The purpose of this research is to provide a nuanced understanding of a nation that struggles with insecurity and inequality, ultimately calling for a policy reform, aimed at promoting ethical resource extraction, and sustainable development. This research will analyze the root causes of the resource exploitation and decades long of turmoil the Democratic Republic of Congo faces. This research will look at how the issue is being resolved and if any improvements to a prosperous nation have been made in recent years. I will also talk about US intervention and its foreign policy reforms to uphold companies, countries and individuals accountable. This paper will also take a look at the migration crisis, along with the extreme human rights abuses being done to the Congolese people.

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

Mechanistic target of rapamycin (mTOR) functions in a protein complex with raptor to control protein synthesis in eukaryotes. A reduction of function mutation in C. elegans raptor is resistant to hypoxic death. This mutation, a missense at amino acid 1033 in the daf-15 gene, is interesting because the mutation site is conserved in all mammals, suggesting that this work could shed light on hypoxic injury mechanisms in humans. The Crowder lab has discovered that a mutation called tm11331 in a gene involved in purine metabolism blocks the hypoxia resistance of the raptor mutation. We hypothesized that the tm11331 mutation restores normal protein synthesis to the raptor mutant and therefore restores hypoxic sensitivity. For my project, I examined this hypothesis by measuring nucleolus size as an indirect measurement of protein synthesis. Four strains were used in this assay: unmutated (wild-type) worms, worms with the raptor mutation, worms with the tm11331 mutation, and worms with both raptor and tm11331 mutations. From previous experiments, we know that raptor mutants have smaller nucleoli than wild-type worms, indicating that protein synthesis rates are lowered in mutated worms. We would therefore expect that protein synthesis rates and nucleolus size would be restored in worms made hypoxia sensitive by the addition of tm11331. For this assay, all strains contained a fluorescent protein that labelled the nucleoli, allowing me to image nucleoli under fluorescence. I processed each image and measured average nucleolus size in worms from each strain. Our data shows that the tm11331 mutation increased nucleolus size in strains both with and without raptor mutation. In fact, the combination of tm11331 and the raptor mutation was not significantly different from wild type. Thus, our data supports the hypothesis that the tm11331 mutation restores hypoxic sensitivity by normalizing protein synthesis.

While flocculation is a desirable trait for brewing yeast because it eases the removal of cells from beer after fermentation, other modes of cell-to-cell adhesion can be detrimental to the brewing process. Mother-daughter separation defects cause cells to form large aggregated clusters which use more oxygen, produce a lower fermentative yield, and require more head space during fermentation. These defects can be caused by mutations to a number of genes, which makes a targeted genetic approach challenging. In this work, we used experimental evolution to eliminate mother-daughter separation defects present in a widely used brewing strain. Cells with this defect are less buoyant and settle faster than non-adhering cells. We used this property to select against cells with this defect by letting the cultures settle and propagating only cells present in the top layer of the media. We propagated top-layer cells for approximately 300 generations (about two months), collected daily optical density measurements, and conducted settling assays. Over time, we found that large, branched cell clusters decreased in frequency in our top-layer samples while the amount of single cells increased, which we confirmed through microscopy and optical density measurements. We characterized the mutations that drive this strain’s separation defect using whole genome sequencing of the evolved and ancestral populations. This project demonstrates how experimental evolution can be used to select against less desirable traits in commercially important yeast strains. Future research could implement similar or reciprocal methods to evolve for decreased or increased flocculation respectively.

Gun violence is a persistent and complex social issue that poses significant challenges to communities worldwide. Within the landscape of gun violence research, there is a recognized need for studies that explore the experiences of marginalized and immigrant populations, such as Somalis, Ethiopians, and multiple other Black immigrant communities. These communities often face intersecting socio-economic, cultural, and systemic factors that shape their vulnerability to gun violence. This study seeks to address this gap by examining the impact of gun violence on the Black immigrant communities in Seattle and surrounding areas, with a focus on understanding the underlying factors contributing to its prevalence and the responses employed by affected individuals and communities. The primary research question guiding this study is: How does gun violence impact the Black immigrant communities in Seattle and surrounding areas? What are the underlying factors contributing to its prevalence? I will conduct an interview study using a mixed-methods approach to analyze crime statistics and demographic data, complemented by creating a codebook. Preliminary findings indicate an increase in gun violence within these communities, reflecting the complex interplay of socio-economic disadvantage, cultural factors, and systemic inequities. By amplifying the voices and experiences of affected individuals, this study advocates for evidence-based interventions and policies that address the root causes of gun violence and promote community resilience. Through a holistic and community-centered approach, this research advances social justice and fosters safer, more inclusive environments for all residents.

Nearly all forms of cardiac disease are characterized by cardiac fibrosis, which contributes to heart failure and arrhythmias due to the accumulation of collagen deposits. Collagen, a crucial extracellular matrix (ECM) protein, is secreted by cardiac fibroblasts—the primary cell type responsible for generating this stiff scar tissue known as fibrosis. Fibroblasts are highly plastic cells that can transition between quiescent and activated states. The Davis Lab has developed a minimally invasive intermittent injury model to cyclically stress cardiac fibroblasts in vivo, allowing for a deeper investigation into the role of cellular memory in regulating the fibrotic response. Notably, we can reduce fibrotic remodeling in this model by inhibiting p38 gene function in the activated population, thereby encouraging a shift back to a quiescent state. My work aims to determine whether the once-activated population is proliferating at the second injury stimulus as well, or if a new population of fibroblasts is proliferating with repeat injury. To address this, I am utilizing genetic lineage tracing and Click-iT EdU technology, which allows for precise biolabeling while also preserving cell morphology and integrity by integrating into the cell's DNA. I am also performing immunohistochemistry staining to detect other proteins of interest that will serve as proliferation markers as well. Based on prior findings in the Davis Lab, we hypothesize that once-activated fibroblasts will go on to activate again when exposed to repeated disease stimuli, but there will be no second wave of proliferation as there was no change in total fibroblast number. 

In an era of increasing political polarization, the ability to engage in meaningful and respectful discourse is more critical than ever. Yet, on college campuses across the U.S., students often struggle to navigate ideological differences, sometimes choosing disengagement over dialogue. The purpose of the three part Civil Discourse Project (CDP) is to use participatory action research principles to understand and address inequity related to civil dialogue and discussions of democracy at the University of Washington. Led by student researchers and staff from UW Brotherhood (BI) and Sisterhood (SI) Initiatives, the three-part project is structured around an iterative cycle of research (i.e. action and reflection) to empower students of color to surface and address social and institutional barriers faced by other students of color within the BI and SI. As a part of the CDP,  this study surveyed 91 first-year BI and SI students through an 11-question online survey in Fall 2024. The goal was to understand how identity shapes engagement with civil discourse. The survey included open-ended, scale, and ranked choice questions assessing students’ prior exposure to civil discourse, their comfort level in engaging with differing viewpoints, and their perceptions of discourse dynamics. Using descriptive and text analysis, the study found that both BI and SI responses exhibited common themes regarding the importance of maintaining composure and respectful engagement during civil discourse. However, the preliminary findings also suggested notable gender differences between the value placed on civil discourse, willingness to seek out civil discourse, and personal comfort while engaging in civil discourse. Specifically, the findings highlighted how a willingness to engage with different perspectives is not always synonymous with being an active discussion participant. These insights can inform ongoing discussions at colleges and universities about fostering equitable and inclusive dialogue across political and ideological divides.

The current understanding of mechanisms of anesthesia and the function of anesthesia-activated brainwide neural circuitry is very limited. Additionally, there is an urgent need to develop new non-opioid analgesic drugs, and targeting anesthesia neural circuitry could provide a novel path to pain relief. To investigate the function of this circuitry, we use a brainwide approach to perform chemogenetic manipulations in a FosTRAP2 transgenic mouse model. Briefly, FosTRAP2 (Fos-2a-Cre) mice receive retroorbital injections of a Cre-dependent virus expressing chemogenetic DREADDs. Mice then undergo isoflurane anesthesia exposure and midway through the exposure, they receive an intraperitoneal injection of 4-hydroxytamoxifen to induce activity-dependent chemogenetic labeling of isoflurane-activated brainwide ensembles. I use behavioral analysis pipelines to analyze how the activation of these ensembles affects thermal nociceptive processing after mice are induced into a lightly anesthetized state and subjected to analgesia testing. Mice underwent the warm water tail withdrawal and hot plate assays. I then use a combination of manual annotation and pose estimation approaches with supervised machine learning using Social LEAP Estimates Animal Poses (SLEAP) followed by Simple Behavioral Analysis (SimBA) to provide insight into behavioral signatures and classifications. I identify a number of occurrences for behaviors such as tail withdrawal, latency to jump, and paw grooming, which is used to infer thermal anti-nociception in open field testing. I also helped develop five distinct behavioral classifiers: rearing, grooming, freezing, circling, and Straub tail response. With the resulting behavioral analysis, I can investigate how targeting brainwide anesthesia-activated neural ensembles produces anti-nociception. Anesthesia, although used for many common procedures, is not widely available to the general public and must be administered by a medical professional. Understanding the mechanisms behind its effect on pain processing is a gateway for revolutionary research that could potentially eliminate the need for opioid medications in the future.

Age-related macular degeneration arises from irreversible photoreceptor loss. Photoreceptors, rods and cones, are specialized cells in the retina that allow light and color detection. My project investigates the role of retinoic acid (RA) on cone and cone-opsin development to understand the timeline of cone specification and development. RA, an endogenously synthesized vitamin A derivative present in the retina during development, drives rod photoreceptor differentiation, but its effect on cone development is still unknown. To understand RA’s role in opsin development, I use a retinosphere (RS) model, an in vitro system to culture human fetal retina. More specifically, I used RS from 70 to 90 days old (D70-D90) and cultured the RS until D100, when the cone-opsin onset occurs. I then fixed, cryosectioned, and immunostained the two conditions for S-opsin, M/L opsin, and NR2E3 (rod marker) and investigated changes in the density of cone opsin-positive cells between the two conditions using confocal microscopy. My findings showed that the condition containing exogenous RA had a decreased density of opsin-positive cells. To confirm that the observed effect is due to RA, I mimic the experiment by instead using WIN18446, an RA inhibitor. I then determined if RA's effects are dose-dependent. My results showed that increasing the concentration of exogenous RA amplified my previous findings. The next step is to understand the timeline of cone specification and development by using RS of a younger age, before cone-opsin onset. These results will allow my mentors and me to use our knowledge about RA to determine if inhibiting endogenous RA synthesis in the retina will play a role in developing therapeutics involving cone regeneration to aid in cone-related macular diseases and injuries.

Hailey-Hailey disease (HHD) is a rare autosomal dominant skin disorder characterized by recurrent epidermal blistering and infections, significantly impacting quality of life. The disease results from ATP2C1 mutations causing deficiency of SPCA1. This Golgi-embedded calcium pump is critical for folding and trafficking proteins, including cadherins that mediate desmosomal cell-to-cell adhesion. Although its genetic cause was identified 25 years ago, HHD remains an orphan disease without any FDA-approved treatments. Drug development for HHD has been hindered by the lack of pre-clinical models as knockout mice failed to replicate the disease. To overcome this barrier, we engineered human cellular and tissue models of HHD to elucidate its pathogenesis and identify therapeutic strategies. Utilizing CRISPR/Cas9, we ablated ATP2C1 in TERT-immortalized human epidermal keratinocytes and generated cell lines with haploinsufficiency or total loss of SPCA1. Mechanical dissociation assays showed SPCA1-depleted keratinocyte sheets had weakened intercellular adhesion. Explaining this phenotype, immunoblots of SPCA1-deficient keratinocyte lysates revealed lower expression of desmosomal cadherins, while immunofluorescent staining showed reduced concentration of adhesive proteins at cell-cell junctions. These effects induced tissue splitting within 3D organotypic epidermis, replicating the key feature of HHD pathology. To define the mechanisms impairing cadherin localization in our model, we performed RNA sequencing, which showed dysregulation of the actin cytoskeleton in SPCA1-deficient cells. We used live confocal microscopy to confirm that SPCA1 depletion altered actin organization in keratinocytes and we hypothesize that this disrupts cadherin trafficking and cell-cell junction stability. Using image analysis software to quantify cytoskeletal morphology, we found that SPCA1-deficient cells had reduced linear actin filaments, which could impact intracellular protein trafficking and keratinocyte migration during wound healing. In sum, our novel pre-clinical model replicated HHD pathology and revealed that actin dysregulation may undermine intercellular adhesion and could represent a new therapeutic target for this orphan blistering disorder.

Alphaviruses such as chikungunya virus (CHIKV) pose a significant threat to global health, yet specific antiviral therapies remain unavailable. In this study, we evaluated combinations of three approved oral directly acting antiviral (DAA) drugs (sofosbuvir (SOF), molnupiravir (MPV) and favipiravir (FAV)) against CHIKV, Semliki Forest virus (SFV), Sindbis virus (SINV), and Venezuelan Equine Encephalitis virus (VEEV) in vitro and in vivo . In human skin fibroblasts, synergistic antiviral effects were observed for the drug combinations MPV + SOF and FAV + SOF against CHIKV, and for FAV + SOF against SFV. In human liver Huh7 cells, the combinations of FAV + MPV conferred additive to synergistic activity against VEEV and SINV strains, while SOF synergized with FAV against SINV strains. In a mouse model of CHIKV arthritis, MPV improved CHIKV-induced foot swelling and reduced systemic infectious virus titers. Combination treatment with suboptimal doses of MPV and SOF significantly reduced foot swelling and decreased infectious virus titers in serum as compared to single doses of each drug. Sequencing of CHIKV RNA from mouse joint tissue revealed that MPV caused dose-dependent increases in mutations in the CHIKV genome. Upon combination therapy of MPV with SOF, the number of mutations was significantly lower compared to single treatment with several higher doses of MPV. In summary, combining approved oral nucleoside analogs confers potent suppression of multiple alphaviruses in vitro and in vivo with enhanced control of viral genetic evolution in the face of antiviral drug pressure. These drug combinations may ultimately lead to the development of potent combinations of pan-family alphavirus inhibitors.

Chronic kidney disease is projected to be the fifth leading cause of death worldwide by 2040. Chronic kidney disease of unknown etiology (CKDu) makes up 70% of CKD cases in places such as India, Mexico, and Sri Lanka, largely through environmental factors. Ochratoxin A (OTA) accumulates in the kidney and is a nephrotoxic mycotoxin that contaminates grain products such as wheat, rice, beer, and most plant-based foods. Chronic OTA exposure has been linked to CKDu in rural agricultural areas, such as Sri Lanka. A prominent family of cell membrane transporters, Organic Anion Transporters (OATs), are one of the main drug transporter families in the kidney. Previous work in our lab elucidated that OAT1/3 and 4 are major OTA transporters. Certain antioxidants, found in common plant-based food products like green tea, coffee, and certain vegetables have been studied to reduce OTA-mediated nephrotoxicity. However, since our preliminary data indicate OAT transporter-dependent uptake into the kidney, we aim to test the competitive inhibition effect of OAT-substrate antioxidants in preventing kidney accumulation of OTA. Potential inhibitors include epicatechin gallate, miquelianan, caffeic acid, luteolin, and myricetin. Competitive inhibition in individuals consuming these products along with OTA exposure could lead to decreased uptake of OTA into the kidney, mitigating toxicity. Our preliminary uptake experiment with those inhibitors indicates that miquelianan reduces OAT3 mediated uptake of OTA by 48%. We will next assess the inhibition potential of miquelianan on OTA with an IC50 curve via mass spectrometry analysis. This study will provide evidence for a potential new mechanism of antioxidant amelioration of kidney toxicity to OTA exposure.

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

As the life expectancy for global populations rises, the prevalence of people affected by age-related morbidity has also increased. Although therapies and treatments are available to alleviate such diseases, they do not effectively address the fundamental cause of all such diseases age. One hallmark of age is cellular senescence. Senescence refers to the state of a cell in which it cannot divide anymore due to factors such as stress or damage to DNA. Although this mechanism is naturally preventative there can be many undesirable consequences. As senescent cells accumulate within aging tissues, inflammatory responses are promoted and may even spread senescence to neighboring cells. This causes more inflammation and elevates the risk of illnesses. Targeting these cells with therapeutics such as senolytic drugs presents a potential solution. A combination of senolytic drugs, Dasatinib + Quercetin (D+Q), has been shown to target and lyse senescent cells, thus increasing lifespan and reducing frailty in mice. This research study involves two groups of mice: old and old treated with D+Q, where D+Q was administered for 24 months. Mandibles were collected to evaluate levels of senescence (CDKN1A and CDKN2A, genes coding for p21 and p16, respectively) through RNA extraction and QRTPCR. Inflammation markers, IL1a and IL1b, were also examined as inflammation is frequently associated with senescence. Preliminary observations have shown decreased transcription of CDKN1A and CDKN2A in treated male mice in comparison to controls (p < 0.05 and p < 0.001, respectively) within aging alveolar bone. In addition, IL1a and IL1b were shown to have decreased expression in the treated male mice in comparison to the controls (p < 0.001, p < 0.05, respectively). This project was funded by the SenNET Grant (AG079753) and funded in part by the Dr. Douglass L. Morell Dentistry Research Fund.

Human activity continues to significantly affect nature, expanding its area of influence via multiple sources. Artificial light at night (ALAN) is a major source of this human interference, originating from urban areas, roadways, and streetlights. Its influence is widespread, disrupting not only ecosystems but also the development, population size, life expectancy, and reproduction of plants and animals. We worked with house crickets (Acheta domesticus) to test whether and how exposure to ALAN throughout juvenile development altered behavior, development, and reproductive investment in the form of maternal hormone provisioning compared to crickets that experienced no light pollution. Here we report that lifelong exposure to ALAN affects cricket development and may influence the hormone provisioning to eggs by female crickets. However, ALAN had no effect on the behavior or movements of crickets. While our result is consistent with some previous findings in animal systems, it contradicts others: we conclude that the influence of light pollution on animal physiology and behavior is likely nuanced, and its effects are dependent on life history, development stage, and ecology.

Multiple System Atrophy (MSA) is a fatal neurodegenerative disease caused by alpha-syn deposition in the brain and spinal cord. This results in severely declined autonomic and motor functions.  In rare cases of MSA, there is pure autonomic system failure, only including dysregulation of blood pressure (BP) control and pelvic organ functions including bowel movement. Blood pressure changes could be extremely dramatic, with uncontrolled drops below 60 mmHg and elevation sometimes over 250 mmHg, resulting in the inability to even stand for more than one minute without feeling faint. Overall, this greatly impacts an individual’s quality of life and mortality. On average, life expectancy after MSA diagnosis is about 6 to 10 years, though this can vary based on factors such as age at onset and symptom severity. Currently, treatment options primarily focus on mitigating symptoms. This case study reports the effect of non-invasive transcutaneous spinal cord stimulation, using on-skin electrodes, on cardiovascular and bowel function. We recruited a male in his 60’s with MSA diagnosed 15 years ago, showing pure autonomic system failure. We measured both acute and long-term effects of stimulation on blood pressure by monitoring continuous BP during stimulation and also had the patient maintain a 24-hour blood pressure log pre- and post-stimulation. Upon examining the data that I analyzed, cervical spinal cord stimulation elevated blood pressure more than thoracic or lumbar stimulation. The participant also recorded his bowel management and stool quality for 5-7 days before and after the sessions. Spinal cord stimulation initiated bowel movements immediately after the intervention. Further research is warranted to better understand the effects of cervical spinal stimulation on blood pressure regulation and bowel function.

Recent technological breakthroughs have allowed important advances in the description of deep reefs (below 30 m). However most research has been restricted to the upper section of deep reefs (down to 80 m) and has primarily focused on fish and coral communities. By contrast, the composition of the lower portion of deep reefs, and of non-coral habitat-forming communities remains limited. This work focuses on how the composition and structure of habitat-forming communities change across the entire depth range of a tropical reef-dominated ecosystem, from 5 to 300 m. Using a combination of SCUBA and manned submersible diving, benthic transects were performed in  Curaçao , an island in the Southern Caribbean Sea. Using a combination of morphology, taxonomy, and trait ecology, I will evaluate the faunal breaks of habitat-forming communities with depth. In addition to providing one of the first descriptions of the diversity and community structure of habitat-forming communities across the entire range of a reef’s slope, this work will contextualize over a decade of deep-reef fish observations conducted at this study site. This study will also provide insights into the vertical reef connectivity and resilience, informing future management efforts of deep Caribbean reefs. 

The metabolite of vitamin A, retinoic acid (RA), plays a critical role in regulating cell differentiation in mammals. RA and its metabolites exist as different geometric isoforms (all-trans, 13-cis, 9-cis, 4-oxo-all-trans, 4-oxo-13-cis .). All-trans-RA is the biologically active isomer, and 13-cis-RA is found as the drug “Accutane” used to treat severe acne. Cellular retinoic acid binding proteins are evolutionarily conserved intracellular proteins that regulate RA tissue concentrations. The all-trans isomer is known to bind tightly to CRABP1 and 2, but little is known about the binding of the other four isomers and metabolites. No data on the binding affinities of the 4-oxo isomers is available. I hypothesize that the RA and 4-oxo-RA isomers that have not been extensively researched, have different binding affinities between the two CRABPs. To test this hypothesis, I use fluorescence spectroscopy coupled with single value decomposition (SVD) analysis and stopped-flow analysis to measure the equilibrium dissociation constant (Kd), association rate constant (kon), and dissociation rate constant (koff) for retinoid binding to CRABPs. My current data generated by the fluorescence spectroscopy method shows that binding affinities of the tested retinoids are comparable between CRABP 1 and 2, except for 13-cis-RA which bound CRABP2 significantly more tightly than CRABP1. (CRABP1 Kd  = 609 nM, CRABP2 Kd  = 70.5 nM) . All-trans-RA (atRA) has the tightest binding to both CRABP 1 and 2, (CRABP1 Kd  = 0.51 nM, CRABP2 Kd  = 0.73 nM), followed by 4-oxo-atRA, (0.39nM, 1.4 nM), 9-cis-RA, (61.5 nM, 96.2 nM), and finally 4-oxo-13-cis (779.5 nM, 743.6 nM) with the lowest binding affinity. These relationships will be further investigated using the stopped-flow method.

Epilepsy is a brain disorder characterized by spontaneous seizures. Many people with epilepsy treat their seizures with antiseizure medicines (ASMs), which must be taken daily, even through major life milestones such as pregnancy. However, there is little evidence on how these medicines, particularly when taken together, influence long-term brain development in children born to mothers taking ASM therapy. Understanding these consequences is crucial, especially for newer ASMs and drug-resistant epilepsy patients that require multiple medications. Therefore, this experimental study investigated how epilepsy therapy impacts birth and developmental outcomes in rodent offspring born to mothers taking multiple ASMs.
Timed-pregnant female rats were orally administered one of the four epilepsy treatments at therapeutically relevant doses during gestation and lactation. Treatments included: placebo, lamotrigine, levetiracetam, or combined lamotrigine and levetiracetam. General characteristics of birth outcomes were monitored, including gestational length, offspring growth rate, and major developmental milestones. No differences were detected in gestational length for our first cohort (22–23 days). Maternal weight gain varied between 78g to 115g, or 30–39% of their baseline weight. No significant differences were detected in litter size (9–15 pups), date of fur development (postnatal day 10, PND 10), or the average date of eye opening (PND 14), with some pups ranging from PND 13 to PND 15. The average mass for offspring was inversely correlated with litter size, but not treatment. These preliminary findings are inconclusive about the impact of ASMs on early developmental outcomes in offspring. Future studies will replicate each cohort and evaluate the long–term cognitive and behavioral effects. Grasping these impacts can guide safer therapeutic approaches for epilepsy patients during pregnancy.

Resilience to aging is a critical biological process that precedes age-related declines in physiological function. Defined as an organism’s ability to respond to physical stress and return to equilibrium quickly despite increasing age, wound healing can help in the evaluation of resilience by indicating the efficiency of repairing physical tissue damage to the body by generating new tissue. Previous correlations between resilience to aging and wound healing suggest that mice with higher rates of wound closure have less cognitive impairment and increased grip strength. GHK-Cu, a peptide that has been shown to accelerate wound healing and skin repair, has been used in topical treatments. Current studies have shown that systemic administration of the GHK-Cu peptide improves cognitive performance in aging mice and lowers inflammation levels. Understanding this role in resilience mechanisms could provide valuable insight into more complex interventions such as multiplexing. A cohort of 20 male 18-month-old C57BL/6 mice was used. Ten randomly chosen mice received daily intraperitoneal doses of GHK-Cu, while ten controls received saline for 19 days. After 3 days, a 2 mm ear punch was taken from both ears. Wound closure was measured on day 3 and day 19 by photographing the biopsy area and analyzing images with ImageJ software. After final measurements, cognitive performance and correlation to wound healing was assessed via phenotypic assays. Tissues surrounding the wound were then stained using immunohistochemistry. TNF-α and VEGF antibodies evaluated inflammation and cell growth respectively and were quantified using QuPath. The GHK-Cu peptide during the experiment showed enhanced wound healing from the physical stressor, suggesting a promising therapeutic strategy to improve recovery from injuries and cognition abilities in aging populations. The findings from this study may inform translational strategies to enhance wound healing and quicker recovery from tissue injury in aging and age-related diseases.

Graphene, a single layer of carbon atoms, is a naturally abundant Dirac semimetal that is turning heads for its interesting electrical properties and tunable phase transitions at nano-scales. Prior research shows novel phases of matter arising when a bilayer sheet of graphene is stacked atop a trilayer sheet of graphene at some small relative angle. This particular geometric configuration gives rise to flat electronic bands near the Fermi level where, at low temperatures, electron-electron interactions dominate the physics of the system. Correlated topological states at integer and fractional filling of these electronic bands have previously been observed in this material, but how these states evolve with twist angle is not well understood. We present our ongoing analysis of Bernal bilayer-trilayer graphene at varying twist angles (0.8-1.7 degrees) to uncover how the geometry of our material changes these correlation-driven states. This work contributes to our rapidly evolving understanding of electron behavior in two-dimensional materials, which has future implications in quantum computing and other electronics innovations.   

