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.

Autosomal Dominant Alzheimer’s Disease (ADAD) can result from a pathogenic variant in the PSEN2 gene, which encodes an integral membrane protein called Presenilin 2. This variant has been shown to result in a harmful change in the balance of amyloid-β types in neurons, which has been hypothesized to increase risk of dementia. The diverse capabilities of Presenilin give reason to hypothesize that there may be other effects of the variant protein that are connected to ADAD pathogenesis. Reduced spine density, a feature of ADAD pathology, may be caused by overactivity of synaptic pruning. This activity is mediated by resident innate immune cells in the brain called microglia. We sought to explore the effects of PSEN2 variants on microglia-neuronal interactions via the assessment of synaptic pruning in a human induced pluripotent stem cell (hiPSC) derived in vitro model. We differentiated CVIA2 isogenic and PSEN2 N141I variant hiPSCs into both microglia and neurons. Utilizing a coculture of both wild-type neurons and microglia with the PSEN2 N141I variant, we performed immunocytochemistry for synaptic proteins Synapsin 1 and PSD95a. We then imaged the microglia and neurons using confocal microscopy. We assessed differences in synaptic pruning by quantifying immunofluorescent signal of Synapsin in microglia. Specifically, we looked at the colocalization of synaptic protein expression with signal from microglia-specific protein Iba1. We hypothesized that the variant microglia would contain a significantly different amount of signal for Synapsin compared to that of a control sample of wild-type microglia and neurons, implying a change to synaptic pruning function. If altered microglial synaptic pruning activity is shown to play a role in ADAD pathogenesis, targeting microglia could become a possible therapeutic treatment for patients.

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

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.

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

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

Presbyphonia, or "aging voice", is one of the most common voice concerns, with prevalence ranging from 19-40% in the older adult (60+) population. Common symptoms of presbyphonia are a strained, weak voice and reduced loudness, which causes communication difficulties that negatively affect mental and social wellbeing. A key factor contributing to presbyphonia is vocal fold atrophy, which is deterioration of the muscle and tissue in the vocal folds. This causes weakness and incomplete vocal fold closure during voice production. Treatment usually consists of voice therapy with a speech-language pathologist (SLP) or vocal fold injections to bulk up vocal fold volume from an otolaryngologist. Currently, the standard for viewing the vocal folds to assess post-treatment change in vocal function is via an endoscope. However, endoscopic examination of the vocal folds relies on perceptual assessment in two dimensions, restricting analysis of vocal fold volume. In this research project, I am using magnetic resonance imaging (MRI) to view the vocal folds in 3D, allowing for a complete analysis of volume in mm3. My goal is to use this novel method to provide new information on which treatments create the best outcomes for patients in terms of vocal fold volume and voice quality. Participants undergo a comprehensive voice assessment conducted by me and a mentor SLP, an initial MRI scan, and then complete one of two treatment pathways: either 4-6 weeks of voice therapy or vocal fold injections. After treatment, they return for another voice assessment and MRI to evaluate the effects. This research is ongoing, but I anticipate that both treatment groups will experience improvement in voice outcomes, consistent with the literature. However, it is unknown if vocal fold volume will increase in both treatment groups, as MRI has not been used to assess post-treatment outcomes in this patient population.  

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

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.

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.

Antibiotic resistance is an increasingly critical concern for the treatment of bacterial infections, rendering new therapy options progressively more necessary. Gram positive bacteria are common infectious agents in skin and soft tissue infections, pneumonia, urinary tract infections, bacteremia, and more. A novel antibiotic candidate, MRS-2541 has been demonstrated to inhibit Gram positive methionyl-tRNA synthetase and decrease bacterial loads of both methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pyogenes in mouse thigh infections to the same degree as currently recommended therapy. This study aims to further characterize the activity of MRS-2541 against Gram positive bacteria including Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus lugdunensis, Staphylococcus saprophyticus, Staphylococcus aureus, MRSA, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus salivarius. I conducted this study by first determining the preliminary minimum inhibitory concentration of MRS-2541 in growth media against each of the aforementioned organisms. I then use these results to guide time kill assays that characterize MRS-2541’s synergy with another antibiotic often used to treat Gram positive infections outside of the United States. Preliminary results demonstrate that MRS-2541 inhibits the above-mentioned organisms. Synergy experiments with MRS-2541 and existing antibiotics will be performed and results will be presented at the symposium. These results will further define the spectrum of activity as well as synergy of MRS-2541, allowing new insight into its candidacy for clinical trials. As a novel antibiotic candidate, the development of MRS-2541 will help address the increase in antibiotic resistance among Gram positive bacterial infections.

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 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. 

Harmful algal blooms (HABs) are threats to a number of species in marine environments. One hypothesis states that excess nutrients in water lead to accumulations of certain plankton species that produce toxins. This can explain some illnesses such as paralytic shellfish syndrome in humans who consume impacted shellfish. HABs can be identified directly, but given the delays involved in analyzing results, other indicators may be used to predict presence of HABs as well. Possession Sound is an inlet of the Puget Sound located between Whidbey Island and the coasts of Everett and Mukilteo, Washington, connecting to the Snohomish River, as well as Saratoga Passage and Port Susan to its North and the main Puget Sound basin to its South.  Since HABs can occur in freshwater and saltwater for different reasons, Possession Sound’s status as a salt-wedge estuary makes it notable as a study site. To investigate the nature of HABs in Possession Sound, I analyzed plankton density data, chlorophyll-a levels, and phosphorus concentration data I collected in 2024 as well as data collected by the Ocean Research College Academy from 2016-2024. Chlorophyll-a concentrations were measured with a YSI EXO Sonde. Phosphorus concentrations of water samples were collected using a Niskin bottle and measured by the University of Washington Marine Chemistry Lab. I analyzed the progression of each parameter temporally and spatially. I expect to see clear spikes in certain plankton species, especially dinoflagellates, that align with similar-timed chlorophyll-a and phosphorus spikes. However, I predict that trends will be the least prominent in phosphorus concentrations due to its greater prevalence in freshwater than in saltwater. Understanding which plankton species are most responsible for HABs and temporal alignment of potential drivers can allow for better prediction of HABs in Possession Sound.

Zostera marina (eelgrass) is one of the many important biological features of Possession Sound, acting as a substrate for many microorganisms, a filter of greenhouse gases, and as protection for many species. The Possession Sound has been marked as a Seagrass Sanctuary by the Department of Natural Resources, which protects and monitors nearshore eelgrasses within the basin. By looking at what kinds of species are found in a marine environment, researchers can assess an ecosystem's overall health. Environmental DNA (eDNA) is a data capture technique used by researchers that picks up DNA traces left behind by organisms, and shows their presence/absence in a given area. The study site, Mount Baker Terminal, lies inside the Possession Sound basin near Everett, Washington, and contains a large eelgrass bed. I collected 10 samples using passive filters submerged at various depths inside and outside the eelgrass bed in 2024 and processed at a WDFW lab. I analyzed these data and 40 additional samples collected by the Ocean Research College Academy from 2021-2024 using similar methods. I hypothesized that there would be more species such as crustaceans, fish, and other plants inside the eelgrass because of its ability to protect and maintain a nutrient-dense environment. These data will help shed light on species richness in each environment, which has potential implications for understanding the overall health of the ecosystem and the critical role eelgrass plays in the estuary.

Possession Sound, located between the city of Everett and Whidbey Island, is a part of both a key economic area and a bustling marine environment. Because of the marine activity, scientists study all sorts of parameters involving the water including noise. Numerous studies have assessed ambient noise in marine environments to investigate the influence of tidal forces on ambient noise. These reports found that tidal noise or “flow noise” is observed around the 0-100Hz range with the most significant impacts observed centered around 25hz. The Ocean Research College Academy operates a SoundTrap ST400 STD hydrophone mounted to Mount Baker Terminal that takes recordings daily for most of the year. Mount Baker Terminal is a small marine terminal operated by the Port of Everett, located just north of the town of Mukilteo. Using data collected from the hydrophone, I took measurements of ambient noise in root mean square amplitude centered around the 25hz range and compared that to NOAA tidal data at Everett, Washington. Using these data I investigated the potential presence of a relationship between the tides and ambient noise. When the initial measurements of root mean square amplitude were compared to tidal data from the area the results showed that tides had no significant impact on the ambient noise at Mount Baker Terminal. Investigating the effects of tides on ambient noise can be crucial to future acoustic research done by researchers in the area as results could be affected by noise created or affected by tides. Future analysis should investigate the impacts of other natural contributors to the soundscape such as rain and wind.

