fentanyl leads to behavioral differences in methamphetamine-seeking but not fentanyl-seeking relative to single-substance rats, suggesting that polysubstance use causes distinct changes in striatal circuitry. Our overarching objective is to determine to what extent pursuit of methamphetamine and fentanyl involves shared neural pathways. How do distinct striatal neuron subpopulations responsive to either methamphetamine or fentanyl regulate drug-seeking in animals exposed to both substances? To investigate this, rats are placed into self-administration boxes and undergo two phases of daily intermittent access drug self-administration. In the first phase of self-administration, lasting 10 days, a novel targeted recombination in active population (TRAP) technology and recombinant viral vector is used to target inhibitory designer receptors exclusively activated by designer drugs (DREADDs) to striatal cells that are activated during fentanyl- or methamphetamine-seeking. For the second phase of the experiment, lasting 28 days, rats are then divided into groups for either self-administration of methamphetamine, fentanyl or a polysubstance model. Using chemogenetic manipulations in polysubstance rats, we will test the hypothesis that inhibition of the striatal neuron subpopulations active during fentanyl-seeking will decrease methamphetamine-seeking whereas inhibition of methamphetamine activated neurons will have no impact on fentanyl-seeking. These experiments will provide important insights and lay the groundwork for future studies into how striatal circuits regulate behavior during single and polysubstance use of opioids and stimulants.

Prostate cancer has a significant heritable component. It is estimated that 10-15% of patients with advanced prostate cancer carry an inherited predisposing genetic mutation, and these patients generally present with a younger age of onset and a strong family history of cancer. The standard in the field of oncology is to conduct short-read DNA sequencing on such patients to find predisposing mutations. While short-read sequencing does well to identify simple mutations that cause disease in many families, our lab concluded that short-read sequencing misses critical mutations in many prostate cancer susceptibility genes. We hypothesized that prostate cancer in many families is due to complex inherited mutations such as genomic deletions, inversions, and mobile element insertions that are not detectable by conventional genomic technologies such as short-read sequencing. To test this hypothesis, our lab specifically recruited prostate cancer patients who, despite having family histories of cancer, did not have any mutations detected via conventional genetic sequencing methods. This project utilizes Nanopore long-read DNA sequencing, which reads DNA in longer fragments and can reliably detect complex mutations. My role is to conduct long-read sequencing on DNA samples from these patients, then analyze the DNA sequence for mutations. I have sequenced 32 patients so far and identified 4 complex mutations through long-read sequencing which were missed by other approaches. These complex mutations include insertions of repeat sequences and duplications which disrupt gene function in BRCA1 and BRCA2. This suggests that, consistent with our hypothesis, some patients who do not have mutations found via conventional sequencing methods do indeed carry causative mutations in well-established prostate cancer risk genes. By finding these mutations, patients can receive more targeted and effective cancer treatment, and undiagnosed family members stand a better chance of catching cancers at earlier stages.

My project intends to discover a DNA aptamer, a single stranded DNA oligonucleotide, that binds selectively to the protein Interleukin-6 (IL-6). IL-6 has an important role in the immune system response and in excess it is known to cause inflammation. Aptamers exhibit binding affinities like that of antibodies but are ~50 times cheaper to produce. The method of aptamer discovery is through SELEX (Systematic Evolution of Ligands by Exponential Enrichment) which involves the selection from an aptamer library that contains 52N random nucleotide region and constant 5’ and 3’ 18 base pair regions for PCR amplification. Positive and negative selection are completed by incubating aptamer libraries with IL-6 or random protein immobilized on magnetic beads respectively. After each round selected aptamer sequences are amplified with a polymerase chain reaction (PCR) with primers that anneal to the constant regions. Reverse primer has biotin on 5’ end that is used later for strand separation with streptavidin agarose. After each round aptamer pool is going to be sequenced using nanopore sequencing platform till the enrichment of IL-6 specific sequences is observed. Binding will be tested through an enzyme-linked immunosorbent assay (ELISA) using the fam on 3’ end. The end goal of this project is to design a cost-effective method of IL-6 depletion from patients blood, allowing for cost-effective method of treatment for overactive immune system inflammation in sepsis patients.

Cyberbullying is repeated, intentional harm inflicted through digital platforms, including social media, messaging apps, and online forums. Most researchers focus on cyberbullying in adolescence, but it continues into adulthood. Young adults (ages 18–25) undergo major life changes and use social media frequently, which increases their risk of experiencing cyberbullying. LGBTQ+ individuals, especially transgender and non-binary people, face higher rates of online harassment. Cyberbullying can lead to severe mental health issues, including depression, anxiety, and social isolation. While existing research focuses on cyberbullying among LGBTQ+ individuals as a broad group, few studies examine its specific impact on transgender and non-binary people. This study employs a mixed-methods approach to investigate cyberbullying in transgender and/or non-binary emerging adults. A survey of transgender and/or non-binary participants aged 18–25 will be conducted using a modified Cyberbullying Victimization Scale to measure three types of victimization: Verbal/Written, Visual/Sexual, Social Exclusion/In-Person Bullying. Participants will report experiences in public online spaces and private online spaces. The study will collect demographic data such as gender identity, racial or ethnic background, level of outness, and social media usage to examine correlations between these factors and cyberbullying experiences. By integrating statistical trends and personal narratives, this research will provide a deeper understanding of cyberbullying in transgender and non-binary communities. The findings will inform social media policies, platform safety measures, and mental health support efforts for LGBTQ+ individuals navigating online harassment.

Leigh syndrome (LS) is the most common pediatric mitochondrial disease, manifesting in the first year of life and leading to early death due to a lack of proven therapies. Like other mitochondrial diseases, LS is caused by gene mutations impacting proteins essential for the mitochondrial respiratory chain, including all complexes. Mutations in NDUFS4, a gene that encodes a subunit critical for structure and stability of complex I, have been linked to LS. Mice with the whole-body NDUFS4 KO exhibit major LS symptoms, particularly epilepsy, along with psychomotor deterioration, progressive neurodegeneration and premature lethality (~P60). Our earlier findings showed that mice with Ndufs4 KO specifically in GABAergic interneurons (Gad2-Ndufs4-KO) exhibit the severe epilepsy and sudden death observed in the global KO mice. These mice represent an excellent model of LS epilepsy, isolated from other clinical manifestations of the disease. LS related epilepsy is often very difficult to treat and indicative of poor disease prognosis. Chronic hypoxia therapy (CHT) has previously shown promise in improving survival and reversing neurodegeneration in LS mice. Yet its impact on seizures remains unknown. In this study, we investigated the efficacy of CHT in ameliorating the epileptic phenotype. Mice with LS epilepsy demonstrated a longer lifespan when exposed to  normobaric 11% O2 than normoxia from postnatal day 35 to day 70. Upon return to normoxic conditions, mice kept in chronic hypoxia die within days. In addition, preliminary thermal seizure tests show an increased thermal seizure threshold in hypoxic mice compared to normoxic ones.  Future studies will evaluate CHT impact on spontaneous seizures using video EEG technique. Our study will aid in the development of a novel therapeutic approach for seizures and related death in Leigh syndrome.

Cervical traumatic spinal cord injury (TCSCI) is a devastating condition that leads to tetraplegia, severely impairing essential life functions and independence. Individuals with cervical TCSCI struggle with hand function, reaching, eating, grasping, and writing, significantly reducing their quality of life. In the U.S., cervical SCI is the most common type of spinal injury, affecting over 300,000 individuals, with approximately 17,900 new cases annually. The long-term disability resulting from TCSCI often necessitates continuous medical care, rehabilitation, and assistive technologies to enhance functional recovery. Our preclinical study evaluates upper extremity dysfunction in rats following cervical TCSCI using behavioral assessments, specifically the Forelimb Reaching Task (FRT) and the Irvine, Beatties, and Bresnahan (IBB) test. These tests provide valuable insights into motor impairments and recovery over time. FRT assesses shoulder movement and fine motor control by placing the rat in a transparent box with side slits, allowing it to extend its forelimb to grasp a chocolate pellet. The grasping behavior is scored on a standardized scale. This test primarily evaluates digit precision and reaching ability. IBB provides a broader analysis of forelimb function, including both proximal and distal limb recovery. In this test, the rat is placed in a cylinder with food, and its grasping and eating behavior are recorded. Forelimb function is later evaluated based on elbow position, paw support, forepaw placement, and digit movements. By comparing these tests, we aim to determine their efficacy in assessing functional deficits and recovery post-SCI. This analysis is critical for refining behavioral assessments and guiding the development of new therapies to enhance motor recovery and improve the quality of life for individuals with cervical SCI.

Although 911 is a universally accessible emergency service for anyone in the United States, civilians utilize the service at different rates. Some people are quick to call over minor issues better suited for the non-emergency line, whereas others are hesitant to call 911 even if a crime has occurred. Existing research suggests that comfort with using 911 and other emergency services varies by social and neighborhood factors, yet the mechanisms shaping this variation remain underexplored. Additionally, social disorganization theory, a theory in the criminology field that hypothesizes that community factors contribute to crime,  suggests that socially disorganized neighborhoods, characterized by low economic opportunity, high residential mobility, and ethnic heterogeneity, contribute to crime and deviance. Drawing on 911 dispatch data from the City of Seattle and neighborhood-level socioeconomic indicators from the American Community Survey (ACS), this study empirically tests the relationship between median neighborhood income and 911 call rates, with homeownership as a potential moderating factor. Using regression analysis, this research evaluates whether social disorganization influences emergency service use in a way that mirrors its impact on crime, with an expected pattern of higher reporting rates in both lower- and middle-income neighborhoods This study is crucial because findings can inform police reform, improve community outreach in Seattle, and provide the basis for future research to further inform the relationship between report rates and neighborhood characteristics in other major metropolitan cities in the United States.

The activation of inflammasomes is a crucial component of the early immune response to pathogens and initiates a form of inflammatory programmed cell death called pyroptosis. During infection, a cytosolic inflammasome-forming protein sensor detects a pathogen to assemble the inflammasome complex, which subsequently activates the protease Caspase-1 (CASP1). CASP1 processes Gasdermin D (GSDMD), inducing pyroptosis through pore formation in the plasma membrane, while also facilitating the release of proinflammatory cytokines, such as IL-1β and IL-18. Adenovirus (AdV) is a common pathogen that causes inflammatory symptoms by infecting multiple mucosal epithelial tissues in the respiratory tract and intestinal tract such as the nose, mouth, and eyes. We wanted to test whether AdV infection could activate one of the main inflammasome sensors in human conjunctival epithelial cells (hCjE cells), which is NLRP1. However, we found that upon AdV infection, NLRP1-mediated cytokine release is absent, suggesting that CASP1 signaling is suppressed. Interestingly, despite the loss of IL-1β and IL-18, pyroptosis remains unaffected. Recent studies indicate that in the absence of CASP1, inflammasomes can activate Caspase-8 (CASP8), leading to the cleavage of Caspase-3 (CASP3) and Gasdermin E (GSDME), resulting in an alternative, incomplete form of pyroptosis. Thus, I hypothesize that during AdV infection, host cells are still able to induce pyroptosis by activating the alternative CASP8-GSDME pathway. To test this hypothesis, we generated and validated genetic knockouts of CASP8, GSDMD, GSDME, and CASP3 in hCjE cells to assess their roles in pyroptosis during AdV infection. These findings will provide new insights into viral immune evasion strategies and inflammasome regulation in epithelial cells.

Recent research shows the lux operon utilized with in-vivo bioluminescence imaging to detect infectious diseases in animal models. Modifications to this operon led to the development of enhanced bioluminescence in Escherichia coli cells. However, expression of this operon has not been optimized for expression in other bacteria, such as Staphylococcus aureus. This study aims to optimize the lux reporter gene expression for Staphylococcus aureus, so luminescence is bright enough to register without specialized equipment. To date, the research has explored Gibson Assembly for cloning the gene sequences into a shuttle vector and efforts to modulate gene expression to reduce toxicity in E. coli.

Load carriage is a human universal used to transport children and other resources (e.g., water). Load placement (e.g., back or side) can vary, which influences an individual's gait. Previous studies have assessed the energetic cost of center-of-mass placement  (COMP) and head-load placement (HLP), but the kinematic changes during combined loads are less understood. Lumbar bending and arm swing amplitude were collected from participants (N=19) using OpenCap as they walked for four load conditions: unloaded (UL), back-loaded (BL), back-loaded-with-empty-bucket (BEB), and head-loaded (HL). All loaded conditions were 7.3kg, approximately 10% of the participant's mass. Conditions were differentiated as COMP (BL) or HLP (BEB and HL). Participants were not habitual head load carriers and used one arm to support HLP (one arm swing). Normal arm swing was maintained for COM conditions. Using a multifactorial ANOVA, COM induces lumbar flexion while HLP induces lumbar extension (p=0.011). Additionally, a difference in arm swing amplitude was found (p=0.058). Normal arm swing (COM) had low swing amplitude while one arm swing (HLP) had a high amplitude, with the highest arm swing occurring during BEB. These findings imply that even when loaded mass is the same, different load positions are associated with kinematic changes that will have important energetic impacts and the potential for changes in skeletomuscular changes particularly via lumbar extension. These data are specifically relevant to understanding the demands placed on individuals around the world who carry water and/or children for long distances, particularly in places experiencing extreme drying during climate change.

Syphilis, caused by the bacterium Treponema pallidum, remains a major global public health concern despite the availability of curative treatment. Cases in the U.S. have increased by nearly 80% since 2018, and congenital cases have skyrocketed by 937% since 2014. Currently, a variety of treponemal and non-treponemal tests exist for syphilis diagnostics. Still, they can be limited by high costs, false positive and negative results, and an inability to distinguish between current and prior infection, depending on the test. Further, the fragility and low protein content of T. pallidum’s outer membrane, coupled with its nature as an obligate pathogen, exacerbates the difficulty of conventional approaches to proteome characterization. Current assays are ultimately incapable of characterizing a high-resolution immune response to T. pallidum in humans. Here, we introduce a phage display and immunoprecipitation sequencing (PhIP-Seq) platform capable of identifying antibody epitopes across the entire T. pallidum proteome. This platform allows for the profiling of antibodies that bind to linear B-cell epitopes. This can further the current understanding of antigenic proteins within T. pallidum, their ability to elicit an immune response in humans, and reveal antigens with the potential as a diagnostic. Utilizing 40 single-draw serum samples from syphilis-infected patients in Peru and Seattle, we characterize how antibody responses differ based on syphilis stage, HIV status, and strain of the infection, and have identified four proteins - TP0136, TP0969, tprK, and arp - as being highly enriched across all patients.

During embryonic development, gene expression is temporally and spatially coordinated to control organogenesis and fetal growth. We previously identified a subset of 140 genes that conferred lethal and sub-viable phenotypes in mice and are likely to be haploinsufficient in humans. These genes presumptively play essential roles in fetal development, but their function is unknown. I aim to uncover the role of these genes in mouse embryonic development using Weighted Gene Co-Expression Analysis (WGCNA). Co-expression analysis will be conducted on mouse embryonic stem cell RNA sequencing data obtained at three different stages of in vitro differentiation and across two different genetic backgrounds, creating a subset of nine samples encompassing 12555 genes. Choosing three different time points allows us to see how expression of our genes of interest changes over time, and choosing two different genotypes (wild type and knock-in) allows us to investigate if expression changes due to a single point mutation. We performed dynamic clustering on this RNA sequencing data to identify co-expressed gene clusters. I will map these gene clusters to biological pathways to make inferences about which cellular processes, metabolic functions, or structural components the genes of interest are involved in. This may indicate the role of these genes in fetal development and help reveal why fetal viability is compromised. In future studies, the functional characterization of these genes will generate new ideas and hypotheses about the basis of genetic disease.

Our sense of touch plays an important role in how we perceive the world. Touch sensation is the result of an intricate interplay between the nervous system and specialized sensory cells in the skin, one such example being the Merkel cell-neurite complex. Within the Merkel cell-neurite complex, Merkel cells (MCs) detect gentle touch signals in the skin and relay them to innervating neurites via synapse-like connections. Many aspects of the MC-neurite complex, including the molecules required for its formation and structure, remain poorly understood. Our lab recently discovered the presence of MCs in the transparent zebrafish skin, making the organism well-suited for study of MC-neurite complexes. Here, we show that Protocadherin-9 (pcdh9), a cell adhesion molecule important in synaptic structure and nervous system organization, is highly expressed in both zebrafish and mammalian MCs. Using a loss-of-function mutation in zebrafish pcdh9, we find a reduction in the number of MC-neurite complexes, but not in the number of MCs, compared to controls. This suggests a role for Pcdh9 in either the formation or maintenance of MC-neurite synapses. Additionally, we observe a higher rate of MCs contacting one another in pcdh9 mutant skin, consistent with a difference in MC spatial organization. In summary, our data indicate that Pcdh9 may regulate one or more aspects of MC-neurite complex formation. We are now in the process of developing tools to further investigate and quantify MC spatial arrangement, and to uncover the ways in which Pcdh9 may affect MC maturation and behavior.

My research is focused on the question of "Why do first-generation Indian Sikh immigrants return back to their origin country?" I am researching about why some migrants return and others do not, specifically the factors that influence the decision-making. My initial research showcased economic motivations being parallel to initial migration as well as return to one's origin country, along with the the influences of the labor market. I hypothesize that return migration in India is driven by the same realities that drive emigration, namely opportunities to develop economically. I conducted qualitative interviews with Indian Sikh immigrants, both those who had returned back to India along with those currently living in a destination country. The subjects were identified through established social personal networks and participants were screened through questions about their migration journey and if they identified as Sikhs. My project is still in progress, however I have completed more than half of my intended goal for qualitative interviews. My preliminary findings suggest that the primary reasons for migration out of an origin country and returning back relates to economic motivations. However social factors, such as conflicts within the origin country and discrimination in the destination country also impact the decision-making processes and intentions of return. The findings of this research are impactful within migration studies, especially as return migration is a relatively new field that is constantly developing. The case study of Sikh Indian Immigrants has not been researched extensively in the past, showcasing why identifying the various factors influencing motivations and intentions is crucial when understanding the patterns of migration. 

Building on the literature of the importance of strategy, this paper explores the relationships between wealth, strategy, and battle related deaths to find out why we may see unexpected conflict outcomes like Ukraine being able to hold back Russian offensives. This paper argues that wealthy actors often use expensive strategies, like strategic air bombing, that are ultimately ineffective at helping win a war and only cause unnecessary casualties, and that less wealthy actors are forced to be more creative with their strategies and this leads to less casualties. To do this, I analyze the relationships between data on rebel contraband (proxy for non-state actor wealth), GDP, and strategies used in war and their effect on battle related deaths. The paper will also cover the ongoing conflicts in Myanmar and Ukraine as a theoretical supplement to this data. Examining these relationships is increasingly important because wars fought in the modern era often see different sides of varying wealth using different strategies. Implementing the discoveries of this paper may give us opportunities to minimize casualties in conflicts by looking at what strategies are the least lethal at what levels of wealth.

Direct Analysis in Real Time Mass Spectroscopy (DART+ MS) is a chemical identification tool that uses a superheated gas stream to ionize chemical samples, producing a distinct chemical signal that can be used to identify the composition of an unknown sample. DART+ MS is used reliably in fields like forensics, food safety, pharmaceuticals, and more recently, environmental protection. At the Wasser Research Lab, at the Center for Environmental Forensic Science, we work to protect endangered species such as African Elephants. Using Direct Analysis in Real Time Mass Spectroscopy, we seek to find if elephant ivory from different regions in Africa has distinct chemical signatures, allowing us to geolocalize ivory samples based on their DART+ MS signatures. Current methods of elephant geolocation include genetic testing, but results can often be ambiguous; By using this completely different, complementary approach, we could improve our estimates of these inconclusive tests. If there is a chemical difference in the ivory of Elephants from the Savannah and Forest regions of Africa, then we can trace the origins of ivory obtained from illegal seizures, aiding in the conservation efforts of African elephants. Chemical distinctions aside, we also hope to answer questions about the effects of certain chemical preservatives on ivory samples and whether the DART+ MS signal varies along the length of the cut of the tusk, establishing best practices for sampling. Ultimately, our goal is to determine if DART+ MS proves to be a reliable and quick method of identifying elephant ivory for conservation efforts. By bridging cutting-edge technology with conservation science, we hope this research will make a significant impact on efforts to combat the illegal ivory trade and wildlife crime. 

