A direct current (DC) discharge is one method for producing plasma. Plasma, the 4th state of matter, is defined as the separation of positive ions and electrons in a gas. A gas transforms into a plasma in an isolated low-pressure area between two electrodes, a cathode and an anode. The DC discharge, particularly the DC glow discharge, has historically been significant for both investigating plasma characteristics and providing a weakly ionized plasma for various uses. This project explores the utilization of Faraday’s Law as a fundamental principle for quantifying plasma currents. A fundamental principle of electromagnetism that I have been exploring on this project is Faraday’s Law, this law is especially useful in plasma physics when figuring out the current flowing through a plasma column or confinement device. The device I am building is called a B-dot probe which will be used to measure the current when the discharge turns on. The B-dot probe is essentially a coil made of conducting wire with a “tail” (twisted pair). Through a series of tests, I have procured the average magnetic field produced by the plasma current. From this average magnetic field and geometric measurements the average plasma current is deduced. Plasma is used everywhere now a days like in your TV and neon lights as well as in nature like the aurora borealis. With this research I hope to make the understanding behind the physics of plasma as well as it's magnetic fields easier to comprehend.

The notochord is a rod-like embryonic structure that plays a critical role in transmitting spatial cues to surrounding tissues, serving as the defining feature of chordates and a vital component of vertebrate embryonic development. Understanding the molecular and cellular mechanisms that govern notochord formation and maintenance is a fundamental knowledge gap in developmental biology. Our lab has previously identified wnt16 to be the second wnt gene expressed in the developing notochord in vertebrates and have found that wnt16^w1001/w1001 zebrafish mutant embryos exhibit significant reductions in notochord height, length, and notochordal vacuolated cell size. The fluid-filled vacuolated cells are osmotically active structures that experience osmotic pressure and rapidly inflate along the confines of the notochord sheath, contributing to embryonic body axis development. Glycosaminoglycans (GAGs) are a family of complex polysaccharides that are predicted to play an important role in vacuolated cell and notochord development due to their regulation of cellular tonic conditions and generation of hypotonic/hypertonic stress. Our study aims to establish potential mechanisms for the maintenance of vacuole cells and notochord development, which we hypothesize to act through the crosstalk between the Wnt16 signaling and GAG biosynthetic pathways. To test this, I performed single-cell RNA sequencing analysis on a zebrafish notochord-specific cell population, identifying five GAG biosynthetic genes expressed in clusters alongside wnt16. By determining expression profiles of these GAG genes in wild-type and wnt16^w1001/w1001 mutants, I aim to uncover the underlying mechanisms of the previously observed notochord phenotype. Furthermore, the notochord directly contributes to spine development, persisting within the nucleus pulposus, a structure entrapped in developing intervertebral discs (IVD) and predicted to be important in maintaining IVD health. As such, the implications of our study extend beyond the bench and may contribute to advancements in treating spinal diseases, particularly intervertebral disc degeneration (IVDD).

Electron paramagnetic resonance (EPR) spectroscopy is a powerful and versatile spectroscopic tool for detecting unpaired electrons in molecular systems. We are particularly interested in using EPR to study protein structure and dynamics. By attaching two spin-labels, which contain unpaired electrons, to different regions of a protein, we can measure the distance between the spin-labels to gain insight of protein conformations. The signal sensitivity is limited by protons on amino acids adjacent to the spin-label. Coupling of the spin-label to these nearby protons causes decay of the EPR signal intensity. This decay is quantified by the phase memory time (T_M). While it is known that the presence of neighboring protons results in a shorter T_M, the quantitative effect these protons have on T_M is not well understood. To understand this effect, I utilize maltose-binding protein (MBP) as a model protein. I place spin-labels on various regions of MBP via mutations and site-directed spin labeling to determine how specific neighboring amino acids affect T_M. Spin-labels at MBP sites with a low number of surrounding protons are expected to have a longer T_M than spin-labels at sites with more surrounding protons. Measuring T_M values of different MBP mutants helps further our understanding of how local protein environments impact signal intensity, enabling us to develop quantitative models to predict T_M values in silico. Such models can be used to computationally determine ideal spin-label sites for proteins that previously could not be studied using EPR due to lack of signal sensitivity, in particular membrane proteins.

Almost every form of cardiac disease is characterized by fibrosis, or the accumulation of collagen, an extracellular matrix (ECM) protein, secreted by the cardiac fibroblast. The buildup of fibrosis is a major clinical burden, as it contributes to diastolic dysfunction, or the heart’s inability to relax, and arrythmias, or an irregular heartbeat. In previous studies, the Davis lab has found that in chronic injury, the heart likely undergoes minor offenses along with periods of rest which accrue over a lifetime. Even when exposed to repeat injury stimuli, the heart is able to recover, and the cardiac fibroblasts can transcriptionally regress. Yet, what remains unclear is when the heart experiences repetitive stress, which is common with hypertension, will these once-activated cardiac fibroblasts have a more aggressive response? And if so, are the activation cues stored in the primed external environment, or are they intrinsic to the cell? To address this, we developed a fibroblast isolation and injection protocol that will ultimately allow us to isolate discrete populations of fibroblasts and study them in hearts void of injury. Our results found that fibroblasts from donor hearts that were subjected to a myocardial infarction injury were detectable at 4 and 14 days post cardiac injection but had little proliferation. However, there was an increase in host fibroblasts recruited to the graft site, many of which were proliferating, and fibrosis was found within these same regions. These results demonstrate that cardiac fibroblasts from the same strain can be isolated and adoptively transferred to other hearts, without exogenous ECM. We can apply this baseline protocol to further examine fibroblast memory in vivo in a model of intermittent hypertension.

Inhalation toxicology is a rising field of study as respirable toxicants become increasingly prevalent in our environment. Our research focuses on commonly inhaled toxicants: diesel exhaust (DE) and electronic cigarette aerosols (e-cig). Exposure to traffic-related air pollution and the use of e-cigs has rapidly increased, yet molecular pathways and health effects, and innate factors that impact health outcomes, remain largely unexplored. To assess cardiometabolic and neurodegenerative effects of DE, we exposed male and female mice (low-density lipoprotein receptor knockout, Ldlr KO) to filtered air or freshly generated DE for 18 weeks while fed a high-fat or Chow diet. We then conducted Object-Recognition and Object-Location Memory neurobehavioral tests to assess cognition, specifically hippocampus-independent recognition memory and hippocampus-dependent spatial memory and discrimination, respectively. We sacrificed mice and harvested brain, liver, and lung tissue for histopathological staining and biochemical measurements, including 3-nitrotyrosine, a biomarker of oxidative stress, via Western blot. To assess cardiopulmonary effects of e-cig aerosols, we exposed different mouse strains to acute (5 days) and chronic (3 months) e-cig aerosols with and without nicotine. We then harvested lung tissue and quantified glutathione (reduced and oxidized), an antioxidant and essential nucleophilic scavenger of electrophiles, via high-pressure liquid chromatography; and protein 3-nitrotyrosine. Statistical analyses of all the results obtained were carried out using R. Initial results revealed sex differences in biomarker levels between control and exposed mice. We plan to expand analyses by measuring an additional biomarker of oxidative stress, 8-oxo-dG. Additionally, we will quantify heavy metal accumulation in liver and brain in DE-exposed mice, along with metabolites of carcinogens such as acrolein in e-cig exposed mice. Forthcoming measurements will provide a more comprehensive understanding of biological responses to exposures and elucidate potential health implications. Our research in inhaled toxicants helps reveal critical insights for emerging public health challenges.

Preterm birth is one of the leading causes of neurological deficits and mortality in neonates. Hypoxia-ischemia (HI), when the brain receives insufficient oxygen and blood supply, is a commonly observed condition among preterm infants. Preterm birth and HI affect the structure of the developing brain, particularly the formation of cortical folds (gyri) of the brain. This process is difficult to study in rodent models as they are lissencephalic and do not have gyrified brains. Ferrets, unlike rodents and more similar to humans, have gyrification – the folding of the cerebral cortex, creating gyri and sulci. Using the ferret as a model, examining changes in gyrification after injury can help us identify and further understand brain injuries like HI and its effects. Preterm-equivalent postnatal day (P) 17 ferrets received lipopolysaccharide intraperitoneally and underwent bilateral carotid artery ligation followed by hypoxia-ischemia plus hyperoxia (HIH). Animals were either non-HIH exposed (controls) or HIH-exposed and randomized to receive saline vehicle, erythropoietin, or therapeutic hypothermia. At P42, ex vivo (n=74) magnetic resonance images were collected. Using ImageJ software, the inner to outer hemispheric ratio was used to set the gyrification index (GI). We assessed the average GI across the whole brain and the peak GI of left and right hemispheres. Kruskal-Wallis test will be used to measure the differences in average and peak GI across treatment groups. We hypothesize that the average and peak GI of injured animals treated with Epo, TH, and saline will be lower compared to control animals. Gyrification can be an essential metric for researchers to analyze brain injuries like HI in preterm neonates. As preclinical and clinical studies for HI continue to improve, gyrification can inform the relationship of folding patterns in the cerebral cortex area, assisting us to examine the potential shared developmental processes between animals and neonates.

Benzalkonium Chlorides (BACs) are widely used as an antimicrobial disinfectant in a variety of food and consumer goods processing. Exposure to BACs has increased significantly due to the COVID-19 pandemic. BACs have been reported in common foods like fruits, milk, and other dairy products, raising concerns about the impact of BACs on human health via oral exposure. Recent work in our lab has reported that BACs are metabolized by cytochrome P450 (CYPs) 4Fs and 2D6 in the liver. However, there is a gap in knowledge regarding how BACs and BAC metabolites are distributed throughout the body, post-oral exposure. We hypothesize that insight into BAC disposition and distribution following an oral exposure route could lead to valuable knowledge of BAC accumulation and subsequent toxicity. In this study, we exposed male and female C57BL/6 mice to deuterated C12- and C16-BACs at 120 μg/g/day for one week via a gel food diet. We harvested liver, lung, heart, spleen, and intestinal section tissues at the end of the study, as well as fecal samples at two time points, and a singular urine time point. Through a targeted BAC and BAC metabolite quantitation analysis using liquid chromatography-mass spectrometry, we found omega-oxidation of the alkyl chain to carboxylic acid followed by beta-oxidation to be a major route of metabolism. Additionally, we found that the liver and big intestine had a higher metabolizing capacity than other tissues and the C16 BACs were preferentially metabolized compared to the C12 BACs. This work provided a deeper look into the disposition and metabolism of BACs and revealed organs that are susceptible to BAC exposure for future studies

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect, requiring patients to undergo multiple invasive cardiac procedures, including pulmonary valve replacement (PVR). However, with recent clinical advances, new tools are needed to optimize PVR timing. We believe noninvasively collected cardiopulmonary exercise testing (CPET) data can provide insight into a patient’s need for PVR. Specifically, we hypothesize that patients with a more severe stage of pulmonary valve dysfunction have a limited ability to increase their stroke volume during exercise, an abnormal response that can be assessed by analyzing the behavior of the oxygen pulse (O2-pulse) curve during CPET. A ‘flattening’ of this curve suggests impaired augmentation of stroke volume and potentially a more urgent need for PVR. This research aims to identify metrics that can characterize patterns in O2-pulse. Data were collected from 44 participants with TOF undergoing CPET PVR evaluation and 10 healthy individuals. To find a maximum O2-pulse, we fit a penalized bilinear regression model to this curve. We extracted 8 parameters to mathematically describe the O2-pulse curve, as well as 20 traditional CPET performance metrics. One important parameter that was calculated is the ‘lost area under the curve’ (LAUC), defined as the area under the two calculated regression lines over time subtracted from the area under the curve as determined if the first regression line were to continue on the same slope as is typically expected during a maximal CPET. This value captures both the change in slope and when participants transitioned from a steep increase in O2-pulse to a relatively flattened O2-pulse. The LAUC, among our other identified metrics, can potentially provide insight into the optimal timing of PVR in patients with TOF. Unsupervised machine learning may be a useful tool to characterize patterns in these metrics and search for clinically relevant patient phenotypes.

Historically, the field of healthcare and broadly STEM has been slow to match the diversity of our communities. This is in part due to attrition in college of key underrepresented groups (Flynn, 2016). One-time events that invite new students with every workshop, also known as touch-point events, allow for broader outreach and accessibility but it is unknown how impactful they can be on students’ self-efficacy. The aim of this study was to analyze how a touch-point event such as Anatomy for Change (AFC) workshops could impact a student’s learning abilities and academic confidence. We partnered with undergraduate student groups at the University of Washington (UW) from historically underrepresented backgrounds in medicine to host each workshop. Within our events, we invited UW School of Medicine students to guide undergraduates in completing various medical case studies. Our study measured the effects of our workshops with pre and post-event surveys given to undergraduate student attendees. These contained open-ended questions as well as scaled questions based on a 5-point Likert scale. For undergraduate students from a variety of racial, ethnic, and gender backgrounds we saw an increased confidence in their ability to learn anatomy, problem-solve in a medical context, and pursue a healthcare field. We also saw that the event increased their sense of belonging in the pre-health space. Our results are promising and indicate that a touch-point event can have a positive impact on a student’s educational journey. Furthermore, such programs can be done across a variety of disciplines and institutions throughout the academic spectrum to promote diversity and inclusivity in education.

Temperature has been shown to impact the physiology and performance of ectothermic organisms including metabolic rate with enzymatic activity. The majority of studies have focused on thermal performance at constant temperatures although organisms experience a range of fluctuating temperatures. Understanding which aspects of performance are affected by fluctuations in temperature can be crucial for predicting how ectothermic species will respond to changes in their environment. Research has shown that ectotherms are more vulnerable to climate change and their growth rates are often temperature-dependent. Previous studies on the cabbage white butterfly (cabbageworm), Pieris rapae, have shown that caterpillars maximize growth at higher temperatures even when higher temperatures are infrequent. Physiological response of P. rapae on fluctuating temperature change will provide an important insight into its ability to adapt and survive to changing temperature ranges. For our study eggs from a lab colony were reared at two different fluctuating temperature regimes (11-35℃ and 18-24℃) until pupation. Our studies measured the overall performance of P. rapae, including egg hatch percentage, growth rate of 4th instar caterpillars, development time from 4th instar to pupation, percent survival, and mass gain at two fluctuating temperature regimes of 11-35°C and 18-24°C. We found that the percent survival was significantly higher at 18-24°C. There was significant mass gain and shorter development time of 4th instar to pupation at 11-35°C. Our results differed from other studies that found growth rate to be greater at 11-35°C. Many studies have found a significant genetic variation in growth rate, development rate, and pupal mass. Future studies using a split sib-family design, may provide insight into the mechanisms of thermal performance in a fluctuating thermal environment. Understanding how fluctuating temperatures impact ectothermic organisms, such as the cabbageworm, can contribute to a deeper understanding of organismal responses to climate change.

Learning management systems (LMS) are used for facilitating communication between instructors and students, disseminating lecture materials, and grading assignments. They collect large amounts of student data, necessary or otherwise, with or without explicit consent from students. Furthermore, they make the data visible to instructors, which could have significant implications for students’ grades and experience in the classroom. My project aims to understand the unique nature of student privacy issues on LMS to inform design solutions. I consider how we can design features on LMS to protect students’ privacy and improve students’ educational experiences. We hypothesize that student privacy controls will improve education and student experiences, creating a more equitable learning environment. Using transcripts from 31 interviews with students who use the Canvas LMS at UW, my mentor and I used inductive thematic content analysis methods to understand themes in students’ attitudes toward these solutions. So far, our research suggests that students are concerned about the lack of transparency and control on LMS and would feel more comfortable with the implementation of a privacy dashboard that would allow customizable, context-appropriate data sharing. According to our findings, key factors influencing student comfort include transparency in data collection and sharing with instructors, concerns about instructor bias resulting from irrelevant data sharing, feelings of surveillance arising from lack of data protections and transparency on LMS, and the level of meaningful control students have over their data on LMS. Our findings indicate that this research could guide the design of student privacy dashboards in LMS, improve instruction by helping instructors facilitate better experiences online, and inform policy impacting the way LMS are used around the world.

Diffusible iodine-based contrast-enhanced micro-CT (diceCT) is a technique used to image soft tissue specimens using 3D x-ray microscopy. Staining soft tissues with iodine (I2KI) solution prior to scanning improves contrast for detailed visualization of internal organs, but iodine staining is also associated with tissue shrinkage which can interfere with quantitative analysis. It has been shown that stabilizing soft tissue with hydrogel can reduce shrinkage. We adopted these protocols for our lab, but, despite using hydrogel stabilization, we observed wrinkles in the external surfaces of E15.5 mouse embryos, qualitative evidence of considerable shrinkage. To quantitatively test for shrinkage, we compared the crown rump lengths (CRL) of mouse embryos measured from photos taken prior to the scanning process and then from diceCT scans. CRLs ranged from 12.4 to 20.0 mm in photos and 11.1 to 16.8 mm in scans. An average reduction of 12% resulted from the specimen preparation process and confirmed tissue shrinkage. Furthermore, the amount of shrinkage was not uniform across the specimens, complicating quantitative analysis based on diceCT. Our first hypothesis was that the iodine solution used to prepare the specimens was too acidic. We measured the pH of this solution and found a range from 4.5 - 6.4. To examine if a neutral pH reduced tissue shrinkage, we prepared specimens with a buffered iodine solution (pH 7.2). DiceCT scans of embryos in buffered iodine solution did not show reduced shrinkage compared to controls in the original solution. Further investigations will focus on other potential sources of shrinkage including the pH of other solutions and the time specimens spend in each step of the protocol. Continuing to investigate sources of tissue shrinkage in diceCT can lead to additional methods for shrinkage reduction, supporting more accurate quantitative analysis of diceCT.

During mitosis, the kinetochore plays a central role in ensuring the proper segregation of chromosomes by connecting them to spindle microtubules, which facilitate the equal distribution of chromosomes to daughter cells. In budding yeast, the Dam1 complex is an essential protein complex that binds the kinetochore to spindle microtubules. The Dam1 complex strengthens the kinetochore-microtubule attachment by self-assembling into a sliding ring around microtubules. This self-assembly occurs at nanomolar concentrations of the complex in the presence of microtubules, but in their absence, appreciable oligomerization occurs at concentrations in the micromolar range. Dimers of the complex predominate in high salt concentrations (500 mM NaCl). This is thought to be due to hydrophobic interactions between the monomers. Yeast strains relying on human histones in place of their yeast histones grow slowly. This slow-growth phenotype is rescued by several different mutations in the Dam1 complex. Preliminary characterization of the mutant Dam1 complexes led to the hypothesis that the mutations that allow the yeast cells to adapt to the humanized histones changed the monomer-dimer equilibrium for the Dam1 complex. To measure the affinity of Dam1 complex monomers for each other, I purified the wild-type and mutant protein complexes and used size-exclusion chromatography and mass photometry to determine the different quaternary structures that arise at different concentrations of the complex. I found that each mutation that enhances growth of yeast strains with humanized histones decreased the affinity of the Dam1 complex monomers for each other. The results of this investigation yielded a greater understanding of the requirements for accurate chromosome segregation.

Autism Spectrum Disorder (ASD) is characterized by distinct social-communication differences and restricted and repetitive behaviors. There is heterogeneity in the presentation of social functioning in autistic individuals, which may be attributed to sleep quality, alexithymia, and anxiety. Insomnia, prevalent in autistic children, was linked to higher levels of autistic traits, specifically, difficulties in social skills and relationship formation. Alexithymia, difficulty in describing and identifying emotions, has been reported in 55% of autistic youth. Anxiety severity, specifically social anxiety, is also negatively correlated with social functioning for autistic youth. This study aims to investigate the relation between sleep quality, alexithymia, and anxiety to social functioning in autistic adults. In a sample of 131 adults (ages 18-26, 51% female), we conducted a multiple regression analysis, with social skills as the dependent variable and sleep quality, alexithymia, and anxiety as the independent predictor variables. Sleep quality was measured with the Pittsburgh Sleep Quality Index (PSQI) questionnaire, alexithymia with the 20-Item Toronto Alexithymia Scale (TAS-20), anxiety with the Adult Behavior Checklist - Self Report (ASR), and social functioning with the Social Responsiveness Scale, 2nd Edition (SRS-2). We hypothesize that sleep quality, alexithymia, and anxiety will each independently impact social functioning. This study contributes to the understanding of factors that influence heterogeneity in social functioning amongst autistic adults. Findings on predictors of social impairment may inform targeted interventions for and benefit the lives of autistic adults.

Current concentrations of carbon dioxide are 420 ppm, a 50% increase since the industrial revolution. Nitrous oxide (N₂O) concentration has increased by 18% since the industrial revolution and is currently 319 ppb. This slight increase may not appear alarming, but since nitrous oxide traps 300 times more heat than carbon dioxide, lowering emissions of this greenhouse gas will help stabilize the climate. One major source and sink of N₂O is production and reduction by microbes, respectively, which have been perturbed by anthropogenic increases of nitrogen. Novel microbes found in low pH (3-6) subsurface sites in Tennessee have been shown to respire N₂O, reducing it to N₂ using both Clade I or II nitrous oxide reductases. Microbes that can reduce N₂O at such low pHs (below 5) are rare but could be beneficial as a sink for nitrous oxide. One such strain is a novel Bacteroidetes that encodes a Clade II nitrous oxide reductase and was provisionally named strain S13. In my experiment, I aim to better understand the metabolic processes of this strain and identify the optimal temperature for growth, using xylose, a 5-carbon sugar, as the carbon source. S13 was then grown in an electron acceptor (N₂O) limiting environment, electron donor (xylose) limiting environment, and fermentative conditions. After the microbes completed their growth, the gas and metabolite concentrations were measured using Gas Chromatography and High-Performance Liquid Chromatography. When grown on xylose, the products produced were hydrogen gas, succinate, and acetate. Optical density of these tubes was measured over the course of their growth to determine growth rates and maximum yield (optical density). This was done at 6 temperatures: 15°C, 20°C, 25°C, 30°C, 35°C, and 40°C. These data indicated that S13’s optimal temperature for growth was 25°C. This information could be utilized in future bioremediation and nitrous oxide control efforts.

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease that causes bone pain and destruction in children. Anti-inflammatory treatments for CNO can be effective, but there are not any FDA-approved medications specifically for CNO use, so there is interest in determining the effectiveness of different treatments for CNO. While CNO etiology is unknown, previous pathology studies indicate osteoclastogenesis plays a critical role in CNO pathogenesis. Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) was shown to inhibit osteoclastogenesis derived from peripheral blood mononuclear cells (PBMCs) in adults with active rheumatoid arthritis. Our objectives are to determine whether osteoclastogenesis is altered in children with CNO and the effect of abatacept, a CTLA-4 analog, on osteoclastogenesis. We collected samples of PBMC and serum from healthy subjects and children with active or inactive CNO. We incubated patient serum samples with CD14+ cells isolated from a commercial PBMC pooled sample with MCSF and RANKL, which are necessary for osteoclast proliferation and differentiation, for 7 days before staining for osteoclasts. To determine abatacept’s effect, we incubated PBMCs from patients with MCSF and RANKL with or without abatacept (CTLA-4 analog), performed DAPI and TRAP staining, and counted osteoclasts using the computer software, Image J. Osteoclasts were defined as TRAP-positive cells with 3 or more nuclei. We intend to use multivariable linear and mixed-effects regression models to estimate the average group effect on osteoclast counts from the serum study and PBMC study and the impact of abatacept on osteoclast counts. Expected statistical results of the Serum and PBMC study include an increase in osteoclastogenesis from PBMCs of children with active CNO compared to other groups, and a decrease in osteoclastogenesis with abatacept treatment. This is an ongoing study, and the results will shed light on the effect of abatacept on osteoclastogenesis and its potential therapeutic use in children with CNO.

Children diagnosed with Autism Spectrum Disorder (ASD), often experience co-occurring language impairments, including grammatical and lexical difficulties. Word segmentation, or the ability to identify word boundaries in continuous speech, is done through statistical learning and identification of speech cues. Recent studies in typically developing infants have shown a linear relationship between the ability to recognize words from continuous speech and the size of an individual's lexicon. The neural activity of the cerebral cortex, specifically the delta frequency band (1-4 Hz), contains the time scale of words and phrases. The delta band was found to track speech rhythm, along with semantic dissimilarity between successive words. Extracting acoustic features from sound signals and their linguistic representations (syllables, words, and phrases) is essential for speech comprehension. This study aims to look at the relationship between delta power recorded via scalp electroencephalogram (EEG) and communication skills in children with and without ASD. 193 participants (ASD = 96) from the NIH study on sex differences in autism were included in the sample. EEG recordings were collected while participants listened to phonemes that were statistically presented to result in 4 learned nonsense words. Parents completed a semi-structured interview on their child’s communication skills. EEG delta power was calculated over frontal, central and posterior regions of interest (ROIs). We expect children with ASD (compared to typically developing children) to have decreased delta power during nonsense word perception and lower delta power will be related to lower communication ability. This study will provide insight into the relation between neural perception of language and verbal communication in children with ASD.

Autism Spectrum Disorder (ASD) is a neurological and developmental disorder that affects around 1 in 6 children and 1 in 65 adults in the United States. Autistic individuals experience difficulties in social communication, interaction amongst peers, and language skills; any of the symptoms of ASD cause an influx of other problems that continue into adulthood; these differences may impact self-esteem and feelings of acceptance. Previous research has shown that a history of mental health concerns is related to worse Quality of Life (QoL) in individuals with autism as they transition into adulthood. This project aims to examine mental health comorbidities and self-reported QoL in adults with autism. 44 autistic adults from the NIH funded study on sex differences in autism were included. Participants completed a self history of current mental health diagnosis (anxiety, depression, OCD, ADHD etc.) and self reported QoL. Participants were grouped into 3 groups based on diagnosis: 1 (no diagnosis), 2 (1 diagnosis), and 3 (2+ diagnosis). QoL scores for each group will be calculated from the World Health Organization Quality-of-Life Scale (WHOQOL-BREF). I predict that individuals with more comorbid mental health diagnoses will have lower QoL scores. These data will inform us of how additional mental health struggles may impact quality of life in individuals with autism.

Multitasking, such as walking and talking, is common for humans and other animals, yet animals are limited in how many behaviors they can perform simultaneously. The neural circuit mechanisms that limit multitasking are not well understood. Uncovering these mechanisms will help us understand how brains seamlessly combine behaviors. In turn, this will improve our understanding of some disorders, such as Parkinson’s Disease, wherein certain symptoms, like difficulties with walking and talking, are exacerbated during multitasking. I am investigating how neural circuits for known behaviors interact to limit multitasking in a genetic model system, the fruit fly Drosophila melanogaster. During the first year of my project, I developed a rig to record complex behaviors and I added optogenetic activation to the rig in order to activate neurons that drive one motor program during single and multitasking contexts. I am now preparing to conduct experiments with this rig, comparing the probability that a fly extends a wing (driven via optogenetic stimulation) while resting (single-tasking) vs. walking (multitasking). I expect that a fly will have a higher wing extension probability while single-tasking than while multitasking. The results of my project will help uncover how neural circuit interactions shape an animal’s ability to multitask.

In response to changing conditions, organisms express genes to optimize the match between their phenotype and the environment. Understanding the mechanisms for how genes are turned on or off is therefore an important research area. One challenge in conducting this research is that many of the proteins involved in regulating gene expression are essential to life, and disrupting their function can lead to death. My research focuses on the essential gene SPT6, which encodes a protein that works with RNA polymerase during the elongation phase of transcription. Recently, the Nemhauser Lab has found that SPT6 also plays a role in transcriptional repression. My project aims to differentiate the role that SPT6 plays in transcriptional activation and repression by disrupting its expression in Arabidopsis. Given that SPT6 mutants do not survive, here I test the use of a new tool that allows me to remove my gene of interest in a particular tissue at a particular time. The tool is based on a molecular switch that relies on serine integrases which can recombine DNA between two specific sequences. So far, I have worked with my mentor to rescue SPT6 mutants with a target that expresses the wild-type version of SPT6. Once the integrase is expressed, the recombination turns off the SPT6 gene and turns on a fluorescent reporter. I express the integrase from a promoter that is active only in the first stages of making a new root, so I can observe the impact of loss of SPT6 function in a cell type unnecessary for plants to survive in lab conditions. This project promotes an understanding of the multiple roles of SPT6 during the transtition from repression to activation, and as SPT6 is highly conserved across eukaryotes, my work in plants may also contribute to understanding human diseases. 

My research explores why conflict breaks out in some contexts but not others. Specifically, I question whether bilateral security agreements and democracy reduce the likelihood of conflict between states in volatile regions. First, I hypothesize that security measures reduce the likelihood of armed conflict because they prevent or reduce dangerous misperceptions, fear, and insecurity, which international relations and political psychology literature identify as catalysts of conflict. Second, I hypothesize that as the democratic health of states improve, the likelihood that they will engage in conflict decreases. This is because democracies share values and norms, institutional and public opinion restraints, and other entanglements that render conflict too costly to be in either’s interest. To test these hypotheses, I will compare bilateral relations between each state dyad in five historically volatile regions: the Middle East, Eastern Europe, the Balkans, Central Asia, and South Asia between 1990 and 2010. For each dyad, I will measure the number and severity of conflicts, the number and type of bilateral security agreements, and the democratic quality of each country. I will test my hypotheses by running statistical analyses including a multivariate regression, controlling for other confounding variables that may influence the likelihood of conflict. From my quantitative analysis, I expect to find that security agreements and democracy decrease the likelihood of conflict. This research is important because we have observed an increased prioritization of forming security agreements in western diplomatic relations during the 20th century as well as foreign policy guided by an understanding that democratic states are less likely to fight each other, especially during the Bush administration. If the US and West prioritize forming security agreements and promoting the spread of democracy, we should understand whether these truly increase security.