The formation of the neural tube is a critical event in embryonic development. Morphogenic signals guide a layer of embryonic cells to fold and create the neural tube, which serves as the precursor to the brain and spinal cord. When the neural tube fails to close properly, neural tube defects arise. Spina bifida is the most common neural tube defect, affecting 1 in 1,000 births. Although surgical procedures can be used to treat it, they often result in complications involving serious disabilities and infections. While neural tube defects are believed to have a multifactorial etiology, which includes a genetic component, proposed causative mutations that lead to the development of spina bifida in humans have yet to be thoroughly examined. Recently, mutations in the gene for a G-protein coupled receptor known as GPR161 were identified in infants with spina bifida. However, the role of GPR161 variants in the development of spina bifida is not fully understood. Utilizing CRISPR/Cas9 technology in human induced pluripotent stem cells, I have generated GPR161 knockout and point mutation lines and differentiated them into neural progenitors in a 2D model while also developing a 3D organoid system. Using these models, I will investigate the downstream pathways involved in the formation and patterning of the neural tube that could be influenced by the mutations. This includes the sonic hedgehog pathway, Wnt pathway, and assessing neural differentiation markers. I will evaluate these markers through various assays, including immunofluorescence and real-time quantitative PCR. Through these efforts, we will enhance our understanding of a genetic component in the etiology of spina bifida while demonstrating the value that induced pluripotent stem cells can have in studying human development and treating human diseases by recapitulating them in human models in vitro.

The goal of this project is to better understand a driver of immune dysregulation in people with Down syndrome, who experience a complex interplay between genetics and immunity, leading to a higher risk of autoimmune diseases. Despite advances in research, the mechanisms driving this heightened susceptibility remain largely unexplored. In the U.S., approximately 1 in every 700 babies are born with Down syndrome each year. Understanding these differences is crucial for developing targeted therapies to improve health outcomes and quality of life. In the Khor lab, we are focused on understanding these mechanisms and how to treat autoimmune diseases common in people with Down syndrome. Preliminary data shows that RNA expression of Duffy, a gene encoding the Duffy antigen receptor for chemokines, is much higher in blood from people with Down syndrome. We want to determine if the protein expression of Duffy follows this same pattern. The Duffy antigen, located on red blood cells, binds chemokines released during inflammation, attracting immune cells to sites of damage. In our experiment, we will use flow cytometry to detect Duffy on RBCs. We expect to find that RBCs from people with Down syndrome express higher levels of the Duffy protein. Our data may reveal a new mechanism of immune dysregulation in Down syndrome and provide insights into how this gene affects the severity of malaria, as the Duffy protein is a receptor for it. This study can serve as a strong foundation for future research on immune dysregulation and infectious diseases like malaria in people with Down syndrome.

Scarcity of usable water has quickly become one of the world’s greatest problems. Most of Earth’s water is saltwater, and much of the limited available freshwater contains harmful contaminants. One type of contaminant, per- and polyfluoroalkyl substances (PFAS), are particularly hazardous as they are toxic to humans and do not naturally decompose due to their strong carbon-fluorine bonds. Of the available methods of removing PFAS from water, including adsorption, ion exchange, and membrane filtration, membrane filtration is an appealing separation technology since it does not require expensive, energy intensive regeneration steps used in adsorption and ion exchange. Our project aims to use molecular layer deposition (MLD) to create polymeric thin films selective to  PFAS for water filtration. MLD involves cycles of dosing and purging reactant vapors to create a thin film layer by layer, allowing for better control over the surface uniformity, composition, and thickness. These thin films, synthesized on polyethersulfone (PES) membranes, will ideally be rejective of PFAS while preserving membrane permeability. We synthesize thin films of various chemistries and measure their water contact angle to determine the impact of hydrophilicity on long- and short-chain PFAS rejection. Here, we provide our measurements of the pure water permeability, long- and short-chain PFAS rejection, and water contact angle of MLD-treated PES membranes.

Assessing how organisms respond to shifting climatic conditions is crucial in the era of climate change to predict species' resilience to environmental changes. This study aimed to explore the effects of heatwaves on grasshopper development and fitness. Specifically, I investigated the reproductive potential of two grasshopper species within the framework of a common garden heatwave experiment. In Spring 2023, we reared the grasshoppers under three heatwave intensity treatments, exposing each treatment group to three heatwaves during set developmental stages. Afterward, I dissected the preserved females frozen for analysis, quantifying the number of primary and secondary oocytes in their ovaries. Oocytes develop into eggs and as such are a metric of reproductive potential. I hypothesized that increased heat stress would result in a decline in fecundity. However, we did not find a significant effect of the heatwave treatment on oocyte count, suggesting any fecundity effects of heatwaves are via a different mechanism. Understanding how organisms respond to changing environmental conditions is key to understanding how ecosystems will change in the coming years, and is important for informing conservation efforts.

Panãra is a Jê language spoken in the Panará Indigenous Land in the Brazilian Amazon by around 730 people. I am an undergraduate research assistant working as part of the larger Panãra Documentation Team at the University of Washington. I am in the process of transcribing, coding, and archiving field notes taken by team members during the summer of 2024. I have employed my experience with Panãra and Portuguese to resolve ambiguities in the notes and to code materials in a standardized, accessible manner. Many letters, such as ⟨b, d, g, z, l⟩, and sequences, such as ⟨-ät-⟩ or ⟨-me-⟩ are impossible due to Panãra’s phonology and orthography. However, these letters may occur in the notes due to transcriber error or Portuguese loans. When I identified suspect items, I had to use my knowledge of Panãra to determine their status. I typed the notes into text format before transferring items into a spreadsheet. In the spreadsheet, I coded part of speech and added lexical items to the ongoing dictionary. My work is a case study in longer-term, multi-researcher documentary efforts in linguistics. Not only will the body of data I code be valuable in further analysis of the language, but the processes developed will be useful in rethinking how documentary linguistics is carried out. In particular I emphasize the need for a coherent vision of data usage, from collection to coding. As the dictionary work moves forward, my next steps will be to give words that have not yet been checked in the field to the research team for the summer and to code the phonological, orthographic, and lexical information for each word into the FLEx database.

Magnetic field models of the Earth used for scientific applications and navigation systems are often mapped using ground and satellite measurements, but are rarely done at high altitudes in the atmosphere. Including magnetic field measurements from the upper troposphere and stratosphere could better inform these models. For this study, we used a MLX90393 magnetic field sensor to measure the magnetic field during a high altitude balloon flight. The sensor has a range of -20°C to 85°C, but temperatures often reach -50°C in the upper troposphere and lower stratosphere. In an attempt to keep the sensor within its operating range, we built an insulated enclosure of Styrofoam and mylar. The enclosure was sealed with weather resistant silicone and chemical hand warmers were placed inside. To improve the accuracy of magnetic field measurements on future balloon flights, we compared magnetic field measurements from a non-insulated and an insulated sensor during a high altitude balloon flight. In addition to magnetic field measurements, temperature and pressure measurements were taken inside and outside of the enclosure using a BMP-180 sensor.

ALAS stands for Adolescent Latinas Advancing Salud mental through Storytelling. Dedicated to empowering young Latinas, providing them with a supportive community and the tools to prioritize their mental health. Through storytelling, ALAS creates a community where these Latinas share their experiences, learn coping strategies, and actively step toward healing and self-improvement. This initiative has been piloted, and the success of the first group of participants has shown just how vital and transformative this program is. The young women who took part in ALAS not only found a sense of belonging but also gained skills that helped them navigate the hardships they faced. Many participants expressed how the program gave them confidence, validation, and a community with an understanding that they are not alone. This presentation highlights the positive impact of the ALAS programs and the potential of the culturally grounded toolset as a proactive intervention for addressing mental health in adolescent Latinas. My qualitative data analysis explores key lessons from two cases and broader data patterns, with considerations for future research. Unfortunately, there has long been a noticeable absence of research and resources dedicated to Latinas' mental health, leaving many young women without the guidance or support they need. A space designed specifically for Latinas, where our unique experiences and cultural backgrounds are understood and validated is more important now than ever. ALAS is working to fill these gaps, ensuring the next generations of Latinas have access to the tools, knowledge, and community that many never had. Mental health is a critical issue, and Latinas deserve to have their voices heard and acknowledged. ALAS is more than just a program. It’s a movement toward change, a step toward breaking the silence around mental health in our communities. Teaching them to embrace themselves and be the change they wish to see.

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

Recent studies have reported that certain tampon brands contain traces of various metals, raising public safety concerns about regular tampon use. Exposure to metals such as lead may pose detrimental effects on cognitive function, the nervous system, and reproductive health, yet little is known about the extent to which these metals are absorbed into the bloodstream from these products.  This project aims to investigate the presence of heavy metals within tampons. We hypothesized that tampons made from cotton would contain higher traces of metals compared to ones that are made with viscose rayon. We selected five widely available brands of varying absorbances and material, categorizing them as either organic (cotton) or non-organic (viscose rayon). To quantify the total lead content, 0.300 g of each sample was digested using a mixture of hydrogen peroxide and nitric acid. To determine the extractable quantity of lead, each sample was submerged in a simulant solution for 24 hours, replicating the acidity of vaginal fluids. To ensure the presence of lead within the sample, tampons with measurable lead concentration were spiked with known amount of lead quantity. Using AA Spectroscopy, quantifiable total lead contents were found in three out of the five tampon samples; Tampon C exhibited the highest lead content of 1.363 µg/g of tampon. Additionally, only one in five tampon samples was found to have significant extractable lead content, with Tampon C containing 0.2184 µg/g of tampon. Our results indicate a higher proportion of detectable traces of total and extractable lead in non-organic tampons compared to organic tampons. Despite these findings, further research is needed to establish whether there are adverse health effects to lead exposure from tampon use.

Political satire is often viewed as a form of indirect political expression commonly employed in authoritarian states like China. When social media is heavily regulated, satire serves as a rhetorical tool to circumvent censorship. However, satire might vary across various types of political discussion, including housing, unemployment, and the overwork culture. While prior research has extensively examined political satire and censorship in China, there is little research comparing how satire functions differently across political discussion themes. This study hypothesizes a correlation between themes of political discussion and the role and characteristics of satire in political discourse by analyzing content on Zhihu, a Chinese Q&A platform. Specifically, it examines (1) the correlation between discussion themes and stance to assess whether satire is a necessary feature for expressing dissent, (2) the prevalence of satire, measured by the proportion of satirical posts within each theme, and (3) the relationship between linguistic ambiguity and satire to determine whether ambiguity is a key strategy for evading censorship. The methodology consists of three main steps: (1) Construct a dataset by creating a random sample from a list of select political discussion themes and scraping the top discussion forums, recommended by the platform's algorithms, to ensure the sample reflects the overall user experience. (2) Qualitative text annotation based on the post's stance, ambiguity, and the presence of satire. (3) Applying natural language processing techniques to examine cross-topic variations in the use of satire and other rhetorical strategies. This approach facilitates a systematic exploration of how different types of public political discussions utilize satire to evade censorship. This research contributes to the broader understanding of political discourse under authoritarianism, offering insights into how citizens navigate the boundaries of permissible speech. 

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

The kidney plays an important role in blood filtration, regulation of blood pressure, acid/base homeostasis, and electrolyte balance. Studying the different kidney compartments provides critical insights into the metabolic mechanisms underlying these essential functions. Ziyu Guo, my research mentor has recently developed a highly multiplexed fluorescence microscopy using semiconducting polymer dots (Pdots) that allows one round of immunostaining and imaging of up to 21 targets. However, this technique is restricted to thin samples (50-100 µm), which may oversimplify biological systems by lacking depth and structural integrity. To overcome this limitation, my research integrates multiplexed fluorescence imaging with ELAST, a technology to transform thick tissues into elastic hydrogels, reinforcing the tissue's structure while allowing for better antibody penetration. This approach allows for simultaneously labeling multiple targets in the thick tissue while preserving tissue architecture. Overall, my project seeks to improve our understanding of kidney architecture in their natural spatial 3D context and further provide insights into disease mechanisms and potential therapeutic targets.

Extracellular vesicles (EVs) are essential mediators in intercellular communication secreted by cells to transfer bioactive cargo that lead to biological effects. The crucial roles EVs have in maintaining biological homeostasis are similarly found within cancer cells in the tumor microenvironment, where they promote cell growth/survival, invasion, and metastasis. Investigating methods to reduce tumor-cell derived EVs could provide substantial remedies for cancer patients. One pathway of interest in cancer is the cellular response to reactive oxygen species (ROS)—highly reactive molecules which tumor cells use for oncogenic signaling, to damage macromolecules, and drive tumor progression. Modulation of ROS levels may yield anticancer effects, but research about the role of ROS in EV biogenesis has not been conducted. To assess their connection, I used MDA-MB-231 human breast cancer cells as an in vitro model for EV biogenesis. My interest in ROS and EVs began when I assisted my graduate mentor in an extensive chemical screen and found kinase inhibitors that altered EV production via an EV isolation protocol. From these hits, I identified ROS-activated pathways that promote cancer progression as important players in EV production. I then tested if chemicals known to directly affect ROS alter EV production by isolating and quantifying EVs and by imaging their production from MDA-MB-231 cells. To provide a comprehensive understanding of the pathway, I validated upstream interactions of EV biogenesis by measuring the production of ROS using a chemical marker that emits green fluorescence when oxidized. From this data, I can determine if there is a direct interaction between ROS and EV production. An understanding of EV biogenesis and its connection to ROS and cancer progression may unveil new opportunities for novel cancer therapeutics.

Inbound tourism plays a crucial role in the global economy by promoting expenses, job opportunities, and creating international connections. In this study, I focus on the impact of China's visa-free transit policy on the labor markets across major entry-exit cities, especially on the employment dynamics in the tourism sector. Using panel data from cities such as Beijing, Shanghai, Shenzhen, etc, I plan to employ a Staggered Difference-in Differences (DiD) model with multiple periods to assess the causual effects of the policy. The control variables are Gross Regional Product (GRP) and domestic tourism activity. My project is still in progress and my anticipated result is that the visa-free transit policy will lead to an increase in employment within the tourism sector as well as have positive spillover effects in related sections.

Children are not merely passive observers; they actively seek to understand the why behind events. A fundamental distinction in causal reasoning is between agentic causes, which attribute outcomes to the actions of an agent like a person, and non-agentic causes, which focus on environmental factors. Do children show preferences for agentic versus non-agentic explanations? Moreover, are they influenced by the outcome’s valence (positive or negative)? This study examines how outcome valence influences children's (4-9 years old) preferences for agentic versus non-agentic causes in situations where the cause is ambiguous. By analyzing their explanatory preferences, we investigate how the valence of outcomes shapes causal reasoning across development. Participants will be presented with scenarios describing everyday events. Each scenario will have a clear positive or negative outcome, and the cause of the event will be ambiguous, with both agentic and non-agentic explanations being plausible. For example, some participants might see an apple falling perfectly into someone's hand (positive), while others see it hitting their head (negative) - events that could be attributed to either a squirrel jumping up and down, or the wind blowing. Participants will then be asked to answer what caused the outcome via a forced-choice task. We predict that children will more often select agentic over non-agentic causes for negative outcomes compared to positive ones. We also expect that as age increases, their choice differences based on outcome valence will be more pronounced. This investigation helps us understand whether agency itself plays a role in early causal reasoning. If children demonstrate a stronger preference for agentic causes in negative outcomes, this may suggest that emotional valence influences how children construct causal explanations. Furthermore, examining children’s explanatory preferences - whether biased toward agentic causes or not - can tell us how they incorporate agency into their developing understanding of causality.

Chimeric antigen receptor (CAR) T-cell therapy offers a promising approach to cancer treatment by harnessing the immune system to target and destroy tumor cells that express a specific cell-surface antigen. While CAR T-cell therapies have been successful in treating blood cancers, their efficacy against solid tumors is limited due to tumor antigen heterogeneity. To address this challenge, we have engineered a universal SpyCatcher003 CAR T-cell system (DB5 CARs) that utilizes synthetic peptide intermediates to target multiple antigens. Peptides are high-affinity biomaterials capable of binding receptors expressed on cancer cells for targeted T-cell killing, but peptides are limited by a short half-life due to rapid degradation in vivo. To overcome this challenge, we have developed peptide co-polymer formulations that are multivalent and exhibit increased serum stability. Additionally, the chemical and structural functionality can be tuned to precisely control the molecular weight and the number of peptides per polymer, enabling simultaneous and multivalent CAR engagement on T cells. In this project, we aim to characterize the serum stability and improve bifunctional loading and targeting of SpyTag003-peptide and folate co-polymer formulations. Preliminary studies demonstrate that SpyTag003 peptide co-polymer intermediates efficiently load onto CARs and exhibit enhanced binding to cancer cells. We hypothesize that SpyTag003 peptide co-polymer intermediates will display superior CAR T-cell activation compared to SpyTag003 peptide intermediate in vitro. We evaluated the serum stability of folate-modified peptide co-polymer intermediates to confirm their enhanced functional half-life and stability. In addition, we assess the cytokine expression and cytotoxic activity of CD4+ and CD8+ DB5 CAR T cells pre-armed with folate-modified peptide co-polymer intermediate. If successful, our approach for universal CAR T-cell therapy could address critical limitations in current CAR T-cell therapies by providing a more comprehensive and durable strategy for targeting heterogeneous solid tumors, ultimately improving treatment outcomes for patients.

Following spinal cord injury (SCI), respiratory function is often impaired due to limited respiratory muscle function. Decreased respiratory function can lead to breathlessness, impaired coughing, reduced exercise tolerance, and increased respiratory infection risks. Previous studies have shown that transcutaneous spinal cord stimulation (tSCS) at cervical and lower thoracic levels can increase vital capacity by targeting respiratory and abdominal muscles in individuals with cervical SCI. This case series study aims to evaluate the effects of tSCS combined with arm crank exercise on respiratory function after SCI. We recruited three individuals with cervical motor-complete SCI, who were randomly assigned to the active tSCS or sham stimulation group. Two participants underwent 24 training sessions with active tSCS. One participant completed 24 training sessions training with sham stimulation. Spirometry was conducted with real-time tSCS at baseline at different spinal locations. Spirometry was also conducted without real-time tSCS before and after 24 training sessions to assess the long-term effect. Forced vital capacity (FVC), forced expiratory volume in one second (FEV1), and peak expiratory flow (PEF) were measured. Out of all locations tested, T6-T7 showed the largest improvement across all spirometry parameters. Participants in the active tSCS group showed improvements in all parameters after 24 sessions. The participant in the sham group showed decreased PEF. The data collected thus far suggests that tSCS may modulate the spinal neural network responsible for respiratory function. Furthermore, tSCS combined with exercise has potential to improve respiratory function in people living with SCI. A larger sample size is necessary to evaluate the long-term efficacy of this novel non-invasive therapy on respiratory function to improve health after SCI.

Transgender and nonbinary individuals (TNB) face significant discrimination in healthcare settings, which is strongly associated with disparities in alcohol use and treatment access. These barriers often result in delayed or avoided care, exacerbating both physical and mental health issues. The literature reflects a lack of comprehensive understanding and research regarding the specific systemic barriers contributing to avoidance of alcohol healthcare among TNB individuals. This study aims to assess how healthcare experiences influence decisions to engage with alcohol healthcare within the TNB community and discusses future considerations for improvement. TNB adults (N = 26) completed an individual qualitative interview either in-person or online. As part of a larger semi-structured interview about alcohol use, participants were asked about their experiences discussing alcohol use and/or receiving alcohol interventions from medical providers. Participants identified as 30.8% transfeminine, 26.9% transmasculine, and 57.7% nonbinary and were between the ages of 18 and 57. The interview was audio recorded and transcribed by HIPAA-compliant Zoom and transcripts were then cross-checked and edited to ensure their accuracy. Ongoing qualitative analysis is conducted in Dedoose to identify emerging themes. Interactive coding procedures included two coders completing deductive codes identified with prior literature and two coders independently using inductive coding to identify new themes. Discrepancies are identified and discussions support reaching consensus. Understanding the intersection of healthcare mistreatment and substance use disorders in this demographic will inform future policies and interventions designed to create more inclusive and supportive healthcare environments for TNB individuals.

Multidrug resistant Gram-negative bacteria are an emerging threat to public health, continuously evolving to survive under an increasing number of antibiotics and evade the immune system. A major feature of these bacteria is a polysaccharide capsule, which prevents their immune detection. Thus, there is a need to therapeutically restore an effective immune response against them. The Woodward Lab verified that bacteriophage tail spike proteins (TSPs) act as opsonins, which coat and increase phagocytosis of bacteria by macrophages as part of a novel phagocytic pathway. To expand on these data, I am assessing how the adaptive immune system is influenced by the TSP opsonization pathway, analyzing markers of T cell activation and macrophage polarization as starting points. I hypothesize that this pathway has distinct effects on antigen presentation, costimulation, and cytokine expression, compared to better known opsonization pathways like complement and immunoglobulins, and that some of these effects are conserved across bacterial species. To first assess this, I infected macrophages in tissue culture with bacteria, with or without TSP, and measured MHC-II and costimulatory marker expression, an increase which would be associated with enhanced ability to induce T cell responses. I did not observe any differences when TSP was added to the infection. To characterize macrophage cytokine expression, I am treating cultured macrophages with TSP and bacteria-specific antibodies, with the latter serving as a point of comparison between the TSP and antibody opsonization pathways, and quantifying proinflammatory and anti-inflammatory cytokines resulting from this treatment. These studies will reveal whether the TSP opsonization pathway promotes or inhibits adaptive immune responses, which would implicate their utility as a therapeutic and contribute to our understanding of the interaction between bacteriophages, bacteria, and the immune system.

Deuterium is the naturally occurring, heavier stable isotope of hydrogen, which comprises a known proportion of the hydrogen in seawater. As evaporated water travels inland, heavier molecules containing deuterium are rained out preferentially. The deuterium/hydrogen ratio (δ2H) in precipitation is controlled by climatic and geographic factors such as temperature, elevation, and latitude. Terrestrial plants use rainwater as their primary source of hydrogen, so this climatic and topographic marker is recorded in their compounds, which allows for their use in the sedimentary record as paleoclimate proxies. In this study I examine δ2H in n-alkanes, the hydrocarbon chains that make up leaf waxes, extracted from plants, leaf litter (duff), and soils across Washington state. Due to rainout effects influenced by the Cascade Mountains’ rain shadow, δ2H is expected to show a trend of depletion across the state. Samples were collected from sites along an east-west transect across the Cascades. I have processed these samples for isotope analysis and am now conducting literature review to compare our results with a global dataset. Preliminary results show the expected depletion of deuterium across the transect and correlation with rainwater δ2H, modeled using the Online Isotopes in Precipitation Calculator (OIPC). My goal is to assess the local trend of δ2H depletion across this gradient through comparison with existing literature, and to examine the poorly-studied pathway of isotopic signature from plant tissue into soils. I am to provide new insight into the pattern of isotopic signals preserved from live plants into soils and sedimentary rocks, and to further explore and refine the use of hydrogen isotopes in sedimentary n-alkanes as paleoclimate indicators. This research is part of a larger study on the persistence of the isotopic signal of the Cascade Mountains’ rain shadow into the rock record to potentially constrain the timing of their uplift. 

Fuels are comprised of thousands of compounds and many compound classes. Olefinic compounds in fuels are known to increase the formation of polyaromatic hydrocarbons (PAHs) and gum formation in engines. The formation of the gums leads to premature engine degradation and lessened fuel efficiency. Various methods, such as molecular bromination, have been developed to detect and analyze these gum-forming olefins. Bromination via molecular bromine has been used in the past, but it has limitations, including high cost and potential environmental harm. As an alternative to bromination, I am using silver-ion solid-phase extraction (SPE) to separate alkenes from other compounds in fuels. Silver ion chromatography selectively retains alkenes, allowing for other compounds to be removed. Selective separation of a compound class will allow me to accurately detect and quantify olefins in fuel. My preliminary results show that olefins can be separated from aromatic compounds, polar compounds, and alkanes with silver ion SPE. I accomplished this by collecting the SPE effluent in measured fractions and analyzing each fraction by gas chromatography mass spectrometry to observe analyte breakthrough. I am developing this method to selectively detect trace olefins in fuels.

The synthesis and characterization of films for interaction with methane and hydrogen is a project with two motivations. 1) TiO2 as a catalyst support has been found to favorably impact the activity in water gas shift reaction, a step carried out alongside Steam Methane Reformation (SMR) in the conversion of methane to hydrogen. We aim to understand the interaction between methane and TiO2 catalyst support deposited on an alumina substrate. A thermal evaporator was used to deposit titanium thin film onto alumina substrates and post oxidized in flowing oxygen at elevated temperatures (200-250°C). We observed evidence for the post-oxidized film to behave like a dielectric and acquire a charge when placed in the path of an electron beam in a Scanning Electron Microscope (SEM). 2) Depositing titanium onto graphite substrate to examine if there is enhancement in hydrogen incorporation into graphite due to Hydrogen Spillover Effect (HSPE).

Commercial pet food (CPF) is not what most people think it is. In the U.S. about 90% of pet owners raise their dogs on CPF, claimed to be complete and nutritionally balanced. Major pet food companies make efforts to hide the fact that their products consist of contaminants such as heavy metals, aflatoxins, heterocyclic amines, and acrylamides. As investigated by Dr. Richard Pitcairn, feeding CPF to animals increases chances of developing cancer and other degenerative diseases. Due to toxins combined with insufficient nutrients, CPF is likely a major factor negatively affecting dogs’ physical health, shortening healthspan (period in life considered healthy), and causing premature deaths. Top causes of death in dogs are illnesses in which veterinarians generally prescribe drugs to treat only the symptoms of these common ailments. However, a focused approach to reduce dog’s susceptibility to disease, by eliminating the potential root cause, should be considered instead. This literature review investigates various threats posed by CPF by analyzing its risk factors and their impact on dogs’ healthspan. Returning dogs' natural diet by including living, raw, nutrient dense food may be the answer in improving dogs’ overall health and lengthening healthspan. Eliminating the overly processed, cooked, and toxic feed and transitioning to a diet of raw food as an alternative poses a chance to reduce common indicators of illness, ultimately resulting in fewer stressful vet visits and allowing owners to spend more time with their pets. Identifying the research gap surrounding the ambiguity of the effects of contaminants in CPF on dog health, this analysis helps to urge studies to be conducted on these contaminants to further pave the path towards creating a healthier dog diet; in addition to prompting more unbiased research on what types of diets are most efficient and effective at maximizing dogs’ healthspan.