The Eastern North Pacific gray whales (Eschrichtius robustus) have a long migration from their breeding grounds in Mexico to their feeding grounds in Alaska. A subgroup of the Eastern North Pacific stock, nicknamed the Sounders, deviate from the migratory path most gray whales follow to feed in the Salish Sea, typically between the months of March and May. Other studies show that gray whales feed on benthic organisms such as ghost shrimp. Studies conducted in the Arctic area of the gray whale migration route have seen sea ice playing an important role in the gray whales being able to enter the areas where they feed. One working hypothesis is that gray whale shifts in migration patterns are the direct result of climate change; this could explain why some of the Eastern North Pacific gray whales enter and feed in Possession Sound. I analyzed sightings data, shared by the Whale Museum and recorded in Possession Sound, WA from 2000-2022. These data, most of which were compiled by the Orca Network, were filtered to identify the number of visitations each month over the study period. Early analysis shows a phenological shift in the time of the gray whale's arrival and departure from Possession Sound. The shift shows an increase in the number of months gray whales are present in Possession Sound, from a March to May visit to a year-round presence. Although these results cannot explain the reason for the phenological shift, future research must look into related shifts in the Arctic ice formation as well as ambient air and water temperature shifts. Future research calculating density of ghost shrimp in Possession Sound will also indicate why this location is favored.

Ocean acidification is the reduction of pH in seawater due to increased carbon dioxide from fossil fuels in the atmosphere and other anthropogenic factors. Ocean acidification causes shellfish such as oysters to experience difficulty building their shells. Acidification trends in the North Pacific Basin are well documented, yet pH trends in Possession Sound, a salt-wedge estuary located in the Salish Sea is less documented. Possession Sound receives discharge from the Snohomish River and has human activity along the shoreline. In this study, the average change of pH in the middle of the North Pacific Ocean was measured and compared to the average change of pH in Possession Sound since 2016. I analyzed data collected from ARGOS Floats located in the central North Pacific Ocean. For Possession Sound, I used data collected from a  YSI EXO Sonde in partnership with the Ocean Research College Academy (ORCA). I collected data on 12 research cruises in 2024. I expect to find a slightly greater decrease in pH within Possession Sound than the North Pacific Basin due to the additional anthropogenic factors present in the Sound. Preliminary analysis shows a slight seasonal change in pH in Possession Sound, but little to no change yearly. I expect the data to show a steady decrease in pH for Possession Sound and the North Pacific Ocean basin every year since 2016. Calculating acidification rates and learning how they differ in various geographical locations, with separate factors, will increase understanding of the impacts of ocean acidification, which may be used in conservation efforts. 

In mammals, the primary mechanism regulating circadian rhythms is the central circadian pacemaker in the suprachiasmatic nucleus (SCN). The 24-hour light-dark (LD) cycle is the primary environmental cue, or zeitgeber, that entrains the SCN and sets its phase by adjusting its timing via phase advancing or delaying. Our laboratory has demonstrated that when mice are foraging outside of their safe nest, cyclic fearful stimuli can act as a nonphotic zeitgeber, entraining circadian rhythms and shifting activity from nocturnal to diurnal. However, the mechanisms of this so-called “fear entrainment” and phase-specific properties of cyclic fear remain unclear. This study examined whether cyclic fear via footshocks differentially entrains activity depending on the circadian phase of exposure. Mice were housed under a 12h:12h LD cycle and divided into three groups based on shock timing: the first six hours of the dark phase, the last six hours of the dark phase, and the middle of the light phase. Both dark phase groups showed delayed activity, with only the early dark phase group exhibiting evidence of entrainment. The mid-light phase group remained nocturnal. To further investigate the interaction between light and nonphotic entrainment, we conducted a follow-up experiment in which mice were placed under constant laboratory conditions (constant darkness) before undergoing cyclic footshock exposure. We hypothesized that, in the absence of light cues, the phase shifts induced by fear would differ from those observed under LD conditions, potentially revealing a distinct mode of nonphotic entrainment. Our findings so far suggest that entrainment to cyclic fear may only be achieved through delays, and that circadian oscillators may use different mechanisms of entrainment in response to photic vs. nonphotic zeitgebers.

In mammals, circadian rhythms are regulated by a hierarchy of oscillators governed by a central circadian pacemaker in the suprachiasmatic nucleus (SCN), which is principally entrained by the light-dark (LD) cycle. Recent experiments in our lab have revealed that cyclic 24-h fearful stimuli can act as a potent nonphotic zeitgeber, entraining circadian rhythms of behavior in mice and rats. This discovery utilized a naturalistic rodent cage with a safe nesting area separated from a foraging area where feeding and drinking occur. While foraging behaviors naturally occur at night, when the foraging area is rendered dangerous by nocturnal aversive stimuli (footshocks), animals entrain behaviors to the shock schedule by shifting activity to the daytime. Under conditions of fear-entrainment, SCN clock gene expression remains loyal to the LD cycle and the SCN is necessary but not sufficient for sustaining diurnal activity. Therefore, we propose the existence of extra-SCN fear-entrained oscillators capable of overriding SCN output and influencing behavioral timing. Here, we subjected 40 mice to either diurnal shocks (DS; control) or nocturnal shocks (NS) under a 12:12 LD cycle. Following confirmation of fear-entrainment, animals were released into constant conditions and sacrificed between 24-36h after the last presentation of footshocks, either CT 1 or CT13. Brains were dissected, sliced, prepared for immunohistochemistry processing, and c-FOS and PER2 protein quantification is currently underway in the SCN, basolateral amygdala, paraventricular nucleus of the thalamus, and dentate gyrus. We hypothesize that c-FOSs and PER2 expression within the SCN will align with the LD cycle, while centers involved in fear processing and memory will exhibit altered levels of c-FOS and PER2 expression in response to time-specific fear. Results from this study may be useful for identifying putative brain regions containing fear-entrainable oscillator(s).

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.

I am currently assisting PhD student Jessica Luo in her research of the Sanmen Wu sound system, a language of the Wu family found in Southeast China. As Jessica writes an article that summarizes the sound structure of Sanmen Wu, I analyze utterances produced by speakers of the language. In my self-guided research, I focus on the sound quality of the consonants and their variations to determine underlying pronunciation. I also connect these variations to historical sound changes from Middle Chinese, its ancestor, into Sanmen Wu. I observe that Sanmen Wu speakers tend to freely alter pronunciations of certain consonants. For example, a speaker may say 部 [pu] or [bu] meaning ‘part,’ the latter only appearing after another spoken word. These two syllables contrast only in voicing, where [p] is voiceless and [b] is voiced. I use Praat, an industry-standard speech-analysis program, to read diagrams that depict the acoustics of these consonants to verify my findings. I am also creating a set of rules that predicts this alternation. One of the conditions is as follows: words with alternating voicing in their consonants change when pronounced within a sentence (‘medially’). Eventually, I will explain these rules, and I predict my explanation is related to the evolution of Sanmen Wu into its current stage. I reason that because the Wu language family stems from Middle Chinese, both of which require contrastive voicing to create distinct words, Sanmen Wu also contains the original underlying variation that exists in Middle Chinese. As such, I attribute this variation to an inherent part of the language rather than random circumstance. Ultimately, I intend to foster a thorough understanding of Sanmen Wu phonology and provide a foundation for further exploration of this topic.

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.

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

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.

Silica nanoparticles have diverse applications in catalysis, imaging, and drug delivery. Tailoring these nanoparticles for specific applications requires precise control over their size, surface chemistry, porosity, and polydispersity. These properties are controlled by a wide range of factors such as reactant type and concentration, pH, reaction temperature, and other synthesis parameters. Due to the large parameter space, determining the optimal reaction conditions for synthesizing silica nanoparticles with the desired size and morphology is time-consuming and challenging. An accelerated experimentation platform integrating automation and artificial intelligence can streamline the selection of reaction parameters for synthesizing silica nanoparticles with targeted size and morphology using machine learning-based iterative design of experiments to optimize material properties. This system uses the Science Jubilee flexible laboratory automation platform to carry out sol-gel synthesis. Small-angle X-ray scattering is used to characterize the sample. The data collected is used to optimize the reaction condition for synthesizing the targeted nanoparticle. We have successfully carried out sol-gel processes and synthesized silica nanoparticles with various sizes and polydispersity using the platform. Currently, we are working on optimizing the selection of sample synthesis conditions.

Since the discovery of DNA in the 19th century, biochemists have been elucidating not only the structure, but unique biochemical environment of each loci. Protein-DNA neighborhoods govern chromatin structure and cellular functions (transcription, replication, etc.). To investigate which proteins and oligonucleotides compose these microenvironments, our lab and collaborators developed DNA oligonucleotide-directed proximity-interactome mapping (DNA O-MAP), a locus purification method using oligo-based ISH probes to recruit horseradish peroxidase (HRP) activity to specific DNA intervals (Liu & McGann et. al. 2024). Once these secondary, HRP-conjugated probes are localized to loci of interest, hydrogen peroxide is added with biotin-tyramide. Hydrogen peroxide activates HRP, forming biotin-tyramide phenoxyl radicals that biotinylate proteins and nucleic acids within 10-75nm. This allows for a scalable, versatile method to investigate these microenvironments. Large scale DNA O-MAP, tiling across several genomic sites, can elucidate insights into biological questions. However, the upstream protocol remains a barrier to its throughput, sensitivity, and reproducibility. In order to ensure this for analysis of tagged proteins, we sought to automate the streptavidin affinity purification protocol onto the Opentrons OT-2 robot. This is where streptavidin-coated magnetic beads capture biotinylated species from lysate. Coupled beads are recaptured with a magnetic rack and pipetting-off of flow-through. Subsequently, several washes cleans up these beads before peptides are digested off via Trypsin/LysC, dried-down, resuspended, and loaded onto a Orbitrap Eclipse LC-MS for proteomic analysis. Purification of streptavidin beads is manually intensive, inherently leading to variation between runs. The Opentrons OT-2 is an open-source liquid handler, allowing our lab to easily transfer methods to others interested in DNA O-MAP. Automating this protocol launches us from technology development to biological application. Here, I present an automated protocol for streptavidin affinity purification and evaluation of its effectiveness via comparison of the automated protocol to our lab's current, manual methods.