Countershading is defined as the difference in color between an animal’s dorsal and ventral surfaces, and can serve one of two purposes: to aid in background matching or to create a self-cast shadow, causing the animal to appear less three-dimensional to potential predators. Studies on primates show that species with more frequent horizontal postures and smaller body sizes exhibit higher levels of countershading, however, these links between locomotion behavior and coloration have not been explored in the vast majority of mammals. The Sciuridae family encompasses over 280 species, including squirrels, chipmunks, marmots, and beavers, which are characterized by a wide array of coat colors and use of different locomotion strata. Here, I analyze the correlation between Sciuridae countershading and locomotion strata using specimens from the Burke Museum. To test this hypothesis, I am collecting standardized photographs of specimens from the Burke Museum spanning 73 species, along with data on natural history from the literature to categorize species based on locomotion strata and nesting location. I expect to find that primarily terrestrial Sciuridae species will exhibit low levels of countershading, whereas arboreal species will exhibit high levels of countershading. I expect species with intermediate locomotion strata to rely on a combination of patterns and varying countershading levels, as their locomotion is more variable. This research sheds light on countershading trends in small mammals in relation to their locomotion strata, while also taking into account nesting behaviors and phylogenetic relationships. By using specimens from the Burke Museum, my data collection also aids in the digitization of specimens. In the future, I hope to use the results of this study to inform research on predator-prey relationships with respect to coloration and visual distractions, along with how these relationships are affected by the environment.

Science is rapidly evolving, yet its advances do not enter classrooms at the same rate. Systems Education Experiences (SEE) is a program in the Baliga Lab at the Institute for Systems Biology (ISB) that accelerates the transfer of scientific knowledge and practices to classrooms. One active area of Baliga Lab research is elucidating the level of resilience organisms have, when faced with complex environmental changes. My role is to design laboratory experiments that investigate this with the model organism Halobacterium salinarum (Halo) and to connect this to broader rules governing natural systems for use in high school classrooms. My first experiment probes the resiliency of Halo with the introduction of a combination of stressors (salt and hydrogen peroxide) and its recovery after population collapse. The second measures the long term phenotypic changes in the population. I wanted to see if after being exposed to a new environment if there was an advantage to having gas vesicles and if it is an irreversible trait that allows Halo to be resilient across a variety of environmental conditions. This relates to broadly applicable rules governing resilience across many systems. This project serves as a model for how all organisms respond to stress. Combinations of stressors in human lives can make us less resilient. However, strategies to quickly prepare, respond, and react can improve outcomes for individuals and the overall population. This project connects to a goal of K-12 science education which is to not just teach academic concepts but to equip students with knowledge that can be applied to all parts of life. Our knowledge on the mechanisms that control how organisms respond to stress is extremely limited. By understanding the biological stress response we can promote resilience in the earth's most vulnerable systems in the wake of climate change.

Current trends indicate that while adolescents and young adults are starting to engage in sexual activity later in life and less frequently, there is a notable shift towards experiences characterized by low commitment and higher risk. Despite numerous studies on sex-related attitudes and practices among young people in the United States, broader insights are necessary to achieve a holistic understanding of the newly emerging landscape of youth sexuality. Against this background, our research examines sexual attitudes and reported behaviors in a sample of 1,200 undergraduate students at the University of Washington. Our study employs a comprehensive survey to identify patterns in sexual attitudes and behaviors among a representative sample. Administering online questionnaires is crucial in ensuring increased reliability and validity of responses on sensitive topics. These include but are not limited to, pornography viewership, kink and fetish interests, sexual self-concept, and more. Preliminary findings indicate a complex interplay between cultural, educational, and social factors in shaping sexual norms and practices among young adults. This study contributes to the broader discourse on sexual health education and highlights the need for nuanced approaches in addressing the dynamic and multifaceted nature of young people's sexual relationships. The results of this investigation aim to inform the foundation of modern sex education in order to address the evolving challenges of today's sexual landscape.

Prominent author and civil rights activist James Baldwin (1924-1987) has found new life on social media in the context of the Black Lives Matter (BLM) movement. BLM is a social and political movement of protests, advocacy, and online activism spanning the past decade. Following incidents of violence and racial discrimination against the Black community, Twitter has been a platform for facilitating societal change, and a significant portion of BLM unfolded on this active forum. Through a comprehensive text analysis of relevant tweets during BLM, our team uncovered notable activity connecting James Baldwin to BLM, current and historical events, and other cultural phenomena that influenced this online discourse. We organized large datasets of various Tweets and dissected their timelines from 2013-2023 to reveal keyword frequencies, engagement, and the prevalence of Baldwin references and quotes, connecting them with ongoing cultural and political contexts. By examining Twitter activity surrounding James Baldwin in the past decade, we wanted to understand how Baldwin’s work contributed to shifts in engagement and public sentiment during this time. Our hypotheses included increased discussions of the author’s work during times of political events and incidents of violence against the Black community. By creating timeline visualizations in Python, we uncovered spikes in engagement and public sentiment of historical events during crucial incidents of the movement, demonstrating how historical literary figures play a role in contemporary digital spaces. We used different language processing techniques for categorizing tweets and extracting patterns. We specifically measured retweet frequencies, hashtag usage, documented valuable keywords, and direct quotes and excerpts from Baldwin’s writing. Our findings provide valuable insights into social media and serve as a resource to understand online perspectives of literature, trends, politics, and social justice.

Acute pancreatitis is an abrupt and painful inflammation of the pancreas that is often associated with serious complications and high mortality rates. Current diagnostic and therapeutic options remain limited, underscoring the need for novel strategies based on the underlying mechanisms of the disease. Our previous research suggests a key role for activin A, a member of the Transforming Growth Factor β (TGF-β) superfamily, in modulating inflammatory responses. Notably, activin A appears to trigger the c-Jun N-terminal kinase (JNK) pathway, a crucial member in macrophage activation during inflammatory diseases. This study aims to explore the role of activin A and the pJNK signaling pathway in macrophages during the pathogenesis of acute pancreatitis. Our investigation involves cell culture experiments using the RAW264.7 macrophage cell line, qPCR and Western blot analysis to identify protein alterations in activin-stimulated macrophages, and transwell migration assays to examine macrophage’s migratory ability toward chemoattractant after activin stimulation. We predict that activin A-stimulated macrophages would have increased JNK activation, increasing macrophage infiltration in inflamed tissues and polarization toward the pro-inflammatory subtype, potentially exacerbating the severe inflammatory response of acute pancreatitis. Our study is expected to reveal novel pathogenic mechanisms of acute pancreatitis and pave the way for the development of more effective diagnostic and therapeutic strategies for this disease.

Activation of Kappa Opioid Receptors (KOR)- either from a stress-evoked release of the endogenous dynorphin neuropeptide or pharmacologically- produces analgesic effects, aversive stress responses, and amplifies behaviors related to drug addiction. Influence on these specific behaviors can be attenuated through naloxone precipitated fentanyl withdrawal to model extreme distress. This was replicated by surgically implanting osmotic minipumps filled with fentanyl in mice for a 7-day period. Saline was utilized as a control against mice pretreated with norBNI (a long-lasting KOR antagonist) versus mice who only received fentanyl in order to determine if there was an effect on behavioral response following the precipitated withdrawal. Once the pumps were removed and fentanyl was eliminated from the system, mice underwent a 2-day spontaneous withdrawal phase prior to pairing 1 mg/kg naloxone injections with the presentation of almond extract. An observed aversion response to the almond odorant would exhibit a conditioned stimulus. The pairing of these components would then associate the negative feelings from withdrawal with introduced extract. The odorant aversion evident in fentanyl-treated mice was significantly reduced by pretreatment with the KOR antagonist norBNI, suggesting that the aversion was mediated by the release of endogenous dynorphin. With the continuation of this experiment, I would expect to see an increase in stress resilience as the KOR system becomes blocked with the administration of an antagonist.

The SAR11 clade are composed of one of the most abundant groups of marine bacteria, composing up to a quarter of planktonic cells in marine environments. These bacteria play important roles in marine biogeochemical cycles. Because they are challenging to culture in the laboratory, they remain understudied, with few publicly available complete genomes. Most of what is known about the genetic diversity of this group comes from metagenome-assembled genomes, which do not capture the full genetic diversity within the group. Our project aims to use non-traditional methods to culture SAR11 isolates from the marine environment and use them for whole genome sequencing. We hypothesize that this work will reveal unidentified genetic diversity within the SAR11 group. This research will yield insight to the genetic and phylogenetic diversity of SAR11 bacteria through the examination of whole genome sequences, and will support future research on this globally important group of bacteria by greatly expanding the number of publicly available complete SAR11 genomes.

Individuals differ in how easily they perceive and internally represent visual and verbal information. However, these differences in information processing style are not all or nothing; individuals vary not only in the direction of attentional bias, but also its strength. Prior research found that when forced to choose between competing visual and verbal stimuli, people exhibit different degrees of bias when selecting what information to attend to. The present study examines whether individuals with greater visual or verbal attentional biases, relative to neutral attenders, show different levels of sensitivity to conflict between visual and verbal information during a categorization task. Data will be analyzed from 185 participants who completed a card sorting task in which they were asked to sort stimuli into one of three card suits. Each trial contained visual (shape) and verbal (word) representations of the card suit. On 75% of trials, the word and shape matched (congruent) and the other 25% of trials contained inconsistent information (incongruent). Our analysis will compare response times on incongruent and congruent trials (incongruency effect) in high- and low-biased individuals, to measure conflict experienced. We hypothesize that individuals showing a greater attentional bias towards either task modality will ignore information that is misaligned with their preferred information processing style, resulting in a smaller incongruency effect. These results would suggest that biased attenders have quicker access to the information that aligns with their processing style, while neutral attenders notice both information types and experience conflict when they are incongruent. Alternatively, if attentional bias is unrelated to incongruency effect magnitude, this suggests that people process information similarly, and experience biases only at the decision phase. This study has important implications for understanding how individual differences in information processing style affect how much information individuals process in situations with attentional competition.

Indigenous populations in Latin America are socially disadvantaged groups that often experience insufficient access to everyday necessities. With climate change raising global temperatures, heat-related illnesses are rising in vulnerable groups, especially among communities in heat-prone environments. The Qom is a population indigenous to the Gran Chaco, a tropical dry ecozone with average summer temperatures well over 90°F ( <33°C). Most of the Qom today are located in the rural Argentinian province of Formosa, and the majority live below the poverty line, further limiting their accessibility to health services. Access to interventions that mitigate extreme heat, such as air conditioning, is also not feasible for most Qom families. The Chaco Area Reproductive Ecology (CARE) program has worked with Qom communities in Formosa for over 20 years, most often in the community of Namqom (~ pop. 5000). A current aim of the CARE program is to gain insight into the therapeutic itineraries that Namqom residents rely on the most, particularly for heat-related illnesses such as heat stroke, heat exhaustion, and heat cramps. If not addressed these illnesses can be fatal, and can exacerbate health conditions for vulnerable individuals. This study aims to identify what factors exaggerate or prevent heat-related illnesses to explore further what type of interventions can be created and implemented within the Namqom community to mitigate this issue becoming more widespread. This poster presents findings from a scoping review to inform our study design. This review will identify and synthesize findings to date on the following topics: (1) human biological and behavioral adaptations to living in the Gran Chaco and similar ecozones and; (2) the specific health risks among vulnerable groups (infants, children, pregnant women, elderly, individuals with underlying health conditions) that are exacerbated by heat stress.

Protozoa are a diverse field of organisms that impact trophic transfer in marine ecosystems, constituting an important link between producers and higher trophic levels. In this study, I focused on determining how protozoan grazing rates differ in nutrient-rich and poor ecosystems. I used a CTD rosette to collect six seawater samples along the equatorial transect of five degrees south to five degrees north at stations: 5°S,2°S, 1°S, 0°, 1°N, 4°N, and 5°N. These samples were filtered to 10 microns and divided into isolated incubation cultures with 0, 25, and 90 percent dilution of 0.2 micron filtered seawater. Change in Chlorophyll was used to infer the phytoplankton growth rate across the dilution factors. Using a linear model of growth rate by dilution factor, a grazing rate was determined for each sample. Nutrients from the water samples were measured for nitrate, phosphate, and silicate concentrations. A series of linear regression analyses of the protozoan grazing rates by in situ nutrient concentrations were then done to determine the correlation between parameters. The growth rates of phytoplankton ranged from -5.2e-4 day-1 to 3.2e-2 day-1. Ambient nitrate, silicate, and phosphate concentrations reached 2.25 mM, 2.18 mM, and 0.46 mM respectively. Surface temperatures reached 30.46 centigrade, and the grazing rate exhibited a decreasing trend with higher temperatures, eventually reaching zero at 30.3 degrees. As eutrophication events become increasingly common due to climate change and anthropogenic pollution, it is important to determine how protozoan communities respond to changes in dissolved nutrients.

Cryo-electron microscopy (Cryo-EM) plays a crucial role in macromolecular complex structure analysis, which helps to understand the cellular mechanism and pathologies to facilitate drug discovery and delivery. However, due to factors such as the target conformational change, damage during imaging, or improper sample preparation, low-resolution maps could be reconstructed and pose challenges to the structural analysis. Prior studies have employed different generative deep learning models to enhance the resolution or readability, performing well most on medium-resolution maps but failing to operate with even lower ones. Here, we proposed another modified diffusion model to enhance the cryo-EM density map resolution, expanding the input range of up to 10 Å. Based on the latent diffusion models, we enable it to work directly in 3D density maps with the conditioning factor to utilize the local resolution estimation rather than a fixed global resolution value for the attention mechanism. Compared with the previous work, the conditioning factor further improves the model's stability and robustness, especially in cases where the structure undergoes conformational changes. Our ultimate objective is to provide an improved and efficient solution for cryo-EM density map analysis, enhancing the process's accuracy and efficiency.

Autism Spectrum Disorder (ASD) is a developmental disorder that is characterized by difficulty in social cognition, communication, and behavior. Social cognition refers to mental processes related to how individuals perceive, process, and respond to social information. Elpers and Coyle (2021) found that there is a correlation between social cognition and general intelligence for adults with ASD. However, there is limited research on this relationship in younger age groups and for individuals without ASD. The goal of this study is to replicate the findings from Elpers and Coyle (2021) examining the relationship between social cognition and the intelligence quotient (IQ) in adolescents and young adults with and without autism. 193 participants (ASD = 96) from the NIH funded study on sex differences in autism were included in the sample. To measure social cognition, participants completed the Reading the Mind in the Eyes Test (RMET), a 36-item assessment measuring Theory of Mind or the individual's ability to recognize that others may have different mental states. Participants also completed the differential ability scale (DAS-2) as a measure of verbal IQ. We expect positive correlations for RMET scores and verbal score, in that as RMET scores increase, verbal IQ scores will also increase for adolescents and young adults with and without ASD. We will also explore how age impacts the scores, as we expect older children and young adults to have more verbal skills, hence performing better on the RMET measure. The results of this study will contribute to our understanding of the relationship between social cognition and intelligence from adolescents and young adults to the existing data that has been previously gathered. 

Understanding the molecular mechanisms underlying the unique regenerative response of rodents from the Acomys (Spiny Mouse) kidney to injury is crucial for advancing regenerative medicine approaches. This study investigates the differential RNA expression profiles of cultured Acomys kidney cells as well as (non-regenerative) laboratory mouse kidney cells under hypoxic and normal culture conditions. The hypoxic culture environment mimics the effect of ischemic injury on kidney tissue. Comparative analysis of mRNA expression between these conditions across the two species can uncover potential factors contributing to Acomys' remarkable regenerative capacity. Observations in this model may provide valuable insights into developing novel therapeutic strategies for treating kidney diseases and promoting tissue regeneration in human patients.

According to some measures, the United States has the largest economy in the world. Despite its massive gross domestic product, US citizens still face high poverty rates across states and counties. Why are there persistent poverty rates and why do they vary across the nation? To answer this question, I hypothesize a negative relationship between welfare spending and poverty rates. Welfare spending is one of the most direct ways that the government can provide money to people experiencing poverty. When people have their most basic needs provided, through welfare programs, they are significantly more likely to get out of poverty. To explore this relationship I use a multivariate regression, controlling for other factors that can impact poverty rates. Through testing this data, I hope to illustrate the importance of adequately funding welfare programs to reduce poverty across the nation. By increasing welfare spending individuals can get out of poverty and communities can thrive, improving the lives of all citizens.

Cannibalism is a widespread phenomenon among arthropods with consequences for population dynamics, stability, pathogen transmission, and epidemiology; while it is common in carnivorous arthropods, incidents of cannibalism among non-carnivorous species are less frequent, and the mechanisms behind cannibalism in these species are still poorly understood. Laboratory observations of Pieris rapae (cabbage white) larvae have found that larvae will engage in cannibalistic behavior under certain conditions. The objective of our research was to better understand the conditions that may cause this herbivorous larva to become cannibalistic. Experiments were conducted on variables of density, food source, food scarcity, instar, instar gaps, sex, and prior experience as possible influencing factors in the likelihood that a larvae will engage in cannibalism. Experiments in density, food source, and food scarcity had groups of larvae monitored for 48 hours at differing densities with a collard leaf, artificial diet, or withheld food. For experiments in sex, instar, and instar gaps inexperienced larvae were monitored in sets of two for 72 hours for cannibalism. For prior experience experiments, larvae that had previously engaged in cannibalism were paired with inexperienced larvae and monitored for another 72 hours. We found that higher larvae densities had a greater percentage of cannibalization. Furthermore, a lack of food source produced significantly higher cannibalization than either artificial or leaf diets. A higher rate of cannibalism was also seen in early instars. Prior cannibalistic behavior increased the rate of new cannibalism events within the first 24 hours of observations.These findings provide insights into cannibalistic behavior in P. rapae, with potential applications to prevent cannibalism in laboratory settings and related disease transmission, understand fluctuations in wild populations, and in agricultural settings to leverage cannibalism as a form of natural population control. Future research aims to isolate other possible factors contributing to cannibalism in P. rapae.

Nectar feeding is an impressive ecological niche for a species to fill as it provides a high energy resource for the species, however, obtaining nectar efficiently and without damaging the flower, which will refill the reward, often requires unique specialized mechanisms that can vary among species. Both Anna’s hummingbirds (Calypte anna), from the United States, and White-naped honeyeaters (Melithreptus lunatus), from Australia, are species of birds that are considered primarily nectivorous and have developed morphology that is apt for nectivorous feeding mechanisms independently of each other. One common morphological feature between both species is their long tongue which has a bristled tip that has important nuanced similarities and differences between them. This research looks to analyze the morphological differences between these independently evolved mechanisms through comparing and contrasting the internal and external morphological features present in the tongues of Calypte anna and Melithreptus lunatus. These morphological comparisons are made from two methods; 1) comparing and contrasting external features through 3D models of the specimens tongues from CT scans compiled by using the program 3D slicer and 2) through using paraffin wax histology with hematoxylin and eosin staining to analyze internal cross sectional differences of tongue morphology between species. Understanding comparative differences like location of structures and which structures are present between these species, belonging to unrelated clades, provides insights into how this nectarivorous niche and associated feeding methods can be addressed in different species of birds that are in turn the main pollinators of coevolved plant species. Understanding these comparisons can add to the larger picture of how nectivorous species feed and what features are important enough for allocating energy towards development, as well as understanding plant-pollinator coevolution among continents.

With the increasing use of lithium-ion batteries, the trajectory of the modern world’s energy needs calls for an improvement in their safety and functionality. Current lithium-ion batteries use a lithium salt dissolved in organic carbonates, which results in a liquid electrolyte with high lithium dissociation and fast conductivity. However, the use of organic solvents makes these electrolytes flammable and prone to combustion in the event of a dendritic formation causing a short. One approach to potentially improving these electrolytes is a solid single-ion polymer electrolyte where the anion is part of the polymer chain to potentially allow higher conductivity and lithium transference numbers. Our approach is to synthesize single-ion copolymers with varying weight percentages of a single-ion monomer (SIM) to control the ion concentration and a monomer with an oligomeric ethylene oxide sidechain (ONDI-12) to lower the glass transition temperature. The goal of my work is to identify the ratio of the two monomers that gives optimal conductivity, improving the potential use of our copolymer as a solid single-ion copolymer electrolyte in lithium-ion batteries. Initial electrochemical impedance spectroscopy measurements of our previous copolymers indicate that lower ion concentrations and lower glass transition temperatures resulted in increased conductivity with 20 wt.% SIM. Building from this work, I synthesized the single-ion monomer (SIM) with an attached anion incorporated into the structure to facilitate lithium cation motion. I anticipate copolymerizing this SIM with ONDI-12 at lower SIM percentages using ring-opening metathesis polymerization (ROMP) and subsequently measuring their conductivity. Identifying the SIM to ONDI-12 ratio that optimizes conductivity will improve our understanding of these materials and potentially advance future polymer electrolyte design.

From 2012 to 2022 violent crime in rural America has either increased or stayed above the national crime rate. At the same time, the amount of firearms in these counties rose dramatically while law enforcement expenditure and poverty reduction stagnated. I theorize that a combination of high poverty rates, increased firearm ownership, and fewer police has contributed to the increase in rural crime over the past decade. As the literature suggests, firearms make it easier to commit violent crimes, fewer police make crime harder to detect, and poverty pushes people into crime due to unstable living conditions. I will evaluate the effect of these three factors on rural crime rates by using FBI Uniform Crime Report, U.S Census Bureau, and RAND Corporation data to perform multivariate regression in order to determine causality. I expect to find a strong positive correlation between these three factors and the rural crime rate. I will use multivariate regression analysis to examine the influence of gun ownership, law enforcement spending and poverty on rural crime rates. By finding the causes of crime in rural communities, I will help identify the areas that local governments will need to address to solve problems of violence.

We collected and compared the spectra of air plasma and argon plasma in a dirty and clean direct current (DC) plasma discharge device. After cleaning the plasma tube we hypothesize the measured plasma spectrum will have fewer lines because it wont have as many impurities. The fourth state of matter, plasma, is matter that has been superheated, causing the electrons to be ripped from the atoms. This forms an electrically charged gas that consists of negative electrons and positive ions. Our plasma was created using a DC plasma discharge device. This device creates a plasma between two electrodes inside of a vacuum chamber. A high DC voltage is applied across the two electrodes and a current flows between them. DC plasmas can be utilized as sputter sources to deposit thin films for solar panels and the purity of the plasma can affect performance. Our vacuum vessel was accidentally contaminated with oil and dirt. To evaluate the effectiveness of our cleaning practices, spectra was measured for plasmas in the vessel contaminated with oil and other dirt and then again after the vessel was cleaned. Spectra, the range of wavelength produced when light is dispersed, emitted by air plasma and argon plasma were measured between 645 nm and 1050 nm with an Ocean Optics ST-NIR spectrometer. Spectra before and after cleaning were compared to measure the effectiveness of the cleaning. Our research provides evidence for the best way to clean DC plasma discharge devices in order to remove impurities. The conclusion of this analysis is imperative for efficient thin film plating using DC plasma.

The planning field includes a diverse array of foci from land use to community development to transportation planning. Planners serve diverse communities but often lack representation within the workplace as planning is still a white-dominated field. This project explores the representation and experiences of Asian women in the planning field, addressing two questions: What are the professional experiences of Asian women working in urban planning in the PNW? How does their identity, specifically gender and race, influence their professional perspectives in the built environment? Through semi-structured interviews with Asian women, this research examines the intersection of race and gender within the workplace culture of urban planning. The interviews explore topics such as pathways into the field, identity in the workplace, and representation. While examining identity, it is important to acknowledge that the identity of “Asian” or “Asian American” encompasses a pan-ethnic and pan-cultural group of people. This research does not attempt to produce a monolithic experience of Asian women in planning. Instead, it produces an ethnographic report on the experiences of Asian American women in urban planning. Interviewees shared awareness of the social perception of their race/gender and racial/gendered stereotypes. While the intersection of identities was important to examine, many participants felt gender impacted the way they were perceived more than their race. The report identifies patterns and produces a reference regarding the culture of the built environment workplace for people with similar identities. Providing examples of representation is important to highlight to prospective and current planners to empower and educate those outside of these identities.

While recent advances in sequencing technology have increased the detection of missense variants in human genes, the functional impact of ~99% of these variants is unknown. Improving our understanding of variant effects will make precision medicine more effective, allowing us to define, test, diagnose, and treat genetic diseases better. One way to understand what variants do is to measure and read out each variant’s effect in cell-based assays. However, there are nearly 9 billion possible single nucleotide variants in the human genome. To measure variant effects in a comprehensive manner, scalable experiments are necessary. Previously, the Fowler lab developed landing pad (LP) vectors to conduct scalable cell-based assays over entire gene variant libraries. However, the current LP design suffers from rapid silencing in cell culture, a phenomenon in which cells deactivate the expression of transgenes, greatly limiting the scope of variant assays. Stem cells are known to rapidly silence most exogenous sequences during differentiation, but they are a target model as LPs embedded in stem cells would allow us to study the effect of gene variation in cells specific to the related disease. Through previous work at the Fowler lab and others, we have characterized a set of promoters, enhancers, insulator sequences and other elements that will provide stable and robust expression of transgenes over time. We hypothesize that combining the LP with this set of elements will allow us to stably express variant libraries regardless of cell context. To test this hypothesis, we have designed a nested LP delivery system that allows us to compare different LPs side-by-side in the same genomic context. By comparing expression levels of transgenes over time, we expect to find that LPs enhanced with a set of stabilizing elements will express stronger signals over longer periods of time compared to LPs that are not enhanced.

Experiencing a stressful situation in the presence of another person can lead to two distinct outcomes: a decrease in fear response (social buffering) or an increase (social contagion). Understanding these phenomena and the factors influencing them is essential for advancing the treatments for anxiety and fear-related disorders. In this study, I am investigating how gender and social context can impact fear response and risky decision-making. To do this, I am using a naturalistic foraging task that allows rats to exhibit a wider range of behaviors and provides data that more accurately reflects real-world scenarios beyond the laboratory. The study involves alternating between paired and single trials where rats (n = 10) venture from a safe nest to retrieve food in an open arena where a realistic aerial predator can emerge. I am measuring fear responses to the predator through various quantitative variables, including the latency to leave the nest, the latency to retrieve the pellet, and the number of attempts made. I have concluded data collection on the male pairs, revealing an unexpected trend: male rats displayed greater fear responses in paired trials, indicating social contagion rather than the anticipated social buffering. This preliminary finding suggests that the presence of a single companion may heighten fear responses. I hypothesize that female rats will show a similar (intensified) trend because they tend to be more cautious foragers.

Latino people constitute the largest minority in the U.S., and diabetes is an urgent health issue that impacts the Latino community at twice the rate as white Americans. Existing literature on Latino populations suggests that culturally competent care is critical for important health outcomes like satisfaction, and interventions to improve cultural competency in diabetes care for Latino patients significantly impact clinical outcomes. However, there is limited research on how Latino patients define culturally competent diabetes care. Previous research in South Asian communities demonstrates that the pathologization of culturally relevant foods may cause diabetic patients to face poor metabolic control and increased risk of complications, leading to higher healthcare costs and lower quality of life. Despite research indicating that food pathologization is a barrier to high-quality diabetes care for some minoritized groups, previous research on diabetes care in the Latino community does not focus on food pathologization in diabetes care.Through an ethnographic study in clinics in the Greater Seattle area, we seek to understand the experiences of Latino people managing type 2 diabetes related to discussing culturally relevant foods with providers. We will recruit Latino patients to participate in structured interviews exploring how providers discuss culturally relevant dietary choices in diabetes care appointments. We will conduct content analysis to uncover themes related to food pathologization and the downstream impacts of how providers discuss food choices with Latino patients. By studying the relationship between possible food pathologization and diabetes care, we hope to contribute to a holistic understanding of the benefits of culturally competent care. Ideally, our findings may help to reduce food-related stigma and prejudice experienced by Latino diabetes patients.

The emergence of induced Pluripotent Stem Cells (iPSCs) have allowed researchers to better study the effects of various diseases and mutations on fetal development. One such way of accomplishing this is the breakthrough of the organoid: a complex, iPSC-derived, 3D structure, that provides biologically relevant models for human systems. Lung Organoids (LO) were developed through this technology. However, the current LO models utilize mature lung phenotypes, which do not consider progenitor stages that may be critical for fetal development and the understanding of diseases that may affect this development in utero. The goal of this project is to provide characterization to the early stages of iPSC LO development: the Embryoid Body (EB) and Anterior Foregut (AFE). Using a previously established protocol, the LOs were fixed with 4% paraformaldehyde (PFA) on day 4 (EB stage) and day 6 (AFE stage), then analyzed with immunofluorescence analysis of the corresponding fetal lung (FL) development markers. 135 day old FL tissue sections were used as a positive control. The markers used to establish characterization were SOX17, a marker for the early endoderm germ layer, OCT4, an iPSC marker for pluripotency, and ECAD, a marker for tissue layer separation and cell migration. We hypothesized that all markers would appear in the EB stage, and the AFE stage would experience an upregulation in SOX17 and downregulation in OCT4 and ECAD. My results confirmed an upregulation of 133% for SOX17 and a downregulation of OCT4 by 58% from the EB to AFE stages. Lastly, as hypothesized, ECAD was present in EBs, but not in AFE. In conclusion, the LO stages proved to be similar to developmental stages of in utero development. Further analysis could help with new disease and mutation models for early development in utero, helping prevent devastating outcomes.

American crows (Corvus brachyrhynchos) make a wide variety of calls, however, the scientific understanding of these vocalizations remains subjective and anthropomorphized. Here, we classify crow calls based on behavioral context using less-biased means. In this study, we recorded crows in pre-roost aggregations and during mobbing events throughout Western Washington. Pre-roost aggregations are daily occurrences where crows gather together for protection starting in the late afternoon. We simulated mobbing events by placing an owl model near a group of at least five crows and playing a recording of a crow in distress. We used a bioacoustics analysis program, Raven Pro, to pull out acoustic variables from our recordings for further analysis (e.g. frequency variables, call duration variables, etc.). We are now using these variables to compare the classification efficacy of two machine learning algorithms, random forest and artificial neural network. Based on preliminary results, our first random forest showed over 90% classification accuracy. We are currently exploring the mean decrease in accuracy per variable in our random forest analysis to identify the most important acoustic attributes when classifying calls with this model. We are in the early stages of using an artificial neural network to predict the contexts of calls based on acoustic variables. Machine learning is becoming increasingly common in biological research, but the techniques used by researchers still vary greatly. Comparing machine learning algorithms and establishing consistent techniques for doing so will improve reproducibility across studies and help us resolve outstanding scientific questions like "what do all those crow calls mean?".

