Wildfires in Western North America have become more frequent and intense in recent years. Wildfire smoke can cause adverse health impacts creating an urgent public health concern. This study compares wildfire smoke preparedness and response plans developed by jurisdictions and institutions in western North America, including counties, cities, states, provinces, and universities. We used qualitative content analysis methods to assess the characteristics of 20 wildfire smoke preparedness and response plans. The majority of the plans included strategies related to air quality monitoring, household-level exposure reduction, and risk communication. Wildfire smoke poses a bigger risk to susceptible and/or vulnerable populations, however, 25% of the plans did not include strategies related to targeted outreach for at-risk populations. Since wildfire smoke plans are a relatively new strategy within emergency response, a “gold” standard set of components has yet to be established, therefore,  significant variations of included plan components exist. To improve these plans, it is crucial to enhance targeted outreach programs for vulnerable populations, develop a standardized framework for preparedness, and integrate plans with existing public health frameworks. Additionally, training for first responders on health impacts and investing in air quality monitoring are essential. Future research should focus on evaluating the effectiveness of outreach strategies, conducting longitudinal health studies, and analyzing the economic impacts of wildfire smoke preparedness. By addressing these recommendations and pursuing further research, jurisdictions can enhance their wildfire smoke preparedness and response plans, ultimately protecting public health more effectively.

Little is known about how male and female Pieris rapae behave during territorial behaviors, making this project particularly significant. Through our previous experiment, we have uncovered intriguing insights into the unique behaviors exhibited by male P. rapae when interacting with pseudo-females (males in disguise). Our observations suggest a complex interplay between competitive instincts and courtship behaviors. Specifically, male Pieris rapae display distinct responses when encountering pseudo-females, indicating a potential recognition of the sex of the interacting butterfly. This recognition may trigger competitive behaviors like a territorial move if perceived as a rival male or foster a display of courtship if perceived as a potential mate. Additionally, we aim to study how female P. rapae interact with other females to determine if there are any behavioral differences in these interactions. By studying the intricacies of both male and female courtship and/or territorial behaviors in P. rapae, this project seeks a deeper understanding of the factors shaping mating systems and reproductive success in this species and beyond.

Post-Traumatic Stress Disorder (PTSD) is one of the most common mental disorders in the world. People with PTSD often have difficulty managing time or have witnessed a traumatic event in the past. PTSD is also associated with memory issues which are characterized by intrusive memories that can cause re-experience aspect of the traumatic event. Through the use of computational models, we aim to investigate the differences in memory retention in spaced vs massed practice presentations. We hypothesize that mass practice will lead to less accuracy in recognition and less intrusive thoughts during retention. Through recruiting healthy adult participants with no history of PTSD or other stress-related psychiatric disorders we get a base data avoiding discrepancies. Participants view visual stimuli as images, either neutral or triggering which are presented in pseudo-order and are asked to rate them based on their valence ranging from neutral to extremely negative. The images are presented under two conditions: mass and space presentation. For spaced presentation, different versions of the triggering image category are presented in no particular order with neutral and filler images in between. For massed presentation, all versions of the triggering image category are presented one after the other with no neutral or filler images in between. 24 hours after the initial presentation of the images, participants are tested on memory retention in the form of image recognition. Participants are asked about the difficulty of recalling the image and how often they think about the image. Having collected data during AUT 24, we were able to understand there is a correlation present between memory retention in mass and spaced recognition in terms of traumatic and non-traumatic events. By collecting data through WIN 25, we will have greater accuracy in terms of significant data.

Language mixing occurs when words and grammar from two languages combine in the same sentence, demonstrating how bilingual speakers creatively use their language skills. Understanding how bilingual children mix languages provides insight into their thinking and navigation between languages. While prior research has focused on noun mixing, fewer studies have examined verbs. Thus, this study aims to investigate how English-speaking bilingual children (ages 4-7) evaluate two verb-mixing strategies: direct insertion (using a verb directly from one language) and indirect insertion (changing the verb to match the grammar of the other language). Participants will be assigned to one of two conditions: one where both characters mix languages and another where only one character does. This allows us to examine how interlocutor context (the conversational partner's language use) and age influence children's judgments. Participants will be introduced to pairs of cartoon aliens having conversations and told that the aliens just arrived on Earth and are learning English; therefore, they may mix their own language with English words. After watching each conversation, children will rate how well the alien spoke using a scale of expressive faces. We hypothesize that children’s preferences for language mixing will be shaped by interlocutor context and age. We predict that younger children will rate direct insertion more positively, while older children will rate both strategies similarly. However, as older children may be more aware of social dynamics, they will rate strategies more negatively when only one character language mixes compared to both. This manipulation allows us to explore how children's developing social awareness influences their judgments of language mixing and expectations of conversational norms. These findings will provide new insights into how bilingual children think about and use their languages as they grow, as well as how language is tied to communication and social connections. 

Chiral molecule sensing has important biochemical applications for detection of disease, as well as cognitive and neurodegenerative disorders. Circular dichroism (CD) has emerged as a powerful spectroscopic tool for probing post-synthetic ligand exchanges of chiral molecules onto originally achiral quantum confined CdS morphologies, manifesting in chirality corresponding to the electronic transitions of the nanocrystals. In this work, we first describe making water soluble quantum dots (QDs) and nanorods (NRs) via ligand exchange with glycine. After this exchange, aqueous chiral thiol solutions are then titrated into glycine capped achiral CdS, and the optical properties are monitored via UV-vis, photo-luminescence (PL), and CD spectroscopies. Preliminary results show we can controllably produce measurable chirality equal to or exceeding previous literature values whilst using orders of magnitude less L-cysteine than previously reported. Moving forward, we intend to correlate growth in CD with changes in PL across a myriad of cysteine derivatives. Additionally, we plan to examine the impact of NR aspect ratio on normalized maximum CD absorption (g-factor).   

Within the field of anesthesia, the process of arousal following general anesthesia is still little understood. Of particular concern is the way a state of pain can modulate arousal, with the nucleus accumbens (NAc) as a brain region of interest as it serves many functions including controlling mood, pain states, and reward motivation. This study investigates how NAc principal cells change their firing during arousal and are influenced by a pre-existing pain state. To assess this, we leverage the partial sciatic nerve ligation model of chronic neuropathic pain to examine the influence of pain state on arousal. We then test groups of mice in their behavioral responses, including open field test, von Frey, hot plate test, and the return of righting reflex as a measure of arousal from isoflurane anesthesia-induced unconsciousness. In some mice, we record 1-photon calcium-related population activity in the NAc to analyze neural activity during arousal from anesthesia. Our findings will serve to illuminate the underlying brain circuitry involved in arousal from anesthesia and the influence of pain state, which can help improve anesthesia recovery and may reveal non-opioid or endogenous mechanisms for pain relief.

Soluble peptides from the HIV-1 (Human Immunodeficiency Virus) envelope heptad repeat-2 domain, known as HIV fusion inhibitors, can inhibit viral entry by blocking formation of the gp41 6-helix bundle required for membrane fusion and infection. However, this treatment is unfeasible because it requires twice-daily subcutaneous injections with high risk and cost. The Lieber Lab is working to engineer hematopoietic stem and progenitor cells (HSPCs) to express HIV fusion inhibitors in vivo, potentially offering sustained protection against HIV. In my work I used SIVmac239 (Simian Immunodeficiency Virus) challenged Rhesus Macaques sera and developed viremia (from another study by Lieber lab). My goal was to test whether anti-gp41 antibodies from these animals cross-reacted with synthetic gp41-derived fusion inhibitor peptides, specifically C46-v2o, C34-SFT, and Enfuvirtide(T20). If antibodies interfered with fusion inhibitors, their therapeutic effect would be severely compromised. In my project, I developed an Enzyme-Linked Immunosorbent Assay (ELISA) to measure antibody titers. These peptides were coated, then blocked with 3% bovine serum albumin, and incubated with diluted Macaque serum to allow antibody binding. I used anti-monkey immunoglobulin-G conjugated with Horseradish Peroxidase for detection of antibody binding. I optimized the serum dilution to 1:200 to reduce background signal and concluded SIV-challenged Macaques had detectable antibody levels against C46-v2o and C34-SFT, but not T20. Ongoing work will determine more detailed IC50 antibody titers in serum samples. Notably, animals with high viral loads exhibited higher levels of antibodies against HIV fusion inhibitors. T20 is a promising candidate for sustained HIV inhibition, as no detectable antibodies means it’s less susceptible to pre-existing immune responses. These findings provide valuable insights into how fusion inhibitors interact with the immune system and help refine strategies for HSPC-based HIV therapies, bringing us closer to a long-term, self-sustaining approach for HIV prevention. 
 

Autism Spectrum Disorders (ASD) are a combination of neurological and developmental abnormalities, with 1 in every 36 children diagnosed worldwide. Brain Selective Kinase 2 (BRSK2) is one of the strongest autism-associated genes, with 35 de novo mutations reported to date. Patients harboring BRSK2 variants clinically present with neurodevelopmental disorders, including speech delay, intellectual disability, motor dysfunction, and behavioral abnormalities. Despite its strong ASD association, the molecular functions of BRSK2 and the mechanisms through which it regulates neurodevelopment remain unclear. My project aims to investigate the molecular role of BRSK2 by identifying its localization in the developing hippocampal and cortical neurons. The function of a gene is reliant upon its localization within the cell. To identify the subcellular localization of BRSK2 during early neurodevelopment, I am analyzing the subcellular distribution of BRSK2 in cultured primary embryonic rat neurons at different developmental time points, using immunocytochemistry and confocal microscopy. To delineate the impact of missense mutations in BRSK2 on its localization, I am analyzing the phenotype of cultured hippocampal rat neurons with GFP-tagged engineered constructs harboring the BRSK2 mutants. My analysis found that both hippocampal and cortical neurons display mostly cytoplasmic BRSK2 localization, with a significant association with the subcellular endomembrane as well as the plasma membrane (PM). Interestingly, BRSK2 was also found at the dendritic spines at day in vitro (DIV) 12. We are currently investigating whether any of these missense mutations disrupt inter-organelle communication between the endomembranes and plasma membrane. BRSK2’s localization in the endomembranes could explain disruptions in protein processing, dendritic development, or neuronal polarity linked with the missense mutations that eventually impact neurodevelopment, leading to autism. Discovering BRSK2’s localization will help contribute toward the future development of targeted therapies for ASD caused by the dysfunction of the BRSK2 kinase.

Prenatal lead exposure is associated with learning and behavior problems, reduced growth, and increased risk of miscarriages. The Centers for Disease Control and Prevention and the American College of Obstetricians and Gynecologists recommend lead exposure screening for pregnant women due to the significant health risks lead poses to their developing fetus. However, there is no nationally recognized screening tool, leading to inconsistent practices and potential gaps in care across the country. This project aimed to address this gap by identifying state-specific screening resources for clinicians and creating a tool to help healthcare providers more easily access these resources. Through web searches, emails, and phone calls to 50 state health departments, 20 state-level screening resources were identified, along with county-level resources in three counties with childhood lead poisoning prevention programs. These resources were compiled into an interactive map directing clinicians to screening resources in their region. This tool is being reviewed for potential use by the Pediatric Environmental Health Specialty Units, an organization that provides free pediatric and reproductive environmental health consultation services to clinicians. The tool addresses the barrier to accessing screening resources, ideally increasing lead screening rates and improving pediatric health outcomes. The findings highlight the need for a national screening tool and provide insights into regional differences in recommended screening practices.

Orientation Patch Count (OPC) is a method of research used by biologists and paleontologists to analyze the complexity of an animal’s feeding surface while inferring their diets; diet and tooth complexity have evolved in concert with one another, which is why this method has been used on reptilian and mammalian (denticular) species. However, it has not been extensively tested on edentulous (toothless) clades. Therefore, my research examines the OPC of an edentulous species - specifically the endangered Madagascar big-headed turtle (Erymnochelys madagascariensis) using  three CT-scanned specimens. Three primary programs were used in order to analyze the quantitative morphometricsof the species: Slicer for processing and editing CT scans from the University of Washington’s Friday Harbor Lab, MeshLab for editing 3D models, and RStudio for data analysis. This research contributes to a broader study on turtle species led by paleontologist Brenlee Shipps, who will apply these findings to extinct beaked clades, specifically dicynodonts.

I investigate whether combining ultra-wideband (UWB) radar with inertial measurement units (IMUs) can produce more robust human pose estimations than using IMUs alone. UWB radar yields precise distance measurements, offering positional data that standard IMUs—sensitive mainly to angular velocity and acceleration—cannot capture. To test this approach, I built an embedded system that integrates a UWB radar module with wearable IMUs, then designed a user study involving everyday movements and targeted exercises performed by a small group of participants. This setup allowed me to collect a diverse dataset under realistic conditions. I processed these data using neural network models, including long short-term memory (LSTM) and transformer architectures, to generate accurate joint angles. I then fed those angles into a 3D skeleton reconstruction model. My preliminary findings suggest that the additional distance data from the UWB radar substantially improves tracking accuracy and reduces ambiguity in limb positioning. This enhanced estimation could lead to more realistic virtual reality avatars, improved fitness tracking, and better physical therapy tools. By overseeing the hardware design, data collection, and model development, I actively demonstrate how interdisciplinary methods can advance human-computer interaction through more precise and accessible pose estimation.

Increased mitochondrial oxidative stress causes fatigue and metabolic dysfunction in muscle tissue. It is unclear whether the oxidative stress is due to elevated production or impaired consumption of reactive oxygen species (ROS). The purpose of this study is to test whether the capacity of the antioxidant defense system is impaired or the mitochondrial ROS production rate is elevated in response to chronic changes in mitochondrial oxidative stress. To experimentally manipulate mitochondrial oxidative stress, we use an inducible mouse model to knockdown superoxide dismutase 2 (SOD2) in skeletal muscle and heart to increase oxidative stress, and exercise training to decrease oxidative stress. Knockdowns (KD) or littermate controls (CON) performed a six-week voluntary wheel running (EX) or sedentary control intervention (SED). Following completion of the intervention, I isolated heart and skeletal muscle mitochondria using differential centrifugation. I measured mitochondrial hydrogen peroxide (H₂O₂) production rate and tested the antioxidant capacity by treating isolated mitochondria with Auranofin (AFN) or 1-chloro-2,4-dintrobenzene (CDNB), which inhibit the thioredoxin and glutathione S-transferase components of the mitochondrial antioxidant defense system, respectively. KD heart and skeletal muscle had similar absolute H₂O₂ production rates compared to CON, but normalized to oxygen consumption the KD had significantly higher H₂O₂ production. Since absolute H₂O₂ production under vehicle conditions was not different, this suggests that the antioxidant capacity adapts to meet the changes in mitochondrial H₂O₂ production. We will collect data from the exercise-trained cohort next month. I expect to see an increase in H₂O₂ production rate and antioxidant capacity in both groups due to the increased mitochondrial biogenesis from exercise training. These results demonstrate that chronic increases in mitochondrial oxidative stress decrease mitochondrial H₂O₂ production capacity from skeletal muscle.

Body dysmorphic disorder (BDD) is a relatively common debilitating psychiatric disorder, marked by a preoccupation with one's physical appearance and associated with significant morbidity and mortality. This preoccupation is due to one's perceived flaws that are not noticeable to others, causing extreme distress and functional impairment. Previous neuroimaging studies have shown how aberration in visual processing is central to BDD. BDD participants often exhibit an unusual focus on high-detail image information (high spatial frequency processing) versus broad image information (low spatial frequency processing), leading to perceptual disturbances. Other research has shown hypoactivation of early cortices, such as V1 and V2, can be found in BDD participants compared to healthy controls when viewing low spatial frequency information. Hypoactivation in visual cortices extends across multiple stimulus categories, indicating a fundamental deficit in integrating low-spatial frequency information. This study aims to isolate and examine low-level visual processing using fMRI and visual mapping techniques to precisely localize the stage of the visual hierarchy where visual processing is altered in BDD. We aim to recruit n=30 participants (n=15 with BDD, n=15 healthy controls), all of whom will undergo clinical diagnostic interviews and behavioral assessments characterizing spatial frequency processing, ending with a spatial frequency processing task involving both low-level and high-level spatial frequency processing. We hypothesize that the results of our research will show that those with BDD will display reduced sensitivity to low spatial frequency stimuli in early visual cortices. If our hypothesis is confirmed, these findings will reveal potential new biomarkers of perceptual dysfunction in BDD, informing intervention efforts to address more fundamental perceptual deficits and identify potential risk markers for early detection of this disorder.

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

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

Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is a fatty acid β-oxidation disease associated with severe hypoglycemia and sudden death. MCADD is caused by biallelic pathogenic variants in the ACADM gene, which codes for a dehydrogenase specific to carnitines C6 through C12. MCADD is included in newborn screening (NBS) and characterized by elevated medium-chain acylcarnitine fats, annotated as C6, C8, and C10:1. Diagnostic testing is performed in plasma. Acylcarnitine results in dried blood spots have been described to differentiate carriers from affected individuals to reduce false positive NBS. Disease sensitivity and specificity, particularly to differentiate carriers from true positive cases, has not been well described in plasma. We posit that MCADD diagnosis will be more accurate if additional ratios beyond the primary disease markers, C6, C8, and C10:1 acylcarnitines, are considered. This study is a retrospective data review of NBS cases that were positive for possible MCADD and diagnostic testing was performed at Seattle Children’s Hospital. Cases are sorted into four groups: MCADD with homozygous disease variants, compound heterozygous MCADD, carriers of MCADD, or true negative. In collaboration with the biostats core service, linear regression models and receiver operator characteristic curves will compare acylcarnitine species and ratios by group. Preliminary results demonstrate that the primary markers associated with MCADD, C10/C2, C10/C6, C8/C2, C8/C10, and C8/Free carnitine, clearly discriminate affected individuals from control cases in plasma. Analysis is in process to compare the different genotypes of affected MCADD from carriers. Uncovering the diagnostic accuracy of plasma acylcarnitine profiles may influence future testing plans and improve the cost-effectiveness of healthcare services. DNA testing remains costly and slow. Additional biomarkers that provide a conclusive diagnosis of MCADD without requiring genetic testing may lead to more equitable patient care.

Changing patterns of human land use near coastal zones have increased the abundance of aquatic habitats where mosquito and midge larvae develop. Salt-tolerant species, such as Aedes togoi mosquitoes and Dicrotendipes enteromorphae midges, have evolved distinct anatomical and physiological mechanisms that allow them to thrive in saltwater environments while also being able to develop in freshwater. While much is known about how freshwater-confined species maintain salt and water homeostasis (i.e. osmoregulation) in dilute freshwater, these processes remain largely unexplored in salt-tolerant species. The main goal of this research was to describe and compare the osmoregulatory strategies of Ae. togoi and D. enteromorphae larvae reared in seawater and freshwater, focusing on how they maintain ion and water balance in saline conditions. Based on information from other salt-tolerant insects, I hypothesized that the rectum of these species is the main organ that excretes salts and will have higher expression of ion pumps compared to other osmoregulatory organs of the larvae. This increased expression would support the secretion of hyperosmotic (salty) urine, a critical adaptation for survival in saltwater. Using immunohistochemistry and fluorescence microscopy, I localized key ion-transport pumps within the rectum and other osmoregulatory organs of Ae. togoi and D. enteromorphae larvae. I identified a high expression of Na⁺/K⁺-ATPase (sodium/potassium pump), and V-type H⁺-ATPase (proton pump) enriched in the anal gills, renal tubules, and the rectum. My findings suggest that the coordinated function of many osmoregulatory organs, and not just the rectum, allows for salt-secretion by marine insects, and this establishes an initial framework of cellular mechanisms among marine insects. This research has implications for predicting future species distributions with rising sea levels, as well as the potential to identify novel targets to control salt-tolerant mosquito populations to mitigate disease transmission in coastal regions.

4.5 million adults in the United States are diagnosed with chronic liver disease. Over time this can lead to cirrhosis, an end-stage condition in which scarring occurs in the liver. Reduced liver function from cirrhosis results in accumulations of neurotoxic substances that induce a spectrum of neurological impairments known as hepatic encephalopathy (HE). The critical flicker frequency (CFF) test is a well-established screening test for HE. Previously we developed Beacon, a novel and portable CFF measuring device that can be administered at home via smartphone app, as an accessible alternative to current CFF measurement devices that are large, expensive, and not intended for at-home use. We found that Beacon produced a CFF measurement that aligned with commercially available devices. While the current Beacon reflects current commercial devices, the efficiency of measurement is bottlenecked by the fact that pairs of flickering light stimuli can only be presented sequentially due to the singular light source. We therefore propose a dual headed version of Beacon that gives the option of flashing two frequencies simultaneously. I designed and developed a version of this dual-headed Beacon with sliding heads as well as an accompanying user interface before conducting a series of user studies, beginning with a pilot study on healthy individuals and progressing to a clinical trial on chronic liver disease patients, to evaluate the impact of the number of light sources and the distance between them on CFF measurement time and repeatability. I hypothesize that the two-headed Beacon will produce a CFF measurement more quickly than the original Beacon and that a closer distance between heads will also produce quicker and more consistent measurements. These findings will help inform the development of future iterations of the Beacon, leading to improved outcomes for chronic liver disease patients.

During inflammation, myeloid-biased hematopoietic stem cells (myHSCs) are crucial for replenishing myeloid cells and platelets. Excessive activation of myHSC during aging and chronic inflammation results in the loss of their regenerative function. We have shown that Semaphorin-4A is a neutrophil-derived molecule that confers myHSC resilience to inflammatory stress and safeguards their epigenetic state, preserving their regenerative function. Sema4AKO mice exhibit excessive myHSC expansion and myeloid bias compared to their wild type (WT) counterparts, particularly in the context of aging. Given that myHSC are positioned at the top of hematopoietic hierarchy, we asked whether myHSC molecular defects due to the absence of Sema4A are “passed down” to mature progeny. In preliminary analysis of aged WT and Sema4AKO mice, we mapped the neutrophil maturation pathway via whole bone marrow RNA Sequencing. Notably, we found that in aged Sema4AKO mice, this process was significantly dysregulated. Moreover, the neutrophil transcriptional signature was abnormal and consistent with excessively activated, pro-inflammatory state. This suggests that neutrophils produced from KO mice may have defective function. To investigate this, we are using a murine ligature-induced periodontitis model to monitor alveolar bone loss as a readout of neutrophil function. Periodontitis is an oral disease that leads to alveolar bone loss and promotes inflammation, specifically production of myeloid cells. The ligatures are placed on the left second maxillary molar and are left on for 8 days. After this incubation period, the mice are euthanized, and bone loss is measured. Since the ligatures are only placed on one side of the mouth, the other side acts as an internal control for bone loss. In our preliminary studies in WT mice, we observed that as expected, ligature-induced periodontitis causes bone loss. Having established this model in our lab, we are starting experiments to examine the impact of Sema4AKO on neutrophil function.

Neotrypaea californiensis, or burrowing shrimp, is a native pest for oyster growers in Washington. The shrimp create networks of interconnected burrows that displace and liquify sediment, suffocating oysters. The pesticide carbaryl was used for decades to effectively control shrimp populations. More recently, the Environmental Protection Agency (EPA) deemed carbaryl an environmental hazard, leading to a vital need for a shrimp control method with minimal non-target effects. Very little is known of the physiology of shrimp that allows them to tolerate environmental extremes. My study aims to understand the tolerance of Netotrypaea californiensis to high concentrations of salts that challenge their ability to regulate internal ions, pH, and metabolic wastes. Using a laboratory-based system whereby shrimp burrow in 6 inch deep sediment in seawater, my research findings revealed that the addition of high concentrations of sodium bicarbonate (NaHCO₃) caused shrimp mortality while high concentrations of regular sea salts did not. This suggested that an ionic imbalance—high levels of sodium and reduced levels of chloride—may be causing shrimp death. To investigate, I collected the gills, a critical organ that regulates systemic ion levels, of shrimp after NaHCO₃ exposure and quantified the abundance and localization of key ion pumps using Western blotting, immunohistochemistry and confocal microscopy. I found a significantly higher expression of Na⁺/K⁺ pumps in the gills with NaHCO₃ exposure, suggesting a major ion-regulatory disturbance caused by NaHCO₃. These data will expand our understanding of how salts that cause ionic imbalance in seawater can disrupt the internal levels of ions that are critical for most biological processes. Findings will be disseminated to Washington oyster growers to aid in the management of their crop.

The importance of accurately identifying infections and wounds is crucial for correct medical treatment. In serious cases, misidentification of infection can cause delay in the healing process and even result in death. Thus, there is a need to simulate the physiological progression of an infection so that medical trainees are better equipped to respond to a real skin wound/infection. Through UW Medicine’s Center for Research in Education and Simulation Technologies (CREST) lab, the dynamic tissue wound modeling and infection simulation project aims to meet this need. Motivation for this research project is rooted in the lack of acceptable physical simulation models despite the educational benefit they provide. The goal of this research project is to engineer high fidelity models of skin wounds and infections that dynamically alter their appearance to create a more realistic simulation for the trainer/trainee. My specific involvement is to create a model of a skin abscess that not only simulates an infection but, when given correct treatment, changes its physiology to reflect said treatment.

In the video game Stardew Valley, the player leaves their corporate job behind to live as a farmer in the countryside, where they manage their farm, battle monsters, and build relationships with townspeople. Importantly, the aforementioned means players play at labor, spending numerous in-game hours doing physical labor (e.g. chopping down trees, tending their farm, fighting monsters) and emotional labor (e.g. giving townspeople gifts, dating). Therefore, through this project, I explore how the identities and experiences of femme-presenting and feminized people of color (POC) impact their gameplay decisions in Stardew Valley, specifically how and why they play at physical and emotional labor. The term "femme-presenting" can apply to anyone who is perceived as feminine by themselves or by others. The term "feminized" is for people who may not want to come off as femme-presenting, but often still do according to systems/society. Over the course of five biweekly meetings over roughly ten weeks, eight participants play Stardew Valley while I observe and ask questions. By reviewing the recorded gameplay footage and our conversations, I examine what each individual player prioritizes (e.g. aesthetics, narrative, money) and why they do so. My analysis of how participants play at labor relies on an understanding of how being a femme-presenting/feminized POC interacts with their additional various other identities (e.g. sexuality, ability, class) to subsequently influence their gameplay decisions. Anticipated results include participants playing at labor in Stardew Valley for the sake of escapism, a sense of control, and to build community. This study reveals the need for further interventions in video game studies which center cozy gaming spaces, femme/feminized communities of color, and feminist theorizing.

Advancements in antiretroviral therapy research are leading to longer life expectancy for people living with HIV (PLWH). Aging is a process that happens with every individual, involving changes in the physical and mental state. However, age-associated symptoms typically occur earlier in these individuals as the disease’s chronic inflammation accelerates the aging process, decrementing PLWH’s lifestyles. Some of the symptoms include fatigue, slower walking speeds, and balance problems. Previous studies prove that exercise is a non-pharmacological method used to improve physical function and wellbeing. Exercise performed at a higher intensity is known to enhance the overall health state of PLWH and generate positive effects on cardiovascular health. The aim of the study is to compare the effects of different exercise intensities on the symptom experience of PLWH. The HEALTH Study is an exercise trial conducted by the University of Washington and the University of Colorado for 120 PLWH aged 50 years or older who reports symptoms of aging and have a sedentary lifestyle. After enrollment, HEALTH Study participants are randomized to either a High-Intensity Interval Training or Continuous Moderate Exercise program lasting for 16 weeks. Participants exercise three times a week in a research center while supervised by trainers. During the study, participants complete many assessments to monitor their physical function and fatigue. The outcome for this study utilizes the HIV symptom index score, collected at baseline (week 0) and post-intervention (week 16). This index score is a 20-question survey that assesses the severity of HIV symptoms, categorized by presence and severity ratings. The end goal of the research is to explore how exercise training can change the symptoms occurring in people living and aging with HIV, creating a strategy for more individuals with HIV to live longer and healthier lifestyles.