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

Veterans and civilians in areas of military conflict are often exposed to explosions, resulting in blast injury: a complex polytrauma experience usually characterized by traumatic brain injury. Blast injury is also accompanied by observable changes to gut bacteria populations. These microbiota alterations influence the gut-brain axis, a two-way communication lane between the digestive tract and the central nervous system (CNS). Changes that impact the axis are linked to neuroinflammation, altered behavior, and more, affecting the overall health of the CNS. In fact, blast-induced microbiota changes are correlated with increased anxiety-like behavior as demonstrated recently in the Schindler Lab, the mechanisms of which are not fully elucidated. The current study aims to investigate the pathophysiology of the gut epithelium after blast exposure, an area no known studies have explored, as a potential route by which the microbiota affects behavior. With collected gut tissue from blasted mice, histological analysis will be carried out using hematoxylin & eosin (H&E) staining and Visiopharm software to measure morphological differences in villus length and smooth muscle thickness between blasted mice and a control group. Generally, short villus length and decreased smooth muscle thickness are signs of high intestinal permeability, which may lead to increased systemic inflammation that eventually reaches the CNS. Further studies will include in vivo assays investigating gut permeability, immunofluorescence histopathology, and fecal microbiota transplant studies to establish a potential causal role of the gut microbiota in driving blast injury outcomes. In short, blast injury is a traumatic experience that affects veterans and military violence victims alike, and understanding the mechanisms by which the gut-brain axis aggravates inflammation and behavior potentially provides therapeutic targets for treatment.

Biodiesel fuel is a renewable and biodegradable fuel that is produced from a variety of sources, such as animal fats or vegetable oils. With its potential to replace petroleum diesel in engines, biodiesel can act as a cleaner and more environmentally friendly fuel. To create biodiesel fuel, a substance, like oil or fat, must react with a catalyst, which allows for a transesterification reaction, converting these substances into biodiesel fuel. Washington alone is home to over 4,000 coffee shops, and as a result, there is significant waste from discarding coffee grounds daily. Spent coffee grounds, the substance being used in this experiment, is a potential upcoming form of effective biodiesel fuel. In order to turn spent coffee grounds into biofuel, the oil within it must be extracted first. Oil is extracted using a method involving a solvent, Hexane, and following that, the oil is presented to two separate catalysts for comparison: KOH (potassium hydroxide) and NaOH (sodium hydroxide). Comparisons can then be made of what catalyst yielded the best fuel burn efficient level, depending on what catalyst the oil was presented to. This ultimately brings up the question of what catalyst is more efficient, in addition to how efficient spent coffee ground oil is as biofuel. Our goal is to answer these questions and contribute to the advancing research of using spent coffee grounds to produce biodiesel fuel. 

In combination with the demand for health services induced by an aging population, the uneven distribution of licensed nurses working in long term care (LTC) as compared to acute care heightens the needs for stable recruitment and retention in the LTC sector. Heavy stigma around work culture, unsupportive management, and chronic understaffing appear to be factors contributing to the nursing shortage in LTC. The purpose of this study is to develop a media campaign that resonates with nurses and nursing students across Washington state, highlighting the fulfilling nature of careers in LTC to combat stigma and encourage a new generation of nurses to enter LTC to deliver high quality care for individuals advancing in old age. We conducted a cross-sectional qualitative study with a quota sampling consisting of 14 nursing students and 27 current LTC nurses. The participants were distributed into 15 focus groups by their position: nursing student or practicing LTC nurse. We translated the interview data relating to what makes LTC careers fulfilling for current nurses, what influences nurses to enter LTC, and the position of nursing students in regards to the attractiveness of LTC nursing into possible themes. From these themes, we plan to create an emotionally engaging marketing strategy focused on increasing LTC recruitment and retention. Our findings will inform the development of interventions that target both prospective nurses and current practitioners, aiming to improve job satisfaction and reduce turnover. Developing interventions that promote careers in LTC is essential to creating a sustainable workforce capable of meeting the growing demand for long-term care, while ensuring the delivery of compassionate, high-quality care for an aging population.

This research project focuses on developing and enhancing an AI auditing system to assess diversity and fairness in large language modeling (LLMs) systems. By replicating an existing Python-based audit framework, originally created by my Principal Investigator (PI), this study extends its functionality to specifically evaluate how race and ethnicity are represented in AI-generated outputs related to professional occupations. The enhanced auditing system cross-references race and ethnicity data with job positions to identify potential biases, providing a deeper understanding of whether AI systems (specifically GPT-4) disproportionately associate certain ethnic groups with specific professions. These findings contribute to the ongoing discourse on fairness in AI, offering insights into how LLM models may perpetuate or mitigate biases in career representation. This research is critical for the development of more equitable AI systems that reflect diversity across various social and professional contexts, highlighting the importance of fairness in the deployment and usage of AI technology.

The impact of microbial communities plays a large role in the lives of all organisms. Numerous thriving communities of microorganisms are present in places we often overlook. Our research investigates the identification of microbial communities present in the University of Washington Bothell's land, specifically the soil, leaves, and mushrooms commonly found around campus. We aim to support future microbiology lab students by identifying additional species that can be used as unknowns and address common issues students face when sequencing and identifying their known microbes. Our team collected 3 samples from 3 different environments, and each microbial strain was isolated, sequenced, and analyzed using Polymerase Chain Reaction (PCR) to amplify the 16s rRNA gene. The resulting genetic sequences obtained were then matched with NCBI BLAST to determine species identity. Additionally, microscopy and gram-staining were used to classify the bacterial isolates based on their structural characteristics. All collected data will be provided to future students to contribute to their understanding of microbial growth and increase the success rate of replicating and identifying their microbes. We aim to encourage further exploration of microbial life in commonly encountered environments and emphasize the significance of microbes in shaping the ecosystems around us. Understanding these microbial interactions can contribute to a broader understanding in fields such as microbial ecology, medicine, and public health.

In the Equatorial Pacific, tropical instability waves (TIWs) are a dominant form of upper ocean variability during the La Niña phase of the El Niño-Southern Oscillation (ENSO). Cold water along the equator is moved westward by strengthened trade winds forming TIWs off the edges of the cold tongue. TIWs have an average period of one month, a wavelength of 1,000 km, and often are characterized by their unique sea surface temperature patterns. It is critical to understand the complex physical dynamics occurring underneath TIWs as they regulate subsurface dynamics (i.e., mixing and internal waves) and ENSO. Here, we investigated the impact of stratification on both the mixed layer and vertical velocity across the TIW field utilizing a Seaglider, an autonomous buoyancy-driven underwater vehicle. In November 2024, we deployed a Seaglider near the equator to sample the TIW field during the La Niña phase for three months as a part of the University of Washington’s Student Seaglider Center. The Seaglider transected numerous TIW fronts collecting oceanographic data along its 1,000 m dives. We used the temperature, pressure, Seaglider velocity, and biogeochemical variables reported by the Seaglider to explore water column stratification and vertical velocities during TIWs. Preliminary results suggest that increased mixing across the submesoscale fronts of TIWs is associated with higher vertical velocities and increased nutrient levels near the surface. The in situ Seaglider data was also compared to data subsampled from the Global Ocean Physics Reanalysis (GLORYS), a dataset from modeled and observational data, to provide large-scale background context. This study increases in situ observation of submesoscale fronts within TIWs which is critical to further resolving small-scale processes within models.

With the growth of immigrant communities in the state of Washington, there has been a noticeable increase in the implementation of one-way dual language programs designed to immerse students from non-English speaking backgrounds into the English language. Although the problem here is that there is a lack of extensive research into the effectiveness of these programs. The key abilities that should be fostered through one-way dual language programs include academic performance, cognitive development, and social-emotional outcomes. These programs typically begin by offering elementary education in the student’s native language, covering core subjects such as basic arithmetic, history, grammar and science in that language. The primary objective of this approach is to develop fluency in the student's native language while gradually transferring this knowledge into English, slowly immersing the student into a full English education. This research aims to assess the effectiveness of one-way dual language programs across school districts in the state of Washington. The study will analyze data from school districts that have substantial immigrant populations, with a particular focus on the quality of the program design and its impact on the academic performance of students. This study will address this gap by analyzing standardized test scores, aggregate data on high school graduation rates, and exploring biliteracy rates. Specifically, in Washington state, the study will examine the number of Seals of Biliteracy attained by high school graduates in districts that have implemented one-way dual language programs and evaluate the correlation between program participation and these outcomes.

Our nanopore experiments consist of small pores over which a voltage difference is applied to draw DNA/RNA strands through the pore. The accompanying ion current depends on the nucleotide present in the pore. This technology has become a standard commercially available method of sequencing DNA. Other nanopore applications of this system are observing the kinetics of enzymes as they process along DNA or RNA. Helicases are one specific enzyme focused on in this study. Generally, these enzymes work to unwind double stranded DNA. In nanopore sequencing helicases are used to control the passage of DNA through the nanopore by yielding slow step-by-step motion of the DNA through the pore. Helicases are adenosine triphosphate (ATP)-dependent enzymes, which means that the concentration of ATP can affect their stepping speed, but also their propensity to backstep. Here we focus on a helicase used in a commercial nanopore sequencing device to learn more about optimizing ATP conditions and other characteristics of the enzyme kinetics in order to optimize sequencing information. Additionally, we will explore how this helicase will process modified DNA bases as well as entirely unnatural DNA bases.

Recent research suggests an association between comprehensive sex education and improved sexual health–demonstrated by lowered rates of STIs and teen pregnancy and higher rates of contraceptive use in states with comprehensive sex education as compared to states without comprehensive sex education. However, there is still an overall dearth of literature regarding the association of sex education legislation and relationship health. Some data suggests that education programs can have effects on relationship health, such as gender equality education programs that predict lower levels of intimate partner violence. Our project aimed to provide insight into how sex education legislation is associated with relationship health indicators by examining the relationship between legislative requirements and relationship health outcomes. We ran a series of t-tests and point biserial correlations, comparing states with comprehensive sex education and those with abstinence only education requirements, and found significant group differences in teen birth rates and STI rates. We also analyzed the association between legislation requiring medically accurate sex education and sexual health outcomes, and found no significant associations. We similarly did not find any significant associations between the requirement of consent in sex education legislation and intimate partner violence rates. Our significant results align with prior literature indicating that comprehensive sex education is associated with lower rates of sexual health outcomes like teen pregnancy and STI rates. Our non-significant findings are more difficult to interpret and could be influenced by limitations in our research, including inadequate sample size and a lack of publicly available databases on variables that accurately operationalize relationship health. Future research might conduct new surveys on relationship health indicators such as happiness, trust, and satisfaction within each state to better operationalize relationship health. These results can inform policy development around sex education in a direction that promotes higher-quality public health outcomes.

Despite widespread drug abuse, treatment options for people in recovery are oftentimes ineffective, as current research fails to cover the full range of the ways in which opioid, stimulant, or other substance contribute to substance use disorders. The goal of our study is to model how polysubstance use disorders operate in the human brain utilizing a translational rat model of addiction. 64 rats were assigned into single or polysubstance cohorts. Each rat was implanted with a jugular catheter, allowing a controlled dose of methamphetamine or fentanyl to be self-administered through a lever press, along with a drug-associated cue light. The cohorts completed a 3 week period of self-administration, followed by extinction, modeling withdrawal and abstinence. After extinction, the animals went through cue-induced reinstatement, a model of relapse. No drugs are dispensed when the lever is pressed, however the light cue continues to be used as a stimulus signal. Within a large dataset following this model, we are looking to uncover patterns related to differences in drug-taking and reinstatement behavior between the different cohorts. Correlations between the rats’ sex, polysubstance use, and other measurements of their behaviors offers a crucial lens of the more nuanced ways in which methamphetamine and fentanyl influence addiction-related behaviors. Methamphetamine and fentanyl function through distinct neural circuits, thus affecting behavior in individual and synergistic manners. To complement the current work, future studies will investigate the neurocircuitry underlying polysubstance use disorders utilizing whole brain imaging. Gaining clarity into how the nervous system responds to the interaction of both drugs present would mean the ability to develop targeted treatments options. Assuming there’s one treatment that works to treat all polysubstance addictions minimizes individual experiences and ignores the reality that we need to better understand the neurobehavioral aspects of addiction so people can get accurate and effective help.

After infecting a cell, HIV-1 reverse transcribes its genome resulting in a double-stranded viral DNA (vDNA) copy of the viral RNA (vRNA) genome. The vDNA is then integrated into the host genome, establishing infection. Upon activation, the integrated vDNA is transcribed resulting in unspliced, partially, or fully spliced vRNA. Fully spliced vRNAs are exported via the canonical host mRNA pathway involving NXF1/T1. Partially and unspliced vRNA require the viral protein Rev, which binds the RNA Rev response element (RRE) sequence, and recruits host CRM1/RanGTP to facilitate nuclear export. Replacing the RRE sequence with a constitutive transport element (CTE) sequence can mediate vRNA export via NXF1/T1, however at a slower rate than RRE-RNA export. This may be due to differences in RRE-RNA and CTE-RNA sizes caused by CTE-RNA having more, and variations in associated proteins. My study aims to identify and characterize the proteins packaged into viral-like particles (VLPs) made from RRE- and CTE-expressing HIV-1. VLPs containing RRE-RNA, CTE-RNA, and synthetic Gag (SG - no packaged RNA) were prepared by the Hu lab (NIH, MD). I was involved in preparing the samples for mass spectrometry (MS) which involved VLP lysis, protein reduction and alkylation, TCA precipitation and tryptic digestion. The samples were then analyzed via LC-MS/MS by the Moritz lab (Institute of Systems Biology, WA). Preliminary results indicate 78 proteins, not present in the SG control, overlap between RRE-RNA and CTE-RNA samples. Many of these are involved in procentriole subcellular localization. Furthermore, 201 unique proteins were identified for RRE-RNA samples and are primarily involved in cell cycle regulation. A total of 109 unique proteins were identified for CTE-RNA samples and are primarily involved in cell adhesion proteins. Additional analysis aims to further assess trends within the sample sets and take into account differences in relative abundance.

The aim of this study is to identify possible differences in Anisakis spp., or “sushi worm”, infection intensities between three different species of wild Alaskan salmon, O. keta (chum), O. nerka (sockeye), and O. gorbuscha (pink), by examining canned salmon samples from three different canning regions from the 2024 season. Species were selected from three different canning regions: Kodiak, Prince William Sound, and Southeast Alaska. Distribution of these parasites among species and location have marine ecology (pinniped health and distribution), salmon biology (physiological and biochemical parasite defense, dietary preferences), and seafood safety implications (marketing, establishing safe food handling protocols) that make it important to establish a baseline dataset.

Strokes and heart attacks caused by a lack of oxygen, called hypoxia, are among the most prevalent form of debilitating diseases in the United States. Hypoxia has been shown to cause hypoxia-induced-fragmentation of the mitochondria altering their size, shape, and distribution (known as the mitochondrial dynamics). However, to what extent these dynamics are involved in hypoxic cell death remains unestablished. The Crowder lab through a C. elegans mutagenesis screen discovered a reduction-of-function mutation in rapTOR that confers strong hypoxia resistance. rapTOR functions in a complex with mTORC1 to control cellular metabolism including mitochondrial function. We decided to investigate whether the hypoxia resistance of the rapTOR mutant is from alterations of mitochondrial dynamics in response to hypoxic injury. To measure the mitochondrial dynamics, I visualized the mitochondria with an outer membrane fluorescent protein, in wild type and mutant worms with and without hypoxic exposure. I analyzed the images blinded to their genotype and hypoxic condition and scored mitochondria as primarily fragmented or tubular, which served as a surrogate for detecting changes in mitochondrial dynamics. For a more quantitative analysis, I utilized image processing MATLAB code and determined differences in images using principal component analysis. My analysis showed hypoxia induces small, rounded mitochondria in C. elegans resembling mitochondrial fission. I found the mitochondria in the rapTOR mutant displayed decreased hypoxia-induced-fragmentation after hypoxia. Then when I combined the rapTOR mutant with a hyperfragmented mitochondria mutant it showed fragmented mitochondria with and without hypoxic exposure. However, the double mutant is also hypoxia resistant, which is not consistent with our hypothesis that mitochondrial fragmentation drives hypoxic cell death. Therefore, we reject our hypothesis and conclude that rapTOR is hypoxia resistant from a mechanism distinct from that controlling mitochondrial fission.

Coaching is a collaborative, goal-oriented process aimed at supporting individuals in achieving personal or professional goals. Coaching originated in workplace settings and expanded in the 1990s to include life coaching. Life coaching has been applied to many specialized areas, including attention deficit hyperactivity disorder (ADHD). Contrasting with psychotherapy, coaching is not intended to treat mental disorders. As such, the intersection of coaching and clinical care has sparked debates about the boundaries between coaching and psychotherapy, particularly when clinical conditions such as ADHD are involved. The COVID-19 pandemic was accompanied by an increase in seeking mental health services for ADHD. This coincided with an apparent influx of new ADHD coaches joining the profession to fill the increased demand. We created the U.S. National ADHD Coaching Survey to better understand the activities and behaviors of ADHD coaches in the U.S. and how ADHD coaching might fit into the broader context of ADHD care. We explore the differences between ADHD coaches who began their practice prior to the onset of the COVID-19 pandemic with those who began their practices following the onset of the pandemic. We distributed this survey to ADHD coaches through ADHD coaching professional organizations, in-person at a professional conference, and through targeted invitations based on web searches of ADHD coaches. We hypothesize that newer post-pandemic coaches are less likely to be members of coaching organizations, more likely to market themselves on social media, and cover a greater variety of session content. I document ADHD coaching workforce trends over time. Additionally, I compare the professional identities and training, referral networks and marketing, and session content of ADHD coaches who began offering their services pre vs post pandemic using independent samples t-tests and chi-square tests. I explore how those differences might impact the current landscape of ADHD treatment and support.

Linear electrochemical impedance spectroscopy (EIS) is widely used in the characterization of electrochemical systems, such as batteries, although the results of EIS are only as good as the scientist's model of their data, as it’s possible to fit multiple models to the same data. Nonlinear EIS (NLEIS) can also be helpful when characterizing batteries - as they are nonlinear devices - and reveal additional information, such as the asymmetry of the charge transfer between charge and discharge. Combining EIS and NLEIS results in multiple, interrelated data sets, which when fit together drastically reduces the set of models that fit the same data, providing a better understanding of battery physics. However, NLEIS is not as widely developed or used as traditional EIS methods. The goal of this research project is to further develop the use of NLEIS for battery characterization in order to combine EIS and NLEIS to ultimately provide a more accurate picture of battery health. To reach this goal, I plan to test fresh and aged lithium nickel manganese cobalt (NMC) pouch cell batteries with my group’s EIS/NLEIS model. Using materials and equipment from the Washington Clean Energy Testbeds, I will then deconstruct these batteries and fabricate coin cell batteries from the harvested electrode materials and run EIS/NLEIS experiments on these coin cells, comparing the results of the coin cells to the results of their parent pouch cells to assess the accuracy and usefulness of the NLEIS model. Advancing battery health testing is critical for the future development and use of batteries, as understanding battery health allows consumers and scientists to make sustainable decisions regarding battery use, recycling, and disposal.

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

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

Surveys leading up to and following the 2024 Presidential election have indicated a substantial proportion of Americans have experienced tremendous anxiety about democracy and the future of the nation. Among minority groups, moreover, anxiety is exacerbated by fears of discrimination, threats of deportation, and feelings of alienation in the U.S. Yet, the limited culturally responsive spaces across our educational institutions that empower students from minority backgrounds to share vulnerable experiences and meaningfully engage in discourse about public policy issues have not grown proportionately to remedy these intensified needs. As such, the University of Washington (UW) Brotherhood (B.I.) and Sisterhood (S.I.) Initiatives are researching the extent to which students of color are empowered to be engaged in civil discourse spaces at the UW, as well as how our institutions can best create community discourse spaces that recognize diverse student needs and perspectives. Thus far, we have developed a focus group protocol and administered two focus groups (one for the B.I. and one for the S.I.), with 4 participants in each group. In examining themes of student civil discourse experiences in our emergent findings, we see that the environments, tools, and practices of campus civil discourse spaces can be better structured to challenge harmful stereotypes and further support authentic exchanges of ideas and experiences across differences in positionality. This work helps situate gaps in the provision of civil discourse spaces at the UW relative to demonstrated student needs and contributes to actionable, culturally responsive approaches for students from all backgrounds to find empowerment in and through civil discourse spaces and ultimately become critically informed agents of social change.

Epilepsy is among the most common neurological diseases worldwide. Over 30 anti-seizure medications (ASMs) are available to treat seizures; however, one-third of people with epilepsy are resistant to their treatment options. The mechanisms behind these pharmacoresistant seizures are not fully understood, but experimental models like the 6Hz or MES mouse seizure models are useful for investigating contributing factors. Recent findings from our lab demonstrate that different brain regions are activated in response to distinct seizure-types, but treatment with ASMs does not alter this activation, regardless of ASM efficacy. Our previous studies used cFOS as a marker of neuronal activity, but since this is not specific to the type of neuron activated, this project focused on calbindin (CALB), a calcium binding protein commonly found in interneurons. We hypothesize that the cFOS immunoreactivity seen in mice who were protected from seizures would be a result of the activation of inhibitory neurons as indicated by increased colocalization between cFOS and CALB-positive neurons. Adult male CF-1 mice were treated with 3 mechanistically different ASMs: cenobamate, levetiracetam, and phenytoin, before being challenged with a focal (6Hz) or generalized (MES) seizure at the time of peak pharmacological effect. Brains were collected 90 minutes after each stimulation and processed for immunohistochemical labeling of DAPI, cFOS, and CALB. Preliminary data suggests that the number of activated CALB cells (e.g., cFOS+CALB cells) did not differ between protected or unprotected mice across brain regions or following certain seizure types. This indicates that the activation of inhibitory neurons might not be a major factor in seizure protection. However, further testing is needed to identify and quantify all inhibitory neuron subtypes to better understand the mechanisms contributing to pharmacoresistant seizures. 

The Thermal imaging-based Temperature After Within-limb Calibration (TAWiC) algorithm has been used and validated by our team in detection of arthritis in the knees of children. It has previously performed well through using a smart-phone FLIR thermal camera attachment. We are now hoping to explore and expand its potential by developing TAWic thresholds to find other inflammatory arthritis in the knee, ankle/subtalar, elbow and wrist joints. Patients 4 years or older with suspected active inflammatory arthritis in at least one knee, ankle/subtalar, elbow or wrist were enrolled at Harborview Medical Center or Seattle Children’s Hospital after consent was obtained. Joint exams were conducted and infrared thermal imaging was obtained through the use of a FLIR One Pro camera by doctors. I analyzed images in MATLAB by manually selecting elbow, wrists, knees, and ankle joints to generate reports and scores for virtual doctor evaluation. With 89 adults and 85 children enrolled, we found the most commonly affected joints in children to be knees while in adults, it was the wrists. Further validation of applying the TAWiC threshold to detect arthritis was conducted, and the sensitivity and specificity of this algorithm for adults with active inflammatory arthritis in the knees were 50% and 83%, respectively. To our knowledge, this is the first reported validation of the TAWiC algorithm for knee inflammatory arthritis in adults. Ongoing and future studies will seek to validate use of the TAWiC algorithm for assessing arthritis in other joints. We hope that in the future, the technology can be used remotely by patients in telehealth efforts to send imaging to minimize costs, increase efficiency, and save time in caregiving efforts.

Urine cultures are the primary method for urinary tract infection diagnosis. Like most culturing applications, these tests often require days to yield conclusive results, causing harmful treatment delays. Additionally, hospitals waste substantial time and resources processing negative patient samples. Predicting culture outcomes before their final result can accelerate patient care and improve diagnostic efficiency by minimizing resource allocation towards culturing negative samples. The goal of this study is to build machine learning models to predict urine culture outcomes and help optimize test order protocols. Using clinical data from the UW Medical Center, containing urine culture results, blood test results, and demographics from over 88,000 patients, I trained Random Forest models, Support Vector Machines, and XGBoost models to predict overall culture positivity and specific infection types (E. coli, Klebsiella, etc.). Predictive parameters included common clinical laboratory tests (complete blood counts, metabolic panels, etc.), as well as demographics (age, sex, and race). To evaluate the predictive performance of these features at different points in the culturing timeline, the data was divided into three subsets: (1) patients with blood work up to 30 days prior to sample collection, (2) patients with blood work up to 30 days prior to their first culture result, and (3) patients with blood work predating their final culture result. Tree-based ensemble models (RF and XGBoost) trained on the latter two subsets yielded the most promising results. The Random Forest model’s AUC (area under the curve), a value between 0 and 1 that measures a model’s ability to distinguish between two classes, was 0.87. An AUC closer to 1 indicates more accurate classifications. The results show that ML models can feasibly predict culture results to optimize operations and enable earlier treatment. Further development of this data pipeline will allow for detailed predictions of specific infection types and concurrent infections.

In vitro models (cells in a dish) are a powerful tool in toxicology, allowing for advanced research in biological mechanisms while decreasing our reliance on in vivo animal models. Reproductive development is a critical endpoint in toxicology and requires a large number of animals, making reproductive studies a priority for in vitro alternatives. The current in vitro testis models are insufficient to recapitulate human reproductive development as they still rely on cells from laboratory rodents due to low human testis tissue availability and the need to capture dynamic developmental stages. To address this, I am developing an in vitro model that recapitulates human spermatogonia development to generate human primordial germ cell-like cells (hPGCLCs) using two induced pluripotent stem cell (iPSC) lines. This approach relies on spontaneous differentiation of the iPSCs using an extracellular matrix overlay. My pilot experiments did not robustly differentiate; therefore, I adapted the protocol to first induce incipient mesoderm-like cells (iMeLCs), which are primed for differentiation to hPGCLCs. I observed distinct cell morphological differences in the iMeLCs relative to control iPSCs using phase-contrast microscopy and found increased expression of Vimentin in the iMeLCs using immunocytochemistry. I am completing additional experiments to visualize expression of the mesoderm marker Brachyury, proliferative marker ki67, and primordial germ cell markers ki67 and SOX17. Using these iMeLCs I will follow the overlay protocol to derive hPGCLCs. I will assess the hPGCLC phenotype using flow cytometry for TFAP2C, a marker of PGCs. The hPGCLCs will then be cocultured with primary testis tissue to drive development towards spermatogonia-like cells (SpLCs), determined by expression of DDX4. The primary tissue will include our labs standard rodent model, as well as human tissue from collaborators at the UW Male Fertility Lab. Developing a fully human in vitro model system will be a powerful tool to study infertility.