Skin serves two key functions: hardened cells at the surface of the skin form a superficial layer to protect against the environment, while the inner layers of the skin are packed with diverse sensory machinery which allow us to perceive and navigate the world. Incredibly, the basal most layer of the epidermis houses stem cells which allow the skin to constantly renew itself, fortifying its protective function and maintaining somatosensation by replenishing all these diverse cell types. Perhaps unsurprisingly, these multipotent and highly active skin stem cells are emerging as an effective way to treat genetic skin conditions, promote wound healing, and rejuvenate ageing skin. To understand how skin stem cells contribute to these different functions, investigators are studying the many niches within the skin which may house diverse skin stem cells. Zebrafish are an excellent model to dissect this topic due to their translucent skin and the many genetic tools available. However, the anatomy and molecular characteristics of zebrafish skin is poorly described. Recently, we performed single cell RNA-sequencing of zebrafish skin and identified seven presumptive skin stem cell subpopulations. Informed by this data, I performed whole-mount hybridization chain reaction, a form of in-situ hybridization, to investigate molecular and spatial heterogeneity in zebrafish skin stem cells. My results have identified three novel skin stem cell subpopulations which occupy distinct spatial domains along the anterior-posterior axis. I found that the appearance of each subpopulation and the establishment of their spatial domain is dynamic throughout skin development. Finally, we have constructed a tool to interrogate their behavioral and functional differences. Moving forward, I aim to determine each subpopulation’s role in skin development, homeostasis, and regeneration, as well as whether they serve as specific progenitors for certain cell types.

The El Niño-Southern Oscillation (ENSO) is the most significant year-to-year climate variation, affecting weather and climate systems worldwide. However, current prediction models, both dynamic and statistical, struggle with accuracy due to the complex mechanism of ENSO. This study introduces a regional temperature and salinity prediction method using a Long Short-Term Memory (LSTM) deep learning model, which is well-suited for identifying long-term patterns in sequential data. The model is applied to three specific regions using in-situ data from Argo floats: the central-eastern Pacific, the central tropical Pacific Niño 3.4 region, and the Western Pacific Warm Pool (WPWP). These regions are chosen because they play key roles in ENSO dynamics. Results show that the LSTM model performs best in the WPWP, where the average mean squared error (MSE) is low (0.03), indicating high accuracy and stability. This is likely due to lower noise in the original data. In contrast, the model performs poorly in the central-eastern Pacific, where the average MSE is much higher (7.03), suggesting instability due to high noise in original data. These findings highlight the potential of deep learning for regional climate predictions and suggest that LSTM models could improve local weather forecasting and fisheries management.

Oceanic currents drive all the world’s major climatic, biological, pollutant and sediment transport patterns. Many complex forces interact to produce the intricate movements of the ocean’s waters. Tidal rectification, a phenomenon caused by the spinning reference frame of the Earth acting together with island geometry and friction, is one such process which dictates how water is circulated around islands, seamounts, and other bathymetric shapes when tidal oscillations are present. Tidal rectification has been described mathematically and compared with physical measurements for many islands, but these islands fall into a few distinct categories. Many are either large and restricted to central latitudes, or small in diameter and found in far northern latitudes. Non-Island formations, such as guyots, and smaller bathymetric features in more central latitudes are not rigorously characterized through the lens of tidal rectification. This study expands the practical characterization of tidal rectification by comparing current speed data around a guyot near Namonuito Atoll, south of Guam, to a theoretical scaling of the potential forces acting on the guyot. I hypothesized that friction-based circulation would dominate over Coriolis-based circulation due to the guyot’s low latitude. Current velocity data was collected along a circular transect around the guyot by the R/V Thomas G. Thompson in December 2024. Preliminary findings, based on a scale analysis, suggest that these two cases are difficult to distinguish. Further research is needed to derive the nature of rectified circulation for small low-latitude islands. A rigorous practical analysis of the effects of tidally-rectified circulation is critical for a deeper understanding of biological processes, sediment transport, and pollutant concentrations around island communities.

The world’s oceans are witnessing a surge in plastic pollution, a consequence of human activities and the growing urbanization of coastal regions. Urban estuaries are complex habitats that are especially good at trapping sediment, carbon, and pollutants, such as plastics. However, our understanding of the extant of plastic accumulation within estuarine sediments remains limited. We determined the first quantification of the total amount of microplastics (>5 mm) in Main Basin Puget Sound, WA – a heavily urbanized estuary – and identified deposition hotspots related to current hydrodynamics. To measure plastic concentrations, we collected both shoreline and shipboard sediment samples and density extracted microplastics using an NaI solution. Extracted plastics were counted and categorized under a microscope. To complement these plastic analyses, energy of the environment was determined using both grain size analysis and extraction of current velocities from LiveOcean, a hydrodynamic model of Puget Sound. We found that plastic concentrations are the highest near land-water interfaces, which are correlated with human population. A range of 50-716 particles per kilogram of sediment was recorded in bottom samples and as much as 1180 particles/ kg were found in shoreline samples. The dominant source of microplastics came from fibers shed from clothing, giving a well-sorted particle size distribution. Furthermore, using the plastic concentration data we developed a predictive model of plastic distribution that relies on Puget Sound currents and could be adapted for other estuarine systems. Providing a comprehensive analysis of the sources and sinks of microplastics in main basin Puget Sound that can be used to inform preventative management on the negative impacts of urban waste.

Discharge planning is an important component of safe and efficient hospital care. We are interested in how patients who live in a baseline unsafe situation conceptualize a “safe” discharge plan. Thus, our study aimed to understand the needs, perspectives, and priorities of patients experiencing homelessness as they prepare to leave the hospital. We conducted qualitative semi-structured interviews in 2023-2024 at a large urban, public, safety-net hospital in the Pacific Northwest. Any adult patient admitted to an acute care general medicine service who was living homeless was eligible. Patients with severe cognitive or mental health disorders that precluded consent process were excluded. This study was approved by our institutional IRB. Patients experiencing homelessness shared their perspectives on discharge planning in three major themes: 1) basic needs, 2) barriers to stability, and 3) role of healthcare systems. Within the theme of basic needs, respondents identified the importance of physical survival: shelter/warmth, protection from violence, and treatment for major injuries or illness. They identified key barriers to stability: loss of property, legal concerns, and financial challenges. While many respondents were hopeful that the role of the healthcare system might be to assist in these issues, they also acknowledged the existence of significant resource constraints. Many reflected on the way that U.S. society views poverty and the impact of policy and funding to what is feasible by healthcare providers. Several participants were aware of interventions that the healthcare system puts into place to achieve better outcomes but noted these may still be out of reach when basic needs are not met. We found that patients experiencing homelessness were overwhelmingly focused on achieving their basic needs, including physical survival and environmental stability. Current discharge processes should be tailored to individual lived experiences, especially with regards to housing status.

Quasars are some of the most luminous objects in the universe. Through analysis of quasar spectra, outflows of gas and dust can be identified by absorption troughs. Outflows that travel at speeds greater than 10% of the speed of light are known as Extremely High Velocity Outflows (EHVOs), and while there have been fewer studies compared to those at lower speeds, they might carry out large amounts of energy due to their higher speeds. The amount of gas in these outflows can be measured and studied through their CIV absorption troughs. However, in some cases, this absorption is contaminated by absorption of other ions at lower speeds. I have developed programming tools to analyze some of these complex EHVO absorption features. I will present the results of applying these techniques to two interesting cases: (1) one of the most luminous quasars in the universe and (2) the fastest known EHVO to date. My work improves the quality of EHVO analysis, resulting in more accurate measurements of absorption of these extreme outflows. This is crucial to obtain better estimates of mass outflow rates and kinetic energies in quasars, of which EHVOs might be some of the largest contributors.

Quasars, located at the centers of distant galaxies, are among the most luminous objects in the universe due to the accretion disks surrounding their central supermassive black holes. By analyzing their spectra, we can observe outflows launched from their accretion disks which grant us insight into their physical and chemical conditions. Some of these outflows, known as Extremely High Velocity Outflows or EHVOs, have been discovered traveling at speeds greater than 10% the speed of light. Due to their extreme speeds, EHVOs carry a significant amount of kinetic energy that could potentially be impacting their host galaxies by either enhancing or quenching their star formation. While outflows traveling at lower speeds have been well studied, there is still much to learn about EHVOs. My project focuses on uncovering the mechanisms that drive EHVOs and the conditions necessary to launch them at such high speeds. To achieve this, I am collaborating with a research team at the University of Nevada, Las Vegas in a theoretical-observational partnership. They generate simulated spectral data of quasar winds using the Sirocco tool, adjusting quasar physical properties such as black hole mass to try and reproduce the conditions that generate EHVOs. We compare these results to observational data from the largest EHVO sample identified in the Sloan Digital Sky Survey’s 16th data release and provide feedback for refining theoretical inputs to better match the data. I will present the results from this work as well as what we have learned from this latest EHVO survey.

Bernini's David (1623) attempted and—in some capacities—succeeded in breaking the barrier between the viewer and the art. David's narrative is only completed through audience participation and then furthered through dialog with the other works displayed in the same space. Bernini's motivation for creating is key to understanding his incessant cultivation of technical skill and his drive to push the boundaries of possibility in Baroque sculpture. The work functions both alone and as a key sculpture in the oeuvre of Bernini. Framing the work with analysis from Wittkower, Wallace, and Lavin, I dissect what made David different from Bernini's earlier sculpture and how David became the precursor for his later work.

Objective. I asses the increased Latino support for Donald Trump and the GOP since 2016, and how the Democratic party was less successful in 2024 with Latinos than in previous elections. Methods. By using a mixed-methods approach that includes an in-depth bilingual content analysis and polling data I can evaluate increased GOP support from Latino voters even under increased threat. Findings. In 2024, Trump demonstrated increased Latino outreach efforts but still failed to capture a majority of Latino voters due to his continued anti-Latino and anti-immigrant rhetoric. However, perceptions of GOP hostility decreased, likely due to rising economic concerns. In comparison, Harris' Latino outreach was much better, however, her policies failed to resonate with Latinos largely due too little to no discussion of comprehensive immigration reform - which typically heightens group identity and thus mobilizes Latino voters. Conclusion. While the media and the campaigns like to discuss the importance of the Latino vote, as they seek their support, the two-party system has left Latino voters behind, effectively ignoring their substantive political wants and needs, increasing the likelihood of a shift of Latinos to the right.

Under India's military occupation, Kashmir has become one of the world's most militarized zones, where systematic human rights violations including enforced disappearances, torture, and sexual violence have been documented. Through analyzing documentary films, visual art, and protest movements, I investigate how Kashmiri women transform individual trauma into collective political action. I focus on two key case studies: the Association of Parents of Disappeared Persons (APDP) and documentary filmmaker Iffat Fatima's "Khoon Diy Baarav." Using ethnographic analysis of films, photographs, testimonies and protest documentation, I demonstrate how these women use memory work and creative documentation to challenge both military occupation and patriarchal structures. The APDP turns monthly protests into spaces for collective mourning while maintaining detailed records that counter official denial. My findings reveal that women's networks employ multiple strategies: preserving memories of the disappeared, creating visual evidence of state violence, building international solidarity through art and film, and establishing alternative archives that document human rights violations. This research contributes to our understanding of how marginalized groups use creative resistance to preserve collective memory and build transnational networks of solidarity under conditions of repression. The implications extend beyond Kashmir to other conflict zones, showing how women's creative activism can effectively challenge dominant narratives while creating powerful spaces for resistance and healing.

Does Universal Basic Income impact educational attainment? Theorists and prior researchers have drawn mixed conclusions on the effectiveness of UBI. While some argue that unconditional cash transfers increase personal goal seeking and human capital investment behavior, increasing educational attainment, others find that UBI negatively impacts educational attainment because it encourages individuals to neglect any investment in their human capital. Despite these arguments, prior research on this topic is extremely limited, which is why it is so important for this paper to investigate these claims. I expect UBI is associated with increased educational attainment because people could use the finances from UBI to support the additional financial and time commitment costs of education. To investigate this puzzle and test my theory, this paper uses Alaska as a case study, as it provides an opportunity to study the effects of UBI through the Permanent Fund Dividend. The Permanent Fund Dividend is a recurring annual payment given to nearly every Alaskan citizen, sourced from the State’s mineral revenue, thus presenting the best large-scale proxy of UBI available to study. This paper will estimate a counterfactual, or synthetic, Alaska without the PFD, which will allow us to infer the impact of PFD on education by comparing real educational attainments with the estimated levels.

This paper explores the significance of U.S. financial assistance to weak democracies and its impact on their political processes, particularly protest movements. In recent history, almost every nation has seen anti-state demonstrations, driven by factors such as war, elections, inflation, or social issues. Domestically, these international conflicts have sparked debate among politicians, scholars, and voters about how U.S. aid should be allocated. While U.S. aid is generally regarded as a stabilizing force that fosters economic growth and democratization, little is known about its influence on political mobilization. Protest as a concept remains underutilized as a mechanism for understanding political dynamics, especially in the context of ongoing global regime changes. This paper examines how U.S. aid shapes protest in weak and transitional democracies. It investigates two competing theories: increased aid either promotes economic stability, discouraging protests, or fosters democratization, which empowers civil society and encourages protests. Using data from transitioning democracies from 1990 to 2020, this research analyzes the frequency of anti-state protests in relation to U.S. economic and military aid allocations.

Neurodegenerative disorders, including Alzheimer’s, are characterized by the accumulation of fibril aggregates—made up of amyloid β-sheet peptides—which were historically thought to disrupt cellular function and contribute to neuronal death. Recent studies have revealed that these plaques are relatively benign; they are preceded by toxic oligomers—peptides that adopt a rare α-sheet secondary structure. These oligomers form decades before the appearance of plaques and have been linked to the neurodegenerative symptoms associated with these diseases. As precursors to full aggregates, toxic oligomers serve as valuable therapeutic and diagnostic targets. Custom peptides designed to bind to α-sheet toxic oligomers can be deposited onto the surface of a well plate to form the basis of a diagnostic assay. Similar to a sandwich ELISA, this soluble oligomer binding assay (SOBA) utilizes a two-antibody system to selectively detect the presence and relative concentration of α-sheet oligomers. In an effort to improve assay repeatability, we attempt to optimize the antibody system used in SOBA experiments. To evaluate assay performance, we test a variety of incubated Aβ oligomer samples and brain homogenates from transgenic mouse models to assess SOBA sensitivity and specificity. In the future, we aim to extend SOBA repeatability studies beyond Alzheimer’s to other aggregation-related disorders, such as type two diabetes and Parkinson’s. By improving the repeatability of this assay, we can enhance early detection methods for Alzheimer’s and related disorders. These experiments serve to develop a standard method for the detection of toxic oligomers, which could pave the way for future neurodegenerative disorder treatments and diagnostic strategies.

Data is the fuel driving AI innovation. Much of the most valuable data is, however, siloed in research centers, hospitals, banks, etc. The onerous processes researchers must go through to access each silo cause a substantial underutilization of AI in many of the most important domains, including healthcare and genomics. AI researchers cannot train models for personalized medicine if they cannot get their hands on enough relevant patient data. One way to provide broader access for research while also retaining the privacy of the original data is with synthetic data generation (SDG), which uses machine learning to generate a set of synthetic data similar enough to the real data to retain its value for research while also anonymizing it. While in some cases a single data custodian (such as a hospital) alone may have enough data to train a generative model, usually, datasets from multiple custodians need to be combined to reach a cumulative size that enables meaningful AI research. The latter is, for example, often the case for rare diseases, with each clinical site having data for only a small number of patients, which is insufficient to train high-quality synthetic data generators. The goal of my research is to generate synthetic genomics data of patients with Neurofibromatosis type 1, a rare genetic condition that causes changes in skin pigment and tumors on nerve tissue. Thanks to our Privacy-Preserving Machine Learning Lab’s inclusion in the National Artificial Intelligence Research Resource (NAIRR) Pilot and our collaboration with Sage Bionetworks, I have access to the TACC Frontera supercomputer at the University of Texas and multiple sets of NF1 patient data. Results of my work on the NAIRR include an empirical evaluation of cross-silo federated SDG algorithms in terms of quality of the generated NF1 data, computational cost, and level of privacy protection.

Nanoparticles are drug delivery carriers on the nanometer-length scale, and are promising targeted drug delivery solutions due to their small size and tailorability. However, current materials used to produce nanoparticles are synthetic and typically lead to large amounts of chemical waste and high costs. To explore more sustainable technologies, the Nance and Roumeli labs established a novel bacterial cellulose nanoparticle (BCNP) platform. BCNPs are formulated with a bacteria that produces cellulose and no byproducts when cultured, allowing for less reagents required and non-toxic biodegradable wastes. To be comparable to synthetic nanoparticles as a drug delivery platform, BCNPs must load and release drugs and be biocompatible with mammalian cells. In this project, I explored the tunability of BCNPs through size modification, performed cytotoxicity studies on a microglial cell line, and carried out drug loading studies. I found that higher mixing speeds during BC culturing led to a smaller BCNP size and variable particle concentration. Through cytotoxicity analysis in cell culture, I showed BCNPs were not toxic. Ongoing studies are assessing BCNP cytotoxicity as a function of BCNP dose. To demonstrate drug loading, I am incorporating catalase, an enzyme with the ability to mitigate oxidative stress markers, into BCNPs to analyze their efficacy in an in vitro model of oxidative injury. These results show BCNPs have the potential to become a sustainable nanomedicine platform and provide an important step towards reducing the environmental impact of synthetic nanoparticles.

Ongoing research towards the realization of the future Solar System Internet (SSI) has demonstrated the potential for using Delay Tolerant Networks (DTN) to create a scalable communications network that overcomes routing complications found in outer space. At present, traditional time synchronization protocols do not scale well in outer space networks, and yet it is unavoidable that some level of time synchronization is required to ensure crucial network functionality (such as scheduled data transmission between nodes) is well supported. The result of this is a necessity to design and implement a scalable, automated time synchronization protocol within the DTN architecture. This presentation covers the development towards one such protocol initially proposed by Moy et. al in 2024. More specifically, we focus on subsequent simulation work with the goal of understanding how implementation details of the algorithm and ramifications of the SSI’s network architecture may affect the convergence behavior of clock times, such as those regarding parameter selection, clustering of nodes in a network, and contradictory setups due to inconsistent knowledge of the network topology between nodes. To address these conditions, we first review the protocol as proposed in 2024. Through simulation, we cover the potential effects of degrees of network clustering and of choosing underlying equation solvers for time convergence on simple network layouts. We conclude with an analysis of a simulation based on the network architecture of a recent DTN experiment campaign involving the International Space Station (ISS). Preliminary results suggest that the convergence of clock times can occur under the tested conditions using the proposed algorithm, but that the convergence behavior and the final “agreed upon” time may differ. These results and future works thereby inspired may be used to inform the scheduling and implementation of the clock synchronization protocol within the network architecture of the SSI.