The external fertilization and transparent embryos of zebrafish make them an informative model of vertebrate embryonic development from the 1-cell stage. In this study, we examine the impact of de novo GTP synthesis on the formation of the embryonic somites, which are embryonic cells which develop into segmented blocks of muscle that run the length of the body. We hypothesize the de novo GTP synthesis is required for the correct patterning of somite borders in zebrafish embryos, and that this process facilitates the formation of a vertebrate body plan. Inosine monophosphate dehydrogenase 2 (IMPDH2) is the enzyme which catalyzes the conversion of inosine monophosphate (IMP) towards the de novo synthesis of GTP instead of ATP. To test the impact of de novo GTP synthesis on somite formation, we inhibited IMPDH2 function with mycophenolic acid (MPA) both before and after somite formation began. MPA caused stronger defects in the somite morphology and embryonic body shape when added to embryos before somite formation began, earlier in development. We performed in situ hybridization against xirp2a to assess the effect of inhibiting IMPDH2 function on the formation and patterning of the somite borders. MPA treatment decreased the definition of somite borders we could observe in the posterior tail. Inhibiting IMPDH2 with MPA produced somites with smooth, round borders instead of the chevron-shape typical of zebrafish. We next conducted immunohistochemistry against IMPDH2 to examine the expression and localization of this enzyme in embryonic cells when GTP conditions are low. In MPA-treated embryos, we observed increased expression of IMPDH2 across the entire embryo. We will next explore how GTP abundance affects activity of the clock, a mechanism which synchronizes gene expression of embryonic cells.

Before a child says their first word, they begin to produce and practice sounds they hear. Early vocalizations play a crucial role in speech development and language acquisition. However, most research on infant vocalizations focuses on children in Western, industrialized societies. This study contributes to the growing body of literature on diverse linguistic environments, specifically examining emergent sounds in the Panãra community, an Indigenous group in the Brazilian Amazon with approximately 700 speakers. Ten infants aged 2-21 months wore recording devices that collected a recording of their language environment over a day. Alongside shared ethnographic observations, I manually annotated selected 30-second audio segments for a fine-grained analysis of child vocalizations. I am currently analyzing the frequency and types of child vocalizations (i.e. vocal play, canonical babbling, variegated babbling) in infants' speech, and I plan to explore how these vocalizations may differ across the age range studied. I predict that child vocalizations will become more complex with increasing age, following pre-speech vocal development stages broadly found across cultures. My findings will contribute to a broader understanding of how language learning varies across cultural settings, vocalization stages, and the role of the environment to language development. 

Depression is one of the most commonly co-occurring mental health conditions among individuals with autism spectrum disorder (ASD) for which there are not currently effective strategies to minimize onset. Given that early caregiver support in autism-specific and general areas of functioning predict the development of a range of adaptive social and behavioral patterns, leveraging caregiving processes in childhood and adolescence may represent one approach to decreasing the risk for psychological disorder. However, current research recognizes that the high levels of stress experienced by many families with an autistic child may undermine the quality of support caregivers are able to provide. As a result, there is limited understanding of caregiving strategies that will reliably confer resilience to depression and that will support the successful implementation of mental health-related interventions in autism. As such, this project assesses caregiver involvement in childhood and adolescence as a predictor of depressive symptomatology in autistic adults, and additionally to evaluate the family environment as a moderator of this relationship. It is hypothesized that there will be a negative association between caregiver involvement and severity of depression symptoms, and that the association will be stronger under conditions of high familial warmth but reversed in family environments characterized by high control or rejection. Taken together, family environment will account for appreciable variations in the effectiveness of parent involvement as protecting against the development of depression. This survey study will lay the groundwork for researchers and autism service providers to develop an informed approach to leveraging parent involvement as a preventative measure against depressive symptoms in adulthood.

Tuberculosis (TB) remains a major global health challenge, causing over a million deaths annually despite being a curable disease. A critical issue is treatment non-adherence, as many patients struggle to complete the required six-month regimen due to a lack of support and access to reliable medical guidance. Improving treatment adherence can significantly increase recovery rates and save lives. This project develops an AI-augmented chatbot powered by GPT-based models to assist Spanish-speaking TB patients. This is done by providing accurate medical guidance, fostering empathy, and enhancing communication between patients and healthcare providers. Integrated into a Human-System Interaction (HSI) interface, the system employs three AI models: a two-step pipeline that classifies messages as informational or emotional to tailor responses appropriately, a few-shot model that generates responses based on examples from prior patient interactions, and a Retrieval-Augmented Generation (RAG) + few-shot model that retrieves relevant medical information from guidelines while maintaining conversational fluency. These models leverage the same underlying technology as ChatGPT, optimizing responses for accuracy, linguistic fluency, and empathy. As part of the research team, I contributed to model development and implementation, ensuring alignment with medical guidelines and human-centered design principles. The chatbot is currently undergoing external evaluation by a multidisciplinary team, including healthcare professionals specializing in TB treatment and AI researchers. Evaluators interact with the chatbot using personas as TB patients, asking medical and support-related questions to assess response quality. They rate the system based on medical accuracy, linguistic fluency, empathy, and other key criteria relevant to patient-provider communication. Insights from this evaluation will guide future refinements, with the goal of improving AI-driven patient support systems in clinical settings.

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that affects millions of people. Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive stimulation typically used in psychiatric conditions such as depression and anxiety. rTMS works by using an electric current to generate a transient magnetic field, depolarizing neurons in a target region and creating lasting changes in brain connectivity via synaptic plasticity. Patients with AD show disruptions in the Default Mode Network (DMN), a network of brain regions typically active during rest and crucial for memory consolidation. We hypothesize that strengthening the DMN through rTMS targeted at the left Brodmann 8AV region, selected for being an easily accessible node of the DMN, will improve memory in AD patients. To test this hypothesis, we are conducting a single-blind, single-arm, randomized cross-over trial of rTMS on early-stage AD patients over a 12 week period with week 1 where we scan for the 8AV region via MRI, during week 3 and 8 being the placebo or treatment week. We measure our primary outcome of the participants’ speed of forgetting —a novel index of memory function—through an individualized, adaptive memory test. To eliminate potential confounding variables, we also measure depression and anxiety symptoms during the 1st, 8th and 12th week of the study. Additionally, functional MRI scans will be analyzed for potential structural or functional differences caused by treatment. Preliminary results from our initial participants have shown promising improvements, and we are hopeful that similar outcomes will be observed in the remaining participants. Successful results would provide a novel target for AD treatment using rTMS, and support further investigation of rTMS as a viable treatment option.

The health risks of particulate matter measuring less than 2.5 micrometers (PM2.5)  include: respiratory disease, cardiovascular issues, and cognitive impairments. Its presence near schools and colleges remains underexplored. This study examines the relationship between PM2.5 exposure levels and academic outcomes in community colleges located in historically redlined neighborhoods across four major West Coast cities: Los Angeles and San Diego in California; Portland, Oregon; and the greater Seattle area in Washington. Using data from the PurpleAir Network, state air quality indices, and community college governing bodies, we analyzed and compared PM2.5 levels near institutions located within historically redlined neighborhoods and institutions located outside those neighborhoods. Leveraging the Python programming language and Google Colab, we examined correlations between an institution’s demographic makeup and transfer rates relative to PM2.5 exposure. Data sets obtained were filtered between the hours of 8 AM and 1 PM during the months of January 2024 through December 2024. Our findings indicate a correlation between higher PM2.5 exposure and lower academic performance for colleges serving predominantly racially marginalized communities located within historically redlined neighborhoods. This research reinforces the role of environmental inequities in shaping educational disparities and highlights the need for targeted policies to address air quality in affected communities.

Brain cells depend on the extracellular matrix (ECM) for structural and functional support as well as sequestration and transport of key ions and neurotransmitters. Structural and compositional changes to the ECM occur in development and in response to injury and disease. Probing ECM structure and composition in real-time in a dynamic living brain would enhance our understanding of the ECM changes that drive disease. In our work, we use organotypic whole-hemisphere (OWH) brain slices to study the interaction between brain parenchymal cells and the ECM. We have applied multiple-particle tracking (MPT), an imaging technique that tracks movement of nanoscale probes with sub-micron resolution, to OWH slices exposed to different stimuli, including oxygen-glucose deprivation (OGD) and mitochondrial dysfunction by rotenone (ROT) exposure.  Our MPT data confirmed that ECM microstructure changes in a time and stimuli-dependent manner and this was associated with changes in cellular composition and morphology. In this study, we measured changes in expression of ECM transcripts using Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) of RNA isolated from OWH brain slices exposed to OGD and ROT. After exposure to 30 minutes of OGD or treated with 50 nM ROT, OWH slices were preserved at 2h and 24h in RNALater buffer for RNA isolation. The 2h time point aligns with the end of the MPT experimental window. Healthy unexposed OWH slices were controls. We measured expression of genes associated with ECM composition and remodeling including tenascin-R, aggrecan, neurocan, MMP9, and TIMP1; markers associated with cellular activation including Ki67, Cd45, Cd11B, and GFAP; inflammation markers including IL-1β, IL-4, IL-6, IL-9, and IL-10; and cell death markers including iNOS, nNOS, TNF-α, and Casp-3. Our results provide a quantitative measure of ECM composition that can be integrated with our MPT and imaging data to better define microstructural dynamics in the stimuli-exposed brain.

Cervical spinal cord injuries (SCIs) often result in impaired locomotion and forelimb mobility. Assessed with a forelimb locomotor scale (FLS), previous research demonstrated improved forelimb locomotion with task-specific physical therapy (PT) training following a unilateral 150 kdyne C6 SCI in a rat model. Improvement in locomotion was calculated using a recovery ratio, which measures the difference in FLS scores normalized to the animal’s baseline score. There was a significant improvement in the recovery ratio (3dpi-14wpi) for animals that underwent task-specific PT training (p ≤ 0.0014). The underlying molecular mechanisms behind this improvement are still unclear. A potential explanation for these functional changes is the task-specific PT-induced increase in brain-derived neurotrophic factor (BDNF) targeted at the injury site. Task-specific PT stimulates neurons, microglia, and astrocytes to release BDNF, promoting neuron survival, growth, and synaptic plasticity. These processes are crucial for mediating the effects of cervical SCI trauma. This study investigates whether BDNF expression in the spinal cord varies in rats that underwent task-specific PT training following cervical SCI. PT-trained rats are hypothesized to have increased BDNF within the spinal cord, especially proximal to the injury site, which would help mitigate SCI trauma and enhance forelimb locomotion and mobility. To this end, we performed immunohistochemistry staining and quantification of BDNF in the spinal cord and compared it across three groups: PT + SCI, SCI-only, and Sham. The expression levels of BDNF in neuronal cells, astrocytes, and microglia were then correlated with their FLS scores to determine if there was a positive correlation between BDNF expression and forelimb locomotion. This would indicate that BDNF supports synaptic plasticity and recovery from SCI-induced trauma.

The identification of synergistic drug combinations remains a significant challenge in oncology due to the large amount of existing drugs and complex interactions between these drugs. In this work, we propose an active learning framework applied to the NCI ALMANAC dataset to efficiently uncover promising drug pairs that conventional screening methods might overlook due to lack of time and resources to handle these nearly countless combinations. Building on established greedy sampling strategies—such as GSx, which selects samples based on maximal minimum distance in the input space, and GSy, which focuses on output diversity—we introduce modifications to potentially enhance sample selection diversity and predictive performance. First, we explore replacing the traditional greatest minimum distance criterion with a greatest average distance metric, hypothesizing that this adjustment captures the overall variability in the data differently than the traditional method. Second, we redefine the improved greedy sampling (iGS) approach by standardizing the distance metrics from both the input (GSx) and output (GSy) spaces using Z-score normalization (or alternative standardization methods) prior to their aggregation, rather than combining them multiplicatively. We conduct a comprehensive comparative analysis against traditional methods to evaluate improvements in model convergence, prediction accuracy, and the ability to identify rare but potent drug combinations. We also explore other active learning strategies as Query By Committee (QBC) and others. Our preliminary findings suggest that these tailored active learning techniques offer a promising pathway toward more efficient and insightful exploration of high-dimensional drug interaction landscapes.

This research study explores the evolutionary adaptations of the TLR7 protein receptor in primates in relation to Flavivirus (Yellow Fever) recognition. TLR7, an important receptor in the immune system, is essential for recognizing single stranded RNA viruses such as Flavivirus. Given the growing prevalence of Yellow Fever in tropical climates, I hope to understand how environmental factors shape immune response. I hypothesize that ecological niches, particularly wet vs dry climates, play a crucial role in the evolution of the TLR7 receptor among primate species. Since Yellow Fever is transmitted by mosquitoes, which thrive in wet climates, these environments are likely driving the transmission of the virus. As a result, wet climates may exert selective pressure on the evolution of TLR7 to enhance immune responses against Yellow Fever in regions where mosquitoes are prevalent. To conduct comparisons of the TLR7 receptors, I will be running Blast, a bioinformatics software that compares genomic sequences across different species. This tool will allow for identification of both conserved and divergent regions in the TLR7 sequences from primate species, including humans, that inhabit wet and dry climates. These variations could reveal evolutionary adaptations influenced by ecological pressures. Through these sequence comparisons, I aim to explore how differences in TLR7 might affect susceptibility to Yellow Fever and other similar viral infections. Understanding how ecological conditions shape immune receptor evolution could also improve our ability to predict how different populations might respond to emerging infectious diseases.

The kinetochore plays a key role during the cell division process, acting as an adaptor between the mitotic spindles and the centromere. The STU1 gene codes for a microtubule plus-end-tracking non-motor protein (Stu1) and facilitates the connection between the kinetochores and mitotic spindles during cell division. It also participates in a checkpoint that ensures proper connections between the spindles and kinetochores before the cell continues into anaphase. Stu1 contains multiple MELT motifs, which are conserved sequences of amino acids that are phosphorylated and targeted by the Mps1 kinase. Mps1 plays a major role in the regulation of segregation and spindle checkpoints. The impact of phosphorylation at the MELT motif on the function of Stu1 is not known. We used a previously constructed CRISPR vector and HDR template to mutagenize the codon within the MELT motif at position 719 in the STU1 gene of Saccharomyces cerevisiae. This mutation would result in a substitution of the amino acid threonine for glutamic acid within the Stu1 protein (stu1-T719E). Threonine is a neutrally-charged amino acid and is used in S. cerevisiae proteins as a phosphorylation site, but glutamic acid mimics a phosphorylation site as it has a constant negative charge. We transformed the CRISPR vector and HDR template DNA into S. cerevisiae cells and recovered transformants. To verify the success of the mutagenesis, we purified genomic DNA from transformed yeast, amplified the STU1 gene via PCR, and then sent for Sanger sequencing. It was found that mutagenesis was successful. This will allow us to move on to the next steps, which include phenotypic tests which will allow us to see if the mutation we made impacts cell division of S. cerevisiae cells. 

Dynamic marine environments require long-term spatiotemporal datasets to successfully monitor and understand patterns in ecosystem composition on a decadal scale. High-resolution photography is often used to compensate for the field logistical constraints associated with marine sites, such as personnel availability or weather conditions, and works well to quickly capture data in the field. However, these photos require extensive manual analysis after the fact. As a research mentee, I asked the question: “Can image annotation with machine learning models provide enough clear data to inform community ecology studies of sessile organisms in subtidal habitats?” Using images collected through transect/quadrat sampling by the Sebens Lab’s Salish Sea Long-term Monitoring Project (University of Washington Biology and Friday Harbor Laboratories), a variation of an open-source model (CoralNet) was trained in the identification of relevant sessile flora and fauna. I then used CoralNet to continue the work of the lab by generating sessile assemblage metrics for a single site in the Friday Harbor Laboratories Biological Preserve. This site included images from transects at two different depths, with sampling from 2014 and 2024. After being uploaded, CoralNet identified 200 random points per image to the lowest possible taxon. I then reviewed all annotations for accuracy and corrected them whenever necessary. This technique greatly reduced the time spent per identification, without sacrificing accuracy. Next, I calculated species richness and Simpson’s Diversity for each quadrat and transect, comparing between depth and year. My analysis showed significant increases in both metrics from 2014 to 2024 and no significant differences between depths, demonstrating a successful report on the dynamics of a subtidal marine community. Application of this method to the entire existing dataset (7 sites, 63 transects per year), and others, provides opportunities to streamline analysis of sessile community composition.

Accurately describing a child’s language skills is difficult, but identifying children with atypical language development adds even more complexity. In an ordinary language assessment session, a Speech-Language Pathologist (SLP) will use both standardized, norm-referenced assessments and non-standardized assessments, like Language Sample Analysis (LSA). However, there is little research about how these different assessments relate to one another. To better understand this relationship, the language abilities of children (n=38) were assessed after turning 6-years-old and attending Kindergarten by SLPs using the following norm-referenced tests: a sound-in-words subtest from the Goldman-Fristoe Test of Articulation, 3rd Ed. (GFTA-3); core language subtests from the Clinical Evaluation of Language Fundamentals, 5th Ed. (CELF-5); and a nonverbal IQ subtest from the Kaufman Brief Intelligence Test, 2nd Ed. (KBIT-2). Then, a 10- to 20-minute language sample of the child’s spontaneous speech was collected for analysis. This project extends from previous research by including participants beyond clinical populations and using multiple sampling contexts to holistically capture the child’s naturalistic speech. I transcribed each language sample with Codes for Human Analysis of Transcripts (CHAT) and utilized Computerized Language Analysis (CLAN) software to automatically compute measures reflecting language skills from the language samples. I will conduct correlational analyses to inspect the associations between measures from norm-referenced tests and measures extracted from language samples. I expect to see significantly positive correlations between several CELF-5 measures and LSA measures of morphosyntactic development (i.e., grammar) that demonstrate a convergence between these two methods of assessment. Correlations between LSA measures and GFTA-3 measures are expected as well but to a lesser degree of association because they do not index identical elements of language. Overall, relationships discovered during this process will lend themselves to further understanding the information we gain from these common tools of language assessment.

Dementia, a growing global health concern, affects the nervous system and leads to severe cognitive impairment, with Alzheimer’s disease (AD) being the most common form, currently impacting nearly 7 million Americans. As life expectancy increases, the prevalence of dementia increases in corresponding fashion, driving research efforts like those of the Darvas Lab, where we study AD and other related dementias using adeno-associated viruses (AAVs) to induce neuropathologic changes. The TDP43 protein is involved in neuropathologic changes such as those in Frontotemporal Dementia (FTD) and in Amyotrophic Lateral Sclerosis (ALS), a primary motor neuron disorder. TDP43, primarily localized in the nucleus, plays a crucial role in regulating gene expression and RNA metabolism. TDP43 pathology in neurons involves the presence of TDP43 in the cytoplasm and its accumulation in cytoplasmic inclusions. To better understand the role of TDP43 in neurodegeneration, we use a mouse model where TDP43 proteins are introduced via AAV, a genetically engineered viral vector commonly used in research. This approach allows control over the timing of neuropathologic changes. Our prior AAV constructs included the Synapsin I promoter, which led to a severe ALS-like motor phenotype due to its expression in spinal motor neurons. However, this model could not be used to study the more subtle effects of dementia due to the extreme nature of the physical pathology. Therefore, our goal is to produce a new model to overexpress TDP43 using an AAV that is exclusive to the cortical brain regions relevant to FTD by instead including the CamKIIα promoter, which exclusively drives expression in the forebrain. I assessed behavioral phenotypes in our mouse model by conducting a Y-maze to evaluate effects on short-term memory, and analyzing neurological scoring to evaluate neuromuscular dysfunction. The development of a more dementia-focused TDP43 model will allow us to more specifically investigate its neuropathology.

Advances in antiretroviral therapy have increased life expectancy for people living with HIV (PLWH), but aging exacerbates symptoms such as frailty, neurocognitive disorders, and bone loss. Pharmacological treatments often present limitations, including side effects and drug interactions. Non-pharmacological approaches like physical activity and diet may offer holistic symptom management, yet remain understudied in PLWH. The aim of this study is to investigate the association between physical activity levels, diet quality, and symptom experiences in older PLWH. We will analyze data from the PROSPER-HIV study, a prospective observational study of 850 participants (over 50% aged ≥50 years) from the Center for AIDS Research Network of Integrated Clinical Systems (CNICS) across four U.S. sites. Key measures include: (a) moderate-to-vigorous physical activity, assessed via accelerometry; (b) diet quality, measured by the Healthy Eating Index-2015 (HEI-2015) from 24-hour dietary recall; (c) symptom burden, evaluated using the 20-item HIV Symptom Index; (d) muscle strength, assessed via handgrip strength; and (e) physical function, measured using the Short Physical Performance Battery (timed walk, chair stands, and balance tests). Descriptive analyses will identify patterns in physical activity, diet quality, symptom burden, muscle strength, and physical function collected at baseline. Linear regression models will examine relationships between symptom burden, physical activity, and diet, adjusting for age, sex, muscle strength, and function. Findings will clarify the impact of lifestyle factors on symptoms, supporting the integration of non-pharmacological strategies into nursing care. The results will inform nursing practice and public health by highlighting the role of physical activity and dietary improvements in symptom relief.

Neutrophils are a type of white blood cell in the human immune system that can migrate through tissues to respond to sites of injuries and infections. In the laboratory, we can recapitulate neutrophil migration under controlled experimental conditions by using a cell line, called HL-60, that was originally derived from a person with leukemia. These cells can be cultured to imitate the behavior of neutrophils, and specifically they are able to migrate while we watch them on the microscope. First, I determined how HL-60 cell migration depends on the physical nature of the substrate they are crawling on. I compared cell migration under three different conditions: 1) uncoated plastic, 2) plastic treated to make the surface stickier for cells, and 3) plastic coated with a protein, BSA, to make the surface less sticky. I found that cells moved faster and with straighter paths on the uncoated plastic. Next, I used a drug, CK666, which is known to inhibit a protein that is important in the assembly of the cell’s actin cytoskeleton, the mechanical driver of cell migration. As expected, I found that the cells moved more slowly in the presence of the drug. Also, I found that the drug made the cells move in less straight paths. Finally, I explored how the HL-60 cells responded when I exposed them to an electric field. Electric fields are thought to arise naturally at sites of skin wounds. I observed that the cells moved toward the cathode of the electric field. I am currently analyzing whether the cells also move faster or straighter when there is an electric field present. In future experiments, I plan to determine whether mutating specific proteins thought to be involved in cell motility can change the behavior of the HL-60 cells on the microscope.

Microglia are innate immune cells in the brain that play an important role in maintaining homeostasis, carrying out immune surveillance, and modulating synaptic plasticity. Through the secretion of cytokines, along with physical functions like synaptic pruning and network refinement via phagocytosis, microglia support the health of neurons and help establish a functional neuronal network. In previous experiments, our lab demonstrated that when cultured with microglia, neurons exhibit more robust morphology and greater synaptic activity. However, it remained unclear whether the beneficial effects of microglia on neurons occur during physical contact between the two cell types, or if the supportive factors secreted by microglia are sufficient to drive this change. To investigate this, I compared the morphology and function of neurons directly co-cultured with microglia, to neurons treated with media conditioned by microglia. In the microglia-conditioned media treatment, I conditioned the microglia media for 24, 48, and 72 hours prior to treating the neurons to determine the optimal conditions for establishing a healthy neuronal environment. To evaluate these results, I conducted immunofluorescence staining for microtubule-associated protein tau (MAPT) and microtubule-associated protein 2 (MAP2), both of which are indicators of neuronal health. I analyzed fluorescence intensity and neurite length to quantify morphological differences in neurons between conditions. To investigate differences in synaptic activity, I carried out micro-electrode array recordings of neurons in each condition. Using data from these recordings, I analyzed the coordinated and overall electrical activity to measure the functionality of the synaptic network in each condition. Given that microglia perform both secretory and physical functions, I expected that neurons directly co-cultured with microglia would exhibit more robust phenotypic and functional characteristics. These experiments provide insight into healthy neuron-microglia interactions and reveal possible avenues towards their dysregulation in Alzheimer’s disease (AD), potentially guiding the development of therapeutics targeting such interactions.

Relative Risk (RR) is a highly interpretable parameter in epidemiology and biostatistics, based on both binary input and outcome. It is frequently used in vaccine development to measure the relative efficacy between two treatment groups.
Researchers are often tempted to use generalized linear models (GLMs) to estimate the logarithmic RR with respect to a set of baseline covariates. However, this approach has inherent flaws, as GLMs do not account for variation dependence in Relative Risk on its nuisance parameters. Richardson et al. have developed an unconstrained and variation-independent doubly robust nuisance model using the log Odds Product (OP).
To expand on this work, we will explore alternative nuisance models—both those developed by us and those from other researchers—and compare their computational robustness to that of the log Odds Product (OP).
Additionally, using the brm R package (which streamlines the methods proposed by Richardson et al.), we will analyze a dataset where Relative Risk serves as the target of inference and compare these results to those obtained using regression methods.

Mycobacterium abscessus is a non-tuberculous mycobacterial (NTM) species that causes severe pulmonary infections, particularly in immunocompromised patients and those with preexisting lung diseases such as cystic fibrosis. Treating M. abscessus infections is challenging due to its intrinsic antibiotic tolerance and capacity to develop multidrug resistance. To identify novel molecules that can target this pathogen and enhance current treatments, we screened a library of FDA-approved drugs (n = 2,400). Our data shows that Netupitant, a drug commonly used to prevent chemotherapy-induced nausea and vomiting, exhibits potent antibacterial activity against a broad range of M. abscessus clinical isolates, including multidrug-resistant strains, with a minimum inhibitory concentration (MIC) ranging from 4 to 16 µg/mL. Furthermore, in combination with amikacin, a standard treatment for M. abscessus infections, Netupitant demonstrated strong synergistic interactions, as confirmed by checkerboard microdilution and time-kill assays. These findings highlight Netupitant’s potential as a novel therapeutic option for M. abscessus, particularly in combination with existing antibiotics. Future studies exploring its mechanism of action and in vivo efficacy could further advance antibacterial drug discovery for difficult-to-treat NTM infections.

Sound is a vibration that is created by an oscillating object and travels in periodic waves of pressure through a medium. Sound waves are characterized by properties such as frequency, amplitude, wavelength, and speed. The purpose of my research was to measure the effects the lower temperature and air pressure present in the stratosphere have on the properties of sound. To conduct this research I custom-designed an Arduino based sensor with a barometer and thermometer that was then attached to a weather balloon. The sensor also had a buzzer that repeated a tone at constant intervals along with a microphone that measured the amplitude of sound across various frequencies as it was necessary to consider the impact that the high wind speeds present in the stratosphere would have on the measurements. As the air becomes colder and less dense it also becomes less elastic causing it to transfer energy less efficiently which in turn leads to a decrease in amplitude. Frequency, however, did not change as it is determined by the source of the sound and does not depend on the properties of the medium. Understanding how changes in the properties of the medium affect the properties of sound opens a path to using sound to illuminate the properties of the medium. Additionally, broadening our understanding of how various atmospheric conditions present on our own planet affect the properties of sound deepens our understanding of how the various atmospheric conditions present on other planets will impact the properties of sound.

Europium (Eu) is a redox-sensitive rare earth element (REE). Eu stable isotopes are promising tracers across different scientific domains, giving quantitative insight to the processes where Eu anomalies are present. Studies on Eu isotopes remain scarce as the chemical separation of Eu from other REEs is challenging due to their geochemical similarities, as well as low concentration of Eu in standard geological materials . Recent development of a high-yield (99.4%) and low blanks (<20 pg, Wu et al., 2024) Eu purification scheme from geological materials using cation exchange resin and extraction chromatographic resin allows for an effective approach to better characterize Eu isotope compositions in various materials. We aim to investigate this method of purification and instrumental analysis technique to obtain  δ 153/151Eu values with a multicollector-inductively coupled plasma-mass spectrometry (MC-ICPMS) instrument. To achieve this, we will replicate the purification protocol established by Wu et al. (2024) with synthetic solutions and digested geological reference materials (GRMs), monitoring the relative intensity of Eu and other matrix elements. We collect pre- and postcut fractions of samples to determine the Eu yields and potential contamination from other elements using MC-ICPMS. To correct instrumental mass bias, Wu et al. (2024) used combined standard-sample-bracketing-internal-normalization method, with internal normalization using Nd and standard reference material NIST 3117a as the bracketing standard. Building on the protocol by Wu et al. (2024), we will additionally investigate the effect of column geometry, acid molarity, as well as instrumental analysis without element doping on yield and precision. The validation of the method used for accurate and precise Eu isotope analysis allows for increased applications of Eu isotope geochemistry.