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.

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.

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.

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. 

Alzheimer’s disease (AD) is a neurodegenerative disease that impacts millions of people and costs billions of dollars annually, with both estimates increasing as our aging population grows. Women are diagnosed with AD at a 2:1 higher rate than men, although the biological drivers of this difference remain elusive. Previous studies have demonstrated that changes to the function of microglia – the brain’s immune cells – observed during AD may be driving disease progression. Furthermore, microglia morphology is related to its function. Thus, we seek to characterize differences in microglia morphology between men and women with and without AD. We hypothesize that microglia from women have, on average, a more disease-associated morphology than those of men, and that differences are exacerbated in individuals with AD. We obtained tissue from the dorsolateral prefrontal cortex of 48 individuals who donated their brains to AD research at UW. We conducted immunohistochemistry (IHC) to stain for microglia markers (IBA1) and two markers of AD pathology (AT8 to stain for phosphorylated Tau and a pan-amyloid β stain). I imaged the samples on a Leica SP8 confocal microscope at multiple depths, which allowed us to compose a 3D rendering of the tissue through an image analysis software called IMARIS. Using IMARIS, I quantitatively measured key aspects of each microglia, such as volume and branching details. Using the data from 12-20 microglia per person, we used multiple regression to test for differences between men and women in both healthy and AD cohorts. We anticipate there are differences in the various measurements of microglial morphology between men and women with AD, which may partially explain the discrepancy in AD rates between sexes. This research is important to better understand the role of sex in AD pathology and help contextualize molecular differences observed in the larger project to which it belongs.

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.

Humpback whales exhibit exceptional maneuverability in water, a trait attributed to the unique scalloped structures (tubercles) on the leading edges of their flippers. This study investigates the influence of such varied tubercles on the aerodynamic performance of wings, using both wind tunnel testing and computational methods. CAD models of the rigid wings were designed for 3D printing. These addressed three variations of the fin morphology, a smoothed base model, one with leading-edge tubercles, and one with tubercles on the trailing edge as well. The fin models feature a swept wing configuration with a concave region before the wing tip, both properties of humpback whale fins. The result of wind tunnel tests at constant, turbulent, wind speeds (Re=10^5) produced plots of the lift and drag coefficients for a varying angle of attack. The experimental results showed that leading-edge tubercles increase the maximum lift and increase the maximum angle of attack before stall occurs at the cost of some additional drag. The addition of trailing-edge scallops reduced drag and raised the overall efficiency to just below the baseline. Computational fluid dynamics (CFD) simulations comparable to the wind tunnel environment and in more turbulent aquatic conditions (Re>10^6) reveal the fluid flow. The tubercles and concave region influence the fluid, reducing span wise flow and the buildup of large tip vortices. The effect of tubercles has already been employed for its influence on stall angle, notably on the rudders of some racing yachts. The studied effect's ability to manage vortices across the wing span may have applications in particle separation, though significant work would need to be done to streamline the necessary manufacturing processes.

Female mammals possess two X chromosomes in every cell, but one is silenced by condensing into a barr body, making its genetic information largely inaccessible. While X inactivation is stable in somatic cells, it is reversible in germ cells, raising the intriguing question of what proteins maintain this silenced state. My project aims to identify the protein composition of both active and inactive X chromosomes in mice. To achieve this, I will use in situ hybridization to target proximal labeling with biotin of X chromosome-associated proteins. This is accomplished by targeting a biotinylation enzyme, such as HRP, to the X chromosomal region, where it will selectively biotinylate neighboring proteins. After affinity purification, these proteins can be identified using mass spectrometry-based quantitative proteomics. To direct the enzyme to the correct location, a two-probe system is employed. The primary oligonucleotide probe complements a specific X chromosome region which also contains landing sites for a secondary probe. Hybridization of the secondary probe which is tagged with HRP enables precise labeling of chromosome-associated proteins. This approach enables in situ biotinylation, preserving proteins in their native context for accurate identification. Since the two X chromosomes are homologous, distinguishing between the active and inactive X requires careful probe design. By utilizing Single Nucleotide Polymorphisms (SNPs) that exist in the X chromosomes, the maternal and paternal X chromosomes can be differentially targeted by primary probes, allowing for homolog specific protein labeling and analysis of their distinct regulatory environments. 

Somatosensory neurons innervate the skin, where their peripheral axons detect signals like touch and pain. The neurons relay stimuli to the brain via peripheral axons in the skin and spinal cord axons in the spinal cord. Given their superficial location, somatosensory axons are susceptible to damage. Axon damage can cause tingling, increased pain, or sensory inhibition, and reinnervation in mammals is often slow or incomplete. I use injury models in zebrafish to study the mechanisms of successful axon regeneration in an adult vertebrate with optically accessible skin. I aim to reveal conserved regeneration patterns of somatosensory neurons. Furthermore, I seek to understand the extent of reinnervation success and observe the prevalence of hyperinnervation post-injury. Using in vivo confocal microscopy and adult zebrafish skin models, I created a methodology to capture somatosensory reinnervation over a three-week span following a scale pluck injury. Zebrafish scales separate epidermal and dermal layers of skin, and scale removal induces regeneration of epidermal skin and surrounding dermal tissue. I use transgenic zebrafish with fluorescent labels for dorsal root ganglion DRG neurons and osteoblast cells Tg(p2rx3a:mCherry);Tg(sp7:EGFP). DRG neurons are the primary somatosensory neuron in adult zebrafish, and osteoblasts allow me to view the scale alongside axon reinnervation. For image acquisition, I designed a 3d-printed chamber for zebrafish mounting and intubation within our confocal microscope. For analysis, I developed Image J macros which use threshold analysis to quantify changes in axon density of specific regions of regenerating axons. Dermal axons tend to regenerate first while superficial axons in the epidermis regenerate secondarily in conjunction with the novel scale. To examine skin layer differences, I separate epidermal and dermal layers to compare the reinnervation trends between superficial and dermal axons. With this data, I can gain insight in the regeneration potential of somatosensory neurons.

The introduction of harmful strains of Escherichia coli (E. coli) in the marine environment negatively impacts ecosystem health. When unnatural strains of E. coli are introduced through pollution events, spikes in animal sickness and death occur, and harm to human health is more likely. Understanding relationships among parameters known for contributing harmful strains of E.coli and parameters more likely to contribute non-harmful strains is important to identify the most impactful parameters leading to harmful E. coli events. Possession Sound, WA is an ideal study site for monitoring multiple parameters associated with the introduction of E. coli to a saltwater environment. The study site includes the second largest freshwater input in Puget Sound, the Snohomish River, which passes many farms on its way to the Sound. The study site is also surrounded by a heavily industrialized port, and a large-density population center. I collected water samples at various depths and recorded animal presence from 2023-2025 at ten separate sites. Using a sterile procedure, I plated water samples onto bacterial plates using Easygel® agar. Overflow and river discharge data were provided by the city of Everett and USGS respectively. Historical data were collected following similar protocols by the Ocean Research College Academy. I hypothesized that increased presence of E. coli would strongly correlate with high river discharge events and combined sewer overflow events more than other inputs, but early analysis does not support this correlation. Further research must consider parameters such as residence time of E. coli, lag time after discharge events, and water chemistry characteristics. 

Eelgrass meadows (Zostera spp.) and Kelp forests (Nereocystis spp.) are both essential habitats in Possession Sound, a saltwater estuary formed where the Snohomish River meets the Salish Sea. Home to many marine species, the Possession Sound has unique salinity levels that provide a rich environment to support marine life. These ecosystems provide vital services such as helping clean the water, sheltering fish, absorbing or filtering carbon, producing oxygen, and protecting coastlines. Given the rich marine habitat that develops in eelgrass meadows and kelp forests, conducting a study of the organisms that reside in the habitat would be beneficial to learn about their condition and influence on life within Possession Sound. To conduct the study, I used eDNA sampling for data collection. eDNA sampling analyzes genetic material from organisms and identifies what species are present in a given environment. I collected samples from two ecosystems at the stations closest to each habitat. MBT (eelgrass) and Kelp Sanctuary (kelp forest). The data I collected from the two sites were sent to the molecular genetics laboratory at WDFW for metabarcoding analysis to identify species using a passive filtration protocol. The data were then combined with historic data to determine the species present in both habitats, specifically focusing on fish and crustacean species. Preliminary analysis suggests that these habitats have similar organisms that frequent each habitat. I expect to see this trend reflected in additional eDNA data, meaning the eelgrass meadows and kelp forests will have similar representative species.