Hydrogel biomaterials have many applications in tissue engineering and drug delivery. Stimuli-responsive hydrogels allow for controlled drug release, dependent on a user-defined trigger. However, current stimuli-responsive hydrogels are case-specific and cannot be used for broader applications, such as targeted disease treatment. Most hydrogels can only respond to one input, making them difficult to use in treating diseases with multiple markers. We developed a fully recombinant protein-based material with protease degradable cross links that follow Boolean logic (YES/AND/OR) in response to multiple inputs to allow for user controlled material degradation and drug release. The protease degradable sequences can be easily switched out before expression depending on the application, making our hydrogel generalizable. The hydrogel will be crosslinked with Boolean logic constructs, each of which are flanked by a click-like chemistry protein system. This allows the crosslinks to be covalently ligated to a linker made from elastin-like polypeptides (ELP), which holds the hydrogel network together. The crosslinks and ELP were expressed recombinantly in E. coli and purified on an ӒKTA Pure (Cytiva). A degradation study was conducted by adding different combinations of proteases to prove that material degradation is dependent on the combination of proteases added. We then conducted rheometry to determine the mechanical properties of the hydrogels, and verified that material stiffness followed the expected logical operation, where correct inputs resulted in material degradation. Finally, we tested the hydrogel’s ability to release drugs by incorporating human epidermal growth factor (hEGF) into the gel and measuring activation of the ERK signaling pathway through a Western Blot. The Western Blot showed activation of the ERK pathway only when the correct combination of proteases was added, indicating release of a bioactive protein drug. If successful, this hydrogel could be used for therapeutic delivery of drugs and broader tissue engineering applications.

Historically, prosecutors have been elected into office based on their “tough on crime” policies. More recently, there has been a rise in the election of “progressive” prosecutors who run on commitments to criminal justice reform. As these prosecutors have been elected, they have faced extensive opposition due to the surmise that progressive prosecutors lead to higher crime rates. While contemporary research has aimed to investigate whether “progressive” prosecutors lead to rising crime, this literature does not address a vital sociological principle: crime is a social construct. Crime, like other social constructs, are recognized and made meaningful through peoples’ shared beliefs, behaviors, and interactions. Previous research explores the media’s role in constructing crime, but does not address its influence on perceptions of prosecutors and their role in fluctuating crime rates. Our research aims to fill this gap. We do so by analyzing media narratives about a sample of “progressive” and non-progressive prosecutors (our categorization is based on Fair and Just Prosecution, a “progressive” prosecutor membership organization). We did two rounds of flexible, inductive qualitative coding to code the ten “most relevant” articles about each prosecutor based on Google News searches. We found that whether jurisdictions with “progressive” prosecutors truly have higher crime rates is less meaningful to the political implications of prosecutors than the public perception of higher levels of crime. The findings from our study hold implications towards the importance of understanding how media-based perceptions influence political consequences for prosecutors or other actors seeking to advance criminal justice reform. Such points to needed shifts towards more accurate, unbiased portrayals of prosecutors and crime within the U.S., ensuring prosecutors who are desired to represent districts are able to do so.

The Acanthocephala are a phylum of parasitic worms commonly found in the gastrointestinal tracts of mammals and birds. They are dioecious, having distinct male and female sexes. Despite their frequent occurrence, there is little research describing the ratio of sexes in acanthocephalans infecting marine mammals. Understanding the life cycles and life history traits of parasites is important to understanding the ecosystem as a whole. This study aims to determine the sex ratio of Corynosoma spp. infecting harbor seals, which will increase knowledge of transmission and reproduction within harbor seals and potential intraspecific competition between acanthocephalans. The results from this study will be used within a larger project to calculate the energetic burden that endoparasites have on their hosts and help inform seal and parasite conservation efforts. To do this, we will first determine key morphological differences (size, weight, body shape, and number of spines) between the sexes, then count the numbers of males and females present in each seal’s gastrointestinal tract. We will calculate the ratio of male to female acanthocephalans within each individual harbor seal and use those values to generate an average sex ratio for acanthocephalans across all sampled harbor seals. Finally, average weights will be determined for each sex to help confirm if there is a size difference between sexes and determine relative biomass differences across the sexes within harbor seal hosts.

Skin-to-skin (STS) care, in which a baby is held directly against a caregiver’s bare chest, has health benefits. However, preterm newborns born before 32 weeks of gestation commonly do not receive STS in the first two weeks after birth in the neonatal intensive care unit (NICU). Research suggests that early STS reduces adverse outcomes such as life-threatening sepsis and mortality within low- and middle-income countries worldwide. Yet, evidence demonstrating the importance of early STS within high-resourced NICUs is limited. To develop evidence-based guidelines for NICU care, it is necessary to examine the relationship between time until first STS and outcomes such as sepsis and mortality. We hypothesize that earlier STS is associated with lower rates of sepsis and mortality. To investigate this, we conducted a retrospective study of very preterm neonates admitted to a level III NICU in Washington state. Newborns were categorized into three groups based on time until first STS: (1) STS within 72 hours of birth, (2) STS between 72 hours and 7 days, and (3) no STS within the first week. We statistically compared the rates of culture-positive sepsis and mortality rates between these groups while also assessing associations with potential confounding variables such as gestational age, birth weight, and fluid intake. Preliminary findings suggest associations between timing of first STS and outcomes of sepsis and mortality, although confounding factors may bias these results and, thus, require future multivariate models to account for confounding variables and their impact on outcomes. Thus, we are conducting an ongoing study to expand the sample size to overcome these limitations. We plan to evaluate the impact of STS on newborn outcomes among other sites to expand generalizability of findings in the future. Ultimately, research on STS care can help improve hospital documentation policies, neonatal care guidelines, and neonatal health outcomes.

The analysis of microbial communities in compost can help identify key microbes necessary for the breakdown of organic materials into nitrogen and carbon which may help to optimize the decomposition process. We chose hot composting because it efficiently produces richer compost in 2-3 weeks at elevated temperatures in contrast to cold composting alternatives which take a longer time. With pre-established workflows already generated, nanopore sequencing technology will provide a detailed examination of bacterial diversity. This study will consist of three compost piles with samples taken every two days for DNA extraction until the composting is completed. PCR amplification of the bacterial 16S rRNA from these extracts and nanopore sequencing of the amplicons will show the types and abundance of microbes in the compost over time. By monitoring shifts in microbial populations across composting stages in different composting materials, we aim to pinpoint crucial bacterial strains that drive organic matter breakdown and the recycling of nutrients. We expect to see thermophilic bacteria (e.g., Bacillus stearothermophilus and Thermoplasma acidophilum) because their enzymes thrive in high-temperature environments. In the future, we hope to culture these microbes and sequence their whole genome through nanopore technology in order to identify key genomic markers that may contribute to composting efficiency.

Mild hyperthermia - defined as raising the human body temperature to 39-42 Celsius - has been shown to improve the effectiveness of systemic therapies for cancer treatment by improving tumor oxygenation and blood flow. High intensity focused ultrasound (HIFU) is a non-invasive, thermal ablative therapy that can be used to induce mild hyperthermia in a small area around the focus. When used in the presence of microbubbles (an ultrasound contrast agent), referred to as bubble-enhanced heating (BEH) HIFU becomes more efficient and increases the treatment area. Further research is required to study the mechanisms of BEH and better understand the complex relationship between microbubble dynamics and the ultrasound parameters. In this in vitro study, I fabricated gel and liquid tissue-mimicking phantoms to perform heating experiments in. The experimental setup consisted of a focused ultrasound transducer aligned to two thermocouples that were placed inside the phantom, one at the focus and one pre-focally. An imaging probe was used to image the phantoms before and after HIFU exposure. During heating experiments, I measured the temperature of the phantom at a single point via thermocouples for 30 s of continuous ultrasound exposure followed by 30 s after exposure has been stopped. I originally hypothesized that as microbubble concentration increases, the temperature elevation would also increase. However, the results showed that for both the gel and liquid phantoms measured at the focus, a higher microbubble concentration does not always result in a higher temperature elevation. This is due to the phenomenon of acoustic shadowing, where the concentration of microbubbles impedes the propagation of sound through the phantom, altering where most of the heat deposition occurs. Future experiments will be performed to confirm these results and investigate further microbubble concentrations and acoustic pressures in order to optimize BEH treatment for future clinical applications.

Most eukaryotes use histones to package the genome. However, many animals package their sperm genomes using specialized DNA-binding proteins called protamines, which package DNA in sperm more tightly to fit inside the sperm head. Based on the transcriptional silencing role of protamines, we hypothesize that protamines can suppress meiotic drivers, which kill other sperm to bias their own transmission. Previously, we discovered that one protamine gene, Mst77F, is required to suppress meiotic drivers on the Y-chromosome in Drosophila melanogaster. Since drive is generally deleterious for transmitting autosomal alleles due to lower male fertility, theories predict that multiple drive suppressors will arise within populations; Mst77F may represent just one such suppressor. We hypothesized that natural variants in distinct genetic loci interact with as well as impact meiotic drive in Drosophila melanogaster. To identify these natural variants, I crossed wild-type flies to Mst77F knockout flies to generate hemizygous Mst77F flies carrying genetic backgrounds from four different populations. I measured the fertility and drive strength by crossing individual hemizygous males from each genetic background to five wild-type females. Using a genetic crossing scheme, I will test for variation in X-linked targets and Y-linked drive in 5 additional populations. This will reveal insights into the mechanism of Y-linked drive and the basis of X-chromosome susceptibility to drive. My study contributes to a better understanding of the pervasive effects of meiotic drive in natural populations and the unexpected function of protamines.

Alzheimer's disease (AD) is the most common form of dementia. Improper cleavage of amyloid precursor protein by a complex containing presenilin 1 or presenilin 2 (PSEN2) can result in pathological amyloid beta plaques. Recent work from the Valdmanis group found novel PSEN2 RNA isoform variants in AD. Specifically, we identified two PSEN2 3'UTR isoforms - a short (507bp) and a long (3976bp) 3'UTR. The 3'UTR harbors essential regulatory elements such as microRNA binding sites and Alu elements that control transcript maturation, stability, and abundance. Here, we sought to elucidate the functional significance of the PSEN2 3'UTR isoforms. To accomplish this, we completed small RNA sequencing to identify microRNA levels in human AD and control frontal cortex brains and used TargetScan7 to map these reads to the PSEN2 3'UTR isoforms. Our analysis identified 53 miRNAs with significant differential regulation in AD frontal cortex bulk homogenate and 76 miRNAs in purified synaptosomes. One miRNA, miR-34c, was significantly downregulated in both fractions. We identified five different miRNAs with significant regulation changes in AD, including miR-326, miR-346, miR-548p, miR-890, and miR-217. Of note, the long PSEN2 3'UTR had nine miRNA binding sites and two Alu elements, while the short PSEN2 3'UTR only contained one miRNA binding site. We next tested PSEN2 3'UTR isoform localization in human AD and control frontal cortex brain tissue using BaseScope in-situ hybridization. We found a marked decrease in PSEN2 expression in AD samples. To develop in vitro PSEN2 3'UTR isoform models, we designed constructs containing the PSEN2 3'UTR isoforms to overexpress in either HMC3 human microglial or SH-SY5Y human neuroblastoma cell lines. In vitro validation results indicated increased long PSEN2 3'UTR isoform abundance to the short isoform. Determining the functional relevance of the short and long 3'UTR of the PSEN2 transcript will further our understanding of AD pathology.

Cardiopulmonary bypass (CPB) is essential for most cardiac surgeries but often leads to systemic inflammation and multiorgan dysfunction in neonatal and pediatric patients. These adverse inflammatory responses are driven by severe shear stress on the blood, contact with plastic tubing, and rapid cooling/rewarming. However, the molecular mechanisms underlying these complications are poorly understood, creating a significant barrier in improving clinical outcomes. The Nigam Lab has identified Interleukin 8 (IL-8) and Tumor Necrosis Factor alpha (TNF-α) as inflammatory cytokines upregulated in blood cells in response to CPB-associated shear stress. We hypothesize that Lamins (LMNA) play a key role in driving these transcriptional responses, as these structural proteins form the nuclear lamina and can sense mechanical forces acting on the cell. To investigate this, we performed in-vitro experiments using THP-1 human monocytic cells to simulate bypass conditions, applying shear stress and collecting samples at various time points to study the cells’ response and recovery from CPB. Using mass spectrometry-based proteomics (MS), we have identified changes in LMNA phosphorylation between sheared and static cells, providing insight into the mechanisms driving LMNA modifications under CPB conditions. We are also employing techniques such as proximity-dependent biotin identification (BioID) to explore kinase interactions with LMNA. Furthermore, to understand how LMNA influences chromatin organization, transcription factor binding, and regulation of inflammatory genes, we will perform greenCUT&RUN to map LMNA localization on chromatin in both sheared and static THP-1 cells. We aim to uncover the specific molecular mechanisms by which LMNA is altered under shear stress and how it influences chromatin dynamics and transcription of inflammatory genes during CPB. Ultimately, this research will help us understand the underlying causes of systemic inflammation post-CPB and inform novel drug targets and therapeutics to enhance the quality of life for pediatric patients undergoing cardiac surgery.

Dravet Syndrome (DS) is a severe developmental epileptic encephalopathy often associated with SCN1A mutations. DS is predominantly caused by a heterozygous loss-of-function mutation in the SCN1A gene, which codes for the pore-forming alpha subunit of the Na_v1.1 voltage-gated sodium channel. The disease is marked by seizures that are resistant to treatment, ataxia, developmental delays, cognitive impairment, and higher rates of premature mortality, primarily due to sudden unexpected death in epilepsy (SUDEP). At this time however, there is no effective intervention against these devastating outcomes. Anecdotal evidence from family members of children with DS suggests that sensory stimulation during these seizures might reduce their severity and duration. This study investigates whether sensory stimulation can reduce SUDEP in DS using a preclinical mouse model with the SCN1A knocked out. We created a closed-loop responsive system that detects seizure onset and triggers sensory stimulation in real time by utilizing piezoelectric sensors, a Teensy microcontroller, and a 12V computer fan to deliver airflow-based stimulation as a response to spontaneous seizures. Using the modified Racine scale, the system successfully identified scale 4 seizures (generalized tonic-clonic while lying on the belly), as well as scale 6 seizures (generalized tonic-clonic with tonic extension). However, it was unable to detect scale 5 seizures (by sudden, erratic jumping movements). Particularly, for scale 6 seizures, typically fatal in all cases, activating the fan completely prevented SUDEP, resulting in zero mortality. In contrast, for scale 5 seizures that went undetected and did not trigger the fan, mortality remained at 100%. These findings emphasize the potential of airflow-based sensory stimulation as a promising, non-invasive intervention for SUDEP. Future research will focus on improving seizure detection algorithms to enhance sensitivity across a wider range of seizure types.

This research focuses on finding patterns in oceanic Planetary Boundary Layer (PBL) by analyzing satellite imagery and the outputs of machine learning (ML) algorithms. The PBL, located in the lowest part of the atmosphere (~1000m) is nearly always turbulent while the flow above the PBL is comparatively smooth. The downward transfer of momentum from the atmosphere above the PBL into the ocean and the exchanges of heat and water vapor between the ocean and atmosphere occur in the PBL. Understanding and modelling these exchanges is an important aspect of climate science. Even though the PBL is turbulent, its flow spontaneously generates organized coherent secondary circulations in the form of small convective honeycomb-like cells (MC) or long wind-aligned overturning rolls (WS). These flow patterns modulate wind-generated cm-scale ocean surface waves. The Sentinel-1 satellite constellation carries microwave (5 cm wavelength) radars that capture very high-resolution images of the ocean surface. The images are 20 x 20 km and are spaced by ~100 km, but sample nearly all the global oceans with each satellite acquiring ~65,000 images per month. The images are analyzed to find patterns indicative of WS or MC structures in the PBL. Several machine learning (ML) algorithms have been developed to analyze these images and predict whether the PBL above the image site contains WS or MC structures. I focus on a subset of 2100 images acquired in a small region of the tropical Atlantic Ocean; each having been hand-classified by a panel of five experts. My goal is to assess the ML models and calibrate a new ML model according to analysis of their outputs. I anticipate analyzing multiple patterns, including variance throughout the day-night cycle, seasonal changes, and geographical trends.

Through the tagging and cleaving of DNA sequences in Saccharomyces cerevisiae, we observe changes in MCM (minichromosome maintenance) protein recruitment, loading, and activation. The functions of MCM2-7 are critical to separate and unwind DNA in preparation for replication. In the G1 phase, MCMs are recruited and loaded to replication origins in an inactive state, within G1 cells. S phase follows, in which the CDC7/DBF4 kinase phosphorylates the MCM, allowing it to fire and initiate DNA unraveling for replication. The regulation of licensing and activation through these phases is crucial to ensure appropriate replication timing (early vs. late) in the genome. By tagging either a histone or one of the MCMs with micrococcal nuclease (MNase), I implement ChEC (chromatin endogenous cleavage) sequencing to cleave the DNA specifically where it surrounds the nucleosome or the MCM complexes. This method allows for precise mapping of the location of MCM binding sites and nucleosomes. We expect to see an increase in MCM helicase complex licensing and firing in regions occupied by less nucleosomes, resulting in regions of earlier DNA replication timing.

Internal pressure sensing gives healthcare providers essential information regarding patient health and can help determine risk factors for many diseases. The current method for this involves the insertion of a catheter to the location where pressure is being measured (e.g. portal vein, cranium, spine), which can be an invasive and potentially dangerous surgical procedure. A promising alternative is to use ultrasound contrast imaging and microbubbles as a pressure sensor. Studies have shown that the magnitude of the subharmonic component of scattered signals from microbubbles varies as ambient pressure changes. However, many acoustic parameters can induce this effect and it is still unknown how to optimize the parameters to maximize the subharmonic response. I perform experiments to determine the ideal acoustic parameters to sense these changes in ambient pressure and apply this knowledge to develop an ultrasound imaging system that can predict these pressures in vitro.

Superatoms are (often inorganic) clusters of several to several hundred atoms in size, that mimic the chemistry of elemental atoms by exhibiting a high degree of valence electron delocalization, effectively creating a unified valence shell over the entire superatom. Our lab works with M₃(solv)_xCo₆Se₈L₆ (M = Cr, Mn, Co, Zn; solv = thf, py; L = PPh₂NTol)  clusters, leveraging the molecular nature of the Co₆Se₈ core to attach three metal “edge sites” held in place by phosphine ligands, arranged such that they serve as an interface between the exterior chemical environment and the inner superatomic core. By swapping the edge metal, we are able to modify properties of the overall metalated cluster, imparting a degree of chemical and electronic tuneability. While investigations into these compounds have shed light on their electronic structure and reactivity, applying these properties in a practical sense has been an elusive and ongoing area of study. In 2021, however, the Nuckolls lab demonstrated a mixture of Co₆Se₈(PEt₃)₆, Cr₆Te₈(PEt₃)₆, and C₆₀ that formed an isotropic crystal structure capable of up to 100-fold increased conductivity compared to crystals of Cr₆Te₈(PEt₃)₆ or Co₆Se₈(PEt₃)₆ mixed with C₆₀ alone. In this work, I am investigating the conductivity of mixtures of various M₃(solv)_xCo₆Se₈L₆ clusters via a 2-probe method. In previous work, our lab has demonstrated the occurrence of charge transfer in the solution phase between clusters metalated with Co and Cu; building off of this, I intend to determine whether such a phenomenon can be observed in the solid state, and to a degree of reversibility that facilitates improved conductivity through the mixture. The observation or lack thereof of such behavior could hold implications for the applicability of metalated clusters in future semiconductor or materials technologies.