As a diverse mammalian clade defined by encephalization and an increased reliance on learned behaviors, primates serve as a uniquely well-suited subject for the study of how environmental factors may influence the diversity of brain morphology. Endocasts, which are 3D models of the cranial cavity, have been proven to be reliable proxies for brain shape and size and provide an accessible method for studying brain morphology. While it has been demonstrated that environment has caused convergent cranial morphology in lemur species, more investigation is necessary to uncover the exact causal variables of these changes and how they affect primates more broadly. In this study, we test the hypothesis that climatic factors contribute to morphological differences in the neocortex, olfactory bulbs, and cerebellum among primate species. For example, food scarcity caused by greater variability in rainfall and temperature may be correlated with investment in regions associated with learning and processing as described by the cognitive buffer hypothesis. Thus, we predict that increased rainfall leads to increased food availability and an increase in neocortex size which is responsible for higher order functions. To test our hypothesis, we obtained CT scans of primate skulls from the Natural History Museum, London, United Kingdom. We then used 3D Slicer to create endocasts from the cranial cavity and quantify endocranial morphology using landmark-based geometric morphometrics. We used phylogenetic comparative methods in R to test whether climate variables like temperature, rainfall, and altitude have induced changes in endocast morphology across species. Our findings will enhance the understanding of the evolutionary mechanisms particular to our own lineage and may help us better predict how Anthropogenic changes to climate will affect the evolution of organisms moving forward.

Correct segregation of chromosomes in cell division relies on kinetochores forming end-on, bioriented attachments to microtubule plus ends. In vivo, kinetochores are known to first bind to the lattice of the microtubule and then transit to the plus end either by tip disassembly or the action of plus end directed motor proteins. Force spectroscopy has recently revealed that kinetochores grip the microtubule lattice asymmetrically. Only ‘on-path’ kinetochores that are pulled toward the microtubule plus end form strong, load-bearing attachments, while minus end directed kinetochores weakly grip the lattice. The weak grip of minus end directed kinetochores limits tension across sister kinetochores and makes them susceptible to detachment by error correction machinery. We seek to investigate the molecular mechanism underlying the asymmetric grip of the kinetochore. We purified recombinant kinetochore subcomplexes and tested them individually for asymmetry. We show that the Ndc80 complex exhibits a similar asymmetry as the kinetochore, albeit weaker, while the Dam1 complex is ambivalent to microtubule polarity. Single molecule fluorescence microscopy shows that kinetochores pulled toward the minus end of microtubules are deformed relative to plus end directed kinetochores. We propose that the asymmetric grip strength of kinetochores arises from a network of interactions between polar-sensitive and polar-insensitive subcomplexes that is disrupted when the kinetochore is pulled toward the minus end of a microtubule. A better understanding of the specific mechanisms of kinetochore-microtubule binding is valuable for understanding control of mitotic progression and could potentially inform more targeted anti-cancer therapies that focus specifically on dividing cells without impacting regular cell function.

The prevalence of food allergies in the United States has increased dramatically, affecting 4 in every 100 children under the age of 18. There are 8 main categories of food that make up the most common food allergies. These foods include eggs, fish, milk, crustacean shellfish, wheat, tree nuts, soy, sesame, and peanuts. Together, these foods create the "Big 8" list: a priority list for the US Food Allergen Labeling and Consumer Protection Act (FALCPA). In this literature review of current treatments for food allergies, we will select the peanut allergy for further research due to the often fatal complications that arise from anaphylaxis following exposure. This review will seek to provide a comprehensive overview of the current types of food allergy treatments and to discuss a cure for peanut allergies. The current solutions available today to treat food-induced allergic reactions include medical treatment (epinephrine), immunotherapy (e.g., "allergy shots'), nutritional support, and simply avoidance. While these solutions are great aids to help alleviate allergic reactions, they do not cure the food allergies themselves. This means that people who have food allergies are not able to consume the foods they want or need. This begs the question, "Is it possible to make a cure for peanut allergies?" The origin of food-induced intolerances stems from the failure of the immune system to ignore, or be tolerant of, food antigens. Previous studies have identified specific peanut antigens that promote allergic responses. Food allergic immune responses are primarily driven by T cells. Potentially, these antigens can be used to isolate peanut-specific T cells in allergic individuals. These T cells could then be analyzed and used to generate cell-based therapies to suppress allergic responses (bystander suppression). This solution could permanently prevent peanut-induced allergic reactions from occurring. 

As the demand for electronics increases, so does the need for efficient recycling methods of electronic waste. The goal of electronic waste recycling is to recover critical metal components that can be used again in future electronics. However, a key challenge is selective separation of metal component mixtures into pure phases. My research in Dr. Zachary Sherman’s lab studies a promising and low-energy solution to this problem involving magnetic separation using external magnets and magnetic fields. Many precious metal ions are magnetizable in the presence of an external magnetic field, and therefore metal ion mixtures can be separated magnetophoretically by taking advantage of differences in their magnetic susceptibility. Using Brownian dynamic simulations to model transport of metal ion mixtures, I have quantified the magnetophoretic separation efficiencies of mixtures of paramagnetic, diamagnetic, and nonmagnetic ions mixtures when exposed to an external magnetic field. I have investigated how separation efficiency is affected by a variety of physical parameters including the strength of the external magnetic field, relative concentrations of ion species, strength of interactions among ions, and the magnetic susceptibilities. I also show that hydrodynamic flows generated by ion motion as well as ion structuring and aggregation have an enormous impact on separation efficiency. These results will guide further research to determine the optimal conditions for selective separation and purification of metal components.

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

Bull kelp (Nereocystis luetkeana), a foundational seaweed in the Salish Sea, is important to native species that rely on it for shelter, food, and protection. Recent studies show that acidweed (Desmarestia ligulata) is outcompeting bull kelp for space. Acidweed also possesses a unique ability to leach sulfuric acid under stressful conditions, which can deter predation. Northern kelp crabs are a major consumer of a variety of kelp species, particularly bull kelp, but have not been observed eating acidweed. To investigate whether kelp crabs graze on acidweed a feeding experiment was conducted. Crabs were offered one of four kelp types – fresh acidweed, stressed acidweed, fresh bull kelp, or stressed bull kelp – and their consumption rates measured for comparison. Crabs consumed less of both acidweed types versus bull kelp. However, stressed acidweed had a higher average consumption rate compared to fresh acidweed. In a follow-up experiment crabs were given bull kelp soaked in either acidweed leachate, sulfuric acid solution, or in fresh seawater. Crabs consumed more leachate-soaked than sulfuric acid-soaked kelp, but fresh bull kelp had the highest rate of consumption overall. Although crabs consumed stressed acidweed when bull kelp was unavailable, their overall feeding rate remained five times lower versus their preferred kelp type. These findings indicate that acidweed’s chemical defenses, combined with the absence of significant predation, may allow it to outcompete bull kelp in the Salish Sea, reducing the abundance and resilience of kelp forests and potentially causing shifts in community structure and biodiversity.

The human gut hosts a dense microbial community that aids in infection prevention. Maintaining this community is crucial for health, as dysbiosis is linked to many diseases. Antibiotics induce dysbiosis by disrupting the microbial community, contributing to resistance. There is a need for antibiotics that specifically target pathogens while preserving the gut microbiome. One approach is to target toxic effectors unique to pathogenic bacteria, minimizing impacts on the microbiome and slowing resistance. Enteropathogenic Bacteroides fragilis (ETBF) is a gut pathogen that induces bowel diseases. The pathogenicity stems from Bacteroides fragilis toxin (BFT), a zinc metalloprotease. BFT induces cleavage of E-cadherin, a mediator of cell-cell adhesion, disrupting tight junctions in colorectal epithelial cells leading to fluid accumulation and colon inflammation. We hypothesize that a BFT-specific inhibitor will prevent the effects of ETBF. We used a structure-guided approach to computationally design peptides targeting the active site of BFT. To aid in testing peptide designs, we generated a ∆bft B. fragilis strain and an inactive point mutant (BFT E349A) to serve as negative controls, and both were confirmed to be inactive. Several candidate peptides were tested, and we identified a candidate with a strong binding affinity (kD = 664 pM). This peptide binds to wild-type BFT and BFT E349A, suggesting it does not target the catalytic site. Despite these findings, the peptide still exhibits anti-BFT activity. Next, we designed generally recognized as safe (GRAS) Bacteroides strains to secrete the peptide for direct delivery to the gut. We observed that the peptide secreted by the GRAS strain significantly reduced E-cadherin release in assays incubating live GRAS bacteria, ETBF, and human colon cancer cells, indicating BFT inhibition. Our results suggest that the designed peptide could be a promising therapeutic strategy to target BFT that avoids the downsides of traditional antibiotic treatments.

Lagomorphs (hares, rabbits and pikas) exhibit a range of specialized locomotory modes and predator avoidance strategies while maintaining similar herbivorous diets. Their close evolutionary relationship and similar trophic role makes lagomorphs an ideal group for examining the effects of habitat and locomotory modes on skeletal morphology. This project examines two aspects of lagomorph morphology to further understand its relationship to the habitat in which those lagomorphs live. The first aspect, limb anatomy, is quantified through caliper measurements and robusticity calculations of the appendicular skeleton. We previously hypothesized a relationship between limb anatomy and digging behavior in rabbits and hares. As an extension of this previous research, we have classified the extent to which each species burrows to further explore the relationships between limb morphology, evolutionary relatedness, and current burrowing behavior. The second aspect is body shape, which is quantified through caliper measurements of the vertebral column and calculated as the ratio between body length and body depth. We previously found no relationship between body shape and locomotory mode. This year, we plan to examine the third lagomorph group (pikas) and increase our hare and rabbit sample sizes to determine whether the patterns that we previously found to be insignificant remain. Further, we plan to compare these different groups using a phylogenetic ANCOVA to correct for evolutionary relationships that may cause bias in our analysis. We predict lagomorphs that burrow will have the most robust forelimbs to allow for greater force to be applied while digging. Additionally, we predict that while greater size will be associated with lower elongation, there will be no significant difference in elongation between groups of lagomorphs, based on our results last year. This project will describe the effect of habitat on skeletal morphology, which could allow for better understanding of extinct groups.

Veterans have high rates of early life adversity and mild traumatic brain injury (mTBI), both of which are risk factors for PTSD. Our laboratory has found that common risk factors for stress and PTSD are exacerbated by increased expression of stress-sensitive gene FKBP5. We are testing whether FKBP5 mediates a synergistic interaction between early life adversity and mTBI to produce symptoms associated with PTSD in veterans. A prior study used illness as early life trauma and concussive blast as adult trauma. In our study, the traumas are better specialized to veterans. I'm exposing C57BL/6 mice to limited bedding and nesting (LBN) adversity pre-weaning and concussive blast trauma post-weaning. Post-natal days two-nine, mice undergo LBN using insufficient bedding, reducing maternal care and increasing stress, simulating housing issues and neglect often endured by veterans in childhood. In week 13, I'm using a blast tube to administer a concussive blast to mice similar to that experienced by veterans from improvised explosive devices, resulting in mTBI. LBN, concussive blast, and sex are the variables. In week 17, I'm conducting Open Field Tests and fear conditioning on subjects to test generalized and novel fear responses and anxiety levels. Mice that endured both traumas should have the most generalized fear. If so, we will have shown that there is a synergistic interaction between early life adversity and mild traumatic brain injury that intensifies PTSD associated symptoms. Mice with both traumas are expected to have the highest FKBP5 RNA levels. We’ll analyze FKBP5 to determine how it participates in serotonin pathways resulting in these symptoms, and whether LBN and mTBI synergize to increase FKBP5 expression. We want to exemplify the role of FKBP5 as it has potential to be used in PTSD and other stress disorder treatments.

Inflammasomes are cytosolic innate immune complexes that initiate pyroptotic cell death and the release of inflammatory cytokines. Inflammasomes are a critical component of the host innate immune response to viral pathogens. The inflammasome-forming sensor NLRP1 functions in barrier defense against a diversity of viral and bacterial pathogens, necessitating multiple modes of pathogen recognition. For instance, NLRP1 directly senses viral infection by detecting viral protease activity. NLRP1 is also activated indirectly by the ribotoxic stress response caused by radiation or toxins. Moreover, NLRP1 has been proposed to directly bind dsRNA. However, it is now understood that dsRNA-induced NLRP1 activation also requires p38-mediated phosphorylation. Thus, it is unclear whether NLRP1 directly or indirectly senses dsRNA. To address how dsRNA activates NLRP1, we reconstituted the NLRP1 inflammasome in inflammasome-deficient 293T cells. We found that reconstitution of the minimal NLRP1 inflammasome responds to viral proteases and other activating stimuli but not to dsRNA. This suggests that NLRP1 is insufficient to respond to dsRNA and instead requires uncharacterized host cofactors. We then hypothesized the NLRP1 response to dsRNA is an indirect event that requires upstream sensing events by canonical dsRNA receptors, and we found that co-expression of RIG-I or MDA5 restores NLRP1 responsiveness to dsRNA in 293T cells. We further investigated this pathway in the context of pathogen infection. During viral replication, dsRNA is generated, and the host has evolved mechanisms to detect it. Since viral dsRNA sensing is detrimental to viral replication, viruses have evolved strategies to evade detection. Notably, influenza A virus (IAV) encodes NS1, a protein that limits dsRNA accumulation. To investigate how IAV potentially counteracts NLRP1 activation by dsRNA, we transfected NS1 into 293T cells reconstituted with the NLRP1 inflammasome system and observed that NS1 significantly attenuated dsRNA-induced NLRP1 activation.

For decades, nanomaterials formed by protein-nanoparticle interactions have been attractive to researchers for applications that include biosensing and drug delivery. Previous work demonstrated bifunctional superfolder green fluorescent protein (sfGFP) genetically encoded with two silica-binding peptides (Car9) can induce the assembly of 10 nm silica nanoparticles (SiNP) in a pH responsive manner. The pH responsiveness arises from an intricate balance between the attraction of protein-decorated SiNP for other SiNPs, and the electrostatic repulsion of SiNP-SiNP, leading to cluster formation at pH 7.5 and dissociation at pH 8.5. In this study, we expand on the work by introducing steric forces using a monofunctional sfGFP variant chemically conjugated to polyethylene glycol (PEG). We investigate how (i) the molecular weight of the PEG extension, (ii) the molar equivalent of pegylated protein to SiNP, and (iii) the use of a mutant bifunctional protein with lower SiNP affinity, influence cluster size and polydispersity. We find that increasing steric hindrances by adding up to 5-fold molar equivalent of pegylated protein to SiNPs, or by using a longer PEG chain, leads to a progressive decrease in cluster size that is accompanied by 6-fold decrease in polydispersity to 10%. We also demonstrate that while cluster size can be controlled in the 1500-800 nm range with the wild-type bifunctional protein, its mutant version enables access to the 250-50 nm size range. We exploit the facts that sfGFP is inherently fluorescent and that our SiNPs encapsulate rhodamine to investigate how cluster size influences the Förster resonance energy transfer (FRET) efficiency between multiple donors and acceptors. We find that whereas ensemble FRET efficiency doubles as cluster size increases from 50 to 230 nm, it only increases by 15% as the assemblies grow to 1450 nm. We discuss the implication of our results for the design of environmentally responsive opto-electronic nanomaterials.

The Pacific sand lance, Ammodytes personatus, is an ecologically important forage fish in the Salish Sea. Adult sand lance bury themselves head first into sandy substrates to avoid predation and hibernate in colder winter waters, whereas juveniles remain pelagic and do not burrow until their first winter. Many head-first burrowing species exhibit cranial skeletal adaptations that facilitate substrate penetration, yet the specific skeletal modifications that enable A. personatus to burrow efficiently remain poorly understood. This study investigates how vertebral mineralization patterns change over development and how these changes may contribute to burrowing efficiency. We analyzed over 345 vertebrae of preserved A. personatus from 20-80 mm SL using a Bruker SKYSCAN 1273 micro-CT scanner. Using hydroxyapatite reference phantoms (25% and 75%) to calibrate grayscale intensity values, we quantified vertebral mineral density. We compared mineralization across three vertebral regions (cranial, mid-body, and caudal) and over ontogeny. We hypothesized that cranial vertebrae would be the most mineralized and vertebral mineralization over ontogeny would increase linearly. Contrary to our initial hypothesis, caudal vertebrae were 1.5x more mineralized than those in the mid-body or cranium, but cranial vertebrae were still more mineralized than those in the middle of the body. This suggests that the tail may play a more significant role in burrowing mechanics than we previously assumed. We identified a significant negative correlation between mineralization and body length in both mid-body and caudal vertebrae. Our data show that as these fish grow, their vertebral regions become less mineralized. This pattern challenges our expectation that adults would exhibit greater skeletal reinforcement for burrowing and instead suggests that juvenile sand lance may experience stronger selective pressures for vertebral mineralization or that adults employ alternative physiological or behavioral adaptations for substrate penetration.

Preterm birth is a leading cause of under-5 morbidity and mortality. No treatments exist to address the neurological complications of premature birth, which include loss of oligodendrocytes and activation of microglia, leading to white matter injury and inflammation, respectively. Our study explored repurposing azithromycin, an FDA-approved antibiotic with anti-inflammatory properties, to mitigate preterm brain injury caused by hypoxia-ischemia. We used a postnatal day (P)14 neonatal ferret model, equivalent to extremely preterm infants. We induced brain injury through a combination of inflammatory stimulus, bilateral carotid artery ligation, and oxygen fluctuations (hypoxia/hyperoxia). Ferrets were randomized into control, vehicle (saline)-treated, and azithromycin-treated groups. Littermate controls were not exposed to injury. Body weights and ex-vivo brain measurements (sulci and gyri widths) were recorded at P21, seven days after injury. Quantitative immunohistochemistry (qIHC) was performed to analyze microglia (Iba-1) and oligodendrocyte (Olig-2) density, and data were analyzed using Kruskal-Wallis tests. In our preliminary findings, post-surgical weights from the azithromycin-treated ferrets were similar to those of vehicle-treated animals. Azithromycin-treated ferrets also showed similar global microglia and oligodendrocyte staining compared to the vehicle group. The vehicle group had lower summed gyri measurements than controls (p=0.04), while azithromycin-treated ferrets had more similar gyri widths to controls (p=0.21). We will continue investigating microglial and oligodendrocyte density using qIHC across additional brain regions using pathology software (VisioPharm), including subregions of each gyrus (cortex, subcortical white matter, and coronal radiata), corpus callosum, hippocampus, and upper and lower thalamus. This will allow us to identify the brain regions most impacted by the injury and investigate if there are regional neuroprotective responses to azithromycin. By deepening our understanding of preterm brain injury and azithromycin-mediated neuroprotection, these findings could lay the groundwork for advancing azithromycin toward clinical trials, offering new hope for saving the lives of the tiniest neonates.

Previous studies suggest that tooth morphology (shape, size, and other features of teeth) strongly correlates with an organism’s dietary patterns, and analyzing dentition is common practice in the field of Biology. Orientation patch count rotated (OPCr), a technique used in establishing dentition-diet correlations, has recently been demonstrated as applicable to turtle triturating surfaces to understand their dietary adaptations. The aim of this study is to add to an ongoing project characterizing the relationship between diet and the cutting/grinding surface in the jaw (triturating surface) in edentulous (toothless) organisms using techniques used in traditional dental topographic analysis. Turtles are a diverse group of edentulous organisms with beaks of keratin to process their food — making them ideal for this study. Specimens of the omnivorous Forest-Hinge Back Tortoise (Kinixys erosa) were micro-computed tomographically (CT) scanned. We reconstructed the CT scans into photogrammetric 3D models using Slicer software. Then, we isolated the triturating surface using MeshLab software. Finally, we read the triturating surface into the R package molaR — resulting in OPCr values that estimate the complexity of their specimen’s triturating surface. Ideally, the OPCr values showcase extreme high triturating surface complexity, as previous research suggests tortoises (Testudinidae) have highly complex triturating surfaces compared with other clades of turtles. Our research hopes to contribute to a new technique for analyzing extinct beaked or edentulous taxa.

Phytophthora ramorum is regarded as a devastating pathogen to many plant species, so its detection and extermination are necessary for a healthy ecosystem. At Clark’s Creek Park in Puyallup, WA, within a stream adjacent to the dog park, P. ramorum was searched for. Rhododendron leaves were used as bait to attract Phytophthora species in various soil samples and the running water of Clarks Creek. Phytophthora from infected leaves was cultured and used for DNA extraction, PCR (with ITS4 and ITS6 barcoding primers), electrophoresis, and DNA sequencing. Bioinformatics analysis revealed that the preponderant species present was Phytophthora gonapodyides. P. ramorum was not detected at the location we surveyed. However, due to our small sample size, the presence of P. ramorum should not be ruled out, and future experiments should continue exploring its potential habitation. If P. ramorum were identified, we would report this data to the USDA for subsequent intervention.

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

Optical metasurfaces used in nanophotonic devices are designed and optimized to display remarkable emergent photonic properties beyond what is possible for single-component materials. Traditionally, metasurfaces are designed in response to a particular incident angle of light impinging on its surface. However, in practice these metasurfaces have limited functionality if the incident angle varies. A metamaterial whose function is independent of incident angle would overcome this limitation and be more efficient in practice. For example, angle independent metamaterials that trap light in solar panels can function efficiently for all solar positions. Because a forward approach of screening many candidate materials through trial-and-error is time-consuming and expensive, in this poster we instead employ an inverse computational-based design strategy. We develop a strategy to optimize geometry/dielectric design of nanoparticles (NPs) metamaterials that have an optical response independent of angle of incidence of light. We leverage a computationally efficient and differentiable electromagnetic simulator based on couple dipole methods, the “mutual polarization method”, to perform numerical optimization of these materials. By encoding multiple incident angles and polarization states into an objective function, we ensure that the optimizer reduces the angle-variation of the metamaterials it designs. We use our inverse design tool to create multilayer plasmonic nanoparticle films, whose extinction spectra are insensitive to incident angle and polarization. We also show that we can use our inverse design method to control the spectral line shape of these NP films. Our inverse methodology will greatly accelerate the development time to synthesize new nanophotonic materials.

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

Knee meniscus tears are common musculoskeletal injuries that have difficulty healing on their own. Required surgical interventions often fail to restore the function of damaged tissue resulting in the need to develop more effective therapies. To do so, it is necessary to develop in vitro models for further investigation of mechanisms of regeneration in the meniscus. To model the mechanical environment of the meniscus, our lab developed a pentenoate-functionalized hyaluronic acid (PHA) hydrogel system with tunable elastic, compressive moduli. However, viscoelastic properties, assessed via stress relaxation time, also dictate cellular behaviors that are favorable for regeneration. The objective of this study is to tune the viscous response within the PHA hydrogel system without significantly impacting the compressive modulus. I hypothesize that viscoelastic properties can be modulated by tuning non-covalent chain entanglement by increasing the amount of un-crosslinked (non-functionalized) HA (UHA) in the PHA hydrogel system. Specifically, I expect that increased entanglement will increase the viscous response without significantly altering the compressive modulus. I performed multiple iterations of stress relaxation and uniaxial compression tests on 0, 0.5, 1, and 2% UHA hydrogels on a dynamic analysis system. I found that increasing the amount of UHA in the hydrogel system had no statistically significant effect on the compressive moduli or stress relaxation half-times, suggesting that modulating the UHA in the hydrogel system allowed me to maintain elastic properties but does not yet allow fine control over the viscous properties. Limitations of the DMA indicate the need to also perform rheological assessments to analyze stress relaxation using constant shear strain. Future directions also include seeding meniscal cells on the hydrogels to assess the impact of viscoelastic properties on the regenerative behavior of meniscal cells. Ultimately, results from these studies will contribute to the development of regenerative therapies for meniscal tears.

Bacteria are constantly under dynamic environmental pressures and must promptly respond to survive. Bacterial general stress responses (GSRs) allow adaptation to perceived environmental changes via two-component and phosphorelay systems. The pathogenic alphaproteobacteria Bartonella quintana uses the body louse as a vector for infecting its target host, humans. It must adapt to two disparate environments, the human bloodstream and the gut of the body louse. Upon niche transfer, B. quintana is able to activate its GSR via a partner-switching mechanism involving an elegant molecular dance between alternative sigma factor RpoE, anti-sigma factor NepR, and anti-anti-sigma factor PhyR. The switching transfers NepR away from RpoE to PhyR, which activates gene transcription. Published works have revealed a molecular mechanism for sequestration via formation of a 1:1 dimer triggered by post-translational modification (PTM). However, a protein data bank (PDB) crystal structure (4QIC) shows a 2:2 tetramer, although it has not been observed in solution. We utilized size exclusion chromatography, multi-angle light scattering (MALS), small-angle X-ray scattering (SAXS), and protein modeling under various buffer conditions to identify conditions favorable for tetramer formation. MALS was chosen to determine the precise molecular weight of our chromatogram peaks, while SAXS was chosen to compare specific chromatogram peak scattering curves to PDB crystal structures and provide an overall shape for relevant peaks. Strikingly, our results revealed the tetramer forms in the absence of phosphorylation in solution, and the dimer is the dominant species under PTM favorable conditions. These results are loosely consistent with the literature but indicate the complexity of the alphaproteobacteria GSR is not fully understood. A possible explanation for the tetramer is that it maintains stress-related transcription despite the absence of a PTM.