Seabirds are considered a strong indicator species for ecosystem health due to their visibility, lack of behavioral and phenotypic plasticity, and high trophic level.  Current declines in seabird populations are often attributed to bottom-up ecosystem control regulating upper trophic level populations. These bottom-up effects might be caused by reductions in marine productivity due to climate change. I performed statistical and graphical analyses on the National Audubon Society’s Christmas Bird Count data from Puget Sound and water chemistry data from the Ocean Research College Academy’s moored and deployable sensors. This allowed me to identify possible relationships between bird populations and water chemistry from 2009 to 2024 in the Possession Sound estuary. My initial analyses demonstrated the expected decline in collective seabirds counted, however certain pelagic species experienced unexpected increases. Further investigation is required to determine whether the increase was caused by ecosystem dynamics or improved count methods. My initial analyses did not indicate any relationship between water chemistry and bird populations. The lack of apparent relationship may be due to the water chemistry changes having impacts on primary productivity and indirect bottom-up trophic cascades, which could have a significant lag time in effects on bird populations. My analysis also does not account for environmental factors in disparate migration sites or breeding colonies that might affect bird populations. 

Sewage system design and heavy seasonal rainfall throughout Washington State pose risks to many marine ecosystems, as stormwater overflow can flush untreated waste into local bodies of water. The estuarine system and status of the Snohomish River as the second-largest freshwater input into Puget Sound make this area especially interesting and relevant to a larger environment. While sewer overflow events pose risks, the extent of their impact on our local water chemistry remains fairly unexplored. Studies conducted across the US suggest that this mix of human waste, debris, and potentially harmful microorganisms and chemicals in hundreds of thousands of gallons at a time can cause significant negative effects on many aspects of marine life, notably dissolved oxygen (DO), to the point of hypoxia. This study seeks to quantify the impact of combined sewage overflows (CSOs) in the Snohomish River and Possession Sound by analyzing trends seen between DO and chlorophyll levels at the mouth of the Snohomish River during low tides occurring before and after major CSO events. CSO outflow data were provided by the City of Everett’s Utilities department and DO and chlorophyll data were collected by a long-term deployed EXO 2 in the Everett marina. I hypothesized that there would be a significant negative correlation between CSO volume and DO levels and a positive correlation between CSO volume and chlorophyll. This research will help assess the risk of hypoxia, an important measurement as many marine species cannot survive in low oxygen conditions, and it will add to an important discussion about how our human systems impact marine life.

Noise pollution from 10 Hz to 200 kHz disrupts marine life and importantly damages cetaceans’ ability to navigate surroundings, communicate, and hunt. Possession Sound supports gray, humpback, and orca whales who all pass through its congested waterways and underwater soundscape. During 2023-2024 a voluntary slow down of commercial vessels occurred in Puget Sound. The results from Quiet Sound showed that 71% of 795 commercial vessels slowed down through the marked zones. There was a 50% 3 dB decrease in sound created and resulted in 72 additional minutes when underwater noise did not reach over 110 dB. One location where noise pollution is prominent is between the city of Mukilteo and the town of Clinton on Whidbey Island. The Mukilteo-Clinton ferries run 21 and a half hours a day, leading them to be a regular contributor to the underwater soundscape and an important factor to assess our environment's health. This study was conducted using data from a SoundTrap 400 hydrophone mounted .4 miles from the Mukilteo ferry terminal. 168 hours of constant data have been gathered between 2021 and 2024. From 1:30 am to 4:40 am, ferries don't run. Noise levels when the ferries don't run were compared to when they do run, which proved to show a significant reduction in overall RMS amplitude. Graphs plotting constant 24-hour RMS amplitude show spikes every half hour, which lines up with the Washington State Ferries (WSF) departure schedule. Future research must identify specific sound frequency signatures for the ferries and compare those frequencies and amplitudes to known values that may harm cetaceans and other marine life.

Fentanyl is a synthetic opioid that has become the leading driver of the U.S. opioid epidemic, contributing to over 70,000 overdose deaths annually. Opioid use disorder (OUD) is characterized by cycles of dependence, withdrawal, and relapse, with most fatal overdoses occurring during relapse, yet existing treatments for OUD do not effectively prevent relapse. Understanding how fentanyl affects brain activity and behavior is critical for developing more effective therapies. I investigated how fentanyl exposure modulates locomotion and the neural activity in the nucleus accumbens (NAc) across abstinence, dependence, withdrawal, and relapse. I hypothesized that each stage would show distinct neural activation patterns and that fentanyl exposure would reduce exploration and locomotion, reflecting compulsive drug-seeking behavior. To test this, I implanted silicon probes in the NAc of mice to monitor neural activity while tracking movement and behavior with high-resolution video. Mice received increasing fentanyl doses over five days, followed by a withdrawal period and, finally, a relapse challenge dose. I analyzed their behavior using deep learning-based pose estimation for correlations with neural activity across different stages of fentanyl exposure. I expect neural recordings to show that fentanyl significantly alters NAc activity, with each phase displaying unique neural patterns. I also expect fentanyl-exposed mice to show reduced exploratory movement, consistent with behavioral inflexibility and compulsive drug-seeking tendencies characteristic of OUD. These findings could provide critical insights into how fentanyl disrupts brain function and behavior, helping to identify new targets for addiction treatment. This research lays the groundwork for future studies on relapse prevention, with the goal of improving OUD therapies and reducing overdose deaths.

The mechanisms guiding the sensory detection of pain and the subsequent sensitization of damaged tissue to mechanical and thermal stimuli are relatively well understood. However, mechanisms guiding the transformation of nociception into the negative feelings associated with pain remain largely unknown. This affective component, notably in chronic pain, translates into an intense emotional impact on patients and can contribute to the development of comorbid psychiatric disorders. The elderly population have a propensity to be socially isolated and face exacerbated effects of chronic pain. In 2021, an estimated 20.9% of U.S adults suffer from chronic pain with persons over 65 years of age having the greatest propensity of acquiring the disease. Due to this, clinical intervention models call for a more holistic approach to pain intervention that incorporates lifestyle and nutritional factors, extending beyond pharmacological treatments. One of these promising non-pharmacological interventions is positive social interaction, which has been shown to alleviate pain and suffering.  Several studies show that humans who maintain strong social bonds recover from injuries faster than people without them. However, it has not yet been evaluated the extent to which this phenomenon occurs in geriatric animals and its relative efficacy as a social intervention to alleviate chronic pain in injured mice. My project seeks to gauge whether social intervention can alleviate chronic pain symptoms in aged mice and to unveil the underlying mechanisms guiding these successful non-pharmacological treatments. I will achieve this through two aims: evaluation of social self-administration as an intervention for chronic pain, and transcriptomic analysis to identify gene expression changes as a result of social interaction. Future research will include miniscope endomicroscopy recordings to visualize cell activity within major brain regions, and comparison of cell ensemble activity between groups of mice will lead to the identification of structures encoding behavioral shifts caused by pain.

Art has long been a cornerstone for revolution. Whereas there are many narratives about artistic interventions in the established norms and systems of oppression within society, there has been less investigation of how the values held within artistic spaces inspire revolutionary change. Artistic spaces produce different modes for thinking about art, its function, and how to create space for its production by all people. I researched these norms within the context of Dutch art cooperatives that emerged from squatting movements in the 1960s and 70s. My research gave me an understanding of Dutch anarchist frameworks and their implications for creating new forms of working environments that prioritize community over capital. In Seattle, I constructed an ethnography to find different values in artistic communities through interviews and experiences in those spaces. I used my research in artistic spaces to map the values held and record how those values implicate different structural frameworks. My main question is how artistic spaces produce different structures that allow for interventions into systems of oppression and to what extent they open opportunities for revolutionary change and individual growth. I measured these through qualitative findings through interviews to find the varying values held within a community and how those are associated with organizational structure. As I continue my research throughout the winter and spring, I anticipate finding the level of collectivity and revolutionary modes of thinking to be based on the organization’s histories within the arts. These findings will implicate how artistic communities vary based on geographic location and the historical norms of that community. The findings will further provide a basis for future understandings of how the arts can create spaces that allow for revolutionary questioning of norms within Seattle and beyond through a historical narrative. 

Many scholars have examined Ancient Rome’s reliance on enslaved labor and many more have investigated the inner workings of the cura annonae (“care of the grain supply”), the state-funded welfare program which provided free wheat to citizens under a certain income level. However, few have studied the foundation role that enslaved and other exploited labor played in the administration of the cura annonae. In this paper, I describe the history of the Ancient Roman food supply, the origins of the cura annonae, and its complex logistics. I outline the steps of the supply chain: the wheat plantations, grain ships, ports, mills, distribution, and bureaucratic administration. Using primary sources, archeological evidence, and scholarly theories, I focus on the instances of labor exploitation within the system. By applying world system theory and dependency theory to the institution of the cura annonae, I show how modern sociological and economic theories can enhance our understanding of the ancient world.