Invasive species have spread around the world, purposefully or inadvertently. Many species do not survive in new environments, but of the ones that do they can thrive. These thriving invasives may crowd out native plants, creating ecosystems of a single plant type, which causes the system to lose ecological functions. Despite the issues caused by invasives, not much is known about the causes of their spread. This project aims to determine which parameters influence the spread of invasive English Holly (Ilex Aquifolium), Cherry Laurel (Prunus Laurocerasus), and Portuguese Laurel (Prunus Laurocerasus). I plotted species locations in Saint Edward State Park which is comprised of a mixed decidous and coniferous forest. As I plotted their locations, I also measured the diameters and height. Using the size data, I will be able to determine the age of the plants which will provide more information into time frames that the plants took root. Additionally, I gathered light and temperature data over a year which I will use to find average lux and temperature in each month as well as each season to create predictive temperature maps of the entire study area. Furthermore, I took soil samples, near the invasive plants and in areas where the plants were absent which I will analyze to see if there is a correlation between soil nutrient loads and locations of the invader’s growth. Finally, using a drone I took pictures that will be used to determine tree species, tree heights, and hillslopes in the area. I will then create maps that use all the gathered data to predict environments that the plants will grow in. The information from this project can be used Park wide to determine areas that these invasive species grow so that park managers can find and remove invasive plants quickly and efficiently.

The project aims to explore and experiment, through critical and creative geovisualization practice and pedagogy, innovative ways to embody, imagine, and represent the more nuanced social and spatial understanding of the Capitol Hill Organized Protest (CHOP). Specifically, we plan to implement qualitative forms of representation and analysis into the CHOP digital geographical archive as new data and layers. It involves analyzing individual graffiti, the messages, and patterns of speech, memories shared in the interactive map, as well as data collected from the field visit and interviews/conversations with the participants of the CHOP through the transformation of various modes of data and analysis that value representation in different ways. It draws on disruptive approaches from black digital geographies and critical and socially-relevant GIS to challenge how meaning is made from digital data. Yet, the project’s objective is not just to map these data and representation in/of the CHOP, but the opposite—remaking and even re-imagining through a process of humanistic sense of place-making. We engaged in multiple conversations with both direct and indirect stakeholders, fostering a comprehensive understanding of the diverse perspectives surrounding the CHOP. Direct stakeholders included individuals who had lived and experienced similar conflicts in Seattle’s history with the WTO protests, which provided invaluable insights that allowed for direct comparisons to the circumstances within the CHOP. Indirect stakeholders include individuals who contributed greatly by offering their perspectives on approaching potential challenges of the project. We put forward critical and creative geovisual processes that can draw connections between local community-based participatory and policy work, and how these diverse evolutions of critical GIS and geovisualization tell a more complex and nuanced story about the CHOP by relating to social, political, and cultural practices and as a way of engaged knowledge production.

Per- and poly-fluoroalkyl substances (PFAS) are colloquially known as “forever chemicals” due to their long-lasting chemical characteristics that allow them to persist in nature. Specifically, their man-made carbon-fluorine bonds are extremely durable which makes them valuable in coating non-stick cookware and waterproof materials. These compounds are so indestructible that they accumulate in waterways and are eventually found in animal tissue. Firefighting foam is the most prominent source of PFAS pollution in waterways, which can accumulate in shellfish such as mussels, which humans often consume and can potentially lead to cancer formation. However, it remains unclear how much PFAS are actually in shellfish in Washington State. Using liquid chromatography tandem mass spectrometry (LCMSMS), we will analyze the amount of PFAS in homogenized mussel tissue samples collected from many different sites within the Puget Sound and surrounding waterways. PFAS levels have not been significantly monitored in shellfish in Washington State, this novel research which will provide valuable insight on the potential bioaccumulation of these compounds in various marine organisms and potentially find associations between the proximity to centers of high population density and PFAS concentration.

As we improve methods of renewable energy production, we increasingly require new energy storage technologies. Current research in clean energy materials seeks to merge the charge transfer capability of a battery with the high surface area charge storage of a capacitor. I am developing new ways to generate materials that are simultaneously electrically conductive and contain high surface area (porosity). The guiding principle to achieve conductivity is charge-transfer cocrystals (CTCs), single-phase materials composed of two molecular subunits in which one is electron-rich, and the other is electron-deficient, promoting electron delocalization between the species and throughout the larger crystal. My approach involves synthesis of a porous molecular electron donor cage composed of various combinations of a metal, primarily nickel(ii) and cobalt(ii), with a dicarboxylic acid bridging ligand and a capping ligand of thiacalixarene (TC4A). This species is integrated in a crystal structure with an electron-poor acceptor of buckminsterfullerene (C60). TC4A-based clusters have been shown to accommodate spherical fullerenes with successful electron delocalization; integration of the porous TC4A cage is a novel approach. I use techniques in organic and inorganic synthesis to create the components as well as molecular characterization techniques of nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy and crystal evaluation techniques of powder/single crystal X-ray diffraction (PXRD/SCXRD). In the early stages of this project, I have generated new materials that I can confirm through a combination of IR and UV-Vis spectroscopy contain metals, bridging ligands, and T4CA. Preliminary diffraction signatures are similar to my target cage, and I will use this new cage to create a porous cocrystal with C60. I am also synthesizing and experimenting with different bridging ligands. My ultimate goal is to demonstrate a new type of hybrid electronic device high in its energy capacity and capable of providing sustained electrical energy at low environmental cost.

Protein kinases have been found to regulate cell processes such as cell growth and adaptive responses to the environment. Thus, they act as excellent targets for tuberculosis treatment. The Mycobacterium tuberculosis (Mtb) genome encodes 11 separate serine/threonine protein kinases (STPKs). One of those STPKs is PknF, which our lab has previously found to be associated with a survival deficit in Mtb. Since Mtb utilizes multiple carbon sources during its infection in vivo, my research project aims to test the effect of perturbing pknF expression levels on Mtb survival in different carbon source conditions. I grew an avirulent Mycobacterium tuberculosis (aMtb) strain that conditionally overexpresses pknF upon exposure to anhydrotetracycline (pknF OE) in different media formulations that provided different carbon sources: glycerol and acetate. I measured colony-forming units (CFU) to quantify aMtb survival in these different growth conditions. I compared survival measurements of the pknF OE strain relative to an empty vector control strain. I found that the pknF OE strain showed a survival deficit by day 7 in both media conditions, with glycerol showing a higher survival deficit compared to acetate. The extent of the survival deficit seems to be affected by which carbon source is provided by the media. Previous literature has linked pknF to the regulation of glucose transport and phosphorylation of glucose catabolism-associated enzymes in the citric acid cycle. Based on this, we hypothesize that these processes may be involved with pknF's observed survival deficit in different media. In follow-up experiments, we plan to investigate how perturbing glucose transport or catabolism influences pknF's survival deficit. These findings can be used to inform future studies on pknF as a potential target for tuberculosis treatment during infection. 

One of the most prevalent issues in regenerative medicine is the impact of spinal cord injuries, as it can lead to an irreparable buildup of inhibitory scar tissue and, thus, paralysis. However, organisms such as Xenopus tropicalis tadpoles are able to regenerate their tails as soon as one week post-injury. By studying how they successfully regenerate, we can start to generate effective therapies for spinal cord medicine. I specifically want to know how quickly neurons populate the regenerating spinal cord and how this repopulation leads to functional motor recovery. To do this, I used the process of immunohistochemistry, where a fluorescent marker antibody binds to specific cells to create a fluorescent image for visualization purposes. First, I amputated around ⅓ of their tail and created clutches of tadpoles stained for a neuron-specific protein. From my imaging, I noticed that the neurons populated the regenerating spinal cord by five days post-amputation (dpa). I became curious about how this regeneration rate impacted their ability to swim. To test this question, we set up a camera with a lightbox to set up Petri dishes of tadpoles. Then, I uploaded recordings of their swimming into a platform called ImageJ to use particle tracking to quantify the paths of each tadpole into measures such as distance, displacement, and velocity. Currently, we are trying to find other antibody markers that can provide more specific staining of neurons so the program can count them. With more specific staining, I hope to count the number of neurons over a set of zero, three, five, and seven dpa tadpoles. This project will help us answer foundational questions about how Xenopus tropicalis tadpoles regenerate functional neurons after injury.

Sub-gram flying robots have transformative potential in applications from search and rescue, to precision agriculture, and environmental monitoring. A key gap in achieving autonomous flight for these applications is the low lift-to-weight ratio of flapping wing and quadrotor designs near 1 gram. To close this gap, we propose a helicopter-style design that minimizes size and weight by leveraging the high lift, reliability, and low-voltage of sub-gram motors. We take an important step to enable this goal by designing a light-weight, microfabricated flybar mechanism and tail wing rotor to passively stabilize the Coin-Copter: a helicopter-style robot. A 48 mg flybar is folded from a flat carbon fiber laminate into a 3D mechanism that couples the tilting of the flybar to a change in the angle of attack of the rotors. The Coin-Copter’s flybar uses a novel flexure joint design instead of the ball-in-socket joints common in larger flybars. This flybar achieved a peak damping ratio of 0.528, an 18.9x improvement from our initial design. Compared to a flybarless rotor with a near 0 damping ratio, our flybar-rotor mechanism can maintain a stable roll and pitch with relative deviations <1°. This research focuses on testing the yaw stability of a near-gram flying robot by incorporating and improving on flybar designs, roll-pitch-yaw test setups, and writing robot control software using pulse width modulation to help precisely control the heading of the Coin-Copter.

Inflammatory bowel disease (IBD) is a chronic autoimmune disease of the gastrointestinal tract, impacting an estimated 3-million people in the United States. IBD can significantly hinder quality of life and is related to increased rates of depression and anxiety.  Treatments focused on medications often do not consider the social determinants of health. Through a holistic approach, the Comprehensive Self-Management (CSM) IBD study at the University of Washington sought to empower patients in their symptom management. Those randomized into the intervention group participated in an 8-week intervention that considered external factors, like exercise, diet, sleep, life stressors, and relaxation, which could contribute to IBD symptoms. Participants were adults over 18-years old. Patients in the treatment and control group completed an end of study interview about their study and intervention experience. This project's aims were 1) to describe the process of interviewing participants; and 2) to examine the major themes associated with participant experience with the intervention based on the end of study interviews. I conducted interviews over the phone, asking patients about their experience with stool samples, satisfaction with the study, food diaries, intervention modules, and most positive or negative aspects of study participation. Both quantitative findings on participant demographics and qualitative findings from the interview surveys are presented. Thematic analysis was used to identify key themes. Some positive themes from the intervention included accessibility, lifestyle changes, and feeling supported. Some challenges included symptom overlap between IBD and irritable bowel syndrome, recalling daily diet, and implementing study skills when disease was inactive. 90% of participants would recommend this study to a friend, and 70% considered study participation to be easy or very easy. These findings will allow for future improvements and/or revisions to the CSM intervention and the interview process. This will help increase the resources available for IBD patients.  

Orofacial cleft (OFC) is a relatively common birth defect that has major impacts on affected individuals and their families. Underlying causes of OFC include genetics and environmental influences. Genome-wide association studies (GWAS) and linkage analyses have revealed genes in which DNA variants are enriched in OFC cases relative to in unaffected individuals in the same ethnic group. Only a portion of the genetic causes have been identified. Here we focus on ARHGAP29, which was identified in several GWAS of OFC. To uncover the role of this gene in craniofacial morphogenesis, and to identify other members of its regulatory pathway, we are working on deleting a paralog of this gene, arhgap29b, in zebrafish embryos. To this end, we have designed four CRISPR guide RNAs that target specific exons in the arhgap29b gene and injected them into zebrafish embryos. We predict that such embryos will a) harbor mutations in the arhgap29b gene, which we plan to test with PCR and sequencing, and b) display abnormal morphogenesis of the face, which we plan to test by microscopy. Alternatively, we may observe a) but not b). In this event we would simultaneously disrupt the other paralog, arhgap29a. These findings will advance our understanding of genes associated with orofacial cleft, hopefully leading to improved diagnosis and underpinning the design of therapies for this disorder.

Autism Spectrum Disorder (ASD) is a complex developmental condition that can affect an individual’s ability to communicate and interact with others. While individuals with ASD can perceive facial structures, they may struggle with remembering and recognizing faces. There is extensive evidence that individuals with ASD atypically process and perceive faces, which can directly impact their ability to understand complex social situations. In this study, we aim to investigate the relationship between facial memory and social responsiveness in children with autism spectrum disorder (ASD) and those that are typically developing (TD). Participants included 399 children (ASD = 280), aged 6-11 from the Autism Biomarkers Consortium Clinical Trials (ABC-CT) study. Clinicians administered the NEPSY subtests for Memory for Faces delayed and Memory for Faces to measure facial memory, and parents completed the Social Responsiveness Scale-Second Edition (SRS-2), 65 question survey measuring social responsiveness. Correlations will be run for NEPSY scores (facial memory) and SRS-2 scores for both ASD and TD groups. We expect the ASD group to score lower on the NEPSY subtests (Memory for Faces and Memory for Faces Delayed) and on the SRS-2 than TD group, and that there will be a negative correlation between facial memory and social responsiveness scores in both groups based on previous research that has shown that children and adolescents with ASD have difficulties in recognizing and remembering faces, and that these difficulties are related to their social impairments. Facial memory impairments play a vital role in the social challenges faced by individuals with ASD, and that interventions aimed at enhancing facial memory skills may have beneficial effects on social functioning for autistic individuals.

Preterm neonates frequently undergo episodes of hypoxia, hypotension, and hyperoxia due to their underdeveloped cardiorespiratory system. As a result, preterm infants are particularly susceptible to brain injury from lack of sufficient oxygen or blood flow. In this study, we use a neonatal ferret model of hypoxic-ischemic-hyperoxic (HIH) brain injury to examine the neuroprotective efficacy of azithromycin (Az), a safe and accessible antibiotic with anti-inflammatory properties that crosses the blood-brain barrier in premature infants. Our HIH ferret surgery model produces global brain injury in Postnatal day (P)14 ferrets, which are developmentally equivalent to extremely preterm neonates. Ferret kits in the surgical group will receive a pro-inflammatory stimulus (E. coli lipopolysaccharide), followed by a bilateral carotid artery ligation and exposure to HIH. Then, surgical animals will be randomized to receive intraperitoneal injections of saline vehicle (Veh) or Az. Control animals will not receive LPS or undergo surgery. We will use a Kruskall-Wallis test to compare P21 ferret weights and brain measurements seven days after surgery to test whether Az is neuroprotective. We will assess pathology using quantitative immunohistochemistry with Iba-1 (microglia) and GFAP (astrocytes) stains. We have two main hypotheses. We hypothesize that 1) ferrets treated with Az will lose less body weight after exposure to inflammation-sensitized HIH than the Veh group, with Az-treated animals being similar in weight to non-injured controls, and 2) normalized brain measurements, corrected for body weight and sex, will show that Veh animals have smaller gyri and sulci measurements than controls, and Az-treated animals will have brain measurements that are more similar to controls. We are optimistic that our experiments will provide evidence that azithromycin is potentially neuroprotective and will offer a promising treatment option for preterm babies with brain injury.

Pediatric patients with End-Stage Kidney Disease (ESKD) and their caregivers often face unfamiliar symptoms and complications, leading to interferences with self-efficacy and self-management, which result in poor clinical outcomes. This uncertainty leaves patients and families wondering: “Is my experience normal?” To address this unfulfilled information gap, we set out to design personal health visualizations that allow pediatric patients to assess their state of normalcy after receiving a kidney transplant. English and Spanish-speaking pediatric kidney transplant recipients and their caregivers were recruited from major transplant centers in the United States, and a standalone network striving to enhance the lives of children with kidney disease (IROC). They participated in three asynchronous Design Sessions involving sharing experiences (DS1), presenting symbolic objects (DS2), and providing feedback on personal health visualizations (DS3) to understand their perceptions of normalcy post-transplant. Data analysis comprised iteratively creating affinity diagrams using the transcripts from DS1 and DS2 to identify thematic areas about participants’ transplant experiences and normalcy. Additionally, we performed classification and statistical comparison using R to evaluate comprehension of DS3 normalcy visualizations. 14 youth (aged 10-21 years) and 16 caregivers participated in the design sessions, revealing diverse perspectives on their experiences. This highlighted the significant need for visualizations that represent normalcy, aimed at enhancing the understanding of patients and caregivers about their health. Our results show the need for normalcy visualizations to include three design principles: incorporating personal values, facilitating peer and self-comparison, and seamlessly communicating abstract concepts to help youth kidney transplant recipients comprehend and contextualize if their transplant experience is normal and what normalcy means to them. Harnessing broader aspects of patients' and caregivers' lives in personal health visualizations can enhance their awareness of progress towards normalcy. This approach helps to empower them to make informed decisions, fostering a sense of normalcy.

Hemophilia A, a severe genetic bleeding disorder affecting 1 in 10,000 people, is caused by genetic mutations inducing an inability to produce a clotting factor necessary to stop bleeding. Current treatment—replacing the missing clotting factor (FVIII)—carries risks like costly long-term injections and inhibitor antibodies in ~30% of patients. Our lab investigates base editing, a promising gene therapy solution aiming to repair the mutated FVIII gene directly to recover the natural production of the clotting factor. Our project uses a dog with a naturally occurring mutation similar to human hemophilia A, as a model for developing the treatment. In Phase 1 of this project, I will use mutagenesis and gel electrophoresis to create a plasmid containing the mutant canine FVIII gene, and other lab members will use hydrodynamic injection to apply it into mouse models. Following the verification of delivery through aPTT phenotypic examination, I will begin phase 2 by developing the CRISPR-Cas9 base editing plasmid. This will include insertion of our sgRNA into an existing plasmid, insertion of CAG promoter, maxiprep to produce a large quantity, and finally gel purification of the DNA. Following confirmed DNA sequencing of the constructs, we will use hydrodynamic injection of a mixture of the mutant canine FVIII plasmid and base editing plasmid into our hemophilia A mouse models and aPTT examination to determine the efficacy of the designed plasmid. Phase 3 will apply the base editing plasmid to treat the dog model, through collaboration with other lab members developing delivery strategies. This research holds immense potential for hemophilia A patients, offering a one-time, potentially curative solution compared to the limitations of current treatments. If successful, we expect the project to demonstrate a recovered FVIII gene and FVIII expression- first in the mouse model, then in the canine.

Traumatic brain injury (TBI) is caused by an external force to the head, resulting in brain injury and is a major cause of death, particularly in adults 75 years and older who are at increased risk of falls which can lead to disability. Humans have a natural response to impact and strain called the Valsalva maneuver, which leads to an increased pressure in the chest and abdomen, which can result in a neuroprotective increase in intracranial pressure (ICP). However, most people are unable to anticipate TBIs and cannot perform their own Valsalva maneuver. Using a ferret model of TBI, the neuroprotective effects of externally-stimulated Valsalva-like response will be assessed. Ferrets are used to model human TBIs because the cortical thickness and layer distribution of their brains are more akin to humans in the ferret compared to rodents. The ferrets will be randomized to one of the three groups: control, TBI+sham valsalva, and TBI+valsalva. To show that the intracranial pressure of ferrets can be transiently increased, an inflatable cuff will be utilized to exert pressure on the abdomen, resulting in a partial Valsalva maneuver. TBI will be induced in the ferrets using a closed-head impact, and the neuroprotective effects of increased ICP from the inflatable abdominal cuff will be assessed using a battery of motor and cognitive tests before and after the TBI event, additionally, brain injury and neuroprotection will be evaluated using histopathology. I hypothesize that the Valsalva maneuver induced by the inflatable abdominal cuff will reduce behavioral deficits resulting from impact. If the behavioral deficits are reduced, this study can work to inform future interventions for TBI, such as environment-sensing wearable devices for high risk populations.

The informational industry’s share of energy expenditures is growing, and the power consumed by network communications has grown faster than others. The growing importance of machine learning (ML), artificial intelligence, and big data will only compound this trend. There is a need for easily manufactured low-cost energy-efficient communications to balance the needs of industry stakeholders and the environment. One such avenue is using perovskite LEDs (PeLEDs) to transmit data over short distances via intensity-modulated light. For PeLEDs to meet the required informational throughput, they must be modulated as frequently as possible without compromising their integrity. The inherent non-linear current-voltage characteristics and charge-carrier behavior of PeLEDs invite experimentation into the signals used to modulate devices at high frequencies. With the use of an automated laboratory testing environment, many high-frequency driving waveforms were used to drive PeLEDs for data on PeLED voltage, current, and photoemission to quantify device performance. Generative ML models trained to associate waveforms with frequency, device lifetime, and power efficiency are then used to generate potentially superior waveforms for testing. This process is repeated iteratively until the best driving waveforms are identified, forming a closed-loop optimization cycle. The expected results of this study are an understanding of how driving waveforms affect key PeLED performance metrics, and which driving waveforms ensure higher frequency, efficiency, and longevity in industrial applications.

Marine microbes produce over half of the world’s oxygen and are major greenhouse gas processors. These tiny organisms are vital to life on Earth as they cycle nutrients through marine microbial communities via metabolic pathways that are not yet fully characterized. We gain insight into how key compounds are cycled throughout different environments and microbial communities by studying transporter proteins as they mediate nutrient uptake and export in microbes. We aim to compare the abundance of transporters between marine microbial communities by translating and processing sequence data obtained from sequencing the RNA in water samples from multiple locations, capturing a diverse range of organism's genetic information. Currently, there is no standard methodology for identifying genes of transporter proteins from environmental sequence data. We developed a bioinformatic pipeline that identifies transporter genes and allows them to be characterized according to a standardized transporter classification system. This pipeline annotates amino acid sequences from oceanic samples with mathematical models to identify transporters and then annotates these results with taxonomic information. The pipeline enables us to compare transporter abundances between different marine microbial communities, which can be used to infer and map nutrient flow through marine microbial communities.

Inflammatory Bowel Disease (IBD) is comprised of Crohn's disease and ulcerative colitis, which are autoimmune chronic inflammatory conditions affecting the gastrointestinal tract. IBD symptoms include abdominal pain, diarrhea, weight loss, and fatigue, which significantly impact patients’ quality of life. Hence, recognizing and researching these symptoms is critical to creating and implementing targeted interventions that can enhance the wellbeing of individuals with IBD. This project’s aim is to analyze the baseline symptoms and quality of life of individuals with IBD who are enrolled in a comprehensive self-management intervention program. For the study, we utilized a randomized controlled trial where 23 participants with IBD, recruited from March to December 2023, completed an electronic survey through REDCap. The mean age of the participants within the sample was 39.39 years, and 78.26% of participants in the sample had Crohn’s disease. In the survey, the participants rated the severity of symptoms (abdominal pain, bloating, fatigue, joint pain, nausea, gas, and urgency) over one week on a scale of 0-10, with larger numbers corresponding to greater severity. Additionally, participants completed a 10-question short inflammatory bowel disease questionnaire (SIBDQ) on a scale of 10-70, in which a score less than 50 indicates poor health-related quality of life. Among all patients, fatigue was the symptom with the highest severity (M: 6.70, SD: 2.51). The following most severe symptoms were bloating (M: 4.22, SD: 2.49), abdominal pain (M: 3.87, SD: 2.16), joint pain (M: 3.83, SD: 3.49), and nausea (M: 3.57, SD: 3.01). The total mean SIBDQ score for the sample was 44.17 (SD: 11.12), indicating low health-related quality of life (<50) among our sample. Our study’s results suggest that future IBD research should aim to create interventions that not only improve quality of life, but also improve extraintestinal symptoms, such as fatigue and bloating, in patients with IBD.

Asthma exacerbations often begin and increase in severity at night. Though animal models have shown molecular circadian rhythm involvement in immune and inflammatory responses, little is known about how circadian rhythms impact responses in humans or diseases such as asthma. BMAL1/ARNTL, CRY1, NR1D1, and PER2 are the genes that form the “cellular clock” by which cells tell time. Our hypothesis is that core circadian gene expression is maintained in an expected, rhythmic manner in epithelial cells from donors with asthma. We use an ex vivo model with human airway epithelial cells cultured at an air-liquid interface in a temperature cycled incubator to mimic the epithelia of the human airway. After temperature cycling to synchronize cellular circadian cycles, RNA collection occurs every four hours over a 48-hour period. After RNA isolation, I perform reverse-transcriptase quantitative polymerase chain (RT-qPCR) on a planned eight donor lines (4 healthy/4 asthmatic) to measure the gene expression of the four clock forming genes. In three asthmatic donor lines, I have found that core circadian rhythmicity is maintained in asthmatic epithelial cells and resembles the circadian rhythm expression in eight healthy donor lines previously analyzed. Shown through a preliminary study conducted by the lab, genes linked to asthma in the IL-17 signaling pathway have altered circadian rhythms of gene expression. In the future, I will use qPCR to study immune and inflammatory genes to confirm the altered rhythmicity across a wider scope of donor lines. In addition, I will analyze gene expression in different subsets of asthma to investigate whether altered circadian regulation contributes to asthma subtypes, such as T2-low which has been linked to IL-17 signaling pathway dysregulation. Investigating the differences in asthma-related circadian gene expression is essential to the development of chronotherapeutics – therapies that take into account time of day.

While discussing as a group what types of experimentation we could potentially do, we had a variety of different ideas. We thought that with the DC plasma source available to us, it would be interesting to compare how the cleanliness of the vacuum chamber impacted when breakdown would occur. For our research, we are using a DC Plasma Discharge device, which creates a plasma between two electrodes inside of a vacuum chamber. A high DC (direct current) voltage is applied across the two electrodes and a current flows between them. Plasma, the 4th state of matter, is a gas where electrons have been stripped from atoms or molecules in a gas. What results is an electrically charged gas consisting of negative electrons and positive ions. The point at which a gas becomes a plasma is called breakdown. Breakdown depends on the pressure in the vacuum vessel, the distance between the electrodes, the type of gas and the voltage applied. A Paschen curve relates the breakdown voltage to the product of the distance between the electrodes and the pressure in the vacuum vessel. Our goal was to see how a dirty vacuum chamber would impact the Paschen curve. We expected that breakdown would happen at lower voltages with the clean vacuum chamber. We obtained data for creating the curve by running the plasma tube and measuring the pressure as the voltage increased while the vacuum chamber was contaminated with oil. We recorded pressure and voltage values for when breakdown occured and repeated this process with different distances. We then gathered the same data after the vacuum was cleaned. The implication of our research is that it will add to information on how the cleanliness of a vacuum chamber determines when breakdown happens in a plasma tube. In the future, more trials could be run and different gases could be tested. 

Community-based Archaeology can allow researchers to interact and cooperate with descendant populations to establish a more ethical and accessible discipline. This past summer, I traveled to Kodiak, Alaska to conduct archaeological fieldwork as part of the Old Harbor Archaeological History Project. This year, the project set out with an added goal; the facilitation of a cultural camp for local Indigenous youth. Serving as a counselor, I aimed to expose Indigenous youth to archaeology by showcasing an ancestral site of their heritage while working with adult community members to create an enriching, and fun, cultural learning environment. Community members of varying ages from Old Harbor, Alaska, joined me at the camp on Sitkalidak Island for this experience. This poster will share my experience in facilitating the cultural camp and discuss the importance of archaeologists' connections with community members. It will also spotlight the knowledge that the archaeological team and Indigenous youth took away from Alutiiq community presenters, including subsistence methodologies as well as Indigenous language, dance, and arts. Ultimately, this poster will demonstrate how community-based work can have wide-reaching, positive impacts on both descendant populations and the quality of archaeological research.

Every forty seconds in the United States, someone suffers from a heart attack or stroke. Heart attack and stroke can be caused by the blockage of blood vessels by small, transient emboli, or clots. The risk of these attacks increases with age, and there are sex and ethnic based inequalities in the prevalence of these thrombotic events. These emboli can form through various pathways. One factor that can affect platelet aggregation is Von Willebrand Factor, which acts as a scaffold for platelets to bind to, creating a stable clot. In our microfluidic devices, I have observed the detachment of small emboli from large platelet aggregations, which I believe can model transient thrombotic embolisms in the body. Von Willebrand Factor is of specific interest to me, as I have observed that higher levels result in larger platelet aggregations, and therefore more emboli detachment events. This project investigated the question: What is the composition of these detached emboli and what part does Von Willebrand Factor play in their makeup? I hypothesized that these emboli will have high Von Willebrand Factor content and a core of activated platelets surrounded by inactivated platelets, which is what allows for the emboli’s detachment and transient nature. I employed flow cytometry, which causes specific components stained by fluorescent antibodies like PAC-1 and P-selectin to light up. This allows me to determine the composition of the emboli in terms of activated platelets and Von Willebrand factor. If my hypothesis that the emboli have high Von Willebrand Factor content is correct, this could have significant implications for treatments for heart attack and stroke, as current antiplatelet therapies do not target Von Willebrand Factor. If we can create more efficient treatments by knowing what the treatments should be targeting, there are countless people whose health can be positively impacted.

The estuarine dynamics of Puget Sound, (Washington, USA) are complex, with high spatial and temporal variability, influenced by factors that control the circulation and mixing of offshore and estuarine waters. However, determining these mixing impacts on a smaller scale can be difficult. Colvos Passage, a distinctive and understudied passageway of Puget Sound, is unlike other channels because surface currents remain consistent in direction regardless of the tides. Here, we investigate mixing in Colvos Passage as water flows into the main basin of Puget Sound during different tidal cycles using Seagliders. We conducted repeat surveys using Seaglider CTD data and fixed position CTD casts at different tidal cycles throughout the winter of 2023-2024. We measured temperature, salinity, and density from Seaglider transects to track the body of water as it exits Colvos Passage into the main basin and provide insight into the complexity of estuarine mixing and circulation. Preliminary results suggest that the body of water in Colvos Passage is well mixed throughout the progression of the tidal cycle facilitating the tracking of this water mass into the main basin. This study is the first from the University of Washington’s new Student Seaglider Center (SSC), a student-run laboratory where students gain valuable experience in testing, deployment, piloting, and scientific planning of refurbished Seagliders. The SSC continues to build on this study to understand circulation in Puget Sound which can support local forecasting and effective pollution mitigation strategies.