Huntington’s disease (HD) is a progressive autosomal-dominant neurodegenerative disease due to the expansion of a CAG-repeat in the huntingtin (HTT) gene. CAG-repeat lengths less than 36 are not associated with disease phenotype, however HD with CAG-repeats greater than 39 causes full disease penetrance, characterized by motor, cognitive, and behavioral symptoms. The onset age of HD symptoms and severity of the disease correlates with the length of the CAG repeat, although there is compelling variability in length and age of onset. Somatic instability (SI) in HD is the occurrence of faulty DNA repair that causes CAG-repeat expansion and continues to lengthen with age. There has been significant research on treating HD but not a treatment addressing both SI and lowering mutant HTT protein. Our lab utilizes multiple therapeutic methods to investigate the relationship between SI and mutant HTT protein with mouse genetic models. More specifically, we devise a CRISPR/Cas9-mediated approach to excise the proximal promoter region in Htt^Q111/+ mice, which have their mutant HTT protein knocked down. My roles in this project include measuring the amount of transcription of the HTT gene from these mutant HTT CRISPR-treated mice to determine whether the amount of HTT gene transcription affects somatic instability. We devised a specially designed qPCR assay to measure the pre-mRNA of the HTT gene. Since these CRISPR-treated mice have been found to have lower somatic instability, we expect the amount of transcription of the HTT gene will directly affect the amount of somatic instability.

Lithium-ion batteries (LIBs) are used in a wide range of applications, including portable electronics, electric vehicles, and grid-scale energy storage. The material composition of the electrodes and electrolyte play a critical role in determining LIB performance. In the cathode, a lithium-containing active material known as LiNi0.8Mn0.1Co0.1O2 (NMC-811) has attracted growing interest to its high specific capacity, high energy density, and reduced cobalt content. However, at high voltages NMC-811 reacts with the liquid electrolyte to form a cathode-electrolyte interphase (CEI) on the surface of the particles. If the CEI is unstable, it can lead to performance degradation as cycling continues. The mechanism of CEI formation remains unclear but is influenced by the NMC-811 particle morphology, cathode structure, voltage, and current density. To better understand these relationships, we are using 3D printing methods to fabricate three-dimensional (3D) NMC-811 cathodes for more fundamental CEI macro-scale characterization work. By producing 3D cathodes with controlled variations in porosity and internal cell pressure, this study investigates how these factors impact, CEI formation, current density profiles and overall NMC-811 cathode performance. My contribution to this research is focused on developing fabrication procedures for the 3D cathode structures, characterizing the cathode structures with optical profilometry and scanning electron microscopy (SEM) imaging, and analyzing the electrochemical behavior of CEI formation during cycling with incremental capacity (IC or dQ/dV) analysis. By using 3D printing techniques to support electrochemical characterization, this research aims to provide insight into the contributing factors of CEI formation in NMC-811 cathodes for LIBs. This work was supported in part by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Vehicle Technologies of the US Department of Energy (DOE) through the Cathode–Electrolyte Interphase (CEI) Consortium.

Extracellular vesicles (EVs) are lipid-bilayer membrane-enclosed structures that cells produce and use for intercellular communication. Within the context of cancer, EVs have been shown to enhance cancer development by delivering cargo from malignant cells to recipient cells to promote survival, proliferation, and invasion. In a previous project, I conducted a chemical screen alongside my graudate mentor and other undergraduates to determine kinases that were important to EV biogenesis. One hit was the JNK pathway, which decreased EV production when inhibited. I studied the pathway in further detail utilizing a variety of experimental techniques to establish its importance for EV generation, and I was able to conclude that JNK regulates EV biogenesis. Another facet of cancer development is oxidative stress, caused by reactive oxygen species (ROS). When unregulated, these highly reactive free radicals and molecules derived from oxygen can damage DNA, facilitate metastasis, and aid in cancer progression. Given that surrounding literature revealed that JNK is activated by ROS, I hypothesized a connection between ROS and EV production. This project aims to more directly uncover the impact of ROS on EV generation by manipulating ROS-related genes in vivo. To do this, I knocked down ROS generator genes such as Dual Oxidase (Duox) in Drosophila melanogaster. I quantified ROS levels by staining the dissected tumor tissues with an ROS probe to ensure that the genes were functioning as expected. Then, I stained the tissues for phospho-JNK as a proxy for ROS quantification and to measure JNK activity. Finally, I conducted live imaging of the tumor tissues to quantify EV generation. I anticipate that impairing ROS generation will inhibit JNK activation, subsequently leading to a decrease in EV production. Understanding how factors involved in cancer development function in relation to each other is crucial for discovering novel cancer therapeutics.

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) senses cytosolic DNA and activates an immune response. This signaling pathway is important for defending against viral infections and regulates cancer immunity. In order to study this signaling pathway, our goal was to develop an in vivo tool using the model organism Drosophila melanogaster to answer questions regarding the activity of STING signaling. To make this STING signaling reporter gene assay, we used molecular cloning to clone the promoter regions of three genes downstream of the STING pathway (Nazo, Srg1, Srg2). We used restriction enzymes to combine the promoter regions with a vector containing the reporter DsRed (sequence for red fluorescent protein). This DNA construct was injected into flies to create transgenic fly lines. When STING signaling is active, the reporter sequence is transcribed and translated along with the STING target genes. Thus, when the transgenic flies are dissected and stained for the reporter DsRed, the images show where and how much STING signaling is active in specific cells in tissue. We tested our reporter line with the antibiotic drug bleomycin which causes tissue and DNA damage that could activate STING signaling. We found that when flies from the reporter line were fed with sucrose containing bleomycin, images of their guts showed areas with high fluorescence that weren’t visible in flies fed with just sucrose. The fluorescent areas also aligned with areas appearing to have cells with broken nuclei, suggesting our reporter line was successful. This tool is useful for any project that needs to detect STING signaling, and is helpful for answering questions regarding the pathway. There are many unknowns regarding what regulates STING signaling and what STING signaling causes which can be further studied with this in vivo reporter.

Integrating complex animal behavior with peripheral physiological recording is critical for revealing the neural basis of behavior. Traditional peripheral physiological recording methods constrain natural behavior due to cable tethers, and manually annotating behavior often introduces subjectivity. We have recently published two pipelines that independently overcome these confounds: (1) mechano-acoustic (MA) devices that provide wireless, minimally invasive peripheral recording based on finely-tuned accelerometers, and (2) a computer vision based machine learning package (Simple Behavioral Analysis, SimBA) for supervised behavioral classification from recorded videos. Here, we developed a comprehensive machine learning model to classify behavioral states using MA device accelerometer data, using SimBA to validate and extend model outcomes. We test this model by analyzing the effect of anesthesia and other consciousness-altering drugs on mice. Lastly, we extend this approach for closed-loop applications. This work contributes to the growing field of bio-signal processing, offers a data-driven approach to automated behavior classification, and provides the groundwork for answering many diverse questions in neuroscience and related fields.

As the effects of climate change continue to worsen, plant species face environmental challenges such as heat stress and drought. Research in plant physiology and how it can be affected by climate change is becoming extremely important, especially when it comes to planning for future conservation efforts. Xylem, a vascular plant tissue that transports water and minerals from the roots up throughout the plant, is a crucial part of plant physiology, particularly when it comes to studying the effects of a changing climate and limited water availability. Xylem staining is a simple and effective way to examine the structure of the xylem by severing plant stems, placing one end in dyed solution, and placing the other end into a staining manifold system made up of pressurized tubing that will draw the solution up the xylem much like a living stem would draw water up from the ground. The dye solution stains the stem and make it clear how fast the xylem is moving water up the stem, or how many active xylem there are, which is extremely useful when observing drought stress effects or potential resistance. However, most xylem staining methodologies were created years ago and are complicated to construct and use, which keeps many labs, including ours, from being able to access them. I am taking an existing xylem staining design and streamlining it using more affordable parts, then writing up a standard operating procedure for the lab on how to use it. Using my manifold, I expect to stain samples from ongoing projects in the lab, take and analyze images, and observe any potential changes in xylem physiology due to drought conditioning or other treatments. Overall, my project makes xylem staining more accessible for my lab and other labs to use for research projects in the future. 

Previous studies have shown that the diet of an organism can provide valuable insight into a variety of characteristics including habitat, behavior, and ecological role. Analyzing dentition is one method used to determine an organism’s diet, but this becomes complicated for edentulous taxa. In this study, we investigated the dietary ecology of Caretta caretta, or the loggerhead sea turtle, through the 3D morphometrics of several CT-scanned skull specimens. We are particularly interested in studying a notable feature on the occlusal surface: the accessory triturating ridge. This structure functions as a way to process food and thus provides important insight into what kinds of nutritional sources Caretta caretta may be drawing from. To analyze and interpret the morphology of the ridge, we took a series of computed tomography (CT) scans and processed them into 3D models using Slicer. We then isolated the occlusal surface in MeshLab and used R to assess variations in morphology. This results in a rotated orientation patch count (OPCr), which we can use to analyze the complexity of the occlusal surface. This acts as a topographic map, with a higher OPCr value likely indicating an omnivorous or herbivorous diet, and a lower OPCr value predicting a carnivorous diet. Because Caretta caretta are known to be omnivorous, we expect to see a higher OPCr value, suggesting that their occlusal surface is more complex than that of other turtles. Analysis of this species contributes to our project's overarching goal of applying morphological analyses to edentulous species and can offer insights into conservation efforts for this ecologically vulnerable turtle.

With the rising popularity of TikTok and its role in widespread information sharing, and concerns about political misinformation on the platform, studying political discourse through immersive ethnographic methods leading up to the 2024 US Presidential Election was imperative. This study, conducted over 12 weeks in the summer of 2024, aimed to uncover the rhetorical and ideological topics and trends salient to Black Republican and Democratic TikTok creators through content analysis. To capture the distinct feeds that a person interested in right-leaning or left-leaning content may see, two partisan personas were created on separate phones. The personas were developed from a seed list of known partisan creators and snowball sampling. A quantitative content analysis was conducted using LabelStudio software on a sample of 120 acquired videos from Black creators across the two research phones. The videos were coded for style, topic, and person of interest, alongside other inductive attributes that emerged during the coding process. Thematic analysis revealed key discursive themes around harm and blame, along with different tactics of evidence used by creators to further their points. We find a divide between left- and right-leaning creators with regard to the institutions and politicians they hold accountable for harms, and the ideologies they perceive being pushed by the oppositional party. This study shows how the affordances of the TikTok platform allowed for, and algorithmically rewarded, infighting within the Black community leading up to the election. Future studies may apply these methods of persona-enabled ethnographic data collection for conducting bipartisan investigation on other online communities, including but not limited to racial minority groups, in gaining a better understanding of prevalent issues within these communities, political or otherwise.

Originating from Functional Analytic Psychotherapy (FAP), the Awareness, Courage, and Love (ACL) model is a widely disseminated approach to building profound social connections and reducing loneliness through the practice of vulnerable self-disclosure and compassionate reflection. This model, however, has not been systematically examined through a cultural lens. This proposal investigates the potential cultural effects of the ACL intervention, focusing on individualism and collectivism. A single-blind design will be conducted with participants from both cultural contexts who will be randomly assigned to either the ACL intervention or an advice-giving intervention. Data will be collected through standardized questionnaires. We hypothesize that the ACL model will be more effective in individualistic cultures, where vulnerable self-disclosure is more culturally normative, compared to collectivistic cultures, which may prioritize group harmony over personal disclosures. The findings from this study will have implications for the cultural adaptation of the ACL model, highlighting the importance of tailoring interventions to different cultural contexts.

The meniscus is a crescent-shaped fibrocartilaginous structure in the knee joint that plays a crucial role in weight distribution, shock absorption, and joint stability. Women experience higher rates of meniscal tears when controlled for sport and tend to have worse clinical outcomes following treatment. While surgery remains the standard treatment, regenerative therapies using human meniscal fibrochondrocytes (MFCs) have shown promise in repairing damaged tissue and improving joint stability. However, repeated culture of primary MFCs on tissue culture polystyrene (TCPS) is known to alter cell phenotype, leading to loss of native function. These phenotypic changes remove our ability to accurately model differences that are seen in vivo, such as sex differences. One approach to mitigate phenotypic change is culturing MFCs in a 3D environment, which more closely mimics the native extracellular matrix (ECM) and helps maintain cell phenotype. Little research has been done to assess whether 3D cell culture systems preserve sex-based differences in meniscal tissue. Sodium alginate beads offer a well-characterized, accessible, and cost-effective 3D tissue culture system designed for fibrochondrocytes. These beads are formed via ionic cross-linking between sodium alginate and calcium chloride solution. Studies have demonstrated that sodium alginate can maintain cell phenotype in chondrocytes, making it a promising alternative to TCPS for MFC culture. To address the issue of phenotypic changes, we cultured MFCs in sodium alginate beads and examined their ability to preserve sex differences in vitro. Previous data from our lab indicates that female MFCs express higher levels of decorin (DCN), a key ECM regulator protein, compared to male MFCs. Therefore, to determine whether the 3D structure of sodium alginate beads better supports the native phenotype of MFCs by maintaining sex differences, we analyzed DCN immunostaining. These findings establish an in vitro system that preserves and facilitates the study of sex differences observed in vivo.

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

Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiovascular disease, impacting the protein interactions responsible for muscle contraction. Aficamten (Afi) is a novel myosin inhibitor that is designed to treat the underlying hypercontractility of HCM by reducing the number of myosin heads available for interaction with actin. In this study, I investigate the mechanism of Afi in both unloaded systems where muscles contract without external resistance and loaded muscle systems where contraction works against an external force. ADP release is the rate limiting step in complex/loaded muscle contraction - comparing how myosin level changes in unloaded systems translate to loaded muscle function provides a detailed mechanistic understanding of how Afi affects ADP release, and thus overall cardiac function. To determine ADP release rates in an unloaded system, pcS1 (porcine cardiac subfragment 1) is incubated with fluorescently labeled pyrene-actin and ADP and is rapidly mixed with a large excess of unlabeled ATP. As unlabeled ATP displaces the ADP bound to the actin.myosin complex, ADP dissociates, leading to actin detachment. This detachment results in a measurable decrease in fluorescence over time, allowing for the determination of ADP release rate constants. I expect Afi to slow the rate of fluorescence decay, indicating prolonged ADP release. To probe the effect of Afi in a loaded system, I utilize the demembranated mechanics assay to measure stress in complex muscle tissue. Subjecting muscle attached between a piezoelectric motor and a force transducer to rapid length steps and decreasing concentrations of ATP, I analyze the relationship between [ATP] and stretch response, providing a proxy for ADP release. I also expect Afi to decrease ADP release in complex muscle tissue. Understanding the mechanism of Afi in both unloaded and loaded models will provide protein and tissue level measurements, offering insight into its therapeutic effects on cardiac muscle function. 

pH is an important parameter for determining the health of aquatic ecosystems in freshwater and marine environments. pH is naturally basic (~8.1) in marine environments, and is controlled by carbonate buffering, carbon dioxide concentrations, and temperature. This differs from freshwater environments, where temperature plays the largest role in determining pH, resulting in naturally more acidic waters with pH levels ranging from 6.5 to 7.8. Global warming is causing rapid temperature changes, which profoundly impact freshwater pH, harming ecosystem food chains. However, long-term lake pH monitoring is limited, largely because robust and pressure-tolerant pH sensing technology have been typically designed for marine environments. This gap in technology limits the technical assessment of marine pH sensors in freshwater settings. Before large-scale and long-term use of pH sensors can begin in freshwater environments, extensive tests need to be completed to ensure the data represents the environment. To conduct this study, we tested the Ion Sensitive Field Effect Transistor (ISFET) pH sensing technology using the Deep SeapHOx™ V2 pH sensor, manufactured by Sea-Bird Scientific, over three months in Portage Bay, off the University of Washington’s Marine Science Building Dock. We collected bi-weekly water samples from the deployment location to determine pH using spectrophotometric analysis, to assess the accuracy and stability of the Deep SeapHOx™ V2 pH readings. Our findings indicated that the Deep SeapHOx™ V2 was functional in freshwater environments but with the regular factory calibration, consistently produced readings approximately 1 pH unit different from the true measurements. Additionally, the sensor exhibited a linear drift over the test period. Both issues could be easily corrected with an in-situ calibration after the sensor had equilibrated to the environment (approximately 1 week). This study contributes to the advancement of freshwater research by expanding the pH sensor technology available for monitoring these ecosystems.

Alcohol is known to cause a number of cognitive impairments including reduced memory and attention and increased risk-taking decisions. Individuals with anxiety and depression also often have characterizations of cognitive impairments, as do individuals who have high levels of impulsivity. However, less is known on whether cognitive performance is worse while impaired among those with high levels of impulsivity or symptoms of anxiety or depression. This study examines whether individual differences in impulsivity, and anxiety and depressive symptoms (ranging from none to moderate) are associated with cognitive performance on attention, memory, and decision-making tasks during alcohol intoxication. Participants included 30 young adult (aged 21-24) drinkers with recent alcohol-related consequences. As part of a larger study, participants completed a baseline survey that included measures of impulsivity, anxiety, and depression. Participants completed a series of cognitive assessments to measure performance on sustained attention, working memory, and risk-taking decisions after peak blood alcohol concentration (BAC) of ~0.10. Anxiety and depression are linked to distractibility, cognitive fatigue, and difficulty maintaining focus, and therefore I hypothesize moderate symptoms of anxiety and depression will be associated with poorer performance in sustained attention compared to those with no symptoms. Additionally, I predict that higher impulsivity scores will be associated with greater cognitive impairment across all tasks, particularly in decision-making and working memory, as impulsive individuals may struggle more with inhibiting automatic responses. Regression analyses will be used to examine these hypotheses. Since data collection occurred at a single time point, this study serves as a preliminary investigation, and further research using repeated measures across different BAC levels is needed. Findings from this study could lay the groundwork for identifying key predictors of cognitive impairment while drinking, particularly by examining how different psychological and behavioral traits interact with alcohol's effects on cognitive performance.

Previous research has suggested that Dynorphin, the endogenous opioid peptide, signals through KOR (Kappa Opioid Receptor) binding and causes negative affective states like anxiety and stress. Dyn-KOR signal activation has been found to instigate drug reinstatement. Based on previous research, questions about why Dyn-KOR signaling leads to drug reinstatement and what level of Dyn-KOR antagonism will mediate this behavior arose. The current project focused on characterizing Dyn-KOR signaling during Cocaine Self-Administration using in-vivo Fiber Photometry recording. Sprague-Dawley rats underwent cranial surgery where I injected a kLight sensor in the Prelimbic Cortex and the Nucleus Accumbens and implanted a fiber optic into each injection site. Chronic IV (intravenous) catheters were inserted into the right jugular vein and then threaded through the right shoulder into a pedestal implanted between the shoulder blades. Rats were attached to IV lines threaded through an operant chamber that was attached to a syringe of 5mg/mL cocaine. Following training, rats would undergo five days of Short Access in the operant chamber for an hour. Following Short Access, rats would go through two weeks of Long Access where they are run in the operant chambers for six hours each day. Fiber Photometry recordings were taken on the last two days of the Short Access week and Long Access weeks. Animals were put through a thirty-day Incubation period where, once over, were injected with KOR agonist U-50 (10mg/kg) and recorded. The day after were injected with KOR antagonist norBNI (nor-Binaltorphimine dihydrochloride, 15mg/kg) and injected with U-50 thirty minutes following and recorded. I collected brain samples from perfusion and fixed samples in 4% PFA (Paraformaldehyde).

The 2013-2016 Northeast Pacific Marine Heatwave (MHW) nicknamed ‘The Blob,’  is characterized by its unusually large spatial extent and duration. We assess the uniqueness of ‘The Blob’ by comparing it to other MHWs with a similar spatial footprint simulated in a large ensemble of climate models. We utilize the Community Earth System Model Large Ensemble Project (CESM LENS2)  as well as Community Earth System Model Forced Ocean Sea-Ice (CESM FOSI) to contextualize the evolution of “The Blob” and determine whether it represents an extraordinary event or falls within the range of expected marine heat extremes in the Northeast Pacific. Using Ocetrac, a Python package used to identify and track MHWs, we analyze the spatial, temporal, and intensity characteristics of MHWs across multiple ensemble members and observational datasets. Our approach allows us to assess The Blob’s uniqueness by examining: (1) Area coverage and persistence, (2) Intensity of sea surface temperature anomalies (SSTa), (3) Frequency of similar events in climate model simulations, and (4) Atmospheric and oceanic conditions prior to, during, and after the MHW. This framework of contextualizing observational MHWs within a larger set of climate model MHWs allows us to compare historical MHWs defined from CESM FOSI to climate model MHWs from CESM LENS2. This research provides the foundation for better understanding of MHW dynamics as well as present a framework for examining the limited number of MHWs in the observational record by contextualizing them in a larger set of MHWs identified in a large ensemble of climate simulations. This research could inform strategies for mitigating the impacts of MHWs on marine ecosystems and coastal communities.

Gaze tracking is a fundamental technology in human-computer interaction (HCI) and is integrated into interactive gaze devices, which serve as essential tools for enabling communication among nonverbal users. Gaze estimation reconstructs the line of sight in a single image by leveraging different kinds of information, such as head pose, face geometry, facial expressions, scene contents, eye model and localization, human-object relationships, and camera parameters. When performed continuously, gaze estimation evolves into gaze tracking, enabling the analysis of visual exploration patterns and fixation points. Through infrared lights, the eye gaze device calibrates by way of tracking the eye’s cornea through planes. Subsequently, users have increased accuracy to interact with pre-established icons manually. However, navigating through different pages on the device can be tedious, adding to the overall challenge of usability. Hence, I outline a framework for integrating predictive modeling into gaze-based interfaces, where convolutional neural networks (CNNs) analyze gaze patterns to infer intended actions, and large language models (LLMs) process contextual cues to refine predictions (i.e., input from auditory interface). Through an initial simulation and qualitative analysis, I explore the feasibility of these models in streamlining navigation and improving response accuracy. Preliminary findings indicate that predictive automation reduces cognitive load and interaction time by 90%, though challenges regarding model precision and adaptability to individual users remain. Future work will focus on refining predictive models to enhance personalization and trust in the modulated eye gaze device in order to reduce cognitive overload while safekeeping ethics.

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

The research project involves designing and building circuits for a pulsed laser and photodetector for a speed of light time of flight measurement device and developing pedagogy and curricula for 200-level experimental laboratory and 400-level senior research project physics courses. We completed project-based learning on circuit principles, Kirchhoff’s Laws, RLC circuits, Thevenin and Norton equivalence, AC signal, phasors, RC filters, oscillators, impedance, diodes, transformers, operational amplifiers, metal–oxide–semiconductor field-effect transistors (MOSFET), and introductory optics and optoelectronics. We performed hands-on training on analog circuits logic and components, CAD design, prototyping, and practical physics applications of analog circuits. Technical lab responsibilities include learning to design analog circuits using a CAD program; ordering the printed circuit board (PCB); testing circuits for functionality, accuracy, and precision; testing the speed of light measurement device for precision with light passing through air and other mediums; and measuring the refractive index of different mediums. Physics education responsibilities include incorporating our work into BPHYS 231 Experimental Physics Speed of Light Lab; developing a pre-lab quiz and lab manual; and providing documented guidance for students on learning objectives, instructions on use of the new speed of light device, lab extensions for BPHYS 231 final projects, and research topics for BPHYS 433 Senior Project. Due to the large scope of this project, the research will continue through Autumn 2025.

Previous literature has identified the relationship between the incidence of concussion and sports played. Further delineations occur between collision versus non-collision sports, contact versus non-contact sports, and athlete gender. We aimed to examine the relationship between incidence of concussion and sport played, and if incidence correlated with increased level of contact or with differences in gender. We undertook this study to better understand why there may be a rise in concussion incidence, especially in non-contact sports and any differences in concussion incidence in sex comparable sports. The cross-sectional study design uses a large data set collected on collegiate athletic teams at universities within the PAC-12 Conference between 2016 and 2022. Each concussion was diagnosed based on the clinical assessment of the evaluating sports medicine physician. The uniqueness of this data is due to diversity in population, broad location of subjects, and sport. I will analyze concussion incidence data from all PAC-12 athletes using descriptive statistics to describe the population and incidence rates to measure differences across the various groups. We believe that our findings will show women’s sports have a higher rate of concussion than men’s. Athletes participating in collision sports such as football may not necessarily be more likely to sustain a concussion than those who play limited or non-contact sports. There has been an increase in reporting, although it is unclear whether the rise is due to an increase in reporting, actual incidence, or a little of both. The information from this study will be useful in determining where additional concussion education and prevention measures should be directed. 

Influenza viruses are a causative agent of seasonal flu outbreaks, which are mitigated through routine vaccination. Due to antigenic drift, many illness-causing strains evolve slower and are therefore, well-characterized. However, new strains occasionally emerge from animal reservoirs through antigenic shift, which can evade pre-existing immunity and cause lethal pandemics. Currently, H5N1 strains are of global health concern. Influenza viruses have two major antigenic surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA), which have opposing functions and depend on a host cellular receptor, sialic acid. HA binds sialic acid for virus entry while NA cleaves sialic acid for viral release. NA is a dimer of dimers with several distinct domains, and two of particular interest: a head domain with sialidase activity and a flexible, hypervariable stalk domain. It is suggested that stalk length alters the range of accepted substrate-enzyme geometries of the NA head. As such, it is hypothesized that stalk length influences NA expression levels, sialic acid cleavage, and head tilting. Recent literature also demonstrates that shorter NA stalks result in reduced viral fitness in human hosts. Characterizing the structural effects of different NA stalk truncation constructs will provide valuable insight into influenza host-virus interactions. HDX-MS is an excellent tool for determining the structural dynamics of NA head regions by measuring local backbone amide solvent accessibility. MS data provides a detailed profile of deuterium uptake kinetics, effectively identifying differences in NA head flexibility across constructs. Additionally, we will use negative stain electron microscopy to observe differences in NA quarternary configuration and head tilting. We plan to correlate structural changes across constructs to changes in NA native function using a variety of NA activity assays in further experiments. This ongoing study aims to inform about how NA stalk length affects the influenza replication cycle, pathogenicity, and broader implications on host immunity.