Discrimination is a long-studied aspect of the minority social experience. For minoritized individuals, it influences mental and physical health, access to resources, economic opportunities, and the internal process of creating and understanding identity. Government anti-discrimination laws provide protections and pathways for minorities to seek justice when they face discrimination. However, current literature critiques the effectiveness of anti-discrimination laws because the burden to prosecute is on the marginalized person, who is more likely to face barriers in doing so. Since anti-discrimination laws are not fully protective, minoritized individuals turn to their community for support. The availability of a supportive community is a vital part of collectively fighting discrimination and providing marginalized groups with resources. This study addresses the influence anti-discrimination laws have on transgender and nonbinary (TNB) individuals in their community engagement. I will compare the impact of anti-discrimination laws in Washington and Idaho on TNB adults’ engagement in their community, measuring the type, frequency, and knowledge of local community events. I will conduct a survey of TNB adults in Washington and Idaho asking about knowledge of state and local anti-discrimination laws. I will combine this with data from the Movement Advancement Project which provides state-by-state anti-discrimination law documentation. I predict that the influence of anti-discrimination laws on varying types of TNB community involvement will depend on the state context. In Washington, with well-rounded protections, there will be a decrease in political advocacy and an increase in community-focused activities. In contrast, in Idaho, with limited protections, I predict an increase in political advocacy and a decrease in community-focused activities. Understanding the influence of anti-discrimination laws on community engagement and how TNB individuals seek support will illuminate potential flaws in anti-discrimination policy, improve policy, and insight into how to better support TNB individuals broadly.

Even among the most progressive liberation groups, hierarchies persist. Since transgender identities were long seen as the "more sexually deviant" margin of gay collective identity, sociological transgender studies are relatively new compared to research on gay identities and cultures which had already reached maturity. This results in a disparity in cultural recognition, public image, and scholarly knowledge between LGB and TQ+ communities. Additionally, research on sexualities and gender identities typically runs parallel in past scholarly work, instead of showing the intersections of sexuality and transness. While there's a significant discourse around trans lesbian women in lesbian communities, trans gay men among gay communities remain neglected. The invisibility experienced by gay trans men could offer us a new perspective on understanding the more subtle, underlying tension within queer communities. Trans gay men's experiences of going through gender transition significantly influence how well they can fit into gay spaces, which are primarily populated by cis gay men. My project focuses on the experiences of trans men engaging in predominantly cis gay men's spaces, such as gay bars and social clubs. The study specifically asks: How does the transition status of trans men who identify as same gender loving affect their inclusion among gay spaces and communities? To address this question, I employ a qualitative methodology using in-depth interviews of 7 participants who are adult same gender loving trans men, out for more than 1 year, and have experience engaging in gay communities and spaces. The results indicate that although blatant transphobia is rare in most gay spaces, it's common for cis gay men to draw an invisible line between trans men and themselves. Alienation and microaggression from cis gay men toward trans men happen often in both public spaces and interpersonal romantic relationships.

Our understanding of atomic physics has driven technology for the past century, but we still know shockingly little about the internal structure of protons and atomic nuclei. Studying quarkonium production in high-energy electron-proton collisions is a potential gateway into probing the mysterious glue that binds nucleons together. In this research we compute the cross section for heavy quarkonium production in nuclear deep inelastic scattering at small-x within the nonrelativistic quantum chromodynamics framework. Our methods decompose the process into independent leptonic and hadronic processes and includes octet contributions from S and P wave states. We employ quantum electrodynamics Feynman Rules to solve the leptonic process, and compute the short distance coefficients for the production of the heavy quark pair within the framework of the Color Glass Condensate effective field theory, which accounts for the effects of multiple interactions of the heavy quark pair with the nucleus at all orders. Our results provide insights into the kinematics of quarkonium production at the future Electron-Ion Collider at BNL.

Pseudomonas aeruginosa commonly colonizes cystic fibrosis (CF) lungs, causing persistent infections even under novel CFTR modulator therapies such as elexacaftor-tezacaftor-ivacaftor (ETI). While antibiotic resistance and patient-specific factors partly explain this persistence, bacterial adaptation to post-ETI conditions likely plays a critical role. Previous findings of functional shifts in bacterial variants point to underlying genotypic changes, yet the genomic basis for P. aeruginosa’s persistence remains insufficiently defined. This work aims to identify the genetic adaptations enabling P. aeruginosa to persist in CF lungs despite the improved airway environment afforded by ETI. We developed a method combining temporal allele frequency shifts and cross-patient recurrence to identify selection. My preliminary analysis revealed algG, a gene involved in alginate biosynthesis, as a promising candidate showing multiple signatures of positive selection. First, algG mutations increased in frequency across two-thirds of sampled individuals. Second, the phylogenetic analysis demonstrated the parallel evolution of algG mutations within individual hosts. Third, statistical testing showed significant enrichment for non-synonymous mutations in algG, indicating protein-altering changes are favored. I am extending this work by developing null models to quantify the significance of observed parallel evolution both within and between hosts, and using protein structural prediction to evaluate the functional impact of identified mutations. This research provides novel insights into bacterial adaptation mechanisms during CF treatment and may guide the development of more effective therapies targeting P. aeruginosa persistence. The findings will enhance our understanding of pathogen evolution within human hosts and have implications for improving treatment outcomes for CF patients. 

The Pacific Northwest (PNW) saw an unprecedented heatwave between June 25 to July 3 of 2021, with temperatures reaching up to 15℃ above the climatological mean. Previous studies have focused on this event’s impacts on plants in Western Washington and Oregon through direct observations, or have focused on the economic implications from poor crop turnout. We used remote sensing data to take a holistic approach and examined how all plants throughout the PNW fared during and after this historical heatwave. We found that solar induced fluorescence (SIF) and near-Infrared reflectance of vegetation (NIRv), two remotely sensed vegetation health markers, had regionally dependent plant responses to the extreme heat. In particular, anomalously high SIF regions coincided with anomalously high photosynthetically active radiation (PAR) regions due to low cloud cover. As SIF has been used as a proxy for gross primary productivity (GPP), our findings begs the question: was the elevated SIF during the heatwave indicative of higher GPP, or was the SIF response an artifact of the higher radiation? Our study aims to further our understanding of how extreme events impact plant health, which is increasingly important as heatwaves become more intense and frequent in the future.

Therapeutic ultrasound with microbubble contrast agents induces biological effects that can be utilized for various clinical applications, and its non-invasiveness enables targeted treatments without harming tissue around the target by concentrating the acoustic energy of ultrasound to a specific location. In cancer therapy, ultrasound can enhance the delivery of chemotherapy by priming tumors or directly destroy cancer cells without surgical risks. While Averkiou lab investigates the effects of ultrasound pulses with microbubbles to enhance the efficiency of drug delivery into cancer cells, this project focuses on studying microbubble behavior during ultrasound-microbubble therapy and developing a technique to monitor their response and effects on surrounding tissues. A tissue-mimicking phantom with a wall-less channel will be used to simulate a vascular environment, allowing for controlled observation of microbubble cavitation. Passive cavitation detection (PCD) will be employed to monitor microbubble responses, with one transducer delivering ultrasound pulses to excite microbubbles and another transducer passively recording the resulting scattered signals. Additionally, this study will explore how excitation pulse nonlinearity influences microbubble behavior by modifying the acoustic conditions. While prior research has primarily focused on peak negative amplitudes when transmitting acoustic pressure, this project will examine the effects of both peak negative and positive amplitudes, potentially revealing new insights into microbubble dynamics and therapeutic ultrasound applications. Differences in microbubble responses to these excitation pulses will be analyzed experimentally and compared to theoretical predictions using MATLAB-based computational simulations. The findings of this study could contribute to optimizing ultrasound-mediated drug delivery and broadening the clinical applications of therapeutic ultrasound.

The opioid crisis is an escalating public health emergency, with fentanyl posing major challenges due to its potency and addictive properties. Current treatments address withdrawal but fail to target persistent cravings and relapse triggers. Under Dr. Susan Ferguson and Dr. Alex Whitebirch, I investigate the neural mechanisms underlying fentanyl addiction using rodent models. This research focuses on dopamine (DA) dynamics within the prefrontal cortex (PFC), a key brain region implicated in addiction. Our approach employs the conditioned place preference (CPP) paradigm, a behavioral test that measures a rodent's preference for a drug-paired environment. DA activity in the PFC is monitored in real-time during CPP via fiber photometry of the GRABDA2m fluorescent DA sensor, expressed in glutamatergic neurons through an intersectional virus strategy. We aim to determine whether the development of fentanyl CPP is accompanied by altered DA signaling in the PFC. DA input to the PFC originates from neurons in the VTA, while pyramidal tract (PT) neurons in the PFC project to the VTA and are implicated in suppressing drug-seeking behaviors. To investigate how PT neurons regulate DA signaling, we use Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) to selectively inhibit them. Investigating the behavioral and neurochemical consequences of PT inhibition will provide insight into whether this pathway enhances or suppresses dopamine release. We hypothesize that our conditioning paradigm will lead to enhanced PFC DA signals associated with entry into a fentanyl-paired environment, and that PT neuron inhibition will further enhance DA signals and fentanyl-associated place preference. My role in this research includes surgical procedures, photometry and chemogenetic experiments, data analysis, and histological processing. By advancing our understanding of fentanyl’s impact on dopamine pathways and the role of the PFC, this project aims to inform the development of more effective therapeutic interventions for opioid use disorder and relapse prevention.

Landslides are one of the main agents of erosion in wet and mountainous regions and can have a long-lasting impact on the landscape. In the Puget Lowland of Washington, landslides are prevalent, especially along steep coastal bluffs. Despite their common occurrence, their triggers are often unknown. In particular, their connection to strong shaking from seismically active faults versus precipitation events is an outstanding problem. The Southern Whidbey Island Fault (SWIF) stretches from Victoria B.C. across Puget Sound into the mainland near Woodinville. The SWIF has produced at least four earthquakes since the last ice age, with the most recent occurring less than 2,700 years ago, evidencing its capability of generating an earthquake up to M7.5. This work quantifies the area, extent, landslide type, roughness of the surface (as a proxy for age), and location distribution of landslides along the coastal bluffs of Whidbey Island. Our ultimate goal is to understand possible links between the landslide inventories in the coastal Whidbey Island area and the activity of the SWIF. Using high-resolution LIDAR elevation data (3 m) we perform a series of topographic analyses using GIS and Python tools to establish a landslide chronology. We use the Ledgewood-Bonair Landslide triggered by a rainstorm in 2013, as a spatial and temporal reference to calibrate our analysis. Our results will shed light on the dynamics of coastal landslides, the feedback between landslide preservation, wave and tidal erosion, and hillslope processes. This study advances our knowledge of cascading hazards from the SWIF and informs risk assessment for the region.

Optimizing cell culture methods for marine invertebrates has proven to be challenging, with only a few immortal cell lines available compared to the thousands that exist for vertebrates. Botryllus schlosseri, a colonial tunicate, is native to the Mediterranean Sea and found within marinas along U.S. coasts and other temperate locations worldwide. In addition to being a sister taxa to vertebrates, B. schlosseri undergoes whole-body regeneration regularly, making it a suitable candidate for cell culture development.The Gardell lab investigates the effects of media formulation on epithelial cell proliferation and longevity. Previously, our lab established a media formulation made of DMEM, FBS, Pen Strep, Gentamicin, Amphotericin B, and Sea Salt as resources for cell growth. Wild colonies of B. schlosseri were collected from local marinas followed by microdissection of their zooid and buds for seeding in vitro. Results from utilizing this formulation showed consistently low cell growth; ranging from an average of ~10 to ~50 cells per seeded tissue within a 5 day period. To promote cell proliferation, we explored modifying the media formulation using various ratios of complete media to seawater with similar total osmolality. By diluting the media with seawater, this simulates a similar environment that B. schlosseri regularly reproduces and replicates in. The results indicated that dilutions of 75% Media with 25% Seawater, and 50% Media with 50% Seawater yielded the most consistent growth and highest cell production within a 5 day period. Given this outcome, continued replication of cell culture with this media formulation is required to ensure consistency of results across B. schlosseri genotypes.  Once medium conditions are optimized I will determine a total estimated cell count, which is necessary to perform a time course experiment that aims to characterize the gene and protein regulation of cells in vitro.

Liver cancer can be diagnosed in the clinic with contrast-enhanced ultrasound (CEUS). This method of diagnosis is qualitative and relies on the comparison of blood flow in the suspected tumor to the rest of the liver. However, observer biases in this method can result in inaccurate diagnoses and delays in treatment. To reduce observer bias, our lab developed a comprehensive and repeatable method of quantifying blood flow in liver tumors from CEUS scans. One problem that reduces the accuracy of this quantitative CEUS method is that tumor blood flow metrics are highly impacted by the motion of the liver, stemming from both breathing and sonographer movement. To solve this problem, there needs to be a standardized method to both detect and correct the motion of the tumor on the CEUS scan. I created an automated MATLAB algorithm to measure the motion of a suspected liver tumor on a CEUS scan and identify frames that cannot be analyzed quantitatively. Compared to a manual realignment and deletion of frames done by an expert (a very time-consuming process), as well as a current motion reduction algorithm based only on respiratory gating, my algorithm was simpler, faster, required less input, and produced similar blood flow parameters. This suggests that my MATLAB algorithm can be used in combination with quantitative CEUS processing to help clinicians diagnose liver cancer more rapidly and accurately.

Technology is an integral part of modern life, extending into elementary classrooms where one-to-one device programs have become the norm. While technology can increase accessibility to education, its widespread integration in early learning environments raises concerns about its long-term impact on students and teachers. This research critically examines the role of gamified learning applications in elementary education, questioning whether they enhance or hinder cognitive development, attention span, and problem-solving skills. Using a mixed-methods approach, I conducted surveys and interviews with educators and students in Seattle Public Schools to assess the effects of technology-driven instruction. Preliminary findings suggest that while applications like Khan Academy focus on educational enrichment, others, such as Prodigy, prioritize engagement through addictive, game-like mechanics. This distinction highlights a growing concern: when profit-driven applications shape learning experiences, students may develop a dependence on digital stimuli. Additionally, teachers face challenges balancing digital instruction with traditional instructional methods. This study contributes to ongoing discussions about the ethics and effectiveness of digital learning tools, emphasizing the need for a balanced approach that preserves curiosity, critical thinking, and human connection in education.

Submarine channels represent the offshore continuation of onshore rivers. The shape of submarine channels captures valuable information about changes on the seafloor caused by fault movement during earthquakes. Many submarine channel systems are observed at the Cascadia subduction zone off the coast of Washington and Oregon. The Cascadia subduction zone is a tectonically dynamic system that exhibits many faults which appear to interact with these channels. These interactions are analyzed by quantifying the shape, or morphology, of the Astoria submarine channel, the offshore continuation of the Columbia River. We quantify channel morphology in ArcGIS Pro and Python in order to answer the hypotheses that 1) channels incise deeper where they cross active faults and 2) channel width is not affected by faulting. Some of these measurements include channel width, depth, width-depth ratios, bank slope, bank angle, cross swath profiles, and longitudinal profile analysis. This will offer insight into the behavior and evolution of faulting at the Cascadia subduction zone and how this affects people living along the Pacific Northwest coast who are at risk of earthquakes and tsunamis.

Approximately 500 million people worldwide live with osteoporosis, a disease of low bone mineral density (BMD) and bone fragility caused by a disequilibrium between osteoblasts, cells that build bone, and osteoclasts, cells that reabsorb bone. Existing osteoporosis treatments are single-action anti-resorptive or osteoanabolic (bone-promoting) drugs, which make them insufficient for individuals with severe disease or those at high imminent risk for fractures. RANK is a receptor on osteoclastic progenitor cells that, when activated by RANK ligand binding, induces osteoclast formation and spurs the translocation of a transcription factor, NFATc1, into the nucleus, where it initiates RANK transcription. The available literature on the topic has traditionally only acknowledged RANK to be present in osteoclasts. Contrary to this view, our lab recently identified Rank in osteoblasts. Thus, my project examines how Rank acts in osteoblasts to regulate bone formation. I hypothesize that in osteoblasts of developing bone, Rank signaling is regulated by Nfatc1 via a positive feedback loop, similar to what occurs in osteoclasts. Using in situ hybridization chain reaction, I found that nfatc1 is expressed strongly and specifically in the same developing skeletal structures as rank+ osteoblastic cells in 3, 5, 12, and 14 day post-fertilization zebrafish, supporting my hypothesis. My ongoing studies focus on identifying the Rank and Nfatc1 interactions that may promote osteoblast differentiation. I am achieving this by analyzing the skeletal phenotypes of a rank loss-of-function mutant I am crossing with a reporter transgene line that fluoresces when Nfatc1 signaling is activated, as well as analyzing fish chronically subjected to FK506—a pharmacological inhibitor of calcineurin, which is required for NFATc1 translocation. My preliminary data suggest that the proposed positive feedback loop between RANK and NFATc1 is conserved across osteoclasts and osteoblasts, revealing potential targets for dual-action (anti-resorptive and osteoanabolic) osteoporosis therapies.

Stress-related factors can have a direct impact on cancer biology and patient outcomes. Exposure to a stressor leads to the sympathetic nervous system (SNS) activating downstream signaling pathways that impact cancer-related processes; SNS activity can be measured with heart rate variability (HRV). Low HRV indicates less ‘autonomic flexibility’ and has been associated with poor health outcomes, while high HRV has been associated with better health outcomes. Psychosocial factors such as resilience, stress, and social support are important for adolescents and young adults (AYAs), but the relationship between psychosocial factors and HRV is unknown. The goal of this study is to examine changes in HRV among AYAs with cancer during a qualitative interview about psychosocial factors. Eligible participants were 12-24 years old within six months of initial cancer diagnosis and undergoing treatment at Seattle Children’s Hospital. Once enrolled, participants wore an HRV sensor while participating in a 1:1 semi-structured interview querying topics including stress, resilience, and social support. I used a commonly reported HRV metric, the standard deviation of normal-to-normal intervals (SDNN) to quantify HRV. I defined baseline HRV as the first 5 minutes of the interview, reactive HRV as 5 minutes at the midpoint of the interview and recovered HRV as the last 5 minutes of the interview. I compared baseline HRV to reactive HRV and recovered HRV. I expect to find that both reactive HRV and recovered HRV are lower (‘worse’) than baseline HRV. Results from this study can give insight on the impact psychosocial factors have on the biomarkers of stress in AYAs with cancer.

Using the University of Washington and its ties to the fossil fuel and weapons manufacturing industries, this paper investigates how industry funding and other ties to colonial and neoliberal universities impact the knowledge and opinions of students. This study analyzes the nature and extent of these ties using archival data collected via public records requests, UW websites, and interviews with student protestors, and then it cross analyzes this information with data collected from an anonymous cross-sectional survey with nearly 900 UW student participants. This survey gauged student knowledge and opinions on the climate crisis, fossil fuels, and fossil fuel companies, as well as (US) militarism, warfare (especially in the case of “israel’s” genocide in Palestine), and weapons companies. The answers for each question had pre-determined rankings of beneficiality of the represented knowledge/opinions to the fossil fuel or weapons industries, based on industry disinformation campaigns and corporate strategies. My analysis shows that the knowledge and opinions of students in the UW college/school with the most ties to the fossil fuel and weapons industries (the College of Engineering) are more beneficial to the industries than those of other students, and the difference is statistically significant for many of the questions. The same held true when comparing departments within this college based on the extent of their ties to the given industries, and when holding constant other factors such as years completed at UW and courses taken related to the climate crisis. The correlation weakened, disappeared, or reversed when only considering students in their first year at the UW and/or who had not taken any classes related to the climate crisis, thus providing evidence that the relationship is causative, supporting the hypothesis that university-corporate ties cause students to develop knowledge and opinions that are beneficial to the industry. 

The findings of this study make sense in the context of, and may bolster, existing research on colonial harms of universities, the relationship between industry funding and research agendas and results, university-corporate ties, and student to industry pipelines. However, none of these specifically study the influence of university-corporate ties on student knowledge and opinions, so this study fills in this important gap in research. This contribution will be important to not only related research but to student movements across the country and their campaigns to urge their universities to cut ties with corporations, particularly those against the fossil fuel and weapons industries at the University of Washington.