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

Biological processes rely on the intricate functions of proteins, which drive essential biochemical reactions. Given their critical role, various methods have been developed to regulate protein functions in biomaterials and in vitro. Enhancing the precision of gene editing is crucial for advancing applications in gene therapy and minimizing off-target effects. My project focuses on integrating photoactivatable proteins with prime editors, a modified version of the widely known gene editor CRISPR/Cas9, to improve spatial and temporal control over gene modifications. By utilizing genetic code expansion, non-canonical amino acids are incorporated into human cells to express photocaged prime editor proteins and altering host genomes. This system enables optical stimulation to precisely regulate protein activity. Through the deployment of well-characterized photolabile groups, we expect to be able to render protein activity controllable in a dose dependent way. A key application of this approach is the development of a photoactivatable prime editor system to induce precise gene edits. Traditional CRISPR/Cas9 methods lack spatiotemporal control over activation. To address this, the system is adapted for use in hydrogels, where two-photon patterning allows visualization of prime editor protein activation in three dimensions. Our study aims to demonstrate the feasibility of optically controlling gene editing with high specificity, offering a novel strategy for advancing cell lineage tracing and gene therapy applications.

Architectural and spatiotemporal aspects of epigenetic regulation and cell behavior are critical for maintaining overall health. Unintentional genetic mutations can create dynamic dysregulation in the epigenome and transcriptomes at the cellular level which is implicated in diseases ranging from fibrosis to cancer. However, our tools to probe and understand these behaviors are limited by a lack of spatiotemporal control. To address this, we propose installing four-dimensional control over the potent CRISPR inhibition transcriptional effectors to establish epigenetic control at cellular scale resolutions.  CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a genetic modification system that relies on Cas9 proteins to splice and deactivate genes as controlled by a programmable guide RNA sequence. CRISPR inhibition relies on a deactivated Cas9 protein that does not directly alter the genetic material in order to sterically hinder transcription. Our work aims to formulate a CRISPR inhibitor system which can unbind from the target DNA with two photon activation via a photo-cageable noncanonical amino acid insertion. This would allow for four-dimensional spatiotemporal control over the system, thus increasing the level of control in epigenetic regulation. Currently, work is being done to test the CRISPR inhibition system in HEK 293 cells that have been lentivirally transduced with both a test sequence and the deactivated Cas9 protein. After testing is completed for this simpler system, we will move toward creating a system that incorporates the photocaged noncanonical lysine variant, giving us control over the CRISPR inhibition system with regards to both space and time.

Tumor angiogenesis is characterized by unregulated blood vessel formation, impairing vascular networks and biological transport. It represents a critical stage in cancer progression, where malignant tumors metastasize and exploit the human body’s resources, which lie in vascular networks. However, the complex tumor microenvironment presents significant challenges in studying tumor angiogenesis and identifying its biomarkers. Towards addressing this concern, hydrogels—water-swollen, polymeric networks—can be used to recapitulate the tumor microenvironment, whose physiochemical properties can be precisely tuned to match that found in vivo. The DeForest Lab has developed methods and techniques in bioorthogonal chemistry and light-based subtractive manufacturing to tune such hydrogel materials with precise and unique 4D control, all at subcellular resolutions. In this project, I will exploit image-guided multiphoton lithography to engineer natively complex tumor vasculature patterns within photodegradable hydrogels. We will further embed tumor vascular spheroids within these hydrogels, providing a platform to model and assay tumor progression in vitro. This study has exciting implications for translational research and preclinical studies, particularly for disease modeling and therapeutic screening, as well as reducing ethical concerns regarding tissue and animal models in preclinical studies.

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

Dialogue/ loving yourself as you would love another recontextualizes the queer coming-of-age narrative by using poetry, drag, and video to embrace abstraction and fragmentation as radical philosophies of self-love. Focused on the ‘girl fag,’ Dialogue/ critiques identity-based systems of queer understanding, examines how the ‘shocking/misplaced’ femininity central to the ‘girl fag’ position separates her from both transness and gayness. The suspension created by this undefinability and the obligation the ‘girl fag’ has to queer abstraction and non-identity performativity is explored through ‘dialogue’ with a dragged-up-self and typical coming-of-age motifs - love, sexuality, physical growth, and discovering passions. The Dialogue/ project consists of a short (20-30min) video poem, the accompanying poetry collection, and a short essay succinctly exploring the mission of the work in academic writing. Visuals of the project celebrate drag traditions and dance as ways to connect with queer ancestry while the sound and writing explore vocal layering, abstract sounds, historical queer languages like Polari, and ‘fag-cent’ inflection. The planned display for this event would include short sections of video, stills, and conversation about project focus and methods. This project is a process of thinking, an of-age-reflection rooted in celebrating the resistance and experience of undefinition. 

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

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

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

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

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

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

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

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

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

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

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

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

The humble toilet, whose sole function is to transport waste away from us, is a machine. This is how the U.S. government wants us to view immigrants right now, as human waste to be discarded. Not as individuals with loved ones, or stories, or a heartbeat. The machine that facilitates these unruly acts of human departure, has a name: Immigration and Customs Enforcement. ICE frames this act of hate as “disposing of the bad guys”. There has been a massive increase of individuals being deported without even so much as due process of law. ICE is a machine that acts as the judge, the jury, and the executioner. Mahmoud Khalil, a student with legal green card status, was detained in March and deported to a prison out of state and away from his legal team. Mahmoud was not given any trial before being unlawfully imprisoned, just flushed away. Mahmoud and his case are well known, but there are more cases like his every day. As you read this, the federal government is attacking UW’s own international students regarding the legality of their visas, making their current legal standing unclear. My painting aims to protest against these governmental threats and acts of terrorism. The toilet, a disarming appliance that everyone in this audience will be familiar with, is here reframed. Who decides what is waste? Who gets to pull the chain? Can we stop them? While the deeper message of my painting might not be obvious at first glance, I hope that the alien and inhuman shape will captivate individuals enough to read my statement and to learn that this toilet is not just a toilet. What can we do about this inhuman machine?

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

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

To function as a tumor suppressor, BRCA1 (breast cancer 1) must dimerize with BARD1 (BRCA1-associated RING domain protein 1). Due to this critical interaction, loss-of-function BARD1 variants are associated with increased breast and ovarian cancer risk. Genetic testing has identified many rare single-nucleotide variants (SNVs) that cause missense substitutions in BARD1. Currently, 85.6% (1,736 of 2,028) of BARD1 missense SNVs are classified as a variant of uncertain significance (VUS) in ClinVar. A VUS classification prevents clinicians from using genetic test results to guide patient care. Consequently, there is a strong need to functionally assess BARD1 SNVs to help resolve VUS. We applied saturation genome editing (SGE) to functionally assess all possible 12,000 SNVs and 2,300 3-base deletions in BARD1. In SGE, we use CRISPR-Cas9, to edit all possible SNVs into a region of BARD1 in haploid cells. BARD1 is essential for cell growth, therefore, cells edited with loss-of-function variants become depleted from the population. We use DNA sequencing to track which SNVs become depleted from the population after 13 days in culture and are likely loss-of-function. All 14,000 variants have completed the full experimental pipeline. We show that 98% stop-gain, 29.6% splice-region, and 14.3% missense variants are loss of function relative to 1.6% of synonymous/intronic variants. The SGE data also agree strongly with current pathogenic/likely pathogenic and benign/likely benign BARD1 variants in ClinVar. Moreover, I have identified previously known and potential new protein-protein interaction interfaces through mapping our SGE data to the surfaces of BARD1’s structured domains. Ultimately, the functional scores for all BARD1 variants provide key functional evidence needed to reclassify BARD1 VUS and provide new insight into the mechanisms of BARD1 function.

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

Our project will be about the intersection of prison with prisoner's sex, age, race, economic standing, innocence, recidivism, and other inequalities. We will focus on a couple of these ideas, for example, finding trends in gender disparities, the economic impact of local prisons, or plea bargains and their effect on prison populations. We will present our findings from a government issued dataset using Python. We would like to introduce how our initial understanding of prison systems have changed from learning with our mentor in the Directed Reading Program. We are planning to use linear regression and decision trees to analyze our data.