Eukaryotic DNA is wrapped around nucleosomes to be packaged into a cell’s nucleus. Nucleosomes are made up of a combination of canonical histones (H2A, H2B, H3, and H4) and histone variants. Histone variants are evolutionarily derived from their canonical counterparts and can replace canonical histones to perform specialized chromatin functions. Given their crucial and widespread functions, mutations of histone genes are correlated with poor prognosis in cancers. Histones and their variants are typically evolutionarily conserved in sequence and function. Therefore, lineage-specific differences in histone repertoires present unique opportunities to understand their functional consequences on genomic organization and biological processes. Here, we study two such changes in the H2A repertoires of budding yeast and fruit flies. Most eukaryotes including humans have an H2A repertoire of canonical H2A and two variants– H2A.X important for DNA damage response (DDR) and H2A.Z essential for gene regulation. However, in yeast, H2A.X entirely replaced H2A, and in flies, H2A.X and H2A.Z are fused into a single variant H2Av. We take two approaches to discover the adaptive advantages of these changes. First, we are studying the evolutionary origins and diversification of H2A repertoires in yeast. We find that many basally branching fungi have a canonical H2A, suggesting that only some yeast have lost canonical H2A. Second, we are recreating the fly and human H2A repertoire in S. cerevisiae. We find that while yeast with a fly-like H2A repertoire have a DDR, it is dramatically reduced compared to wild-type yeast. This raises the intriguing possibility that a fly-like repertoire might lead to a trade-off of compromised DDR in fly genomes. We are now analyzing how DDR-dependent processes like meiosis are altered in fly-like yeast. By leveraging the power of evolution and yeast genetics our work will reveal the biological consequences of unexpected histone innovation.

The variation in traits associated with fitness often results in selective pressures, thereby influencing the phenotypic traits observed in populations across diverse environments. The exploration of differences among individuals within and between populations has consistently been a key emphasis in evolutionary biology, seeking to understand how organisms adapt to a range of environments. In this research, I analyzed pelage color variation in the least chipmunk (Tamias minimus). Focusing on intraspecific variation—differences observed within a species—I conducted a quantitative analysis of pelage brightness across populations distributed throughout the range of the least chipmunk. This species is well-suited for this study because of its extensive geographic range, encompassing a variety of environments that span from semi-arid shrub steppe to high-elevation forests. I investigated the relationship between chipmunk habitat, utilizing various environmental variables, and pelage brightness. I predicted that precipitation and temperature would influence the brightness of the pelage, which often corresponds to the ability of an individual to camouflage or thermoregulate in their environment. To test this hypothesis, I photographed 334 museum specimens and measured the mean and standard deviation luminosity (two measurements of brightness) along four dorsal stripes and the head. I then extracted environmental variables using the GPS coordinates for each individual, these included 19 bioclimatic variables, elevation, latitude, net primary productivity and other variables related to geographic location. To examine the influence of environmental factors on the pelage color, I conducted generalized least squares analyses and principal component analyses in R. The initial results of my research indicate that the pelage color of a population is influenced the environment. Most notably, there is a significant correlation between pelage color and precipitation. In habitats with increased precipitation, such as forests, chipmunks tend to exhibit darker colors, whereas in regions with low precipitation, like deserts, individuals often display brighter pelage.

Our research aimed to investigate the microbial diversity in Pieris rapae larvae obtained from three distinct settings: wild-collected larvae, larvae fed with leaves in a laboratory setting, and larvae fed with a standard artificial diet. Additionally, this investigation sought to identify the factors contributing to developmental delays in artificial diet-fed larvae, while also investigating the underlying cause of increased cases of infection and mortality affecting the laboratory colony. Initial observations indicated that wild larvae exhibited the fastest development and appeared healthiest, followed by those fed with leaves, both settings showing the lowest instances of disease and mortality. Conversely, the artificial diet group experienced developmental delays and frequently succumbed to disease before pupation. Based on these observations, we hypothesized that variations in microbial composition within different diets and environments contributed to the disparate outcomes. Furthermore, we speculated the possible identification of bacterial strains with known associations with promoting or hindering larval success. To analyze the larval gut microbiome, a specialized contraption was designed for sterile frass (feces) collection. Frass, skin, artificial diet, and leaf surfaces were swabbed onto TSA media, enabling the isolation of distinct colonies and species. Morphological characteristics, gram staining, and Sanger sequencing data of the 16S rRNA gene were used to identify the bacterial colonies at the species level. The identification of six bacteria at the species level yielded intriguing results, with particular interest surrounding Bacillus subtilis and Bacillus thuringiensis. The presence of B. subtilis exclusively in the artificial diet group suggests its potential involvement in the developmental delay observed in the larval population fed by artificial diet. Conversely, the identification of B. thuringiensis implicates a potential bacterial infection, which could explain symptoms experienced by the colony. These findings have potential implications for enhancing larval outcomes in colonies or, in contrast, pesticidal applications in an agricultural setting. 

Marine microbial communities produce and cycle organic matter in the ocean. Some of this organic matter is in the form of metabolites, small, organic biomolecules that are present both inside of microbial cells and dissolved in seawater. Studying metabolite dynamics provides insights into the fate of a significant portion of marine primary production as well as microbial community interactions that influence short and long term carbon storage in the ocean. Here I analyzed both dissolved (extracellular) and particulate (intracellular) metabolites from the 2019 Gradients 3 (G3) research cruise that were collected along a latitudinal transect. Sampling stations spanned the North Pacific Subtropical Gyre, an area with low nutrients and primary productivity, to the North Pacific Subpolar Gyre, an area with higher nutrients and primary productivity. I extracted particulate metabolites using a modified Bligh and Dyer extraction and dissolved metabolites using cation-exchange solid phase extraction. I acquired metabolite data using liquid chromatography mass spectrometry and processed the data using Skyline software. In both dissolved and particulate samples, metabolite pools were dominated by compatible solutes, compounds organisms use for handling osmotic stress, as well as amino acids. Metabolite abundances in both phases largely increased traveling northwards along the transect, reflecting increases in productivity, microbial biomass, and nutrients. However, certain metabolite concentrations did not follow this trend, suggesting that differences in microbial community composition or physiology may play an important role in regulating the synthesis of these compounds. These results show how varying environmental conditions affect the composition of organic matter produced by marine microbial communities. This information can be used in to predict how marine primary producers will store and use carbon in a future changed ocean.

Acute pancreatitis (AP), inflammation of the pancreas in response to injury, is the leading cause of hospitalizations for gastrointestinal disorders in the US. Severe AP is correlated with a 30% mortality rate and treatment options are limited to supportive care. Our lab has previously reported that increasing serum levels of activin A, a TGF-β family member that regulates inflammation, is correlated to severity of AP in humans. Additionally, activin A has an established role in immunomodulation of neutrophils, which are critical innate immune cells driving AP. Our project aims to test the hypothesis that activin A promotes neutrophil activation and infiltration in AP. We performed qPCR on HL-60 cells treated with DMSO and/ or activin A to identify changes in the mRNA expression of immune activation genes, including CD11b, CD66b, and TNFɑ. We will also perform transwell migration assays on HL-60 cells treated with DMSO and/ or activin A to observe differences in neutrophil migration in vitro. We also intend to perform Western blot analyses, probing for pAKT and pERK, to identify the mechanism of activin A-induced neutrophil stimulation. We observed an increase in immunostimulatory mRNA in neutrophils treated with DMSO, which was further increased by activin. Additionally, we anticipate activin A and DMSO stimulation to promote neutrophil immunomodulation via the ERK pathway and increase neutrophil migratory capacity. The results of this project can provide more evidence that activin A can be a biomarker useful for risk stratification of patients with AP and allow for individualized treatments.

Previous work has shown that short-term treatment of rapamycin (an mTOR inhibitor) in aged mice can increase lifespan, improve heart function, attenuate inflammation in gingiva and periodontal bone, and remodel the oral microbiome toward a more youthful state. Nevertheless, important questions arise of whether the beneficial effects of rapamycin persists. Here, we demonstrate that rapamycin continues attenuating periodontitis in old mice even following an 8-week cessation in treatment. Quantitative Real-Time PCR analysis was used to determine expression levels of inflammation markers attributed to periodontitis. Quantitation and analysis were completed by first standardizing target genes relative to ß-actin and GAPDH expression. Data were analyzed where appropriate using one-way analysis of variance (ANOVA) with post-hoc Tukey test for multiple comparisons, where p-values <0.05 were considered statistically significant. Statistical analysis was completed on GraphPad Prism 10.0. Our findings show elevated levels of inflammatory cytokines IL-1a and IL-1b and bone turnover markers NFATc1 and MMP13 in aged alveolar bone were decreased after rapamycin treatment, and the attenuation persisted. Additionally, PI3K-α and PI3K-γ expression, both upstream of mTOR, associated with periodontitis, and elevated in old mice, were inhibited to levels of young mice, and results persisted. These findings demonstrate that the potential therapeutic effect of rapamycin persists in attenuating periodontitis and suggest that a drug dosage regimen can potentially be optimized.

My research project aims to combat inflammation and fibrosis caused by biomaterials and implants by developing a deeper understanding of the effect of CID on macrophage phenotype. Non-degradable biomaterials can provide long-term stability in the body but can elicit a foreign body response, such as inflammation. The project involves engineered M1 cells which were created and published by the Giachelli and Scatena Lab within the Department of Bioengineering at UW. We have two groups of mice: one control group that has been injected with engineered TLR4 (Toll-Like Receptor 4) cells but not given the CID (Chemically Induced Dimerizers) drug, and another group that has been injected with both the engineered TLR4 cells and given the CID drug. Previous in vitro studies have demonstrated that the engineered TLR4 cells activate the proinflammatory M1 macrophage phenotype when treated with CID. Activation of the proinflammatory M1 phenotype is expected to result in alteration of the healing process, including altering the collagen quantity and structure. At this stage in the project, we have tissue samples from both these groups, and I am currently analyzing these samples using both H&E staining and Picrosirius Red staining thus allowing me to measure healing parameters, like density of collagen. At the same time as data collection, I am using ImageJ to obtain measurements and expect to see the group with CID have a denser collagen structure around the material than the group without CID since CID causes activation of the M1 phenotype. Conducting the analysis on these tissue samples will help address the effect of CID on healing parameters, such as inflammation, and help us develop a better understanding of the roles that M1 and M2 phenotypes play in the healing process.

Autism Spectrum Disorder (ASD) impacts many different aspects of the individual’s functioning, especially cognitive and social functioning. Previous research has found that social pragmatic problems were positively associated with problems with inhibition and emotional control. Additionally, research has shown a relationship between greater executive function challenges and more social challenges among 6-12 year old children, however, no significant sex differences were found between executive functioning (EF) and social challenges. This study leveraged a large sample of sex matched adolescents with and without autism to investigate the relationship between executive functioning and social functioning. 318 participants (ASD =163), ages 8-17 from the NIH funded multisite study on sex differences in autism were included. Parents of participants completed the Brief Rating Inventory of Executive Function (BRIEF), a 86-item questionnaire with eleven sub-scales that measures executive functioning ability. Parents also completed the Social Responsiveness Scale -2 (SRS-2), a 65-item questionnaire with five sub-scales that measures autistic traits. Correlations within ASD and TD groups will be conducted between BRIEF EF subdomains and SRS social communication index. In addition, sex differences will be analyzed for BRIEF and SRS scores within each diagnostic group. We expect that the ASD group will have elevated scores on BRIEF and SRS compared to the TD group, consistent with greater executive functioning challenges and more autistic social traits. Within the ASD group, greater executive functioning difficulties will be related to more autistic social behaviors. This research can help understand more about the variability between EF and social functioning in individuals with autism.

Vertical velocities are a fundamental component of ocean flow and are vital to characterizing global circulation. However, vertical velocities are small compared to horizontal velocities and are thus difficult to measure. Previous studies attempting to estimate them ignore the impacts of topography, mesoscale eddies, internal waves, and spatial variability. Novel estimates from the Argo float array allow for direct estimates of vertical velocities. This project will focus on comparing these new Argo estimates with vertical velocity observations from moorings in the Southern Ocean. The Southern Ocean is an important site of vertical volume transport for mass ocean circulation with global implications, particularly the Antarctic Circumpolar Current which dynamically links many of these interactions. We expect vertical velocity characterized by moorings to maintain coherency with Argo float estimates. Differences may occur, however, due to mismatches in spatial resolution between Argo-based estimates and mooring-based estimates, which rely on mass conservation across larger scales. In comparing novel Argo datasets to known mooring values, we gain a more complete understanding of vertical velocities in the Southern Ocean which have direct implications for data assimilation in models and parameterization of energy pathways.

Phytoplankton play a pivotal role in marine ecosystems by providing essential nutrients and energy to heterotrophic microorganisms through the release of low molecular weight (LMW) metabolites into the dissolved organic matter (DOM) pool. Ectoine, a compatible solute primarily sourced from bacteria, acts as a safeguard against osmotic stress. In this study, we investigate the intricate interaction between phytoplankton and bacteria consumers by comparing the growth dynamics of two diatom species, Thalassiosira pseudonana and Thalassiosira oceanica, in the presence of ectoine. Cultures of T. pseudonana and T. oceanica were cultivated under axenic, controlled conditions, and their growth was monitored using measurements of relative fluorescence units, cell enumeration techniques, and metabolomics analysis. Our hypothesis suggests that samples with ectoine will exhibit higher metabolite abundance and growth rates compared to those without. Through a comparative analysis between cultures supplemented with ectoine and those without, this research endeavors to shed light on producer-consumer interactions within controlled laboratory settings, offering valuable insights in the complex microbial dynamics prevalent in oceanic environments.

Open-top light sheet (OTLS) microscopy enables the volumetric imaging of large tissue specimens for research and potential clinical assays. No destructive sectioning is required, allowing the tissue to be used for standard downstream assays (e.g. H&E and molecular analyses) after the 3D pathology process is completed. While our typical 3D pathology workflow uses many of the same reagents as standard formalin-fixed paraffin-embedded (FFPE) histology, including xylene and ethanol along with a food-grade cinnamon oil (ethyl cinnamate), we would like to show that our processes do not negatively impact the quality of molecular biomarkers in valuable archived clinical specimens (FFPE). In previous research, we qualitatively demonstrated that tissue morphology and immunohistochemistry markers were unchanged before and after our 3D pathology workflow. Here, we aim to quantitatively assess the effects of our processing methods on FFPE breast carcinoma tissues using standard ER and HER2 immunohistochemistry (IHC) and HER2 fluorescent in situ hybridization (FISH) analyses, as well as nucleic acid integrity metrics (RIN scores, RNA bulk yield, signal quality). We hypothesize that the molecular characteristics of our processed specimens are statistically equivalent to those of unprocessed specimens. To demonstrate this, I have obtained two adjacent 3-mm diameter punch biopsies from 26 archived (FFPE) breast specimens. For each specimen, one sample will undergo our standard 3D pathology workflow. I will then submit both samples to pathology labs for quantitative comparison of standard clinical biomarkers (e.g. HER2 and ER expression) and nucleic acid integrity metrics. We will demonstrate that our lab’s 3D pathology protocols do not negatively impact tissues in terms of molecular characteristics, which will be important for clinicians to allow our nondestructive 3D pathology methods to be performed on valuable archived tissue specimens, and for our methods to more-easily translate into standard clinical practice.

Tumors generally spread and remain in one individual; however, transmissible cancer differs. Detected among Tasmanian devil and dog populations, transmissible cancer is defined as whole cancer cells spreading among individuals in a population. Recently, Bivalve Transmissible Neoplasia, a transmissible cancer found among bivalve species, was discovered among soft-shell clams (Mya arenaria) on the East Coast of the USA and Canada; however, it has not been reported in any populations of soft-shell clams on the West Coast. Preliminary data showed that BTN was present in at least one West Coast soft-shell clam population. We focused on testing for BTN among soft-shell clams sampled from multiple sites in Washington State and determining which sub-lineage of BTN can be found among the West Coast soft-shell clams. I extracted DNA from the hemolymph of 37 soft-shell clams from Similk Bay to test for the presence of BTN using quantitative PCR (qPCR). The results indicated that soft-shell clams from Similk Bay tested negative for BTN despite an exposed population nearby in South Skagit Bay. I also analyzed DNA from soft-shell clam BTN from South Skagit Bay and Triangle Cove, Washington, to identify specific genetic markers to diagnose the specific sub-lineage the Soft-shell clams derived from - East Coast, USA or Prince Edward Island, Canada. An SNV in the COI gene specific to the Canadian sub-lineage of BTN was not found, and insertion sites of the Steamer retrotransposon specific to the USA sub-lineage of BTN were present among the West Coast soft-shell clams BTN samples, showing that the BTN on the West Coast arose from the USA sub-lineage. Given these results, analysis of more sites will provide information on how far the USA BTN sub-lineage has spread among West Coast areas and possibly how neoplastic cells can transmit among softshell clams across a body of water.

As global demand for renewable energy grows, new avenues emerge to design cost-effective routes for enhancing energy storage and capture, such as high-capacity batteries and next-generation solar cells. This study focuses on characterizing the underlying dynamics of model energy storage and conversion materials in response to oscillating stimuli. The near-term goal is to develop a generalizable method of doing this that may be adapted to a wide array of different materials. The long-term goal is to apply this method to understand the fundamental chemical dynamics involved in the function of these materials, ultimately accelerating progress in improving ion storage media for batteries and enhancing photovoltaic efficiency. The first target is to selectively detect vibrational signatures associated with electron accumulation in response to an applied potential in semiconducting nanoparticles, with applications as anode materials for alkali metal ion-based batteries. I aim to do this by developing a phase-sensitive detection method using lock-in amplification, which allows measurement of small spectral signals that would otherwise be undetectable due to noise. To hit this target, a well-studied, reversible ferrocene/ferrocenium system was subjected to alternating current (AC) electrochemical modulation and probed using visible light. The electrical signals induced in these materials were analyzed at characteristic frequencies. By monitoring the spectral fingerprints of each ferrocene and ferrocenium, I will extend the application of these spectroelectrochemical methods to the model titanium(IV) oxide (TiO₂) electrode. Moving forward, this method to probe reaction dynamics may be applied to analyze the stabilizing effect of performance increasing modifications on anode materials within alkali metal-based batteries.

Although physical activity benefits children's health and development, most children do not meet the recommended 60 minutes of physical activity per day. Additionally, barriers to physical activity, such as lack of access to staffing or equipment at low-resource schools, can exacerbate population-level health disparities. With the goals of promoting physical activity in children and tackling health inequities, 13 schools across WA state were recruited for participation in this study with support from the Office of Superintendent of Schools (OSPI). Schools were randomized to either receiving a Physical Activity Coordinator (PAC) (n=4) or being an Active Control school (n=9). The purpose of this study is to investigate the PAC program's impact on children's physical activity at school and how children feel about physical activity. Data was collected via student surveys and observations before school, during lunch, and after school using the System for Observing Play and Leisure Activity in Youth (SOPLAY) method. Metrics collected via SOPLAY include area conditions, the number of children engaged in physical activity, the type of their physical activity, and the type of social interactions. Using our collected data, we are now working to analyze the impact of the PAC program and anticipate finding increases in some of our collected metrics. As part of the team, I worked on data collection through school observations, data verification, and data analysis. These findings are important because investing in building healthy habits in our children will pay dividends for their current and future health. Hopefully, the lessons learned through this study can be applied on a broader scale to help promote physical activity and tackle systemic health inequities.

Genome-wide association studies demonstrate an association between the single nucleotide polymorphism (SNP) rs3184504 and many autoimmune diseases, including Type 1 Diabetes (T1D). The rs3184504*C allele encoding for arginine is mutated to encode for tryptophan in the rs3184504*T risk allele, resulting in a loss-of-function of the adaptor protein SH2B3, a negative regulator of various tyrosine kinases and cytokine receptors. The SNP is uniquely enriched in humans of European descent. Isolation of the SNP rs3184504 is challenging due to its presence in a linkage disequilibrium region. To normalize this donor variability we used a CRISPR/Cas9 system in human peripheral blood mononuclear cells (PBMCs). CRISPR guides target exon 4 of the SH2B3 gene to be cut by the Cas9 enzyme. This cut is then repaired by a green fluorescent (GFP) repair template cassette delivered by an adeno-associated virus (AAV) containing homology arms for the flanking SH2B3 sequence. The insertion of GFP permits the identification of the SH2B3 KO cells. Our previous experiments on SH2B3 KO mouse lines demonstrated heightened signaling response after IL-2 stimulation in T cells, particularly in CD8+ naive and effector cells and CD4+ effector cells. To test this in primary human T cells, we will stimulate our edited SH2B3 KO cells with IL-2 and use flow cytometry to compare differential responses between edited and unedited T-cell populations. We expect to see similar results in our edited cells. Successful gene editing of PBMCs to model the human SH2B3 disease haplotype enables us to more accurately study the biological underpinnings of T1D, ultimately providing new avenues for which to treat T1D.

Quantum dots are nanometer scale semiconductor particles that have been extensively studied over the past decade. Colloidal quantum dots are dispersed in solution, and so can be easily deposited on a surface. This allows them to act as highly versatile quantum sensors. I am studying cadmium selenide quantum dots doped with manganese (Mn:CdSe). They possess a spin of 5/2, meaning they have six spin states, each corresponding to a different quantized energy. These six energies can be probed with photoluminescence spectroscopy, and theoretically appear as six distinct peaks in the spectrum. This allows us to use spectral analysis to read the spin state of a dot. Due to the Zeeman effect, the spin state energies are sensitive to applied magnetic fields. A simple sensing procedure first initializes the spin state, allows it to evolve under some magnetic field, and reads out the final spin state. My work focuses on the initialization and readout of the spin. For this purpose, I previously built a monochromator to characterize the quantum dots under pulsed excitation at various wavelengths, power, and temperature. I am measuring their properties using photon counting correlation measurements, photoluminescence spectra, and lifetime measurements. The goal of these results is to characterize the properties of these Mn:CdSe quantum dots to lay the groundwork for their development as a highly sensitive quantum sensor.

In a recent breakthrough, bullvalene, renowned for its “shape-shifting” molecular nature with over 1.2 million degenerate isomers, has been successfully integrated into polymer backbones. This integration addresses challenges in solubility and thermal properties crucial for tailoring polymers used in manufacturing diverse products ranging from phone screens to organic solar cells. This project aims to deepen our understanding of the interplay between fluxionality and thermal properties by examining the thermal stability of small molecule bullvalene models. Through extrapolating insights for bullvalene-substituted polymers, our research seeks to contribute to the advancement of the development of advanced materials suited for varying thermal conditions. We synthesized small molecule bullvalenes to mimic polymer chains, subjecting them to diimide reduction to suppress fluxionality before comparison with their fluxional counterparts. Their thermal properties were characterized using Thermogravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC). Key findings reveal a decrease in glass transition temperature upon reduction of bullvalene, highlighting the impact of fluxionality on thermal stability. Future work will delve deeper into exploring the thermal properties of small molecule models, providing insights into polymer behavior. We anticipate bullvalene as an internal plasticizer capable of modulating rigidity, solubility, and thermal properties within different classes of polymers, thus enabling a more efficient and cost-effective large-scale industrial production of a wide array of polymeric materials.

Bioconjugation, or the covalent linkage between a biomolecule and another chemical group, creates hybrid "conjugates" that exhibit the properties of both biomolecules and exogenous moieties. The N-termini of proteins often fall outside of their final fold, making the N-terminus an optimal site for conjugation while preserving a protein’s native folding and bioactivity. Consequently, N-terminal modification of proteins and peptides has been a long-standing goal in fields like drug delivery, biotherapeutics, and cellular imaging. However, the current techniques for N-terminal protein conjugation are limited by either the introduction of bulky protein assemblies at the conjugation site, the need for multiple costly and complicated steps, or low site selectivity. In this project, we aimed to develop an improved route for N-terminal bioconjugation. We created a generalizable platform for single-step purification and near-scarless N-terminal bioconjugation of proteins by leveraging the chemistry of the atypically split intein VidaL. To evaluate the effectiveness of our platform, we first examined the kinetics and reaction conditions of VidaL bioconjugation, confirming its ability to modify the N-termini of proteins successfully and selectively. Then, we used our platform to conjugate an alkyne, biotin, or FAM-biotin moiety to the N-termini of fluorescent proteins (EGFP and mCherry), a model enzyme (beta-lactamase), and a model growth factor (EGF). Through measuring fluorescence and conducting nitrocefin and proliferation assays, I found that, regardless of the moiety added, bioconjugation did not impact the native function or activity of these proteins. In the future, we expect that this platform's ability to easily N-terminally bioconjugate proteins with minimal impact on their functionality will find use across the growing fields of applied chemical biology.

Healthcare workers struggle to find a work-sleep balance, especially during periods of night shifts which according to Likitha Shaik (a clinical researcher at Hennepin Healthcare), results in a 37.7% increase in patient harm and medical errors, highlighting the urgent need for effective solutions. Researchers have proposed polyphasic sleep cycles as a solution to optimize healthcare workers’ sleep by managing accumulating sleep debt. Polyphasic sleep consists of two or more sleeping periods a day that happens to align with the chaotic and unpredictable schedules of healthcare workers, especially those in emergency medicine, trauma surgery, neurosurgery, OB/GYN, and critical care medicine. This literature review investigates how biological and lifestyle factors affect sleep optimization in healthcare workers. Biological factors include age, circadian rhythm, melatonin production, and sleep disorders. Lifestyle factors include physical activity, nutrition and hydration, stress and mental health, and temperature regulation. I constructed this literature review through research using peer-reviewed and popular sources that highlighted the connection between said factors and sleep optimization. The findings of this literature review demonstrate how healthcare workers can best incorporate polyphasic sleep cycles in consideration of the aforementioned biological and lifestyle factors. By understanding how individual factors affect the optimal use of polyphasic sleep, we can start incorporating these findings into staff training and medical school curriculums, especially regarding sleep medicine. Consumer sleep technologies, such as sleep-tracking smartwatches, will also greatly benefit from this research as they can better meet the specific needs of an individual and can be used more frequently in clinical settings. Implementation of these findings is not only crucial to decrease medical errors while enhancing alertness and performance quality among healthcare workers, but also to potentially set new standards for workplace well-being across various professions requiring extended night shifts and/or chaotic sleep schedules.

El Niño is an atmospheric-oceanic phenomenon characterized by the periodic warming of the sea surface in the eastern equatorial Pacific. Profiling data from Argo floats in the eastern equatorial Pacific is used for this research. An Argo float is an underwater profiling technology that can record and transmit real-time data of various ocean parameters at different depths. This technology supports the analysis of temperature, salinity anomalies, and other nutrients. In addition, a numerical model will be developed to simulate the progression of El Niño and evaluate its regional oceanic impacts. With both observational data and modeling output, this research aims to enhance the understanding of the dynamics of El Niño-induced impacts on oceanic parameters at a broader global scale. Based on the current data, I have discovered a clear variation in temperature and salinity according to the annual average. The El Niño Southern Oscillation (ENSO) indicator also suggests that the 2023-2024 El Niño is very strong and still in its development phase.
 

The COVID-19 pandemic heavily affected individuals’ lives, not only through disease transmission but downstream effects such as unemployment and worsening mental health. People living with HIV (PLWH)—as a marginalized and vulnerable population—experience greater mental health risk and life challenges than the general population, which the COVID-19 pandemic exacerbated. Studies that investigate PLWH’s wellbeing during the pandemic are few. In this study, I conducted a mixed-methods study in Qingdao, China using interviews and surveys to explore the effects of COVID-19 and associated policies on the wellbeing of PLWH. My overarching aim was to understand personal experiences of wellbeing, mental health, and factors specific to PLWH before, during, and after the COVID-19 pandemic. Collaborating with Qingtong, an NGO working with PLWH in Qingdao, China, I conducted 15-minute semi-structured interviews with a total of 17 HIV+ individuals whose median time had been living with HIV was 6 years (+/- 2.32). I asked questions about life and wellbeing changes due to the pandemic and challenges they faced. I qualitatively coded the interview transcripts, and found three themes, including (1) Social embodiment, support, and stigma of living with HIV, (2) COVID’s physical and mental effects on PLWH, and (3) Medication access changes over the pandemic. Overall, I suggest that mental health issues experienced by PLWH were not caused by their HIV status solely but by systemic factors such as COVID-19 policies and geographic disparities in accessing medication. Therefore, I advocated that the management of PLWH and relative policies need to be further strengthened in order to respond to any future public health emergencies and to ensure the wellbeing of this population.

Hypoxia-ischemia (HI), or brain injury caused by a lack of blood flow and oxygen to the brain, is a leading cause of infant mortality and morbidity. Contrasting between ages, the effects of HI tend to be more severe in younger neonates. Curcumin, a dietary compound derived from turmeric, exhibits anti-inflammatory, antioxidant, and antiapoptotic properties, but is not bioavailable in molecular form, thus may serve as a neuroprotective treatment when loaded into synthetic nanoparticles to allow for effective absorption and crossing of the blood-brain barrier, forming the treatment NanoCurc. Gestational ages of 37 weeks through 42 weeks are all considered term neonates, yet their brain continues to develop and differ significantly in response to treatments against HI. Using the rat Vannucci model of unilateral hypoxic-ischemic brain injury, we studied the in vivo effects of NanoCurc in neuroprotection, in P7, P10, and P13 rats, equivalent to 34, 38, and 42 weeks’ gestation, respectively. Tissue is collected 72 hours after unilateral carotid artery ligation surgery, followed by tissue staining and analyzed by tracing the healthy tissue versus damaged tissue, to calculate the average percent area loss in treated and untreated rats. I hypothesize that in all ages, neonatal rats treated with NanoCurc will have lower injury in comparison to those treated with saline (vehicle), while the treatment will be more effective in younger rats in comparison to older ages. In the future, NanoCurc treatment may be used as a neuroprotective agent in reducing the effect of HI in preterm and term infants. If NanoCurc provides a stronger neuroprotective effect in the younger population, it may serve to target infants most severely affected by HI, potentially creating personalized treatment for gestational ages.