Due to considerations such as dose reduction, or physical limitations of the scanner, computed tomography (CT) images must sometimes be reconstructed from sparse-view or limited-angle sinogram data, resulting in a loss of image quality. In recent years, there has been a great deal of interest in using neural networks to improve image quality in these scenarios. In this work, we implement three neural network architectures – denoising convolutional neural network (DnCNN), U-net, and transformer – and apply them to sparse-view and limited angle problems in both a post-processing and iterative, “plug-and-play” reconstruction context. In post-processing, the neural network is applied to the final image to remove artifacts, while in the plug-and-play approach, it is incorporated into the algorithm that reconstructs the image from the sparse-view or limited-angle data. Based on standard image quality metrics, the post-processing approach with the U-net is found to give the best image quality. The plug-and-play approach, while not always providing the best image quality, is able to ensure fidelity with the sinogram data.

My project aims to improve sanitation in mental health and maternity hospitals in Ethiopia by introducing pressure-washing cleaning services. This initiative goes beyond routine cleaning, it restores dignity and safety to healthcare facilities where poor hygiene discourages patients particularly expectant mothers from seeking essential care. By reducing contaminants and improving cleanliness, the project will create a more welcoming environment that encourages hospital births rather than home deliveries driven by unsanitary conditions and odors. To achieve this, I am providing pressure-washing equipment to underserved hospitals and clinics focusing on four hospitals and three clinical facilities in urgent need of sanitation improvements. Additionally, I am engaging with smaller underserved clinics that play a vital role in delivering essential healthcare services to their communities. This project presents multiple challenges including identifying high-need facilities managing equipment distribution and coordinating regular cleaning schedules. I am actively involved in every aspect from logistical planning to hands-on implementation. My role requires strong project management and problem-solving skills to ensure a tangible impact with limited resources. Beyond logistics, this work demands an understanding of the experiences of vulnerable patients. Effective communication with hospital staff and government officials is crucial for building trust and aligning our efforts with their priorities. This experience is helping me grow as a leader improving my ability to mobilize communities around a shared goal while remaining sensitive to cultural and systemic challenges. Ultimately, this project is about more than sanitation—it is about transforming healthcare spaces into environments where patients feel safe respected and encouraged to seek the care they need.

Indium phosphide (InP) quantum dots are a high-performing semiconductor material used in optoelectronic applications due to their tunable electronic properties and low toxicity compared to cadmium-based quantum dots. However, InP quantum dots are currently synthesized at or above 180°C because of the high energy input required for nucleation and growth of the covalent nanocrystals. This study explores the synthesis of small InP clusters at lower temperatures by investigating reaction conditions that can produce InP with reduced energy consumption. Using the precursors indium carboxylate and P(SiMe₃)₃ in a nonpolar solvent toluene, we systematically investigate the evolution of InP clusters at room temperature and 60°C via UV-Vis absorbance spectroscopy. The formation of atomically precise InP clusters was observed at room temperature after 23 days. To speed up the reaction, we investigate adding a polar aprotic solvent or amines to promote the formation of InP at low temperatures. Including 20% of N-Methylpyrrolidone in the solvent mixture with toluene allows InP to be formed in 2 hours. Amine additives interact with the indium cations to modulate their reactivity, therefore we investigate adding varying equivalents both to the pre-formed atomically precise cluster, and to the indium and phosphorous precursors in toluene. We found that adding up to 100 equivalents of benzylamine per cluster did not promote the growth of InP clusters. Our findings contribute to the understanding of how InP forms at low temperatures for scalable, environmentally friendly production.

Glaciers have long been used as the bellwethers of climate change, given their ability to store gases, dust, microbes, and other environmental materials in their layers; tracking their recession has also been an important visual indicator of climate change. In this research, I examine how anions in newly exposed vary with depth. To do this, I took samples from exposed vertical ice faces on the Coleman glacier, on the north face of Mount Baker. Samples were thawed and analyzed using ion chromatography.  Trace amounts of chloride, nitrate, sulfate, and phosphate were found in each sample. The ion concentrations showed no trend with depth, and the ice itself appeared uniform. This is in contrast from vertical cores taken from solid ice in numerous other surveys, which show distinct annual layers and variation. This suggests that the ice at vertical faces has different properties from that at the top layers, including in its ability to trap environmental markers. Further research is needed to confirm this difference and examine which of these markers is most affected. Increased understanding of these markers could give more insight into how glaciers change over time and interact with their environment.

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

The increasing concern over global warming has driven interest in clean energy solutions, with piezoelectricity emerging as a promising alternative. Piezoelectric materials generate electric voltage under external mechanical forces, offering an innovative method for energy harvesting. This work derives a system of partial differential equations (PDEs) and their accompanying boundary conditions that describe the coupled elastic-electric behavior of an Euler-Bernoulli piezoelectric beam. Under the quasi-static approximation for the electrical field, the assumptions of Euler-Bernoulli beam theory, and the constitutive relations for the 3-1 piezoelectric coupling mode (i.e., voltage is generated in a direction perpendicular to external mechanical force), we develop a Hamilton’s variational principle to derive the governing equations and boundary conditions for the piezoelectric Euler-Bernoulli beam. The obtained equations consist of Gauss’s law of electrostatics and the Euler-Bernoulli beam equation that are coupled due to the piezoelectric effect: apparent electric charges that depend on elastic deflection appear in Gauss’s law, while apparent mechanical forces and moments that depend on the electric potential appear in the Euler-Bernoulli beam equation and its boundary conditions. The derivation from first principles, as well as the study of the governing equations constitutes a fundamental framework for analyzing piezoelectric beam behavior, with implications to the improvement of design of piezoelectric energy harvesters.

In their books Pihkal and Tihkal, Dr. Alexander and Ann Shulgin describe their experiences ingesting 234 psychoactive compounds, most of them newly synthesized by Dr. Shulgin. The goal of this project is to use natural language processing techniques to map the semantic space of the Shulgins’ qualitative comments and determine what commonalities, if any, exist between compounds of similar molecular structures. I first created a TF-IDF matrix to determine the importance of each word for each compound. I then applied three clustering techniques (k-means, DBSCAN, and affinity propagation) to group compounds based on their meaning and used UMAP after each technique to graph the clusters in two dimensions. Unfortunately, despite attempting different combinations of pre/post processing and hyperparameter tuning, each method resulted in only weakly associated clusters. My next analytical method is using Sentence-BERT modeling to compare the semantic meanings at the sentence level. Since sentences hold more meaning than single words, I anticipate that this technique will differentiate the compounds to a greater extent, therefore leading to more visibly divided clusters. I also have the compounds clustered by similarity in molecular structure and determined the most common words associated within each group. By quantifying the subjective experiences of these psychoactive compounds and mapping them to molecular structures, this knowledge could allow us to synthesize molecules to obtain a desired effect on a patient’s consciousness. This could in turn aid in synthesizing new medications to treat mental health disorders.

Latine people constitute the largest minority in the US, yet the prevalence of diabetes within the Latine community is nearly twice that of White Americans. Latine populations also experience food insecurity at higher rates than the national average, which heightens their risk for chronic conditions like type 2 diabetes (T2D). While nutritional counseling is critical for T2D care, there is limited research on the barriers to effective counseling, especially for minoritized identities. Understanding how Latine patients relate to counseling and barriers to adherence is an urgent health concern with significant implications for addressing health disparities. This study investigates both micro (e.g., provider pathologization of culturally relevant foods) and macro (e.g., food access) barriers to following nutritional guidance for Latine people with T2D. Previous research in South Asian communities shows providers pathologize culturally relevant foods, leading to poor metabolic control, increased complications, higher healthcare costs, and lower quality of life. Food insecurity exacerbates outcomes, with food-insecure diabetic patients reporting less control over their diets despite understanding dietary requirements. However, these barriers remain unexplored for Latine people with diabetes in the US healthcare context. Through a qualitative study in Greater Seattle, we seek to understand the experiences of Latine people managing T2D by conducting structured interviews on barriers to following nutritional counseling. Content analysis uncovers themes related to micro and macro barriers. We aim to enhance culturally competent healthcare to overcome barriers preventing Latine people with T2D from following nutritional guidance. By amplifying the voices of Latine patients, we can inform providers on more effective ways to interact with this population and develop tailored care plans.

Plasma, a fluid consisting of highly charged particles, is the single most abundant state of matter in the universe, yet our understanding of its properties remains incomplete. One common method of generating plasma is by inducing a large voltage difference between two charged electrodes in a low-pressure environment, referred to as direct current (DC) plasma. Understanding the relationship between plasma temperature and spectral line intensity as a function of external parameters, such as voltage, pressure, and position, is crucial to optimizing plasma-based processes. This study analyzes these dependencies systematically to help build a further understanding of the spatially dependent properties of DC plasmas. We extract electron temperature from spectroscopic measurements by analyzing line intensities assuming a Maxwell-Boltzmann electron energy distribution. The intensity of spectral lines is related to electron energy via the Boltzmann factor, allowing for temperature determination through a logarithmic plot of intensity ratios versus upper energy levels. By varying voltage and pressure, we identified trends in intensity and temperature, providing insights into plasma behavior. Our results suggest that higher discharge voltages correspond to an increase in electron temperatures, indicating a direct relationship between voltage and temperature. These results provide a greater understanding of plasma-based processes, paving a path toward greater efficiency in applications such as semiconductor manufacturing, surface treatment, and materials processing.

Most human activities engage multiple brain regions simultaneously, but our ability to study this is limited by our capability to run experiments. Electrophysiology is the data-collecting technique of placing electrode probes into the brain to record the electrical activity of neurons. Currently, researchers performing electrophysiology use one or two probes. However, to record activity across many regions, researchers must use multiple probes which introduce new kinds of challenges such as ensuring accurate and reproducible positioning of several probes to target specific areas in the brain, managing probe movements to avoid collisions with each other, and preventing probes from breaking during insertion. Brain-wide coverage will require five, ten, or more probes, amplifying the challenges researchers face with just one or two probes at a time. Over the past two years, I have been developing an automation platform that can solve these challenges in electrophysiology. A key innovation is the integration of a computer-vision-based probe tracking system being developed in collaboration with the Allen Institute. This probe tracking system ensures probes can be accurately positioned on brain regions repeatably and detect when probes fail to insert into the brain, so movements are stopped before damage occurs. The automation platform will also route and manage electrode probes during experiments, preventing collisions with each other and the rig. Together these improvements ensure that electrophysiology experiments can be performed in a reliable, safe, and reproducible manner, but perhaps the biggest improvement the platform provides is efficiency. On average, it takes 15 minutes to insert one probe into the brain, meaning brain-wide experiments using eight probes may need two hours to insert manually, increasing stress on subjects unnecessarily. With automation parallelizing the process, we can reduce insertion times from 15 minutes per probe to 15 minutes flat making brain-wide electrophysiology a viable tool in neuroscience.

Humans have limited ability to regenerate tissue lost from traumatic injury or amputation. Growth factors have the potential to induce the regrowth of damaged tissues, such as bones and joints in a mouse model of digit amputation. However, to achieve this in a clinical setting, a minimally invasive drug delivery system that permits the controlled release of multiple growth factors is needed. To this end, we are using micron-sized, bioactive hydrogels (microgels) to investigate the spatiotemporal release of growth factors in the presence of an external magnet, which helps direct microgels to the wound site. Optimizing the drug release profile requires an understanding of the biophysical properties of the microgels and their surrounding tissue. We hypothesize that the magnetic force needed to translocate a microgel is directly related to its size and stiffness and to the tissue microenvironment’s pore size and stiffness. Meanwhile, the release rate for growth factors is expected to be inversely related to microgel diameter and stiffness. To investigate these hypotheses in silico, we developed two computational finite element (FE) models. First, we used COMSOL Multiphysics to characterize the magnetic force exerted on a microgel by a permanent magnet. Magnetic forces were measured by varying the distances between the microgel and magnet. Second, we used FEBio to model microgel movement through tissue, taking into account how microgel and tissue mechanical properties (e.g., Young’s modulus, Poisson’s ratio) influence translocation. Future work will compare simulation results to in vitro data of microgel translocation and protein release. By using FE analysis to model biomaterial behavior, we will be able to better predict drug dosing at the wound site to induce musculoskeletal tissue regeneration.

Liver fatty acid binding protein (FABP1) is highly expressed in the liver, kidney, and gut and is known for its role in binding endogenous lipids. FABP1 has also been shown to bind drugs and modulate metabolism in the liver. A high frequency single nucleotide polymorphism (SNP T94A) in FABP1 is shown to correlate with nonalcoholic fatty liver disease. We hypothesize that this SNP also affects drug binding. To evaluate drug-FABP1 binding, I measure equilibrium dissociation constants (K_ds) by fluorescent displacement assays for both FABP1 wild-type and T94A using two fluorescent probes, 11-(dansylamino)undecanoic acid (DAUDA) and 8-anilino-1-naphthalenesulfonic acid (ANS). FABP1 has a large binding pocket that can accommodate 2 ligands simultaneously in a ‘high affinity’ and ‘low affinity’ binding site. When DAUDA-FABP1 or ANS-FABP1 are titrated with a drug, a drug-FABP1-probe ternary complex is formed rather than the probe being fully displaced. This complicates data analysis and suggests that endogenous lipids may change the affinity of drugs for FABP1. Therefore, I use multiple fluorescent probes with different binding affinity to obtain drug K_d values. I use singular value decomposition (SVD) to isolate individual fluorescent components from the overall observed fluorescence spectra. I then estimate drug and probe K_ds for FABP1 T94A and T94T by fitting the fluorescent change due to binding to dynamic models in COPASI software. From forward and reverse titrations, DAUDA K_d for FABP1 wild-type was found to be 0.194 µM while ANS binds more weakly (K_d = 1.38 µM). From DAUDA displacement assays, diclofenac was found to have a K_d of 3.90 µM for wild-type FABP1 and 3.78 µM for T94A. I anticipate measurement of K_ds for 8 other drugs using both DAUDA and ANS in the coming months. The developed methods will enable evaluation of FABP1’s role in drug disposition.

Erbium(III) doped cerium oxide nanocrystals are promising candidates for spin qubits in quantum computing and information science applications. Our goal is to tune the synthesis and composition of Er-doped CeO2 nanocrystals for monodispersity and desirable optical properties, particularly the intensity and lifetime of near-infrared emission features unique to Er3+. We optimized previously reported methods for making Er-doped CeO2 by altering the concentration of erbium, presence of water, and the amount of time allowed for the reaction to progress. These nanocrystals were then analyzed using several techniques, including transmission electron microscopy, X-ray diffraction, and photoluminescence spectroscopy. Our results indicated that by omitting water from the synthesis, the sizes of the nanoparticles decreased significantly. Additionally, smaller concentration of erbium(III) dopant in the nanoparticles correlated with a longer lifetime of photoluminescence intensity.

The ventral tegmental area (VTA) contains dopamine (DA) expressing neurons, which are critical for reward processing in the brain. DA neurons are tightly regulated by inhibitory GABA-expressing neurons; these GABA neurons have recently been found to be present in distinct subpopulations in the VTA. Opioids disrupt this regulation by inhibiting VTA GABA neurons via mu-opioid receptors (MORs), leading to increased DA activity and reinforcing drug-seeking behavior. However, the distribution of MORs across distinct VTA GABA subpopulations remains unclear. This study uses multiplexed in situ hybridization to map MOR (Oprm1) expression in genetically distinct GABA populations characterized by their expression of Pnoc, Crhbp, and Cbln4. Preliminary findings suggest differential Oprm1 expression, with Pnoc and Cbln4 populations showing high Oprm1 expression patterns, while Crhbp contains little Oprm1 expression. These results highlight the heterogeneity of VTA GABAergic neurons and provide insight into the mechanisms underlying opioid addiction, which may inform future therapeutic strategies.

Manduca sexta is a model lepidopteran insect organism which has been widely used in the field of chemical ecology due to its impressive olfactory senses. Odorant reception plays an important role in locating nectar sources, mating, and ovipositioning. Insects detect volatile chemical compounds (VOCs) present in their complex environment primarily through their sensory organ antenna. Each antenna is made up of thousands of olfactory receptor neurons (ORNs) and each neuron detects specific odor molecules with specific odorant receptor proteins. The whole genome sequencing of Manduca sexta has identified the major chemosensory receptor proteins: odorant (ORs), ionotropic (IRs) and gustatory (GR) but the role of each receptor is still unclear. In this project, we are investigating the role of female-biased odorant receptors OR5 and OR6, which might be involved in detecting VOCs present in their environment and play an important role in mating and oviposition. To investigate the role of these ORs, we have generated mutant strains by using a CRISPR/Cas9 approach and we are checking their effect on odor detection and oviposition behavior by comparing them with wild type strains. We are also performing an RNA-FISH experiment to visualize the ORs and locate the olfactory sensory neurons in the female antennae. In addition to this, we are also working on developing a neurogenetic tool which will allow us to measure the neuronal activity in response to different olfactory stimuli by generating a pan-neuronal BRP-GCaMP6s transgenic line.

All mammals experience a slowdown of cardiac pacemaker rate with aging. The main mechanisms to explain that phenomenon are related to alterations in the ionic currents that underlie the diastolic depolarization phase of the action potential. We have previously reported that pacemaker cells from old mice have reduced L-type calcium currents. We further explore the mechanism underlying that reduction, testing cell hypertrophy and alteration in the scaffolding of L-type calcium channels as potential mechanisms. To test for cell hypertrophy, we combined immunostaining and high-resolution imaging to map the HCN4-positive pacemaker region of isolated upper heart explants from young and old mice. We compared cell length, width, and area between young and old cells. We also determined these morphological parameters in HCN4-positive enzymatically dissociated pacemaker cells. We found no significant difference in cell dimensions or area between ages, ruling out hypertrophy as a potential mechanism. We used mass spectrometry to identify expression changes in scaffolding proteins essential for calcium channel organization at the plasma membrane. Through this approach, we identified a large reduction of caveolin 3 as a possible mechanism. Caveolin is a protein essential to forming signaling microdomains between calcium channels and other proteins. Using western blotting, we confirmed a 50% reduction of caveolin 3 in isolated pacemaker tissues from old animals. Using proximity ligation assay and super-resolution microscopy, we showed altered recruitment of L-type calcium channels into caveolae. Our findings suggest that the age-associated decrease of L-type calcium current is caused by a reduced insertion of these channels in caveolae.

Acetylcholine (ACh), a neurotransmitter known for its roles in neuromuscular function and cognition, has recently been implicated in immune regulation, particularly in the context of Type-2 immunity. The Type-2 response combats parasites at mucosal and cutaneous sites and plays a role in allergic diseases like asthma and food allergy. In the intestine, Type-2 inflammation involves a dramatic remodeling of the intestinal epithelium via the activation of intestinal epithelial stem cells (ISCs), which results in the hyperplasia of specialized effector-like secretory cells such as goblet and tuft cells. These epithelial cells then produce factors that talk back to the epithelium, such as Ach, and factors that promote Type 2 immune responses, such as the cytokine interleukin-25. Tuft cells are the only intestinal epithelial cells that express choline acetyltransferase, the enzyme for ACh synthesis. Recent work suggests that during helminth infection, tuft cells release ACh in response to IL-13 signaling, implying a role for ACh in regulating epithelial responses. However, its specific function in epithelial remodeling and Type-2 immunity remains unclear.This project aims to investigate ACh’s epithelial intrinsic role in Type-2 immune responses using an in-vitro enteroid model of the intestinal epithelium. Enteroids, 3-D cultures derived from stem cells, model the epithelium without immune cells, allowing for a focused examination of epithelial-intrinsic factors in immune responses. By culturing and treating enteroids from wild-type and tuft cell-deficient mice with ACh, we will assess its effects on goblet cell proliferation, inflammation, and stem cell renewal during injury regeneration responses. I hypothesize that ACh enhances the pro-Type-2 inflammatory response in enteroid epithelial cells, leading to heightened immune activity. This research will advance our understanding of the neuro-immune axis in the gut and may have implications for parasitic infections and allergic inflammation.

Hyalella azteca are freshwater amphipod crustaceans abundantly found throughout North America and are frequently used in toxicology for water and sediment toxicity testing. As freshwater bodies change due to anthropogenic climate change, understanding chronic, sublethal impacts to aquatic life is critical. Amphipods are known to have a higher tolerance to heavy metals (i.e. Cu²⁺) and road salt (i.e. NaCl) compared to other aquatic invertebrates, however, these contaminants may have subtle, sublethal consequences on their ability to smell and detect chemical cues for survival and reproduction. This research identifies the combined impacts of environmentally relevant levels of Cu2+ and NaCl, on the olfactory system and olfactory-related behaviors of H. azteca. H. azteca underwent acute 96 hour exposure to control, Cu2+ (30 µmol/L), and combined Cu2+ (30 µmol/L) and NaCl (5 ppt) contaminated freshwater. I recorded daily measurements of survival, and utilized qPCR to examine changes in the expression of key olfactory genes that we predicted would be modulated in response to these multiple stressors. I assessed the olfactory-associated foraging behavior to determine changes in their detection of an attractive food cue when exposed to Cu2+ and NaCl, which would indicate olfactory impairment. Preliminary results show that amphipod survival is not impacted by Cu2+ and NaCl contamination but changes to their olfactory system occur. Therefore, U.S. Environmental Protection Agency water quality standards for heavy metals and salt may not mitigate long-term, sublethal effects on aquatic animal populations as it relates to this important sensory modality.

Certain species exhibit the remarkable ability to regenerate their appendages, a process that requires complex metabolic pathways to facilitate the cellular proliferation needed to regrow tissue. Among these species, Xenopus tropicalis, the Tropical Clawed Frog, serves as a great model for regeneration studies because of its transient regenerative capacity. X. tropicalis tadpoles exhibit the ability to regenerate their tails, but this capability is gradually lost after metamorphosis. This unique characteristic allows for direct comparison of regenerative and non-regenerative processes within the same species. Previous work from the Wills lab indicates that genes encoding the enzymes of the pentose phosphate pathway (PPP), which generates precursors of biosynthetic molecules such as nucleotides and lipids, are highly expressed during tadpole tail regeneration. Although tail regeneration has been well studied, the variation in hind limb regenerative capacity across developmental stages and the metabolic pathways involved remains unclear. Hence, I performed a live imaging study to determine the developmental progression of hind limbs and assess their regenerative potential. This data suggests a decrease in success as the tadpole gets older. Immunohistochemistry staining of mitotic cells in developing limbs shows that proliferating cells decline as regeneration competency decreases. I hypothesized that genes for the PPP enzymes would also be expressed during successful limb regeneration, which was confirmed by in-situ hybridization. Together, these findings indicate that the regenerative capacity in limbs of X. tropicalis is stage-dependent and that PPP genes are expressed during all stages of regenerative capacity. This provides insights into the role of metabolic reprogramming in appendage regeneration, with the potential for translating it into non-regenerative species like mammals.

Stiffness measures derived from MR Elastography have shown value in guiding treatment decisions and monitoring effectiveness of therapies for liver disease but it requires extra hardware, longer scan duration and is susceptible to motion and breathing artifacts. Recent studies have revealed a strong linear correlation between water diffusion and tissue stiffness, demonstrating that Diffusion Weighted MRI (DWI) can be used to estimate stiffness values in liver tissue. DWI-derived stiffness values may help evaluate treatment-induced changes in breast cancer but to our knowledge, this has not yet been tested. The purpose of my ongoing study is to calibrate DWI estimates of tissue stiffness for the breast by optimizing DWI parameters (diffusion weightings, or ‘b-values’) and  calibration coefficients (a, b), evaluating the potential of stiffness measures for monitoring response to neoadjuvant chemotherapy (NAC) in breast cancer. We collected baseline and early treatment MRI exams from 25 patients undergoing NAC in this IRB approved study along with their treatment outcomes based on pathologic response post completion of NAC. I evaluated  the stiffness values obtained from different b-value pairs (low b-values: 100/200; high b-values: 800,1500,2000 s/mm²) and calibration coefficients(a,b=-9.7,13.9:-10.8,17.5:-8.8,21.2) and compared it to the invasive breast cancer stiffness values reported in literature. I also evaluated the performance of the optimized parameters to predict treatment response. The optimal b-value pairing (b=200,1500s/mm²) and coefficients a=-9.7,b=13.9 produced stiffness values consistent with literature. Using this approach, the performance for predicting treatment outcomes between responder and non-responder groups was AUC=0.84. These preliminary findings suggest that DWI based virtual elastography could serve as a non-invasive tool to assess tumor stiffness and track treatment efficacy, potentially improving breast cancer management.

This investigation is based on the famous intermediate axis theorem, often called the tennis racket theorem. This theorem describes why objects with three distinct moments of inertia, around three different axes, have an unstable rotation around the intermediate axis (the axis with the intermediate moment of inertia) while the axes that have the largest and smallest moment of inertia have a stable rotation. This phenomenon can be observed in rotations of everyday objects like tennis rackets and phones. By videotaping rotations of different objects with three distinct moments of inertia around three axes, and visually examining the intermediate axis, one can notice the instability of the intermediate axis compared to the stability of rotations about the other two axes. We mathematically analyzed the motion around three axes using Euler’s equations of rotations, the equations governing the dynamics of a rigid body undergoing rotational motion. We solved the differential equations demonstrating the instability around the axis with the intermediate moment of inertia. This behavior was also simulated in MATLAB using Euler’s equations of rotations. Our graphs of velocity as a function of time for rotation around the three axes, demonstrated and justified the visual observations from the videos. These experimental and computational approaches can lead students to a comprehensive understanding of the intermediate axis theorem.

Fluoride intake is essential for dental health, yet excessive consumption can lead to fluorosis, a condition negatively affecting teeth and bones. Tea, one of the most widely consumed beverages globally, naturally accumulates fluoride, making it a significant but often overlooked dietary source. Black tea is the most popular type of tea consumed in the U.S. In this study we compared fluoride levels across six brands of black tea and investigated how brewing conditions and water sources affect fluoride concentrations in tea. We brewed black tea from six locally popular brands (Lipton, Tazo, Fortnum & Mason, Twinings, Tetly, and Harney & Sons), using two water sources (distilled water and Seattle tap water), with four samples for each brand using both water sources. We brewed 50 mL of water at 100°C, then we let each sample of the tea sit for 5, 10, and 20 minutes. Ion chromatography was used to measure fluoride concentrations at each time interval. We compared these values to the U.S. Environmental Protection Agency's (EPA) recommended fluoride level of 4.0 mg/L. Our results help characterize the variation between brands and the influence of brewing duration on fluoride release. These findings contribute to a better understanding of fluoride exposure from tea consumption, helping consumers make informed choices about their dietary fluoride intake.

Beaver dams can function as natural filters helping decrease pollution in streams, creeks, and rivers. Beaver dams slow down the water flow in a creek or river, forming ponds that help trap excessive nutrients. An excess of nutrients such as phosphate and nitrate can cause eutrophication, leading to increased algal blooms that can produce toxins and ultimately deplete oxygen in the water. This study investigates the ion levels of chloride, fluoride, phosphate, nitrate, sulfate, and bromide upstream and downstream of the major beaver dam at Pipers Creek in North Seattle's Carkeek Park over the course of a year to better understand the long-term impacts of the dam. We collected three water samples at each of eleven sites along the creek, eight upstream from the dam, and three downstream. Ion chromatography was used to measure the concentrations of anions at each site. The results of this study help elucidate the role of beavers in moderating water quality and provide important baseline data documenting seasonal variations in the nutrient load at Pipers Creek. These findings can also be used to better understand the impact of new beaver dams in other freshwater systems.