Nitrous oxide (N₂O) is an important greenhouse gas that depletes stratospheric ozone and is 300 times more potent than carbon dioxide (CO₂) over 100 years. Emissions have increased by 40% since 1980, and N₂O has been accumulating in the atmosphere at an unprecedented rate due to its long lifetime. The rapid rise of N₂O emissions primarily come from soil microbes that respond to the increased usage of agricultural fertilizers which help supply global food demand. Other notable sources include combustion, wastewater treatment, and industrial processes such as nitric acid production. Despite the importance of N₂O, atmospheric observations have limited spatial coverage. Remote sensing presents an attractive solution to dramatically increase spatial sampling. Here we assess the feasibility of using remote sensing to measure N₂O concentrations from sub-orbital platforms. Sub-orbital remote sensing platforms provide a testbed to determine the future viability of space-borne measurements. Our work uses an airborne instrument: the Airborne Visible InfraRed Imaging Spectrometer (AVIRIS). AVIRIS is a full spectral range airborne imaging spectrometer that measures the radiance of the Earth’s atmosphere from 380 - 2510 nm wavelengths. We hypothesize that band ratios from AVIRIS can be used to detect N₂O plumes. We begin by selecting the highest emitting point-source facilities in cloud-free flight tracks. Preliminary plumes will be verified by shape and direction according to meteorological data and consistency with facility layouts. We first test this methodology on CO₂, as previous studies have demonstrated successful detections with AVIRIS. CO₂ will serve as a proof of concept before applying our method to N₂O, which is more challenging to detect due to its lower atmospheric abundance and weaker spectral signature. 

Children of immigrants are uniquely situated in the United States. They share parts of both their American identity and upbringing, along with that of their parents’ and relatives’ homeland(s). Previous research has shown that because of these identities, children of immigrants are more civically engaged than any other group of young people. However, more research is needed to understand what is most effective for this population along with broader implications for these individuals. Utilizing the Youth-Parent Socialization Panel Study of 1965-1997 from the Inter-University Consortium for Political and Social Research, I examine different civic engagement methods including civic education and community involvement and the effect on children of minority groups as opposed to their majority group counterparts. Furthermore I predict that these methods have a positive long term impact on measures of civic engagement, while also having a stronger effect on minority groups.

For state policymakers concerned with road safety in the United States, tamping down on drunk driving is front of mind for good reason; alcohol-impaired crash fatalities rose from less than 11,000 annual deaths before 2020 to over 13,000 annual deaths in 2021 and 2022. To combat drunk driving, policymakers have turned to a variety of policies such as zero tolerance laws, stricter punishments for DUI charges, or lower per se illegal blood alcohol concentration (BAC) rates, the latter of which this paper focuses on. As of this writing, every state with the exception of Utah maintains a 0.08% BAC legal limit despite the National Transportation Safety Board long recommending states lower their BAC legal limit to 0.05%. Accordingly, several state assemblies such as those of Washington, New York, or Hawaii have recently considered or are actively considering lowering the BAC legal limit. These bills have sparked intense discourse on whether a 0.05% BAC legal limit unfairly punishes responsible drinkers who may not be impaired yet blow a BAC over 0.05% on a breathalyzer test, and thus excessively disincentive drinking outside the home and unreasonably hurt the food and service industry. Thus, this paper uses difference-in-differences analyses to measure the effect of BAC policies on drinking habits, specifically alcohol consumption, and whether people substitute drinking at bars and restaurants with drinking at home. I rely on evidence from the state of Utah, which passed HB155 “Driving Under the Influence and Public Safety Revisions” in 2017, a bill that lowered Utah's BAC legal limit from 0.08% to 0.05% effective December 30, 2018. 

In Escherichia coli, the Cpx system is understood to be a two-component cell envelope stress response system. In Pseudomonas aeruginosa however, the Cpx system is largely unstudied. Based on predictive modeling, the Cpx two-component system in P. aeruginosa is thought to involve interactions with two novel accessory proteins, PA3203 and PA3207. Previous genetic analysis in our lab has indicated that PA3207 acts as a negative regulator of Cpx signaling, while PA3203 promotes activity of the system. I evaluated biochemical interactions between these two proteins using the Bacterial Two-Hybrid assay. I generated N- and C-terminal fusions to two functional domains (T18 and T25) of an adenylate cyclase enzymatic reporter. Adenylate cyclase activity, occurring when T18 and T25 were brought into proximity by fusion protein interactions, was measured by a qualitative color assay on MacConkey agar. By this method, I confirmed functional interactions between PA3207 and cytoplasmic signaling domains of both CpxS and CpxR. Interactions between PA3203 and CpxSR were also detected, but were more dependent on the orientation of protein fusions. These findings indicate that CpxSR signaling is regulated through protein-protein interactions with multiple accessory proteins, a unique mechanism among bacterial two-component systems.

6PPD-Quinone (6PPD-Q) is a toxic transformation product of the tire rubber additive, 6PPD, that has been identified as the primary cause of Coho Salmon (Oncorhynchus kisutch) mortality in watersheds impacted by roadway runoff. Recent studies have focused on quantifying the lethal concentration of 6PPD-Q, identifying the major sources, and predicting the environmental release from rubber products. Organic chemical release from solids is typically evaluated with solvent extraction where organic solvent and solid are contacted, releasing the leachable chemicals for measurement. However, different solvents and methods introduce inconsistencies in leaching data from different laboratories. This study evaluates the impact of solvent choice on 6PPD-Q extraction from crumb rubber. I will quantify 6PPD-Q concentrations in methanol, ethyl acetate, or acetone during storage after rubber extractions. Determining the best solvent for 6PPD-Q that promotes the most recovery and stability is essential for data quality. After this study, desorption and resorption rates of 6PPD-Q onto various crumb rubbers will be measured.  These studies aim to improve study design for leaching assessments and enhance our understanding of the persistence and mobility of 6PPD-Q in the environment.

The project aims to design a multi-modal sensor network with VLF antennas will be implemented to model the ionospheric D-region in real-time. In consideration of not having ground truth data, such a network will address the ill-posed problem of inverting with robust regularization techniques. High-data-rate acquisition, high-data-rate processing, and dynamically adaptable auto-tuning will be included in our design. Drawing on experience with the NeSSI, modularity and a digital bus for centrally processed, real-time processing will be part of a standardized, modular sensor network that will be designed. The D-region, an upper atmospheric dusty plasma, controls radio wave propagation via fluctuations in charge. Numerical simulations in our work simulate such occurrences as HF to UHF range radar echoes, validated through experiments in radar labs. Ionospheric instabilities in occurrences such as SAPS events generated through space weather result in GPS and Starlink communications outages. 3D electrostatic fluid and gyrokinetic equations are included in our model, which is significant for describing such instabilities. Real-time observation, predictive maintenance, and reliability in communications networks are enhanced through such studies.

The use of data visualizations in qualitative research varies widely across disciplines, yet there is little consensus on how these visuals are constructed, evaluated, or effectively integrated. This project employs a data-driven literature review to systematically explore these differences and examine the broader intersection of qualitative research and data visualization. We analyze existing studies from qualitative research journals and evaluate them through the Grammar of Graphics framework. Rather than establishing a rigid standard, this research develops a systematic approach to assess and enhance how qualitative data visualizations are used. By mapping various qualitative fields along a spectrum, we identify key factors—such as disciplinary norms, methodological choices, and technological advancements—that influence the adoption and presentation of data visuals. The produced framework does not merely classify the presence of visualizations but examines their function, effectiveness, and alignment with different epistemological stances. Ultimately, this study aims to improve the clarity, accessibility, and impact of qualitative findings by providing a structured understanding of how data visualizations are utilized. By systematically mapping these variations, this study not only reveals the diverse ways qualitative research engages with visualization but also provides a foundation for more intentional and impactful integration, ensuring that visual tools enhance both the interpretability and communicative power of qualitative findings across disciplines. This study is ongoing, and we will present preliminary findings and their implications on the relationship between qualitative research and data visualization.

Heart disease remains the leading cause of death in the United States, with the limited regenerative capacity of cardiac tissue resulting in long-term functional deficits following injury or defects. There is a critical need to develop physiologically relevant engineered heart tissues (EHTs) for disease modeling, drug discovery, and even cardiac surgery. Extrusion-based bioprinting offers a promising approach to generate EHTs with high spatial precision using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). However, most extrusion-based bioprinting methods rely on hydrogel-rich bioinks to achieve desirable rheological properties, often leading to low cell densities that limit tissue functionality. Here, we show that the cell’s properties can be leveraged to form high cell density bioinks with suitable rheological properties, without the need for excessive hydrogel content. Using these boinks, we bioprinted cardiac tissues (400 M cells/mL) around flexible polydimethylsiloxane (PDMS) posts (2mm diameter) to assess contractile force output and electrophysiological characteristics. The printed cells began spontaneously beating after two days, maintained high viability (>80%), and formed mechanically robust tissues with strong structural integrity. These findings highlight the feasibility of high cell-density bioprinting for cardiac tissue engineering and provide a foundation for future work aimed at generating complex, functional EHTs with high cell-density and spatial precision.

Current methods of cancer immunotherapy, such as CAR T-cell therapy, can treat blood cancers. However, treating solid tumors with T-cells remains a challenge, as the necrotic cores of solid tumors are a toxic environment for human immune cells. Bacteria are inexpensive, easy to genetically modify, and have many species which can colonize tumors. Bacteria, therefore, have potential to be an effective alternative to T-cell based treatments. Our challenge is to engineer E. coli bacteria to secrete immunomodulatory payloads upon colonizing the tumor microenvironment. This could be a useful avenue for immunotherapy, especially if the bacteria could produce multiple cargos with synergistic effects. However, we have limited data on what therapeutics E. coli can secrete, and whether it can secrete multiple therapeutics simultaneously. In the fall, I tested whether known E. coli secretion tags could export immunomodulatory minibinder proteins designed by the Baker lab. These minibinders interact with cytokine receptors on tumor cells and are hypothesized to reduce rates of tumor metastasis, which could make them effective anti-cancer therapeutics. Through western blot analysis, I successfully detected secretion of one of these candidate minibinders. My next step is to test whether it can be secreted together with another designed cytokine, Neo-2/15. I anticipate that combining cargos might lower each individual therapeutic’s secretion, since expressing multiple proteins may increase the cell’s burden past its secretion capabilities. If secretion or expression is observed, I will work on optimizing secretion of each therapeutic. The results of this experiment will broaden our understanding of E. coli’s potential as a delivery mechanism for individual and combined therapeutics, open future avenues to test more human immunomodulatory therapeutics and combinations thereof, and hopefully someday facilitate more effective forms of cancer immunotherapy.

Kaposi’s sarcoma (KS) is a cancer caused by Kaposi’s sarcoma-associated herpesvirus (KSHV). While most KS tumor cells are latently infected, where KSHV is inactive, all current treatments for herpesviruses target lytic infection. The Lagunoff lab has shown that latent KSHV infection, similarly to cancer cells, induces the Warburg effect, in which glycolysis is used as an energy source rather than oxidative phosphorylation. Inhibition of lactate dehydrogenase (LDH), an enzyme that catalyzes the last step of glycolysis, increases cell death specifically in latently infected cells. This indicated that the KSHV-induced upregulation of glycolysis was necessary for the survival of these cells; however, it is unknown how KSHV induces this requirement. The goal of my proposal is to determine the viral mechanism for the induction of the Warburg effect in latently infected cells. During latent infection, only the KSHV-latency-associated-region (KLAR) of the viral genome is expressed. KLAR encodes 4 genes: vFLIP, vCyc, LANA, the kaposins, and a cluster of 12 microRNAs. I hypothesized that one of the genes or miRNAs is necessary and/or sufficient to induce the requirement for glycolysis in latently infected cells. To test for necessity, I am using KSHV recombinant viruses that have a deletion in vFLIP, vCyc, the kaposins, or the entire miRNA locus to infect endothelial cells. To test sufficiency, our lab has created lentiviral vectors that contain one of the KLAR genes or the miRNA locus to overexpress these genes in endothelial cells. I anticipate that vCyc and/or the miRNA locus might exhibit necessity/sufficiency, since prior studies have identified these as important for the regulation of other metabolic pathways. Understanding KSHV’s alteration of specific metabolic pathways in latently infected endothelial cells provides novel therapeutic targets for the inhibition of latent KSHV infection and ultimately KS tumors.

Functional assays on intact tumor biopsies play a key role in drug testing, personalized oncology, and cancer research by allowing scientists to better characterize tumor biology. However, these assays usually rely on antibody-based fluorescent labeling. Fluorescent labeling, while well-researched and reliable, is labor-intensive, semi-quantitative, and cannot provide real-time data. In this project, we designed and created a sensor that addresses these issues by using electrochemical aptamers. Our sensor features a 24-well, multiplexed electrochemical setup that detects concentrations of Cytochrome C (CytC), a cell death indicator, with high affinity and specificity. We found that we were able to quantitatively track increasing CytC concentrations in real time as microdissected tumor samples were being treated with various cancer drugs. In the future, this sensor could be expanded to work with more biomarkers, paving the way for clinical use, real-time tumor response monitoring, and high-throughput oncology drug screening.

In mathematics, a symmetry of an object is an invertible mapping from the object to itself. In classical geometry, symmetries are described by group actions. However, group actions are not enough to capture all of the symmetries of some objects. In particular, algebras have symmetries given by Hopf actions of quantum groups called quantum symmetries. In this project, we aim to classify the quantum symmetries of gentle algebras given by Hopf actions of generalized Taft algebras. Path algebras are algebras associated to a directed graph. All finite dimensional algebras can be understood as quotients of path algebras including gentle algebras. The directed graphs associated with gentle algebras can be obtained by gluing copies of particular directed graphs with 1-4 edges. Our approach is to start by classifying Taft actions on these smaller directed graphs. Then, we will determine how these actions glue together to give us Taft actions on any gentle algebra. There is a known parametrization of Taft actions on path algebras, and this project is a step in generalizing this to Taft actions on any finite dimensional algebra.

Premature neonates are particularly vulnerable to electrolyte and fluid imbalances due to their increased insensible fluid losses and immature kidney function. Clinicians carefully monitor and document electrolyte and fluid intake. However, research suggests that saline flushes, small volumes of sodium chloride solution administered to clear intravenous lines after medication delivery, are a source of electrolytes and fluid in the NICU that are often unaccounted for. In the first week after birth, frequent medication administration leads to multiple flushes, and the relative contribution of flushes to total sodium and chloride intake may be substantial for the smallest newborns. Particularly, sodium imbalances contribute to pathologies and have been associated with adverse health outcomes, including intraventricular hemorrhage (IVH) and all-cause mortality. Understanding the impact of saline flush administration on fluid and electrolyte balance is essential for developing evidence-based neonatal care guidelines. We hypothesize that saline flushes in the first have greater relative contributions of sodium, chloride, and total fluid intake for smaller and more premature newborns. To investigate, we are conducting a retrospective study of very preterm newborns admitted to a level III NICU in Washington state. We will statistically compare sodium, chloride, and total fluid intake before and after accounting for saline flushes, and we will descriptively analyze the amount of each in relation to gestational age and birthweight. We will additionally evaluate via univariate models how sodium intake with and without inclusion in total fluid intake correlates with serum sodium daily values. This ongoing study aims to expand the sample size to increase our ability to perform multivariate regression models to account for confounders which may bias our findings. Ultimately, results from this research can improve neonatal care guidelines, helping clinicians optimize sodium, chloride, and fluid intake. 

Cerebellar development relies on the coordinated proliferation and differentiation of progenitors from the ventricular zone (VZ) and rhombic lip (RL). To systematically map their spatiotemporal dynamics, we performed EdU pulse labeling by injecting pregnant mice with EdU and collecting embryonic cerebella at daily intervals over five consecutive days as well as an acute half-an-hour post EdU injection. EdU labeling identifies actively dividing progenitor cells at the time of injection. As development progresses, EdU+ cells can be tracked to study their differentiation and migration, revealing the temporal dynamics of VZ and RL progenitor-derived neurons in the cerebellum. Using multiplex immunohistochemistry with VZ- and RL-derived cell-type specific markers, we tracked the spatial distribution and differentiation of EdU-labeled cells, distinguishing VZ- and RL-derived progenitor lineages. Additionally, we outline a strategy to isolate EdU+ cells for single-cell RNA sequencing (scRNA-seq) and ATAC sequencing (ATAC-seq), enabling a comprehensive molecular characterization of progenitor fate transitions. This approach provides a high-resolution developmental trajectory of cerebellar progenitors, offering new insights into the regulatory mechanisms driving cerebellar neurogenesis and their disruptions in neurodevelopmental disorders.

Tame knots, which are equivalent to a polygonal knot with a finite number of sides, have well-studied invariants; conversely, wild knots that exhibit infinite and pathological behavior are difficult to study and classify. Knot mosaics, introduced by Lomanoco and Kauffman, are an example of a complete invariant for tame knots. Our project aims to expand the existing formal system of knot mosaics to develop an invariant for wild knots. We define n-singular mosaic tangles, the mosaic analog of tangle insertions in pseudoknots and singular knots, and we formalize a system of infinite insertion that generates a wild mosaic to represent certain wild knots. We also intend to define wild mosaic equivalence moves to capture the notion of wild knot equivalence in the mosaic setting. This gives insight to many wild knots explored in existing literature and provides methods to generate and classify new examples.

The Type 4 pilus (T4P) in Neisseria gonorrhoeae, and other bacterial species, is a protein system responsible for host-cell adhesion of the pathogen. Insight into the structure of this system necessary for N. gonorrhoeae pathogenesis can aid the development of novel therapeutic avenues. PilC, the adhesin located at the tip of the T4P, is essential for the initiation of pilus assembly, DNA transformation, and host-cell adhesion. It is believed to interact with a complex of minor pilin proteins to initiate pilus assembly, but the mechanisms of this process are unclear. My project aims to develop an amber-codon suppression system to investigate the function of PilC and its interactions with minor pilins and host cells. Based on computational modeling, the last 12 amino acids of PilC form a beta-strand that binds to the minor pilin PilK to initiate piliation. I designed a mutated version of the PilC gene by inserting an amber stop codon (sequence “TAG”) before the genetic code for this beta-strand. When expressed in gonorrhoeae, the mutated gene leads to a loss of T4P. Next, I aim to genetically modify an existing tRNA to read an amber stop codon. I hypothesize that such a tRNA, known as an “amber suppressor,” when expressed in the non-piliated cell, should rescue the defect in PilC by reading the amber stop codon, thus enabling translation of the complete, functional protein. The resulting cell should change from non-piliated to piliated, confirming that the final beta-strand of PilC is essential for T4P formation. Once I develop a functional amber-suppressor system in N. gonorrhoeae, I intend to study other domains of PilC and the minor pilins essential to T4P biogenesis, by extending the system to enable site-specific incorporation of non-canonical amino acids with useful properties.

Given the pressing challenges of climate change caused by human interference in natural systems, the civil engineering industry must adopt more sustainable solutions. One approach is the use of supplementary cementitious materials (SCMs), as cement production is a major source of CO₂ emissions. This ongoing study investigates the use of zeolite as an SCM in pervious concrete. During the summer of 2024, over a dozen pervious concrete specimens were cast with 0%, 25%, and 50% zeolite powder replacing traditional Portland cement. Zeolite, a naturally occurring mineral formed from volcanic eruptions millions of years ago, has been shown to adsorb pollutants and, when used as an SCM, can reduce CO₂ emissions from cement production and potentially increase the material's levels of strength. To assess the impact of zeolite on the mechanical and hydraulic properties of pervious concrete, tests on compressive strength, porosity, and permeability shall be conducted during the Winter 2025 and early Spring 2025 quarters. Results will be shared as laboratory tests are conducted and data is analyzed. The filtration capacity of pervious concrete for different types of pollutants, both with and without zeolite, is a key focus for future phases of this research project.