Democracies run on information, and decisions made by a democratic body are only as good as the objectives facts that voters have access to, which form the basis for political opinion. Access to information has never changed as drastically or rapidly in the United States as it did during the propagation of internet service that occurred in the period between 2000 and 2016. The effect of the internet as a source of information is theoretically ambiguous. Some herald it as a tool for the democratization of information, making knowledge easily searchable and available to all. Others lament the internet’s role in spreading misinformation, particularly through social media. To investigate the relative magnitude of these effects, I employ county-level data on home broadband connections from the Federal Communications Commission as well as voter perception survey data collected by the American National Election Studies. Controlling for social and partisan determinants, I analyze this period of internet expansion in order to determine the effects of broadband access on voters’ perceptions of objective politically relevant statistics, such as national inflation and unemployment trends. These perceptions are then compared to the real statistics during these periods to determine whether internet access has made voters more or less informed on political issues. Though my analysis is still ongoing, I anticipate disambiguating the competing effects that the internet has on information acquisition and determining which is predominant in influencing the formation of political perceptions. These findings contribute to our understanding of the social ramifications of internet access—a new and still-developing field—and inform future efforts to regulate the flow of information online.

Pseudomonas aeruginosa (Pa) is an opportunistic pathogen that infects the airways of people with cystic fibrosis, a genetic disease that increases susceptibility to lung infections. Pa uses an intercellular communication system called quorum sensing (QS) that allows bacteria to sense cell density and coordinate behaviors among the population, including regulation of virulence. In the laboratory strain PAO1, there are three complete QS systems in Pa that are regulated by the transcription factors LasR, RhlR, and PqsR. PAO1 QS is organized hierarchically with LasR regulating RhlR, and the hierarchy is influenced by the transcription factor MexT that delays RhlR activity. However, it is unknown if QS hierarchy is found widely in Pa strains. My project tested whether the QS hierarchy exists in clinical isolates of Pa. We obtained 3 clinical isolates with intact lasR, rhlR, and mexT genes and created lasR and mexT knockout mutants for each strain to test the effects on RhlR activity compared to wild-type. To measure RhlR activity, we transformed each strain with a RhlR reporter plasmid. We found that a PAO1 mexT mutant shows greater RhlR activity compared to wild-type, while each clinical isolate showed similar RhlR activity between wild-type and the mexT mutant. We observed lower RhlR activity in clinical-isolate lasR mutants compared to wild-type, demonstrating LasR-dependent QS like PAO1. In PAO1, a ∆lasR∆mexT double knockout mutant restored RhlR activity. Interestingly, in clinical isolates, we observed no change in RhlR activity in these ∆lasR∆mexT double knockout mutants as compared to the lasR mutant, indicating MexT is not regulating QS hierarchy in these clinical isolates. Altogether, the clinical isolates displayed a LasR-dependent QS architecture similar to PAO1, but this was not dependent on MexT. Thus, my work points to undiscovered factors that influence QS architecture and highlight the diversity of QS regulation in strains of Pa.

Harbor seals (Phoca vitulina) are one of the most prevalent marine mammals along the West Coast of the United States. In the Salish Sea, harbor seal populations have increased significantly since the Marine Mammal Protection Act of 1972, and the population is now considered to be at carrying capacity. These seals prey on many species of fish and invertebrates and are themselves a major component of the diet of local transient killer whales. Harbor seals can frequently be seen resting in groups on land at places called haul-out sites. They are known for their high site fidelity, meaning that the same seals consistently return to the same sites. These haul-out sites are frequently dominated by a specific sex or age range. This study investigated whether specific seals are more likely to be re-sighted in smaller groups or with other specific individuals within the haul-out site. Using SealNet, an AI facial recognition system, I analyzed photographic data from 750 images from the Ocean Research College Academy’s (ORCA’s) long-term data collection that were taken from haul-out sites at the mouth of the Snohomish River. SealNet identifies individual seals by analyzing facial features and comparing them across photos, assigning a similarity score for each photo and ranking them in descending order. The results of this research are aimed at determining if harbor seals exhibit more complex social structures within haul-out sites. Understanding the social structure of harbor seals can help provide insight into their cooperation, competition, and overall population dynamics. This study focuses on haul-out sites while the majority of interactions occur in the water, so further study is needed to better understand the dynamics of this population.

Everett’s Naval base, train tracks running parallel to the shore, and robust recreational/commercial boat traffic add to the increasingly loud acoustic environment of Possession Sound. Several studies have linked elevated sound pressure levels to reducing the acoustic communication space and disrupting critical behaviors such as feeding, breeding, and communication in marine fish and invertebrates. Ongoing research within the Salish Sea has highlighted some habitats like seagrass meadows (Zostera marina) and kelp forests (Nereocystis spp.) that can aid in mitigating the effects of noise pollution on underwater communities on top of being a foraging habitat, shelter, and critical nurseries for various species. Although the Salish Sea as a whole has seen dwindling kelp forests and eelgrass meadows in recent years, Possession Sound nonetheless contains both habitats. For my study, both Z. marina and N. ssp. were present around the perimeter of Hat Island, 5 nautical miles from the Port of Everett. I collected 8 seven minute recordings using a deployable hydrophone (SoundTrap 300). Preliminary analysis has revealed distinct biological sounds, primarily within the 0-5 kHz range, and are denoted as a part of the biophony of the soundscape. I analyzed the soundscapes using ‘Root Mean Square’ (RMS) amplitude formatting, because it indicates the equivalent steady state energy value of oscillating sound waves. I utilized RMS amplitude measurements for comparison inside the habitats to the appropriate counterpart outside the habitats (exclusion zone is a minimum distance of 100 meters from the previous recording). Future analysis will expand with continued gathering of ambient soundscape data into early spring to ensure the utilized dataset can represent multiple seasons and atmospheric conditions as well.

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

Additive manufacturing, particularly 3D printing, often produces surface ridges, especially for complex geometries, that require post-processing to achieve a smooth finish. Laser ablation is an effective technique for smoothing these surfaces, but precise identification of ridges is crucial for optimizing the process. This study explores the use of machine learning to detect and ablate 3D print ridges, improving the accuracy of laser smoothing. A convolutional neural network (CNN) was trained on greyscale images of printed surfaces, learning to segment ridge regions from background material. From there, image processing filters and a line transform was applied to gather line defining information to be converted into DXF, a readable file for the laser software. The trained model was integrated into a graphical user interface (GUI) to automate ridge detection and guide the laser for targeted ablation, minimizing manual intervention. The system was validated on test parts, demonstrating overall efficiency and accuracy in ridge identification. Other experiments were done to determine proper laser and process parameters to achieve an accurate and smooth surface finish. The experimental results showed improved surface uniformity. The automated approach made laser smoothing efficient and scalable for industrial and manufacturing applications. By leveraging machine learning, this method advances the precision and repeatability of post-processing in 3D printing, reducing labor costs and improving final product quality.

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

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

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

There is a crucial need for a vaccine that produces a robust immune response against Human Immunodeficiency Virus (HIV), particularly for those without access to effective treatments. We investigated the immunogenicity of a novel self-amplifying RNA (RepRNA) vaccine for HIV in non-human primates (NHPs). RepRNA vaccines encode subgenomic sequences that enable the self-amplification of additional copies of RNA, inducing strong immune responses with lower doses of RNA. The repRNA was formulated with a lipid nanocarrier called LION (HDT Bio), which protects the RNA from degradation and enables its delivery into the cell. This platform has shown success in a licensed SARS-CoV-2 vaccine, suggesting it may be similarly promising as an HIV vaccine. I aim to evaluate whether the RepRNA/LION vaccine can elicit robust systemic and mucosal responses in NHPs. I hypothesized that the vaccine would increase HIV-specific T-cell responses in PBMCs and induce HIV Env-specific antibody production in nasal and rectal secretions. To investigate the immunogenicity of this vaccine, we vaccinated twelve cynomolgus macaques, divided into three groups, with HIV Env and/or HIV Gag-Env. To determine vaccine efficacy, I measured the frequency of antigen-specific T-cells in blood using interferon-gamma (IFN-γ) Enzyme-Linked ImmunoSpot (ELISpot) assays because activated T-cells secreting IFN-γ help eliminate infected cells. I also assessed HIV Env-specific Immunoglobulin A (IgA) levels in nasal and rectal secretions using Enzyme-Linked Immunosorbent Assays (ELISAs) because IgA is key in neutralizing pathogens at mucosal surfaces. My preliminary results show an increase in IFN-γ production after the first vaccination, which indicates a systemic antigen-specific T-cell response. We will continue to run assays to see if further vaccination doses can induce more robust immune responses. Results from this study indicate that the RepRNA/LION HIV vaccine may be a promising approach to induce mucosal and systemic immune responses against HIV.