Low-income communities are often disproportionately exposed to air pollution. High concentrations of pollutants such as particulate matter under 2.5 µm (PM2.5) and human aerosol emissions, including carbon dioxide (CO2), have been linked to various health and cognitive issues. Performance arts, including singing and playing instruments, produce human aerosol emissions and are considered high risk for airborne disease transmission. Our study evaluated the accumulation of CO2 and PM2.5 in high-risk environments (band classrooms) in low-income public schools in King County (WA), to determine whether there is a correlation between accumulation rates and Title 1 designation. Title 1 designation, which provides government funding for schools with a high percentage of students from low-income households, was used to represent low-income communities. We compared four middle schools that qualified for Title 1 designation to one school that did not qualify. Concentrations of CO2 and PM2.5 were measured using the Aranet4 Home CO2 sensor and a PurpleAir Classic sensor for PM2.5. We took a baseline measurement of both concentrations when the classroom was unoccupied. We then analyzed the change in concentration rates when classes were in session, taking into account classroom size and number of students. Our data showed concentrations above recommended levels at 1,370 ppm (parts per million) for CO2 in one of the Title 1 schools suggesting that Title 1 schools may be at greater risk of poor indoor air quality, though additional studies are needed. This additional exposure to pollutants and human aerosol emissions in already high-risk environments like band classrooms may lead to increased airborne disease transmission, highlighting the disparity in healthy learning environments. These classrooms require additional measures to maintain healthy concentrations of CO2 and PM2.5 to reduce the risk of airborne disease transmission particularly in low-income communities. 

The balance of ions in soil and water directly impacts sustainable agriculture, human health, and livestock well-being. Small family farms, such as the one in this study, often depend on well water for household and agricultural use, making water quality essential for both food safety and long-term farm viability. This study investigates the spatial distribution of key anions, including nitrate (NO₃⁻), nitrite (NO₂⁻), and phosphate (PO₄³⁻), in soil and well water across a small family-operated farm in Woodinville, WA. These ions were selected due to their roles in plant growth, soil chemistry, and potential health effects on humans and animals. The farm sustains 68 animals, including chickens, cows, donkeys, alpacas, llamas, sheep, quails, and horses, and provides food and water for seven residents. Soil and water samples were collected from distinct zones, including livestock pens, vegetable fields, and tap water from the farm’s well, to evaluate how land use influences ion distribution. Soil samples were collected at multiple sites; ions were extracted from the samples using a  common water extraction method. Ion chromatography (IC) was employed to quantify anion concentrations and assess spatial variability. While this study does not determine definitive sources of the ions, analyzing variations in these ion concentrations near crop fields and livestock areas can help assess potential nutrient leaching and runoff. This type of comparative analysis of soil and well water samples helps quantify potential risks to both farm operations and the health of residents and livestock. This research underscores the importance of ongoing water and soil quality monitoring to ensure the sustainability of small-scale farms that rely on well water and homegrown food, while offering insights for improved land and resource management practices

As climate change increases temperature, Pieris rapae caterpillars' feeding habits may be affected. As their feeding habits are altered, P. rapae may begin to migrate to different plants; this can be detrimental for agriculture because these defoliating caterpillars are pests. P. rapae caterpillars are known to feed on Brassica species, including collards and kale. It is also shown that caterpillars increase their feeding rate at higher temperatures (Kingsolver 2000). However, little is known about how temperature influences their feeding preferences. In this experiment, we find the consumption rate of P. rapae 4th instar larvae eating kale (Brassica oleracea var. sabellica) and collards (Brassica oleracea var. viridis) to find consumption preference between these two plants at 14°C, 23°C, and 35°C. Larvae were placed on a moist filter paper in petri dishes containing 2 collard and 2 kale leaf disks placed in an alternating fashion. Petri dishes were placed in three separate incubators set to the three temperatures. We predicted that P. rapae would have a preference for collards since they are reared on collards in the lab and they would increase their consumption of the preferred plant. We also examined the percentage per hour of each leaf eaten and compared this data between types of leaves and temperatures. The data showed that as temperatures increased, the consumption rate of P. rapae caterpillars also increased. Though, there was no change in preference as the P. rapae caterpillars consistently preferred collards over kale. This suggest that higher temperatures from climate change will increase the rate at which caterpillars eat, but will not affect preference. It is important to consider the change in consumption rate of caterpillars with temperature when aiming to prevent crop damage in the face of climate change.

Safe drinking water in schools is crucial for children's safety and academic performance. While Seattle Public Schools has tested for some contaminants, such as lead, the district's responsibility for ion-specific testing for anions such as phosphate, bromide, nitrite, nitrate, chloride, sulfate, and sulfite is less clear. High concentrations of anions pose potential health risks, including reduced oxygen in red blood cells, higher risks of tumors in children, and diarrhea. This research investigated the anion concentration in water fountains across seven high schools in the Seattle Public Schools. Twenty-one water samples were collected from seven public high schools and analyzed for anion concentration using ion chromatography. Results were compared to the Environmental Protection Agency's (EPA) maximum contaminant level (MCL). All test samples were below the EPA's MCL. These results suggest that the drinking water in these schools does not pose potential risks to students from anion contamination. While regular monitoring and management are still necessary to maintain safe drinking water, Seattle Public Schools have met the safety requirements for anion concentration in their drinking water. 

As individuals experiencing homelessness age, their healthcare needs become increasingly complex. People over age 50 are the fastest-growing group experiencing homelessness, yet there is little knowledge about specific subgroups, particularly older homeless veterans. The aim of our study was to explore the experiences of older veterans and non-veterans experiencing homelessness, with a focus on contextualizing the unique barriers to accessing healthcare and maintaining stable housing in each group to better understand how these factors impact healthy aging. Using a qualitative research design, we developed a semi-structured interview guide in collaboration with key informants from Compass Housing Alliance. We recruited participants aged over 50 who have recently exited homelessness and are living in Permanent Supportive Housing (PSH). We conducted forty-five-minute interviews with veterans (6-10 participants) and non-veterans (6-10 participants). The questions focused on daily living, work, healthcare, connection & community, access to structural support services, and perceived impact on aging well. We recorded and transcribed these semi-structured interviews, which we coded to identify key themes. Additionally, all participants completed a basic survey to capture demographics such as length of time homeless, age, and gender. After the initial thematic analysis, we had a second session with participants to check the accuracy of the identified themes. The qualitative approach of this study provides new data directly from those with lived experience. This study offers critical insights into the unique challenges faced by aging veterans in comparison to non-veterans in PSH, exploring gaps in healthcare access, limitations of healthcare services, and the role of housing stability for older adults. This research is significant to policymakers, healthcare providers, and housing organizations seeking to tailor support to the heterogeneous groups within the aging homeless population.

Transient ischemic attack (TIA) patients can still experience a recurrent stroke due to platelet-rich thrombi despite being on dual antiplatelet therapy (DAPT) consisting of acetylsalicylic acid (ASA) and a P2Y12-inhibitor. One pattern these patients have was an elevated von Willebrand Factor level (VWF), a blood clotting protein that tethers platelets to the endothelium. VWF unfolds under shear, exposes its A1 domain to which surface receptor GPIb-IX-V of platelets can bind. DAPT targets platelet activation by inhibiting thromboxane A2 synthesis and blocking ADP binding to P2Y12, but it does not directly address shear-mediated activation of platelets via VWF. Even with DAPT, platelets can still bind to VWF via GPIb-IX-V under a high shear rate. To understand the interplay between elevated VWF levels, DAPT, and platelet thrombus formation under shear flow, we used a microfluidic device to analyze platelet-rich plugs for (1) platelet activation, (2) aggregation size, and (3) contractile versus drag forces to withstand embolization. Those characteristics are measured in a healthy platelet-plug control and a platelet-plug doped with 6-fold VWF level, both with and without DAPT. We found platelet-plugs with DAPT still maintain activation, and activation level becomes higher when DAPT is combined with elevated VWF level. Platelet-plugs with DAPT and/or elevated VWF have larger aggregate size than control, and aggregate size is highest when DAPT is combined with elevated VWF level. While contractile force dominates in control, it becomes similar to drag force with DAPT and/or elevated VWF. We suspect the large size, reduced contractile force and maintained activation of platelet-plugs with elevated VWF can make the plug prone to embolization caused by the drag force. This result can shed light on the limitations of DAPT when VWF level is elevated, and introduces the possibility of screening patients for high VWF to tailor antiplatelet therapies. 

The focus of this research was to test the effectiveness of a silicone-based paint in the marking of Pieris rapae in a manner that was non-invasive and durable. Previous studies have tested other marking methods but have faced challenges such as harm to the organism. By using a paint made from red cabbage (Brassica oleracea), I aim to minimize the harm to larvae in current marking methods while retaining durability under moist conditions. This experiment examined both the durability and health effects of cabbage-based paints on P. rapae caterpillars. Preliminary experiments tested a water-based version, which did not appear to affect survival but faded under moist conditions, and a silicone-based version, which withstood moisture but raised concerns about potential effects on health due to the additional ingredients required for the silicone base. My research continued testing the cabbage paint with a cosmetic-grade dimethicone base and aimed to determine the extent that the cabbage paint may have on caterpillar health and survival. Survival experiments were conducted on 4th and 5th instar caterpillars to determine larva mortality rates when exposed to the pigment. Weight change experiments were conducted from the 4th instar to pupation to be used as a metric of the overall health of the larvae. I conclude that the silicone-based cabbage pigment is a promising marking method for larger caterpillars, offering improved durability and minimal impact on overall health compared to many conventional methods. These findings contribute to the development of safe durable marking techniques suitable for ecological research on soft-bodied insects.

Duchenne Muscular Dystrophy (DMD) is a severe neuromuscular disease caused by mutations in the dystrophin gene and characterized by progressive muscle wasting. Dystrophin protein is essential for the stabilization of muscle fibers; without it, continuous muscle damage eventually has devastating consequences in the skeletal, cardiac, and respiratory systems. While prior AAV-mediated editing strategies have been effective in targeting these mutations, there are significant immunological concerns from the uninterrupted expression of bacterial gene editing components. This project utilizes the mdx mouse model of DMD to address these concerns by developing methods to turn gene editing on and off using novel drug-responsive pA regulator vector constructs. I have been part of this project from the start, contributing to the assembly of the expression constructs using bacterial cultures and standard cloning techniques relying on restriction enzymes and high-fidelity cloning kits to piece together our editing constructs. Initial data was acquired from cell culture tests where I helped perform quantitative dual-luciferase reporter assay analyses. Subsequent in vivo experiments were performed by delivering adeno-associated viral vectors, carrying our constructs, into mdx mice via retro orbital injection. Activation of editing activity was achieved via three intraperitoneal injections of Tetracycline.  During analyses, I played a significant role in processing muscle tissues to extract proteins, DNA, and RNA for quantitative assays. Ultimately, our cell culture tests identified two lead pA regulator sequences exhibiting favorable activation levels at therapeutically relevant Tetracycline doses. Initial in vivo tests are promising, showing drug responsive editing and dystrophin expression in mice. We anticipate that our follow up tests will restore sufficient dystrophin expression and improve muscle function, without persistent editing activity. Overall, the outcomes of these studies could have significant implications for a multitude of genetic conditions amenable to genome editing and may help accelerate translation of effective methods towards clinical trials.

Viral evolution theory hypothesizes that specialist strategies increase fitness by reducing interspecific competition, while generalist viruses increase fitness by accessing multiple hosts. However, specialism may come at the cost of infecting few hosts, while generalism may reduce fitness in any single host. These tradeoffs have been demonstrated in Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus infecting multiple salmonid species. High rates of viral replication have been observed for specialized subgroups in their respective hosts, while lower rates of replication across multiple hosts have been observed for the generalist subgroup. However, the host-virus mechanisms underlying these replicative differences are unknown. Here, I aim to characterize the early innate immune response of sockeye salmon, the ancestral host of IHNV, to specialist and generalist subgroups at target tissues. Specifically, I seek to test whether sockeye salmon display distinct transcriptomic responses to IHNV specialist and generalist subgroups in the kidney 2 days post-exposure (dpe). To accomplish this goal, RNA was extracted and sequenced from kidney tissue of individuals 2-dpe following exposure to specialist (n=9), generalist (n=9), or control (n=4) IHNV treatments. Overexpressed and underexpressed genes will be identified between each subgroup and control samples. These genes will then be used for pathway enrichment to compare differences in transcriptomic response. Replicative rates have shown a difference between specialist and generalist subgroups of IHNV 2-dpe in the kidney; therefore, we expect to observe differences in the number and magnitude of over- or underexpressed genes and enriched pathways between hosts exposed to specialist and generalist subgroups. Results from this study will aid in characterizing evolutionary mechanisms underlying viral specialism and generalism, understanding host innate immune response and evasion strategies, and identifying biological markers associated with response to viral exposure. This knowledge will be critical in predicting future disease outbreak and informing disease mitigation strategies.

Protein subunit vaccines are highly used today as an alternate vaccine platform to older vaccines such as live-attenuated viruses. They contain a protein antigen of the virus or bacterium that can be recognized and targeted by the immune system, and an adjuvant that amplifies the immune system response to this protein by widely putting the immune system on alert. The most commonly used adjuvants pose the risk of possible adverse reactions and are not created to target specific immune pathways, but rather stimulate general inflammation. To design a vaccine adjuvant that generates a more targeted immune response, we are using the self-assembling protein nanoparticle, I53-dn5, to display a CD40 binder that mimics the T Cell ligand, CD40L, by binding to B cell surface receptor CD40. We aim to create a particle that can replicate the binding interaction between B and T cells in the lymph node responsible for triggering antibody maturation, and B cell proliferation and differentiation. We hypothesize that this multivalent display of CD40 binder will generate potent B cell responses allowing us to respond to an antigen more effectively than current adjuvants. We are utilizing computational protein design methods like RFDiffusion, ProteinMPNN, and AlphaFold2 to optimize this display, and testing these designs in vitro for stability and ability to elicit downstream signaling effects of the CD40/CD40L interaction. This research holds two promising innovation potentials. The first is creating higher potency adjuvants by stimulating specific signaling pathways for use with protein subunit vaccines. Secondly, these materials can be used as a more stable and potent molecule in biochemical assays such as being an alternative to feeder cell lines in B cell support culture.

The timing of flowering in Arabidopsis thaliana is tightly regulated by environmental cues that induce the expression of FLOWERING LOCUS T (FT), a mobile signal responsible for floral induction. Recent studies have identified FPF1-LIKE PROTEIN 1 (FLP1), a gene co-expressed with FT in phloem companion cells, as a potential regulator of flowering. Given FLP1’s genetic similarity to known flowering regulators, we hypothesize that it functions as a mobile flowering-promoting signal. Using predictive protein interaction modeling with AlphaFold 3, followed by Bimolecular Fluorescence Complementation (BiFC) and Yeast-Two Hybrid assays, we confirmed that FLP1 interacts with key proteins in the shoot apical meristem. Overexpression of FLP1 leads to early flowering in Arabidopsis, while loss-of-function mutants exhibit delayed flowering, supporting its role in floral induction. Interestingly, while FLP1 homologs generally promote flowering across species, a contrasting effect in Brachypodium distachyon has been observed, where overexpression of its homolog (BdFLP1/BdFLP7) delays flowering. This unexpected result raises critical questions about the molecular basis of functional divergence among FLP1 homologs. To investigate this, we are introducing BdFLP1 and BdFLP7 into Arabidopsis to assess their effects on flowering time and to determine whether structural differences or distinct protein interactions underlie their divergent functions. Through molecular cloning, transgenic expression analysis, and biochemical assays including western blotting, immunoprecipitation, and mass spectrometry, we aim to elucidate the role of FLP1 and its homologs in flowering regulation. Understanding these mechanisms will provide deeper insights into conserved and species-specific pathways controlling floral induction. This knowledge is essential for improving crop adaptation strategies in the face of climate change, highlighting the broader significance of our research in plant developmental biology.

Plants' defense mechanism against herbivory is integral to both resistance in nature and the global food supply. Glycine max or soybean, is one of the most widely grown crops in the world, and suffers substantial losses from pests, including many Lepidopteran species. Related legumes, including cowpea, and common bean, can respond to Lepidopteran herbivory by detecting Inceptin-11 (In11), a short peptide found in larval oral secretions. The protein responsible for this ability, Inceptin Receptor (INR), is not found in soybean. The aims of this project are two fold, firstly introducing INR into soybean lines and testing for improved resistance to Lepidopteran herbivory, and secondly studying the effects of INR on defense gene expression in soybean, in order to better understand mechanisms of herbivory resistance. The first step in this project was to create soybean lines which consistently express INR. This was done by sending our INR construct to collaborators, who used it to inoculate multiple soybean lines, then breeding the corresponding lines until response to In11 was seen in all offspring. We will then test larval beet armyworms (Spodoptera exigua) on both INR- and INR+ lines. We expect the INR+ lines to have significantly lower S. exigua growth, indicating an improved immune response. We are also infiltrating INR- and INR+ lines with both In11 and flg22 (a well studied bacterial elicitor) for RNA sequencing of the early immune response. We expect genes involved specifically anti herbivory mechanisms being upregulated when compared to flg22. These two prongs allow us not just to demonstrate the viability of stable transgenic herbivory resistant lines, but to uncover the molecular mechanisms involved in that resistance, allowing for future scientists to better engineer the next wave of pest resistant crops.

According to the CDC report in 2022, Indigenous women experience 58% of intimate partner violence cases, which is one of the primary causes of homicide. The Reauthorization of the Violence Against Women Act (VAWA) has been credited for expanding protections for Indigenous women. This included increasing the provision of crimes under Tribal Jurisdiction and creating a pilot program for Alaskan Natives to prosecute non-Native offenders in villages. However, this policy reveals a gap between written law and people's experiences. This study examines the effectiveness of VAWA strategically, what demands were left out, and what those gaps represent in demanding changes through intersectional advocacy. In this qualitative research, I created a codebook to analyze the VAWA Congressional hearings from 2009 to 2022 to track the evolution of policy reforms from Indigenous activists. Applying a high-level textualized analysis by gathering a literature review, I utilized the framework of intersectional advocacy, which identifies the extent to which laws and interventions can create meaningful linkages across issues experienced by multiple marginalized people. VAWA remains to be a product of limitations in representation and holistic change to advance the needs of Indigenous people. Expected findings suggest that future policy reforms move beyond analyzing the issue through the lens of individuals to a community-based perspective. Intersectional frameworks will become a cornerstone of future policy work by propelling conversations centered around restorative well-being and healing. Creating bridges between people's lived experiences and legal institutions is foundational to creating critical correspondence. 

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

Injustice has permeated the criminal legal system and its punitive regime for as long as this society has existed. The rapidly expanding American carceral state arose from a myriad of retributive policies and legislation that became prevalent throughout the last quarter of the twentieth century. There is currently an abundance of research focused on the effects of incarceration on people of diverse racial, ethnic, and socioeconomic backgrounds. A crucial gap in prison reform research remains the effects of this system of punishment on LGBTQ+ people. My research endeavor aims to address that fact and reveal how individuals with queer sexual or gender identities have been impacted by this system within Washington State. The institutions that exact punishment in this state operate both on a heteronormative apparatus and a gender binary. My thesis involves placing formerly incarcerated LGBTQ+ people at the forefront of prison reform research to highlight their distinctive adversities and establish policy proposals to ameliorate them. I conducted interviews with people who fit this demographic to bring to light their lived experiences and discover what practices, policies, and changes they want to see implemented. The findings illustrate a need for reform in areas including programming opportunities, support systems, healthcare accessibility, gender-affirming care, therapeutic services, housing assignments, reentry assistance, and equitable treatment overall. Incarcerated LGBTQ+ individuals are subjected to exacerbated punishment from correctional staff and other incarcerated individuals, which leads to difficulties with interpersonal dynamics and an overall suppression of identity. Faced with heightened vulnerabilities while incarcerated, LGBTQ+ people maintain resilient attitudes as they reenter society and positively transform their lives. The voices of this community in this research illuminates the necessity of addressing LGBTQ+ rights within prison reform efforts.

Determining the genus of a graph—the smallest surface on which it can be embedded without edge crossings—is a fundamental problem in graph theory with applications in circuit design, transportation networks, and data visualization. Existing genus computation methods often require extensive case-by-case analysis, and the problem is NP-hard in general. To address this, we developed and analyzed PAGE, a novel algorithm that efficiently determines a graph’s genus by enumerating non-backtracking closed directed trails and optimizing search iterations. We established an upper bound on its runtime as O(n(4m/n)^(n/t)) for graphs of girth t and implemented performance optimizations using hash sets for cycle tracking and adjacency list storage for rotation systems. We then conducted empirical comparisons against existing methods, including SAGEMath and MULTI_GENUS, demonstrating PAGE’s superior scalability, particularly for large 3-regular cage graphs. These results suggest PAGE’s potential to improve genus computation, contribute to open problems in topological graph theory, and enhance applications in fields requiring efficient graph embeddings.

In this work, we present two new geometric properties of ellipses that emerged while studying problems related to mass transportation. The first property states that if we shrink the ellipse proportionally and consider any tangent to the smaller ellipse, the two points where this tangent intersects the original ellipse always sum to the point of tangency. This reveals a fundamental symmetry in how ellipses scale and interact with their tangents. The second property describes a special set of interior points that arise by tracing how tangents from a fixed boundary point behave across a family of smaller ellipses. We prove that this set forms another ellipse, exactly half the size of the original, centered at the midpoint between the origin and the fixed boundary point. These findings offer new insights into classical geometry and may have potential applications for problems in mathematics and other fields. 

In this project, we study the order polytopes of generalized snake posets, a particular family of polytopes (geometric shapes with flat sides) defined in recent work by von Bell and coauthors. We specifically investigate triangulations of these polytopes, which are subdivisions of the polytopes into simplicies (arbitrary-dimensional generalizations of the triangle). To do so we examine their secondary polytopes. The secondary polytope of a polytope is a related polytope in which each vertex corresponds to a triangulation of the original polytope and each edge corresponds to a bistellar flip (a specific type of transformation between triangulations), capturing the combinatorial relationships between different triangulations in a geometric object. Von Bell and coauthors conjecture that the secondary polytopes of order polytopes of snake posets have multiple unusually nice properties similar to those of the associahedra, a well-known family of polytopes that admit nice combinatorial descriptions and appear in many areas of mathematics. The overall goal of this project is to prove these conjectures. Collaborating with fellow undergraduates Molly Bradley (University of Pennsylvania), Mario Tomba (Dartmouth), and Katherine Tung (Harvard), I have written code to compute details of the smallest examples of these secondary polytopes, proved related theorems/results, proposed some new conjectures based on observed patterns in the examined examples, and made partial progress towards proving multiple of the von Bell conjectures. This project is ongoing, and we continue to explore multiple ways to approach the conjectures and more broadly understand the secondary polytopes.

Autism is a neurodevelopmental condition characterized by social-communication differences and restricted, repetitive behaviors (American Psychological Association, 2013). While racial disparities in autism prevalence have been documented, not much research has examined how these differences appear in autism screening measures. This study investigates racial differences in Autism Spectrum Quotient (AQ) scores among non-autistic Asian and White adults to assess potential biases in autism screening. Using data from three NIH-funded studies (COBRA, BEAM, and The Korean Study), AQ scores from 166 participants (n=102 White, n=64 Asian) will be analyzed through t-tests and Repeated Measures Analysis of Variance (ANOVA) to compare total and subscale scores. Preliminary observation suggests that non-autistic Asian participants may be more likely to score higher on the AQ, raising concerns about false positives in autism screenings. Understanding these differences will help improve diagnostic accuracy, reduce disparities, and promote equitable access to neurodevelopmental resources.

Asian Americans are victims of anti-Asian racism, but recent studies have also shown that they have a different role in perpetuating anti-Blackness and White supremacy. Our research aimed to specifically examine whether White and Asian Americans perceive a difference between anti-Blackness and White supremacy. We ran a qualitative study where anti-Blackness and White supremacy were defined for Asian and White American participants, who were then asked to write about their racial group’s relationship with those phenomena. We defined anti-Blackness as the belief that Black people are inherently inferior to others, and the corresponding practice of them being given insufficient power. Similarly, we defined White supremacy as the belief that White people are inherently superior to others and the corresponding practice of them being given disproportionate power. A few research assistants and I rated the similarity between the responses on anti-Blackness and White supremacy on a Likert scale from 1 to 7, with 1 indicating “not similar at all,” and 7 indicating “very similar.” We then performed a two-sample t-test (a type of statistical data analysis in psychological research) on this data to compare the responses between the Asian and White American participants. As expected, we found that the Asian American participants rated anti-Blackness and White supremacy as being more distinct than the White Americans did. The p-value for this data analysis was a statistically significant 0.004. These findings establish a foundation for future studies on the Asian American role in anti-Blackness and White supremacy. I have also conducted data analysis and ran participants for two such studies, which examined whether reminders of anti-Blackness caused Asian Americans to take more responsibility for anti-Blackness and show more solidarity with African Americans more than reminders of White supremacy.

First-generation college students (FGCS), those first in their families to pursue or complete a college degree, are a widely studied demographic across psychological research. However, much of the literature on FGCS examines their mental health and life experiences through a deficit framework, focused on systemic obstacles to success and categorizing students as “at risk”. Additionally, some research fails to recognize the importance of intersectionality, viewing FGCS’s mental health as separate from its systemic, social, and institutional contexts. To better highlight the assets and intersecting identities of FGCS, this strengths-based presentation explores existing literature about their mental health experiences, describes their risk and protective factors in developing mental health symptoms and conditions, and proposes mental health initiatives for FGCS and, specifically for, Latine FGCS. I use insights from interviews with Latine FGCS as illustrative examples to further demonstrate the importance of considering context and intersectionality in this area of psychological research.

Overgeneral Autobiographical Memory (OGM) is a common symptom of depression and Post-Traumatic Stress Disorder (PTSD). Instead of remembering specific details, individuals with OGM can only describe past events from their lives in general terms. The "trauma hypothesis" suggests that OGM emerges because individuals suffering from PTSD tend to reduce the number of details they retrieve about their memories to avoid remembering their trauma. However, this hypothesis does not fully explain how this avoidance is learned, or why avoidance spreads from traumatic memories to all autobiographical memories. To this end, we propose a computational model of OGM that integrates theories of memory retrieval and trauma with reinforcement learning. In this model, multiple episodic memories are nodes in an interconnected network, and memories are retrieved when visiting that node in the network. The more nodes that are visited, the more detailed that autobiographical recall will be. On the other hand, visiting more nodes comes with an increased risk of encountering a traumatic memory, which comes with negative emotional valence. The decisions about whether to visit another node or terminate the retrieval process are made using reinforcement learning, which takes actions based on predicted outcomes. By obtaining a greater understanding of OGM through this model, we hope to improve treatments for PTSD that specifically targets its effects on memory. 

The King County Brightwater Treatment Plant includes a marine outfall pipe anchored to the seafloor that discharges highly treated effluent from the Seattle metropolitan area into Puget Sound, Washington. Since 2009, as part of an eelgrass survey study, King County biologists have collected annual video footage of the outfall pipes from which they witnessed the abundance of organisms colonizing the pipe at all depths. Consequently, in 2012, King County biologists launched a ten-year project assessing the effectiveness of the high-density polyethylene (HDPE) outfall pipe at providing habitat for marine organisms and the composition of organisms it houses. Using a  remotely operated vehicle (ROV), they placed thirty plates of HDPE material adjacent to the outfall pipe at 100ft, 300ft and 600ft depths. Sets of replicate plates were then retrieved after 2, 5, and 10 years of deployment, at which time King County staff immediately took photos of each plate for analytical assessment. In this study, we analyzed the photos for percent live cover and composition of marine organisms inhabiting the pipe material, all across depths and time intervals. We hypothesized that the wastewater outfall pipe can function as a habitat; and the extent to which different organisms, their identifications and abundance, likely vary by depths due to the environmental conditions at different levels of depths. We found that percent live cover increased over time but did not vary across depths, and that certain phyla consistently dominated cover on the plates but dominant groups varied across depths. These findings allow experts in the field to consider using outfall pipes to provide additional habitats for marine organisms, and to assess communities of organisms at depths that are less accessible. 