Alcohol and cannabis are associated with increased rates of sexual risk behaviors, especially unprotected sex, and decreased perception of the risk involved in unprotected sex. However, little research has explored the relationship between the context of substance use (e.g., partner presence, simultaneous alcohol and cannabis use) and sexual risk behaviors. Multilevel models tested if simultaneous alcohol and cannabis use with a romantic partner present was associated with a greater likelihood of sex, sex while intoxicated, or unprotected sex compared to using only alcohol with a romantic partner present. Young adults (n=409, ages 18-25) who reported using alcohol alone at least three times and alcohol and cannabis simultaneously at least once in the last month were recruited from the Seattle area. Participants completed six two-week periods of twice-daily surveys over two years. Items measured alcohol and cannabis use, presence of others during use, whether sexual intercourse occurred, condom use, and intoxication during intercourse. Analyses were conducted on 308 participants who reported the presence of a romantic partner during use at least once. Simultaneous alcohol and cannabis use with a partner present was associated with significantly higher rates of sex while intoxicated compared to days when only alcohol was used with a partner present. No other associations were found. Although there was no increase in the likelihood of sex or unprotected sex on simultaneous use days with a partner present (versus alcohol-only days with a partner present), there was an increased likelihood of sex while intoxicated. The increased likelihood of sex while intoxicated on simultaneous use days with a partner present could lead to issues with consent and harmful emotional/psychological outcomes (e.g., guilt, regret, lowered self-esteem, worse self-image). Future work could expand the definition of sexual risk behaviors to include these outcomes of sexual encounters rather than focusing exclusively on protection.

Public discourse on prison labor often centers on its ethical implications, yet little research has been conducted on its impact on local labor markets. The Prison Industry Enhancement Certification Program (PIECP), a federal initiative that allows private companies to employ incarcerated individuals at prevailing industry wages, offers a unique opportunity to assess these impacts. Currently, there are 45 correctional facilities which use the program, and they partner with 222 businesses. This empirical study examines how participation in PIECP influences local labor markets by analyzing changes in wages across sectors and metropolitan statistical areas (MSAs) to inform public policy discussions on the role of prison labor in the U.S. economy. Using a difference-in-differences research design, I compare regions where prisons implement PIECP employment with those where certified facilities do not engage in the program. Data from the National Correctional Industries Association and the Bureau of Labor Statistics will be used to quantify these effects. This research aims to provide insights into how prison labor through this program affects local labor markets.

Glycogen Synthase Kinase 3 (GSK3) is a well-studied enzyme that is implicated in many diseases due to its regulatory role in numerous signaling pathways, both known and unknown. The scaffold protein Axin binds to GSK3 and the substrate β-catenin (Bcat), specifying GSK3 so that it primarily acts within the cancer-implicated Wnt signaling pathway. My project seeks to determine if GSK3 is recruited to other potentially unknown signaling pathways by other scaffold proteins that compete with Axin and each other to bind GSK3 at its Axin-binding site. A previous proteomics and computational experiment identified five proteins that potentially interact at this interface of GSK3. Five peptides were designed from the theorized binding sites of the proteins to evaluate whether these proteins compete with Axin. I am using an engineered mammalian cell line to indirectly measure cellular levels of GSK3's substrate, Bcat, and test whether the peptides are capable of displacing Axin from GSK3. When GSK3 is both active and bound to Axin, it causes degradation of Bcat; when GSK3 is inactivated or unbound from Axin, Bcat builds up in the cell. Lithium chloride is a known pathway-independent GSK3 inhibitor that will be used to compare the effect of the peptides on the amount of Bcat, and thus the effect on the amount of Axin-bound GSK3. Displacement of Axin by these peptides indicates that the proteins specify GSK3 for signaling pathways in a similar mechanism to Axin, and that in normal cell states, some equilibrium exists between pools of pathway-recruited GSK3. Understanding the equilibrium between these binders and their associated signal pathways would give insight into how overexpression of one can cause the development of disease states such as cancer.

Polymer networks, materials comprised of interconnected polymer chains, have been the subject of research interest for decades and have, particularly in recent years, found use cases in a variety of applications. Despite their broad use cases these materials are limited by their inherent tendency toward brittleness. One strategy for increasing the toughness of polymer networks is to introduce mechanochemically reactive groups in the crosslinks of a network instead of in the load-bearing primary polymer chains. Previously reported scissile crosslinkers have typically relied on strained ring structures or unusually weak covalent bonds for selective bond scission, introducing challenges such as difficult synthetic procedures and high design complexity. My collaborators at Johns Hopkins University have developed a novel, synthetically accessible crosslinker design that allows for selective mechanochemical bond scission via the replacement of a single carbon atom with silicon. They demonstrated that this scissile crosslinker doubles the toughness of a polymer network prepared by controlled polymerization. In my project I incorporated this crosslinker into a liquid resin compatible with free radical vat photopolymerization, 3D printed this new material, and mechanically characterized it through tensile testing. My work demonstrated that the same toughening effect occurs on polymer networks that are much less controlled and that this strategy for network toughening is compatible with 3D printing, which allows for the fabrication of more complex constructs. In conjunction with the expedient synthesis of this new crosslinker my project demonstrates that this approach to network toughening has the potential for large-scale applications.

Chronic pain is a public health crisis that has been clinically demonstrated to disrupt reward learning and motivation in affected individuals. Previous literature has indicated that Calca neurons in the parabrachial nucleus (PBN) play a key role in the sensory and emotional processing of pain and become hyperactive in chronic pain models. Despite this, how PBN Calca signalling impacts adaptive decision-making in a positive-reinforcement context remains unclear. This study aims to explore how chronic PBN Calca hyperactivity impacts learning and motivation. Using chemogenetics, a technique that selectively modulates neuronal activity, we chronically activated PBN Calca neurons in transgenic mice. These mice were then tested in a two-phase positive-reinforcement operant conditioning paradigm to assess how chronic PBN Calca activation altered learning rates and motivation compared to controlled animals. In phase one, mice underwent a fixed ratio schedule in which they learned to press a lever during a distinct cue to obtain a food reward. In phase two, mice underwent a progressive ratio schedule in which they had to press a lever an increasing number of times to obtain a food reward. We hypothesized that chronic activation of PBN Calca neurons would impair both learning rate and motivation. With this work, we hope to clarify the impact of centrally-mediated chronic pain on motivational and cognitive processes, which could inform the development of future therapeutic strategies.

Syphilis, caused by Treponema pallidum (T. pallidum), remains a significant global health concern, with increasing cases worldwide. Doxycycline post-exposure prophylaxis (Doxy-PEP) has emerged as a potential strategy to prevent infection. However, widespread use raises concerns about the possibility that doxycycline-resistant T. pallidum strains might emerge and spread. This issue is alarming since doxycycline is a second-line therapeutic for syphilis and is often used in patients with allergies to beta-lactams or when beta-lactams are unavailable due to shortages. If genetic resistance to doxycycline were to develop in T. pallidum, it could undermine the effectiveness of Doxy-PEP and further narrow the range of treatment options for syphilis. To address this concern, I developed a restriction fragment length polymorphism (RFLP) assay to detect potential doxycycline resistance mutations in T. pallidum. This assay analyzes the 16S rRNA gene region of T. pallidum where most likely mutations could develop based on the analysis of other resistant pathogens. The assay was optimized using three synthetic 16S rRNA gene constructs containing the resistance-associated mutations and DNA from a wild-type T. pallidum strain (Nichols) as controls. The presence of mutations in the amplified control DNA was assessed by restriction digestion with the AluI, RsaI, and SfaNI enzymes, which can selectively cut wild type and mutant sequences and reveal specific mutations. The analysis of 60 archived samples from syphilis patients collected in the US, Madagascar, Argentina, and Sri Lanka is ongoing. Results will provide data on the frequency of doxycycline resistance mutations in T. pallidum, if any are found in this selected group of specimens. Developing a rapid, cost-effective surveillance tool is essential for monitoring potential resistance and preventing treatment failures when doxycycline is used.

Natural growth factors like fibroblast growth factor (FGF) are essential for maintaining pluripotency in induced pluripotent stem cells (iPSCs). However, current limitations of native growth factors include signal instability, off-target pathway activation, and dependence of xenogenic components for production. To address these issues, we developed a synthetic protein, C6-79C, which consists of six scaffolded subunits of a de novo designed FGFR1/2c binder, mb7. While mb7 functions as an FGF pathway inhibitor, the hexameric C6-79C acts as a receptor tyrosine kinase (RTK) agonist, providing more isoform-specific and prolonged signaling compared to native FGF. We formulated SynGrow, replacing FGF with C6-79C in minimal E8 media, and compared its performance against commercial media. Our study focused on three objectives: (1) comparing the expression of pluripotency markers (Oct4, NANOG, SOX2, and TRA1-60) in cells grown in SynGrow versus commercial media, and (2) evaluating morphology and viability under different media change regimens (daily, every other day, or no change). iPSCs grown in SynGrow exhibited superior morphology compared to those in mTeSR (commercial media). Pluripotency markers (Oct4, NANOG, and SOX2) were expressed at similar levels in both media, with SynGrow also showing higher expression of TRA1-60 across passages, confirmed by flow cytometry. Future evaluations will assess germ layer marker expression following directed differentiation. Our findings demonstrate that synthetic protein-based media formulations, like SynGrow, can effectively replace native growth factor-based media. This approach offers stable, prolonged, and xeno-free alternatives for stem cell culture, with broad implications for improving reproducibility and safety in regenerative medicine and cell-based therapies. 

Leigh Syndrome (LS) is a neurodegenerative disease due to the dysfunction of mitochondria. This disease usually begins in infancy and affects approximately 1 in 40,000 individuals, with children experiencing a progressive decline in their cognitive and motor functions often accompanied by severe treatment-resistant epileptic seizures. Mutations in Ndufs4, the gene that encodes a subunit of mitochondrial complex I have been linked to LS. Using mouse models, our lab has previously demonstrated that GABAergic interneurons play an important role in the pathophysiology of LS. Specifically, mice with Ndufs4 knockout (KO) in GABAergic neurons located across all brain regions exhibit seizures. However, seizures in epilepsy patients and animal models typically originate from forebrain structures. In this project, we examined whether inactivation of Ndufs4 in GABAergic neurons of the forebrain alone is sufficient to cause seizures in mice. To inactivate the Ndufs4 gene in the interneurons of the forebrain, homozygotes floxed Ndfus4 (Ndufs4flx/flx) mice were crossed with Dlx56Cre+ mice. Ndufs4flx/flx; Dlx56Cre+ mice obtained from this cross were used as experimental mice. We hypothesized that mice carrying the gene KO in this region will exhibit seizures and related mortality. Thermal seizure testing was conducted on 9 experimental mice and 10 control mice. Our results show that mice with Dlx56Cre KO exhibit a high seizure susceptibility to both spontaneous and thermally induced seizures. In addition, these mice exhibit a very reduced life span with nearly all mice dying by age P60. These findings indicate that inactivation of Ndufs4 in GABAergic neurons of the forebrain is sufficient to induce seizures and mortality in mice.

Technologies like CRISPR-Cas9 have emerged as promising tools for gene regulation and single nucleotide editing. The field has recently developed mRNA responsive base editors that can edit a genomic scratch pad and record mRNA expression and abundance in bacterial cells over time. RNA responsive base editors can let us retroactively study gene expression that can result in phenotypic differences. However, in complex heterogeneous communities, such as biofilms, monitoring the phenotype and expression of individual cells in real time is challenging. Pairing fluorescence signals to levels of mRNA can convey spatial information about how individual cells behave differently in complex communities. Our goal is to achieve mRNA-responsive base editing to generate fluorescent reporter output. To accomplish this, we will utilize the two existing systems, Rptr, which performs mRNA-responsive base editing, and CRISPR activation (CRISPRa), which can activate a fluorescent signal. These two systems will simultaneously perform base editing and CRISPR activation within the same cell. For this purpose, we will prototype orthogonal CRISPR systems that can independently recruit either activators or base editors through RNA hairpins attached to the guide RNA. My work focuses on designing synthetic fluorescence reporters with installed stop codons that can be modified with base editing and then activated with CRISPRa. My reporters will allow for rapid prototyping of mRNA responsive base editing with RNA hairpin recruitment. We can then find our best performing RNA-recruited base editing system to use in a multiplexed effector system. Ultimately, this integrated approach will couple mRNA expression with a fluorescent reporter read out, allowing us to monitor individual bacterial cells within complex populations.

Elevated levels of metals such as copper (Cu) and manganese (Mn) are often observed in liver failure patients, individuals with Wilson’s Disease, and those with hypermanganesemia with dystonia or workplace exposure. The binding of Cu and Mn to proteins such as albumin and ceruloplasmin poses difficulties for their removal through dialysis. The primary objective of this research is to evaluate the effectiveness of adding albumin in dialysis in removing these toxic metals. We explored different blood and dialysis flow rates and dialysate albumin concentrations to find optimal conditions for Cu/Mn removal. We also explored cheaper Food and Drug Administration (FDA) approved alternatives to albumin that may be effective at removing Cu/Mn. Additionally, due to Human Serum Albumin’s (HSA) limited supply and blood bank pricing, albumin from other mammal species were used to make treatments feasible. In this study we used albumin from several species and three low-cost albumin alternatives to remove Cu/Mn in a closed-loop dialysis process. We digested the biological samples with Nitric Acid and Hydrogen Peroxide on a hotplate and analyzed the atomic compositions of the biological samples using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). We measured the percent reduction of each toxic metal normalized by albumin concentration and found that 20 mL/min and 150 mL/min of Bovine Serum Albumin (BSA) dialysate resulted in a significant percent reduction compared to the negative control. For albumin alternatives, Dextran Sulphate showed promise by notably increasing Cu percent reduction compared to the negative control. Despite the encouraging data, a larger sample size is needed to make a conclusive statement. Although Mn had little variance with different dialysate flow rates or albumin, charcoal columns demonstrated an effective near 100% reduction at both 20 mL/min and 120 mL/min of dialysate flow rate. Further replication studies are needed.

Adolescents and young adults often experience barriers to accessing inclusive, high-quality, and youth-friendly healthcare. Despite growing attention to these disparities, few standardized tools exist to assess or encourage youth-friendly practices across healthcare settings. This project, conducted under the Adolescent Health Team at the Washington State Department of Health, asks: What criteria define a youth-friendly healthcare environment, and how can these be translated into a sustainable certification model? To answer this, we employed a mixed-methods approach. We conducted a landscape review of existing youth-focused health frameworks, analyzed qualitative feedback from community partners and youth advisory groups, and iteratively developed criteria through stakeholder engagement. Branding materials and an informational flyer were designed to enhance accessibility and understanding of the certification. A draft patient satisfaction survey was also created to capture ongoing youth experiences in certified settings. Preliminary findings highlight key themes in youth feedback, such as the importance of inclusive language, provider relatability, and confidentiality and privacy in care settings. These themes directly shaped the final set of certification criteria and informed outreach materials. This work contributes to the field by piloting a novel framework for Youth-Friendly Certification in Washington State. Findings underscore the value of youth-informed design in public health initiatives and provide a replicable model for other regions seeking to improve healthcare access and equity for young people.

Aging is a significant risk factor for many chronic diseases. Understanding longevity interventions can help prevent these illnesses. When mitochondria fail to function correctly, energy production decreases, leading to diseases and shorter lifespans. This study investigates a potential longevity intervention and utilizes Ndufs4-/- mice, a model for mitochondrial disease resembling a human condition called Leigh Syndrome. Mice carrying this mutation have shortened lifespans and neurological impairments. This study aims to determine whether the Sirt3 gene is required for an extended lifespan when using Adefovir Dipivoxil (ADV) injections in a Ndufs4-/- mouse model. In prior experiments, ADV has been shown to increase the expression of genes involving fatty acid oxidation, allowing cells to break down fats for energy. This increase in energy production has been shown to extend the lifespan of Ndufs4-/- mice. ADV is hypothesized to work through a similar pathway as Rapamycin to influence fatty acid oxidation. Rapamycin inhibits the mTOR complex, which influences the CEBP-Beta complex to produce a high LAP/LIP ratio. This shift in the LAP/LIP ratio enhances fatty acid oxidation, extending lifespan. However, in Ndufs4-/- mice lacking Sirt3, a mitochondrial protein, Rapamycin fails to extend their lifespan. This study determines whether ADV works through the same pathway as Rapamycin, specifically if it requires Sirt3 to exert longevity effects. To investigate this, Ndufs4-/- mice are crossed with Sirt3-/- or Sirt3 +/+ and given ADV injections starting at 10 days of age, continuing until the end of their lifespan. I am responsible for genotyping experimental animals and ensuring the correct genetic profile before enrolling them in the study. My role includes administering ADV injections, tracking weight changes, and monitoring the onset and progression of disease.

Cardiopulmonary bypass (CPB) is a conventional way to treat the majority of cardiac surgeries. CPB is used during heart surgeries to circulate blood out of the patient's body in order for surgeons to operate on the heart. However, CPB has led to inflammation and multiorgan dysfunction especially leading to post CPB complications in neonates. Lack of questioning and understanding behind the complications of the technique have posed issues for improvements to clinical outcomes. Specifically, lack of understanding of molecular mechanisms and CPB-associated post surgery inflammation have posed obstacles to improvement of methods in recent years. To better understand these mechanisms, we performed mRNA and ATAC sequencing on circulating leukocytes from neonatal CPB patients. Notably, IL-8 and TNF-α were strongly upregulated in leukocytes. To explore these findings, I performed in-vitro experiments of running THP-1 human monocytic cells to CPB-like conditions, including high shear stress and cooling/rewarming. These experiments were collected and studied at times pre and post shear, and recovery post shear. Experiments regarding blood plasma changes were proposed and this plasma was similarly collected during varying conditions pre and post bypass. ELISA kits were run on antigens AREG and EREG to determine how antigen binding changes with shearing. Sheared then rested samples were found to show a significant increase in antigen binding in both kits AREG and EREG. Sheared and processed samples also showed an increase in binding when compared to the static samples. I have shifted my focus from plasma experiments to investigating the effects of commonly used plasticizers on blood composition. Specifically, I am analyzing how these plasticizers influence changes in blood and plasma using a PIPSeq kit.

Mutations in the RAS gene family are common in various cancers and are estimated to occur in approximately 19% of cancer patients. We utilize the model organism C. elegans to study RAS genes because it sends signals in the worms the same way it does in humans. C. elegans only have one RAS family gene, encoded by let-60, making it simpler to study than the three in humans. The let-60 G13E mutation is a gain of function (gf) mutation also found in cancer patients and is characterized by a glycine to glutamic acid amino acid mutation at residue 13. The mutation is phenotypically marked by neoplasias - pathologically abnormal growths of tissue, effectively constituting tumors. Despite genetic uniformity of C. elegans in the controlled laboratory environment, not all let-60 gf worms develop neoplasias. Preliminary findings show that the penetrance of neoplasias is approximately 81% in the MT2124 strain, which developed the let-60 gf mutation via mutagenesis, and 93% in the ARM219 strain, which developed the mutation via CRISPR technology. Previous reports have identified chaperones as affecting RAS activity, My study aims to identify the effects of heat shock proteins hsp-17/CRYAB  and hsp-70/HSPA5 in C. elegans on the penetrance of neoplasias driven by the let-60 gf worms. Neoplasias shorten lifespan, so I measured their effects on survival in worms with and without the let-60 gf mutation, sorting them by tumor count. I hypothesized that the genetic backgrounds with a lower penetrance and expressivity of let-60 gf will have fewer tumors on average and observe a longer lifespan compared to strains with a higher penetrance of the mutation. Understanding the role of heat shock proteins in neoplasia penetrance could provide insights into potential therapeutic targets for RAS-related cancers.