Zinc oxide (ZnO) is a promising host material for spin defect qubits due to its direct and wide band gap, low spin-orbit coupling, and ability to be isotopically purified to eliminate the nuclear spin bath [1]. Progress in developing practical devices in ZnO critically depends on superior defect optical and spin properties, provoking a search for advantageous new defect candidates. A particularly promising class of impurities in ZnO are shallow neutral donors. Along the column of shallow donors in ZnO (Group IIIa), attractive qubit properties have been observed, including a longitudinal electron spin relaxation time approaching 0.5 seconds from Ga donors [2], and a strong hyperfine (100 MHz) interaction from In donors [3]. Hyperfine interaction strength increases going down the column [4]. This trend prompts the investigation of the next Group IIIa element, thallium. In contrast to the spin 9/2 115In nucleus, all stable isotopes of Tl have nuclear spin 1/2, improving the prospects for full control of the nuclear spin manifold. Tl ions were introduced through ion implantation and annealing, allowing for control of donor concentration and spatial extent within the sample. Through low-temperature photoluminescence spectroscopy, we observe a sharp, excitonic line exhibiting Zeeman splitting consistent with a neutral donor, the first optical signature reported for thallium-doped ZnO. We present progress towards conclusively identifying the donor. This work provides an example of the purposeful creation of and search for a novel semiconductor defect. This material is based upon work supported by the Air Force Office of Scientific Research under award number FA9550-23-1-0418. [1]: X. Linpeng et. al., Phys. Rev. Applied 10, 064061 (2018). [2]: V. Niaouris et al., Phys. Rev. B 105, 195202 (2022). [3]: X. Wang et al., Phys. Rev. Applied 19, 054090 (2023) [4]: Phys. Rev. B 25, 6049 (1982)

The interaction between the kinetochore and spindle microtubule serves as a checkpoint during the transition from metaphase to anaphase in the cell cycle. Bipolar microtubule attachment and tension sensing is required for successful segregation of sister chromatids, and progression through the cell cycle. Incorrect attachment will lead to cells containing excess genetic material, or not enough; both of which will compromise the cell's survival. Proteins that make up the kinetochore, such as Dsn1, are still being investigated for their role in chromosome segregation. Dsn1 is a protein located in the MIS/MIND complex, bridging kinetochore subcomplexes involved in microtubule attachment and tension sensing. Phosphorylation is known to alter the structure and function of proteins. We were interested in whether phosphorylation events impacted the function of Dsn1. We aimed to mutate the DSN1 gene at codons that code for amino acids known to be phosphorylated. Specifically, we targeted two threonine amino acids at sites where mass spectrometry analysis has confirmed Dsn1 is phosphorylated: T380 and T386. We transformed yeast with a vector expressing the CRISPR-Cas9 system engineered to target a DNA break in the DSN1 gene, and a homology directed repair DNA molecule (HDR) that would induce mutations changing the target codons to valine (T380V and T386V) during the repair of the break. After obtaining yeast transformed with these DNAs, we amplified this region through a PCR reaction and sent out the DNA for Sanger sequencing to confirm the presence of our intended mutations. The integration of the dsn1-T380/386V mutations was not successful, however sequencing data supported the function of the CRISPR vector since an off-site mutation was present near the T380/386 site. We are repeating the mutagenesis with a longer HDR template, and hope to show the role of phosphorylation of these sites in the function of Dsn1.

Chronic Recurrent Multifocal Osteomyelitis (CRMO), is an autoinflammatory bone disorder that is notable by the recurrent bone lesions with potential long-term complications that include growth impairment in pediatric patients. Growth impairment can be illustrated through z-scores for weight and height. Z-scores represent how far a patient’s weight and height measurements deviate from the average for their age and sex. Z-scores below -1 and -2 could indicate the negative disturbance by CRMO or inadequate treatment. Standard second-line treatments for CRMO include bisphosphonates, disease-modifying antirheumatic drugs (DMARDs), and tumor necrosis factor inhibitors (TNFi). Bisphosphonates are frequently prescribed pediatric medications for their ability to improve bone health and reduce inflammation. However, the impact of these medications – alone or in combination with DMARDs and TNFis – on growth patterns are understudied. Medication practices may demonstrate varying results on height and weight outcomes in CRMO patients. CHOIR included prospective longitudinal data from >500 patients from multiple sites across continents, which allows us to compare the effects of these treatment regimens on the change of Z-score. We expect that the proportion of patients with low Z-scores is similar across all groups before the treatments. By gathering patients based on treatment regimen, this review will compare the prevalence of lower z-scores. Understanding these correlations is vital for identifying whether certain treatments contribute to growth improvement, offering insights into optimizing care for CRMO patients.

Type 2 immunity is the immune response activated by allergens and parasites, and recently type 2 immune cells were discovered to have pro-tumor functions. We are working to understand how tumors activate and regulate a type 2 immune response using a mouse model (Apc^Min/+) which mimics pre-malignant human colorectal cancer. This project focuses specifically on the role of mast cells; a key component of type 2 immunity attributed with both pro- and anti-tumor properties. Mast cells are known to infiltrate tumors, and previous work in the lab has shown that the intestinal epithelial cytokine IL-33 promotes activation of Apc^Min/+ tumor-associated mast cells leading to a pro-tumor response. We hypothesized that mast cells and IL-33 would be colocalized in these tumors because of this association. While immunofluorescence (IF) imaging and reverse transcriptase, quantitative polymerase chain reaction (RT-qPCR) results confirmed an upregulation of IL-33 in tumors, IF data did not support the colocalization hypothesis. To further understand the role mast cells may have in type 2 immune response activation, the antibody c-Kit was used to deplete mast cells from Apc^Min/+ mice and I compared expression of the enzyme Arginase 1 and cytokine IL-13 to control Apc^Min/+ mice using qPCR. These targets both serve as measurements of type 2 immune response “outputs”. Data showed a decrease for both targets in the mast cell-depleted mice, which supports the idea that mast cells have a role in activating the type 2 immune response in tumors. Additionally, we made a novel observation of intraepithelial mast cells residing within the tightly packed epithelial tumor cells, which is one way we have come to better understand the morphology of the Apc^Min/+ tumors. We continue to explore where cells and molecules are located in these tumors because this facilitates our thinking about how interactions may be taking place.

Understanding the structure and habitat preferences of deep-reef fishes is crucial for effective conservation management. Mesophotic ecosystems, occurring between 40 and 150 m, are understudied ecosystems with limited biodiversity assessments, although their importance in supporting species of commercial interest is established.  In particular, very few studies have described mesophotic fish assemblages in the Mediterranean, where essential fish ecosystems face increasing pressures from human activities. This study investigates fish species composition, abundance, and depth distribution at two sites in the Aegean Sea (Eastern Mediterranean).  Fish observations were collected by technical rebreather divers from the surface to 90 meters depth, along with information on habitat and fishing pressure. I will complement this dataset with information collected from the IUCN to identify patterns in species distribution, vulnerability, and habitat associations. This study will provide valuable insights into the community structure and habitat associations of mesophotic fish assemblages, ultimately contributing to conservation strategies that protect vulnerable marine ecosystems in the Mediterranean.

HIV incidence among adolescent girls and young women (AGYW) is disproportionately high in East and Southern Africa, highlighting the urgent need for effective HIV prevention counseling for this population. Our study addresses critical gaps in HIV prevention for AGYW in Kenya, particularly regarding HIV education and engagement in prevention services, by leveraging the trusted role of nurses to support AGYW and overcome barriers related to stigma, misinformation, and interpersonal dynamics. Nurse navigators are a promising intervention within family planning clinics, though accessing contraception via pharmacies is common among AGYW in Kenya. Prior pilot studies show the feasibility and acceptability of delivering HIV Pre-Exposure Prophylaxis (PrEP) within a pharmacy with PrEP-trained nurses. The purpose of this current study is to evaluate the effectiveness of integrating nurse navigators and long-acting PrEP agents on PrEP uptake and continuation among AGYW seeking contraception at pharmacies in Kisumu, Kenya. A 2-armed non-blinded cluster randomized control trial is being conducted in Kisumu among AGYW (n=1900) seeking contraception at pharmacies. The study randomized 20 pharmacies to receive (n=10) or not receive (n=10) nurse navigators to support PrEP delivery. We anticipate that the implementation of nurse navigators and long-acting PrEP agents in pharmacy settings will significantly improve access to and engagement with HIV PrEP among HIV-negative AGYW in Kenya. Additionally, the study will qualitatively evaluate the acceptability, feasibility, and client satisfaction of delivering long-acting PrEP agents within pharmacies with nurse navigators to support PrEP use. While the study is ongoing, our preliminary data illustrates positive experiences among AGYW with nurse navigators, including feelings of safety, trust, and educational improvement. This study can confirm the efficacy of nurse navigators in improving engagement in health management and education for AGYW in Kenya. Further exploration of the effectiveness of nurse navigators in service to other populations should be conducted. 

An estimated 4.3% of children in the United States have disabilities, a prevalence that has been steadily rising in recent years. Children with motor disabilities often face significant delays in achieving independent mobility, with many lacking access to powered mobility devices during critical early developmental stages. Early access to these devices fosters exploration, social interaction, and cognitive development, highlighting the need for timely assessment and intervention strategies. Discussions with practicing pediatricians highlight their strong interest in data-driven tools to better inform clinical decisions to support mobility, independence, and timely care. This study leverages the Permobil Explorer Mini, a powered mobility device for young children, to evaluate motor, cognitive, and social-emotional development through the Assessment for Learning Powered Mobility (ALP). Preliminary data collected from nine participants reveal correlations between key parameters and developmental progress, demonstrating the potential of data-driven approaches to enhance therapeutic outcomes. A classification model is being developed to predict ALP scores by identifying relevant features and refining model performance. Current accuracy is 50%, with efforts underway to address data sparsity through expanded data collection and validation. Additionally, a diagnostic interface is being designed to integrate the classification model, providing data visualization and tracking for pediatric clinicians. Built using React and optimized for tablets, the system incorporates AWS for secure storage and Python for preprocessing and model application. Iterative feedback from clinicians ensures usability and clinical relevance, aiming to improve diagnostic accuracy and inform therapeutic decision-making in pediatric care. The final product will undergo real-world testing in pediatric hospitals to evaluate the effectiveness of the interface and classification model.

Fear extinction, the process of extinguishing conditioned fear responses, plays an essential role in the treatment of anxiety disorders. Research has shown that fear regulatory mechanisms appear to be modulated by fluctuating endogenous hormones, such as estradiol, resulting in altered fear extinction strength at different phases of the menstrual cycle. This project explores the neural and physiological mechanisms of fear extinction across different phases of the menstrual cycle. This research addresses a significant gap in the literature, as women are historically underrepresented in fear extinction studies despite experiencing higher rates of anxiety disorders. I hypothesize that participants in the early follicular phase will exhibit attenuated fear extinction and recall compared to those in the mid-luteal phase. Using a combination of skin conductance response, pupillometry, and self-report measures, I will assess fear responses during acquisition, extinction, and recall phases of a basic fear conditioning paradigm. Additionally, functional MRI will be employed to investigate brain activity. Specifically I expect to see attenuated activity in the ventromedial prefrontal cortex, a brain region which appears to modulate amygdala activity, in the early follicular group. Our study aims to provide a comprehensive understanding of how menstrual cycle phases influence fear extinction, leading to more effective and tailored exposure therapy protocols for women.

Climate change has affected every part of the world. However, nowhere is affected more than the Arctic. More and more arctic ice melts every season, and while the environmental implications are disastrous, it may open up positive new opportunities for trade and recreation, bringing life into small, dwindling Arctic economies. One area of the Arctic that will see increased use in the future is the Northwest Passage (NWP). The once icelocked and barely usable trade route has the potential to influence the economy of all territories it touches, primarily Alaska. Current data indicates that the melting ice along the NWP will have a positive impact on the Alaskan economy. This Literature Review predicts the possible quantitative impact on the region. Strategically positioned Alaskan communities, such as Nome, have fragile infrastructures which will have to adapt to increased commercial demand from cruise ships and recreational vessels. While it is unlikely that trade will have much of an impact economically as most of the ships will not stop along the route, it is likely that the increase in cruise ships will stimulate forced economic and infrastructural growth for these communities. Additionally, as this region of Alaska is mostly undisturbed, there needs to be more study into the environmental impacts of economic growth in the area. Considering the possibility of the NWP becoming a well traveled route is essential in order to help prepare small towns for potential economic booms. An overview of the research suggests that while trade in general may not impact the overall Alaskan economy, the potential increase in tourism via cruise ships and other recreational vessels has the potential to overwhelm the infrastructure of smaller Alaskan cities, even as it jump-starts their economies.

Alzheimer’s disease (AD) is the most common cause of dementia in the aging population and is characterized pathologically by the presence of amyloid plaques and tau neurofibrillary tangles in the brain. However, other co-pathologies are often present along with AD, such as TDP-43 pathology. TDP-43 pathology, which was first described in other forms of neurodegenerative disease, has more recently been observed as a common co-pathology in AD, particularly in older individuals. The pathology is characterized by aggregates of hyperphosphorylated TDP-43 in the same brain regions as the tau pathology of AD, including the hippocampus. The combination of AD and TDP-43 pathology is associated with accelerated cognitive decline, greater brain atrophy, and increased AD pathological burden, particularly tau. In past studies, it has been suggested that there may be a potential synergistic relationship between tau and TDP-43 co-pathology in model systems. However, there is limited data on the relationship between quantitative tau and TDP-43 in human post-mortem tissues. This project explores the correlation between tau protein and TDP-43 in the aged brain using a quantitative neuropathological approach. We identified brain donors from the University of Washington BioRepository and Integrated Neuropathology (BRaIN) lab with pathology-confirmed high levels of AD pathology and varying degrees of TDP-43 co-pathology, along with a matched group of donors with high AD pathology and no TDP-43 co-pathology (n=8 per group). We use immunohistochemistry to stain the frontal cortex and hippocampus of each donor for hyperphosphorylated TDP-43 and different forms of pathologic tau. We quantify pathologic protein burden on digitized slides using the image analysis platform HALO and assess the relationship between tau and TDP-43 burden and cognitive function. This work will expand our understanding of the relationship between tau and TDP-43 pathology and ultimately provide new avenues for potential diagnostic and therapeutic approaches.

Dopamine plays a critical role in learning, motivation, and emotional regulation, yet its influence on the interplay between positive and negative stimuli remains unclear. This study examines how dopamine receptor 1 (D1) and dopamine receptor 2 (D2)-expressing neurons in the central amygdala (CeA) contribute to fear generalization and its reversal through reward-associated cues. Using fiber photometry, we recorded neuronal activity in Drd1-Cre and Penk-Cre (highly co-expressing Drd2) mice during Pavlovian reinforcement learning, fear generalization, and reward-mediated fear reversal to assess their roles in adaptive behavior. During positive reinforcement, both Drd1 and Penk neurons responded to reward, but only Drd1 neurons developed a response to reward-associated cues. In contrast, during fear generalization, both neuron types were activated by aversive stimuli, with Penk neurons exhibiting stronger responses. Notably, when reward-associated cues were used to reverse fear generalization, Penk neurons displayed an enhanced response to fear cues, whereas this effect was absent in Drd1 neurons. These findings reveal a dopamine-dependent mechanism in the amygdala that regulates fear generalization based on reward history. Understanding how dopamine receptor signaling shapes the balance between fear and reward processing offers valuable insights into potential therapeutic strategies for fear-related disorders. 

The topic of abortion has been heavily debated throughout countries, with many religious groups being for or against the medical procedure. From there, the movements "Pro-life" and "Pro-choice" have been constantly tossed around in the media, portraying one group as wrong while the other group is right. Pro-choice arguments stem from how women globally have been denied abortion rights. In contrast, Pro-life arguments stem from religious beliefs and focus on the morality of murdering a potential life. Unfortunately, stances around this subject become increasingly unfair when authorities favor one side. An example is The Global Gag Rule (GGR), the "Mexico City Policy". This policy is a governmental policy that states how NGOs and non-US territories will lose US health funding if they have any information promoting abortion. What occurs is that once a Republican president is in office, this policy is reinstated. Reinstation of this policy means that NGOs, governmental agencies, and health clinics will be ineligible to receive funding, meaning that they have no choice but to give up their abortion services to continue receiving monetary aid from USAID. On the other hand, revoking this policy, which a Democratic president typically does, means that abortion support has no part in the eligibility for US foreign aid. While this may seem like sometimes there should not be an issue when it is reinstated or revoked, the constant back and forth in this policy causes a human rights regression.

User-controlled cell behavior is useful for studying wound healing because the isolated therapeutic effects of individual signals can be observed at the wound site. Aptamers are single-stranded oligonucleotides that fold into three-dimensional structures that can capture and inhibit proteins. The biological capacity of cells to deploy traction forces as a release mechanism for extracellular proteins can be engineered through clever deployment of aptamer-bound proteins with peptide handles. Scientists at the Imperial College London recently synthesized TrAPs: Traction Force-Activated Payloads that enable precise control of cell behavior using such a strategy. We bound photocaged TrAPs lacking adhesion handles to functionalized collagen hydrogels. Peptide immobilization was then selectively patterned using 365 nm light to spatially confine cell access to captured vascular endothelial growth factor (VEGF). After surface seeding endothelial cells, observations were made regarding changes in cells’ physical characteristics as a result of  protein release. Through SELEX (Systematic Evolution of Ligands by Exponential Enrichment), TrAPs can be designed for any target protein in the extracellular matrix. The wide scope and biorthogonality of this project allows for many applications in medical technology and user-controlled cell fate. 

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

Critical care outcomes vary significantly across healthcare settings, and resource-limited environments often lack high-quality data-driven insights that can improve patient care. In particular, there is a strong need to understand whether insights derived from high-resource settings such as the US can be readily applied to more resource-constrained healthcare settings. To this end, here I systematically compared ICU populations between hospitals in India and the University of Washington Medical Center (UWMC) to assess differences in laboratory test dynamics and clinical outcomes (mortality, sepsis, blood transfusions, etc.). Using ICU datasets containing >100,000 patients, I applied clustering algorithms to segment patient populations based on lab test time series data. Clustering was performed across stratifications of age, sex, and admitting diagnosis to capture variations in population health. Resultant clusters demonstrated up to a threefold stratification in mortality rate (3% to 15%), with similar stratifications for other outcomes. Additionally, dimensionality reduction techniques (Uniform Manifold Approximation and Projection [UMAP], t-Distributed Stochastic Neighbor Embedding [t-SNE], etc.) were used to visualize population differences. To identify the strongest predictors of clinical outcomes, I used Cox proportional hazards model to quantify the impact of individual lab tests on patient outcomes. The analysis revealed distinct differences in lab test significance between UWMC and Indian ICU populations. Key lab tests such as Blood Urea Nitrogen and Hemoglobin were strong predictors of adverse outcomes across both cohorts, but their relative importance varied between the two settings, suggesting differences in disease progression, healthcare practices, and marker utility. These findings highlight the need for region-specific risk models and emphasize the importance of integrating time-series lab data into ICU decision-making. Understanding these differences can inform the development of more generalizable risk stratification models and improve critical care strategies in resource-limited settings, ultimately advancing global healthcare equity.

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

Traumatic brain injury (TBI), characterized by a physical impact to the skull, is a significant health concern among veterans, athletes, and the elderly, with over 200,000 TBI-related hospitalizations in 2020. TBI causes shearing forces and physical damage to the brain, resulting in increased risk of neurodegeneration and mental health problems. When they expect an impact, humans brace, exhaling against a closed airway in what is known as a Valsalva maneuver. This prevents venous return from the head, pressurizes the vascular network in the brain, and increases intracranial pressure (ICP) in a way that may protect the brain from TBI. We aim to mimic a Valsalva-like response (VLR) through external abdominal stimulation and measure corresponding ICP changes. First, we performed a 3mm-wide craniotomy in anesthetized ferrets and implanted a pressure transducer inside the brain to collect baseline pressure readings. After skull closure, VLR was performed both supine and upright (body at 45°), either physically (pVLR, 80-120mmHg by abdominal compression using a blood pressure cuff, n=4) or electrically (eVLR, bilateral 25-30mA stimulus of the rectus muscles, n=4). pVLR resulted in a 2-4mmHg increase in ICP over 2-5 sec. By comparison eVLR resulted in a larger and faster ICP increase - 3-7mmHg with an onset of 250-750ms. Consequently, we will utilize eVLR to modulate ICP in a TBI model to determine whether it is neuroprotective. Ferrets will be assigned to control or randomized to receive a TBI impact with either sham eVLR or eVLR. Animals will be subjected to baseline (pre-TBI), acute, and long-term behavioral testing. Additionally, we will perform brain cell specific histological staining. Results from behavioral testing and histology will inform us of the potential neuroprotective effects of eVLR against TBI and provide future direction towards translating the findings into a wearable device for at-risk individuals.

Some older individuals exhibit the pathological hallmarks (i.e., amyloid-beta plaques and tau-containing neurofibrillary tangles) of Alzheimer’s disease (AD) yet remain cognitively intact, a phenomenon known as resilience. Microglia, the primary immune cells of the central nervous system are important for clearance of debris and responding to injury in the brain. When exposed to aggregated proteins, they can release inflammatory molecules toxic to neurons.  Because neuroinflammation has been implicated in neurodegeneration, understanding how microglia interact with Aβ could provide insight into immune mechanisms that support cognitive preservation despite AD pathology. In patients with AD who have dementia, it is known that their microglia cluster around amyloid-beta (Aβ) plaques which possibly contribute to damaging inflammation.  Whether microglia in resilient individuals share the same relationship to plaque is unknown. This study investigated whether microglia in resilient individuals differ in their spatial relationship to amyloid plaques compared to non-resilient individuals in the dorsolateral prefrontal cortex. Using confocal montage images from postmortem human brain tissue where immunofluorescence stained for Iba1+ microglia and PanAβ+ Aβ plaques, I quantified the proportion of microglia clustering around Aβ in three groups: 1) individuals with symptomatic AD, 2) cognitively intact individuals with AD pathology (resilient), and 3) cognitively intact individuals with no/low AD pathology (resistant). By generating 2D surface reconstructions, I measured microglia-Aβ overlap and proximity to assess colocalization patterns. I identified differences in microglia-Aβ colocalization between these three groups. This approach can help understand how microglial interactions with Aβ may contribute to resilience mechanisms and could inform novel therapeutic strategies for AD.

In 2023, the World Health Organization (WHO) estimated that there were 263 million malaria cases and 597,000 deaths globally. Parasites of the genus Plasmodium are the causative agent of malaria, deposited into the dermis of a human host through the bite of a female Anopheles mosquito carrying infected sporozoites (spz). From the dermis, spz migrate through the bloodstream and into the liver where they infect hepatocytes, producing potentially thousands of merozoites from a single hepatocyte which then enter the symptomatic erythrocytic stage of the disease. Higher numbers of CD8+ T cells per infected hepatocyte have been associated with Plasmodium clearance and because eliminating all infected hepatocytes during the pre-erythrocytic stage prevents malaria onset, identifying causes of CD8+ T cell recruitment provides critical insights for malaria prevention. The liver is one of the most sexually-dimorphic organs in both mice and humans, leading us to utilize immunohistochemical light microscopy to observe CD8+ cells in inflammatory foci, defined as abnormal concentrations of hepatic nuclei including at least one CD8+ cell. Using digital pathology software, we quantified these in female, male, and orchiectomized male (ORX) BALB/cJ mice that were either unvaccinated or repeatedly vaccinated with radiation-attenuated spz allowing us to assess the role of androgens in this recruitment. We found that following challenge with the rodent malaria wild-type parasite Plasmodium yoelii spz, vaccinated mice had more inflammatory foci and CD8+ cells than unvaccinated mice while intact male mice had fewer CD8+ cell and inflammatory foci than ORX or females of similar vaccination status. These findings suggest that androgens reduce recruitment of CD8+ T cells to inflammatory foci, providing a potential explanation for the reduced parasite clearance in male mice compared to their female counterparts. Further studies should explore the mechanism behind this reduced recruitment to inform important decisions in malaria vaccinology and translational medicine.

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

Lentivirus is a well-established gene-editing tool commonly used in cellular research. Recently, its widespread adoption has led to the development of numerous protocols for the transduction of primary human T-cells. However, generating high-titer virus for large vectors remains a challenge, and there is a need for optimized protocols – particularly for creating Base Editor lentivirus for a 15 kb vector. By developing a method to estimate transduction efficiency in primary human T-cells using viral titers, significant reduction to the waste of valuable human samples could be achieved. To address these challenges, we tested various variables—including plasmid concentration, media formulations, and transfection reagents—within infection protocols to optimize lentivirus production and improve T-cell transduction efficiency. By refining the protocol for creating Base Editor lentivirus, we aim to base-edit autoimmune-associated variants in human CD4 T-cells and assess their impact on T-cell effector function. This work is crucial for advancing base editing technologies in the Ray Lab and will contribute to the broader field of immunology.

Courts are often assumed to be neutral bodies far removed from the political sphere. International courts even more so given their distance from domestic politics and policymaking. Yet over the last sixty years, the European Court of Human Rights (ECtHR) has profoundly shaped law and policies across Europe and it is increasingly the site of political and legal mobilization by a wide array of interests. In this project, we examine how and why interest organizations have accessed the ECtHR and how this has affected the development of human rights in Europe. To study this dynamic, we utilize judgment data from the European Court of Human Rights database (ECHRdb) covering the time period 1960-2022. Utilizing the ECHRdb data and Court policy documents, we then created an original data set for a comparative case study of two areas of law: environmental protection and work/business. Conducting exploratory analyses using R, Python, and Tableau, we examined general trends in organization participation in the cases, as well as variation across the two policy areas. Historical case law analyses also enabled us to identify key judgments that have been critical to the development of European law. Through our analyses, we identified repeat players (organizations who strategically use the court over time), longitudinal change in the court’s policy impact cases and change in violation rates. Our findings highlight that the Court has a direct impact on domestic policy and serves as a forum for political mobilization. Our data also suggests that “learning” both by the Court and repeat interest organization players shapes the degree the Court expands the law and the success of organizations in important cases. These findings may also help answer larger questions on the impact of international courts in sensitive areas of domestic policy including climate change and worker’s rights.

In the study of the consonants of the world’s languages, certain consonants, specifically those made through the glottis, are less studied than consonants made using primarily the lungs, despite being geographically widespread. In particular, there is very little large-scale research about the acoustic (sound) variability in their production in connected speech. In the present study, we investigate the acoustic variability present in the realization of implosives (consonants made from lowering the glottis and blocking air in the mouth at the same time) from the online corpus of Hausa and kiSwahili. The corpora used was from Common Voice which contains recording of speakers reading sentences. This data was downloaded for each language, then hand corrected and noted for implosives and their equivalents. We used this data to investigate the variability between the consonants in Hausa and kiSwahili and we discuss this variability in the realization of the consonants. We anticipate finding important differences among implosives in these two languages and hope to apply this knowledge to other languages with implosives. This research is part of a larger effort to document the variability among consonants made using the glottis in languages all over the world.