This research delves into the impact of economic conditions on the macroeconomic health of Israel, specifically focusing on low-income individuals. The study defines the economic conditions of these individuals based on their income levels, employment status, access to education, and availability of social services. The economic health of Israel is measured using a data-driven and multi-faceted approach, which considers various macroeconomic indicators such as Gross Domestic Product (GDP) growth rates, unemployment rates, inflation rates, and income inequality indices. Additionally, other factors such as investment levels, productivity rates, and fiscal balance are taken into account to assess Israel's economic health. By analyzing patterns and trends in these indicators, a more comprehensive understanding of the state of the economy can be formed, which goes beyond basic income measures. This approach forms the foundation for assessing the impact of taxation policies on the overall economic performance of the nation, allowing for a more nuanced understanding of the economy. The research methodology involves collecting and analyzing economic data from Israel, including income distribution, unemployment rates, education access data, and social services availability. The study aims to determine how these specific factors contribute to the economic conditions of low-income individuals and how they interact with each other and the broader economic environment. Preliminary findings suggest that enhancing the economic conditions of low-income individuals could have a positive impact on Israel’s overall economic growth. The research aims to deepen the understanding of these dynamics and identify potential strategies for improving the economic conditions of low-income individuals, thereby enhancing Israel's economic growth. The implications of this research could inform policy decisions and contribute to economic development strategies in Israel. Furthermore, the study will make relevant comparisons with policies from other countries to identify potential solutions or factors that could influence Israel's economic performance.

Black phosphorus (bP), an allotrope of phosphorus, is a 2D Van der Waals material composed of corrugated layers of phosphorus atoms. Few-layer bP is a semiconductor with interesting physical properties, including relatively high carrier mobility and layer-dependent band gap. These properties may be harnessed for applications including nitrogen fixation photocatalysts, thin film transistors, and sensing devices. One limitation that must be overcome before bP can be used in devices is its degradation into phosphoric acid when exposed to oxygen, water, and/or light. Finding passivation methods is crucial for the future use of bP in electronics or photochemistry. As each passivation treatment changes bP’s electronic properties, it is important to find protection methods that are compatible with each use case. To investigate possible methods to reduce surface degradation, we exfoliate bP in solution and treat it with a passivation candidate. We then use ultraviolet-visible light (UV-Vis) spectroscopy to track the amount of unoxidized bP that remains in solution during ambient exposure. Since bP absorbs strongly across the UV-vis region, while the decomposition products, phosphorus oxides, do not, UV-vis is an ideal method for measuring degradation. Possible treatments include attaching alkoxy or thiolate groups via peroxides or disulfides to bP edges to protect the particularly reactive dangling bonds, treatment with radical scavengers such as butylated hydroxytoluene, or noncovalent protection with Tetracyanoquinodimethane (TCNQ).

For the past two decades, Korean pop music, also known as K-pop, has garnered a massive fanbase that grows in number by the day. These dedicated fans gather together online in places that are often referred to as fandom spaces and engage in various activities, interacting with one another through mediums such as tweeting, consumerism, and activism. This study aims to explore these behaviors and the culture that is cultivated within fandoms as it pertains to K-pop and its growing fanbase. Through the use of Benedict Anderson’s theoretical framework for nationalism— imagined communities which describes people who feel comradeship through the mere fact of shared citizenship despite never having met one another— the question of whether or not the internet encourages the creation of an imagined community for K-pop fans is asked. Further, this study will consist of reviewing literature, online ethnography, ethnographic interviews, and auto-ethnography to explore the topic at hand. The combined effort of these methods hopes to confirm the existence of an imagined community in the K-pop fandom and to overall analyze the group behaviors that have developed and are prominent within its ever growing base. Ultimately, this study may also pose the question of how the internet is able to cultivate various imagined communities across fandoms pertaining to different objects of fanaticism such as television shows, video games, and celebrities, and how cultures are created through the means of social media.

The aim of this study was to analyze the three-dimensional deformational changes in the tongue base during natural chewing in a minipig model. Eight 7-8-month-old Yucatan minipigs were used in this study. Under anesthesia, eight 2mm ultrasonic piezoelectric crystals were implanted in the tongue base forming a cubic-shaped configuration, representing the right/left dorsal (RDL-LDL) and ventral (RVL-LVL) lengths, anterior/posterior dorsal (ADW-PDW) and ventral (AVW-PVW) widths, right/left anterior (RAT-LAT) and posterior (RPT-LPT) thicknesses. After the minipig was awakened after anesthesia withdrawal, unrestrained feeding was offered for 10-15 minutes. The amplitudes and onsets for each dimensional change of the crystal-circumscribed region were measured from the start of the jaw opening phase of chewing, and up to 21 concessive chewing cycles were measured. The phases of jaw opening-closing/power stroke during chewing were determined from the simultaneous electromyographic recordings. The duration measurements represented the chewing cycle lengths. The ADW was set up as the reference dimension for the onset calculation (zero point) due to its most stable nature during chewing. All measured dimensions showed either increased (peak/elongation) or decreased (valley/shortening) signals from the baseline. Overall, lengths (RDL-LDL and RVL-LVL) are either shortened or elongated depending upon a given chewing side. The widths (ADW-AVW and PDW-PVW) increased, and the RPT-LAT thickness increased while RAT-LPT thickness reduced during jaw opening of chewing. RDL showed the largest shortening (-42.28% valley-amplitude) while LDL showed the largest elongation (21.15% peak-amplitude, p ≤ 0.05). Earlier onsets occurred in shortening and later onsets in elongation (1.41% to 10.53%) in relation to the reference. Last, the duration of the chewing cycle was 0.45-0.58 seconds. The findings of this study showed a specific kinematic pattern of the tongue base in chewing. This will contribute to a better understanding of the biomechanics of the oropharyngeal function.

Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiovascular disease. Traditional therapies focus on treating the symptoms of the disease and do not directly treat the underlying functional changes. Myosin modulators are a novel class of pharmaceutical agents designed to treat patients with cardiomyopathies by directly modulating cardiac myosin function in the sarcomere. Compounds including Mavacamten (Mava) and Aficamten (Afi) reduce myosin function, measured through its ATPase activity. In this study, I investigate how these small molecules affect the multiple turnover kinetics of the ATPase cycle. Porcine cardiac heavy meromyosin (pcHMM) is rapidly mixed with a two-times excess of fluorescently labeled ATP (mant.ATP) in the presence of actin and fluorescence is measured over time. Calculating the length of time, tau (τ), until the fluorescence has returned to 50% of the peak value estimates the time taken to hydrolyze all the mant.ATP, and is used to calculate the rate constant of ATP hydrolysis (kcat). Both Afi and Mava increase τ and decrease kcat, while a lower concentration of Mava is required to reach similar inhibition as Afi. I also utilize the In Vitro Motility assay to measure the ability of myosin to move actin and compare the effects of Mava and Afi with stopped-flow data. Preliminary results indicate that both Mava and Afi inhibit actin filament velocity, with Mava requiring a lower concentration, similar to stopped-flow. I will discuss how each modulator affects ATP turnover with a direct effect on catalytic activity and extend those results to the functional consequences of these myosin inhibitors. Insight into the impact of these myosin inhibitors on the myosin actin cross-bridge cycle will help provide tailored treatments to patients who are impacted by HCM.

 In geomorphology, computer simulations of synthetic landscapes can help us understand the dynamics of tectonics and surface processes. However, there are always limitations to the applicability of these models to real-world observations. Thus, contrasting computer-derived synthetic versus natural measurements is key to validating our model-derived hypotheses. The main goal of this project is to compare geomorphological markers from synthetic topography from landscape evolution models of strike-slip faults to topographic observations derived from photogrammetric techniques of the Salar Grande Fault in Northern Chile. To accomplish this goal, the project involves four steps. First, the generation of a high-resolution digital elevation model (DEM) from drone images collected in the Salar Grande Fault using Agisoft Metashape software. The second step involves using the constructed DEM to measure and quantify geological markers near the Salar Grande Fault through ArcGIS. Third, the quantification and measurement of the same markers in synthetic topography. And finally, the comparison between our observations. Our results will consist of offset channels and valley spacing measurements to reveal if features from arid landscapes such as the Salar Grande Fault are consistent with model predictions for slow-slipping faults. This project helps to test insights from models and impacts our understanding of how to use geomorphic indicators to study strike-slip faults in arid environments that develop under sporadic erosional processes.

Recent advancements in the ability to measure and manipulate large-scale brain activity with high resolution have significantly enhanced our understanding of the coordination of brain-wide activity, a crucial aspect of brain computation. My project develops a novel system for simultaneously recording and inducing brain activity in mice, using calcium imaging and optogenetics to measure and manipulate brain activity, respectively. This system creates a more streamlined approach to measure activity across the entire cortex against stimuli and behavior, enabling comprehensive study into the mechanisms of inter-area brain activity. The experiments are done with conscious mice in a setup that includes custom software and hardware control using MATLAB, and data is analyzed using Python. One challenge is that the red optogenetic laser can cause aberrant visual responses. When the laser is near the retina, some of the light can travel through neural tissue and hit retinal neurons, ultimately starting a neuronal signaling cascade. An aberrant visual response can interfere with optogenetic effects. I have determined that laser powers greater than 1 mW can elicit this off-target visual response and that we can diminish the response to the laser using a noisy, flickering visual stimulus. When the flickering stimulus is present, the laser power needed to cause a visual response is increased by 100%. In the future, we will use the combination of techniques to understand what brain-wide mechanisms underlie goal-directed behaviors. By measuring and manipulating cortex-wide activity while a mouse completes a task, we can investigate communication between different parts of the brain and identify the mechanisms that impact learning. This technique has implications in more advanced studies of synaptic plasticity, computational modeling, and brain-wide cognition, offering promising new avenues for neuroscience research in the future.

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), sulfur dioxide, and hydroperoxymethyl thioformate (HPMTF), all of which 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 monthly resolution in an ice core, the measurement size is smaller than previously measured by an order of magnitude, at about 1 µg S per sample. We will develop a method to isolate 1 µg of sulfur from an ice core sample by concentrating the sulfur using an anion-retaining resin, precipitating with barium chloride, and drying in an oven. We will quantify the efficacy of our method using a stable isotope mass spectrometer compared to laboratory-prepared standards. We expect that we will reduce our sample size by an order of magnitude (to 0.1 μg sulfur) and improve the accuracy by 50%. Quantifying sulfur isotopes at this resolution will provide information about the seasonality and change in phytoplankton sulfate production.

Cortisol is a stress hormone that plays a role in several vital processes throughout our body, including immune and metabolic regulation and stress responses. Typically, cortisol follows a diurnal pattern, peaking in the morning and gradually declining as the day goes on. More blunted cortisol diurnal slopes have been associated with chronic stress and poor sleep. In Autumn Quarter 2023, we investigated the relationship between diurnal cortisol patterns and hours of sleep among 20 University of Washington (UW) students as part of a class project. Over three days, participants self-collected saliva samples immediately after waking and at 8 PM and answered daily survey questions about sleep, stress, and behavior. Saliva samples were analyzed by students for cortisol concentrations using an in-house enzyme immunoassay protocol. We calculated the diurnal slope by finding the quotient of the difference between the AM and PM cortisol concentrations and the difference between collection times. For this study, we calculated the average slope across the three sampling days for each individual, and the average hours of sleep across the three days. We found that sleeping less than 7 hours per night was associated with a blunted cortisol response. We are investigating if this pattern replicates across UW students using prior class data sets from 2020-2023. Understanding the relationship between these variables, including how sleep interacts with hormones like cortisol, is crucial for gaining insight into how stress influences students' academic performance and can inspire further research.

Western U.S. wildfires are a growing threat to human lives, societal infrastructure, and global climate. While it is well known that meteorological factors impact wildfire intensity and growth rate, quantitative relationships between meteorology and wildfire are scale-dependent. For example, a recent study evaluating all recently observed California wildfires found that explosive fire growth was strongly related to short periods of strong winds and dryness. However, that study used data from a global atmospheric reanalysis (which cannot resolve local winds). As such, even the strong relationships found between meteorology and wildfire growth may have been underestimated. Given the potential consequences involved in predicting and mitigating future wildfires, it is important to understand the real-world accuracy of previously determined fire-environment relationships. To do so, this project compares how local meteorological observations from Remote Automated Weather Stations (RAWS) differ from reanalysis observations during known wildfires. The seasonal and spatial variation in the different relationships is also evaluated. Analysis has shown that the RAWS network is dense enough to adequately represent conditions at each fire being examined. Early results indicate that RAWS and reanalyses have similarly timed wind events during the max growth period. These results are promising, as they indicate that global atmospheric reanalyses can be used as a proxy for ground observations in remote terrain when analyzing periods of extreme wildfire growth.

The Kappa Opioid Receptor (KOR) is one of four opioid receptors found in the body and has an endogenous ligand known as Dynorphin. Binding of Dynorphin to this receptor has been shown to mediate some responses to stress, increase addiction risk, affect learning behaviors, and can provide analgesic effects. I am interested in learning how stress-induced activation of the dynorphin-KOR system affects addiction risk by identifying where in the brain dynorphin acts and how KOR activation affects brain function. I studied "where" by doing injections into specific regions in which Dynorphin is expressed and observing the mechanism of activated KOR. As a part of my project, I was tasked with performing stereotaxic viral infections of two different viruses in order to further study this system and its pathways. To allow for selective targeting of KOR expressing cells, the mice used have a gene for Cre Recombinase placed after the KOR promoter. This creates an environment where all neurons with expressed KOR also have Cre Recombinase in the cytoplasm. From here, I inject double-floxed inverse orientation viral vectors into specific KOR-expressing regions of the brain. The reversed virus is able to find its way into many cells but is only able to be inverted and properly expressed in cells containing Cre Recombinase. Functions of the active virus may differ but there are two primary examples used in my projects. The first is p38 CRISPR, which uses CRISPR-Cas9 technology to knockout the p38 mitogen-activated protein kinase gene, a protein kinase expressed after KOR activation. The second is a reactive oxygen species sensor, as ROS are associated with depalmitoylation and subsequent deactivation of the receptor. The use of a stereotax with this technology allows for precise targeting of different brain regions depending on the location relative to landmark sutures on the mouse skull.

De novo sequencing of peptides is a key technique in proteomics mass spectrometry for detecting and quantifying proteins from biological samples without the use of a reference protein database. This is necessary when working with organisms with low proteome coverage in extant databases, such as in metaproteomics, and in circumstances where the space of possible peptide sequences is extremely large, as in immunopeptidomics. Currently, all state-of-the-art de novo sequencing methods employ deep learning models. However, the majority of the available data used to train these models comes from mass spectrometry experiments that use the enzyme trypsin to digest proteins into peptides. Consequently, these methods exhibit a strong learned bias toward peptides generated by tryptic digestion, and degraded performance when applied to spectra generated by alternative digestion enzymes. This bias limits the models’ ability to generalize to other settings, where the use of alternative digestion enzymes can preserve sequence features that are lost from tryptic digestion. We approach this problem by modifying the state-of-the-art deep learning model, Casanovo, to incorporate an explicit representation of the digestion enzyme as part of its input. We then train Casanovo on a set of spectra digested using a wide variety of enzymes, providing the enzymatic context to the model to facilitate learning the diverse spectral and peptide patterns inherent in non-tryptic digests. We observe that our enzyme-aware model learns enzyme-specific digestion rules and shows significant improvements over the control model on enzymatically diverse data. The enhanced generalizability of our model will enable proteomics researchers to improve the robustness of their de novo sequencing workflows in settings that employ non-tryptic digestion.

The purpose of this experiment was to visualize and record the different rates of expansion for multiple gases as they are launched into the higher parts of Earth’s atmosphere with a High-Altitude Balloon (HAB). The ideal gas law models the behavior of a gas that of which its molecules occupy no volume and have no intermolecular forces (IMF). It is a simple equation; however, it cannot model gases accurately. On the other hand, Van der Waals equation for non-ideal gases better resembles the behavior of a real gas as it includes what the ideal gas law lacks. To test this, we filled three syringes with three different gases to the same volume. We chose to test argon, helium, and nitrogen. We secured the syringes to a container, which served as the payload for the HAB. We also placed an altimeter, thermometer, and a barometric pressure sensor inside the container. Then, we connected the sensors to an Arduino to record each piece of data synced to a stopwatch that is displayed in the container on a screen. Finally, we secured a camera to the container facing the stopwatch and syringes to record the gasses’ volume. Because helium has the weakest IMFs out of the three gases, we believed helium would expand at a higher rate as atmospheric pressure decreases compared to the other gases. The results from our experiment serve as a good example of how far the behavior of real gases deviate from ideal gases modeled by the ideal gas law. Depending on how close our measured values reach the calculated values from the ideal gas law, we can predict which situations the ideal gas law can model the behavior of a particular gas relatively accurately.

Ferrate is an effective technology for water treatment applications because of its capabilities as an oxidant, coagulant, and disinfectant. Furthermore, ferrate is an environmentally benign chemical derived from a ubiquitous mineral on the Earth’s surface. However, ferrate rapid reduction to ferric species reduces its oxidation capacity. Ferrate-coated sand has been proposed as a better deployable method for ferrate in water treatment applications. Sand has a high composition (>80%) of silica (SiO₂) which has been demonstrated to stabilize ferrate reactivity and increase its oxidation capacity. A previous study on the treatment of phenol, a common surface water contaminant, showed that ferrate-coated sand was better at degrading phenol than ferrate only (in the absence of sand). However, the study was conducted in pure water matrices. Here, we are evaluating the oxidation of phenol by ferrate-coated sand in the presence of effluent organic matter and trace metals (i.e. copper). Organic matter is ubiquitous in the environment and can impact contaminant remediation efficiency. Studies have detected trace metals in surface waters which can pose environmental and health risks. Through batch tests, we observed that effluent organic matter hinders the stability of the ferrate-coated media and reduces its oxidation capacity. The results of this study will provide information about the ferrate-coated sand reactivity and capacity for the treatment of complex water matrices.

Human Immunodeficiency Virus (HIV) is a rapidly evolving pathogen with no effective vaccine for eliciting broad protection against HIV infection. The HIV Envelope protein (Env) is a trimeric glycoprotein that is responsible for host-cell membrane fusion and infection initiation. As the only protein on the HIV virion surface, Env is the sole target for neutralizing antibodies. Characterizing the local structural dynamics of Env provides valuable insight into HIV host-virus interaction mechanisms. HDX-MS is an excellent tool for determining structural dynamics by measuring local backbone amide solvent accessibility. Generally, less structured protein regions uptake deuterium more rapidly compared to buried regions or those that are stabilized by secondary structure. We can use mass spectrometry to measure the kinetics of deuterium uptake for peptides throughout the Env protein. HDX-MS provides a detailed portrait of local structural dynamics and order, effectively identifying switching between completely closed prefusion and more open conformational states. A particular HIV Env isolate, A4, is of interest due to its unusually dynamic nature compared to other well-studied Env isolates, such as BG505. Dynamic Env exhibit more conformational flexibility, allowing them to sample various intermediary conformations between open and closed. We hypothesize that this attribute could increase HIV resistance to broadly neutralizing antibodies (bnAbs) that selectively target the closed Env conformation to prevent virus entry in immune cells. We may be able to correlate antibody binding to local dynamics measured in A4 versus BG505 Env trimers to verify this hypothesis. Biolayer interferometry will be applied to quantify antibody association and dissociation rates, as well as binding affinities. These studies will advance existing knowledge in Env-based vaccine therapeutics to improve immune responses to HIV.

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease that mainly affects children and adolescents. Disease monitoring is challenging as reported pain is not reliable and imaging is not always obtained at all clinic visits. To date, patient-reported outcomes used in CNO research have not yet been validated in this population. The Patient-Reported Outcomes Measurement Information System (PROMIS) questionnaires, validated in other pediatric rheumatic diseases, are administered to patients enrolled in the prospective multisite Chronic Nonbacterial Osteomyelitis International Registry (CHOIR) since 2018. Our objective was to assess the convergent and responsive validity of the PROMIS instruments in patients with CNO. Patients with CNO consented and enrolled in CHOIR. Self-reported PROMIS questionnaires of fatigue, pain interference (PI), pain behavior (PB), mobility, upper extremity (UE), physical activity (PA), and strength impact (SI) were administered to patients. External validation surveys were administered to assess patients’ perception of the difficulty of use of limb/back/jaw, fatigue, sadness, and worry on a 0-10 scale, disease status, and status change. More than 1,000 clinical visits from 184 patients were associated with self-reported PROMIS questionnaire entries. PROMIS scores correlated significantly (p<0.01) with patient-reported variables and physician global assessment (PHGA). The correlation with function and PHGA was good for Mobility, PB, and PI. All PROMIS scores, except physical activity, correlated significantly (p<0.05) with patient-reported disease status. After effective treatment when the clinical disease activity score improved by at least 2.5 points, the change of PROMIS scores from Mobility, PB, PI, and UE was significant. PROMIS questionnaires provide valuable information about the disease status of children with CNO and correlate well with self-reported functional and other psychosocial domains. Mobility, PI, and PB show sensitivity to change after effective treatment or with disease status change. These instruments are useful for CNO clinical disease monitoring and research.

The placenta is a crucial fetal organ providing oxygen and nutrients to the developing infant. Placental cell models, which are derived from immortalized or placental cancer cells, are typically used to study the organ. The use of placental cell models is important because human samples are difficult to obtain, and placental physiology is highly species-specific. However, our understanding of these models and how they compare to placental tissue samples is limited. This project aims to determine which placental cell model most directly reflects the gene expression of the human placenta. We obtained twenty-eight RNA sequencing datasets from the HTR-8/SVneo, JEG-3, JAR and BeWo placental cell models as well as human placental villous explants and primary trophoblast cells using the Gene Expression Omnibus database. Fetal sex was determined by quantifying expression of the Y-chromosome for each of the models. From this analysis we identified that HTR-8/Svneo was of female origin, while JEG-3, JAR and BeWo was of male origin. A clustering analysis was also conducted which identified groups of genes that showed similar expression profiles across the groups of cell lines and placenta tissue. This was subsequently used within a pathway analysis to identify which biological pathway defined the cluster. Pathways are chains of reactions leading to products or changes in a cell. The analysis showed at 22 of the 53 clusters were enriched for 1 or more pathways, which helps provide insight into the biological functions of these clusters and indicates biological processes that may be different between these models. With this information we have created an interactive web application. This site allows users to search a given gene and identify the expression data across all the models. This tool aims to provide a resource to the placental biology research community in further investigations of the placenta.

Understanding the complex neural mechanisms underlying motivated behavior and reward processing is crucial for advancing our knowledge of addiction and related disorders. In this study, we explore the role of neurotensin (NTS) peptides in modulating dopamine neurons within the ventral tegmental area (VTA), a key brain region implicated in reward processing. Previous research has highlighted the reinforcing effects of optogenetic stimulation of NTS inputs from the lateral hypothalamus to the VTA. However, a gap remains in understanding how NTS signaling interacts with other brain regions involved in motivated behavior. Our research addresses this gap by investigating the contribution of NTS and fast neurotransmitters in circuit-specific behavioral activation within the VTA. We hypothesize that distinct NTS inputs differentially influence motivated behavior in a combined NTS and GABA/glutamate-dependent manner through optogenetics and circuit mapping. We employ a multidisciplinary approach combining optogenetics, CRISPR gene editing, and behavioral assays to achieve this. Specifically, I utilize optogenetic stimulation to selectively activate NTS inputs from diverse brain regions, including the periaqueductal gray (PAG) and the pedunculopontine tegmentum (PPTg), targeting specific input regions via unilateral injections of AAV1-FLEX-Chrimson-mCherry. Control mice receive AAV1-FLEX-mCherry alone to ensure the specificity of our manipulations. Following surgical procedures and acclimation to the experimental setup, I conduct behavioral assays on mice, specifically Real-Time Place Preference (RTPP) and open-field testing to assess the effects of optogenetic stimulation on locomotion and anxiety-related behaviors. Subsequently, we investigate the mediating role of NTS and neurotransmitters by employing CRISPR viruses to target genes related to different components of neurotransmission. By integrating cutting-edge techniques with behavioral assessments, our study aims to elucidate the intricate interplay between NTS signaling, fast neurotransmitters, and specific circuit activations within the VTA. These findings contribute to our understanding of reward processing and hold potential implications for developing novel addiction treatment strategies.

Quantum point defects are imperfections in a lattice that occur exclusively at or around a single point. In zinc oxide (ZnO), such imperfections can arise when implanted atoms replace zinc atoms adjacent to vacant lattice sites. This substitution leads to unpaired electrons, contained in the potential well of the vacant site, that act as standalone atomic systems. Such systems are often utilized in quantum sensing or employed as qubits; their effectiveness in these roles is qualified by their spin, optical, and charge properties, uniquely determined by the lattice material. Ab initio simulations have predicted promising spin defect behavior in ZnO implanted with vanadium, niobium, and titanium ions. Theorized properties of such defects, such as magnetic insensitivity, would be exceedingly useful for applications as a robust and coherent qubit. Therefore, the goal of this project is to create, observe, and eventually characterize these novel defects to determine their effectiveness for quantum information applications. To do so, I first determine the photoluminescent spectral profile of non-implanted ZnO samples using confocal fluorescence microscopes across various temperatures and excitation wavelengths. Then, we introduce the substituent atoms to the samples with an ion beam. After, we anneal the sample, subjecting it to high temperatures and prompting the ions within to move throughout the lattice and reattach themselves near vacancies, creating the defect. I then fluoresce the implanted sample to prompt a transition between the energy levels of the defect. If it is present, the defect’s relaxation emits a photon of a characteristic frequency unique to the defect. Thus, comparing pre and post-implantation spectra of the sample’s photoluminescence allows us to confirm the existence of the defect, gain insight into its structure, and, in later projects, examine its optical, electronic, and magnetic properties.

The impact of wildfire smoke and disaster exposure on agricultural and forestry workers in the Pacific Northwest (PNW) is a critical concern amid intensifying climate change. As extreme weather escalates, disparities affecting this vulnerable population are likely exacerbated. The purpose of this study is to describe and analyze the extent of wildfire exposure among agricultural and forestry workers in the PNW states of Washington, Oregon, and Idaho. In this research, I ask, “How do multiple wildfire exposure metrics vary among agricultural and forestry workers compared to other people in the PNW, and what are the spatial patterns of these exposures?” Using American Community Survey data from 2006-2012, this project applies R and ArcGIS to conduct a spatial quantitative analysis. I link wildfire metrics (wildfire burn zones, annual and average wildfire particulate matter (PM2.5) concentration, and annual and average number of smoke waves) at the census tract level in the PNW to discern patterns and correlations between these metrics and farmworker distributions. Preliminary results indicate higher exposure to wildfire smoke among agricultural and forestry workers vs. the general population, with the highest smoke exposure in Washington. Expected findings include discernible patterns in exposure levels, providing insights for targeted interventions and resources to mitigate exposure for vulnerable populations. Agricultural and forestry workers in the PNW face unique wildfire and disaster exposure risks. These findings could inform future strategies aimed at safeguarding the health of agricultural and forestry workers amidst ongoing climate changes. This research highlights the urgency of addressing occupational exposures and health risks in an evolving environmental landscape.

The basic reproductive number (R₀) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has varied over the course of the pandemic. Phylodynamic analysis uses genetic samples to estimate R₀ by combining a phylogenetic tree model with an epidemic model. Previous research has used phylodynamic analysis to study how government policies and non-pharmaceutical interventions influence the R₀ of SARS-CoV-2. We collected publicly available phylogenetic tree data from published research on selected island nations during the first two years of the pandemic. We studied island nations due to their stricter travel limitations in order to reduce external variables. We estimated transmission rate, incubation period, and sampling probability of the virus in each nation using a birth-death exposed-infectious (BDEI) model implemented in the Python software package PyBDEI. These estimates were used to calculate R₀ for each nation. We validated our data analysis pipeline with sample data and utilized subsampling methods to reduce compute time. We then conducted a comparative analysis of COVID-19 pandemic intervention responses between the island nations using our estimates of R₀. Lower estimates of R₀ provide evidence that supports the effectiveness of specific policy interventions in decreasing viral spread. Our results can inform policymakers which intervention methods to use in case of future similar outbreaks by coordinating evidence-based policies across regions.

Net primary productivity (NPP) is a major component of the carbon cycle. NPP is defined as the amount of carbon biomass produced by primary producers over a given period of time and area. The NPP exceeds 100 billion tons of carbon per year on Earth and half of it comes from the ocean through phytoplankton. The equatorial Pacific ocean is the largest tropical ocean on Earth and subsequently the largest oceanic source of CO2 to the atmosphere. Despite its importance, NPP in the west equatorial Pacific is poorly characterized due to the lack of data. Previous research suggests that strong upwelling is associated with increased nutrient concentration in the euphotic zone leading to an increase in primary productivity. However, the western equatorial Pacific is known for weaker upwellings compared to the eastern and central equatorial Pacific.This study was conducted aboard the R/V Thomas G. Thompson from December 28, 2023, to January 12, 2024, with the goal of identifying and quantifying the critical variables that have a substantial impact on NPP in the region including temperature, chlorophyll, dissolved nutrients, and current speed. NPP was measured using in-situ oxygen incubations, and was compared to NPP calculated from satellite data, which tend to typically overestimated or underestimated NPP in the region. Results of this study provide important information for refining satellite models to comprehend CO2 emissions into the atmosphere.

According to the Kaiser Family Foundation, almost half of the US population resides in areas with a shortage of mental health professionals. The United States Census Bureau states that 26 million Americans do not have health insurance. Without insurance, a single mental health session can cost hundreds of dollars. Due to these factors, people are looking for alternative ways to address their mental health issues. The purpose of the research being conducted is to create conversational AIs that provide many benefits that a psychotherapist could offer, such as engaging the user in deep conversations, building relationships with the user, and providing apt responses, while avoiding some demerits like patient disclosure and preconceived bias. The research being conducted makes use of Machine Learning and Natural Language Processing models in its development, which is unlike most other popular mental health chatbots that uses a decision-based approach to find the best responses. The anticipated goal of our study is to better understand user comfortability and challenges with the AI therapist that is in development and how to better optimize it for a wider audience. By developing an AI solution that provides the benefits of a psychotherapist, we can better address the mental health crisis and worker shortage in America that predominantly affects low-income and underrepresented communities. The expected result would be a live chatbot application that can understand the mental health issues of the user, and provide advice and suggestions relevant to the user's concerns and issues.