Dehydration is a silent but pervasive health risk, particularly for older adults in assisted living home settings, where prevalence rates can reach up to 60%. Medications that increase fluid loss place seniors at a heightened risk, leading to severe complications including urinary tract infections, falls, cognitive decline and hospitalisations. Caregivers continue to struggle to monitor fluid intake effectively, with less than 10% maintaining consistent hydration logs. Existing hydration monitoring solutions are often invasive, expensive and poorly suited for non-medical care settings. To address this critical issue, we developed a novel, non-invasive hydration monitoring system designed for elderly care environments. Unlike existing methods that rely on highly variable sweat salt concentrations, our approach leverages ultrasound-based elasticity measurements to assess hydration status. Changes in hydration levels alter the biomechanical properties of skin and muscle, affecting the speed at which ultrasound waves travel through tissue. By using a dual-transducer system to induce and measure shear wave propagation, we can quantify hydration status in real-time. The device provides both quantitative readouts for longitudinal tracking and intuitive qualitative feedback, similar to a blood pressure monitor's high-normal-low classification, ensuring ease of use without specialised training. Initial testing demonstrates promising accuracy and usability, positioning our solution as a practical solution to improve hydration management, prevent dehydration-related complications, and enhance quality of life for elderly residents. By empowering caregivers with a reliable, accessible hydration monitoring tool, our solution has the potential to significantly reduce healthcare costs, improve patient outcomes, and transform hydration care in aging populations. 

This research examines the statistical interactions of genetic risk scores and behavior data from wearable devices, including physical activity and sleep measures, to predict Major Depressive Disorder (MDD) symptom onset. MDD is a widespread mental health issue, with nearly all indicators of mental health worsening from 2013 to 2023 and 30% or more current children experiencing mental health symptoms. Research shows that lifestyle changes, such as improving physical activity and sleep behavior, can alleviate early-stage MDD symptoms. But, many people are unaware of their genetic vulnerability to MDD, leaving them unprepared for potential challenges. This study uses the Adolescent Brain Cognitive Development (ABCD) dataset, the largest U.S. longitudinal study of brain development and child health. ABCD provides extensive psychometric, demographic, genetic, and wearable data for research. This study uses genetic and wearable tracking data to predict MDD severity and support early interventions. It also investigates how genetic risk levels inform how physical activity and sleep patterns must change to mitigate MDD symptom severity.  This study will calculate polygenic risk scores (PRS) for ABCD subjects and improve prediction accuracy for non-European populations using state-of-the-art bioinformatics tools. Then, this study will utilize mixed effects modeling to analyze additive and interactive effects of PRS, wearable data, and depression severity scores. Lastly, this study will program machine learning (ML) models to provide variable importance and accuracy results. The goal is to create a personalized, data-driven approach to MDD prevention and empower individuals to take proactive steps toward mental well-being based on a comprehensive view of their genetic and behavioral factors.

Exoplanetary studies suggest that massive outer planets, such as Jupiter in our Solar System, play a crucial role in shielding inner planets from excessive asteroid bombardment, thereby contributing to long-term orbital stability. The Kepler-11 system is a tightly packed configuration of six planets that lacks a known massive outer planet protector. In this project I investigated the stability of Kepler-11 planets under varying levels of asteroid impact modeled using a combination of n-body simulations in 10,000-year segments, Monte Carlo methods, and statistical extrapolation. These results were then further extrapolated using Poisson statistics to estimate the system’s long-term evolution over millions of years. I ran simulations as the system is currently known and with a Jupiter-like planet to assess its role in deflecting or capturing incoming objects. Preliminary findings suggest that in the absence of a massive outer planet, asteroid impacts on the inner planets increase significantly, leading to cumulative orbital drift and potential long-term destabilization. These results highlight the importance of massive planets in preserving planetary system stability and suggest the possible existence of an undetected distant massive planet or a densely packed outer system that has maintained Kepler-11’s current planetary configuration.

CdCr₂X₄ and ZnCr₂X₄ (X = S, Se) spinels are ferromagnetic semiconductors, with reported bandgaps between 1.3-2.5 eV. With the advent of spintronic devices, a renewed technological interest in materials with coupled magnetic and optical properties has caused a resurgence in the study of these magneto-optically active spinels. Despite prevailing interest in their magnetic structure, the semiconductor luminescence of these materials is not well studied. We have prepared these materials in-house to study the magneto-optical coupling of this bandgap transition. We are also beginning to prepare these materials as nanocrystals for the first time as a way of accessing alloyed and shelled varieties. We started by synthesizing the non-magnetic In³⁺-based analogous sulfide and selenide spinels as nanocrystals, establishing a starting point to prepare the Cr³⁺-based spinels. We then introduced Cr³⁺ ions, which occupy the In³⁺ sites, into the lattice during the solution-phase synthesis. We aim to make the pure chromium-based nanocrystal spinels, along with a concentration range of Cr³⁺ ions in the In³⁺-based lattice. Our goal is to explore the relationship between the Cr³⁺ concentration gradient and the magneto-optical properties of these materials. We have characterized the composition and optical bandgap energies of these spinels with X-ray diffraction, photoluminescence, and UV-Vis absorption spectroscopy. We have begun tuning the bandgap energy of the nanocrystals by preparing mixed anion alloys with different ratios of Se and S ions (i.e. CdCr₂(Se_1-xS_x)₄; ZnCr₂(Se_1-xS_x)₄) and examining the bandgap shift with photoluminescence excitation spectroscopy. Future work includes utilizing magnetic circularly polarized luminescence (MCPL) to probe the magnetization of the lattice emission, letting us conclude how the optical properties of the semiconductor are coupled to its magnetism.

Upon nerve injury and neurodegeneration, neuron regeneration is crucial to maintain proper function. However, this natural process happens infrequently and slowly. Neuron regeneration is known to be mediated by the activity of nerve growth factor (NGF) in neurons, which binds to two receptors: tropomyosin receptor kinase A (TrkA) and p75 neurotrophin receptor (p75NTR). Previous studies have shown that engaging the receptor p75NTR activates a signaling pathway that also triggers a pain response, thus it would be ideal to have a ligand that only activates TrkA for neuron regeneration without initiating the pain response. In collaboration with the Institute for Protein Design (IPD), this study investigated an AI-designed TrkA agonist that specifically binds to and activates only the TrkA receptor. We used fibroblasts transdifferentiated into neurons as a model to study the efficiency of this TrkA agonist. Western blotting was used to study the phosphorylation of the proteins downstream of TrkA in the signaling pathway, such as pPLCγ, pAkt, and pErk, and the activity of transient receptor potential vanilloid 1 (TRPV1), a calcium channel that indicates the sensitivity of a neuron. Immunofluorescence staining was used to examine the expression of calcitonin gene-related peptide (CGRP), a neuropeptide involved in pain perception. We found that the designed TrkA agonist generates a similar level of activation of downstream proteins as NGF while successfully preventing the expression of pain response markers. Directly injecting NGF as a treatment for neurodegenerative diseases is generally not considered viable as it often induces significant pain, therefore this TrkA agonist has the potential for therapeutic use.

Parkinson’s disease (PD) is a neurological disorder that affects patients’ movement, balance, and coordination, primarily due to the death of dopaminergic neurons. Traditionally, researchers use MPTP, a neurotoxin that destroys dopaminergic neurons, to replicate the motor symptoms of PD. However, this approach captures the later stages of the disease, making it difficult to develop early stage interventional treatment with this model. There is a long prodromal, or early, phase of PD, in which neuronal cells and circuits are changing before the neurons die and cause overt motor symptoms. A critical gap exists in our understanding of the early progression of PD due to the lack of robust primate models of this phase of the disease process. In an effort to create a prodromal phase model of PD, we made intrasnasal and intracranial injections of a pathological form of the protein alpha-synuclein (aSynPFFs) extracted from human PD patients, and used it in macaques. We quantified the motor changes in macaques using a modified version of Unified Parkinson’s Disease Rating Scale (UPDRS), which has 14 categories that each define a movement function of interest scaled from 0 to 3 (no symptom to highly impaired). To improve the detection of the changes, we used a deep learning software called DEEPLABCUT (DLC) to track the subtle motor changes seen in the macaques after exposure to aSynPFFs. By using quantitative approaches to assess motor function before and after aSynPFFs exposure, we hope to establish a timeline of neurodegeneration associated with PD in primates. Such a model would provide an important platform to assess therapies to halt neurodegeneration associated with PD.

The future of clinical research is expanding towards sampling that can be completed from the comfort of a participant's home. Blood samples allow for the collection of ribonucleic acid (RNA), which is relevant for gene sequencing that can track the progression of a disease. However, venous blood draws require trained phlebotomists at a healthcare facility, which may not be readily accessible in some areas. Dried blood spots are an existing remote sampling method, but rapid degradation of RNA and low blood volume can limit the scope of analyses that are possible. Previously, our lab developed homeRNA, which interfaces with the Tasso-SST (Tasso Inc.), a lancet-based device that draws blood from the upper arm. The addition of the engineered, spill-resistant container creates a channel through which participants can draw their own blood, stabilize the blood with RNAlater (Thermo Fisher Scientific), and ship the sample to a laboratory for analysis. The homeRNA+ project improves upon the original homeRNA by integrating a commercially available blood collection tube for better compatibility and doubling the maximum blood collection volume. Feedback from study participants over the United States across all age and race demographics generally find the blood collection process painless and the stabilization easy to perform. We expect samples to also have sufficient RNA integrity and yield for downstream analysis. The project serves a number of nationwide and global collaborators, including academic institutions like New York University and Boston University. I assist in receiving and processing biological samples from remote collection, ensuring proper handling by safely unpackaging, logging, and preserving returned samples in cold storage for future analysis. Additionally, I serve as a study coordinator by meeting with collaborators, manufacturing high volumes of kits in a timely manner, and managing inventories.