Dopaminergic signaling within the striatum plays a crucial role in modulating reward and aversion, shaping behaviors such as food-seeking and consumption. While striatal dopamine release has been implicated in reinforcement learning and decision-making, the spatial and temporal dynamics of dopaminergic activity along the anterior-posterior axis of the striatum during consummatory behavior remain poorly understood. We investigated the role of dopamine in the striatum during the consumption of multiple solutions by employing a trial-based multi-spout behavioral paradigm with head fixed mice. To record the dopamine activity in the ventral and dorsal striatum, we utilized multi-site fiber photometry to record the fluorescent biosensor GRAB-DA2m along the anterior-posterior axis. Food restricted mice were given varying concentrations of sucrose as rewarding stimuli, while water restricted mice were given varying concentrations of sodium chloride as aversive stimuli. Our results revealed that dopamine responses scaled more across concentrations in the anterior regions of the striatum compared to the posterior regions. Additionally, we found more distinction between dopamine responses for the various concentrations of the aversive solution compared to the rewarding solution. Lastly, posterior striatal dopamine responses had a more rapid onset upon stimulus consumption, whereas anterior regions exhibited delayed responses, highlighting region-specific temporal differences in dopaminergic encoding. These findings refine our understanding of dopaminergic circuitry within the striatum and how dopamine-mediated responses to rewarding and aversive stimuli regulate feeding behaviors. By exploring this pathway, we offer potential insights into the mechanisms underlying disorders characterized by dysregulated reward including eating disorders and obesity.    

The locus coeruleus (LC) is a major neuromodulator source with widespread projections to distinct functional targets that influence arousal, anxiety, learning, and other behavioral states. Our lab has previously shown LC excitation triggers the release of norepinephrine (NE) into the basolateral amygdala (BLA). Recent studies suggest LC terminal stimulation may release DA into the dorsal hippocampus (dCA1) enhancing novelty-associated spatial learning. Our recent data show LC stimulation evokes DA release. Previously, release across regions, paradigms, and behaviors typically associated with LC have not been characterized, due to difficulty in separating DA from NE using traditional sensing methods. Due to this, the relationship between the LC and other DA systems remains unclear. To understand the mechanisms by which the LC may release DA independently of the ventral tegmental area (VTA), a major DA source, we have employed optogenetic stimulation to evoke release from neuron terminals and quantify the release dynamics of NE and DA. We used fluorescent biosensors to detect NE and DA, captured by a fiber optic cable and amplified to observe the relative dynamics of DA release. These sensors have tuned affinity and selectivity for NE and DA and use fluorescence as a proxy for neuromodulator release. In this project, we aim to elucidate how and under what conditions the LC is releasing DA across regions with different functions during aversive and appetitive behaviors. These data will enhance our understanding of the LC neuromodulator signaling that can become maladaptive and afflict anxiety, addiction, and more, and also demonstrate that the release of DA from the LC is dependent on the behavior induced.

The ability to pattern three-dimensional microscale cultures opens new avenues for examining the effect of nonplanar mechanical environments on mammalian cells and tissues. Our lab has developed a method for generating suspended tissues with spatial control using open microfluidic principles called Suspended Tissue Open Microfluidic Patterning, or STOMP. STOMP utilizes spontaneous capillary flow and capillary pinning to pattern suspended, multi-region tissues. Using similar microfluidic principles as STOMP, we have developed a method to pattern large (cm-scale) models via semi-open microfluidic channels called Suspended Nonplanar and Planar, or SNaP, geometries. I design these devices with computer-aided design, fabricate components on stereolithography 3D printers, pattern devices with standard pipettes, and culture resulting tissues for short- and long-term time periods to model biological scenarios. With the broad statement that human tissue is generally nonplanar in mind, my research focuses on three different geometries of tissue, 1) a sinusoidal wave, 2) a transwell-like mogul, and 3) a multi-region dome, where each nonplanar geometry enables a different biomedical investigation. The sinusoidal wave construct allows us to ask if cells embedded in tissues with varying frequencies of undulation experience changes to cell morphology due to the topology of their environment; the transwell-like mogul enables investigation of cell proliferation of cells grown at or within an air-liquid interface; and the multi-region dome facilitates the study of tissue interfaces where a diseased region of cells meets a healthy region of cells, all within a single contiguous tissue. I am currently exploring these questions through multiple cultures where different device versions and/or multiple cell types are engaged to collect biological readouts which demonstrate SNaP as a translatable platform for the investigation of questions in biomechanics and regenerative medicine.

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

Biodiesel, "an alkyl ester of fatty acid" and type of biofuel, can be used for fueling vehicles and can be produced via transesterification, the process of using the alcohol methanol along with a base catalyst (usually sodium hydroxide) to break down oils and fats that have many triglycerides into fatty acid methyl esters (FAMEs) and glycerol. The viscous triglycerides are broken down into ester bonds and free fatty acids (FFAs), which are not ideal for biodiesel synthesis because FFAs have high melting points, unlike FAMEs. Thus, biodiesel synthesis should be conducted in a manner that reduces the number of FFAs while having a high breakdown of triglycerides into ester bonds. Transesterification that involves alkali/alkyl (like the bases sodium hydroxide (NaOH) and potassium hydroxide (KOH)) as a catalyst can cause soap-FFA reactions, resulting in "emulsification" challenges (Cheng et al 2013) (Hasan et al 2017). KOH and NaOH both can cause soap formation if they interact with triglycerides and esters. Furthermore, KOH produces more soap that NaOH, but KOH also helped produce more biodiesel than that from NaOH at 0.2 mol concentration (Van Gerpen et al 2006). What are the effects of NaOH and KOH on the fuel value of the biodiesel produced over the course of eight weeks? If KOH is used to synthesize biodiesel, then the biodiesel's fuel value form KOH will be higher than that form NaOH. Although the research project is currently in progress, the anticipated result is that KOH better catalyzes transesterification (via causing more heat combustion of ethanol) than NaOH for producing biodiesel. The results' significance determines which catalysts are used to produce more biodiesel. This is because the amount of biodiesel produced can be used for daily life purposes like faster transportation without having to refuel automobiles as frequently.

Members of the gut microbiota produce an array of bioactive metabolites that impact many aspects of host metabolism, immunity, and behavior. However, the mechanisms by which these metabolites are generated remain poorly understood and the biosynthetic enzymes are largely understudied. Recently, our laboratory discovered a family of gut microbial amidases that were found to affect hunger-related biological pathways in malnourished children. These amidases hydrolyze N-acyl ethanolamines (NAEs), lipid messengers with known roles in satiety, visceral pain, and inflammation. Using one of these family members as a model amidase, I am exploring and defining the catalytic mechanisms that are responsible for NAE hydrolysis and the production of a new class of gut microbial metabolites, N-acyl amino acids (NAAAs). I used computational models to predict specific residues that might be important for the amidase activity. I then cloned mutant enzymes into an E. coli expression vector, induced recombinant protein expression, and tested the ability of the purified mutant enzymes to hydrolyze labeled NAEs using liquid chromatography - tandem mass spectrometry (LC-MS/MS). These analyses have pinpointed residues that are important for substrate recognition and binding. My work is advancing our understanding of the selectivity of these intriguing gut microbial enzymes and the regulation of NAAAs in the gut lumen. These efforts are expected to generate the knowledge required to engineer more selective enzymes that produce metabolites of known bioactivity.

Hydrogen sulfide (H₂S), known for its distinct smell of rotten eggs, is recognized as the third endogenous gaseous signaling molecule, alongside nitric oxide and carbon monoxide. Often described as a double-edged sword, H₂S exhibits both cytoprotective and cytotoxic properties depending on the biological context. A 2018 study suggested that H₂S enhances the efficacy of doxorubicin (Dox), an anticancer drug, by promoting apoptosis and reducing colony formation in HepG2 cells, even restoring drug sensitivity in resistant cells. However, my preliminary experiments indicated a protective role of H₂S in HepG2 cells under stress, particularly when treated with NaSH (an H₂S donor). Rather than inducing apoptosis, H₂S appears to support cell proliferation and regulate reactive oxygen species (ROS) production. My research project aims to identify H₂S -dependent pathways in HepG2 cells under oxidative stress. Using Dox as a stress inducer, I conducted viability and cytotoxicity assays, demonstrating that supplementation with 250 µM NaSH at 0 and 12 hours significantly restored cell survival. To investigate the molecular mechanisms, RNA-seq analysis identified 2,996 differentially expressed genes in the H₂S + Dox group compared to Dox alone. Principal component analysis (PCA) revealed distinct transcriptomic profiles, while KEGG enrichment analysis highlighted significant alterations in genes within the PI3K-Akt pathway. To further validate these findings, I plan to perform flow cytometry and western blot analysis. While the role of H₂S continues to be debated, my data suggest a protective function in liver cells against Dox-induced stress via the PI3K-Akt pathway. Understanding these mechanisms could pave the way for new therapeutic strategies aimed at maintaining or increasing H₂S levels to support cell health in diseases characterized by oxidative stress, such as cancer and diabetes.

The small ubiquitin-like modifier protein, SUMO, regulates the activity of many cellular processes through covalent modification of proteins. These modified targets include the protein components of chromatin; histones H2A, H2B, H3, and H4. Chemical modification of histones directly regulates gene expression, necessitating an understanding of the role of each type of modification. The identification and role of histone SUMOylation has been described for H4 in human cells; however, SUMOylation of H2B in human cells has been recently observed but not yet characterized. SUMO is shown to impose a predominantly repressive effect on many cellular processes and proteins that it targets. Therefore, I am working toward identifying the role of H2B SUMOylation to either add to this narrative or describe novel functions of SUMO. To accomplish this, I have purified wild-type histones and SUMO-histone fusions through bacterial expression followed by size-exclusion and affinity chromatography. The purification of several of these proteins has not been described yet; therefore, I designed the purification for these proteins using unique methods, like solubilizing tags, to obtain the product. I reconstituted the purified proteins into octamers, the protein complex that DNA wraps around, and purified the octamers away from other oligomeric forms of the histones via size-exclusion chromatography. I further reconstituted the octamers into mononucleosomes by condensing DNA around them to mimic SUMOylated nucleosomes in chromatin. I hope to then subject the mononucleosomes to in vitro biochemical assays to observe changes in the modifications that regulate other chromatin-associated proteins. A better understanding of the complex dynamics at play during gene expression and repression is needed to identify stronger, safer, and more sustainable therapeutics. Furthermore, SUMO is implicated in a wide array of diseases, such as Alzheimer’s. Therefore, the results of this study will increase our understanding of gene regulation and provide insight towards treating related diseases.

“In Africa, whenever an old man dies, a library burns down.” –Amadou Hampâté Bâ. Malian writer, historian, and ethnologist Amadou Hampâté Bâ’s quote underlines elders as keepers and purveyors of knowledge, culture, and wisdom. As “libraries” worth prioritizing and preserving, Black grandmothers’ stories and cultural inheritances (material possessions, cultural traditions, rituals, language, etc.) have been integral to the matriarchal traditions and culture characterizing people of African descent. Yet, at key periods, African Americans have experienced threats to our collective ability to document, preserve, and pass down our “libraries” because of a lack of financial resources and technological support. Black grandmothers experience multidimensional oppressions and rarely have a chance for self-representation. What are the ways black grandmothers experience erasure in the digital age, and within their communities through displacement? How are we responding? How can researchers mitigate, document, and disrupt their erasure? To conduct this work, we collect oral histories, document cultural inheritances, and create data visualizations to digitize their "libraries." We document, preserve, and amplify Black culture and history by sharing the lived experiences of Black grandmothers. The Black Grandmother Worldmaking Library is a collaborative, community-based model for gathering, archiving, and digitizing distinct aspects of our “libraries” beginning with the stories and cultural inheritances of Black grandmothers experiencing mass displacement in Seattle’s Central District and along the Gullah Geechee Corridor. The project offers a readily accessible digital resource for Black grandmothers to contribute to and control the stories we tell about their lives. The Black Grandmother Worldmaking Library aims to repair what we are taught about Black grandmothers, to reclaim their narratives and culture using firsthand accounts, and to preserve their legacies.

Maintaining the integrity of genetic material and preventing changes over time is essential for normal cellular function. This genomic stability is directly affected by the DNA replication process. Replication must be both accurate and efficient; mutations that affect DNA replication can cause genomic instability and changes in the genetic makeup of the cell. Through a genomic instability screen in mice, researchers discovered a single base pair mutation in a highly conserved gene required for unwinding DNA during DNA replication. The presence of this single base pair substitution, called Chaos3, in both copies of the gene causes female mice to develop mammary tumors. We have found that in the yeast Saccharomyces cerevisiae, the corresponding Chaos3 mutation decreases activation or “firing” of some replication origins—the sites where DNA replication begins. Chaos3 does not affect all early firing origins in the genome; rather, origins near centromeres are specifically affected, thereby delaying replication of those centromeres, causing chromosome loss. We found that when an affected origin is replaced with an unaffected one, firing levels are restored to wild type function and that chromosome loss is rescued. To further understand what components are essential for timely DNA replication, and why only a subset of origin sequences are sensitive to the Chaos3 allele, I am focusing on the origin sequences directly. I am mutating the origin sequence itself and separately deleting different genes whose products have potential interactions with origin sequences. My research aims to advance the understanding of the role these genes play in the activation of origins for timely DNA replication and how the Chaos3 mutation may be interrupting normal function of these processes. This knowledge can help identify key molecular mechanisms that drive cancer development in higher eukaryotes.

Copy number variation (CNV) is associated with genetic disorders in humans. One particular kind of CNV is a gene triplication in which the central copy is inverted. How such structures arise is poorly understood but is of great interest because of their association with cancer and other genetic disorders. We find similar amplified structures in budding yeast Saccharomyces cerevisiae, and therefore, we can use yeast to understand the mechanism that generates them. The Brewer and Dunham labs have proposed Origin Dependent Inverted Repeat Amplification (ODIRA) as a model that explains inverted CNVs. To understand which proteins/enzymes contribute to amplification, we are implementing gene deletions to observe the effect on the production of these ODIRA amplification events. ODIRA events are rare and thus large sample sizes are required to detect them. To streamline their identification, I am developing a system that uses color as a visual indicator of CNV. When a single copy of the bacterial gene, VioA, is expressed in yeast it produces light purple colonies; in multiple copies, the colonies are a darker shade of purple. I am inserting a single copy of the VioA gene into a region of the yeast genome that undergoes inverted triplication events. Simply scanning plates for dark purple colonies will enable me to screen for ODIRA events quickly and measure their frequency. Using this visual indicator will allow me to rapidly screen different yeast mutants and determine the role they play in the ODIRA amplification mechanism.

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

Since the ban on sports betting was struck down by the supreme court in 2018, 38 states have legalized betting in some form. In the third quarter of 2023, sports betting generated over $500 million in tax revenue for state governments. Many of the impacts that seem obvious when thinking about the consequences of legalizing sports betting have already been studied, so in this paper I analyze effects that are further downstream in the causation chain. Specifically, I look at how the legalization of sports betting has affected marital relationships as measured by state-level divorce rates, mental health outcomes as measured by depression rates, and substance abuse issue measured by the number of alcohol related hospitalizations and rehabilitation center bookings. I utilize the staggered rollout of legalization across the country to conduct a difference-in-differences analysis to accurately measure the magnitude of each of these effects. Additionally, I investigate the potential additional damages caused by the legalization of online gambling compared to only in-person gambling. Of the 12 states who have yet to legalize any form of sports gambling, most of them have some form of legislation on the table to decide the future of sports betting in their respective states. Within these legislative sessions, and eventually if these measures are on state ballots,legislators and voters will be asked to personally weigh the pros and cons that are associated with the legalization of sports betting and this paper's aim is to be a small part in helping inform these decisions.

Xylazine is a veterinary sedative that has become a common adulterant in fentanyl products due to its ability to prolong the euphoric effects of fentanyl. Adulterated drug mixtures containing xylazine have been linked to an increased risk for respiratory depression and fatal overdose. Existing treatments for overdose such as naloxone do not work against xylazine and there is currently no FDA approved reversal agent for xylazine toxicity. Monoclonal antibodies (mAbs) are a promising therapeutic option to reverse drug overdose and can be used to target small molecules by sequestering them in the bloodstream and preventing their passage into the brain. Previously, we made a series of xylazine haptens and formulated them into vaccines where they were found to induce strong antibody responses, reduce brain to serum ratio of xylazine, and mitigate respiratory depression in Sprague-Dawley rats. Based on the protective effects of our xylazine conjugate vaccines, we hypothesized that we can create an effective reversal agent by isolating xylazine specific mAbs. In this study, we immunized mice with xylazine conjugate vaccines to generate antibodies specific against xylazine. We then used the secondary lymphoid organs of the vaccinated mice to establish stable mAb producing cell lines using hybridoma technology. Hybridomas were screened with ELISA and lead candidates were selected and sequenced for further characterization. We will conduct in-vitro characterization assays to quantify binding affinity, functional activity, and thermostability of our lead mAbs. Furthermore, in-vivo studies will assess the efficacy of our mAb lead candidates in rodent models.

TBC domain containing kinase (TBCK) is an understudied protein with three domains: a pseudokinase; Tre-2, Bub2, and Cdc16; and rhodanese, and is highly expressed in the brain. Homozygous mutations in TBCK cause a rare neurodegenerative disorder in children, which clinically presents as syndrome infantile encephalopathy, brain atrophy, cerebellar hypoplasia, and muscle hypotonia. Two mutations in particular, Arg126Stop and Arg511His in the pseudokinase and TBC domains respectively, are commonly found among TBCK patients. The progression of the disease is characterized by a global regression in brain development, severe intellectual disability, and premature death in acute cases. The pathogenic mechanism underlying TBCK syndrome is unclear, but past studies show that TBCK patient neurons demonstrate aberrant metabolite buildup in the lysosome likely resulting from abnormal lysosomal activity. Immunoprecipitation mass spectrometry was performed for wild type TBCK in both N terminal and C terminal tags, revealing a preliminary list of both known and unknown interactors for TBCK. To further investigate the early developmental implications of mutant TBCK, CRISPR/Cas9 directed mutagenesis is being used to generate two induced pluripotent stem cell (iPSC) lines harboring the Arg126Stop and Arg511His mutants for subsequent differentiation into neural progenitor cells (NPC) and neurons. Immunofluorescent imaging of the mutant NPCs will confirm the recapitulation of growth and lysosomal defects present in patient cells. To analyze the effect of TBCK mutation on lysosomal function/content, we will immuno-isolate lysosomes through lysosome immunoprecipitation (Lyso-IP) and identify proteomic changes through mass spectrometry. While providing a crucial in vitro cell model of two common patient mutations, these experiments will offer critical insight into cellular dysfunctions that contribute to TBCK disease states.

Non-syndromic orofacial cleft (OFC), comprising cleft lip, cleft palate, or a combination of the two, is among the most common structural birth defects. OFC has both genetic and environmental underpinnings, though the genetic contribution is only partially understood. Members of the same gene regulatory networks associated with OFC are candidates to harbor the “missing heritability” for OFC. Van der Woude Syndrome (VWS) is an autosomal dominant condition characterized by cleft lip and/or palate, and lip pits. Mutations in IRF6, encoding the transcription factor Interferon Regulatory Factor-6, account for approximately 70% of VWS cases, mutations in GRHL3, a transcriptional target of IRF6, account for 5%, and it was recently found that mutations in PRKCi, encoding a kinase, account for 5% more. Published data support that IRF6 is phosphorylated and thereby activated by RIPK4. However, the kinases PRKCi and IKK1 are also required upstream of IRF6 activity. Regulatory interactions within this kinase cascade are unclear. The goal of this project is to shed light upon the kinase cascade encircling IRF6 to illustrate genetic causes of VWS and non-syndromic OFC and ultimately improve patient outcomes. I hypothesize that IRF6 phosphorylation is dependent upon RIPK4, which is activated by IKK1 and downstream of PRKCi activity, and all components are necessary for IRF6 activation. To test this hypothesis, I am conducting experiments injecting mRNA products from our genes of interest into zebrafish embryos and detecting phosphorylation activity within the harvested protein through immuno-precipitation and mass spectrometry analysis to determine protein-protein interactions. I anticipate that in the absence of RIPK4, the pool of Differentially Expressed Genes (DEGs) will align with the pool of DEGs in the absence of IKK1 and IRF6 respectively. Implications of these findings will ultimately give a stronger understanding of the molecular foundations of VWS and non syndromic OFC.

Poor sleep quantity and quality are associated with increased risk of negative health outcomes such as chronic conditions, depression, and anxiety, which ultimately impact overall well-being. The present study aims to investigate the association between perceived stress and sleep quality among college students. A sample of 113 college students in the United States completed an online survey that asked questions about their sleep and perceived stress. Perceived stress was assessed using the Perceived Stress Scale (PSS; Cohen et al., 1983) and sleep quality measured through the Pittsburgh Sleep Quality Index (PSQI; Buysse et al., 1989). Sociodemographic data were also collected. Results indicate that college students with higher perceived stress reported poorer sleep quality. Given that perceived stress and sleep were correlated, we conducted additional analyses to compare levels of stress and sleep quality among different sociodemographic groups. We found that international students exhibited lower perceived stress and better sleep quality compared to domestic students. Furthermore, college students who reported lower family income, and those whose native language was not English experienced higher perceived stress and poorer sleep quality across both groups. Taken together, the data demonstrate an association between perceived stress and sleep quality and highlight differences in both variables based on immigration situation, as well as linguistic and socioeconomic factors. Further longitudinal studies could be helpful to determine the temporal relationships among these variables and the long-term role that they play in health. 

Neonatal hypoxic-ischemic encephalopathy (HIE) occurs when the brain receives insufficient oxygen and blood supply before or during childbirth. HIE is a leading cause of neonatal mortality and morbidity that may also affect later brain development, specifically gyrification - folding of the cerebral cortex creating gyri and sulci. The nonhuman primate (NHP) brain is gyrified, similar to humans, making NHPs a highly translatable model to examine brain development after injury, which has not been well-studied in HIE. In our nonhuman primate (NHP) model of neonatal HIE, we induced injury through in utero umbilical cord occlusion (UCO) for 20 minutes, mimicking the cause of HIE in humans. Twenty-two term-equivalent pigtailed macaques (Macaca nemestrina) underwent UCO and were randomized to no treatment (n = 11) or treatment with therapeutic hypothermia and erythropoietin (TH + Epo [5x1000 U/kg]; n = 11), while non-UCO animals served as controls (n = 7). All animals were delivered via cesarian section. Injury severity was determined by physiological parameters (Apgar score), lactate, and pH levels after resuscitation. To evaluate the impact of injury on gyrification, we will utilize magnetic resonance imaging (MRI) taken 6-months post-injury to measure the gyrification index (GI). GI will be calculated by taking brain’s inner-to-outer hemispheric ratio; the inner trace following the contours of the gyri and sulci, and the outer trace following the circumference of the cerebral cortex. We hypothesize that global and regional GI will be altered in animals exposed to UCO, corresponding with decreased brain volume and greater injury. We also hypothesize that treatment will mitigate some of these changes, leading to a GI closer to control. These results will help determine whether hypoxia-ischemia alters the trajectory of cortical development, as well as the association between injury severity, brain volume, and gyrification.

The first-in-class capsid (CA) binding antiretroviral, Lenacapavir (Len), inhibits viral spread at multiple steps in the viral life cycle. Structural studies show that Len interacts with an FG-binding pocket between the N-terminal and C-terminal domains of adjacent CA monomers resulting in destabilization of the CA core lattice. Three key binding functional groups within Len that interact with CA were identified. Subsequently, six Len analogues (Lenalogs) were designed and synthesized. These Lenalogs vary by the removal or replacement of one of the identified functional groups. My work investigates the impact of Len and Lenalog binding on CA assembly rate, as well as, the structure of the assembled protein. Using an IPTG  E. coli expression system and ion exchange chromatography, I have expressed and purified CA protein. I induced in vitro assembly of the purified CA protein by the addition of inositol hexakisphosphate (IP6) in both the presence and absence of Len or the Lenalogs. Relative to Len, LL-10.4 and LL-15 promoted assembly, LL-14 was similar, while LL-11, LL-19 and LL-20 promoted assembly to a lesser extent. Samples with LL-10.4 and LL-15 were chosen for cryo-EM analysis as these promoted assembly to a greatest extent. CA was assembled on lipid vesicles (templated CA-like particles or CLPs) by the Dick lab (Emory University, Atlanta, GA), and these were subjected to cryo-EM data collection and analysis. Both LL-10.4 and LL-15 bound to the FG-binding pocket like Len. Negative stain transmission electron microscopy and light scattering will be used to further assess the effect of Len and Lenalogs on assembly kinetics. My work will be used to inform the design of next generation CA-targeting antiretrovirals.

Decision During Drinking (D3 study) is currently developing a mobile app aimed at reducing negative alcohol-related outcomes with a focus on young adults. D3 offers modules to educate users on identifying cues that influence their decisions, understanding their values after drinking, and engaging in practices to avoid such experiences. I have aided in the design of the prototype of the D3 program, both creating new features and adapting previously developed features. The current study assesses core aspects of human centered design on two of the D3 study features I helped to create in Figma. The first is an activity that compares participants’ perception on alcohol expectancies to alcohol’s physiological effects. The second is a “roadmap” planning tool that guides users to create action plans to cope with specific drinking cues, linking each plan to personal values. By using an iterative design approach from research participants’ feedback, I refined the user interface (UI) to improve the features. I am adapting measures on usability (i.e. System Usability Scale) to assess the metrics for these features specifically. Data is being collected from online surveys on the usability of these features. I predict that the final usability score would be higher than the industry-standard threshold (e.g. score of ≥ 70), so the features will provide a seamless and intuitive user interface. Based on the improvements, if deemed usable, these feature designs could be applied to other clinical app developments. 

Washington State is known for its progressive policies and support for transgender and nonbinary (trans) populations (i.e., trans-progressive). However, some studies suggest that there are still barriers to healthcare access. This study explored trans Washingtonians’ perspectives of these policies and experiences in access to non-discriminatory healthcare. The Priority Assessment in Trans Health Study conducted semi-structured interviews in August 2023 – March 2024 trans adults (n=24) living in Washington State. Interview topics included access to sexual health services, policy awareness, and community resilience. Themes were identified via inductive thematic analysis using Dedoose. Participants were more willing to visit hospitals that have anti-discrimination policies over those that do not, citing safety as a main contributing factor. Although, many were not aware of the anti-discrimination policies that their clinics had in place.  Some noted the presence of pride flags and trans health posters were signals of safety for trans individuals in these settings. However, some participants believed these endorsements feel performative without actionable follow through and described their personal discriminatory experiences in these hospitals. Additionally, participants noted that the lack of necessary training for trans healthcare makes obtaining care, particularly emergency care or intersectional care  difficult. Lastly, participants emphasized that the national structure of the American healthcare system as a barrier to accessing trans-specific care (e.g. need for multiple referrals). While Washington’s state-level policies supporting trans healthcare create an initial sense of safety, they often fail to address the root structural inequities which perpetuate healthcare inaccessibility. To bridge the gap between performative action and genuine inclusion of trans adults, accountability must be prioritized at all levels: from hospitals holding their employees accountable for discriminatory behavior to reforming medical education.

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

Geographic Information Systems (GIS) are a powerful framework that enables the analysis of spatial data, or information connected to a location, that can be applied to a variety of fields, such as public health, policy, agriculture, and environmental management. With these frameworks, we can create maps to convey specific data or general information, make comparisons between data sets, and quantify spatial characteristics. In this study, I utilized a GIS framework together with Real-Time Kinematic Global Navigation Satellite Systems (GNSS RTK) methods to collect spatial data regarding hiking trails throughout Saint Edward State Park in Kenmore, Washington. I hypothesize that the positional accuracy of data collected via GNSS RTK is significantly better than positions collected via methods that do not incorporate differential correction. To test this hypothesis, I will collect differentially corrected positional data along trails in the park and compare them to uncorrected data gathered between 2013 and 2015 from the same trails. Comparisons will be made using a t-test to determine whether there is a statistically significant difference between the mean differences of each data set. Furthermore, I will use this spatial data to visualize more accurate trail locations, indicate areas requiring maintenance, and decommission unofficial trails that are harmful to the ecology in the park.