Alphaviruses are arthropod-borne viruses that are responsible for febrile illness, chronic arthralgias, and premature deaths worldwide. Yet, there are no existing vaccines or therapeutics for the treatment of alphaviral diseases. Despite the limited size and coding capacity of alphavirus RNA genomes, most alphaviruses can adapt to multiple, evolutionarily divergent vertebrate and insect host species. As such, alphavirus RNA genomes and proteins carry host-specific adaptive features to compensate for the differences between hosts, such as body temperature (28°C in insects vs. 37°C in vertebrates) and methods of host immune response. Previous experiments have shown that continuous passaging of the dual-host alphavirus Sindbis virus (SINV) in Adedes albopictus (C6/36) cells results in a gain of fitness in said cells and a loss of fitness in human embryonic kidney (HEK293T) cells, resulting in a mosquito-adapted SINV (SINV^M). Using a modified long-read sequencing method (MrHAMER), we identified an assortment of fixed mutations that were serially acquired over the course of mosquito cell adaptation. Interestingly, multiple synonymous mutations were mapped to the 5' end of the SINV RNA genome, which is known to adopt functionally important RNA structures necessary for virus replication and genome packaging. Additionally, non-synonymous mutations were acquired within the viral structural genes. In this study, I aimed to understand the functional consequences of these two classes of SINV^M mutations with regards to viral fitness in insect and vertebrate cells. Furthermore, I assessed if the phenotype of these mutants were influenced by host body temperature by incubating the infected HEK293T and Vero cells at both 28°C and 37°C. We envision that studying these mutations will allow us to better understand the selective pressures influencing alphavirus evolution and potentially identify host-specific viral determinants of infection. Ultimately, this knowledge will allow us to identify ways to intervene at different stages of the alphaviral transmission cycle.

Since their introduction to clean energy applications, organic-inorganic lead halide perovskites have received great attention for their potential to create highly efficient, manufacturable and cheap solar cell devices. To make effective perovskite solar cells, charge transport layers are used to remove electrons and holes from the bulk perovskite semiconductor, increasing current, voltage and power conversion efficiency. Phosphonic acid self-assembled monolayers (SAMs) are a common hole transport layer. The phosphonic acid binds to the transparent conductive oxide electrode while an organic head group forms the SAM/perovskite interface. This head group is key for charge transfer and voltage characteristics, but the structure-function relationship is still poorly understood. My project investigates the role that deposition techniques and electronic structure play in the optimization of this SAM/perovskite interface. Expanding from the standard two step spincoating SAM/perovskite deposition method, I explored whether the codeposition of the two layers or the addition of a SAM solvent wash step produced an improved interface. I also fabricated films using several different SAM compositions to test for performance trends and improvements compared to the current field standard SAM, Me-4PACz. I collected photoluminescence lifetimes, quantum yields and solar simulation measurements to evaluate film performance. Preliminary data shows that neither the washing step nor codeposition add any performance benefit, but the single step codeposition achieves a more streamlined manufacturing method. Two of the new experimental SAMs performed comparably to Me-4PACz. These results encourage codeposition of the SAM/perovskite interface as the most efficient method to create high quality devices and show promising alternatives to the industry standard Me-4PACz SAM.

Corepressors are proteins found in all eukaryotes that work with DNA-binding proteins to repress many genes. Keeping some genes off, yet ready to quickly turn of if needed, is essential for development and physiology. Our project aims to identify interacting proteins that work with TPL, a conserved plant corepressor, to form a transcriptional repressor complex. To uncover these proteins, we created a visually screenable plant line containing RUBY, a reporter that expresses throughout the plant, turning it dark pink to purple. We next created a synthetic repressor dCas9-TPL and guide RNA (gRNA) construct that binds to and represses the RUBY reporter. Roots of plants with both constructs appeared whitish-pink, indicating dCas9-TPL is transcriptionally repressing RUBY. We then mutagenized 40,000 individuals from this line using the chemical Ethyl methanesulfonante (EMS), which creates new point mutations in random locations throughout the genome. We identified 257 individuals from 129 mutagenized families with dark pink roots, which show that repression by dCas9-TPL has been impaired. Many of these adult plants had phenotypes in addition to appearing pink, including miniaturization, infertility, and irregular growth patterns, suggesting that the mutations we found are affecting other pathways that require TPL. Using Mendelian genetics, we are currently characterizing the mutation types (i.e. homozygosity, recessive, or dominant) as well as establishing complementation groups. We will then backcross the lines with the parent line to eliminate extraneous mutations and perform whole genome sequencing to determine the precise mutation causing loss of repression. This will also tell us if repression was due to mutating a TPL interactor, or mutating one of our reporter or repressor constructs. By finding genes required for TPL to act as a corepressor, we hope to understand conserved mechanisms of corepressor activity across diverse eukaryotes.

With future ferry fleet modernization and electrification in the 10-year horizon, this research aims to explore user experience on the classic Washington State Ferries using these questions: How does the design of a historically significant space like the Washington State Ferries affect the experience for riders who heavily rely on the ferry – focusing specifically on what they do once they are on the ferry? Through this exploration, what pain points of riding the Washington State Ferries can be identified for future improvements? By taking user research approaches that identify the user as the expert of the product and acknowledging the idea that the design of spaces and places create unique experiences, I explore these questions through multiple research methods. I conducted field observations of 3 different ferry routes and distributed a user experience survey. Based on survey results, I will recruit participants to engage in my photovoice research, prompting participants to take pictures of significant aspects of their personal ferry experience and discuss them during an interview. I anticipate a unique relationship – both positive memories and experiences of the ferry coupled with frustrations about the process of onboarding or offboarding and the inconsistency of the schedule. This work is significant in capturing the experience of riders who are reliant on the ferry as their sole mode of transportation to the islands for various purposes such as commuting, medical appointments, and visiting family. It also is an important way to capture the historical significance of older ferries as change is on the horizon with ferry fleet turnover and future electrification goals.

Targeted therapeutics are a class of chemotherapeutics that block specific cellular functions in order to inhibit tumor proliferation. One such targeted therapeutics is a class of drugs known as tyrosine-kinase inhibitors (TKIs) which work by inhibiting the human epithelial growth factor. However, TKIs, like many cancer therapeutics, can fail eventually. This is known as drug resistance. Drug combinations or "cocktails" are a way to combat this issue, where drugs work together by attacking different angles of tumor proliferation. I aim to quantify the differences in intracellular concentration of cancer drugs by combining a bulk cell viability assay and microscopic data. For this project, I will use four different drugs representative of separate drug classes: lapatinib and afatinib, two different types of TKIs; Verapamil, a calcium-channel inhibitor, and Chloroquine, a drug that inhibits the progress of the cell cycle. First, to find the optimal concentration between combinations of different drugs, I ascertained the bulk differences in cell survivability using the MTT assay, a biochemical assay that measures the optimal inhibition of drug concentrations. Then, at and around the optimal inhibitory concentration, we will quantify the TKI uptake of different drug combinations. This is done at a single-cell level using the novel imaging technique of Stimulated Raman Scattering (SRS) microscopy, allowing us to determine the optimal drug combination that would increase the uptake of TKIs in cells. Results of SRS show that cells treated with drug combinations show higher TKI uptake when compared to cells treated with only one TKI. I predict that this particularly stands between drugs of a different class and is concentration specific. Combining the cell viability assay and a non-invasive microscopy technique, we can better understand the mechanisms behind how non-typical cancer therapeutics can be used with cancer treatments to lessen drug resistance, streamlining future therapeutic developments.

Our team conducted a study to understand the public attitudes towards creating human brain organoids (HBOs), a relatively new technique in neuroscience used to study brain development and disease. HBOs are structures derived from human donor stem cells and they mechanistically mimic certain aspects of the human brain. The goal of this study was to explore the values, priorities, and concerns that a sample of the general public has towards brain organoid research. An online survey was sent to 801 participants through Qualtrics. Respondents were asked to answer 51 yes or no, multiple choice, ranking, or open-ended questions, and provide their demographics. My colleagues and I qualitatively analyzed the open-ended responses to 3 questions using ATLAS.ti to code and identify themes in the general public’s opinion about brain organoid research. We found intriguing preliminary findings; 333 statements were supportive of the research and did not express concerns; for example, “it’s [brain organoids] created for research, thus it’s like hair, can be discarded”. 86 statements expressed concern about the potential future uses of brain organoids, for example: “it’s taking the first steps on the way to cloning…Dracula like”. Finally, 41 statements questioned the ethics of brain organoid research explicitly, for example: “people like to abuse things and this is no exception…[researchers] would end up using this for very harmful and unethical practices”. In open-ended responses, respondents expressed strong positions on the implications of brain organoid research, whether supportive or concerned. Further analysis of the open-ended responses is ongoing, and we plan to identify more themes. Increased knowledge of public opinions on brain organoid research could be valuable because it can help researchers improve informed consent for future studies, increase understanding of common misconceptions and concerns in the field, and influence how this type of research is regulated and conducted.

Evidence suggests that comprehensive sex education supports the overall well-being of students. Despite this evidence, a majority of U.S. states require their schools to implement curricula such as abstinence only programs that can reinforce negative sex and gender stereotypes. Our research assesses the needs of health/sex educators so that they can effectively implement comprehensive sex education. To support these teachers and curricula, our research team collaborated with local public schools, distributing surveys and facillitating focus groups to determine needs, experiences, perspectives, and more. Preliminary results suggest that teachers hold a variety of views regarding their experiences teaching health/sex education. The results of our literature review, analyses, and community engagement will be used to develop resources and recommendations for teachers and administrators. 

The diversification of many vertebrates was spurred by the use of novel food resources, and jaw morphology provides clues about the adaptations associated with dietary diversification. The external dimensions along the mandible reflect the strength to resist bite forces, which are associated with the diet's physical properties. Variations between different species may reflect adaptations of the jaw to specific diets. Using the mandibles of 60 Chiroptera species, we quantified the external dimensions at interdental gaps to generate mandibular strength profiles. Insectivores showed the greatest within-guild variation in jaw shape, while nectarivores had noticeably gracile symphyses. Further, insectivorous bats showed deep jaws at the canine, which may be associated with the use for prey capture. At the same time, frugivores have deep jaws at the posterior molars, possibly linked to adaptations for crushing seeds and pulp. When compared to measurements of bite force collected in the field, there was a remarkable and significant correlation between field-gathered and inferred bite force profiles. These results show that mandible strength profiles reflect dietary adaptations in bats, and demonstrate the reliability of this method in inferring the mandibular force profiles from preserved (non-living) specimens. These results indicate that this method can be used to further our understanding of the dietary behavior of species with few living specimens or that are extinct.

North American Beavers (Castor canadensis) are a semi-aquatic species in the family Rodentia and agents of biogeomorphic change in watersheds. Research in the last 20 years has demonstrated that beaver activity can reduce downstream flooding and significantly improve water quality. Beavers have inhabited the North Creek Wetlands (NCW) at the University of Washington Bothell (UWB) since 2008. In Autumn 2023, they constructed several dams that inundated the northern third of the wetlands, creating a new opportunity for studying the impacts of the dams on surface water dynamics in the NCW. I want to estimate how much water the beaver dams are holding back in the NCW and how that impoundment affects sediment movement and water quality above and below the dams. To address these questions, I have estimated water storage in the northern third of the NCW using both aerial drone photography and previous site documentation. Sedimentation is being investigated with sediment traps placed throughout the affected area. Water temperature, turbidity, and dissolved oxygen are being measured at several sampling sites that have been used for many years for water quality testing, providing significant baseline data against which to compare final results. I anticipate that results will indicate the beaver dams have increased NCW water storage, increased sedimentation in the northern third of the NCW, and are improving water quality in the North Creek before it discharges into the Sammamish River. Understanding the impacts of beaver activity on the NCW will help the UWB and local stakeholders to better balance the risk of flooding near campus with the beaver’s benefits to water quality and reducing downstream flooding and may inform future actions by the UWB Facilities Services and Campus Operations Department.

One of the characteristics of Autism Spectrum Disorder (ASD) is a difference in the individual's social skills compared to non-autistic individuals. It has been documented that within the autistic population there are sex differences in social skills. Females tend to engage in more social interactions, have better communication skills, and also display more masking behaviors when compared to males. To understand the underlying factors contributing to sex differences in social skills, this study investigates the potential link between sex differences in social functioning and structural brain metrics. Social functioning of each participant was assessed by self-reported measures on the Social Responsiveness Scale, Second Edition (SRS-2), and structural measures were collected from preprocessed T1-weighted MRI scans. Statistical analysis will be performed on the collected data to identify any correlations between answers on the SRS-2 and the structural properties of different regions in the brain, specifically those considered to have a role in social cognition. It is hypothesized that structural brain differences will help explain sex differences in autistic traits associated with social functioning. Identifying these differences between males and females could offer novel insights into the observed sex differences in autistic traits presentations.

Each winter, the northeastern U.S. experiences powerful storms that cover cities in snow and ice, which result in millions of dollars in damage, halt travel, and disrupt essential services. Yet, the type, intensity, and distribution of precipitation is unique to each winter storm. This research project aims to provide a greater understanding of the precipitation properties and distribution in snowstorms, through focusing on a major winter storm that occurred over the Midwest on 17 February 2022 and was the target of a research flight conducted during the Investigation of Microphysics and Precipitation for Atlantic Coast-Threatening Snowstorms (IMPACTS) field campaign. Radar data collected during this research flight provides a unique perspective of the vertical cloud and precipitation structure, and numerical model fields provide the environmental context of the structures observed in the radar measurements. This storm had a frontal boundary, or a strong thermal contrast, that provided lift needed for the production of precipitation and had sub-freezing temperatures so that the precipitation fell as snow.This frontal boundary consisted of warm air originating from southern latitudes riding over colder air originating from northern latitudes. Analysis of the vertical cloud and precipitation structure from radar data and the in situ cloud particle measurements collected during the flight revealed that regions of higher reflectivity had larger particles and greater ice water content, compared to regions with lower reflectivity. The analysis also includes examining how the cloud particle properties are different depending on the origin of the air masses (from the north or south) that form the storm. By relating the temporal and spatial information regarding the air masses to the high-resolution radar and microphysics data collected by the IMPACTS airborne instruments, the results of this analysis will ultimately support increasing the accuracy of snow prediction.

Biological processes depend on the intricate functions of proteins, which serve as the driving force in vital reactions. Given the importance of proteins in biological processes, several methods have been developed to control their functions in biomaterial and in vitro. Current methods often rely on secondary fixatives and caustic chemicals, posing risks of functional impairment in target proteins. To address these limitations, my project focuses on modifying cells with non-endogenous machinery, enabling expression of photoactivatable proteins – those with photocaged amino acids installed at essential locations, and using them to optically stimulate protein function. This strategy enables the triggered activation of target proteins with light, mitigating the risks associated with chemical interventions. We predict that the degree of protein activation can be controlled in a dose-dependent manner by manipulating light exposure duration and intensity. Genetic code expansion is used to integrate noncanonical amino acids, site specifically, into proteins expressed in bacteria and mammalian cells. By incorporating these photoactivatable proteins into biomaterials and living cells, our research aims to gain insights into fundamental cell signaling processes through control of targeted proteins. By analyzing biological mechanisms at the molecular level, we can guide cell processes and make informed decisions regarding cellular behavior and fates.

The nitrile imine produced by photolysis of 2,5 dimethyltetrazole undergoes a cross-linking reaction with the amide group in peptide-tetrazole conjugates and tetrapeptide-nucleotide complexes. In our work, we synthesized various peptide conjugates furnished with 2,5-diphenyltetrazole phototag. Upon laser pulses at 250 nm, nitrile imine intermediates can be generated by loss of N2 from tetrazoles. These nitrile imines can then crosslink with other parts of the molecule that contains amide groups. These crosslinking reactions are quite effective, achieving about 50% conversion with just two laser pulses at about 2 mJ. We could detect the formation of crosslinked products by tandem mass spectrometry. The UVPD-CID-MS3 spectra of these conjugates showed unique fragments including internal fragments of peptide sequence, indicating possible crosslinking. Moreover, we can confirm the structures and compositions of these crosslinked products using UV–Vis action spectroscopy and cyclic ion mobility mass spectrometry (c-IMS). By comparing experimental and calculated data, we confirmed the presence of nitrile imines and certain crosslinked products. We also explore thermal chemistry when nitrogen gas is lost from the peptide-tetrazole conjugates, and it seems to be a mildly energy-consuming process. The extra energy from breaking down tetrazoles is likely driving the reaction towards forming crosslinked structures involving peptide amide groups. Digging into the mechanism of this reaction, we found the proton transfer as the initial step, followed by a series of steps like cycloaddition and breaking of certain chemical bonds. Interestingly, other reactive groups, like cysteine thiol, do not interfere with this process. Within the complex of peptide conjugate and 2′-deoxycytidylguanosine, the intermolecular crosslinking efficiency is over 80%. The CID-MS3 and optimized structure showed the nitrile imine selectively targets guanine. In particular, the discovered reactivity of peptide amide groups toward nitrile imines appears promising as it provides potential clues to cross-link structure elucidation and conformational analysis.

 During gestation, a human fetus is fully dependent on the placenta which provides oxygen, nutrients, regulates waste transport, and acts as an immunological barrier. Glial Cells Missing Transcription Factor 1 (GCM1) is a transcription factor (TF) that plays a crucial role in placental development. Our goal is to understand the downstream effects of GCM1 knockdown on genes necessary for placental development. The BeWo choriocarcinoma cell line is a model of placental syncytiotrophoblasts cells which undergo a cell fusion process called syncytialization to form multinucleated cells that help exchange nutrients. BeWo cells were treated with Forskolin (FSK) to induce syncytialization to represent syncytiotrophoblast cells. RNA sequencing was conducted after GCM1 knockdown using siRNA to quantify downstream gene expression changes. BeWo cells were treated in 4 different conditions: FSK, GCM1 siRNA (GCM1 KD), FSK treatment first then GCM1 siRNA treatment (FSK + GCM1 KD), and lastly, GCM1 siRNA treatment first and then FSK treatment (GCM1 KD + FSK). In the GCM1 KD group, a total of 533 genes exhibited significant differential expression (FDR < 0.5), when compared to control BeWo cells, with 236 genes upregulated and 297 genes downregulated. Subsequently, in the FSK + GCM1 KD group, 961 genes were significantly altered, where 386 were upregulated and 575 were downregulated. In the GCM1 KD + FSK group, a notably higher number of genes, 7,165, displayed significant differential expression, with 3527 genes being upregulated and 3638 genes being downregulated. We also identified a number of biological pathways such as focal adhesion and adherens junction that may be crucial to GCM1-induced syncytialization. Overall, our results will improve our understanding of how GCM1 coordinates gene expression in the placenta during pregnancy.

Understanding how DNA folds in three dimensions is crucial for deciphering cellular function. Chromosomal contacts are interactions between different DNA regions. These contacts hold key information about tissue-specific characteristics, such as gene expression and regulation. However, current predictive models for genome folding primarily focus on within-chromosome interactions, largely ignoring variations across tissues and the role of interactions between chromosomes (trans-contacts). To address these issues, we developed TwinC, a machine learning model that predicts trans-contact maps from pairs of nucleotide sequences. To build TwinC, we used a convolutional decoder coupled with an encoder architecture that can be configured to employ transformers, convolutional networks, or a hybrid approach. Preliminary results suggest that the convolutional architecture achieves performance comparable to Orca, the current state-of-the-art in sequence-to-contact predictions. TwinC is trained and evaluated on contacts measured in two human tissues and one mouse tissue. We are experimenting further with other encoder architectures, fine-tuning the model, and investigating how it generates its predictions. This research will provide valuable insights into the underlying biological mechanisms responsible for chromosomal contacts and lead to an improved, high-performance model for predicting trans-contacts.

Located in the Southern Pacific Ocean, American Samoa was formed nearly 400 thousand years ago due to hotspot volcanism. As these eruptions occur, ash and volcanic rock fragments settle and leave behind texture, roughness, and clast sizes that are identifiable using mapping techniques such as backscatter analysis. The 2024 Oceanography Senior Thesis cruise aboard the R/V Thomas G. Thompson, produced bathymetric and backscatter maps utilizing the Multibeam Kongsberg EA302 to identify the boundary of such deposits and the thickness of sediment that has been deposited on it, indicating relative age and formation of volcanic features on the seafloor. This study focused on the islands Ofu-Olosega and Ta’u, and we located several intact and exploded cinder cone. Sediment cores were collected to quantify the grain size of the basalt that erupted violently out of these hot spots. We hypothesized that the grain size would correlate with distance from the caldera, with larger clasts sinking closer to the eruption site, and fine sediment carried farther. This was found true, but there were also large grain sizes radiating away from the initial cinder cone site, indicating the presence of other eruptions on the seabed. Multiple landslides were documented on the southern and northeastern slopes of Olosega Island. These landslides display key features such as steep amphitheater headwalls, blocky ridges, and hummock aprons. The landslides were classified as either slumps or debris avalanches based on these characteristics and compared to other volcanic hotspot landslides within the Pacific region. We hypothesized failure deposits would be identifiable in the seabed up to 30 km away from the caldera, and found them to be graphically obvious for about 21 km.

Sensory processing is a process in which the nervous system receives, processes, and integrates incoming sensory input from the environment to allow individuals to perceive and respond to their surroundings. Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social and behavioral skills. Many individuals with ASD experience hypersensitivity to sensory stimuli, thus individuals with ASD may experience more difficulty when navigating the world around us. These sensory challenges may result in increased anxiety symptoms. The purpose of this study was to explore the relationship between sensory processing and anxiety in autistic and typically developing (TD) adults. 256 participants (ASD = 149) ages 18-35 from a NIH funded study on sex differences in autism were included. Participants completed two self-report questionnaires: “Sensory Processing 3-Dimensions Scale” (SP3D) measuring sensory processing difficulties in auditory, visual, and tactile domains, and the “Screen for Adult Anxiety Related Disorders'' (SCAARED), measuring the intensity or frequency of anxiety symptoms and assessing four factors of anxiety (panic disorder, generalized anxiety disorder, separation anxiety disorder, and social phobis disorder). Correlations will be used to compare SP3D scores and SCAARED scores. Given the hypersensitivity to sensory stimuli in ASD, we hypothesize the effects of anxiety symptoms will be increased in the ASD group who experience more domains of hypersensitivity. The results of this study will contribute to a greater understanding of the effect sensory sensitivity has on anxiety in adults with ASD.

Nanofibrillated cellulose (NFC) can be produced from lignocellulosic fibers using a novel peracetic acid (PAA) oxidation treatment in combination with mechanical treatment. The nature of lignin - the glue that holds fibers together in a plant - present on the fibers is not well researched. In order to explore this, we will start by taking different samples of cellulose fibers extracted from wheat straw, each with a different lignin content and treating them with a low dosage of PAA to oxidize the fibers. Then we will run Klason chemical analysis and Shimadzu High-Pressure Lignin Chromatography (HPLC) to collect data on the lignin and sugars present in the treated fibers. We then mechanically fibrillate them via high-shear blending to produce NFC and compare the yields of NFC of each lignin level. NFC itself has a high specific strength and specific surface area and is biodegradable. Due to its unique physical and chemical properties, NFC can be used in various applications from smart food packaging, to building materials, sensors, bioplastics and more. Using our findings, the lignin content within the fibers can be tuned at the processing level to best suit certain applications. The ability to maximize the final lignin content of NFC can increase yields and potentially lower operating costs significantly. We aim to prove that NFC can be produced from high-lignin cellulosic fibers to minimize chemical input and lower energy demands with the goal of reducing the environmental impact of the process.

Birth asphyxia is the inability of a newborn to begin and maintain breathing. Twenty-three percent of neonatal deaths globally are caused by birth asphyxia. Birth asphyxia results in a neurological injury called hypoxic ischemic encephalopathy (HIE). Rapid HIE screening within six hours after birth is crucial to identify neonates at risk. Unfortunately, the diagnostic equipment is impractical for low resource settings because it is costly ($20/test and $5,000 for equipment) and requires technical staff, that are in short supply, to operate. We hypothesize that a cost-effective device can be developed for HIE analysis. pHast Cam quickly screens for birth asphyxia and HIE in infants via a paper-based blood pH sensor. The device combines an inexpensive pH sensitive dye, a smartphone camera, and a fixture that controls the imaging environment to quickly identify acidosis from samples. A low-cost paper-based strip is made with a water-soluble resin doped with a pH-sensitive dye, bromothymol blue (BTB), and a membrane to filter out red blood cells. The fixture removes lighting variation. The smartphone camera records the pH indicator image, and an algorithm captures, reduces noise, and accesses color change. pHast Cam incorporates four features: 1) accurate assessment of acidity within 0.05 pH units, 2) require only a few microliters of sample, 3) use electrical hardware and software only from the smartphone, and 4) affordability. At this stage, we have achieved a regressive linear model that predicts buffered solution acidity (y=-589.32x+4684.05 R2=0.9857), with 95% confidence interval of 0.04 pH units. In the future, we will transition from measuring buffered solutions to blood-plasma. Ultimately, we expect pHastCam to screen for birth asphyxia, and other acid-base disorders, by quantifying plasma pH in neonates so that timely therapeutic interventions and plans to address long-term complications may occur.

The Tanginak Spring site on Sitkalidak Island, Alaska contains lithic technologies dating back to 7,500-6,000 cal BP. This is one of the earliest records of human activity in the Kodiak archipelago and contains key artifacts reflecting how the settlement developed and how people adjusted to the island environment. The prevalence of stone tool technology on Sitkalidak Island begins an operation examining how scrapers are used in the process of modifying wood and skins. I investigate how the prevalence and types of lithic scraper technology changed through time. Shifts in stone technologies related to bifacial projectile points and blades allude to shifts in technology and activities performed at the site. I use typological and technological analysis through visual inspection to examine the scrapers and their use wear, which reflects how long these artifacts were utilized and for what purpose. Additionally, I apply a stratigraphic analysis to investigate how scraper types change through the layers of the site. Analyzing the stratigraphical location of tools within this assemblage allows me to evaluate ideas about relatedness in the technological sequence through scraper morphology. This examination contributes to an ongoing investigation of changing scraping activities through time at the site. Continuing to explore the progression of scraping technology in the Kodiak archipelago can provide context to how people began to sustain their livelihoods on the island during a period of significant climatic cooling.

Oxygen deficient zones (ODZs) are large, naturally-occurring regions of the world's oceans where dissolved oxygen concentrations drop to low levels—less than 10 nM. These regions are important to the biogeochemical cycling of carbon, nitrogen, methane, and sulfur and are expected to expand as ocean temperatures rise due to anthropogenic climate change. Located above and below the anoxic ODZ core are oxyclines where dissolved oxygen concentrations change rapidly with depth. The deep oxycline extends into the deep ocean supporting an understudied microbial community adapted to these low-oxygen conditions. In this study, I examine a metagenomic library previously generated from a water sample collected at 1000 meters on the RR1804 POMZ cruise to determine both the diversity and genetic potential of microbes in the deep oxycline. I found that three groups of prokaryotes dominate in the deep oxycline: the cosmopolitan alphaproteobacteria, Pelagibacter ubique (20%); the uncultured candidate phylum SAR324 (16%); and archaea of the phylum Thaumarchaea (12%). I generated metagenome-assembled genomes (MAGs) from this sample to determine the genetic potential of this microbial assemblage. By examining these MAGs, I expect to find genes encoding for processes such as low-oxygen stress responses, alternate terminal electron acceptors, and carbon-fixation pathways. By better understanding the contributions of the deep oxycline microbial community to biogeochemical cycles, we can more accurately predict how nutrients will be consumed and regenerated in ODZs as they expand.

Autism Spectrum Disorder (ASD) is a neurological disorder that affects social and behavioral development. Although there are no known biological markers of ASD, low birth weight and presence of an older sibling with an ASD diagnosis have been identified as elevating risk for ASD, such that between 7 to 15% of low-birth-weight infants and 20% of infant siblings will be diagnosed with ASD. One confounds to interpretation of outcome is use of clinician observational measures versus parent reports of behavior. For example, parent and clinician ratings showed strong correlation for motor skills but weak to moderate for communication skills. As altered communication skills are “red-flags'' for autism, understanding the relationship between sources of information is important. This project looks at the concordance between clinician administered and parent completed measures of communication in a longitudinal study of infants at elevated risk for ASD. Fourty-nine participants from an NIH funded longitudinal study of social and nonsocial development from 6 - 36 months were included. Infants were grouped as typical-likelihood for ASD (TL, n=24), or at elevated-risk for ASD, including, low birth weight (ER-LBW, n=17), and infant sibling of children with ASD (ER-Sib, n=8). At 12 and 24 months of age, parents completed the Vineland Adaptive Behavior Scales (VABS), a clinician administered parent interview that includes expressive language (EL) and receptive language (RL); and clinicians completed the Mullen Scales of Early Learning (MSEL) with the infant to assess EL and RL. We expect ER group to have the highest concordance between parent and clinician report and EL concordance to be higher than RL because it is easier for parents to assess their child’s spoken language compared to language understanding. If parent rating shows high concordance with clinician rating, this could inform the use of lower cost questionnaires for screening and diagnosis.

My research is an analysis of the pervasive issue of gender-based violence faced by women in India. Despite the presence of constitutional safeguards, the entrenched patriachal norms, and the prevalent misogyny in Indian society continue to deny women the healthy and peaceful lives they rightfully deserve. By analyzing pre-existing data along with data collected from interviews conducted with women between the ages of 35-45 from village Gumtala in Punjab, I have conducted a study to examine the relationship between postponed age of marriage and gender-based violence. It's through the lens of these women, I argue that decades of suppression in the name of culture have normalized violence against them. I conducted this study with careful consideration, ensuring that the questions posed in the semi-structured interviews were sensitive to the unique backgrounds and experiences of the women involved. Through the method of convenience sampling and qualitative analysis of interview data, I identified patterns of gender based violence and socio-economic factors. The results of my study suggest that early marriage not only increases women's vulnerability but also fosters economic dependence and social isolation of young brides that fuels the act of dowry practices causing marital abuse.These findings are not only essential in creating awareness regarding the vulnerable state of these women but also help me pose possible policy interventions by the Governmnet of India. My research has allowed me to argue how raising the legal marriage age for women to 25 mitigates gender-based violence, allowing women more time to pursue education and build financial independence before marriage. This study is an ode to all the women who are denied a voice.