Glioblastomas (GBMs) are highly aggressive brain tumors with poor patient prognosis, necessitating improved preclinical models to evaluate therapeutic strategies. My lab develops cerebral organoids from human pluripotent stem cells, seeded with primary patient tumors to model GBM progression and therapeutic screening. Developing biologically relevant neural organoids provides a platform for integrating patient-derived GBM samples, enabling disease modeling and treatment testing. This study aims to optimize the embedding, cryosectioning and immunofluorescence (IF) staining protocols used to screen key molecular markers and cell populations within the organoids to validate their suitability for GBM tumor engraftment. Fixed organoids, along with embryonic and adult mouse brain tissues, are embedded in OCT to preserve structure and cryosectioned (12–20 μm). IF staining is optimized by adjusting fixation time, permeabilization, blocking reagents, and antibody concentrations to improve specificity and reduce background fluorescence. Markers analyzed so far include SOX2 (neural precursors), PAX6 (radial glia), FOXG1 (forebrain), and TUJ1 (neuronal differentiation). Mouse brain cryosections from newborn (P0) and adult (P56) stages serve as positive controls to validate antibody specificity and distinguish true signals from autofluorescence or non-specific staining. Images are acquired via Olympus scanner and analyzed using OlyViA and NIH Fiji (Enhanced ImageJ). Current efforts focus on optimizing section thickness for clearer images and refining blocking conditions to minimize non-specific binding. We expect the detected fluorescent markers will mirror known cellular and tissue expression patterns, confirming that the organoids exhibit normal human fetal neurodevelopmental characteristics and are biologically relevant for GBM modeling. Future work will expand marker validation to include GFAP (astrocytes), DCX (neurogenesis marker), TBR2 (intermediate progenitors), OLIG2 (oligodendrocyte progenitors), PTPRZ1 (radial glia), IBA1 (microglia) and other cell lineage-specific markers. Establishing reliable staining and imaging conditions is a crucial step toward developing our organoid model to be suitable for exploring GBM tumor biology and potential therapeutic responses.

Although much has been explored regarding introductory physics students' everyday ideas about energy, it is often still taught in much the same way as it was 30 years ago (e.g., balls falling off cliffs, roller coasters, skateboarding). During that same time period, the climate crisis and society’s energy consumption has become a culturally important topic that is largely neglected in physics courses. At a community college in the Pacific NW, instructors introduced activities from Levy et al. (2023)  “An Energy Unit Fueled by Climate Change” to the physics curriculum, aiming to explicitly tie energy topics to climate change issues. Post implementation of the unit, we asked students to share their views of the relevance of and relationship between energy topics in physics and their society, specifically in the context of climate change. Using a phenomenographic qualitative analysis, we examined students' written reflections and coded their responses into similar themes. In this presentation, we share the results of our analysis and recommend a more robust integration of the culturally relevant topic of climate change into introductory physics education.

According to the CDC, there are over 42,000 female deaths from breast cancer a year in America. In particular, triple negative breast cancer is a clinical subtype that lacks estrogen, progesterone, and HER2 expression, making it more aggressive and harder to treat compared to other subtypes. There is an increased demand for targeted treatments such as immunotherapy, but little is still known about the disease’s immunological progression. Thus, we aim to integrate multiplexed imaging techniques with computational algorithms to capture immune distributions and uncover unique immune spatial architectures. We will study the immune interactions  between neutrophils and different T cell populations as they play an important role in immune signaling in the tumor microenvironment. This is important as neutrophil interactions are currently not well understood. Using a cohort of multiplexed immunofluorescence (mIF) images, we will characterize helper, cytotoxic, and memory T cells as well as neutrophils using the following biomarker panel: CD3, CD4, CD8, CD45RO, CD66b. Custom-trained CNN-based models using spectrally unmixed data for each marker is used for phenotyping with high accuracy. We annotated cells from our dataset to generate the training dataset for these phenotype classifier models. After phenotyping, we utilize spatial point pattern analyses (e.g., G-Function) to identify spatial interactions such as clustering effects between the immune cell phenotypes. We also compute patient level metrics such as the median nearest neighbor distance between pairs of phenotypes and custom-designed inter-phenotype clustering scores. Finally, we utilize Kaplan Meier analyses and log-rank test to correlate the above spatial metrics with recurrence-free survival.

The He6-CRES collaboration experiment aims to take precision measurements of nuclear beta decay spectra to search for exotic currents of the weak interaction, which would indicate a deviation from the Standard Model of particle physics. The sources used for the investigation of beta decay in the experiment are helium-6 and neon-19, which are created via use of a Tandem Van de Graff particle accelerator. For neon-19, a 12 MeV proton beam is incident upon the target gas sulfur hexaflouride. At this energy scale, it is possible for unstable isotopes, in addition to neon-19, to be created. As such, it is necessary to place upper limits on possible contaminants. The focal point of this project is the determination of the maximum amount of radioactive contaminants that are created when producing neon-19, and the methods in doing so.

Adenomyosis is a painful gynecological condition with a prevalence ranging from 20-35% in symptomatic patients. Current detection methods, ultrasonography and magnetic resonance imaging, are suboptimal and definitive diagnosis frequently relies on hysterectomy, prompting more research for less invasive diagnostic tests, which is the aim of this study. We enrolled 108 women undergoing hysterectomies, after post-operative histopathology diagnosed women with adenomyosis (n=46) and other benign conditions (n=62). Cervicovaginal lavage (CVL) and vaginal swab samples were collected. CVLs were used for global metabolomic data, as well as immunoproteomic profiling. We conducted 16s rRNA microbiome profiling on vaginal swabs. The integration of datasets was performed using MetaboAnalyst and MetOrigin. No significant differences were found in body mass index, menopausal status, co-occurring conditions, and parity between patient groups. Pathway enrichment analysis revealed co-metabolic pathways pyrimidine metabolism, D-amino acid metabolism, arginine and proline metabolism, and histidine metabolism as the most enriched in the adenomyosis group. Using least absolute shrinkage and selection operator (LASSO) for biomarker selection, multivariate receiver operating characteristic (ROC) analysis revealed that a model based on metabolomics dataset has an area under the curve (AUC) of 0.852, predictive accuracy (PA) of 77%, and Youden's Index (J) of 0.607. Compared to immunoproteomics and microbiome models, which had a PA of 68.8% and 66.5%, respectively, combining metabolomics with immunoproteomics resulted in an improved PA of 74.8%, while combining metabolomics with microbiome led to a PA of 74.3%, both outperforming their individual counterparts. Three-omics integration in a multivariate model resulted in an AUC of 0.859, PA of 77.4%, and J of 0.624, with metabolites being the top predictive features in the model. Our study identified that global metabolomics is the best single omics predictor of adenomyosis. Multi-omics integration increases performance metrics. Overall, this study identified key metabolic biomarkers for diagnostic development and assessment in future studies. 

Antibiotic treatment is commonly used to manage bacterial infections in very preterm infants (defined as born before 32 weeks of gestation) admitted to the neonatal intensive care unit (NICU). Because immediate treatment is crucial to treat life-threatening sepsis, antibiotics are often administered empirically before microbiology test results confirm infection. As a result, it is common practice that some infants without confirmed infection receive multiple days of antibiotics, which can disrupt the newborn’s developing microbiota. Research suggests that empiric antibiotic therapy is associated with adverse long-term outcomes, including retinopathy of prematurity (ROP), a disease of the eyes, and bronchopulmonary dysplasia (BPD), a chronic disease of the lungs. Understanding the implications of empiric antibiotic use is essential for developing evidence-based guidelines for preterm infection management. We hypothesized that empiric antibiotic exposure is associated with higher rates of ROP,  BPD, and mortality after adjusting for confounding variables. To investigate this, we are conducting a retrospective study of very preterm newborns admitted to a level III NICU in Washington state (N = 55). We statistically modeled the association between the number of days exposed to antibiotics within the first 14 days after birth and the incidence of ROP, BPD, and all-cause mortality after 2 weeks from birth. Preliminary findings indicate a non-significant trend toward higher rates of ROP, BPD, and all-cause mortality (after 2 weeks) with longer duration of empiric antibiotic therapy within the first two weeks. We are conducting an ongoing study to expand the sample size and refine statistical models to account for additional confounding variables. Research on the effects of empiric antibiotic use can improve clinical practice guidelines for treating unconfirmed infection and reduce potential harms associated with early antibiotic exposure.

In the Puget Sound region, some lowland lake ecosystems have been contaminated with metals from the former ASARCO copper smelter located in Ruston, WA. Arsenic, a toxic metalloid, has accumulated in various parts of lake environments from this contamination. Chinese Mystery Snails (CMS) are a ubiquitous freshwater snail species that feed on periphyton, an environmental compartment found to hyperaccumulate arsenic (Hull et al., 2023). This feeding could be a key entry point of arsenic into our food chain. Our research has utilized CMS to test the hypothesis that trophic transfer of arsenic occurs through consuming periphyton and their gut microbiome is altered as a result. To test this hypothesis, our lab conducted a feeding-based arsenic exposure with lab acclimated reference lake CMS. These CMS were either fed algae wafers (control) or periphyton obtained from a high arsenic concentration lake. Trophic transfer of arsenic and gut microbiome alterations were not observed in the food-based arsenic exposure. This led us to hypothesize that waterborne arsenic exposure is an important route for bioaccumulation in CMS, with arsenic concentration correlating to gut microbiome changes. To test this, we conducted a comparative waterborne experiment, exposing CMS to arsenic concentrations of 0, 20ppb and 200ppb. At the end of the exposure, 16S amplicon sequencing was performed on CMS gut contents to assess how the varying arsenic concentrations affect microbiome composition. Whole-body arsenic quantification was conducted using ICP-MS to determine the degree of arsenic bioaccumulation that occurs at different concentrations. 

Washington state has one of the lowest cardiovascular disease (CVD) mortality rates in the nation, yet significant disparities in CVD burden and access to high-quality cardiovascular care persist and little is known about the effect of socioeconomic and cardiovascular care access factors on CVD burden and outcomes disparity. Here we investigate how the distribution and accessibility of comprehensive cardiovascular care impacts cardiovascular outcomes and burden across the Washington State counties. To assess cardiovascular healthcare accessibility, we catalogued hospitals offering cardiovascular services, determined physician density, and calculated the distance of care types to the county population center. The strength and relationships between these accessibility metrics, selected socioeconomic, and behavioral risk factors were compared against select cardiovascular disease outcomes. Data was obtained from public health records and healthcare datasets and were assessed using linear, logarithmic, and logistic regression models. Area Deprivation Index (ADI), Median Income, and College Education were the top socioeconomic (SES) predictors that positively correlated with improved cardiovascular disease outcomes and burden across counties. While proximity of cath lab and emergency services were not strongly correlated with improved cardiovascular outcomes and mortality, proximity of coronary intervention and cardiothoracic surgery were moderately predictive of cardiovascular disease outcomes and mortality. Surprisingly, the density of primary care, emergency services, critical care, and cardiology physicians was weakly correlated with improved cardiovascular outcomes, while the density of neurologists was moderately correlated with improved cerebrovascular outcomes and the density of cardiothoracic surgeons was moderately correlated with improved cardiovascular outcomes. Cardiovascular outcomes, burden, and healthcare resources vary widely across Washington state counties. Overall, higher SES and immediate accessibility, availability, and proximity of specialized cardiovascular care were most highly associated with improved cardiovascular outcomes and higher median ADI percentiles across counties, highlighting the critical need for targeted and specialized cardiovascular care and expansion of accessible interventional services.

Osteoporosis is the most common metabolic bone disease in the United States and worldwide. Genome-wide association studies (GWAS) have identified numerous loci associated with bone mineral density (BMD), however, the target genes at most of these loci remain unknown. Multiple GWAS have identified the TNFRSF11B-COLEC10 locus to be associated with BMD. TNFRSF11B, tumor necrosis factor receptor superfamily, member 11B, is a gene that encodes for osteoprotegerin (OPG), a key regulator of bone resorption. COLEC10, collectin subfamily member 10, encodes a C-lectin family protein involved in neural crest cell migration, endocrine function, and the nervous system, though its role in bone remains unknown. While TNFRSF11B is presumed to be the target gene at the TNFRSF11B-COLEC10 locus, we have obtained preliminary data that loss of COLEC10 in zebrafish results in altered bone morphology. However, these animals were mosaic for mutations in COLEC10, preventing a uniequivocal determination of its role in bone. The purpose of my study is to map genotype-to-phenotype relationships in COLEC10 and TNFRSF11B germline mutant zebrafish. Mutants for COLEC10 were generated by ENU mutagenesis as part of the Sanger Mutation Project. Mutants for TNFRSF11B were generated by our lab using CRISPR. I will genotype both mutants using Polymerase Chain Reaction (PCR) and gel electrophoresis. I will scan the adult fish (90 days post fertilization) using micro-computed tomography (microCT), and then utilize FishCuT for the segmentation and analysis of the vertebral column of each zebrafish. The primary outcomes will be the tissue mineral density (TMD), volume (Vol), thickness (Th), and length (Le), in the centrum, haemal arch, and neural arch of each vertebra. By determining whether COLEC10 is a gene of major effect compared to TNFRSF11B, my research will help to elucidate COLEC10’s skeletal function and its potential role as a casual gene underlying genetic risk for osteoporosis.

DNA computing utilizes the unique properties of DNA molecules to process information while still in molecular form and enable the programmable control of matter at the nanoscale. However, a major limitation is the low reading bandwidth of DNA circuit outputs with fluorescent-based reporters, which hinders scalability and practical applications. Nanopore sequencing is an advanced DNA sequencing technology capable of rapidly detecting single molecules of DNA as they pass through a nanoscale pore, unlike traditional sequencing methods that require amplification. My research seeks to overcome this barrier by integrating DNA computing architectures with nanopore sequencing technology to achieve high-throughput readout and real-time monitoring of circuit kinetics. I am designing DNA-based reporters that encode DNA circuit outputs in a format compatible with nanopore sequencing. These reporters have distinct sequence signatures that can be efficiently read by Oxford nanopore sequencing devices, enabling high-throughput, real-time parallel sequencing. My work involves designing and engineering these reporters, validating their function through experimental assays, and optimizing their compatibility with nanopore platforms. By bridging DNA computing with nanopore sequencing, this research has the potential to expand the capabilities of molecular computing, making it more practical for real-world applications. Beyond computing, this approach could enhance biosensing and diagnostic technologies by enabling rapid and precise detection of molecular signals. For example, DNA circuits could detect specific disease biomarkers, with nanopore sequencing providing an immediate readout. Since nanopore sequencing is a more accessible and portable technology, it could be better deployed in low-resource settings, broadening DNA computing's impact on global healthcare and research. Ultimately, this work not only advances DNA computing but also has implications for broader fields such as DNA nanotechnology and personalized medicine.

Alcohol consumption is known to influence individuals' perceptions and engagement in various activities, often altering how they experience different social, recreational, and everyday tasks. Understanding the effects of alcohol on enjoyment is crucial for identifying potential risks associated with alcohol use, particularly among college students. This research study aims to explore how college students perceive their enjoyment of activities like household chores, social interactions, and leisure when alcohol is consumed, compared to when alcohol is not consumed. Given the prevalent drinking habits among university students, particularly in social settings, it is important to examine how alcohol may shape their experiences in everyday life. Participants are fraternity and sorority-affiliated college students at a large public university who are enrolled in a larger study focused on increasing the availability of and engagement in substance-free social activities. The study is currently collecting data and anticipates a sample size of N = 300.  Participants will complete an online survey of self-report questionnaires. The Substance-Free Reinforcement Survey (SFRS; Correia et al, 2002) will be used to assess participants’ enjoyment of a variety of activities with and without alcohol use. Participants were asked to rate their enjoyment on a scale from 0 (unpleasant or neutral) to 4 (extremely pleasant). Activities included social and individual activities, such as group gatherings, personal leisure activities, and household chores. We will conduct t-test to evaluate whether there are differences in enjoyment between activities experienced while use alcohol versus activities experienced without alcohol. The study’s results will provide valuable insights into the relationship between alcohol use and student engagement in everyday activities. These findings could ultimately inform interventions aimed at reducing harmful alcohol consumption while promoting healthier and more fulfilling social and recreational behaviors. Understanding these dynamics can lead to more effective strategies for addressing alcohol-related risks on college campuses. 

This study investigates the physical mechanisms driving spatiotemporal variability of

barrier layers in the Western Tropical Pacific (WTP) along 149°E, with a specific focus on the

La Niña phase of the El Niño-Southern Oscillation (ENSO). Barrier layers, which separate the

surface mixed layer from the thermocline, regulate ocean-atmosphere interactions and influence

climate dynamics. This research assesses the relative contributions of freshwater input from

precipitation, and wind stress on barrier layer formation and thickness. Data were collected

during a research cruise in January 2025 aboard the R/V Thomas G. Thompson from an

Underway Conductivity Temperature and Density (UCTD) sensor for temperature profiles, and

public-source meteorological data for atmospheric conditions (ERA5). Seven stations, spaced

two degrees apart in latitude, were sampled along a transect from 4°N to 15°N. Each station

provided data to analyze barrier layer thickness, with spatiotemporal variability determined by

comparing different formation mechanisms across stations. Spearman Correlation analyses were

used to determine dominant factors influencing barrier layer thickness and variability. We found

that barrier layer thickness in the WTP shows a general positive but statistically insignificant

relationship with freshwater (ρ 0.32 and p-value 0.48), and a general negative but statistically

insignificant relationship with wind stress (ρ 0.18 and p-value 0.70). During La Niña conditions,

these effects are expected to drive variability, with thicker layers forming in regions of high

precipitation and weak wind stress. Increased freshwater input enhances stratification, while

strong wind stress likely promotes surface and subsurface mixing, leading to barrier layer

thinning. Understanding these dynamics has implications for improving ocean-atmospheric

interaction climate models in the tropical Pacific.

Carbon fiber reinforced polymer (CFRP) is a composite material consisting of carbon fiber and cured resin layers. Its usage is especially prominent in Washington state, whose aerospace sector generates over 70 billion dollars in revenue each year and supports more than 250,000 jobs. Despite its relatively high material value of more than $40 per pound, around two million pounds of CFRP waste are sent to landfills in Washington each year. Assessments show that the costs of this waste and its disposal are a significant financial expense for manufacturers, potentially exceeding hundreds of thousands of dollars. Additionally, the complex and high-temperature manufacturing process required to produce CFRP is extremely energy intensive and generates high levels of greenhouse gas emissions. My research seeks to identify the current state of CFRP recycling in the Washington aerospace sector and examine its potential to address these industry-wide economic and environmental concerns. Through conducting market analysis of aerospace manufacturers in Washington, I will collect data on current levels of CFRP recycling and understand to what extent these recycling processes are effective in reducing environmental impact and improving business profitability. I aim to identify the main barriers that manufacturers face when attempting to implement recycling processes, in order to establish what developments would be necessary to expand the adoption of CFRP recycling across the industry. I anticipate that by identifying these developments and the processes required to achieve them, there will be opportunities for increased collaboration between aerospace manufacturers and CFRP recyclers. With Earth’s resources rapidly depleting and demand for CFRP steadily rising, CFRP recycling is a critical solution that will ensure that aerospace manufacturing can be sustainable, circular and economically feasible.