Alternative-technology (alt-tech) platforms like Telegram, Truth Social, and Rumble have emerged as self-proclaimed free speech hubs, appealing to distrust in governments and tech companies. While alt-tech platforms remain niche, they play a growing role in political communication and have contributed to real-world events, such as the January 6 Capitol attack. Despite their influence, research on these platforms remains limited compared to mainstream social media studies. This study develops a typology of five right-wing alt-tech platforms—Rumble, Truth Social, Gab, Gettr, and Telegram—analyzing their ownership structures, monetization models, and content moderation policies. By examining how these platforms’ designs and financial incentives influence content production and user behavior, the study aims to provide insights into their role in shaping online information ecosystems. Prior research has examined individual alt-tech platforms, such as Bitchute, and broader comparisons between mainstream and alt-tech platforms. However, this study offers a comparative analysis focused exclusively on alt-tech platforms, identifying patterns in governance, incentive structures, and policy enforcement. Findings from this research could inform policymakers on potential regulatory approaches, including ownership transparency, antitrust interventions, and content accountability measures. Additionally, technologists and platform developers may leverage these insights to design more transparent governance frameworks for alternative digital spaces. By addressing gaps in current social media research, this study enhances public understanding of alt-tech platforms and their growing influence in digital discourse and political communication.

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

Heart disease is linked to one in every five deaths in the United States, indicating the need for more research on causes and possible treatments. Dilated cardiomyopathy (DCM) is an inherited cardiomyopathy characterized by a decrease in contractile function, which often leads to heart failure and death. DCM is a disease of progressive remodeling and is often not diagnosed until later in life once a patient becomes symptomatic and the progression of disease is difficult to discern. By understanding the specific molecular etiology of DCM, treatments can be specialized and better prevent progression to end-stage heart failure. One protein associated with DCM is the motor protein myosin. In the Regnier Lab, we study the dilated cardiomyopathy-associated myosin mutation R369Q to better understand the molecular mechanisms leading to DCM. To explore this, I used Human Induced Pluripotent Stem Cells (hiPSCs) that have been CRISPR-edited to contain the mutation, differentiated into cardiomyocytes and cultured on patterned surfaces to promote maturation and alignment of the contractile organelles called myofibrils. I electrically paced and live-imaged these cells to capture single-cell contraction to compare differences in sarcomere shortening and quantify cell-level effects of the R369Q mutation. I also analyzed flat glass imaging to measure cell area and potential differences in sarcomere alignment. My goal is to better understand how the structural and functional differences on a single cell level fit into the context of a DCM mutation's effects in the heart. Ultimately this will allow a better understanding of the R369Q mutation’s pathogenic effects and give better insight into how possible future treatments can potentially combat the effects of DCM.

DNA concentration sensing is important for accurate reagent input measurement and output data collection for various molecular biology applications, such as genomics, biotechnology, and clinical diagnostics. Common use cases for DNA concentration sensing include polymerase chain reaction (PCR), gel electrophoresis, and enzymatic assays. Off-the-shelf spectrophotometry systems, used today to measure DNA concentration, require an aliquot of DNA to be pipetted onto a sensor. The sample is then discarded to avoid contamination. Our goal is to develop a novel, cost-effective, and contactless method of containing and directly measuring DNA concentration in individual microliter droplets in real-time. Advantages of contactless containment are: (1) no sample is lost to adhesion to the container, (2) no spectral signature from the container material is added to the sample’s spectrum, and (3) samples can be weighed without contact for closed loop control of sample mass. To contain the droplets of DNA without contact, we use an acoustic levitation system. This system emits focused ultrasonic sound to lift, move and contain liquid droplets in air without making direct contact. Since DNA absorbs ultraviolet (UV) light at a wavelength of 260 nm, we use a low-cost, off-the-shelf spectroscopy sensor to build a portable DNA concentration measurement system within the levitation system to measure the amount of 260 nm UV light absorbed by the DNA. Preliminary results show that the device can distinguish samples containing different concentrations of DNA. Further research will focus on enhancing the device’s sensitivity and expanding its application to other fields related to biology.

Joubert Syndrome (JS) is a rare neurodevelopmental condition characterized by the presence of the molar tooth sign (MTS) on axial brain magnetic imaging (MRI). Patients typically display hypotonia (muscle weakness), ataxia (impaired coordination), and developmental delays. JS can be caused by dysfunction of any one of over 40 genes. Differences in genes, commonly referred to as DNA variants, can be classified based on their potential to cause human genetic conditions. Pathogenic or likely pathogenic variants, thought to be condition-causing, are anticipated to change how the gene functions. Typically, both copies of a gene need to be affected to cause JS. The purpose of this project is to evaluate the genetic causes of JS in patients with one confirmed pathogenic variant and another variant of uncertain significance (VUS). For this purpose, I selected two patients for whom we had fibroblast cell lines, each with one pathogenic variant and one VUS in the JS gene, CC2D2A. Patient UW320-3 carries c.1558C>T (pathogenic) and c.685_687del (VUS). Patient UW456-3 carries c.3452T>C (pathogenic) and c.248-5_248-4insAAGTTT (VUS). To assess the pathogenicity of these two VUS, I performed western blot analysis with a  CC2D2A antibody, measuring protein size and quantity in these patient cell lines. I anticipate lower CC2D2A protein levels due to both copies of the gene being impacted. If the CC2D2A protein levels are significantly reduced, that would provide strong evidence for the variants in CC2D2A being causal in these two patients. Validating the pathogenicity of these variants of uncertain significance will help to further identify novel genetic causes of JS in our cohort, increase our overall understanding of the recessive mechanisms of JS, and allow us to report more precise genetic causes to families.

Assessing one’s circadian phase is important to both clinicians and researchers. The gold standard method of estimating circadian phase involves identifying the clock time when melatonin levels increase when under dim light (<5 lux), called Dim Light Melatonin Onset (DLMO). This method involves collecting 8 hourly saliva samples, starting in the afternoon and finishing one hour after habitual bedtime. As external conditions can mask markers of circadian phase, such as bright evening lights inhibiting melatonin production, this method requires strictly controlled conditions (i.e. no eating, drinking, standing 30 minutes before each sample). This increases money and time cost of studies assessing circadian phase, and it reduces the accuracy and accessibility of DLMO assessments. The current study (n=17) attempts to validate a new method of estimating circadian phase, developed by Dr. Achim Kramer at Charité University, based on a one-time collection of hair follicles (HFs). Participants collected their own HFs in the morning before arriving at the lab to complete an evening DLMO assessment. I verified dim light levels via lux meter, ensured participants did not stand, eat, or drink 30 minutes before providing each saliva sample, and recorded the exact time of individual participants’ sample collection. I assayed saliva samples for melatonin levels to estimate DLMO. HF samples are processed at Charité University using the RNA levels of different relevant genes. We predict the circadian phases calculated by this method will significantly correlate with those of the DLMO assessment. If validated, this method would reduce the time burden on participants from ~8 hours to a matter of minutes. Reducing the cost of circadian phase studies will benefit researchers and clinicians alike, including for those living in remote areas or in areas with less healthcare access.

Greater than 70% of the volcanism on Earth occurs along mid-ocean ridge spreading centers and plays a significant role in cycling elements into and out of the seafloor due to hydrothermal circulation. My study investigated how temperature and chlorinity/conductivity were changing in two submarine hot springs (hydrothermal vents) from September 12, 2023 – January 7, 2025, with linkages to earthquake activity. I chose this time interval due to heightened seismic activity and inflation of the volcano in recent time indicating an impending eruption at Axial Seamount is likely within a year. These data inform the underlying plumbing system and were utilized to test the hypothesis that the plumbing systems of two ~350°C hydrothermal vents (Escargot and Diva) are not interconnected in the shallow subsurface. Data utilized were from the Ocean Observatories Initiative – Regional Cabled Array (OOI-RCA) underwater observatory and Axial Seamount Earthquake Catalog. These allowed for examination of phase separation and perturbations occurring in each vent. The RCA Instruments utilized were two sensors that stream live temperature and resistivity (converted to chlorinity/conductivity) measurements from the volcano 300 miles offshore. These data, in addition to pressure data from a Bottom Pressure-Tilt sensor (BOTPT) and the Axial Seamount Earthquake catalog are being analyzed with Python to correlate earthquakes to temperature and chlorinity/conductivity and examine lunar-driven tides. Five statistically significant perturbations/events were documented and analyzed. Findings from an additional perturbation showed the occurrence of possible brine release from the subseafloor due to heightened inflation from the magma chamber. This work helped inform on process linkages leading up to an eruption and the sequestration of subsurface brines and their possible release post eruption into the overlying ocean with impacts on novel brine and metal tolerant organisms in these extreme environments. 

Methane is one of the most attractive targets for controlling near-term climate change due to its short lifespan and high potency (34 times that of CO₂). Methanotrophs are bacteria that can consume methane and convert it into CO₂ and biomass. There is growing interest in using these bacteria to mitigate greenhouse gas emissions from sources such as landfills, agricultural feedlots, and abandoned coal mines. However, a key challenge is that to achieve large scale methane sequestration, as well as economic viability of deploying these in the field, we have to significantly improve the growth of methanotrophs at low concentrations of methane. Regulatory genes play an important role in determining how bacteria allocate energy. By deleting specific regulatory genes and measuring the growth rate of these mutants under low methane conditions, we can assess their importance in helping the bacteria survive and thrive in nutrient-limited environments. Using this approach, we can also replicate mutations that have naturally emerged in strains cultivated for over a year under low methane conditions. This allows us to confirm whether these mutations provide a growth advantage. By identifying and testing key genes involved in low-methane growth, we are guiding efforts to engineer a more efficient and resilient strain for real-world applications.

According to the literature, consensually non-monogamous (CNM) individuals experience lower levels of jealousy than their monogamous counterparts (Conley et al. 2017; Edlund et al. 2022); however, scales commonly used to evaluate jealousy were created using a mononormative lens that assumes dyadism. As extradyadic sexual and emotional relationships are permissible in CNM configurations, we theorize that the current scales used to evaluate this population are not properly capturing the experiences of CNM individuals. To test this, we have modified scale items to target the unique relational experiences of this population. CNM and monogamous participants will complete the study online and will be recruited from the crowdsource platform, Prolific, and CNM social media groups. Participants will answer a series of questions to tap into jealousy across a range of experiences, including original and CNM modified questions. In addition, to assess the downstream consequences of jealousy often studied by relationship researchers, participants will answer a series of questions assessing relationship satisfaction, trust, and well-being. Participants will also provide open-ended responses to questions asking about their experiences with jealousy to better understand CNM experiences that we may not fully capture quantitatively. We predict that CNM individuals will indeed experience lower levels of jealousy commonly experienced in monogamous relationships (as found in previous work; Conley et al. 2017) compared to monogamous individuals; however, they will be more likely to experience jealousy on questions that better capture relationship dynamics in CNM relationships. We will be presenting preliminary results; implications of this work and future directions will be discussed.

How do state policies in abusive litigation cases within domestic violence law impact state-wide case outcomes? Through this research, I investigate how state legal protections affect case outcomes for defendants in abusive litigation cases within domestic violence law. Abusive litigation, a form of coercive control, allows abusers to exploit the legal system to intimidate and financially drain their victims, perpetuating harm even after separation. While domestic violence laws addressing physical and emotional abuse are well established, their impacts are well understood. In contrast, legal protections against abusive litigation are less common, and little systematic research has explored their effectiveness. In this study, I examine how varying state-level policies—such as vexatious litigant statutes, protective order-linked restrictions, and financial remedies—shape outcomes like dismissal rates, compliance with court orders, and survivor access to justice. By analyzing state-specific legal frameworks and state-wide case data, I aim to demonstrate that robust protections significantly enhance judicial efficiency and equity for defendants. My findings will provide critical insights into the intersection of domestic violence law and procedural justice, offering evidence-based recommendations for policy reform. 

Robotic movement between waypoints—specific points a robot must travel to—is often perceived as stiff and choppy. This is primarily because paths between these points are typically treated as straight lines. A more effective solution for smoother robotic motion involves forming polynomial curves composed of points–or re-discretizing points–rather than linear segments. The process begins by calculating the diameter of the robot’s orbit, which is determined by computing the maximum distance between any two points. With the orbit dimensions defined, a polynomial trajectory can be fitted to the points and constrained within the robotic arm’s circumference, resulting in a smoother and more fluid movement pattern. The use of this approach of spline trajectories as compared to straight line segments will be demonstrated for a robotic application being used to emulate spacecraft motion for relative proximity operation.

Girls in Afghanistan have been denied their rights numerous times in history, with restrictions on clothing, work, movement, education, and more. In this project, I explore the persistence of Afghan girls' fight for freedom through underground education and provide a timeline reflecting work on the underground education system. This opens the discussion on what more can be done by powerful global organizations in the context of ever decreasing rights for Afghan women brought upon the events of the Taliban takeover in 2021. My research highlights the brave and selfless Afghans who have committed themselves to empower Afghan girls through underground education by hearing their stories. The goal here is to counteract the continuous turn of limitations on Afghan women's rights that are holding back prosperity in Afghanistan. This examination of underground education and the people who make it possible paves the way for positive intervention. This research will primarily be based on qualitative data and some data visualization.

Nucleotides are essential for diverse cellular functions, from DNA synthesis to signaling pathways. Inosine 5’ monophosphate dehydrogenase (IMPDH) is a highly conserved regulatory enzyme in the de novo pathway for guanine nucleotide synthesis. Humans have two isoforms of IMPDH, and both are highly regulated to maintain appropriate levels of purine nucleotides required by the cell. Mutations in IMPDH2 have recently been linked to dystonia, a neurological disorder. Through collaborations with clinicians, this work examines emerging mutations in IMPDH2 that have been identified in patients (ages 2-12) with neuromuscular symptoms such as hypotonia, developmental delay and impaired motor skills. All of the disease-causing mutations are located in or nearby the regulatory domain of the enzyme, desensitizing it to normal feedback inhibition by the downstream product GTP, and causing the enzyme to be hyperactive. In this research project, I am assaying these IMPDH2 mutants in the presence of potential IMPDH2 inhibitors to identify small molecules that will inhibit the hyperactive mutants. I am testing six small molecules, four of which are natural compounds derived from traditional Chinese medicine. The other two are mycophenolic acid (MPA) and ribavirin (RBV) which are previously established IMPDH inhibitors used for immunosuppression and hepatitis. I am also using electron microscopy to understand the effects of these inhibitors on the structure of IMPDH2. My preliminary data shows that MPA and RBV exhibit inhibitory activity on the disease mutants. I have also characterized new disease mutants as collaborators have connected with us. This led to the discovery of a new mutant that is hypersensitive to GTP inhibition, making it the only mutant that has behaved differently. I anticipate that the other small molecules will inhibit but not as strongly as RBV and MPA. The long-term goal of this work is to identify drug candidates for treating IMPDH2-related disorders.

This research focuses on improving speech understanding for individuals with hearing loss caused by a gene mutation affecting the stereocilin protein (STRC). The STRC mutation, which impacts the outer hair cells in the cochlea, is the second most common genetic cause of inherited hearing loss, affecting approximately 14.36% of individuals with mild to moderate hearing loss. Although this mutation doesn’t cause profound deafness, it significantly impairs the ability to distinguish speech, especially in noisy environments. The project proposes the use of spectral contrast enhancement (SCE), a signal processing algorithm that sharpens the auditory spectrum to improve speech clarity. Previous studies have shown that the SCE algorithm benefits cochlear implant users with poor spectral resolution, and this research adapts the algorithm specifically for those with STRC-related hearing loss. By enhancing spectral content, the algorithm helps make speech more intelligible in complex listening situations, such as background noise. I am conducting a behavioral evaluation with normal-hearing participants, simulating STRC-related hearing loss via the online platform Gorilla. The experiment measures hearing thresholds, word recognition with and without the SCE algorithm, and speech clarity ratings to assess the algorithm's efficacy. With the help of Dr. Yi Shen, I designed the experiment and created the user interface for the test. The current step involves adding more words into the SCE test for comparison with and without the algorithm, allowing for a comprehensive evaluation of the algorithm's impact on speech recognition and clarity. This work represents a significant step forward in audiology by applying precision medicine to hearing loss treatment. It aims to provide a tailored, evidence-based solution for individuals with STRC mutations, improving their ability to communicate in everyday settings and enhancing their overall quality of life.

The ecosystem of microbes found in the gut, or the gut microbiota, plays a vital role in host health, influencing the immune, digestive, and central nervous systems. Research suggests that the microbiome may be linked with the development of neuropsychiatric disorders, presenting the possibility that altering the microbiome could influence the risk of these conditions. Recent research has explored this link within the context of Parkinson’s Disease (PD), a neurodegenerative disorder primarily known for its effects on motor control. PD patients often suffer from chronic constipation for years prior to diagnosis. Although the mechanisms of this gut-brain relationship are still unknown, many studies have highlighted the potential involvement of the gut microbiome in the development of PD. I explored the specifics of this relationship by developing a metabolic model trained on metagenomic data from PD case-control studies, using a microbial community-scale metabolic modeling (MCMM) approach. MCMMs may provide detailed mechanistic insights into the gut-associated etiology of PD, potentially allowing for the development of preventative therapies that prevent the onset of PD, which could revolutionize our current system of retroactive treatment of the established disease.

Diet is one of the most significant contributors to an organism’s morphology, as without morphological features to acquire food the organism will cease to live. Previous studies have quantified these morphological features in toothed taxa using Rotated Orientation Patch Count (OPCr) but not in edentulous taxa. Previously, we obtained OPCr from several turtle species using photogrammetry, created 3D models with Slicer, edited them down to just the triturating surface in MeshLab, and ran statistical analysis in R. Specifically, I worked on the unique, endangered turtle species Carettochelys insculpta (n=6) using CT scans obtained from MorphoSource to add to our photogrammetry data. However, the OPCr values obtained from these meshes discarded more surface area and were significantly lower than the meshes made from photogrammetry. To increase the surface area counted in the OPCr and potentially get results more comparable to the photogrammetry meshes we experimented with decreasing the percentage of patches discarded during analysis in R from 1% to 0.1% and tried smoothing the meshes in Slicer using a factors of 0.3, 0.5, and 0.7. A simple T-test was used to determine significant differences. To increase the number of available specimens and compare turtle species with different diets – durophagous and omnivorous respectively – Malaclemys terrapin specimens (n=5) were used in addition to the Carettochelys insculpta specimens. We expect to find increased surface area and higher OPCr values when increasing the percentage of patches discarded from 1% to 0.1%. We also expect that smoothing will increase the amount of surface area counted at both 1% and 0.1%. As a result of this study, we hope to create a better method for processing CT scans for morphological analysis of the triturating surfaces of turtles, and to develop a methodology for determining diet in any edentulous organism.

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

The meniscus is a fibrocartilaginous tissue that sits in the knee and acts as a stabilizer and shock absorber. Meniscus tears are a prevalent injury among athletes in contact sports. Severe tears often do not heal, even with surgical intervention and synthetic replacements. Our lab seeks to develop treatments that encourage functional regeneration of the original cartilage-like tissue. A critical initial step toward this goal is understanding the specific cell types within the meniscus and the specific extracellular matrix (ECM) proteins that these cells produce.  Our ultimate goal is to find the cells that can best regenerate the damaged matrix after injury. My project entails comparing NIH/3T3 cells, a well researched immortalized mouse fibroblast cell line, to the cells of interest: human meniscal fibrochondrocytes (MFCs), the predominant ECM-synthesizing cells within the meniscus. I am comparing the expression of known and newly-identified ECM protein markers at different stages of in vitro cellular growth via fluorescent antibody staining and confocal microscopy. These images can be compared using analysis tools like ImageJ to quantify the amount and localization of matrix protein expression. I will use relevant quantifications, including  the percentage of total cells expressing each protein and the percentage of surface area covered by each protein. 3T3 cells are far more robust and resilient than MFCs, they replicate more readily, and I hypothesize that they will produce a greater quantity of ECM in a given timeframe. However, as both cell lines are fibroblasts, I expect the localization and percentage of cells expressing each protein to be similar. Comparing the expression and localization of ECM proteins across these two different cell types allows us to better characterize MFCs in a robust way, contributing a novel functional characterization to the literature.

Clinical ventilation methods - where a patient’s breathing is supported by a cannula, a mask, or in severe cases, tracheal intubation – are often used to support patients in ICUs (intensive care units). Given the high risks associated with intubation, a key question is whether a patient's level of care can be de-escalated. This question is crucial in the context of newborn children (or neonates) who are especially fragile.  To address this question, we developed machine learning models to predict ventilatory support outcomes in neonates. Using a multi-center dataset of 6,538 neonates from ICUs (Intensive Care Units) across 121 Indian cities, we extracted time-based snapshots of each patient’s clinical status at 6-hour, 12-hour, and 24-hour intervals. For each snapshot, we utilized features related to vitals (heart rate (HR), respiratory rate (RR), etc.), demographics (e.g., highest HR, highest RR, etc.), and ventilation states (e.g., room air, nasal cannula, noninvasive ventilation, intubation). We trained Random Forest models, with hyper-parameters optimized via 5-fold cross-validation, using a 70-30 train-test split, to predict three outcomes: (1) mortality, (2) escalation of ventilatory support (“step-up”), and (3) successful discharge. Model performance was evaluated using the area under the receiver-operating-characteristic curve (AUROC). Predicting at 6, 12, and 24 hrs, the best models achieved out-sample AUROC values of 0.79–0.87 for mortality, 0.81–0.85 for step-up, and 0.68–0.70 for discharge. The most predictive variables for mortality, escalation, and safe discharge were the highest past FIO2, and the presence of a cannula for escalation and safe discharge, respectively. These findings suggest that machine learning can provide early warnings of clinical deterioration, reducing unnecessary intubations and improving neonatal respiratory care. By enhancing risk stratification, particularly in resource-limited settings, this approach may guide more timely and judicious use of tracheal intubation and contribute to improved neonatal outcomes.

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

Despite the widespread use of general anesthesia, our understanding of mechanisms by which anesthetics and analgesics induce unconsciousness remains limited. This study used a transgenic mouse model (FosTRAP2) to investigate neural circuits that are active during isoflurane-induced anesthesia. FosTRAP2 mice were retro-orbitally injected with an AAV-PHP.eB virus expressing Cre-conditional DREADDs (designer receptors engineered to be activated by designer drugs), which was followed by general anesthesia exposure, where 4-hydroxytamoxifen was injected to chemogenetically label isoflurane-activated cells brain-wide with DREADDs. We subsequently implanted the mice with wireless mechano-acoustic (MA) devices to record peripheral physiologic data such as heart rate, respiratory rate, temperature, and physical activity. To determine the functional impact of isoflurane-activated circuits, chemogenetic reactivation was induced via clozapine-N-oxide (CNO) injection, with concurrent video recording for pose estimation with Social LEAP Estimates Animal Poses (SLEAP), and behavior classification with Simple Behavioral Analysis (SimBA). Combining both physiologic data and machine learning provided us with an experiment pipeline that allowed us to better study brainwide isoflurane-activated neural ensembles. We found that reactivation of these circuits led to a significant reduction in heart rate, body temperature, physical activity, accompanied by a reduction in typical active behaviors, such as grooming and rearing. By gaining a deeper understanding of how general anesthetics alter neural circuits, we hope to uncover the complex relationships between brain activity and consciousness, with important implications for improving anesthetic practices and developing novel sedatives or analgesics in the future.

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

As the sensitivity and capabilities of modern synchrotron facilities continue to develop, so does the field of computational material sciences in an effort to meet the demand for analysis of new properties in various systems. 3d transition metals are of special interest due to their wide range of conductive and optical properties. Traditionally, local bonding environments are characterized in terms of group symmetries, but this has limitations in complex systems. Linearly polarized emission of x-rays from these 3d materials can provide information about local anisotropy, and valence-to-core (VtC) x-ray emission spectroscopy (XES) is especially sensitive to oxidation state, ligand environment, and bond length. The purpose of this project is to use local geometric and electronic information to formulate a measure of local anisotropy. This metric is evaluated against real-space Green's function calculations of linearly polarized XES, where we apply a supervised machine learning approach trained on this metric to predict differences in the polarized spectral shapes. Polarized spectroscopy techniques are critical for a wide range of applications including the development of microelectronics, nanostructure characterization, analyzing anisotropy within quantum dots, and studying the polarization sensitivity of non-linear optics. An accurate formulation of this continuous anisotropy parameter will provide researchers with quick and inexpensive computational insight. For the development of new functional materials, this metric can be used for searching databases efficiently, allowing researchers to select the candidates that will provide a more ideal signal of any polarization dependent properties.

The early 20th-century publishing landscape in England remains largely undocumented in a structured dataset, despite the availability of bibliographic records in The English Catalogue of Books. Issued annually by Publishers’ Circular, these catalogs document books, laws, and government reports published in the United Kingdom from the mid-19th to early 20th century. Digitized versions, made available through the HathiTrust digital library, contain Optical Character Recognition (OCR)-generated text that often includes errors and inconsistencies, making automated data extraction challenging. Our project focused on refining and formatting bibliographic data from these files by developing tailored regular expressions and Python-based parsing techniques for each catalog year. This work was a necessary step toward the eventual creation of an open-access dataset covering books published between 1900 and 1928. In Summer 2024, we refined parsing methods to identify and correct inconsistencies in the raw OCR text for catalog years 1902–1922, building on prior work. These improvements increased the number of extracted publication entries by 15.4% across the catalog collection, adding approximately 16,500 additional book records. The structured data enabled content analysis of bibliographic trends, including authorship patterns, publisher prominence, and thematic categorization. Using SQL-based keyword searches, we examined colonial publication networks, identifying the prevalence of colonial discourse and associated geographical trends. Additionally, we parsed Hebrew-language publications to analyze Jewish authorship and the locations of Hebrew book publishing in early 20th-century England. By structuring historical bibliographic data, this project provides a valuable resource for researchers studying literary trends, publishing industry shifts, and broader cultural patterns. Our work contributes to ongoing efforts to digitize The English Catalogue of Books and deepen insights into the evolution of the British literary landscape.