Typical data visualizations in neuroscience flatten 3D space into just two dimensions, limiting researchers ability to observe spatial relationships. To overcome this limitation, we have previously developed rendering tools to support exploratory 3D visualizations, specifically for neuroscience data. In this project, I am expanding the renderer to allow users to display and explore additional non-spatial dimensions of their data. These new tools will allow users to explore additional dimensions of their dataset such as time, stimulus properties, or the spatial position of an animal. For example, to explore time, I have developed an interactive slider bar that dynamically updates the 3D display and a corresponding linked 2D plot, providing a clear depiction of neural activity with relation to specific events. Scrolling along the 2D plot enables users to pinpoint their position in time relative to stimulus onset, with the 3D display concurrently adjusting to reflect the data from that specific snapshot in time. These functions are packaged into the API of the renderer, streamlining the process for users to transform raw data into intuitive and interactive visualizations. Reducing the complexity of the code expands the accessibility of these new features, making them more approachable for new users who may be less familiar with coding. By supporting additional dimensions, users will be able to develop visualizations that are tailored to their individual research projects. My objective is to create research tools that are versatile, applicable to a range of projects, and accessible to individuals with diverse levels of experience, including students and researchers of varying programming backgrounds.

Upconversion (UC) is a non-linear optical process where a material absorbs two lower energy photons and subsequently emits one of higher energy. Currently, inorganic UC materials used in lasers and photovoltaics are primarily lanthanide-based. However, a few transition metals also exhibit UC, such as Re4+ , Os4+, Ti2+, Ni2+, and Mo3+, and due to their high oscillator strengths, d-d transitions, and a strong ligand field dependency, offer the potential for greater tunability and efficiency in upconverting optoelectronics than their than their lanthanide counterparts. The goal of this work is to increase Re4+’s PLQY by isovalently doping low-phonon vacancy-ordered double perovskites (A2BX6 : A = Cs+, NH4+; B = Ti4+, Zr4+; X = Cl-, Br-) with rhenium to minimize non-radiative decay that can occur through defects and lattice vibrations. This has been attempted via schlenck line synthesis of the host lattice and coprecipation and ion-exchange doping procedures. While [ReX6]2- has previously demonstrated near-IR to visible upconversion in the bulk, this work aims to characterize its upconversion mechanism on the nanoscale with variable temperature and time-resolved photoluminescence. If made successfully, the colloidal stability of Re4+:Cs2TiBr6 nanocrystals would allow for new post-synthetic processing avenues including electrohydrodynamic inkjet printing and core-shelling, and new applications in flexible electronics.

The intersection of data visualization and qualitative research has seen a lack of importance within the scientific field. Its potential to advance the field is diminished due to the challenges researchers face when working with qualitative data and the lack of appropriate visualization methods. WordStream is a qualitative data visualization type that aids researchers in visualizing nuanced perspectives of qualitative data. Within the user study, we purposefully recruited participants who have a background in STEM education research along with qualitative methods. We present a user study of two WordStream-based platforms, Journal Data Dashboard and WordStream Maker, that surveyed participants in STEM education research who use qualitative methods to garner insights. A mixed-method study allows us to examine visualizations and a questionnaire to explore our topic. Our initial study consists of 4 respondents, with a plan to increase to 10 respondents. We apply a Likert scale to our questionnaire to investigate and measure the ease of use and usefulness. Additionally, our method analyzes open-ended questions regarding trust, envision use, and desired features. Through quantitative and qualitative analysis, we report user preferences between the two qualitative visual analytic platforms. Two themes emerged: (1) Users prioritize functions that increased their visual control to explore the data in context; (2) Users’ perspectives reflect a strong context of use in evaluating the WordStream functions related to their areas of expertise. Preliminary findings from four participants show that users prefer the Journal Data Dashboard to the WordStream Maker for ease of use and usefulness. The study is ongoing, and we will present additional data and the implications of the findings for improving Wordstream and designing other qualitative visual analytics.

Periodontal disease is a prevalent oral disease most frequently found in older adults, and left untreated can lead to inflammation, bone loss, and patients may lose their teeth. Treatment of periodontitis includes repeated maintenance by a dentist and surgical procedures. These treatments can be invasive and time-consuming and do not target the underlying molecular changes that occur during the aging process. Previously, the mTOR pathway was shown to decrease inflammation and bone loss during periodontal disease in aged mice. Here, we investigate if targeting a marker upstream of mTOR, called colony-stimulating factor 1 receptor (CSF-1R), can recapitulate the effects of targeting mTOR. CSF1-R plays a role in inflammatory diseases by regulating myeloid cell lineages such as macrophages and osteoclasts. We hypothesize that inhibiting CSF-1R will decrease the expression of inflammation markers associated with periodontal disease in aged mice. Real-time quantitative PCR was used to identify relative expression levels of various inflammatory markers involved during aging and periodontal disease, including IL1-a and IL1a. Quantitation and analysis were completed by first standardizing target genes relative to ß-actin and GAPDH expression. Data was analyzed where appropriate using one-way analysis of variance (ANOVA) with post-hoc Tukey test for multiple comparisons, where p-values <0.05 were considered statistically significant. Statistical analysis was completed on GraphPad Prism 10.0. Our analysis demonstrates that CSF-1R inhibition decreases multiple cytokines involved during periodontal disease and major isoforms of the PI3K pathway. These findings indicate the importance of the CSF1R signaling along the mTOR pathway and possible implications for future research. This study was supported by the VitaDAO/Molecule Longevity Fund to Dr. Jonathan An, Oral Health Sciences

Recent studies have shown that pedagogical approaches like hands-on lessons, representative and near-peer mentoring, as well as culturally responsive teaching increase Science Technology Engineering and Math (STEM) engagement in classrooms, specifically those with underrepresented minority (URM) students. URM students interested in pursuing STEM show increased engagement and confidence from holistic outreach programs, unfortunately, there is a dearth of URM instructors who also have the necessary technical know-how. However, new AI tools based on Large Language Models (LLMs), like ChatGPT-3.5, have been shown to increase the productivity of software developers, with the largest productivity gains being for non-experts. Therefore, we propose a study on the effects and limitations of LLMs as an educational tool for supporting students and instructors of various skill levels in both facilitating programming classes for URM students and bringing embedded systems projects to completion. We will instruct 40 hours of culturally relevant Arduino course content to 25-35 URM students. We will allow ChatGPT-3.5 to be used as an educational tool without explicitly telling students to use it as a means of understanding perceptions and hesitations around the tool from URM communities. As our lab’s previous research has seen a significant increase in productivity and project completion with the use of LLMs with novice programmers, we aim to see students who choose to use ChatGPT-3.5 program and complete their projects faster than those who choose to not, as well as an implicit understanding of prompt engineering over time. We anticipate that exposure to the tool will cultivate an interest in exploring other AI and LLM opportunities. Lastly, we hope that implementing LLMs within the curriculum will increase the number of available near-peer instructors to teach these courses by aiding content-inexperienced instructors, thus aiding in closing the digital divide.

Prostate cancer is the most common type of cancer amongst men in the U.S. It relies on androgens that bind to the androgen receptor (AR), which increases the transcription of genes associated with the growth and proliferation of the prostate cells. For the AR-driven prostate cancer (ARPC), current treatments involve decreasing androgen levels (Androgen Deprivation Therapy) or inhibiting the ARPI (Androgen Receptor Pathway Inhibitors). However, around 15% of patients develop resistance to these treatments, resulting in a type of prostate cancer called neuroendocrine prostate cancer (NEPC). NEPC cells are no longer dependent on AR activity, which makes this subtype difficult to treat with the current treatment options in the clinic. To better understand the biology of NEPC, we focused on gene expression at the protein synthesis level and found that NEPC has a decreased level of a tRNA called Arg-TCT-1-1. Following Arg-TCT-1-1 tRNA overexpression in NEPC, we detected elevated expression of AR downstream targets via qPCR and western blot. NEPC with high Arg-TCT-1-1 also responded to an AR inhibitor called enzalutamide as measured by cell viability assays. To further investigate the role of Arg-TCT-1-1 in prostate cancer, we used shRNA-mediated knockdown of this tRNA in prostate cancer cells with high AR expression and measured changes in gene expression. This study will provide important insights on the role of Arg-TCT-1-1 during the differentiation process from ARPC to NEPC.

Ultrasound elastography (USE) is an emerging technique used to measure in vivo tissue elasticity, or stiffness. The present study applies USE to examine tissue property of the tongue in a minipig animal model. The long-term goal of this research is to examine the association between tongue stiffness in relation to obesity and obstructive sleep apnea (OSA). Eight Yucatan minipigs, 7-8 months-old, were used for this study. USE data were collected for the caudal tongue from the submandibular region with sagittal orientation and for the left masseter muscle when the pig was under sedated sleep in the lateral position. The USE data are collected as video clips, and image frames are extracted and then analyzed with custom-developed software that converts image pixel colors to stiffness values. Multiple video clips are recorded at each site for each study. For each video clip the USE values in extracted ROIs are averaged over 10-20 frames, producing an average circular elastography ROI. The USE pixel values are then averaged over the video clips acquired in each region of the tongue and the left neck muscles. I have processed the tongue video clips to extract blocks of USE measurements that will be compiled to summarize the tissue stiffness and USE data quality for each animal. This procedure will also be applied to the masseter muscle images to produce reference tissue stiffness values for each animal. These data will provide a set of normal baseline stiffness values that can be compared to animals with obesity and OSA in ongoing research studies.

Superconducting materials have various important applications, including, but not limited to, MRI machines, low-loss power transmission, and computing. The current carrying capacity, Jc, of superconductors depends on the dynamics of vortices, penetrated magnetic flux lines whose motion introduces energy loss. This motion can be induced by current-induced forces and thermal energy (creep). Thankfully, material defects can slow down vortex motion, resulting in a dramatic improvement in Jc. In a recent study, it was found that the ultimate theoretical lower limit to the vortex creep rate depends on the Ginzburg number, Gi, which in turn depends on material-specific parameters such as the coherence length, penetration depth, and critical temperature, Tc. The typical approach to minimizing creep is to modify the defect landscape to reach our proposed lower limit. In this study, we aim to reduce the theoretical lower limit itself by tuning the Ginzburg parameter in multiple superconductors, through doping, and verifying that we do indeed observe slower vortex creep. If successful, this approach could lead to extremely slow creep rates in materials and therefore unprecedently high current carrying capacities. We expect to see a direct correlation between the square root of Gi and the measured creep rate, indicating that a reduction of Gi allows for significant increases in Jc.

Lake Washington is home to a complicated metapopulation of Oncorhynchus nerka. There is a potentially native population of sockeye spawning in the Sammamish River and tributaries with at least two history variations - typical sockeye that migrate to the ocean and return as adults, and residual sockeye that remain in freshwater and return at a smaller size. Historically, there was also a native, genetically distinct, freshwater-only population of O. nerka called kokanee. Thought to have been eliminated from Lake Washington in the 20th-Century, recent genetic evidence indicates that a small population of native kokanee remains with a single cohort spawning every third year. We are comparing spawning ages for sockeye, residual sockeye, and native kokanee by extracting otoliths (mineralized structures in the ear containing annual rings similar to tree trunks). Otoliths are mounted on slides, viewed under a light microscope, and aged by counting the number of rings present. We expect ocean going sockeye to be age 4 (typical for sockeye); kokanee to be age 3, reflecting the 3-year cycle in kokanee abundance; and residual sockeye to be younger than typical sockeye. Lack of information prevents a clear spawn-age expectation for residuals. A large run of kokanee returned in 2020 and another was expected in the fall of 2023. Surprisingly, a sizable run was present in 2022. We hypothesize that the 2022 run was composed primarily of early-returning 2-year-olds while the 2023 run were typical 3-year-olds. We are comparing the age distributions of kokanee from runs in 2022 and 2023 to test this. Kokanee are remnants of a once abundant population. It is important to have a better understanding of kokanee relative to sockeye and residuals as a basis of conservation; much remains unknown. This study will also help interpret potential differences in spawning ages between similar life history variants.

Traditionally known for its toxicity, hydrogen sulfide (H₂S) also possesses physiological roles as an endogenous gaseous signaling molecule in multiple biological processes. Previous research has demonstrated changes in levels of H₂S-producing enzymes during oxidative stress, hypoxia, and inflammation in various tissues including the liver and heart. H₂S protects cells from cytotoxicity in part by promoting the synthesis of glutathione, neutralizing reactive oxygen species, and inhibiting apoptosis signaling pathways. Thiol methyltransferases TMT1A and TMT1B can methylate endogenous H₂S to methanethiol. TMT1B has been shown to have a potential role in mediating the toxic effects of methanethiol. Gene silencing of TMT1B was found to significantly alleviate the observed cytotoxicity induced by methanethiol in human bronchial epithelial cells (16HBE). Methanethiol may induce harm to human respiratory tract cells, and understanding the mechanisms involved, including the role of TMT1B, could potentially lead to insights for mitigating these harmful effects. Doxorubicin (Dox) is a widely used chemotherapy drug for the treatment of various cancers but can induce oxidative stress in cells. In my preliminary experiments, I assessed the cell viability of HepG2 liver cells that were supplemented with various concentrations of NaSH (H₂S donor) and sodium methanethiolate (NaSMe, MeSH donor), followed by Dox treatment. Supplementing the cells with H₂S significantly increased cell viability in the presence of doxorubicin, while the methanethiol had no effect. The goal of my project is to identify H₂S-dependent protective pathways during cellular stress in HepG2 versus cardiomyocytes. My preliminary data indicates that both H₂S and its metabolite, methanethiol, may alter cellular responses following treatment of exogenous compounds that induce cellular stress such as CoCl₂, hydrogen peroxide and Dox. My goal is to pinpoint genes altered during the stress response. This understanding of H₂S-dependent pathways may pave the way for designing novel therapeutics that maintain or enhance H₂S levels.

How much global warming will the Earth experience? This depends mostly on how quickly fossil fuels and other heat trapping gasses are phased out. We used reduced-complexity climate models to calculate whether a given emissions scenario meets temperature targets and other global effects. Our research starts with writing code that pulls and compiles the most recent data on various global environmental factors. This is used alongside existing data that break down emissions by industrial sectors, such as agriculture, electricity and transportation as well as by fuel, such as coal, oil, gas and land use. Using the updated historical data, we created various scenarios that ramp down emissions to zero over a specified number of years into the future. These scenarios were run through the Finite-amplitude Impulse-Response (FaIR) model to create plots demonstrating the resulting effect on global temperature. Additionally, we are considering the current decarbonization trends in our analysis. We noted current rates of decarbonization and continued these trends into the future to determine how much warming the earth will experience as a result. This data can be compared to the critical two degrees of global average temperature increase. By running these models, we can use current trends to estimate if we will exceed two degrees of global warming. Additionally, by modifying the rate of emission reduction, we can see what economic changes need to be made to stay under two degrees of global warming.

There are three enzymes that S-methylate thiols: thiopurine methyltransferase (TPMT) and two enzymes that our lab has recently identified, alkyl thiol methyltransferase 1A and 1B (TMT1A and TMT1B). These enzymes have been studied predominantly because of their role in drug metabolism. Thiopurines, potent chemotherapeutics, are inactivated through thiol methylation by TPMT. While there are not many drugs that contain alkyl thiols, nearly every alkyl thiol-containing drug is metabolized via S-methylation, presumably mediated by TMT1A or TMT1B. With any drug used there is a possibility of drug-drug interactions (DDI) that can lead to a drug concentration in the cell that is above the therapeutic index, leading to toxicity. Thus, it is important to have a method that allows for quick determination of possible DDIs in the body. In this work, using ligation cloning and nickel affinity chromatography, I recombinantly expressed and purified TPMT from bacteria. I then developed an absorbance-based high throughput assay to compare the substrate specificity of TPMT with that of recombinant TMT1A and TMT1B. I determined that TMT1A and TMT1B preferentially methylate alkyl thiols, while TPMT exclusively methylates thiols involved in a conjugated electron system. Although these enzymes serve a crucial role as drug metabolizing enzymes, it is not known if these enzymes have a function beyond drug metabolism. To study the endogenous role of these enzymes beyond drug metabolism, I am utilizing my developed assay to screen for compounds that can specifically inhibit TMT1A, TMT1B, and TPMT. In addition, the assay is optimized in order to screen for potential drug-drug interactions that might result due to interactions with TPMT. Based on literature, I expect most benzoic acid derivatives and similar structured compounds to result in DDIs.

Perinatal asphyxia or hypoxia, where the infant brain does not receive enough oxygen or blood flow, commonly occurs in premature newborns and is one of the leading causes of neonatal mortality worldwide. Survivors often have altered white matter with cognitive impairments, motor deficits, and increased rates of cerebral palsy. There is currently no standard treatment for preterm brain injury, so there is a critical need to research neuroprotective strategies as well as ways to assess their impact. The ferret is a promising model species for studying preterm brain injury due to its gyrified brain and white-to-gray matter ratio, which are similar to that of the human brain. The gyrification index (GI) can be used to assess cortical development and is calculated using magnetic resonance imaging (MRI) images. These are analyzed using ImageJ software to perform hemispheric tracing by dividing an internal trace, including the gyri and sulci, by an external trace that excludes them. A higher GI is indicative of a larger cortical surface area. This project seeks to evaluate the effects of postnatal (P) age on post-hypoxic-ischemic (HI) gyrification in two ferret models. In both models, HI ferrets underwent bilateral carotid artery ligation and exposure to hypoxia, differing by date of surgery, with randomly assigned control animals not undergoing surgery. Model One ferrets underwent surgery at P10 (extremely preterm equivalent) and tissue collection at P70, and Model Two ferrets underwent surgery at P17 (late preterm equivalent) and tissue collection at P42. I hypothesize that GI will be affected by HI injury, with both age of injury and age of assessment altering GI relative to control animals. Contextualizing age differences in GI could help inform future therapy regimens to treat infants with premature brain injury.

In this pilot project, we conducted think-aloud interviews with undergraduate students who had recently completed CHEM 142 as they worked through a set of multiple-choice, general-chemistry questions in order to investigate the levels of cognition they exhibited during problem solving. In collaboration with members of my research group, I designed recruitment materials and selected eight undergraduate interviewees from a pool of around 50 volunteers, with attention to diverse identities— including race, gender, sexuality, disability, prior courses in science/math, and parent’s educational background—as such identities and experiences may influence what problem-solving skills one has acquired. I co-developed the interview format, and conducted two of eight interviews. Participants were asked to narrate their approach while solving four multiple-choice CHEM 142 questions, then to critique the questions in terms of relative difficulty. The questions we used were previously characterized according to Marzano and Kendall’s New Taxonomy of Educational Objectives by a group of chemistry educators from our research group. I developed and refined a modified version of Marzano’s Taxonomy inspired by Teodorescu’s work in introductory physics (Teodorescu et. al., 2013), and am using it to code the interviews according to cognitive level exhibited by the interviewees. My preliminary results suggest that students approach a particular question in a variety of ways, engaging different levels of cognition. Students who display mastery of a concept tend to utilize lower cognitive levels, apparently due to familiarity with the concepts. Students who seem less familiar with or state they are struggling with a topic tend to employ more cognitively demanding strategies, whether or not they arrive at the correct answer. I will also discuss a comparison of the cognitive level exhibited by students to the level predicted by previous group members for each question, and any observations unique to different student identities.
 

This study presents a design research project to create high-fidelity prototypes for culturally inclusive and responsible Indigenous e-publications, specifically targeting the Cherokee community. The initiative addresses the issue of knowledge transmission, which has traditionally relied on oral traditions, by leveraging digital platforms to record and organize traditional ecological knowledge. Using Cherokee Earth Dwellers (Teuton & Shade Family, UW Press, 2023), a comprehensive book on Cherokee culture, as a primary source, the project integrates audio and video with text from the print book to craft a multimodal educational resource. The methodology is grounded in 10 usability heuristics and participatory design principles, involving members from the Cherokee community in the design process to ensure the final e-publication meets their needs and expectations. Drawing on previous research in Indigenous studies, co-design workshops, participatory sciences, and human-computer interaction, the project aims to produce an interactive e-publication as a vital resource for Cherokee educators and youth, enhancing access to Cherokee culture for educational purposes through digital mediums, thus fostering language revitalization and cultural education. Anticipated outcomes include design guidelines for research towards Culturally-inclusive, Relational and Responsible web design.

Inflammatory bowel disease (IBD), a chronic autoimmune condition encompassing ulcerative colitis and Crohn’s disease, significantly affects individuals' health and quality of life. This study centers on patient activation and self-efficacy, which are critical concepts in the management of IBD. Patient activation—encompassing an individual’s understanding, abilities, and confidence in managing their health—is measured using the Patient Activation Measure. Similarly, self-efficacy, which relates to one's confidence in carrying out behaviors necessary to achieve specific performance goals, is assessed by the Self-Efficacy for Managing Chronic Disease Scale. These factors are essential as they enable patients to actively participate in their healthcare, potentially improving outcomes. This study aims to explore patient activation and self-efficacy among individuals with IBD enrolled in a Comprehensive Self-Management Intervention. Participants in a randomized controlled trial completed baseline measures and follow-ups at 3 and 6 months. By assessing change in baseline to 3 months in patient activation and self-efficacy, the study seeks to understand how this comprehensive intervention influences the self-management behaviors of individuals living with IBD. We expect that patients receiving the intervention will exhibit enhanced self-efficacy, indicating a positive direction in IBD self-management practices.

The aorta is responsible for transporting blood to all of our organs and extremities. During an aortic dissection, a tear develops in the intima (inner) and media (middle) layers of the aorta, causing a rapid influx of blood and a consequent separation of the adjacent layers. Type A aortic dissections (TAAD) refer to aortic dissections proximal to the left subclavian artery – the aortic segment nearest to the heart. The mortality rate of TAAD is shockingly high: roughly 50% for both acute and long-term survival. There are numerous factors contributing to long-term survival, and current literature has primarily focused on medical/surgical interventions to prevent disease progression. There is comparatively little data regarding epidemiology and social determinants that are relevant to long-term survival. This project aims to analyze the impact that socioeconomic factors, gender, and race have on short-term and long-term surgical outcomes of TAAD patients. A TAAD surgery database at the UW Medical Center is the primary point of investigation. In this study, I am assisting with the primary analytical design and statistical analysis of our data through the use of the R programming language, which will be done in conjunction with a biostatistician. I am also responsible for helping synthesize and communicate our findings in the form of an abstract and manuscript. Preliminarily, we have begun to see correlations between the aforementioned population characteristics and short-term surgical outcomes. As we continue with more complex statistical analyses, especially regarding long-term survival, we expect to see noticeable differences between patients of different socioeconomic, gender, and/or ethnic groups. Our project has the potential to benefit all TAAD patients. A better understanding of health disparities among these patients will allow for the identification of modifiable risk factors and targeted use of resources, thus improving care and outcomes in all associated populations.

Though Seattle’s reputation is for economic and technological prosperity, some Seattle high schools do not nurture students with the academic and professional rigor needed to partake in their local economy. This project examines the relationship between poverty and income in the City of Seattle and secondary education outcomes in Seattle Public Schools (SPS). The project puts forward the concept and practice of community mapping and GIS (Geographic Information Systems) for representation and visualization. Conducting a mixed-methods research using both qualitative and secondary research analyses, we uncover education narratives and outcomes in SPS while considering socioeconomic and political influences. SPS and state government online databases provided relevant information such as school graduation rate, college-readiness index, census tract poverty percentage, average annual income, and income inequality. We also conducted an online survey on SPS counselors, inquiring about their perception and input behind local socioeconomic contributions to the SPS curriculum and school life. In visualizing our research data, we utilized ArcGIS Pro, sectioning Seattle by SPS school zones and census tract, organizing our data by poverty percentage and income level through bivariate analysis, and juxtaposing them with education outcomes in SPS. Altogether, employing a social community investigation in conjunction with our mapping process allows for a deeper geospatial analysis that can be used as a tool to highlight socio-economic issues. In light of the socio-economic problems in Seattle, SPS counselors infer that other variables such as rich community sentiment, domestic and scholastic support, extracurricular involvement, and an overall meaningful life balance can contribute to successful education. Though our work establishes the relationship between high poverty percentage, low income, and poor education outcomes, we found that specific education metrics such as graduation rates do not necessarily entail success beyond secondary education. We proposed to use other metrics, such as the college readiness index, to infer education outcomes more accurately.

Titanium dioxide is a compound that has been used in the realm of nanotechnologies for decades. Titanium dioxide is used as a protective and high-refractive index optical coating. It also has strong mechanical and chemical stability. This is also true of other ceramics throughout the Washington Nanofabrication Facility with compounds such as aluminum oxide, titanium nitride, and aluminum nitride. With this in mind, the goal is to explore the best conditions to reactively sputter titanium dioxide. Thus, I developed a series of experiments including a screening for significant factors, and a following set of experiments using previous results to find an optimum point. In order to produce titanium dioxide in a physical vapor deposition environment such as the sputter tool utilized, the chamber holding the designated surface was pumped down and exposed to a chamber filled with argon, whose function was to hit the target titanium and a percentage of oxygen designed to react with the titanium in order to form titanium dioxide. By generating experiments designed to better understand how titanium and oxygen would react within the sputter tool, there was an aim to better screen for factors and understand the surface composition of the titanium dioxide. The desired outcome of this research is to build a working titanium dioxide recipe that optimizes deposition. Based on preliminary testing, the ideal outcome is likely produced under low pressure and higher power conditions. Future goals may include uniformity and accuracy within titanium dioxide, but also with other materials. With the implementation of this recipe, which is both optimized for the deposition of the material as well as its applicability for the lab, other recipes utilizing similar methods are desired. With a working titanium dioxide recipe, titanium and aluminum nitride recipes can better be developed.
 

Malaria, caused by parasites belonging to the genus Plasmodium, accounts for roughly 600,000 deaths per year, with the most vulnerable population being children under 5 years old. The current available malaria vaccines show limited effectiveness in children. After being deposited by the bite of an infected mosquito, Plasmodium travels through the bloodstream and invades liver hepatocytes, causing an asymptomatic infection. Within hepatocytes, Plasmodium multiplies until the hepatocyte bursts, in which they are released into the bloodstream to cause a symptomatic infection. To develop an effective vaccine for children, it is critical to understand the immune response to liver stage Plasmodium infection in children. However, our current understanding of immune responses in children compared to adults, specifically in the liver, is limited. During Plasmodium infection, CD8 T cells in the liver are able to confer sterilizing protection. The main goal of this study is to identify differences in the spatial location of immune cells in human liver tissue across ages. We are currently utilizing a combination of RNAscope and immunofluorescent assay (IFA) staining to visualize CD8αα+ T cells expressing the promyelocytic leukemia zinc finger (PLZF) transcription factor, which distinguish them from conventional CD8+ memory-like cells as innate-like T cells. These unconventional cells play a key role in autoimmune responses in the liver. We are doing further spatial analysis on Imaris to gather quantitative data on these samples. We hypothesize that children would express higher levels of CD8αα+ T cells expressing PLZF because they do not produce memory-like cells as well as adults, and thus lack an efficient response to infections. The results of this study will help us better understand the differences that age may cause in immune cell types and quantities, and how this can be used to develop a more effective malaria vaccine for children.

Communities in the Pacific Northwest region of the United States face a risk of harm from earthquakes and tsunamis, which cause significant health impacts. There is currently limited research on the specific vulnerability of women and gender minorities to natural disasters in the Pacific Northwest. This study examines how gender identity affects risk perception and disaster preparedness for residents of this region. This study asks: what individual or communal resources can Pacific Northwest residents access during a disaster, what are their experiences with disasters and disaster planning, and how do these differ across gender identity? I developed an online survey instrument alongside other undergraduate fellows with the Cascadia Coastline and Peoples Hazards Research Hub (CoPes Hub). The survey was completed by hundreds of residents of Washington, Oregon, and California in February 2023 and remains open. The study utilizes crosstabulations of current data from this survey, as well as interview data currently being collected by CoPes Hub fellows from 18-30 year old transgender residents of the Pacific Northwest (n = 10). I expect to find that women and gender minorities have less access to resources and have unique perceptions of disaster risk and preparedness compared to cisgender men. Identifying existing gender differences in disaster preparedness can inform further research into the root causes of these disparities, as well as targeted disaster policy that eliminates barriers to resilience for people of all genders.

Mild cognitive decline with increasing age commonly affects millions of people beginning as early as middle age. It can progress to more severe levels of cognitive impairment including dementia associated with Alzheimer’s disease and irreversible brain damage with eventual death. Therefore, treatment before the onset of dementia would be the most effective way to prevent the devastating loss of normal daily living and death as an outcome. However, few drugs have been shown to be successful in preventing the progression of mild cognitive decline to more severe cognitive dysfunction. One candidate drug we are testing is the naturally occurring peptide GHK (glycyl-L-histidyl-L-lysine), which is known to have regenerative and anti-inflammatory properties in the brain. In order to test this peptide, we treated middle-aged male and female C57BL/6 mice with GHK as a copper complex (GHK-Cu) or saline using a novel intranasal atomizer daily for two months. We then conducted behavioral tests to assess learning and memory, and then mice were euthanized to collect brain samples for special stains for biomarkers of brain aging including the presence of non-neuronal microglia, brain-derived neurotrophic factor, and synapse integrity. Our preliminary observations from behavioral tests show that mice treated with intranasal GHK-Cu performed better in learning and memory tests than mice treated with intranasal saline. The brain aging biomarker tests I completed show that the neuropathology markers associated with aging are less severe in mice treated with intranasal GHK-Cu. Such a positive outcome provides the rationale to do further preclinical testing as a way to move toward clinical studies designed to treat mild cognitive decline and prevent the devastating progression of irreversible neurodegeneration.