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

Cave formations, also called speleothems, are natural archives of past climate conditions. Analysis of these speleothems can provide information about environmental changes over thousands of years. Church Mountain Cave is in the Northeast Cascades and is distinctly characterized by its unusually predominant speleothems, which is relatively unusual for western Washington. This project explores the potential of Church Mountain and other caves as paleoclimate archives. I begin with a characterization of Church Mountain Cave, focusing on cave morphology, stratigraphic and structural position of the cave, and forming a hypothesis of cave formation and fault activity. This classification will allow for a detailed view on Church Mountain Cave and the factors impacting speleothem formation. We also characterize a range of speleothems from other caves using trace element and isotope analysis, with the eventual goal of using uranium-thorium dating to establish precise ages and stable isotope analysis with oxygen isotopes to infer past temperature, precipitation patterns, and other environmental factors. By refining regional paleoclimate reconstructions, we can improve predictions of future climate trends and extreme weather events. Additionally, this study underscores the importance of caves as climate archives and highlights the need for conservation efforts to protect these valuable and fragile environments for continued scientific research. 

This research project aims to investigate the perceptions of physical disability among able-bodied college students, with a focus on how the duration of the disability influences these perceptions. Despite increasing awareness and advocacy for disability rights, stigmatization and misconceptions persist within educational environments, potentially affecting the social integration and academic experiences of disabled students. Furthermore, individuals with permanently disabling physical impairments may experience different treatment than individuals who are temporarily disabled by acute injuries. Though anthropological mixed methods research on the perception of disabilities is not uncommon, my research is focused on the difference in the perception of congenital (e.g. cerebral palsy) or acquired permanent physical disabilities (e.g. traumatic limb loss) compared to that of temporary disabling acute injuries (e.g. traumatic fracture). I hypothesize that there is a difference in the treatment of people with permanent versus temporary disabilities; students with permanent disabilities are regarded as “more disabled” than those with temporary disabilities and are considered “less capable” and “less threatening”, and therefore more likely to receive pity and unsolicited help from abled students. They may also be perceived as “less intelligent” despite having no mental impairment. This study's findings fill the gap in the existing body of knowledge on the effect that the duration of physical disability has on its perception. My research employs a mixed-methods approach, combining anonymous surveys and qualitative interviews to explore the attitudes and beliefs of students at UW regarding their peers with physical disabilities. By understanding how the duration of disability affects perceptions, universities can better address the specific needs and challenges faced by disabled students, promoting a more equitable and empathetic academic community.

Cancer immunotherapy, specifically Adoptive Cell Therapy (ACT), has revolutionized treatment approaches using genetically modified T cells to recognize and eliminate cancer cells. However, tumors combat this by creating an immunosuppressive tumor microenvironment (TME) blocking effective antitumor immune responses.  Dendritic cells (DCs) are innate immune cells that act as messengers between the innate and adaptive systems.   In the Oda lab we have designed Dual Costimulatory Receptor (DCRs) that combine a FLT3L or CD40L ectodomain with different costimulatory endodomains (e.g. CD40, 4-1BB, OX40), to provide both T cell-extrinsic and -intrinsic costimulatory signals.  These DCRs are expressed on the surface of antigen specific T cells, and the combination of these signals allows for enhanced tumor antigen presentation and dendritic cell activation, leading to an increase of the immune response to target and destroy cancer tumors. I will investigate how incorporating DCRs on T cells will enhance ACT effectiveness. I hypothesize these DCR signals on T cells will enhance dendritic cell function in the TME, allowing for increased T cell activation and antitumor immune responses. To test this, I will conduct in vitro coculture experiments to determine how DCR-T cells, dendritic cells, and pancreatic cancer cells interact together. I will study the interactions of these immune cells using live cell imaging technology such as the Incucyte. Additionally, I will analyze the phenotypes of our distinct cell populations via flow cytometry.  This research aims to enhance the development of immunotherapy for Pancreatic and all solid cancers by improving the recognition of cancer cells from the immune system. These results could help pave the way for improving solid tumor cancer treatment.

Serotonin serves a vital role in the regulation of stress responses, and variance in the release of serotonin was found to contribute to various mental illnesses such as anxiety and depression. Current mental health treatments heavily rely on Selective Serotonin Reuptake Inhibitors (SSRIs). While these medications are generally effective, there are patient populations for whom SSRIs show limited efficacy. Recent studies found that in response to stress, the expression of the FKBP5 gene also increases and modulates many neuronal pathways including serotonin. This experiment determined whether manipulating FKBP5 gene expression in the dorsal raphe (DRN) directly correlates with serotonin release in the basolateral amygdala (BLA), an established neural circuit for fear. To manipulate FKBP5 gene expression, an adeno-associated FKBP5-Cre virus was injected into the DRN of Pet1-Cre transgenic mice, causing up or downregulation of FKBP5 in the DRN. To gauge the effects of FKBP5, fiber photometry was used to measure the release of serotonin following optogenetic activation of the DRN-BLA pathway using a 5HT GRAB sensor injected into the BLA. We hypothesize that increased FKBP5 expression in the DRN will increase serotonin release to the BLA, and as FKBP5 expression is decreased, the release of serotonin to the BLA will decrease. Success in modulating serotonin release using FKBP5 gene expression will expand therapeutic targets in mental illness research, mitigating the gap in treatment efficacy for patients who have undergone ineffective SSRI therapy.

In genomics, large-scale experiments commonly exploit DNA libraries, transforming them into a biological system to assay their effects. In these experiments, smaller DNA constructs provide increased transformation efficiency, such that larger libraries can be screened. Previously, we observed a 3-fold increase in the DNA transformation rate in the fruit fly Drosophila melanogaster when we reduced the size of the DNA construct to approximately 1/6 its initial size. Further improvement of this transformation rate will be dependent on a number of features, including the ease of production of tens of micrograms of minicircles, the ability to create a library of minicircle constructs, and the presence of a PhiC31 attB site to allow integration into the D. melanogaster genome. There are no existing minicircle production methods that address all these needs; thus, we are developing a DNA minicircle production approach that should address them. We use asymmetric PCR to produce single-stranded DNA (ssDNA) that is then circularized. We use these ssDNA circles as templates for rolling circle amplification to generate large quantities of double-stranded DNA (dsDNA). Following debranching and digestion of the DNA, we use a serine recombinase PhiC31 and its recombination directionality factor gp3 to recombine small dsDNA fragments into dsDNA minicircles. To date, we have produced linear single-stranded DNA using asymmetric PCR, ligated the linear ssDNA into circular ssDNA, and performed in vitro recombination using PhiC31 and gp3 to make minicircles from small dsDNA sequences. We are now working to combine all parts of the procedure into one continuous workflow and to measure the method’s efficiency and yield. This procedure will be vital for large-scale genomic manipulations of D. melanogaster, and should thereby improve the scale of these experiments. The approach should ultimately increase our understanding of genetic variation as we can assay it in D. melanogaster.

Gene arrangements are observed in human diseases such as cancer and developmental disorders. In developmental disease, gene triplication with an inverted central copy is observed, while a hallmark of cancer are palindromes, or inverted repeats of DNA. Therefore, testing one mechanism of gene arrangement in an easily studied organism like the  budding yeast Saccharomyces cerevisiae may shed some light on the human genome and disease generation. Yeast cells grown for >200 generations in sulfate limiting media are enriched for triplication of the high affinity sulfate transporter SUL1 with the center copy inverted, as amplification confers a selective advantage. To explain how such a triplication occurs, the Brewer and Dunham Labs proposed a model called Origin Dependent Inverted-Repeat Amplification (ODIRA). The ODIRA mechanism requires a DNA origin of replication and short, inverted repeats flanking the SUL1 gene. During DNA replication, an error of the replication fork, or fork regression, causes annealing of leading and lagging strands to create a hairpin intermediate. The intermediate then replicates and recombines into the genome, forming interstitial triplications, with the middle copy inverted. While the proposed mechanism explains the observed triplication in yeast, the specific proteins involved are not yet known. The genes I've chosen to test are the DNA helicases MPH1 which prevents cross-over between ectopic sequences, and RRM3 which relieves replication fork pauses. Both are predicted to regulate necessary steps of the ODIRA mechanism, making them good candidates for genes that may be involved in these triplications. By deleting each gene, I can then measure the frequency of ODIRA events in those strains and compare them to wild-type strains. Increased ODIRA events in the knockout strains may implicate their role in the ODIRA mechanism and prompt further study of these genes and how they might affect copy number variation in humans.

Dynamics of activity across the cerebral cortex at the mesoscopic scale – coordinated fluctuations of local populations of neurons — are essential to perception and cognition and relevant to computations like sensorimotor integration and goal-directed task engagement. However, understanding direct causal links between population dynamics and behavior requires the ability to manipulate mesoscale activity and observe the effect of manipulation across multiple brain regions simultaneously. Here, we develop a novel system enabling simultaneous recording and manipulation of activity across the dorsal cortex of awake mice, compatible with large-scale electrophysiology from any region across the brain. Transgenic mice expressing the GCaMP calcium sensor are injected systemically with an adeno-associated virus driving expression of the ChrimsonR excitatory opsin. This strategy drives expression of the blue-excited calcium indicator, GCaMP, in excitatory neurons and red-excited Chrimson opsin in inhibitory neurons. The light channels of the imaging and the opsin do not interfere. We demonstrate widefield single-photon calcium imaging and simultaneous galvo-targeted laser stimulation over the entire dorsal cortical surface and find that the spatial and temporal resolution of the stimulus is suitable for targeting many specific cortical regions in short periods of time. The calcium indicator responded to the laser within 30 ms, and the activity returned to baseline within 100 ms after laser offset. The area of effect was as small as 3 mm² for the lowest laser power or as large as 10 mm² for the largest laser power. Moreover, the preparation is stable over many months and is thus well-suited for long-term behavioral experiments. The ability to stimulate and measure anywhere on the dorsal cortical surface of the brain will allow us to design computational models describing how causal manipulation impacts neural dynamics, especially in the context of designing closed-loop systems to control neural activity and behavior. 

Visual word interpretation involves both phonology, sound-based processing common in alphabetic languages, and orthography, visual pattern recognition common in logographic languages. Previous research suggests that word recognition in alphabetic languages, such as English, activates the left inferior frontal gyrus (LIFG), and logographic languages, such as Mandarin, engage the visual word form area (VWFA). The goal of this study is to investigate the neural and behavioral differences between native English speakers and native speakers of logographic languages when processing English phonemes. I hypothesized that native English speakers would show more activation in the LIFG whereas native logographic language speakers would show more activation in the VWFA. Participants completed a rhyming judgment task based on English phonemes while undergoing functional magnetic resonance imaging (fMRI) to measure neural activation. English proficiency was recorded through both self-report and the Nelson-Denny Comprehension test. Behavioral results suggested that native logographic language speakers had significantly longer response times and lower accuracy compared to native English speakers. Both self-reported and objectively measured English proficiency were negatively correlated with response times and positively correlated with accuracy. Although the neural analysis did not yield statistically significant results, there was a trend of increased VWFA activation in native speakers of logographic languages compared to English.

The ability to recognize that others have mental states, separate from us, and that these states are not always accurate portrayals of reality, is central for theory of mind (TOM). This capacity becomes particularly crucial when children explain causal relationships, as they must integrate their understanding of causality with their awareness of other's knowledge states. Skills like this are essential for effective communication and reflect a key developmental milestone in both cognitive and social reasoning. This study examines how children process causal scenarios while considering and tracking the knowledge states of multiple people. We will examine how children (ages 4-7) perform with conjunctive causal relationships, where two separate effects must combine to produce an outcome (e.g., watering a plant and giving it fertilizer causes it to bloom). Children are asked to explain how the outcome happened, and what knowledge each character has. The children will be given four causal events, varying in content, and follow the same causal structure, where each character is only aware of one cause (A or B). After the scenario, children will answer open-ended questions to assess their recall of what each character knows and test their understanding of how the outcome (C) occurred. We predict that younger children will recognize the causal outcome but struggle to differentiate knowledge states, while older children will demonstrate an improved ability to tailor their explanations based on other's perspectives. This study extends beyond previous studies that primarily focused on children's passive evaluation of explanation as our study will investigate children's active role in generating explanations tailored to different character's knowledge states. Our findings will contribute to the understanding of how the development of TOM shapes children's ability to understand and reason about causal relationships.

Rhabdomyosarcoma (RMS) is a rare pediatric cancer that begins growing within soft tissue and becomes deadly with rapid tumor growth, eventually leading to therapy resistance and metastasis. Today, drug therapy options remain scarce in relapsed patients, resulting in significantly lower 5-year survival rates compared to patients with localized disease. Recent research in other cancers has implicated the hyperexpression of an oncogene, YBX1, and an immune checkpoint marker, PD-L1 in driving therapy resistance and immune response evasion of cancer cells. YBX1 is an RNA-binding protein that improves the survival of stem-like cells in RMS. Additionally, PD-L1 is a protein expressed on the surface of tumor cells that binds to PD-1 on T lymphoid cells and aids in the evasion of T-cell-induced cell death. We hypothesize that the combination drug therapy with atezolizumab, a PD-L1 inhibitor, and SU056, a YBX1 inhibitor, will synergistically inhibit tumor growth by increasing immune cell activity. I performed intraperitoneal (IP) transplantation of RMS tumor cells derived from a zebrafish RMS tumor line (‘3.2T’) using a syngeneic line of zebrafish, ‘CG1’. The drug treatment study consists of 4 experimental groups (SUO56 or atezolizumab only, two-drug combination, and vehicle control) receiving two drug injections via IP route over 7 days. I quantified tumor growth over 7 days via ImageJ/Fiji software. Additionally, we use RNAscope (RNA-targeted in situ hybridization) to determine mRNA expression levels of various tumor-associated immune cell markers, including CD4 and CD8 for T lymphocytes and PAX5 for B lymphocytes. Based on our knowledge of YBX1 and PD-L1, we expect to see a greater reduction in tumor growth and an improved immune response with combination therapy compared to single-drug treatments. Completing this research will address the current lack of effective therapies in treating relapsed RMS patients and possible combination therapies for improving RMS patients’ survival.

Westfield Southcenter Mall, located in Tukwila, Washington, is one of the largest malls in the nation, and like many malls, its aging retail spaces and surrounding strip malls are becoming less viable. With rising housing costs and a growing regional population, it is clear that spaces like Southcenter must be transformed into affordable, mixed-use districts that can provide housing, vibrant community spaces, and accessible transportation options. This project explores how Southcenter Mall can be redesigned using New Urbanist principles to foster a thriving community. Using site visits and global case studies of recent successful mall redevelopments, it analyzes the current shortcomings of Southcenter Mall and proposes a more successful mixed-use alternative. The final deliverables include a 3D model mock-up of a revitalized Southcenter that includes affordable housing, ground-level retail, and an overhauled transportation framework prioritizing pedestrians and cyclists.

There is an existing ideology prevalent in our culture that radicalized, and gendered subjects are expected to endure copious amounts of pain when it pertains to their menstrual cycles. I call this into question and aim to explore alternative methods of alleviating dysmenorrhea beyond hormonal contraceptives and SSRIs. Focusing specifically on BIPOC menstruating populations, I have been the primary investigator of a study examining the effects of community dance and affinity spaces on menstrual pain management. Participants come into the dance studio weekly to engage in various open dance practices with others, in addition to journaling, guided massage, and discussion. The dance practices range from traditional Chinese practices like Qigong to local community dance practices like Dance Church. In addition to weekly sessions, I host quarterly BIPOC Jams open to the public, to share the knowledge with the wider community, cultivating a space for BIPOC to engage in freedom dreaming, community building, and collective healing. I will explore what a future of community healthcare would look like, moving away from Western models of healthcare that focuses solely on the individual. Drawing from practices like community acupuncture where the healing experience happens with others rather than in isolation, I am curious to investigate how having a shared dancing experience impacts and shifts the emotional and physical well-being of participants. I am exploring the care relationships that form in BIPOC affinity spaces and how dance as a language facilitates a different type of embodied healing. I will be presenting the structure that I have used for weekly sessions and the BIPOC Jams. I will also share excerpts of participant experiences and reflections from both spaces. I am drawing upon existing theories around care work, somatic abolition, and pain management to develop a practice of community care that builds upon existing discourse. 

Traumatic brain injury (TBI) results from a blow to the skull that causes shearing forces in the brain. Elevating intracranial pressure (ICP) at the moment of impact may protect the brain from TBI by stiffening the brain tissue and decreasing shearing. When they expect an impact, humans naturally brace and perform a Valsalva maneuver (exhaling against a closed airway), which momentarily elevates ICP. In a ferret TBI model, we conducted abdominal compression using a blood pressure cuff to induce a Valsalva-like response (VLR) and determine whether VLR resulted in neuroprotection. The ferret model was chosen for its gyrified brain structure and white to grey matter ratio that closely resembles the human. TBI was induced using a CHIMERA (Closed-Head Impact Model of Engineered Rotational Acceleration) device, which is designed to deliver high-energy, controlled skull impacts. Initial work showed that the abdominal compression procedures increased ICP. The TBI study involved a total of 36 adult ferrets of both sexes randomized into three groups: (1) a sham control group exposed to isoflurane with a cuff but no compression, (2) a TBI group with a cuff but no compression, and (3) a TBI group with a cuff and abdominal compression. Baseline behavioral assessments (CatWalk, Novel Object Recognition, Swim Test, and Open Field) were conducted one week prior to injury. Post-injury behavioral testing, using the same assessments, was performed at 24–48 hours and 8 days post-TBI to evaluate functional outcomes. On day 8, ferrets were euthanized, and their brain tissue was collected and assessed for neuropathological outcomes. We hypothesize that abdominal compression will mitigate deleterious TBI outcomes. If these findings are supported, this intervention could improve the lives of those at risk of TBI and contribute to ongoing research in the field.

Can early adverse experiences possibly enhance cognitive functions? The current literature pertaining to children and youths with adverse experiences suggests that they often present extensive deficits, potentially showing less working memory, later language disorders, and lower impulse control (Ellis et al., 2020; Dannehl et al., 2017; Dixon et al., 2023; 2016; Snow, 2021). However, this deficit-based perspective is incomplete – the hidden talents framework suggests that children possess adaptive strengths of unique skills that emerge under stress and in particular, adverse environments. Children and youths with experiences of adversity show social and cognitive adaptations, revealing enhancements in certain domains (Ellis et al., 2020). Here, we examine a facet of their adapted strengths: cognitive flexibility in adulthood as a response to childhood unpredictability, defined as the rate of alterations or instability in the individual’s childhood environment. We propose that adults with prior experiences of childhood unpredictability develop enhanced cognitive flexibility to adapt to unpredictable environments. In this experiment, we will recruit a normative sample of 180 adults and measure their cognitive flexibility along with experiences of childhood harshness and unpredictability using the Perceptions of Childhood Harshness and Unpredictability scale and the Number-Letter Task. We predict that participants who experienced a high level of unpredictability will demonstrate more cognitive flexibility compared to those who experienced high general childhood harshness. Preliminary analyses from the UW psychology participant pool indicate similar trends, suggesting that higher childhood unpredictability correlates with increased cognitive flexibility, while higher childhood harshness is associated with lower cognitive flexibility. Framing cognitive flexibility as a form of adaptation from unpredictable environments is imperative to pivot the current narrative toward children’s hidden talents – revealing that children are resilient, adaptive individuals with unique abilities to overcome adversity. 

Individuals with Stage II/III severe periodontal disease were recruited from the Graduate Periodontics Clinic at the University of Washington School of Dentistry using an approved IRB (STUDY00016871). Subgingival plaque samples were collected from four tooth sites: an active inflamed site, two adjacent tooth sites, and a distant healthy tooth site. Sterile paper points were inserted into the gingival sulcus for 30 seconds. DNA was isolated and extracted using the Qiagen AllPrep DNA/RNA Mini kit (Cat. #80204), then purified and concentrated using the Zymo Clean & Concentrator (Cat. #D4014) kit. 16S rRNA libraries were generated and sequencing was performed on the MiSeq platform (Illumina, San Deigo, CA, USA) using 300bp paired-end chemistry. Raw reads were processed and analyzed using Qiime2 and the DADA2 algorithm to generate amplicon sequence variants (ASVs), which were then classified using the expanded Human Oral Microbiome Database (eHOMD). Differences between tooth sites were assessed within and across individuals. Correlation between taxonomic levels and clinical data was also assessed. Data analysis is still being performed at this time. Based on previous literature (Pawolski et al, 2005, Kerns et al. 2023), we expect that a subgingival community gradient radiates from tooth sites affected with periodontal disease toward distant healthy sites. We aim to resolve this within individuals using ASVs for the first time. Additionally, we anticipate an increase in disease-associated bacteria within actively inflamed tooth sites, such species within Porphyromonas, Tannerella, and Treponema genera. Furthermore, we anticipate a gradient of perio-pathic disease-associated bacteria will decrease in relative abundance the further away from active diseased sites. We expect that results from our study will highlight the presence of a subgingival microbiome composition and enrichment of specific gram negative perio-pathic disease-associated species within clinically healthy tooth sites in patients with active periodontal disease despite the absence of clinically observed inflammation.

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

The short-term goal of this research project is to integrate and apply machine-learning tools to magnetic resonance imaging (MRI) data housed within a queryable, large-scale MRI database. Long-term goals seek to develop tools to better identify patterns of pathology within multimodal MRI data. Imaging approaches such as morphometric and connectivity analyses provide a means of uncovering the brain’s seizure onset zone in patients with epilepsy, known as the epileptogenic zone. MRI is the standard reference protocol for non-invasive evaluation of epilepsy. This is due to the fact that a majority of epilepsy patients have visible lesions on brain MRI scans. However, a number of epilepsy patients are MRI-negative, defined as having no visible lesion. To improve lesion detection in MRI-negative patients, machine learning has been applied to multimodal MRI as a means to detect subtle patterns of changes. However, these studies are limited by small number of patients or included only a few epilepsy pathologies. Working with a team from the Department of Radiology, I established a structured database integrated with raw MRI data, computational post-processing results, and clinical metadata. In the present study I will examine how available machine learning techniques can be replicated and utilized on the data within this integrated database. As the database accumulates MRI data from a larger number of epilepsy patients with and without visible MRI lesions, we hypothesize that this integration will uncover subtle abnormalities not detected through qualitative MRI. This form of individualized brain mapping we predict will provide new insights into seizure networks and ultimately enhance efficacy of non-pharmacological based treatment approaches such as enhancing accuracy of surgical resection of the epileptogenic zone.

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

Parents play a significant role in shaping adolescent alcohol use. The specific role of adolescent decisional freedom—the extent to which adolescents independently make decisions— has yet to be examined. I conducted a brief literature review on adolescent decisional freedom, and this study explores its links with alcohol use within distinct developmental periods. Data from baseline to year 6 follow-up of the National Consortium on Alcohol and NeuroDevelopment in Adolescence study (N=831) were tested for cross-sectional associations between decisional freedom and alcohol use phenomenology (i.e., drinking days per average month, past month alcohol consumption, quantity of drinks during average drinking period, and binge drinking days in the past year and month). Separate models were tested for early adolescence (ages 12-14), middle adolescence (ages 15-17), late adolescence (ages 19-20), and emerging adulthood (ages 21-24). Adolescent decisional freedom was measured using a self-report 5-point Likert scale across distinct domains (e.g., spending money, drinking alcohol, time spent with friends). Gender and age of first drink were covariates, and each model examined associations between decisional freedom and gender. Regression results consistently linked lower decisional freedom to lower alcohol use across all phenomenology in early adolescence (bs ≤ −.41, ps < .01). For middle adolescence, the protective effect of limiting decisional freedom only emerged for drinking days per average month (b = −.29, p < .01) and quantity of drinks during average drinking period (b = −.46, p = .001). In early and late adolescence, the association between lower decisional freedom and fewer past month binge drinking days was stronger for boys (bs ≥ 0.43, ps < .05). These findings suggest that increasing control over early adolescents’ decisional freedom, particularly for boys, and flexibly granting greater decisional freedom over time may protect adolescents from harmful decisions associated with alcohol use.

The Campanian stage of the Late Cretaceous (84–72 million years [Ma]) was a dynamic interval for North American ecosystems and included the zenith of dinosaur diversity and the regression and transgression of the Western Interior Seaway (WIS). Most studies that investigate vertebrate biodiversity during this interval focus on dinosaurs, whereas few focus on changes in herpetofauna (lizards, frogs, and salamanders). Herpetofauna are important indicator species of ecosystem dynamics, because they are fragile to ecosystem change. Vertebrate microfossil sites are ideal for studying herpetofauna diversity dynamics through time because they can produce large sample sizes, sample aquatic environments, and are plentiful through stratigraphic intervals. The Judith River Formation (JRF) of north central Montana is rich in vertebrate microfossil sites, preserving ~4 Ma of the Campanian (~79–74 Ma). Here we aim to document patterns of herpetofauna diversity change in the JRF by quantifying herptile taxonomic richness and relative abundances using specimens from three temporally separated microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (76.5 Ma), and Clamfetti (~75.2 Ma). We collected sediment samples from these sites over four years and processed them via underwater screen-washing techniques. Presently we have studied 470 herptile microfossils (600 planned). Our preliminary results show changes in the taxonomic diversity across the sampled sites. Taxonomic richness of herptiles varies through the formation, first increasing and then decreasing. Salamanders have the highest relative abundance, lizards decrease in relative abundance, and frogs fluctuate. We hypothesize that taxonomic patterns are influenced by the impact of WIS cycles on water supply in ecosystems: amphibians thrive in wetter environments, whereas lizards are more terrestrial. These preliminary results reflect a connection between diversity patterns and extrinsic drivers not observable through the analysis of dinosaur fossils. Our continued analysis will provide more fine-scale resolution of herptile diversity during the Campanian.

Adoptive cell therapy with CAR-T cells has shown promise in hematological malignancies, but efficacy in solid tumors remains a challenge in part due to CAR-T cell exhaustion and antigen heterogeneity. However, the vast majority of preclinical models do not recapitulate the tumor-immune interactions that produce these barriers. To study CAR-T therapy in a rigorous model that recapitulates tumor-immune barriers, we adapted a Kras^LSL-G12D/+;P53^f/f (KP) genetically engineered mouse model (GEMM) of lung adenocarcinoma. However, adapting the KP-GEMM model for various target antigens, genetic drivers of disease, or interfacing with the vast array of powerful genetic mouse models is resource intensive which prohibits widespread utility. Here, we propose a defined, modular system for generating GEMM for CAR-T preclinical studies using the Sleeping Beauty (SB) transposon system. The proposed system uses polyethylenimine (PEI) to deliver SB transposon encoding oncogenic Kras^G12D and P53^R175H dominant alleles as well as our target antigen hROR1, in vivo to wild-type mice. We demonstrate that in vitro PEI successfully introduces genetic cargo into lung epithelial cell lines, while SB transposons mediate stable integration and expression. Next, we will test this in vivo. This system affords the induction of tumors with specific oncogenic driver mutations and specific tumor antigens on any genetic background. Ultimately, we expect that this approach will streamline preclinical use of GEMM in preclinical research. 

Behavioral flexibility is the ability of an animal to adapt to environmental changes, crucial decision making and goal directed behaviors. Impaired behavioral flexibility has been linked to psychiatric disorders such as depression, anxiety, and substance use disorders. Emerging research suggests that psilocybin, a psychedelic drug that acts on serotonin receptors, may improve behavioral flexibility by promoting adaptability in responses to new information. Given the growing literature exploring the impact of psilocybin as a therapeutic treatment for psychiatric disorders, this study aims to explore the effects of psilocybin on the use of behavioral strategies on a complex spatial set-shifting task. Long-Evans rats were trained on an elevated plus maze with two start arms, north and south, and two reward arms, west and east. The task requires rats to alternate between two strategies: alternation and place. The alternation phase required rats to switch between reward arms (go West, then go East), and the place strategy required choosing the same arm (e.g. go West) continuously. Rats must determine the correct strategy and implement it; once 12 out of 15 trials are accurately completed, an uncued switch in the correct strategy will occur, requiring adaptation to a new strategy. Once animals were well-trained on the task, a single dose of psilocybin (1mg/kg) or saline was administered 10 minutes prior to a session and their behavior was analyzed. Metrics such as performance, and flexibility scores were assessed to determine the impact of psilocybin on behavior. Preliminary findings suggest psilocybin improves behavioral flexibility compared to the saline group, though overall performance remains relatively stable. These results provide insight into the potential of psilocybin as a therapeutic tool for conditions characterized by behavioral rigidity; even in wild-type animals, psilocybin improves flexibility, indicating the possibility for mitigating more severe impairments in flexibility seen in psychiatric disorders.