In 2020 Seattle experienced a divide in support behind three separate movements, Black Lives Matter, Stop Asian Hate, and The Kisaan Morcha/Farmers Protest. These three movements represent a key identity of three minorities within the region, Black, Japanese and Desi-Americans. The division between the three has long-standing roots within 20th century Seattle, and is full of moments of allyship and division. Each group has dealt with White racism and division in their own ways, but it's the way these narratives have fed into the societies that effects the relationship we see today. My research will focus on three time frames of Seattle History: Early 1900's (1910-1920s), Mid 1900's (1930s - 1950s), and Late 1900s (1960s - 1990s). Each of these sections represent a different timeframe for Seattleites: Settlement and the formation of communities, Civil Rights Era, and Modern implications/results. Each section will conclude of three main subsections that creates the basis of my argument. They will be based on: discrimination in the Workplace, Social Identity, and Economic Mobility. What I will be arguing is while each community has dealt with their own levels of discrimination and set-backs, Black Seattleites have constantly dealt with the brunt of the racial actions from White Seattleites, and have reaped the least amount of benefits compared to the other two communities. 

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

Western media has perpetuated society’s perspective of the nursing role through a sexual lens rather than a professional. Nurses face high levels of sexual harassment and violence, with some studies showing up to 80% of nurses experiencing some form of sexual harassment in the workplace at some point in their career. The relationship between the media’s sexualization of nurses has led to an increase in harassment and violence in the profession, as well as proliferating the stereotype of ‘sexy nurses.’ In this literature review, I examine both the media and cultural perception of the nurse and the data surrounding sexual harassment and violence of nurses in the workplace. We know that workplace harassment can lead to increased rates of burnout and staff turnover, if the image of nursing is changed then we can create a healthier work environment with higher levels of job satisfaction and safety.

In this experiment we will look into the relationship between different mushroom species' toxicity and copper concentrations. Due to their wide variety of biochemical characteristics, mushrooms can be either extremely toxic or edible. Mushrooms contain different amounts of copper, an essential trace element that may affect a mushroom's toxicity. Using Atomic Absorption Spectroscopy, we evaluated the amount of copper of several mushrooms. Our early results show that mushrooms with higher copper concentration tend to be more toxic. This shows that copper content may be a useful marker of the toxicity of mushrooms, giving foragers important information and assisting in the development of food safety protocols. Our research is to be continued as we’re going to test on more mushrooms to get a better understanding on how copper could affect the production of toxic compounds.

The rising impacts of climate change driven by fossil fuel consumption highlight the need for sustainable alternative energy sources, such as biodiesel. Biodiesel is a biodegradable diesel fuel made primarily from vegetable oil or animal fats. Currently, biodiesel production predominantly relies on vegetable oils, which contribute to over 85% of production costs and raise concerns regarding higher consumer costs and environmental sustainability. To mitigate this issue, this study examines the potential of using animal waste, specifically beef tallow,  as an alternative feedstock for biodiesel production. The United States produces 20% of beef in the world, leaving large amounts of waste that go unutilized. Instead of relying on plants and crops for biodiesel, which requires large-scale cultivation of crops like soybean and palm that contribute to increased greenhouse gas emissions, beef tallow offers a resourceful alternative due to its widespread availability. The production of biodiesel from vegetable oil and beef tallow is done through transesterification with the catalysts NaOH and KOH to facilitate the conversion of the fats to biodiesel. Upon synthesizing the biodiesel, a soda can calorimeter is used to analyze how much of the biodiesel is able to be burned and the amount of heat released from the reaction to determine the fuel value. The aim of this study is to evaluate the fuel value of beef tallow to determine its potential as a more viable alternative to vegetable oils for biodiesel production.

Sensorimotor adaptation is the ability of the brain to adjust future movements made by an individual in response to feedback signaling movement error. I am conducting an experiment using a virtual display system in order to manipulate visual feedback associated with arm movements when a subject reaches toward a target. My experiment consists of a baseline phase, followed by an adaptation phase, and finally, a de-adaptation phase. In the baseline phase, the cursor is aligned with the true movement of the sensor, in the adaptation phase, the position of the cursor is displaced by 30° counterclockwise relative to the true position of the sensor, in the de-adaptation phase, the cursor is aligned with the sensor again. Time can be a factor in how people learn motor skills, specifically time intervals between practice trials performed, also known as inter-trial-intervals (ITIs). I am conducting this visuomotor experiment with varying ITIs in between practice trials in the adaptation and de-adaptation phases with 20 human subjects. The subjects sit at the virtual display system strapped to an arm sled with their finger taped to an electromagnetic sensor which controls a cursor and reach towards a target. The subjects are divided into four groups, 7-second ITI only for adaptation, 7-second ITI only for de-adaptation, 7-second ITI in both adaptation and de-adaptation, and no 7-second ITI in in either adaptation or de-adaptation. I will collect data on each subject's response, which is the reach direction relative to the target to see if the amount of adaptation in reach direction is enhanced for groups practicing with the 7-second ITI.  

While some species cannot persist in urban areas, coyotes (Canis latrans) thrive in cities in part thanks to their varied diet and creative scavenging. Urban coyotes consume more anthropogenic foods and have more diverse diets than wild populations, and the quality of the anthropogenic foods they consume varies with the landscape of the city. In addition, consumption of particular anthropogenic foods can bring coyotes into conflict with resident human populations. What are coyotes eating in Seattle, and what does their diet composition say about the specific urban environments they inhabit? DNA metabarcoding, a technique used to genetically identify the species present in a sample, provided an initial idea of coyote diet composition. However, the metabarcoding data lacks resolution for plants, invertebrates, and some anthropogenic foods. This study investigates the diet composition of Seattle’s coyotes through traditional scat analysis, building on previous metabarcoding work to identify key diet items. Traditional analysis allows for better identification of plant and invertebrate species via the identification of hard-items such as bones, exoskeletons and seeds, and can provide additional resolution where metabarcoding primers lack specificity. In particular, traditional analysis contextualizes the dietary role of chicken— the presence or absence of physical items such as feathers clarifies if coyotes are eating domestic chickens or anthropogenic foods. I estimate the percent composition of each item in a given sample and compare these results to the metabarcoding data in order to compare the strengths of traditional and genetic techniques for diet analysis. My anticipated results provide valuable information regarding the dietary role of invertebrates, the plants coyotes consume and disperse, and if coyotes are consuming domestic chickens— highlighting the advantages of traditional analysis used in conjunction with metabarcoding. These results will help refine the methods of omnivore diet research and inform action to prevent human-wildlife conflict.

Autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) are neurodevelopmental conditions that are known to co-occur with decreased sleep quality and quantity. ASD is characterized by social communication differences and restricted, repetitive behaviors and interests.  ADHD is characterized by inattention and/or hyperactivity/impulsivity. Previous research found higher instances of sleep disruptions within adults with ADHD as well as autistic populations compared to neurotypical adults. However, quantitative data around the associations between ASD and sleep disruptions is sparse.  This leads to our research question which is, how does sleep disruption affect autistic, autistic + ADHD adult’s sleep quality and quantity compared to neurotypical adults? We hypothesize that ASD+ADHD and ASD adults have experience higher sleep disruptions (fewer hours of sleep and lower quality) compared to non-autistic adults. Participants included autistic adults (n=66), autistic adults with ADHD (n=39), and non-autistic adults (n=221) enrolled in the NIH-funded COBRA and BEAM studies, which investigated how the brain processes sensory and visual information.  Autism diagnoses were confirmed using standard assessments (such as Autism Diagnostic Observation Schedule, 2nd Edition, Autism Quotient) by clinicians.  Participants self-reported ADHD diagnoses, sleep quantity (hours per night on weekdays, hours per night on weekends), and sleep quality (over the past week on a 4-point Likert scale). An ANOVA will be used to compare sleep quality and quantity between diagnostic groups. Understanding neurodivergent populations’ sleep quality and quantity helps improve public health communication around sleep health, which is particularly important population health issue given the link between sleep, mental and physical health. Finally, identifying populations most in need of sleep interventions helps us address the increased number of adults with sleep disturbance and disorders.

Alzheimer's Disease (AD) is a neurodegenerative disorder with classical behavioral and pathophysiological presentations such as memory impairment, cerebral vascular alterations, and most notably, the accumulation of amyloid-beta plaques and tau fibers in humans. While these symptoms are hallmark signs of AD, the severity of these symptoms differs for individual patients. As such, clinicians face challenges in misdiagnosing or giving a late diagnosis using a few of these AD markers. My research project aims to characterize AD through 3 concurrent modalities with the goal of early diagnosis and better quality of care for AD patients: [1] motor activity using a motion capture chamber, [2] spatial memory and learning using Barnes Maze Trials, and [3] real-time cerebral hemodynamics with ultrafast contrast-enhanced ultrasound (CEUS) in a rat model of AD. This project utilized control wild-type (WT; n=3) and transgenic (AD; n=3) rats. We hypothesize that the WT and AD rats will express similar movement and cognitive metrics measured until they are 12 months old, whereas the AD rats show a gradual motor decline and cognitive impairment. The 12-month metric is used as a benchmark set by prior research using this rat model. Intravital CEUS imaging will be conducted at 16-19 months old. We expect CEUS imaging will reveal that cerebral blood flow in the parietal and hippocampal regions of the brain is reduced, and microvascular response is impaired in AD rats. The expected outcome of all 3 experiments is that there is a strong correlation between motor and cognitive decline with impaired hemodynamics in AD rats. Results from our study will allow for systematically chronologizing the progression of AD in greater detail than before which allows for greater diagnostic ability.  

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

The mandible plays a central role in the mammalian skull as it is responsible for feeding. Various selective pressures, such as diet, habitat, and climate shape mandibular morphology across mammals, and in this study, we investigated their impact on mandibular evolution of primates and carnivores. This relationship will allow us to understand how environmental factors collectively impact the evolution of various species. In our previous research, we found that diet accounts for only 21% of the variation in mandibular morphology of primates. In this study, we extended our investigation to additional factors such as climate and habitat. We hypothesized that habitat and climate will affect mandibular morphology by driving adaptations in jaw structures to meet various functional demands of different environmental conditions. We tested these hypotheses by analyzing a database of 3D scans of primate and carnivoran mandibles from natural history museums. Mandibular shape and size were quantified using geometric morphometrics of the digitized 3D models. Habitat and dietary data were sourced from the carnivoran and primate literature, and climate data was obtained from WorldClim for species with matching habitat and diet information.  We used regressions and ANOVAs to evaluate the relationships between mandibular morphology, diet, habitat, and climate. Our research may be helpful for future primate and mammal studies focusing on the selective pressures on the evolution of the mandible.

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

The LISA (Laser Interferometer Space Antenna) mission is a joint NASA and ESA venture that will measure gravitational waves at frequencies that earth-based antennas cannot capture, such as waves caused by EMRIs (Extreme Mass Ratio Inspirals). Before LISA is launched in 2035, it is paramount to learn how to analyze the mission data. My research identifies successful MCMC (Markov Chain Monte Carlo) parameter estimation techniques for EMRI signal data. Using simulated LISA data and exploring a range of system parameters in Python, I implemented different MCMC parameter estimation techniques (number of walkers, parallel tempering, etc.) on different kinds of EMRI signals and measured the match between the injected and recovered parameters, as well as examined the likelihood and corner plots to optimize search strategies. With these preliminary results, researchers can better incorporate MCMC parameter estimation techniques for EMRIs into their analysis as they receive data not only from single sources but many overlapping sources at once to determine a "global fit", which recovers likely parameters for all sources detected. Then, general relativity can be tested as any deviations from expected behavior could indicate gravity acts differently than previously predicted. Furthermore, learning about the population of supermassive black holes via their recovered parameters provides insight to their relationship to galaxy evolution.

Gynogenesis is an asexual reproduction strategy where sperm is necessary for fertilization, but the resultant offspring have no paternal DNA and two maternal sets of chromosomes. This strange reproductive strategy has never been observed before in nematodes (round worms), until a few years ago when a previous student at Ailion Lab observed the phenomenon when investigating the hybrid offspring of two species of Caenorhabditis roundworms; C.Becei and C. Nouraguensis. On their own, neither of these species exhibit asexual reproduction. Furthermore, C. Nouraguensis females normally produce haploid eggs, but when cross bred with C. Becei, they began to produce almost only diploid eggs. It is known that asexuality has arisen from previously sexually reproducing species, but the exact mechanisms of this evolution are unknown. This research project uses CRISPR techniques to attach fluorescent proteins to key structures involved in meiosis, which can then be imaged to reveal any irregularities which could explain the production of diploid eggs instead of haploid. The main goal is to understand the cellular mechanisms which facilitate such a dramatic change in reproductive strategy. 

Lepidosauria is a clade of reptiles including Rhyncocephalia and Squamata, constituting much of the diversity of living reptiles. Squamates include lizards and snakes, and are the most species-rich group of lepidosaurs. Rhyncocephalians were more diverse and widespread in the Mesozoic Era, but today are represented by a single living species, the tuatara of New Zealand. Lepidosaurs first evolve in the Triassic Period, making their fossil record from this interval critical to understanding the evolutionary origins this group. New lepidosaur fossil material from Petrified Forest National Park has been recovered from screenwashing sediment from the Kaye Quarry, a fossil bearing locality within the Sonsela Member of the Upper Triassic Chinle Formation. Three mandibles of unknown taxonomic affinity from the Kaye Quarry have been selected for anatomical description and phylogenetic analysis. All three mandibles display labiolingually compressed, recurved teeth, along the majority of the dentary. Two dentaries display a larger conical tooth, protruding dorsally from the anterior end of the mandible. Other mandibles recovered from the Chinle Formation display similar dental anatomy, indicating these specimens belong to the clade Rhynchocephalia. There are currently no lepidosaur fossils known from the Sonsela Member of the Chinle Formation. Sectioning and computed tomography (CT) scanning will be used to create detailed three-dimensional images of the mandibles for the basis of anatomical description and phylogenetic analysis. CT scanning hosts the potential for internal morphology including tooth implantation and neurovasculature.

A subset of voltage-gated potassium channels, Kv2s, are responsible for the majority of the perisomatic delayed rectifier current in pyramidal neurons of the neocortex. Mutations in these ion channels and their associated proteins cause developmental epilepsy, but the cellular mechanisms underlying this remain less clear. Previously, we have shown that the two members of the Kv2 family of voltage-gated potassium channel α-subunits, Kv2.1 and Kv2.2, are expressed differently depending upon the type of neuron in rodent primary sensory and motor neocortex. There are two major subclasses of layer 5 (L5) pyramidal neurons in the neocortex, extratelencephalic (ET) and intratelencephalic (IT) neurons, that are distinguished by their projection targets and laminar distribution. ET neurons, enriched in L5b of the neocortex, send projections to subcortical structures, whereas IT neurons, primarily located in L5a, project within the telencephalon. In rodents, ET neurons are enriched in Kv2.1, but not Kv2.2. Here, we tested whether these features extend to the association cortices of primates, particularly the prefrontal cortex and temporal cortex, which are essential for various higher-order cognitive functions, including recognition, attention, and planning. Using immunohistochemistry against Kv2.1 and Kv2.2, we showed that these subunits have distinct laminar distributions in the dorsolateral prefrontal cortex (dlPFC) and temporal cortex (TCx). Kv2.1 was predominantly expressed in L5b, whereas Kv2.2 was more concentrated in layer 2 (L2) and L5a. Using a tarantula toxin, Guanxitoxin (GxTx), to block the Kv2-mediated current, we found that, similar to what we observed previously in rodents, the role of Kv2 channels differs depending on the L5 neuron type. GxTx makes L5 ET neurons fire repetitive bursts, whereas GxTx makes L5 IT neurons less excitable. Together, these results support distinct roles for Kv2.1 and Kv2.2 in regulating excitability across ET and IT neurons in the association cortex of the macaque. 

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

American crows (Corvus brachyrynchos) are intelligent birds that use a diverse range of vocalizations to communicate in varying behavioral contexts. We aimed to interpret these calls objectively to broaden our understanding of how crows use their vocalizations to communicate, and how specific acoustic factors change relative to the behavioral contexts in which they are used. To do this, we recorded and analyzed vocalizations of crows in two behavioral contexts: pre-roosting and mobbing. Pre-roosting is a routine behavior, occurring before sunset, where crows group together before traveling to their roost sites. Mobbing is a situational behavior where groups of crows harass a predator with approaches and calls to repel it. In this study, we initiated mobbing by playing the audio of a distress call (made by a crow when restrained by a predator) and displaying a model owl. Using a bioacoustics analysis program called Raven Pro, we extracted acoustic variables from our audio recordings, such as frequency, duration, amplitude, etc. Using these variables, we created machine learning models to differentiate pre-roost and mobbing recordings. Further analysis showed frequency-related variables were crucial during mobbing behavior. To clarify how frequency/pitch is related to mobbing, we modified the frequency of a typical crow call to match the peak frequency of a distress call and vice versa. We then played these modified calls back to wild crows and monitored their responses. Our results showed altering call frequency significantly influenced mobbing behavior. Lowering the pitch of distress calls to decreased mobbing responses. Conversely, increasing the pitch of a typical call did not induce mobbing behavior comparable to a distress call. These findings demonstrate acoustic variation in crow vocalizations is context-dependent and thereby expands our knowledge of crow social communication.

This research examines the barriers to aging in place for older adults in Seattle and explores how community-focused housing solutions can address these challenges to support long-term stability and well-being. Situated within the context of affordable housing policy and aging equity, the study specifically addresses the displacement pressures influencing the housing needs of older adults in Seattle. The project investigates strategies for scaling community-based housing solutions to enhance housing stability and facilitate aging in place. The analysis integrates stakeholder interviews and qualitative conceptual content analysis of the collected data. Expected findings include policies that increase funding for senior-focused affordable housing, streamline review and application processes, and expand innovative housing strategies. The final report will present scenario-based solutions and strategies for aging in place, offering actionable policy recommendations and insights on expanding community-based housing models to address the unique challenges faced by older adults in Seattle. This work is significant as it tackles housing stability and displacement issues for older adults, proposing sustainable community-focused housing solutions to enhance equity and community resilience.

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

Morphological control in nanocrystal synthesis is crucial for tailoring material properties in magnetic, thermoelectric, catalytic, and renewable energy applications. In this study, we explore the synthesis of anisotropic single-phase Cu2Se nanorods (NRs) via cation exchange from CdSe NRs. Transmission electron microscopy and X-ray diffraction were employed to characterize the resulting nanocrystals. The synthesis of Cu2Se NRs remains challenging due to limited Se precursors suitable for shape control and identifying the kinetic conditions that lead to morphological selectivity. We have since shifted our focus to reaction conditions required to perform Cd-to-Cu cation exchange. Our work aims to refine synthetic parameters, including solvent compositions, hot injection temperatures, and concentration of Cd precursor to establish a reliable pathway for monodispersed nanorod formation and demonstrate precise morphological control. These insights will contribute to the Cossairt Lab’s broader efforts to advance nanoparticle synthesis for classical and quantum light emission, catalysis, renewable energy, and magnetooptical technologies.

Patient reported outcomes (PROs) trackers have been developed into digital health applications used by patients to self-report symptoms. They allow for improved patient-provider communication, symptoms and quality of life outcomes. The Electronic Self-Assessment and Care Tool (eSAC) is one such PRO tracker with personalized education that was adapted for patients with ovarian cancer. Past studies have validated and demonstrated the effectiveness of the eSAC precursor, ESRA-C, in patients with cancer. The purpose of this quality improvement project is to ascertain barriers to patient use of eSAC and address barriers via patient education. The project includes patients from the University of Washington Medical Center’s Gynecological Oncology ambulatory service. We will interview patients at the clinic to gather insights into their experience using the eSAC program using a script approved by the clinic nursing administration. We will also make phone calls to prompt and guide eSAC usage prior to in-person or telehealth clinic visits. Responses from patients will be noted to include patient’s reflections about eSAC and their perceived barriers and benefits to using the program. The expected outcome is to see an increase in the use of eSAC after student interventions and understand barriers of usage. Preliminary results have revealed varying levels of patient acceptance, with notable barriers being age, comfort with technology usage, and lack of provider review. Benefits have included ease of usage if they are able to access eSAC correctly. This project will help explore the feasibility of a digital PRO tracker and educational system with this patient population and assist in guiding future efforts of designing a system that can acceptably and effectively be implemented in clinical practice.

Young children are highly vulnerable to wildfire smoke, especially those in historically marginalized communities where environmental and health disparities persist. This research examines 2023 survey data on childcare facilities in different Home Owners' Loan Corporation (HOLC) zones—particularly Grade B (more desirable), Grade C (working-class), and Grade D (historically marginalized)—to prepare for and respond to wildfire smoke. Childcare providers in historically redlined areas (HOLC Grade D) are more affected by wildfire smoke compared to those in more desirable HOLC zones (Grades B and C). I conducted data cleaning and standardization, renaming columns, binary-coding responses, and categorizing each response by HOLC zone. I classified communication methods into media (e.g., phone, TV), person-to-person (e.g., parents, supervisors), and unknown/other. Wildfire response actions were grouped into behavioral changes (e.g., bringing children indoors), temporary physical changes (e.g., closing windows, air cleaners), and permanent modifications (e.g., installing air filtration systems). I structured the dataset in Python to analyze trends and generate visualizations, including pie charts, bar graphs, and tables, to explore response patterns across roles, facility types, and zones. Preliminary findings suggest disparities in preparedness and response strategies. Childcare providers in historically redlined areas reported higher levels of children affected by wildfire smoke exposure, both indoors and outdoors, compared to those in less marginalized zones. While media alerts were the most commonly reported information source, teachers relied more on “unknown” sources, highlighting gaps in communication. This research aims to understand smoke inhalation risks for young children, provide childcare settings with feasible risk management options, and influence policy strategies to make adaptation measures more accessible for vulnerable communities.

Previous studies have found a correlation between the complexity of an animal’s teeth and its diet. However, not all vertebrates have teeth, such as turtles, which is problematic because dental topographical analysis has not been completed on toothless—or, edentulous—animals. Regardless of whether a species has teeth, we can use the measurement OPCr (orientation patch count rotated) to quantify the complexity of a surface, and subsequently use that value to analyze species’ diet. OPCr calculates the number of separately oriented patches on a 3D surface. A higher OPCr value indicates a more complex topography. To obtain OPCr values, we edited CT scans of the turtle species Malaclemys terrapin in Slicer and MeshLab, then analyzed the resulting model using the R package molaR. From this, we obtained OPCr values. However, R struggles to analyze meshes at a higher resolution, so we use various downsampling filters in MeshLab to make the models usable in R. One such filter is Quadratic Edge Collapse Decimation (QECD). The algorithm behind QECD is QSLIM, which reduces the complexity of polygonal meshes by eliminating edges based on error metrics from quadratic formulations, but still preserves the original shape as much as possible. Currently, we downsample all meshes to just 10,000 faces before reading them into R. My role in this project is to determine whether we can reliably use higher resolution scans by altering the number of faces to be slightly higher at 15,000 and slightly lower at 5,000, then examining the impact of these resolutions on OPCr values. So far, our analysis shows that importing a higher resolution mesh tends to give higher OPCr values, and a lower resolution gives a lower OPCr value.

This study investigates the interactions between drag and grazing flow over a Helmholtz resonator array under varying resonance conditions, using three-dimensional Particle Image Velocimetry (3DPIV) in a subsonic wind tunnel. By adjusting the resonators’ natural frequencies, we examine how velocity fluctuations influence the local boundary layer in the vicinity of, and downstream from, the resonator orifices. Additionally, we evaluate the effects of resonance tuning on grazing flow to enhance our understanding of fluid–structure interactions in acoustic liner systems. These findings provide insights into drag modulation mechanisms and inform future steps in noise attenuation, aerodynamic efficiency, and both active and passive control strategies.

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

Ochratoxin-A (OTA) is a ubiquitous food contaminant linked to nephrotoxicity and carcinogenicity. Yet, its exposure risk and metabolic pathway in humans remain poorly understood. This research aims to investigate the intrinsic clearance of OTA in the human liver and to identify cytochrome P450 (CYP450) isozyme(s) responsible for its biotransformation. I employed a substrate depletion assay on OTA-treated human liver microsomes and used ultraviolet–visible spectroscopy to determine the kinetic parameters of clearance rates. To identify specific CYP450 isozyme(s) involved in metabolism, a parallel substrate depletion assay was conducted with recombinant CYP450 supersomes at defined intervals. Findings from this study reveal human susceptibility to OTA-induced toxicity and offers insight to our understanding to the hepatic metabolism of this widespread dietary toxin. Future research will explore human proximal-tubule specific OTA bioactivation, ultimately guiding regulatory decisions and public health interventions to reduce OTA-associated health risks.

Individuals with spinal cord injury (SCI) often experience reduced exercise capacity due to impaired cardiovascular control, which limits their participation in rehabilitation and daily activities. Although epidural spinal cord stimulation (eSCS) has demonstrated efficacy in restoring activity tolerance, its invasive nature and high cost hinder its widespread clinical adoption. To overcome these limitations, this research aims to develop a non-invasive, closed-loop transcutaneous spinal cord stimulation (tSCS) system that automatically adjusts stimulation levels based on real-time physiological signals. As a validation study for the hypothesis that exercise tolerance can be modulated using tSCS with activity dependent stimulation intensities, electrocardiogram and photoplethysmography data were collected from four SCI participants during exercise. I processed these cardiovascular signals using Fast Fourier Transform for heart rate variability (HRV) analysis in Python. I am also involved in developing a predictive machine learning model responsible for controlling tSCS intensity to improve exercise tolerance. It estimates exercise tolerance metrics, such as oxygen consumption volume, based on the HRV parameters. In the system, data are transmitted via Bluetooth Low Energy (BLE) protocols from physiological monitoring units to a processing unit, after on-board computation it then performs automatic adjustment of stimulation intensity. I have established a stable BLE connection within the system, and the final integrated system is anticipated to enhance rehabilitation outcomes by improving cardiovascular control during exercise and providing a clinically viable method to restore exercise capacity in individuals with SCI. Future studies will focus on optimizing algorithm efficiency for real-time performance and validating the system through clinical trials to further assess its impact on rehabilitation outcomes.