Gas-phase emissions from sea-spray generate aerosols which are an important source of atmospheric halogens. Halogens (chlorine, bromine, and iodine-containing species) are important in the atmosphere because they affect the abundance of greenhouse gasses such as ozone and methane. The Bermuda boundary Layer Experiment on the Atmospheric Chemistry of Halogens (BLEACH) is a campaign that studies the abundance and cycling of atmospheric halogens. Filter samples from field campaigns are often frozen to preserve them for future analysis. However, after freezing a mixture of anion standards that replicate atmospheric composition for measurement on an Inductively Coupled Plasma Mass Spectrometer (ICP-MS), total aerosol iodine showed a tenfold increase in concentration in two separate trials compared to room temperature. Understanding the impact of freezing filter samples on aerosol iodine is crucial in interpreting BLEACH observations and could change the understanding of aerosol iodine speciation in the scientific community. I investigated this total iodine enrichment after a series of experiments on frozen and room temperature laboratory standards using Ion Chromatography (IC), which measures iodate and iodine separately. The tenfold iodine enrichment observed after freezing measured on ICP-MS was not replicated in IC trials. The total iodine ratio of frozen to room temperature was 1.1 on the IC and 9.8 on ICP-MS. Our results also show that the ratios iodide/iodate are the same for frozen (1.3) and room-temp (1.3) samples, suggesting that the conversion between iodide and iodate is not responsible for the enrichment in ICP-MS. Our observations of total aerosol iodine concentrations in Bermuda’s atmosphere are consistent with previous studies in the same region. This either suggests that the iodine enrichment after freezing is unique to the “simulated atmosphere” standard prepared in this study, or all field observations using ICP-MS may be overestimated by an order of magnitude.

Serratia marcescens is an opportunistic pathogen that can infect multiple human organs and is responsible for many healthcare-associated infections. It has a mortality risk of up to 58% and early diagnosis is crucial for timely treatment. S. marcescens secretes a unique restriction endonuclease, which has been recognized as a virulent factor and thus can be used as a diagnostic biomarker. To detect this restriction enzyme biomarker, I have designed and investigated a model system using novel restriction endonuclease mediated DNA strand displacement (resDSD), adapted from the enzyme-free DNA strand displacement (DSD) reaction. In a typical DSD circuit, a DNA input “invading” strand invades a duplex DNA substrate, replacing the previous incumbent strand through branch migration to reveal a fluorescence molecule. In contrast, my resDSD circuit employs a restriction endonuclease enzyme input. In my design, the toehold region is concealed and blocked by a strand that the restriction enzyme can cleave. Once cleaved, the toehold region is exposed, allowing an invading strand to hybridize and initiate the DSD cascade. This study represents the first demonstration of the resDSD system. To validate the concept, I used commercially-available restriction endonuclease BamHi instead of S marcescens’ endonuclease. I will also modify E. coli 5-alpha competent strain (c2987h) to secrete BamHi in place of S. marcescens. By investigating this innovative resDSD approach, I aim to establish a reliable method for detecting bacterium such as S. marcescens based on its secretion of the restriction endonuclease. Such a diagnostic tool could contribute to early detection and prompt treatment of infection caused by this opportunistic pathogen or similar pathogens in healthcare settings.

Nickel phosphide (Ni2P) nanoparticles have been gaining attention due to their ability to catalyze various clean energy-relevant reactions, e.g., the hydrogen evolution and carbon dioxide reduction reactions; however, Ni2P has been known to corrode in aqueous electrolytes. Studies have indicated that nickel phosphide alloys have shown a small amount of oxidation to nickel phosphate at oxidizing potentials or complete dissolution at more aggressively oxidizing potentials. However, understanding of the speciation and kinetics of oxidation is limited. Therefore, we aim to understand the corrosion mechanism of Ni2P in neutral buffered electrolyte; which we hypothesize to show significant conversion to nickel phosphate at oxidizing potentials. First, I synthesized colloidal Ni2P nanoparticles from NiCl2 and tris(diethylamino)phosphine [P(NEt2)3] in oleylamine. Techniques such as powder X-ray diffraction, transmission electron microscopy, and thermogravimetric analysis confirmed the formation of uniform 5 nm diameter nanoparticles. Next, we probed the electrochemical corrosion of Ni2P through anodic polarization and operando X-ray absorption spectroscopy (XAS). In order to prevent premature oxidation of Ni2P, all procedures were performed in an air-free environment which posed many challenges for the preparation of the electrochemical cells, especially the operando XAS cell. Finally, we found that Ni2P nanoparticles corrode upwards of 0.4 V vs RHE and can no longer be restored when anodically polarized beyond 0.6 V vs RHE. Future experiments will probe the corrosion of Ni2P in acidic and basic electrolytes. This study aims to understand how Ni2P can be used industrially to replace rare and expensive metals, such as platinum, as electrocatalysts to electrify the petrochemical industry and reduce greenhouse gas emissions.

Group B Streptococcus (GBS) is a gram-positive bacterium that during pregnancy, can cause invasive disease including preterm-births, stillbirths, pneumonia, sepsis, and meningitis in newborns. Although GBS commensally resides in the vaginal tract, as a pathogen the bacterium can employ numerous virulence factors, including the serine rich repeat glycoprotein (SRRs) adhesins. GBS expresses one of two SRR’s (Srr1/Srr2) in a strain-dependent manner, and both can bind fibrinogen to increase GBS adherence to vaginal epithelial cells, increasing pathogenicity. Both proteins are heavily glycosylated, yet the role of glycosylation on protein function and GBS virulence remains unknown. Previously, our lab has conducted in vivo studies infecting pregnant mice with mutant GBS strains that do not express SRR or express an altered SRR glycoform. Data from these studies show that a decrease in vaginal colonization and ascending infection is seen for the SRR deletion mutant, while SRR glycomutants exhibited increased virulence compared to the wild-type strain. To further explore these findings in a more mechanistic manner, I will conduct a series of in vitro experiments to examine the host-pathogen interactions and immunological mechanisms of these mutants. Specifically, I plan to examine the role of neutrophil killing as an immune modulator of GBS pathogenesis and how susceptibility to killing changes when SRR glycosylation is altered. In addition, these GBS mutants will be used to explore whether the SRR adhesin and its glycosylation is important in inducing vaginal epithelial-mesenchymal transition – an important cellular pathway that predisposes vaginally infected mice to uterine infection and will test the susceptibility of the GBS SRR mutants to entrapment via fibrin clots. By examining how the SRR adhesin and its glycosylation impacts vaginal colonization and downstream disease-associated events, we aim to elucidate the role of SRR glycosylation in GBS virulence and identify new antimicrobial targets that can decrease GBS pathogenicity.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by difficulties in social communication and interaction, and restricted or repetitive patterns of behavior or interests. ASD is associated with features beyond its core characteristics, including alexithymia and anxiety. Alexithymia is characterized by difficulty recognizing and describing one’s own emotions, it influences physical and mental health, and it is associated with symptoms of anxiety. Despite current research demonstrating the correlation between alexithymia and anxiety in both ASD and the general population, there remains a significant research gap in how alexithymia and autism traits individually and collectively influence anxiety levels among the participants. This study has two aims: 1) To explore the relationship between alexithymia and anxiety in participants with ASD and TD. 2) To analyze the role of alexithymia as a mediator of the relationship between autism traits and anxiety in adolescents and young adults. This sample includes 149 participants (93 ASD) ages 15-34, from the NIH funded study on sex differences in autism. Measures included alexithymia via the 20-Item Toronto Alexithymia Scale (TAS-20), anxiety via the Screen for Adult Anxiety Related Disorders (SCAARED), and autism traits via the Social Responsiveness Scale (SRS-2). We will first conduct regression analyses to examine the relationships between alexithymia, anxiety, and autism traits. Then, we will employ Preacher and Hayes’ INDIRECT Method to investigate the mediating role of alexithymia in the relationship between autism traits and anxiety. We expect to see a significant relationship between alexithymia and anxiety in both groups and the relationship between alexithymia and anxiety in the ASD group to be significantly different than TD group. Understanding the relationship between anxiety and alexithymia could aid in the development or improvement of interventions for anxiety in people with ASD.

Some genes are on all of the time in most cells, and carry out functions that are essential for life. Unsuprisingly, essential genes are difficult to study, as interfering with their function leads to death. One such critical component is the multi-protein Mediator complex, which is found at every eukaryotic promoter where it coordinates activation of gene expression. My project focuses on one of the core components of the Mediator complex, MEDIATOR21 (MED21). While MED21 is required for gene activation, the Nemhauser Lab recently found that it also plays a role in repression of gene expression through interaction with the corepressor protein TPL. I would like to be able to differentiate the role MED21 plays in activation versus repression using the plant model Arabadopsis. This work is made more complicated by the fact that most mutations in MED21 lead to lethal phenotypes. As an alternative I recently developed a new technology called a molecular switch that turns off MED21 in certain tissues or in reponse to addition of a chemical. The molecular switch relies on the expression of serine integrases that recognize, and recombine the DNA between, two specific DNA sequences. By expressing an integrase portein from a promoter that is only expressed in secondary roots, I can study MED21 loss of function in a small pool of stem cells while the rest of the plant is wild type and healthy. Plants that have undergone this cell-type-specfic switch exhibit several abnormal root phenotypes including agravitropism, increased root formation, and more root hairs. My next experiments include uisng a switch from wild-type MED21 to a mutant form incapable of binding to the corepressor TPL. This study will help us better understand the role MED21 plays in repression versus activation, and how state switching contributes to organogenesis.

The world is in dire condition and our energy and environmental future need to be secured. Through a historical look at the field of Futures Studies, the World's Fairs, the Hanford Site, and solar power, we will gain insights on how to implement R. Buckminster Fuller's framework of Comprehensive Anticipatory Design Science to address future energy and environmental challenges. This literature review analyzes Fuller's essay "Humanity's Critical Path: From Weaponry to Livingry" (1983) and its implications for the future. Comprehensive Anticipatory Design Science, as conceptualized by R. Buckminster Fuller, is an approach that begins with the entirety of a system, anticipates future needs, and applies accumulated knowledge to create an omnicooperative society. Examining two of Fuller's artifacts — the World Game and Dymaxion Map — we gain insight into how to give everyone access to a global accounting system of resources available to inform future policy decisions. From this research, we learn how to leverage Design Science to change our projected future. Through an exploration of the Hanford Site, we gain an understanding of what dangers nuclear technology poses. A detailed overview of the World's Fairs and those involved in strategic national planning projects informs how past decisions were made that led to this dire situation. This work seeks to determine whether observing the development of solar energy technology can conserve our petroleum reserves, fissionable materials, and transition our society to the participatory, sustainable, and renewable future that Fuller envisioned. This research unveils the significance of Fuller's ideas by addressing the risks and benefits of nuclear technologies and alternative renewable energy sources that could be employed. Further research into Fuller's concepts at the intersection of complex energy solutions and sustainability will provide us with feasible options to our dire climate crisis.

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is one of the deadliest pathogens in human history. The aim of this project is to begin probing the metabolic reprogramming that occurs in Mtb during treatment with isoniazid (INH), a commonly used frontline drug. Unpublished work from a collaborator has identified several common metabolites that change the minimum inhibitory concentration of INH needed to kill 99% of cells in a culture. The amino acid serine -- which is well known to be involved in one-carbon metabolism through interconversion with glycine -- was found to be of particular interest due to the increase in Mtb susceptibility to INH observed in serine-supplemented culture. To further explore this effect, I have generated timecourse growth curves using an avirulent Mtb (aMtb) model while under INH treatment with and without serine. I started cultures of aMtb at log-phase growth under the following conditions: without any additives, with serine, with INH, and with both INH and serine. I then plated aliquots of defined volumes on solid media to observe colony forming units (CFU) that assess how many cells were present in each culture. I repeated CFU plating 4 and 7 days after each culture was created, which gave me sufficient data to analyze the growth patterns of aMtb under these various conditions. My findings require validation but suggest serine supplementation may play a role in lowering INH tolerance in Mtb. If this result is found to be accurate, this may implicate one-carbon metabolism as a pathway with downstream effects on Mtb tolerance to INH.

In recent years, there has been a stark decline in bee colony populations. Many studies believe neonicotinoids to be a significant contributor to this problem. Neonicotinoids are insecticides that are often used in farming or agricultural settings. One of the neonicotinoids suspected to play a role in the bee colony decline is Imidacloprid. Imidacloprid is believed to directly negatively affect the navigational skills of bees. It interrupts their homing abilities, making it difficult for them to relocate their hive after coming in contact with Imidacloprid. Previous research projects have been conducted to study the affect of Imidacloprid on bees, but the proportion of Imidacloprid to the bee itself is not realistic of what they would be affected by in a veritable agricultural setting. Here we demonstrate an extraction protocol based on sample clean-up with both ion-exchange and reversed phase separations prior to targeted gas chromatography-mass spectrometry (GC-MS) analysis. This protocol is similar to the QuEChERS (Sigma, St. Louis, IL) method, however, the extraction protocol presented here shows how capturing and concentrating the Imidacloprid while washing away the other matrix components can help improve sensitivity and selectivity for Imidacloprid. Our targeted detection strategy involves selected ion monitoring (SIM) to decrease limits of detection. Initial findings show that C-18 separation is optimized by adding a centrifugation step prior to SPE (solid phase extraction). As we continue to develop a targeted detection strategy for Imidacloprid, the hope is that the strategy will be used in future farming and agricultural environments to determine if the level of neonicotinoids being used in specific fields is detrimental to the bee colony population in the area. 

The endangered Western Pond Turtle (Actinemys marmarata) was once a broadly distributed species across a large range from Western Washington to as far south as Baja, Mexico. However, unprecedented amounts of population loss driven by exploitation as a food source, wetland development and the destruction of habitat began to plague this species beginning in the early 1900s. As a result, the Washington State Department of Fish and Wildlife (WDFW) and the Woodland Park Zoo created six reestablishment sites that proved to be successful, elevating the number of turtles from 150 in the 1990s to around 900 individuals today. Threats to this species persist, making it more crucial than ever to locate new reintroduction sites to increase population numbers and promote self-sustaining populations. Our analysis is focusing on determining if the Union Bay Natural Area (UBNA) could be a potential 7th reestablishment site through the utilization of a habitat suitability index (HSI) with ArcGIS Pro and comparisons with Klickitat County and Pierce County sites. We anticipate that UBNA displays the habitat characteristics capable of promoting occupancy by the Western Pond Turtle. Furthermore, given UBNA’s popularity as a bird watching hotspot, we will also establish a kiosk intended to raise public awareness, educate the public about its threats, and display a map demonstrating their current and potential re-establishment zones as shown by our analysis. This kiosk includes a website linking the general public to a survey allowing visitors to record turtle sightings that can be accessed by future researchers. This study has widespread implications in terms of wildlife conservation, endangered species recovery and the management of threatened species.

Amid Earth’s two periods of glaciation known as the Snowball Earth, evidence has been found for the survival of photosynthetic eukaryotic algae. Therefore, there must have been warm areas — with liquid water, or very thin ice permitting photosynthesis underneath — where microbial activity survived extreme cold. Previous research found that inland seas in the subtropics, like the Red Sea, were likely areas for refugia because friction from the seafloor and sidewalls, and relatively high sublimation thins the ice. However, this is only one criteria for a refugium. Deep inside the inland sea, it must also be warm enough to prevent freezing and allow water and nutrients to circulate and replenish regularly. Using the Community Earth System Model version 2, I analyze data from simulations of the Snowball Earth Climate with a simplified supercontinent geometry to understand the conditions for this warmth, as well as the robustness and frequency of warmth. We expect the warming to mainly appear along the north and south ends of the supercontinent due to the effect of Hadley convection cells at the equator. However, in our most recent runs, the model has exhibited unexpected instabilities in the occurrence of ice. After we adjust the topography of the continent, atmospheric carbon dioxide concentration and land solar radiation absorption to identify stable areas of warmth, I will continue with running the model to compare temperature data with other climate variables like wind speed, snow depth, and solar flux. Understanding the conditions of the Snowball Earth will give insight on how the climate has evolved in the past, and how it may evolve in the future: which is becoming increasingly important as the Earth faces dramatic change today.

Achieving consistent targeting of multiple simultaneous probes during electrophysiology experiments is a challenging and time-consuming process. Even with a planned insertion trajectory, experimenters still have to go through a lengthy process of positioning and inserting each probe. Electrophysiology experiments are increasingly focused on brain-wide coverage, requiring three or more simultaneous probes motivating researchers to accelerate their processes to reduce the duration of the experiment and the corresponding stress levels of their subjects. To improve the efficiency and reproducibility of multi-probe electrophysiology experiments, we developed two frameworks: a communication platform to allow software control of hardware micro-manipulators and an automation platform to perform multiple synchronous probe insertions. Each existing manipulator platform has proprietary software for programmatic control, which is rarely cross-platform and often exposes inconsistent interfaces. To standardize manipulator communication, we developed a Python server that acts as a generic cross-platform application programming interface (API). This platform ensures that client applications only need to interface with one API to be compatible with many different manipulator platforms connected across various computer operating systems. Building on top of this communication platform and an existing trajectory planning tool, Pinpoint, we next developed a system that automates the insertion process for multiple probes, saving time. The automation system provides three guarantees for researchers: first, that probes will reach their intended targets without manually introduced errors in targeting; second, that experiments can be repeated exactly to improve reproducibility; and third, that movement speeds are limited to low levels for reduced tissue damage. Because our software drives multiple probes simultaneously, complex multi-probe insertions are more manageable. Taken together, these open-source tools for communicating with hardware manipulators and automating multi-probe insertions enable the next generation of reproducible, high-efficiency, brain-wide electrophysiology data collection.

In the context of computer-aided design, researchers have studied how to reconstruct an input geometry in CAD by decomposing it into CAD primitives. Such reconstruction is useful for creating CAD designs for manufacturing applications. What we want to study is also object decomposition but towards a different goal: understanding object affordances and interactability. For example, a handle of a basket can be grasped or hung from a sticky hook, and we recognize this affordance or functionality because it has a certain shape (e.g. hook or rod). Prior research has identified eight types of shape primitives that are common in everyday objects, but the existing tagging process requires a high degree of modeling expertise. We aim to create a more automatic and easy-to-use tagging tool. Our proposed research is to develop user-in-the-loop methods for tagging shape primitives given an object geometry. This takes advantage of human intuition for how objects function and interact. We start with building an interface, where users sketch over the input mesh to indicate the region for fitting and select the type of primitive to be fit. On top of this, we plan to crop the selected mesh data to generate a reduced mesh that encompasses only the area selected by the user. Finally, we utilize differentiable rendering techniques to automatically optimize the shape parameters of user-selected primitives to fit our reduced mesh data. With this tagging tool, we can enable more people without modeling expertise to tag objects. Data generated with this tool can support future research that studies object affordances with learning, as well as improve applications in robotics, product design, and assembly design like FabHacks.

Cellular senescence is one hallmark in the biology of aging in which cells stop growing and accumulate over time. These cells secrete factors called SASP, or senescence-associated secretory phenotype, which may be involved in inflammation and cancer. A cancer that most often occurs with age is cancer of the tongue. Investigating tongue cancer has been primarily in animal models that have induced cancer, thereby losing the opportunity to study the impact of aging on cancer. This project evaluated cellular senescence in aged male and female mice tongues and tested the effect of inhibiting mTOR via rapamycin, an intervention that improves the health and extends lifespan in animal models. RNA from tongue specimens was isolated and Real-Time PCR was used to quantify the levels of SASP expression. Histology was completed to visualize the tongue structure. The results show differences in aged male and female mice in senescence markers p16 (Cdkn2a) and p21 (Cdkn1a). There were also significant increases in major markers such as IL-1A, IL-1B, and TNF-a. Treatment with rapamycin decreased SASP expressions in older mice. Further research is needed to test how these SASP markers relate to aging and oral cancer. Future experiments include conducting protein assays and overexpressing these SASPs to determine if they increase the risk for oral cancer in mice. This project is important because these markers can become valuable tools for clinicians to diagnose oral cancer in older adults before its onset. This will provide more time for them to implement preventative measures and treatments, increasing the survival rates in the fight against cancer and age-related diseases.

The Strand Lab Benzene Team quanitified the removal of benzene by a genetically modified plant (2E1 pothos ivy) under concentrations similar to home environments. The objective is to make this houseplant available to the public and develop a practical home biofilter that uses a genetically modified (GM) houseplant. The development of a genetically modified pothos ivy with the 2E1 gene provides means to degrade volatile organic compounds (VOC), for example, benzene. My partner developed extraction procedures while I developed the analysis procedures for influent and effluent samples concentrating benzene so that analysis could be done by injection of the concentrated extracts on gas chromatography with flame ionization detection (GC-FID). I created calibration curves with external standards to help quantify the concentration of benzene within a sample. GC-FID was used to measure benzene area peaks for both the influent and effluent samples from which benzene concentrations in conjunction with the standard curves could be calculated. Our findings reveal a 65% removal of benzene by the A9 transformant of pothos ivy containing the cytochrome P450 2E1. The wild-type plant showed no significant benzene removal. The development of this GM houseplant offers a promising solution for indoor air purification, potentially mitigating health risks associated with the exposure of benzene and other VOCs. Furthermore, the potential commercialization of GM houseplants could influence the biotech industry to expand the application of biofilters beyond the home environment such as office spaces, schools, and hospitals. 

In this study, I investigated distinctive electroencephalogram (EEG) patterns associated with processing social and nonsocial information in both typically developing individuals and those with Autism Spectrum Disorder (ASD). A total of 139 youth and young adults aged 10-24 years participated, including 63 individuals with ASD (23 females, 40 males, mean age = 17.57) and 76 typically developing youth (35 females, 41 males, mean age = 17.47). Data collection occurred across four sites as part of the multisite ACE Network GENDAAR Wave 2 study (R01 MH10028, Pelphrey). EEG data were collected using a 128-channel Geodesic sensor net, concurrently capturing live social and nonsocial attention responses. During the social condition, participants viewed videos featuring social stimuli (vignettes of women telling or singing nursery rhymes), while during the nonsocial condition, they viewed videos of objects (dynamic toys). Additionally, all participants underwent assessment using the Vineland Adaptive Behavior Scales-2 (VABS-2). I calculated power spectral density (PSD) values for 8 channels based on the 10-20 system across various frequency bands, and performed analysis using this data. The results indicated a main effect of condition (social vs. nonsocial) at several frequency bands and electrodes. Furthermore, a main effect of the group revealed higher alpha power in typically developing individuals compared to those with ASD. Notably, no significant relationships were observed between Vineland Adaptive Behavior Scales-2 (VABS-2) subscores and neural responses. This study highlights a difference in neural activity during attention to social vs. nonsocial information in both groups of participants and underscores the importance of understanding these neural correlates in individuals with ASD.

Preliminary work has shown that long-term arsenic exposure affects the relative partition of bacterial species in freshwater lake microbiomes. Our current hypothesis is that arsenic acts as a selective pressure for tolerant and resistant bacteria in all compartments of the lake microbiome. I have attempted to confirm this hypothesis by taking a larger sample size of periphyton, water, sediment, and Chinese Mystery Snails (CMS) in summer of 2023 for Next Generation Sequencing (NGS) and arsenic quantification via ion-coupled plasma mass spectrometry (ICP-MS). Samples were taken from non-contaminated to highly contaminated local lakes in the South Puget Sound area, all with open access to the public. I performed DNA extractions and processed the samples for ICP-MS. I have also cultivated lab-acclimated CMS for experimentation with the feeding of high-arsenic sourced periphyton vs. sterile algae wafers to observe whether the snail gut microbiota and their innate immune system are affected by direct arsenic consumption. Upon receiving NGS and ICP-MS results, I determined relative fractions of bacterial species across the various lakes in correlation to their respective arsenic contamination levels. Ongoing work involves the optimization of a quantitative polymerase chain reaction (qPCR) assay of arsenic metabolizing genes aioA, arrA, arsC, and arsM. These genes are widespread across bacteria and confer resistance/tolerance to arsenic via respiratory arsenite oxidation, respiratory arsenate reduction, inorganic arsenic detoxification, and organic arsenic methylation, respectively. The overall goal of this project is to determine how arsenic exposure shapes interactions between microbes and their hosts in a complex aquatic ecosystem, and the implications of these changes for the total lake ecosystem including humans, fish, and birds. 

Evolution is a challenging topic that high school students often struggle to grasp. The yEvo project, a collaboration between genetics labs and high school biology classrooms, seeks to address this issue by giving students an active hands-on experience in evolution using yeast as a model. Over the course of a school year, yEvo students expose yeast to a selective pressure (such as antifungal drugs), and the natural mutation rate creates beneficial mutations that increase in frequency due to selection. Whole-genome sequencing and computational analysis of the ancestor versus evolved populations reveals changes in the genome that were selected over the course of the experiment. However, the resulting raw mutation data is difficult for students to interpret, thus motivating a need for an intuitive, interactive method to visualize sequencing results. Built using R shiny, a first draft of the yEvo mutation browser consisted of a chromosome diagram with each classroom’s mutation data mapped, a pie chart of mutation types, and a gene viewer depicting the altered sites in each mutated gene. Our work focuses on upgrading the user interface to make it more intuitive, optimizing the backend data processing for more streamlined data filtering, and adding features that allow users to upload and interact with their own datasets. This tool will enable students to more easily interpret the results of their evolution projects. Students will be able to view their classroom data, compare it to other datasets with the same condition, visualize mutation clusters in the genome, and see how each mutation changed the genes. In the future, the yEvo browser can be outsourced and used as a framework for data visualization for other model organisms that can serve to benefit the genetics community as well as educators.

Teaching engineers about design processes is difficult. In a typical engineering curriculum, students get multiple experiences doing design but less often get to learn about design. Understanding the context and breadth of design is important. Therefore, in this work, we ask the question, “How might we offer a breadth of design perspectives to students?” To approach this problem, we created a resource by crowdsourcing attributes of “good” design. We invited design and engineering researchers and educators to respond to the prompt, “When you talk to someone and say “Good designers do ‘X’”, what are the top 4 or 5 things you list? I’m looking for ‘off the top of your head’ answers.” 34 people responded with 179 statements, resulting in a rich resource to show the breadth of design processes. We’ve used this in multiple spaces, and in this poster we’ll describe how we used this in a seminar of 25 undergraduate and master’s students from multiple majors. We engaged the students with an in-class activity with the statements and asked them to create a visual representation inspired by the collection. We performed an inductive thematic analysis of student reflections to that in-class activity, as well as their reflections at the end of that class. From our analysis we found that the collection of responses helped students (1) gain an interdisciplinary awareness that there are many possible perspectives and different ways of defining good design, (2) understand that learning and adaptability are important elements of design, and (3) experience the importance of deep and personal reflection about their own values and motivations. This collection helped students understand the breadth and personal nature of design processes. We offer this resource to support engineering educators who hope to broaden the way they teach design.

Autism spectrum disorder (ASD) is a neurodevelopmental condition that affects social and behavioral development. Although autism is most associated with social difficulties, it is also correlated with issues such as sleep disturbances. Previous literature suggests that 50-80% of autistic individuals experience sleep difficulties. One common feature of autism is differences in sensory processing compared to typically developing (TD) individuals. These differences may result in behaviors that are detrimental to sleep habits. This project aims to identify the relationship between sensory processing and sleep quality in autistic and TD adults and to identify a type of sensory concern that correlates to increased sleep disturbance. 150 participants (ASD = 94) ages 18-25 from the (National Institutes of Health) NIH funded multisite study on sex differences in autism were used in the analysis. Participants completed self-reports on sensory systems using the Sensory Profile, and on sleep quality using the Pittsburg Sleep Quality Index (PSQI). The Sensory Profile scores participants among 4 quadrants: low registration, sensation seeking, sensory sensitivity, and sensation avoiding. The scores reflect the participants sensory systems compared to their age range separated into five groups. The PSQI takes participant responses and assigns a score with “0” being no difficulty and “3” being severe difficulty across 7 components of sleep. Component scores are then summed for a global score. A t-test will be performed to compare the mean global PSQI score for the five groups across each quadrant on the Sensory Profile and for autistic and non-autistic populations. We expect to see higher mean global PSQI scores for those with autism and for those with higher Sensory profile scores within the ASD population. Increased differences in sensory processing in autistic individuals is important to investigate because studies have shown that filtering out sensory input is key to falling and remaining asleep which leads to improved quality of life.

An important and universal aspect of cancer cells is the ability to proliferate rapidly. Rapid proliferation imposes specific metabolic demands which are often targeted for cancer therapies, and yet these demands are not well understood. A crucial aspect of cell metabolism is from the Tricarboxylic Acid (TCA) cycle. The TCA cycle is amphibolic, both catabolic and anabolic, and disruptions in the cycle are implicated in the onset and progression of various human cancers. Succinate Dehydrogenase (SDH) and Fumarate Hydratase (FH) are two TCA cycle enzymes that are tumor suppressors, proteins that when lost contribute to the malignant phenotype. In the TCA cycle, SDH catalyzes the conversion of succinate to fumarate, and FH catalyzes the subsequent step of fumarate to malate. Due to this proximity, one may predict SDH and FH mutations would have similar metabolic effects. However, this prediction, surprisingly, does not hold true. Paradoxically, loss of SDH generally impairs cell proliferation by disrupting synthesis of the amino acid Aspartate, a crucial output of mitochondrial respiration. Our lab recently discovered that SDH-deficient cancer cells adapt to overcome this metabolic deficiency by downregulating Complex I of the Electron Transport Chain (ETC). By downregulating Complex I, SDH-null cells increase the capacity of alternative aspartate synthesis pathways aside from the usual TCA cycle dependent pathway to enable faster proliferation. For SDH-null cells, treatment of a Complex I inhibitor improves proliferation for reasons discussed above. However, when FH-null cells are treated with the same Complex I inhibitor, there is a decrease in proliferation rate. It is not well understood why this difference exists, but characterizing it can provide insights on the roles of these enzymes and could inform better treatments for SDH and FH linked cancers.