South Thurston County's car-dependent and low-density built environment can affect the health and economic wellness of its residents. This research investigates the barriers that residents face in getting to work, their daily needs, and things-to-do. What are the best strategies to improve the built environment that provides access to employment, necessities, and entertainment for people in south Thurston County’s SR 507 and Old Highway 99 corridors? A process of observations, community surveys and interviews with government and other agency officials will allow for an understanding of current conditions in the study area, personal viewpoints of community members, and constraints that the government agencies and other organizations might face in making improvements. This project will include investigation into design, policy and economic practices. A free or low-cost guide that would allow rural governments to make economically smart design and planning changes, and help make towns more self-sustainable, will be created after understanding this research. As innovation in planning and re-urbanization occurs increasingly in the United States’ larger metropolitan areas, rural and tribal communities, too, deserve an opportunity at urban core making, simplifying the daily lives of its residents, and maintaining health and wellness for all.

This project examines how industries' return-to-work policies influence public transit ridership patterns across various business sectors in the Puget Sound area. By analyzing ORCA card data from local transit agencies and reviewing company policies, the research tracks the impact of policy on industry ridership trends from January 2018 to January 2025, spanning the pre-pandemic, pandemic, and post-pandemic periods. The findings provide insight into industry-specific ridership changes, revealing which industries in the Puget Sound area have experienced the most significant shifts in public transit ridership post-COVID-19, and how return-to-work policies may have influenced these changes. The results of this research can be used by public transit agencies to focus and adapt their strategies to engage low-ridership sectors. This work can also help advance equitable, sustainable, and resilient public transit systems, particularly in the context of evolving remote work policies.

Chloroplasts are central to plant immunity and act as a hub for immune signalling and defence-related hormone synthesis. The essential chloroplast-localized protein FtsHi1 is a component of the FtsHi import motor and is vital to translocating proteins across the chloroplastic membrane. Viral-induced gene silencing (VIGS) of FtsHi1 in Nicotiana benthamiana results in a bleached phenotype, indicative of decreased translocation of essential chloroplastic proteins and decreased chlorophyll synthesis. Previous work identified herbivore-induced kinase 1 (HIK1) as a potential interactor of FtsHi1. HIK1 is a receptor-like cytoplasmic kinase (RLCK) implicated in the immune response to caterpillars. FtsHi1 contains a predicted RLCK phosphorylation site, indicating possible phosphorylation of FtsHi1 by HIK1, which could promote defence signalling over photosynthesis. This project aims to test the impact of phosphorylation on FtsHi1 function and its role in protein translocation across the chloroplastic membrane. This work utilises engineered FtsHi1 variants, which mutate the serine phosphosite to either mimic FtsHi1 phosphorylation (Ser→Asp), prevent it (Ser→Ala), or recapitulate the wild-type protein sequence. To test the phosphosite mutation effects, FtsHi1 VIGS knockdown of N. benthamiana leaves will be transiently modified using Agrobacterium tumefaciens bacteria to express WT or phosphorylation-modified FtsHi1 constructs. The resulting colour phenotype for each construct will then be compared to the bleached phenotype of TRV2:FtsHi1 plants and the phenotype of wild-type plants. I hypothesise that the FtsHi1 phospho-null mutant will result in a rescue phenotype similar to wild-type FtsHi1, whereas FtsHi1(phospho-mimic) will retain the bleached phenotype.Examining FtsHi1 phosphorylation enhances our understanding of its potential interaction with HIK1 in herbivory-induced plant defences. Future studies will explore FtsHi1's role in defence mechanisms, with implications for engineering herbivory-resistant crops. 

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

Individuals with Stage II/III severe periodontal disease were recruited from the Graduate Periodontics Clinic at the University of Washington School of Dentistry using an approved IRB (STUDY00016871). Subgingival plaque samples were collected from four tooth sites: an active inflamed site, two adjacent tooth sites, and a distant healthy tooth site. Sterile paper points were inserted into the gingival sulcus for 30 seconds. DNA was isolated and extracted using the Qiagen AllPrep DNA/RNA Mini kit (Cat. #80204), then purified and concentrated using the Zymo Clean & Concentrator (Cat. #D4014) kit. Whole genome libraries were generated and whole genome sequencing was performed on a NovaSeq X (Illumina, San Diego, CA, USA). Relative abundance of species-level assignments represented by clusters were determined, and best matched genomes were then used to generate species pangenomes for comprehensive multi-genome wide read mapping and gene-level analysis. Taxonomic and gene level functional analysis was also performed. Data analysis is still being performed at this time. Based on previous literature (Basic and Dahlén, 2023), we anticipate that the activity of certain microbial metabolic pathways associated with oral disease and their functions will be heightened in the active disease site and lower on the non-affected site within strain-level disease-associated bacteria, such as those of the Porphyromonas, Tannerella, and Treponema genera. Specifically, we expect amino acid fermentation and lipid metabolism activity to be increased in the active disease site. We expect that results from this study will highlight the presence of heightened activity of bacterial metabolic pathways and functions at the strain level associated with specific gram negative perio-pathic disease-associated species within clinically healthy tooth sites in patients with active periodontal disease despite the absence of clinical observed inflammation.

The proximal tubule (PT) and glomerulus are vital blood-filtering components of the nephron, the functional unit of the kidney. The components’ micro-scale sizes and intricate three-dimensional structures are critical to kidney function, although accurate in vitro modeling has proven difficult. Limitations in fabrication techniques have forced size scaling and imprecise morphology in models. In this study, we addressed fabrication limitations using multiphoton ablation to etch intricate, three-dimensional proximal tubule and glomerulus vessels in collagen hydrogels. We sought to demonstrate model viability by introducing human proximal tubular epithelial cells (hPTECs) and human umbilical vein endothelial cells (HUVECs), respectively, through cell perfusion. However, we encountered a significant challenge: due to the small diameter and high curvature of the micro-scale channels, the cells tended to aggregate, disrupting cell profusion and cellularization throughout the vessels. Cell aggregation was especially prominent in the glomerulus model due to the more tortuous and complex geometry. While our cellularization trials on native-scale models proved it is feasible to perfuse cells throughout the vessel, we still need to refine cellular profusion and cellularization. To improve cellular profusion and cellularization, we are first studying a 1.5-scale glomerulus model. The scaled model's increased vessel diameter and lower curvature demote cell aggregation and enhance the ease of cell profusion. We anticipate that cellularizing the 1.5-scale model will provide a deeper understanding of the variables facilitating cell profusion that we can use to improve native-scale vessel cellularization. Fabricating native-scale, accurate in vitro PT and glomerulus models is crucial for developing a deeper understanding of hemodynamic influence on kidney function. These findings contribute to the fabrication of more biomimetic in vitro PT and glomerulus models that will pioneer therapeutics and the understanding of kidney physiology and pathology.

Hypertrophic Cardiomyopathy is the most common form of hereditary heart disease affecting ~1:500 individuals, characterized by progressive thickening of the left ventricular wall. The first mutation linked to this disease was the heterozygous R403Q mutation in human beta-myosin heavy chain (β-MHC). Conflicting reports of contractile kinetics between human myectomy samples vs transgenic mouse and rabbit models motivated us to study the molecular mechanisms of altered contraction in a CRISPR/Cas9 gene edited human inducible pluripotent stem cell line. Following differentiation to cardiomyocytes (hiPSC-CMs) and maturation in culture, we isolated sub-cellular contractile organelles called myofibrils. Myofibril contractile kinetics from this line had slowed force development and cross-bridge detachment, with reduced maximal force compared to the WT line. hiPSC-CMs were cast into fibrin matrices to form three-dimensional, engineered heart tissue (EHT) for measures of twitch force and contractile kinetics. At 1Hz stimulation, heterozygous mutation EHT’s exhibited a hypercontractile phenotype compared to WT EHTs, with slowed relaxation kinetics. Since the penetrance of our heterozygous R403Q hiPSC-CMs is unknown, we are now studying a homozygous iPSC-CM line where 100% of the β-MHC is mutated. This will allow us to assess the direct contribution of the mutation to the disease contractile phenotype. We will repeat the myofibril and EHT measures of contractile properties and perform stopped flow kinetics analysis on isolated myosin to determine ATP turnover and ATP hydrolysis product release rates. This will provide molecular mechanistic insight of the contractile abnormalities, allowing development of therapeutic interventions that specifically target the mechanisms that alter contractile function. 

In the wake of the Trump and Biden administrations, during which movements such as Christian nationalism and religious deconstruction brought civil religion into the public eye, scholarship regarding religion as it interacts with politics becomes increasingly relevant. My thesis aims to investigate the role of Christianity in the political communication of our two most recent presidents, arguing that public religiosity is not diminishing in America -- rather, it is in a constant state of evolution to fit an ever-changing nation. This content analysis compares Trump's and Biden's usages of Christian language to one another as well as to former presidencies, addressing the question of how religious rhetoric is shifting in American political discourse. Through creation of a codebook of more than one hundred Christian keywords, which are then applied to presidential communication such as State of the Union addresses (accessed through The American Presidency Project), I determine the frequencies and contexts of religious mentions within Trump's and Biden's communication. Using programs such as Atlas.ti, I measure, analyze, and visualize Trump's and Biden's individual invocations of Christian talk. I hypothesize that Donald Trump's use of religious language increased over the course of his presidency as well as being significantly concentrated in self-referential contexts. Meanwhile, Joseph Biden's religious language is expected to be concentrated in contexts of national crisis, mainly taking the form of Biblical quotations. Overall, findings are expected to demonstrate that Christian language in the American presidency is not broadly declining, but rather used in more niche contexts. This project contributes to the vast field of religious and political scholarship by comprehensively analyzing not just the frequency but also the context of religious language in these presidencies, supporting the notion that public religion is a living entity that functions as a sociological and cultural phenomenon.

Remembering ‘when’ things happened is difficult relative to ‘where’ things happened. One reason for this may be because time is an abstract concept while locations are concrete. Many cultures worldwide use space to represent time to get around this problem. A common representation is a mental timeline: a linear mental model of time. For most Western adults, the mental timeline flows from left-to-right: representing the past on the left and the future on the right side of space. Previous research suggests that U.S. adults recall the order of events more accurately when items are presented from left-to-right, rather than nonlinearly or from right-to-left, indicating that adults spontaneously organize temporal order in terms of a mental timeline. However, it is unknown what memory processes influence this benefit. We examine the relation between the mental timeline and temporal memory by assessing both encoding (committing to memory) and recall (remembering) phases. In this study, adults first view triplets of images arranged from left-to-right, right-to-left, or nonlinearly (encoding). Then, images are shown individually, and participants identify whether the image appeared first, second, or third within the triplet (recall). We record participants' responses and their pupil dilation. We predict that item location will affect participants’ errors. For example, they might be more likely to incorrectly remember an image as ‘first’ if it appeared on the left, even if the triplet was presented right-to-left. Additionally, we expect adults to exert greater mental effort when encoding triplets presented nonlinearly or from right-to-left, indicated by increased pupil dilation. These results will provide insight into how the mental timeline interacts with temporal memory beyond memory accuracy measures. The pupil dilation measures will reveal the role of mental timeline in the encoding process, and errors will reveal its role in the recall process.

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

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

The ability to manipulate and ligate proteins has been a driving force in advancing our understanding of the complex regulation of biological processes in space and time. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy in biomacromolecular engineering, enabling precise control over protein modifications, stability, and functionality. This is particularly useful in understanding protein function and interactions, as well as modulating protein activity, including immobilization of protein-based signals within materials triggered by cytocompatible light. One proven system known for its specificity and ease of use is SpyTag/SpyCatcher, a peptide-protein pair capable of irreversible ligation via isopeptide bond formation. Recent work has demonstrated the ability to control SpyTag/Catcher ligation using cytocompatible light due to its non-invasive nature and spatiotemporal (i.e., 4D control) manipulation of protein signals on a biologically relevant timescale. However, the application of this reported photoligation strategy is hindered by the use of genetic code expansion which limits protein yield, entails additional orthogonal protein machinery, and involves translational incorporation of a non-canonical amino acid. To address these challenges, we aim to develop a photocontrolled protein ligation strategy using native protein activity while maintaining spatial and temporal control. We predict this strategy will enable dose-dependent reconstitution of ligation by varying light exposure duration and intensity in native protein systems while sidestepping challenges associated with genetic code expansion. We intend to use this strategy to further assess our capability to control split protein reconstitution and for future applications in directing complex cell fate, which has significant utility in stem cell biology and regenerative medicine.

Neonatal tracheal intubation (TI) is a high-risk procedure requiring careful coordination to minimize complications and improve outcomes. The Personalized Intubation Neonate Safety (PINS) Bundle was developed to enhance team communication and optimize intubation practices for neonates at risk. The bundle incorporates five key domains: patient risk assessment, treatment threshold for intubation, premedication plan, equipment specification, and provider selection with escalation strategies. At the University of Washington Neonatal Intensive Care Unit, eligibility criteria for the PINS bundle include neonates requiring non-invasive respiratory support with >30% FiO₂, those meeting surfactant administration criteria (≥30% FiO₂ and PEEP 6 on NCPAP), already intubated and mechanically ventilated infants, those with difficult airway diagnoses (e.g., craniofacial anomalies, large tongue, micro/retrognathia), and extremely preterm infants (<1000g or <4 weeks old). We will evaluate the impact of PINS implementation by comparing intubation attempts and adverse events before (January – June 2024) and after (July – December 2024) the bundle’s introduction. Data was adjusted to exclude ineligible patients, ensuring comparable cohorts. Primary outcomes include the number of intubation attempts before success and the incidence of tracheal intubation adverse events (TIAEs). We hypothesize that PINS implementation will be associated with a reduction in intubation attempts and TIAEs, reflecting improved preparation and procedural success by the healthcare team. By standardizing an individualized pre-intubation plan, the PINS bundle aims to enhance neonatal safety and streamline team response during intubation. Findings from this study will inform future clinical protocols and may support the broader adoption of personalized intubation strategies in the NICU. Further assessment of long-term outcomes for infants will strengthen the bundle’s clinical utility.

Cascadia Subduction Zone, a major fault off the Pacific Northwest coast, has a history of producing powerful earthquakes. These events highlight the need to understand the region's earthquake probability. This study aims to conduct a sensitivity test on the earthquake probability in the Pacific Northwest, evaluating partial and full rupture scenarios. The study analyzes 32 different earthquake chronologies derived from the earthquake catalog and perturbs them to assess how the probabilities vary with changes in data. As a result, we found that the Southern Oregon and Northern California regions face the highest risk, with a 34-49% chance of a partial rupture and a 28-32% chance of a full rupture within 100 years. Within the next 50 years, probabilities are 17-20% and 13-15%, respectively. The relatively small changes in probabilities suggests that the estimates are robust, indicating that changes in data do not significantly skew the overall probability assessment. These findings emphasize the need to implement hazard mitigation strategies to protect vulnerable Southern Oregon and Northern California communities from future earthquake events.

The Campanian stage of the Late Cretaceous (~84–72 million years [Ma]) was a dynamic interval for North American ecosystems including the evolution of angiosperm plants and the regression and transgression of the Western Interior Seaway (WIS). These dynamics likely impacted terrestrial fauna across the continent. Most studies investigating biodiversity in western North America during the Campanian focus on a single group (e.g., dinosaurs or herpetofauna), whereas few investigate diversity patterns of multiple taxa. This approach is imperative because comparing diversity patterns among taxa can provide rare insight into the synecology of animal communities. Vertebrate microfossil sites are ideal for such a study because they preserve large sample sizes, multiple taxonomic groups that likely coexisted, information about environmental conditions, and they sample multiple stratigraphic intervals. The Judith River Formation (JRF) of north central Montana preserves ~4 Ma of the Campanian (~79–74 Ma) and large regressive and transgressive cycles of the WIS. This formation, which is contemporaneous with the Dinosaur Park and Two Medicine formations, is also rich in vertebrate microfossil sites. To examine vertebrate diversity patterns through this critical interval, we compared taxonomic richness and relative abundances of Dinosauria, Squamata, and Lissamphibia from the JRF from three temporally distinct microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (~76.5 Ma), and Clamfetti (~75.2 Ma). Over four years, we collected and screenwashed fossiliferous, bulk-sediment samples from these sites. Thus far, we have recovered 998 and aim to recover 1,200 specimens total. We use our data and knowledge from the literature to evaluate the extrinsic factors (e.g., seaway regressions) that drove diversity changes in the JRF fauna.  Our preliminary results suggest a connection between diversity patterns and WIS cycles. We observe shifts in relative abundances and richness near the onset of the WIS transgressive cycle. 

Tuberculosis (TB) remains the world’s deadliest infectious disease, claiming over 1.25 million lives annually—surpassing malaria and HIV in mortality. TB’s causative pathogen, Mycobacterium tuberculosis (MTB), continues to spread rapidly due to inadequate access to accurate molecular diagnostic tests. The most commonly used tests include sputum-based and tuberculin skin tests, which require follow-up visits and have suboptimal sensitivity, particularly within certain patient populations. Moreover, these assays cannot identify emerging drug-resistant strains (DR-TB) that have reduced susceptibility to first-line antibiotics. Our aim is to design a diagnostic tool to detect cell-free DNA (cfDNA) in urine and identify the infecting strain to ensure patients receive appropriate antibiotics. To achieve this, we are developing a probe-ligation assay with single-nucleotide specificity. Current implementations are limited by the low specificity of ligase, leading to false positives and an inability to differentiate between mutated MTB strains. We hypothesized that Flap Endonuclease-1 (FEN1) could confer a specificity advantage by integrating a second enzymatic “check” into the process. The protocol involves a ligation reaction with MTB genome-derived targets and two probes, each containing a DNA flap with additional nucleotides. To detect the ligated product, FEN1 must cleave these flaps before the ligase catalyzes the repair of the nick between probes. To experimentally observe this, we carried out several ligation reactions containing FEN1 and ligase with wild-type and mutant targets, followed by PCR or gel electrophoresis to measure ligated product formation. We evaluated the efficiency and precision by analyzing the amplification profiles of WT targets and mutants containing SNPs neighboring the ligation site. Our data about whether FEN1 confers a significant specificity advantage remains inconclusive, but the double enzyme reaction is functional and could be further exploited in future experiments with additional optimization or modifications to enzymes or DNA probes.

Grasses (family Poaceae) are highly diverse (~11,800 species), cover nearly 40% of Earth’s ice-free land surface, and play critical ecological and economic roles. Grasses have evolved a variety of unique traits, including an exceptionally high accumulation of silicon in the form of biological silica bodies (phytoliths) in some lineages. Silicon accumulation confers resistance to both abiotic and biotic stresses, including drought and salinity resistance, herbivore defense, and structural support. Despite the role of silicon in the enormous success of grasses, a clear picture of the exact drivers of silicon accumulation in grasses across species and environments has not yet emerged. I hypothesize that elevated silicon concentrations are primarily driven by environmental stress, most notably high temperatures and low precipitation. To test this hypothesis, I used X-ray fluorescence to analyze the leaf silicon concentration of 482 grass leaf samples, encompassing approximately 200 species across all 12 grass subfamilies. Using occurrence records from online databases, I identified the realized climate niche and its environmental conditions (e.g., temperature, precipitation) for each sampled species. The next step is to collect geolocation data from each individual sample, which will be combined with the climate niche data of its species. By comparing the relationship between a plant’s climate niche, its individual growing conditions, and its silicon concentration, a better understanding of environmental drivers of silicon will begin to emerge. Preliminary results taking into account only climate niche and silicon concentration showed no relevant correlations, illustrating the need for individual growing condition data. Because many of the stresses that silicon helps to alleviate are also those that will worsen under climate change (high temperature, drought, insect herbivory), an improved understanding of the environmental drivers of silicon accumulation will allow us to better prepare for the impacts of climate change on our agricultural and ecological systems.

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

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

Plants utilize molecular patterns in order to detect threats to the plant. Through the recognition of molecular patterns by their associated receptor, plants are able to initiate an appropriate immune response, measurable by the increased production of reactive oxygen species (ROS). In the model organism Arabidopsis thaliana, the pathogen associated molecular pattern flg22 is detected by the pattern recognition receptor Flagellin Sensitive 2 (FLS2) to initiate intracellular signaling. The immune signaling kinase Botrytis-Induced Kinase 1 (BIK1) is then phosphorylated by FLS2 to transduce the immune signal, initiating ROS production. However, A. thaliana lacks a group of immune signaling kinases related to BIK1 called Herbivory-Induced Kinase Like Kinases (HLKs), which are present in multiple species including tobacco (Nicotiana benthamiana) and common bean (Phaseolus vulgaris). The goal of this project is to determine the role of HLKs in immune signaling. To investigate the role of HLKs in immune signaling, A. thaliana were transformed with transgenes to express HLKs or overexpress BIK1. Stably transformed A. thaliana lines were then bred to produce progeny that are homozygous for the transgenes. These lines are treated with flg22 in order to initiate an immune response. ROS is used to measure the immune response of each transgenic line, where HLK expressing individuals are compared with BIK1 overexpressing individuals as a control group. I anticipate that HLKs will increase the ROS production when compared with the controls, signifying an increased immune response, since HLKs are related to the native BIK1. An understanding of the role of HLKs in FLS2 immune signaling in the model organism A. thaliana can be applied to crop species that employ HLK mediated immune signaling.

Understanding the impact of the solvent environment on the electronic properties of modified DNA is essential for their use in nanoelectronics and in medicine. We modeled the impact of counterions in metal modified DNA (mmDNA) using ab-initio density functional theory to model wet and dry conditions. The orbital wavefunctions and charge transport properties were compared for a variety of test conditions, looking at effects for a single basepair as well as a longer DNA chain, using the Thymine-Mercury-Thymine mmDNA basepair as a case study. Preliminary results from single base pair calculations indicate that chlorine counterions in wet DNA do not significantly affect the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, while in dry cases, orbital wavefunctions are more localized and at lower energies, albeit with a similar bandgap. In most calculations, the LUMO localizes on the central metal atom. These findings suggest that longer DNA molecules could potentially form a channel for electron transport along the metal atoms, effectively functioning as a nanowire with a conductance dependent on solvation and counterion presence. With a more accurate model of DNA as a nanomaterial for bioelectronics, it will be possible to develop smaller, more efficient devices operable in biomolecule-friendly environments.

Robots must be able to pick objects from densely packed shelves in order to automate industrial warehouses. Dense packing gives rise to challenges in grabbing targeted objects efficiently as the shelves can be clustered, objects can be stacked, and the target object can be obstructed from direct reach. The goal of this research project is to create a new gripper combined with reinforcement learning to manipulate objects within a shelf without multiple attempts or repositioning of the robot arm. The new gripper design includes four fingers that are linear actuators with vacuum units and suction cups attached to the ends of each finger. Additionally, each finger contains a time-of-flight sensor at the tips which provide spatial information for different objects within the shelf. I integrated time-of-flight sensors into the multi-fingered gripper and filtering algorithms for the sensor’s data. I modified the previous vacuum ejector unit which only provided support for one unit to four vacuum ejector units. I also conducted a series of experiments that provided cases where the new gripper design proved to be better than the previous design. We also collected suction cup vacuum data and trained a neural network to predict the success rate of suction cup attachment. The results of this project will inspire new designs for increasing the success rate of robotic grasps within densely packed environments.

It is estimated that ~15% of all cancers are caused by oncogenic virus infections. Two of the top seven cancer-causing human viruses are members of the gammaherpesvirus family: Epstein Barr Virus (EBV) and Kaposi’s Sarcoma Herpesvirus (KSHV). Our lab uses Murine Herpesvirus 68 (MHV-68), a mouse gammaherpesvirus with shares significant genetic homology to KSHV and EBV, as a model system to understand how gammaherpesviruses alter the metabolism of their host during lytic infection to promote their replication. We recently metabolically profiled MHV-68 infected host cells at various time points during the lytic infectious cycle. Our data showed nucleotide metabolism is significantly induced in MHV-68 infected NIH/3T3 cells, revealing a potential antiviral target. This study investigates the antiviral efficacy of Methotrexate (MTX), an FDA-approved nucleotide biosynthesis inhibitor currently used to treat cancer, rheumatoid arthritis, and psoriasis. MTX inhibits dihydrofolate reductase (DHFR), an enzyme crucial for producing thymidylate and purine nucleotides, which are essential for de novo nucleotide synthesis. We hypothesized that MTX can block MHV-68 production and be repurposed as an antiviral drug. To test our hypothesis, we first determined a safe concentration of MTX in NIH/3T3 cells using both qualitative (microscopy) and quantitative (trypan blue exclusion) cell viability assays. Next, we infected NIH/3T3 cells with MHV-68 and treated them with a safe level of MTX or solvent control. After 48 hours, we assessed viral production in control vs MTX treated cellular supernatants via viral plaque assays. Our results revealed that MTX significantly suppressed MHV-68 virion production by ~50-fold. These findings suggest that targeting host metabolic pathways could be an effective antiviral strategy against gammaherpesviruses in humans. Further research is needed to explore the use of MTX as a broad viral therapy against other viruses.

We are developing a RNA scaffold-based CRISPR activation and inhibition system to controllably tune gene expression in  primary immune cells, which will allow us to manipulate and increase production and function of immune cells, vastly increasing their efficacy in fighting diseases such as cancer. Here we target Bcl11b, a key T cell transcription factor necessary for progenitor cell commitment to the T cell lineage. CRISPR activation and CRISPR interference (CRISPRai) enable activation or repression of targeted genes. Due to the large size of dCas9 activator and reperessor fusions, it is not possible to express the necessary machinery in primary mouse T cells. Thus, we are developing a CRISPRai system where the gRNA (guide RNA) contains an additional RNA hairpin to recruit RNA binding protein-effectors, enabling activation and repression in the same cell. To optimize the efficiency of CRISPRi in T cells, we are 1) cloning and testing a repressor domain for its ability to drive gene silencing and 2) testing alternative RNA base pairs (BP) and hairpin pairs. We are testing these optimizations in a T cell progenitor cell line which has turned on Bcl11b with a downstream YFP (fluorescent) reporter. Here, YFP expression, which we measure using flow cytometry, is directly correlated to Bcl11b expression levels. We hypothesize that an alternative validated RNA hairpin BP in conjunction with a novel compact transcriptional effector will result in decreased levels of YFP expression compared to the existing system.

Carpels are invaluable floral organs that have undergone myriad innovations in flowering plant evolution, providing fruits and seeds. Carpels consist of a pollination site (stigma), pollen growth area (style), and a region containing ovules (ovary) which become the fruit after fertilization. Understanding carpel development and evolution is fundamental for efforts to increase food production. A decreased abundance of insect pollinators due to anthropogenic climate change has made this pursuit all the more urgent. The plant genus Thalictrum comprises perennial herbs in temperate regions that have repeatedly transitioned from insect to wind-pollination in their evolutionary history. Hence, they are ideal to investigate the adaptations and genetics that decrease reliance on insects for reproduction. A key feature of wind pollination is a longer stigmatic surface that increases pollen capture. I am taking a candidate gene approach, examining homologs of the stigma development gene families STYLISH (STY) and NGATHA (NGA). I am characterizing the role of NGA and two STYLISH gene copies in our model species, Thalictrum thalictroides. Previous work has found that silencing one of the STY gene copies results in the loss of stigma development, while the function of the other copy remains unknown. In other genera, altered NGA expression has been shown to alter stigma development. To characterize the function of both NGA and STY, I am implementing Virus-Induced gene Overexpression (VOX) by infiltrating tubers with Agrobacterium transformed with Tobacco Rattle Virus (TRV) carrying an overexpression construct. STY genes will be overexpressed, and NGA will be both overexpressed and silenced using Virus-Induced Gene Silencing (VIGS). I will characterize the phenotypes resulting from these treatments to determine the functionalization of STY and NGA. By dissecting the genetic basis of floral adaptations to wind-pollination in this system, I hope to contribute solutions to enhance crop production in the face of pollinator decline. 