The purpose of this research is to examine myoregeneration and tissue effects on the tongue base following surgical injury and adipose tissue accumulation in minipigs. Twenty, 8-9 months old Yucatan minipigs were studied. Eight minipigs were assigned as the control group, and other 6 same-sex pairs were used as intervention groups. In each pair, one was intentionally fed to obesity (BMI>50) and the other one with normal weight (BMI < 35) received surgical ablation of the tongue base. BrdU was administered intravenously to track muscular cell proliferation and myofiber formation, with injections given 15 days and 2 days before the termination, respectively. Tongue base samples were paraffin-embedded and cut into 7µ sections for routine H&E, Trichrome, and immunohistochemical staining. Quantitative cell counts and semi-quantitative analysis of labeled cell density and differentiation were performed using the grid system and coding approach to examine muscular responses to the injury and adipose tissue infiltration. The anticipated result will be: 1) fewer muscle satellite cells in the control group; 2) increased adipose cells occupying the spaces between myofiber; 3) significantly more active myoregeneration, with a higher presence of satellite cells in the surgical group. The outcome of this study will elucidate the potential capacity of the tongue base to respond to wound injury and adipose tissue infiltration.

Cardiovascular diseases are the leading cause of morbidity and mortality in the United States. Among the many contributing factors, mishandling of intracellular calcium (Ca2+) dynamics plays a crucial role in the etiology of cardiac diseases including heart failure, and arrhythmogenic disorders. Cardiac ryanodine receptor 2 (RyR2) channels play a central role in excitation-contraction coupling by regulating Ca2+ release from the sarcoplasmic reticulum (SR). Abnormal activity of the RyR2 by impairing Ca2+ release from the SR results in sudden death in many cardiac disorders. Thus, regulators of RyR2 could provide a novel therapeutic target in several heart diseases. Our initial studies implicate the role of the chloride intracellular channel, CLIC4 in modulating the activity of RyR2. We identified CLIC4 as a mitochondrial-associated endoplasmic reticulum membrane protein. The absence of CLIC4 induced faster Ca2+ release from SR, indicating abnormal RyR2 activity. Further, co-immunoprecipitation studies indicated an interaction between RyR2 and CLIC4. Moreover, we found that the absence of CLIC4 increased myocardial infarction upon ischemia-reperfusion (IR) injury in mice. Thus, based on our findings we hypothesize that CLIC4 by either stabilizing RyR2 in a closed state or by regulating the anionic gradient across SR modulates the  RyR2 activity. In this study, we will map the domain in CLIC4 specific to interaction with RyR2 and modulate its activity. We will systematically clone and express various N- and C-terminal truncated CLIC4 constructs to investigate their interaction with RyR2. Further, we will determine the effects of these constructs in modulating calcium release from RyR2. Our studies could aid in the development of a peptide-based therapeutic approach to modulate RyR2 activity in cardiac diseases.

The global pandemic of obesity has increased the prevalence and burden of metabolic diseases, including type 2 diabetes and cardiovascular disease. Obesity and its comorbidities are frequently associated with hypogonadism (low levels of testosterone (T) in men), and both preclinical and clinical evidence support a causative role of hypogonadism in predisposing individuals to metabolic diseases. However, the mechanisms remain unknown. One potential mechanism arises from our recent discovery that in mice, surgical castration (reducing T levels) amplifies the pro-inflammatory response to consumption of a high-fat diet, specifically leading to activation of astrocytes within the hypothalamus, a brain region critical for regulating whole-body metabolism. Concomitantly, there is a striking reduction of the anti-inflammatory neuropeptide neurokinin B (NKB; encoded by the Tac2 gene) in the same brain region. Therefore, we hypothesized that T limits astrocyte inflammation via enhanced NKB-neurokinin-3 receptor (NK3R) signaling. Using primary astrocytes harvested from newborn mice, we found that T and dihydrotestosterone (DHT; a non-aromatizable androgen) increase the expression of tachykinin genes like Tac2. Further, androgen treatment blunted the proinflammatory response of primary astrocytes to lipopolysaccharide (LPS), a sepsis-inducing bacterial cell wall component. To assess the anti-inflammatory capacity of NK3R signaling, we co-incubated astrocytes with the NK3R agonist Senktide and LPS, finding a significant attenuation of proinflammatory cytokine expression. Together, these data suggested that androgen receptor signaling might constrain astrocyte inflammation through induction of NKB-NK3R. However, the ability of DHT to reduce cytokine expression in response to LPS was preserved in the presence of Osanetant, an NK3R antagonist, indicating that the anti-inflammatory actions of androgens are independent of NK3R signaling. These findings form the foundation for future pharmacologic and genetic interventions in obese mouse models to further clarify the role of astrocyte T and NK3R signaling in hypogonadism-associated metabolic diseases.

Enteric neurons regulate intestinal immunity, motility, and other functions. However, they are not in direct contact with the intestinal lumen. This creates the question of how they can sense microbes in the intestine. Intestinal epithelial cells are in direct contact with the lumen and have also been described to regulate immune responses to pathogens. We hypothesize that enteric neurons that regulate intestinal immunity are activated by intestinal epithelial cells. To test this hypothesis, my goal was to identify if there are physical interactions between specialized types of intestinal epithelial cells and enteric neurons. To achieve this, I utilized whole-mount preparations of the intestine of mice, imaged by 2-photon microscopy, where sensory epithelial cells and enteric neurons were labeled by immunofluorescence. I further applied advanced computational analysis of the obtained 3D images of the intestine to quantify cellular proximity. By integrating these approaches and performing precise spatial mapping and statistical evaluation, I identified interaction patterns between specialized sensory epithelial cells and enteric neurons. This research provides the spatial fundaments of interactions between intestinal epithelial cells and enteric neurons, which provides the basis for neuronal sensing of luminal signals and control of intestinal immunity, with broader implications for gut health.

Climate change and anthropogenic pollution have led to a rise in coral bleaching events. These bleaching events cause the loss of corals’ symbiotic algae cells, depleting coral colonies’ energy and leaving them vulnerable to starvation and death. This study aimed to understand whether the sex of gonochoric corals (in which colonies are either male or female) has any correlation to corals’ growth and development, with implications for corals’ response to bleaching events. For the gonochoric species Porites compressa, preliminary results indicate that female colonies develop their gametes earlier in the year compared to males. Energy conserved to produce these lipid-rich eggs may limit the overall growth of female colonies. However, unlike male colonies, females might be able to resorb their eggs to better recover from bleaching events. In summer 2023, twenty-four P. compressa colonies from Kāne‘ohe Bay, HI were stained with an alizarin dye, sexed as male or female based on sperm/egg histology, and returned to the reef to measure one year of skeletal growth. Following their collection in the summer of 2024, eighteen surviving colonies were scanned using an Artec Spyder to produce 3D models revealing colony surface areas and volumes. We then cut cross-sections of each colony to reveal their alizarin growth bands from 2023, allowing us to determine the amount of growth from 2023-24. We anticipate that differences in growth rates will show that female colonies are saving energy by limiting their growth, leaving them less susceptible to bleaching compared to male colonies. 

Porphyromonas gingivalis is a Gram-negative bacterium that is a major contributor to periodontal disease. It is also linked to the development of systemic inflammatory diseases like rheumatoid arthritis. Outer membrane vesicles (OMVs) modulate cell-cell interactions between P. gingivalis cells and export cargo to the cell’s surroundings, but their biogenesis mechanisms remain unclear. Peptidylarginine deiminase (PAD) is an OMV cargo protein that catalyzes the post-translational citrullination of many P. gingivalis proteins. Others have reported that inhibiting PAD in P. gingivalis decreases OMV production and increases biofilm density. A study from our lab found that the deletion of lpxF was also affecting biofilm formation and OMV production in a similar manner. The inclusion of the C4’ phosphatase on lipid A inhibited OMV production, reducing biofilm dispersal. This is presumably due to the reduced delivery of OMV cargos that drive dispersal. We hypothesized that strains with different lipid A structures will have different OM proteomes because of the differences in trafficking and stable interactions with membrane lipids. To begin investigating these potential interactions between outer membrane proteins and LPS, I optimized an outer membrane (OM) isolation protocol so that I can consistently isolate OM from P. gingivalis regardless of strain. I followed up the isolations with Western blots as a quality check so that the samples could be prepared for comparative proteomics analysis. OM, OMV, and whole cell fractions from strains 33277 WT/ΔlpxF and 381 WT/ΔlpxF were sent to a core facility for the comparative proteomics analysis by LC-MS-MS. Our preliminary results suggest that PAD activity is reduced in ΔlpxF because the citrullination of proteins decreased versus WT in whole cells. This led us to our hypothesis for future studies; that lipid A structure influences PAD activity.

Eukaryotic cells contain many membrane-bound organelles and rely on precise vesicle trafficking to transport cargo between them and maintain organelle function and identity. Functional defects in Adaptor Protein complex 3 (AP-3) disrupt vesicle trafficking, leading to disorders such as albinism, seizures, and neutropenia. In Saccharomyces cerevisiae, AP-3 carries cargo from the late Golgi to the lysosomal vacuole, but how it dissociates from the carrier vesicle is not clear. Adenosine diphosphate (ADP)-ribosylation factor 1 (ARF1) regulates AP-3 recruitment and shedding, relying on GTPase-activating proteins (GAPs) for proper function. AGE2, an ARF1 GAP, functions redundantly with GCS1 to regulate ARF1 (Schoppe, 2020), thus AP-3 trafficking. This study aims to identify the interaction site between AP-3 and AGE2 to better understand AP-3 shedding molecularly. Using AlphaFold3, the Merz lab predicted a conserved alpha-helix region in the AP-3 subunit Apl5 C-terminal domain (CTD) as a potential interaction site. To test this hypothesis, I introduced substitution mutations in Apl5 CTD and conducted spinning disc confocal microscope experiments to assess AP-3 pathway defects with a GNSI reporter, which enables to quantify AP-3 function via fluorescence distribution. My results show no statistically significant difference in trafficking defects between wild-type and mutant strains, suggesting that the predicted site is either not a binding site, or not necessary for AP-3 and AGE2 function. Although this study yielded a negative result, it refines our understanding of AP-3 shedding. Future studies will explore alternative regions on Apl5 subunit of AP-3 to identify the true interaction site and uncover the molecular mechanism of AP-3 shedding.

Over 200,000 doctors and nurses in the U.S. who use live X-ray imaging (fluoroscopy) to guide medical procedures are exposed to harmful radiation. Over time, this exposure increases their risk of cancer, cataracts, and other health problems. The current solution, which involves wearing heavy lead aprons, provides some protection but does not entirely block radiation. Furthermore, these heavy lead aprons often cause long-term problems, such as chronic back, neck, and joint pain in over 50% of users. Over the past two years, I have helped develop a new portable radiation shield designed to provide full-body protection while reducing physical strain. This shield features telescoping poles that adjust for ergonomic positioning and support large lead sheets while remaining compact, easy to maneuver, and compatible with sterile environments. To evaluate its effectiveness, a phantom model is used to measure scattered radiation during live X-ray imaging. Two shielding methods are tested: a standard lead apron and the portable shield we have created. Radiation sensors are placed at the head, neck, chest, and legs to compare exposure levels. A paired t-test determines whether the portable shield significantly reduces radiation compared to the lead apron. At least 30 test trials per shielding condition are conducted to ensure accurate results, with a target of ≥95% radiation reduction. Based on our initial calculations, I expect a 15-fold decrease in radiation exposure with our portable shield compared to traditional lead aprons. This research evaluates a new way to protect healthcare workers from harmful radiation exposure while reducing physical strain and helping improve safety in medical settings. 

Fat, oil, and grease (FOG) in residential wastewater presents significant environmental challenges, contributing to the formation of fatbergs that disrupt wastewater systems, increase treatment costs, and heighten public health risks. Traditional methods, like commercial enzymes, are only temporarily effective and require constant maintenance. The goal of this research is to develop Engineered Living Materials (ELMs) comprising a yeast strain, Yarrowia lipolytica, within polymeric matrices for sustained FOG degradation. Y. lipolytica is known for its ability to efficiently degrade hydrophobic FOG components due to its diverse lipase enzyme expression. I encapsulated engineered Y. lipolytica strains in UV-cured poly(ethylene glycol) diacrylate (PEGDA) hydrogels. The findings showed sustained lipase activity and robust cell growth, confirmed by enzyme assays and confocal microscopy. However, over 28 days, significant degradation of the PEGDA-based ELMs occurred, likely due to the breakdown of ester bonds by lipolytic enzymes. To address this, I switched to a thiol-ene polymer network composed of tetra-PEG-allyl and PEG-dithiol, which is expected to resist degradation more effectively. I confirmed the viability and lipase production in these thiol-ene ELMs using the same methods. Varying polymer chain lengths in the thiol-ene network influenced Y. lipolytica growth patterns and morphology, including a shift toward hyphal growth—a filamentous form typical of its dimorphic nature. These changes were influenced by the polymer network’s architecture and material stiffness. Moving forward, I will investigate how hyphal growth impacts FOG degradation and assess the long-term mechanical properties of these thiol-ene ELMs. I expect these ELMs to remain stable over time and reduce FOG concentrations in simulated wastewater. Ultimately, this research aims to provide a sustainable solution for wastewater treatment, addressing the environmental, economic, and infrastructural impacts of fatbergs.

Spinal cord injury (SCI) is a destructive neurological and pathological state that causes major motor, sensory and autonomic dysfunctions with an estimated global rate between 250,000 and 500,000 individuals every year. Many therapeutic strategies have been proposed to overcome neurodegenerative events and reduce secondary neuronal damage. Available treatments are limited and only provide supportive relief to patients with lifetime disability. The severity of impairment is related to the function of the remaining viable neural resources since the central neurons cannot yet be repaired or replaced, only reorganized.   Use-dependent movement therapies have been proven to increase neuronal plasticity. In addition, electrical stimulation can directly induce neuronal plasticity, enhancing therapeutic efficacy. Using a well-known rat model of Acute Spinal Cord Injury (ASCI) available in our laboratory, we hypothesized that targeted, activity-dependent spinal stimulation (TADSS) with physical retraining enhances motor recovery after SCI by facilitating and directing intrinsic synaptic plasticity in specific spared motor circuits below SCI. Long-Evans rats will undergo training and testing for pellet reaching four-legged assessment test, and CatWalkXL test for 4 weeks followed by a moderate to severe unilateral dorsal spinal contusion at the C4/C5 border ipsilateral to the dominant forelimb, resulting in a marked and persistent inability to extend the elbow, wrist, and digits for injured group. Following injury, a neurochip is implanted which delivers closed-loop electrical stimulation below the lesion point throughout the weekdays of training (for 6-8 hours per day). All groups will resume training for another 40 weeks and data will be collected and analyzed. Based on our initial data, we expect to prove that electrical stimulation combined with physical training improves the functional recovery of limb use after acute unilateral spinal cord injury.  

The cerebellar ventricular zone (VZ) is the primary source of progenitor cells that give rise to all cerebellar GABAergic neurons, including Purkinje cells (PCs) and interneurons (INs). While the VZ has been well studied in mice, much less is known about its role in human brain development. In this study, we investigated how progenitors and neurons form in the human cerebellar VZ, using in situ hybridization, immunohistochemistry, and single-cell RNAseq analysis. Our findings reveal several key differences from the mouse model. We found that Purkinje cells are generated during a brief two-week period, even before the cerebral cortex begins to develop. Interneurons, on the other hand, start differentiating a few weeks later and mature on a timescale of months to years. A unique feature of human cerebellar development is the presence of specialized inner and outer subventricular zones (SVZ), which are absent in mice. Most differentiation occurs in these regions, with the first wave taking place in the outer SVZ. Additionally, we observed variations in Purkinje cell arrangement and number, including a subset of Purkinje cells that continue expressing cell cycle genes, suggesting a more complex and prolonged developmental profile compared to mice. By characterizing these developmental processes, our study provides new insights into human cerebellar development, highlighting important structural and temporal differences from animal models. These findings may have implications for understanding neurodevelopmental disorders.

Sulfate aerosols cause pollution and affect climate by influencing cloud properties and incoming solar radiation. Emissions and abundances of sulfur-containing aerosols are one of the largest sources of uncertainties in global climate modeling. The largest biogenic and most uncertain emission source of sulfur aerosols is from phytoplankton in the form of dimethyl sulfide (DMS). In the atmosphere, DMS is oxidized to methanesulfonic acid (MSA) and other compounds that can form sulfate. Historical emissions of DMS are studied by measuring MSA concentrations in ice cores as a proxy for DMS oxidation. Declining levels of MSA have been found in ice core records, implying that production of DMS has also been decreasing; however, anthropogenically driven changes in atmospheric chemistry have altered the ratio of MSA to sulfate produced from DMS over time. To better understand DMS oxidation mechanisms and its relationship to the production of MSA and sulfate aerosols, we need more recent ice core records of MSA and sulfur isotopes of sulfate (δ³⁴S(SO₄^2–)) at higher temporal resolution. To measure δ³⁴S(SO₄^2–) at seasonal resolution in an ice core, rather than an annual resolution, the measurement size is smaller than previously measured by an order of magnitude, at about 1 µg S per sample. We will develop a new method to isolate samples containing less than 1 µg of sulfur from an ice core sample by separating SO₄^2– from other major ions in the sample using an ion chromatograph. We will quantify the isotopic ratio of sulfur in our samples by using an Orbitrap mass spectrometer. Quantifying sulfur isotopes at this resolution will provide information about the seasonality and change in phytoplankton sulfate production.

Cellulose nanofibres (CNFs), produced from sustainable plant resources, are an emerging class of renewable structural biopolymers. Through surface modification via carboxylation and control of fiber length and aspect ratio, CNFs are open to wider usage through further modification of the carboxylated site. However, an understanding of the foundational specific thermodynamics and kinetics of cellulose defibrillation and surface charge modification has not been developed and generalized, hindering widespread adoption of this biopolymer in applications. Additionally, the current fabrication methods for carboxylated cellulose nanofibers (C-CNFs) require harsh solvents and limit reusability. Thus, this study utilizes a deep eutectic solvent treatment (DES) containing citric acid, oxalic acid, and iron(III) chloride to guide the defibrillation of bacterial cellulose (BC) fibers and their carboxylation. We controlled the ratio of the DES components, normalized by the weight of the BC, and determined the reaction rate of bacterial cellulose carboxylation. Through electron microscopy (EM) and zeta potential analysis of titration results, we determined the morphology and composition of the carboxylated BC and surface charge. This work provides insights into the kinetic and thermodynamic interplay that governs the surface charge modification and defibrillation of bacterial cellulose, offering a foundation for further application.

Understanding how blood flow can be influenced by the use of drag-reducing polymers (DRPs) is crucial for addressing secondary injury mechanisms in spinal cord injuries (SCI). SCI disrupts spinal blood flow due to increased intraspinal pressure, altered vascular topology and increased resistance, exacerbating hypoperfusion resulting in hypoxia additional cell death. Thus, mitigating the impact of these secondary mechanisms is critical for better outcomes. We hypothesize that DRPs may reduce vascular resistance by reducing turbulent flow in injured spinal cords; specifically, by reducing the effect of flow separation in larger vessels. The major experiments of this study are to (1) test multiple DRP concentrations to find optimal restoration of hemodynamics after injury and (2) to design 3D models of in-vivo vasculature structures based on ultrasound scans. We have currently tested 2 different DRP concentrations and determined an ideal injection volume in a non-injured rat to increase blood flow—we hope to further these experiments via an injury model and analyzing effects of DRP. Hemodynamic analyses will be conducted from contrast-enhanced ultrasound (CEUS) scans at baseline, post-DRP injection at 30, 60, 90 minutes where a microbubble bolus injection will be delivered. Specifically, we will examine arrival time delay (ATD) which represents relative vascular resistance and area under the curve (AUC) which represents total blood flow volume. Preliminary results showed improvement of flow attributed to the DRP injection (~ 15-20% decrease and increase in ATD and AUC respectively). I will also design 3D models of intraspinal vessels informed by imaging and bioinks to explore blood flow behavior in controlled in vitro settings. Combined, these studies will serve to understand how DRPs can be effective as mitigating secondary injury mechanisms of SCI and improve recovery