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

Flowering plants are important sources of agricultural crops and are diverse in flower and fruit structures. To study how this diversity has evolved, I am developing a new plant model system in the order Ranunculales, an underrepresented clade that will help bridge the knowledge gap within dicotyledonous plants, where most of the angiosperm diversity is found. A key tool in model system development is the ability to transform plants to study gene function, therefore, I aim to develop a method for genetic transformation. Specifically, I am implementing the tried and true  “floral dip” transformation method of Arabidopsis using Agrobacterium tumefaciens in Myosurus minimus, tiny mousetails. This is a small, fast-growing plant that produces many seeds, making it feasible to generate and propagate stable transformants. As proof of principle, I am expressing fluorescent proteins (GFP and YFP) and a visual reporter called RUBY, which causes transformed plants to produce red pigment. I found red color on the petals of treated plants, suggesting that transformation is working in Myosurus. I am currently validating this phenotype by planting the seeds on antibiotic selective media. I expect to see that certain individuals are resistant to antibiotics, while others die, which will allow me to identify the genetically transformed plants. By developing this transformation method, I will be able to test the function of candidate genes of interest in this new model plant species, which will further enable the investigation of gene network evolution in flowering plants. Increased understanding of gene function provides opportunities for engineering crop species to have beneficial traits for agricultural purposes. 

Birdsong in the Machine is a soundscape composition that explores the evolving relationship between natural and artificial worlds through the story of the Streaked Horned Lark (Eremophila alpestris strigata), a threatened coastal songbird native to the Pacific Northwest. The central research question is: How can artificial intelligence (AI) and machine learning (ML) enhance environmental storytelling to amplify the voices of endangered species and reimagine human-nature-technology relations? By integrating AI-generated audio, wildlife recordings, and digital sound processing, this project critically examines the paradoxical role of technology as both a disruptor and preserver of ecological systems. Inspired by my lifelong connection to technology and deep appreciation for the natural world, Birdsong in the Machine reflects on the impacts of technological progress on the Streaked Horned Lark. The project draws from Donna Haraway’s A Cyborg Manifesto and the works of Bernie Krause and Thom van Dooren, challenging the perceived divide between the natural and artificial. It envisions a future where these realms coexist harmoniously, fostering collaboration rather than conflict. This composition combines recordings of the lark’s song and habitat with AI-generated audio, using machine learning models to emulate and predict natural soundscapes. Digital audio processing techniques integrate these elements into a cohesive narrative. Bibliographic, archival, and ethnographic research reinforce the ecological and artistic focus of the composition. Through its juxtaposition of organic and AI-generated sounds, Birdsong in the Machine illuminates the paradox of technology’s role in ecological degradation and preservation. The soundscape fosters empathy and awareness for endangered species while reimagining relationships between humans, nature, and technology. Future directions will explore the ethical implications of using AI in ecological art and expand collaborations with scientists and digital artists. Ultimately, this piece stands as both environmental advocacy and an artistic experiment, challenging audiences to rethink their place in the interconnected natural and artificial worlds.

Variations in floral structures influence how plants are pollinated, showier flowers are more attractive to pollinators, while wind-pollinated plants benefit from having smaller, inconspicuous flowers that produce increased amounts of pollen, and have the appropriate morphology to receive pollen from the wind. The genus Thalictrum contains species that range from insect-pollinated to wind-pollinated. Certain transcription factors are known to affect the stigma, the area of pollen reception that consists of papillae, and to increase stigmatic papillae length. By better understanding the genes that influence stigma morphology, this gene could be used in economically important crops to increase their stigmatic surfaces and consequently the likelihood of pollination. In this study, we use in situ hybridization to analyze gene expression of candidate genes for stigma development in the genus Thalictrum, which has had multiple transitions from insect to wind pollination in its evolutionary history. We selected three species representing the range of stigma morphologies found in Thalictrum. I will test the hypothesis that expression of my candidate genes will correlate with stigma morphology, such that the short (capitate) stigmas characteristic of insect-pollinated species will exhibit restricted areas of gene expression just prior to stigma development, while the more elongated stigmas of the wind-pollinated species will show an extended temporal and spatial domain of expression, with mixed-pollinated species lying in between. Thus, this work will provide a connection between developmental genetics and morphology to improve understanding of the wind pollination syndrome.

The transcription factor LEAFY (LFY) controls the development of flowers in angiosperms, but it is found in all lineages of land plants, including those that do not flower. In the non-vascular plants like moss, LFY promotes the first cell division in the zygote, and in early vascular plant representatives like ferns, LFY controls stem cell activity. Ferns are the sister lineage of seed plants, making them an ideal model to study the evolution of LFY. The model fern Ceratopteris richardii has two copies of the LFY gene, while most angiosperms have one, and the two genes are expressed at different levels across development, suggesting the possibility of sub- or neo-functionalization. In this study, we use transgenic C. richardii plants overexpressing one or both LFY genes to determine their function across development. Since LFY is expressed in sperm cells, I set up assays to observe C. richardii sperm cells during fertilization and determine the role that LFY may be playing in fern sperm development and reproduction. To test whether the two fern LFY proteins interact with each other, I perform yeast two-hybrid assays, which will provide insight into whether the genes play independent roles or share overlapping functions. Determining the function(s) of LFY in ferns will help uncover the evolutionary history of this important plant transcription factor and how it came to control the crucial role of initiating flower development.

With the increasing prevalence of large wildfire events, especially near urban areas, the identification and quantification of combustion-derived air pollutants is critical. The collection, quantification, and identification of particulate air pollutants, also known as aerosols, provide important insights into air pollution sources, evolution, and health effects. To improve capabilities in this area, with funding and support from the Beckman Foundation, we have designed and developed an aerosol collector that uses high-voltage Dielectric Barrier Discharge plasma and Electrostatic Precipitation (DBD-ESP) to collect and desorb target nanosized aerosols (30 nm – 800 nm) containing components typical of woodsmoke, such as levoglucosan and phenolic compounds, among others. The DBD-ESP is integrated with an Ultra-Portable Time-of-Flight (TOF) Mass Spectrometer (UP-ToFMS) to produce online, near real-time analysis of the chemical composition, mass, and size of target aerosols. Based on preliminary collection and desorption testing, we expect to have a 75% collection and desorption efficiency of submicron aerosol particles within 5 minutes. The DBD-ESP has an internal volume of less than 2 cm3 and an overall external volume of around 1 L. Once coupled with the UP-ToFMS, the overall ultra-portable system will be no larger than 0.095 m3 and weigh around 35 kg, enabling the remote sampling of aerosols from wildfire events while still yielding high-quality mass spectral data.

Since 1947, the Japanese government has been constrained by Article 9 of its Constitution, renouncing war as a means to settle international disputes and preventing the existence of an offensive military force. With the Security Treaty between the United States and Japan signed in 1951, the United States is obligated to defend Japan in exchange for the continued existence of American military bases on Japanese soil. In this research, we explore whether it is in America's interest to encourage Japan to amend or repeal Article 9, considering the security risks stemming from a stronger China and combative North Korea. In our policy recommendation, we used scholarly sources to discover three distinct challenges to regional and global security if a change to the status of Article 9 was to be pushed forward: Japanese public opinion and governmental concerns, the potential antagonization of regional adversaries, and the polarization of American allies with long-standing colonial histories with Japan. To address these concerns, we utilized a qualitative approach, exploring various narratives and opinions on the issue at stake. We found a diverse set of viewpoints, which we used to compile a recommendation for Japan to amend Article 9 to allow for the collective self-defense of its neighbors and allies when attacked. This research has significant implications for Japan's role in the future of East Asia, designating the state as a key military and economic power under America's Free and Open Indo-Pacific. With the culmination of our project, we found a clear path to upkeep and enhance America's time-honored relationship with Japan while maintaining its strategic leadership in the region. As previous efforts to remilitarize Japan have broken down due to several factors, our findings provide insight into the most suitable direction for the United States as a key player in the broader Asian region.

Undocumented youth are a highly politicized group in the United States and Israel, two nations who are themselves composed mostly of recent migrants. Recently, Israel and the United States introduced temporary policies to attempt to address the "issue" of undocumented youth. In 2006, Israel enacted the Temporary Arrangement for Grant of Status for Children of Illegal Residents (TAGS) policy. This one-time program granted legal residence to undocumented youth in Israel. Just six years later, President Obama announced the Deferred Action for Childhood Arrivals (DACA), a policy that granted undocumented youth protections from deportation, a work permit, and sometimes access to certain benefits. In this study, I conduct a comparative analysis of DACA and TAGS to evaluate how both states restrict and expand pathways to citizenship for undocumented youth. I conducted a literature review of the policies and experiences of undocumented youth utilizing large research organizations such as the Migration Policy Institute, academic journals such as the International Journal of Intercultural Relations, and local news sources such as Haaretz and i24News. I argue that through their limited criteria and application, both policies function as a "gatekeeping" mechanism, creating a liminal status of citizenship through their narrow eligibility criteria and temporality. These policies also contribute to state-building through reinforcing a hierarchy of 'deservingness' and belonging in both States (Lee, 2004). As the relationship between the US and Israel continues to evolve and undocumented migration continues to be a politically charge topic, it is pertinent that undocumented youth, one of the most vulnerable groups, continue to be a topic of study.

I investigate the effects of scopolamine-induced cholinergic disruption on the working memory performance of rhesus macaques. Working memory plays a critical role in cognitive function and relies heavily on cholinergic signaling in the brain. To explore this relationship, I designed and implemented a delayed match-to-sample (DMTS) task to optimize the accuracy and reliability of the data collected. The DMTS trials involve three phases: stimulus, delay, and choice. Monkeys are presented with a sample stimulus they must memorize. After a variable delay period of 5 to 30 seconds, they select the target image from a set of options. Performance is tracked by calculating the percentage of correct, incorrect, and omitted responses. Daily DMTS sessions provide longitudinal data on memory performance, allowing me to analyze patterns before and after scopolamine administration. I am also learning to analyze spike-spike coherence to investigate changes in neuronal synchronization associated with memory performance. Upon inducing amnesia-like conditions under scopolamine, an M1 muscarinic antagonist, the delayed match-to-sample task evaluates memory performance under baseline and drug-induced conditions. The primary objective of my project is to understand how scopolamine-induced disruptions affect working memory performance and to investigate the underlying cortical mechanisms involved. Based on existing literature and preliminary observations, I anticipate observing a measurable decline in memory performance following scopolamine administration, with older macaques likely exhibiting more pronounced deficits compared to younger macques. This project aims to contribute to the understanding of how cholinergic mechanisms influence working memory performance and to provide insights into the cognitive impairments associated with neurodegenerative diseases.

Rotated orientation patch count (OPCr) is a measurement used to quantify the complexity of a 3D surface. OPCr has previously been used to analyze tooth complexity, showing a correlation between complexity and diet in lizards, crocodilians, and mammals. We applied this technique to toothless taxa, with the goal of determining if there is a correlation between the complexity of the occlusal surface of a given species of turtle and its diet category. OPCr is determined by analyzing a 3D mesh of the occlusal surface of turtle specimens, with meshes based on both photogrammetry and CT scans of turtle skulls. Photogrammetry and CT scans are fundamentally different. Photogrammetry is a 3D mesh created from a series of surface images of an object, where the lighting and shadows cast on the object potentially distort its complexity. CT scans are not subject to these errors, and are typically more consistent provided the scan is made properly. However, there is little research analyzing the impact of different scanning techniques on the surface complexity of the resulting mesh. This project is therefore a comparison of photogrammetry and CT scans: do models made from these different methods produce significantly different OPCr scores? Nineteen specimens previously digitized using photogrammetry have been CT scanned. I created 3D models from the CT scan data and analyzed their surfaces using OPCr. I then compared the OPCr values produced by the CT scan models to the photogrammetry counterpart of each specimen. We hypothesize that statistical analyses will show no significant difference between the two methods of digitizing specimens.

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

TDP43 is an RNA/DNA binding protein that forms pathological aggregates in most amyotrophic lateral sclerosis (ALS) and half of frontotemporal lobar degeneration (FTLD) cases. Knockout of TDP43 in animal models leads to neurodegeneration and motor deficits, but overexpression of wildtype TDP43 leads to the same events; therefore, TDP43 protein homeostasis is critical to prevent ALS/FTLD. To achieve this homeostasis, TDP43 autoregulates its own mRNA splicing, resulting in multiple TDP43 isoforms. Although some of these isoforms go through nonsense mediated decay, other isoforms result in unique proteins with differing C-termini. This leads to variable cellular localization. It is unknown if these alternative, protein-coding isoforms are predominantly associated with ALS/FTLD or if aging changes the frequency of these isoforms. To determine how TDP43 overexpression yields different isoforms and interacts with aging and ALS-like symptoms, the Darvas Lab created a novel approach to overexpress human TDP43 (hTDP43) via Adeno-Associated Virus (AAV) delivered through retro-orbital injection, leading to ALS-like motor deficits. We tested this AAV in young and old mice cohorts. Then, to determine if Tardbp alternative splicing is linked to ALS-like symptoms and aging, I designed and validated primers and protocols to measure the nine Tardbp mRNA isoforms in mice via quantitative real-time polymerase chain reaction (qRT-PCR). I have started to determine if hTDP43 overexpression leads to differential splicing compared to mice injected with a sham-control AAV in these old and young mice. Once this is done, we will clone the most interesting differentially spliced isoform in an AAV and inject that AAV and a full-length TDP43 AAV into mice to see if the spliceform causes increased toxicity, manifesting in worsening motor deficits and mortality.

Currently, nearly 10% of Americans have type 2 diabetes (T2D), placing it among the most common chronic diseases in the United States.  Growing evidence points to brain neurocircuits that regulate glucose homeostasis as potential targets for developing novel therapeutics to treat T2D. Recent studies have revealed that the brain can induce sustained remission of hyperglycemia in rodent models following intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1). FGF1 stimulates the MAPK/ERK signal transduction system, which translates signals from the activation of cell surface receptors into gene expression changes within the cell nucleus. Following FGF1 injection, tanycytes and astrocytes are sites of transcriptional changes related to the ERK pathway. Inhibition of MAPK/ERK signaling blocks FGF1-induced diabetes remission. Like other growth factors, FGF1 requires integrin signaling to elicit the full spectrum of its cellular responses.  The integrin receptor αvβ3, which is implicated in the chronic cellular response to FGF1 is expressed in hypothalamic neurons and tanycytes and is required for FGF1 to induce sustained activation of MAPK/ERK signaling. To determine if integrin signaling in tanycytes is required for FGF1 to induce diabetes remission, we utilized adult, male, diabetic mice expressing either floxed Integrin β3 (ITβ3) or floxed Integrin αV (ITαV). Mice received a single 500µl injection of TAT-cre or heat-inactivated TAT-cre into the 3rd ventricle. TAT-cre administration inactivates the expression of genes encoding either ITβ3 or ITαV. Next, each cohort received a single icv injection of either FGF1 (2 µg) or saline vehicle. Food intake, body weight, and blood glucose measurements were taken daily throughout the investigation.  Our data demonstrates that the ability of icv FGF1 to induce lowering of blood glucose levels is not blocked by knockout of either ITβ3 or ItαV in tanycytes suggesting that integrin signaling isn't required for FGF1 to induce diabetes remission.

Plasma cell neoplasms are characterized by the secretion of large amounts of monoclonal antibodies into circulation. Monoclonal gammopathy of undetermined significance (MGUS) is a precancerous plasma cell neoplasm that can develop into a cancer called multiple myeloma. Glycosylation of the antigen-binding (Fab) light chain fragment of monoclonal antibodies is a risk factor for MGUS progression to myeloma. However, heavy chain Fab glycosylation may also occur and be a risk factor for progression, but this has not yet been investigated. In this study, I identify whether heavy chain Fab glycosylation occurs on monoclonal antibodies isolated from MGUS and myeloma patient serum, to help determine whether it should also be investigated as a risk factor of disease progression. I isolate intact antibodies to optimize antibody fragmentation and dissect them into light chain, heavy chain, total Fab, heavy chain Fab, and fragment crystallizable region (Fc) fragments. To do this, I purify IgG from serum from patients with plasma cell neoplasms. I either reduce these purified IgG samples using dithiothreitol into heavy chain and light chain fragments, or cleave them using IdeZ enzyme into total Fab and Fc fragments. I separate and purify reduced heavy chain and light chain fragments using high pressure liquid chromatography, and the cleaved total Fab and Fc fragments using an affinity matrix.  I buffer exchange the fragments through dialysis or using filters, and assess fragmentation and purity using SDS Page gel electrophoresis. After optimizing these protocols, I will isolate pure antibody light chain, heavy chain, total Fab, heavy chain Fab, and Fc fragments from MGUS and myeloma patients and healthy controls. This will enable subsequent glycosylation analysis and characterization. We anticipate that our results will lead to an improved understanding of antibody glycosylation in plasma cell neoplasms and provide insight into their potential role as risk factors for disease.

We measured the functional traits of two species of moss (Homalothecium fulgescens and Rhytidiadelphus loreus), native to the Pacific Northwest, to better understand the complex relationships mosses have with other plants in their environment. Mosses play important roles in facilitating other plants around them by increasing moisture and nutrient availability and decreasing the effects of wind. Our research questions aimed to understand how these functional traits of mosses affected seedling growth of 4 native seeds. We measured the water retention and moss thickness of these mosses under control and drought conditions. We watered the control mosses twice a week with 50 mL of deionized water, and drought mosses once a week with 50 mL of deionized water. We measured moss thickness and water retention, then examined the correlation between them. We added seeds (Lupinus succulentus, Pseudotsuga menziesii, Lolium perenne, Castilleja miniata) to these pots to see how mosses and their functional traits impacted seed germination. We found seed germination to be related to less moss mat thickness. We found that more seeds grew in Rhytidiadelphus loreus pots despite having less thickness in comparison to Homalothecium fulgescens pots. We found seed germination to be less related to controlled conditions as our results showed that there were more seeds germinated in Rhytidiadelphus loreus under drought conditions than Homalothecium fulgescens in both conditions. In addition, an unplanned fungus (white rust) infected the moss pots. We examined how quickly this infection impacted seedling growth under drought and non-drought conditions. Homalothecium fulgescens was more prone to the infection compared to Rhytidiadelphus loreus. Less seeds grew under infected condition overall.  

Underground storage organs (USO) allow plants to retreat underground during periods of resource scarcity and/or abiotic stress. These adaptations help plants survive seasonal climates and have evolved repeatedly across the vascular plant tree of life. USOs develop as modifications of various plant tissues, including root, leaf, and stem tissues. The non-model plant Bomarea multiflora (Alstroemeriaceae) offers a unique opportunity to study the development and evolution of USOs as it has two types of USOs (rhizomes and root tubers), allowing for direct comparison. B. multiflora’s dual USOs and its phylogenetic position within the monocots makes it a good candidate for future development as a model species for USO development. Here we analyze a transcriptomic dataset of four distinct tissue types in B. multiflora: aerial shoot, rhizome, fibrous root, and root tuber tissues. We use ZigZag, a recently developed hierarchical Baysian model that determines the probability of active expression for each gene in each tissue type. We found 56 genes differentially expressed between individual tissues and 29 between root vs. shoot tissue. We review these genes and describe avenues for future investigation of USO developmental pathways within monocots.

Extreme operating temperatures in rocket engines severely degrades their lifespan, function and reusability. One mitigating approach to help cool rocket engines and extend their lifespans is called Regenerative Cooling, which has been a method actively used in liquid rocket engines (LREs) since 1923. The cooling system utilizes many narrow coolant channels to draw heat away from the liquid propellant near the rocket nozzle. However, experimental research on these channels is rarely done as they are very small and a single channel is difficult to manufacture for basic research testing thereby causing many researchers to look to non-experimentally tested CFD (Computational Fluid Dynamics) simulations to perform their studies. Our experiment aims to fill the gap between simulation and practical testing by testing scaled up models with V-shaped ribs based on a study done by Zhang et al. These scaled up models would allow for more easily obtainable thermal distribution, stress, and pressure data while also being simpler and cheaper to manufacture. We believe our data could offer an alternative to non-tested CFD simulation data and, as access to experimental data increases, result in the expansion of this area of research.

Our goal is to establish water quality baselines and ongoing trends for streams and tributaries of two separate watersheds, both of which drain into Lake Washington through Lake Forest Park, a city in the northwest part of King County, WA. This project is the first intensive multiple-site survey of urban King County watersheds using certified Washington State Department of Ecology methods. In three teams of 4-5 college students, we conducted monthly field tests of 16 sites along tributaries and sub-basins of the McAleer Watershed, and of 6 sites within the Lyon Creek watershed. We used a YSI ProDSS multiprobe meter and a Hach DR 900 colorimeter to collect measurements of air and water temperature, water turbidity, conductivity, % oxygen saturation, dissolved oxygen, pH, total suspended solids, and nitrate and phosphate levels, used Coliform Bacteria R-Cards to measure the quantitative presence of water-borne E. coli. Analysis of these water quality indices for these sites over a 12-month period will allow us to evaluate the overall health of the greater watersheds, and possible causes of poor conditions. Our data will contribute to other conservation research efforts supporting urban watershed health. This work was undertaken as a research project by undergraduates participating in the Urban Stream Ecology Internship and Training (USE-IT) program, funded by a Seattle Waterworks grant to the Stewardship Stream Initiative (SSI), an initiative launched by the Lake Forest Park Stewardship Foundation in 2024.

Electromagnetic launchers currently use a combination of magnetic forces and complex electronic timing to propel objects. One example is the US Navy EMALS system, which uses a linear electromagnetic launcher to launch aircrafts from aircraft carriers. However, using complex electronic timing introduces more failure points within the system, increasing its complexity, making such systems susceptible to being disabled by external electromagnetic interference. Inspired by the design of Tom Stanton, this project explores a new approach that removes the digital-based electronic timing and replaces it with a mechanical timing system that can be used to propel drones or other payloads into the air quickly and efficiently. The goal of reducing the design’s complexity is to create a launcher that is a reliable method for drone and payload deployment. By removing electronic switching and using a mechanically driven circuit closure, this project develops a durable, efficient launch system. The prototype is built using 3D-printed components, powerful magnets, and a coil on a sled with contact arms that touch the conductive rail to complete the circuit. Rather than lining the rail with multiple coils, stationary magnets replace the coils with alternating currents to provide the acceleration when the coil becomes powered. The results allow us to have a competitive design that provides a practical alternative to the typical electromagnetic launchers. Expected results include improved durability, reliable performance due to the simplification of electronics, and reduced energy losses. Our research provides a new way to launch drones or other payloads to be integrated into systems where they would be less susceptible to external electromagnetic interference and jamming.

Although being in nature has been associated with benefits including health and well-being, many people do not spend time in nature. Some studies have focused on the reasons why people do not spend time in nature; however, both in this research and in nature and health research, the term "nature" is inconsistently defined. Without a concrete definition of nature, it is unclear what participants consider nature and if this affects their reasons for not spending time in nature. This work is part of a larger experiment looking at students at the University of Washington's reported time in nature, and whether or not having a definition of nature impacted people's responses to nature-related questions. Here, we identify the underlying reasons given for the individual's not spending time in nature. Additionally, we examine whether having a definition of nature which includes urban nature affects reasons why participants report spending no time in nature. Out of 1,573 participants, 273 individuals (17%) responded that they had spent no time in nature in the previous week. They were then asked to explain why they spent 0 hours in nature that week. Common themes included being too busy with school, work, and other responsibilities. Notably, one theme emerged, "feels limited by place" in which participants stated they do not spend time in nature because they "live in Seattle". Preliminary results indicate that when nature is defined, the theme feeling limited by place did not occur, meaning receiving a definition of nature appears to affect the qualitative reasons given for spending no time in nature. This study highlights the importance of defining nature while also providing valuable insights into the reasons why some might prefer to not spend time in nature, as well as barriers that prevent students from spending time in nature.

Plants defend themselves against invading pathogens and herbivores using immune receptors that detect molecular signals associated with danger. Two types of plant immune receptors are the leucine-rich repeat (LRR) receptor, receptor-like kinases (RLKs), and receptor-like proteins (RLPs) through which signal transduction may proceed through the cell. Coreceptors like SERK3/BAK1 and SOBIR1 pair with LRRs to facilitate intercellular communication. We studied a specific LRR receptor, the inceptin receptor (INR) that recognizes an eleven amino acid-long peptide chain known as inceptin-11 (in11). Given the close interaction of LRR and its coreceptors, and considering that we still don’t fully understand how INR recognizes in11, we investigated its three-dimensional structure to analyze the mechanism of ligand binding and signal activation. Through predictive modeling in Alphafold of homolog RXEG1, a carboxy-terminal loop out domain was identified as a facilitator in the binding interaction between INR and the BAK1 coreceptor. To explore this mechanism, we introduced targeted mutations in the domain’s K-X5-Y motif to potentially change its ability to recruit BAK1. When a ligand attaches to a receptor, its conformation change allows signals to pass through the cell membrane. We constructed a library of 36 single and double mutants in the K-X5-Y motif and coexpressed them with a luminescence-based reporter construct in Nicotiana benthamiana to screen their activity. We expect that a mutation at K or Y or both will affect BAK1 recruitment, leading to phenotypes that are hypersensitive or inactive. Insight into LRR-RLP coreceptor interactions could open doors to further INR-immunology research alongside better modeling of BAK1 protein binding. Targeting immune-related peptides in this screen could significantly advance cultivation programs for INR expressing organisms.

Infertility, the inability to conceive after one year of unprotected intercourse, affects about 15% of the global population. Nearly half of couples diagnosed with infertility have a contributing male or sperm factor (male-factor infertility). Preparation of purified sperm is an important component of fertility treatments. Most purification techniques rely on centrifugation, although the effects of centrifugation on sperm motility (movement) and DNA integrity are not well understood. Our objective is to manipulate centrifugation g-force and time settings following sperm preparation to investigate potential impacts of centrifugation on sperm quality for fertile and infertile men. Our hypothesis is that the highest centrifugation g-force and time will result in reduced motility and maximum DNA damage. Participants with normal semen parameters are recruited. A semen analysis is performed to determine volume, concentration, and baseline motility, which is measured using an automated visual sperm analyzer. Motile sperm are isolated via “direct swim out,” a standard purification technique. Nine different centrifugation settings are applied to the sample (time and g-force parameters studied: 7, 30, and 60 minutes, and 250xg, 600xg, and 800xg), and motility is evaluated. For each condition, DNA integrity is assessed with a COMET assay (uses single-cell gel electrophoresis to detect double-stranded DNA breaks). Preliminary results from 11 participants (ages 26-35) demonstrate substantial variability in motility for each participant. We observe that while the highest centrifugation g-force and time condition (60 minutes at 800xg) reduces motility for some participants, it has the opposite effect for others. Data collection for motility analysis and DNA integrity assays are in progress and will continue over the next three months. This project aims to provide high quality evidence to support current laboratory practices in sperm preparation, an essential part of fertility treatments.

Nature has long been a source of inspiration when it comes to tackling engineering challenges. Taking this inspiration from nature, our study aims to emulate the behavior of burrowing animals in order to efficiently dig into granular media. The pacific razor clam utilizes its retractable foot muscle to burrow itself while simultaneously expanding and contracting its shell to fluidize the surrounding sand. Our goal is to create a digging device that approaches the digging efficiency of pacific razor clams of 21 J/m. Our hypothesis is that the interaction of vibration and fluidization is key in burrowing performance. We built a cylindrical robotic model composed of both soft and rigid materials, equipped with a vibrational motor and a downward-facing nozzle. We adjusted the energy devoted to vibration and flow to optimize burrowing efficiency as a function of energy per depth.  Preliminary results suggest that a combination of both local fluidization and vibration improves burrowing efficiency over using them independently. We anticipate that different combinations of flow and vibration are optimal for different burrowing stages. By understanding nature's efficient digging techniques, we can create a reliable anchoring system for sensor arrays and underwater vehicles to aid in the study of our oceanic ecosystem.