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

Salivary glands are organs in the mouth which produce and secrete saliva, a multifunctional fluid crucial for processes including oral cavity lubrication, digestion, and antimicrobial functions. Diabetes mellitus has been associated with salivary gland dysfunction and harmful oral consequences including severe tooth decay and disrupted wound healing, yet it is not currently known what cell populations are affected in salivary glands and how this disease affects cell organization, function, and metabolic response. One model for diseases in human tissues are organoids, three-dimensional multicellular systems derived from stem cells which self-organize to mimic the structure and function of tissues in vivo when given the right cues. Dr. Devon Ehnes in the Ruohola-Baker Lab recently created a protocol to develop salivary gland organoids from induced pluripotent stem cells (iPSCs), and through additional culture in a high-glucose media along with inflammatory cytokines, this organoid has been used to study how diabetes affects salivary glands. Preliminary analysis has suggested acinar and ductal cell dysfunction and mitochondrial stress as causes of salivary gland dysfunction, but further work is necessary to understand how this diabetic environment leads to changes in cell function and mitochondrial activity. Here, I use a human iPSC-derived organoid model to assess how diabetic conditions affect the expression and localization of the acinar marker AMY1A, the ductal marker KRT19, the cell stress marker FOXO1, and the mitochondrial marker ATPB to determine the mechanisms for salivary gland dysfunction in diabetes.

Alzheimer's disease (AD) affected approximately 6.9 million Americans aged 65 and older in 2024, and it is projected to rise to 13 million by 2050 (Alzheimer’s Association, 2024). AD is characterized by progressive cognitive decline, but sleep disruption is an often overlooked symptom that emerges early in the disease's progression. Evidence suggests that AD-related sleep disturbance may originate from dysfunction in the circadian system, particularly in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN regulates sleep-wake cycles, and recent findings from de la Iglesia lab have shown that specific SCN neurons exhibit a daily rhythm of fiber expansion and retraction. This study aims to investigate how aging and AD affect SCN structural plasticity; this could help explain circadian disturbances in AD patients. I aim to identify the age at which abnormal circadian phenotypes emerge in a mouse model of AD which shows circadian disruptions. We are currently comparing activity patterns of AD mice ages 6 to 16-months old with their wild-type littermate controls using behavioral running wheel data. We hypothesize that the AD mice will exhibit a decreased mean total sleep and shorter circadian period in constant darkness. While these symptoms are common with aging in healthy mice, we expect that they will appear earlier in AD mice than in their wild-type littermates, as disrupted sleep is an early-onset symptom of AD. Future studies will assess whether these symptoms are associated with deficits in daily structural plasticity of the SCN. By elucidating the relationship between AD, SCN neuronal structure, and circadian rhythm disruptions, this research aims to provide insights into the mechanisms underlying sleep disturbances in AD patients. Understanding these processes could potentially lead to the development of targeted interventions to mitigate sleep disruptions and slow disease progression in AD patients.

The King County Brightwater Treatment Plant includes two twin outfall pipes that were installed in 2012, and discharge approximately 36 million gallons of highly treated effluent into Puget Sound daily. After observing colonization of the pipes by marine organisms, King County biologists launched a ten-year study examining the impact of effluent discharge on motile and sessile species on and near the outfall over time. They placed plates of the pipe material, high-density polyethylene (HDPE), on the seafloor, with replicates near the effluent discharge diffusers and approximately 300 ft away. King County retrieved the replicate plates after 2, 5, and 10 years and, photographed each plate for subsequent image analysis. In this study, we analyzed the photos to investigate whether there was a measurable effect of effluent discharge on the abundance, identity, and size of organisms colonizing the plates. We concluded that effluent discharge likely does not affect percent live cover, number of taxa, or the identities of taxa present. However, some motile species may be more abundant in the absence of effluent discharge, and there may be some effect of effluent on the size of some species. These abundance and size differences are worth further investigation as they may indicate that, although highly treated, effluent discharge from the Brightwater Treatment Plant impacts some species' demographic rates, like survival and growth rates, and the water quality of the Puget Sound. Our results indicate that even highly treated effluent impacts the surrounding water and the species that depend on it and that further research is needed to fully investigate the impacts of wastewater discharge in the Puget Sound ecosystem.

Per-Arnt-Sim (PAS) domains are ubiquitous protein modules that enable cells to detect and respond to environmental signals. For instance, circadian rhythm regulators leverage PAS domains to sense stimuli and initiate protein-protein interactions critical for maintaining biological oscillations. Structurally, the sensory region of PAS domains detects environmental cues—such as fluctuations in phosphorylation levels—while the effector domain converts these signals into cellular responses, including altered gene expression or protein interactions. Inspired by this natural framework, our project aims to design de novo sensory domains that selectively recognize tyrosine phosphorylation, a key post-translational modification in cellular signaling, through association/dissociation between bound and unbound states regulated by the phosphorylation/dephosphorylation cycles. During the design phase, we prioritized synthetic peptide targets for initial proof of principle and systematically deployed computational pipelines: (1) Rosetta introduced phosphotyrosine modifications into pre-designed protein-peptide heterodimer scaffolds; (2) iterative LigandMPNN with Rosetta FastRelax optimized binding interfaces to accommodate the phosphotyrosine modifications; (3) RFdiffusion Partial Diffusion enhanced the structural diversity around promising designs with the aim of improving affinity and specificity; and (4) Chai-1 and AlphaFold enabled in silico folding and structure-based filtering of final candidates. High-confidence designs will be expressed and purified from E. coli, and then undergo in vivo characterization via size exclusion chromatography (SEC) binding assays and enzyme-linked immunosorbent arrays (ELISA) to quantify their binding affinity, specificity, and the function of phosphorylation-dependent switching. Validated scaffolds will then be integrated with pre-designed effector domains to assemble fully de novo PAS domains. This modular platform establishes a foundation for designing phosphorylation-sensitive biosensors. Future adaptation to natural phosphorylation sites could yield programmable tools for interrogating signaling networks, advancing synthetic biology, and enabling precise manipulation of cellular communication pathways.

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

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

Caffeine is one of the most widely consumed stimulants globally, yet its effects on explicit memory remain an area of active research. This literature review examines how caffeine influences explicit memory, particularly in short-term recall and recognition memory in young adults ages 18-22. By synthesizing findings from recent peer-reviewed studies, we explore the neurochemical mechanisms, focusing on caffeine’s role in modulating adenosine receptors, enhancing neuronal activity, and affecting hippocampal-dependent memory functions. Some studies indicate that caffeine improves attention and alertness, which can indirectly support memory formation. However, other studies suggest that excessive intake or habitual use may lead to adverse effects, particularly if it disrupts sleep patterns or increases anxiety—both of which are known to impair memory. These conflicting findings highlight the complexity of caffeine’s effects and the challenge of drawing definitive conclusions. Beyond individual consumption patterns, methodological differences across studies like varying dosage intake and testing periods also contribute to conflicting findings. Variations in participant characteristics, experimental designs, and memory assessment methods make direct comparisons across studies challenging. Some studies focus on immediate recall, while others examine delayed retrieval or recognition memory, further adding to the variability in reported outcomes. By critically evaluating existing research, we aim to clarify the relationship between caffeine and explicit memory while identifying research gaps that future studies should address. Given the widespread use of caffeine among young adults, particularly for academic performance, a deeper understanding of its cognitive effects is essential. Investigating how caffeine influences memory under different conditions—such as varying levels of stress or sleep deprivation—could provide valuable insights. Future research should also refine methodologies to isolate caffeine’s specific effects on explicit memory in young adults.

The sensation of acute pain is fundamental to survival, indicating tissue damage that motivates an animal to engage in adaptive protective behaviors. Chronic pain, however, is persistent pain beyond typical recovery window and serves little adaptive function. The negative emotional component inherent in chronic pain contributes to the development of comorbid psychiatric disorders such as depression, social aggression, and social withdrawal. Our research aims to understand the bidirectional relationship between pain and social behavior, by evaluating mechanical sensitivity and changes in social motivation, reward, and interaction following a neuropathic injury. Using social self-administration (SSA), pair-housed mice were placed in operant chambers and underwent voluntary lever press trials for the reward of social interaction with their cage mate. Mice also underwent mechanical hypersensitivity response assays called von Frey where increasing weights of plastic filament were applied to the hind paw. Following baseline von Frey testing and the acquisition of the SSA task, mice then received a spared nerve injury (SNI) to induce neuropathic pain. After surgery recovery, mice were returned to the lever press and von Frey trials at different post-operative windows. Pain sensitivity was determined by the filament weight in which the animal withdrew their paw during von Frey. Changes in social behavior were measured via changes in lever press frequency and interactions during trials. Behavior changes were quantified using Simple Behavior Analysis (SimBA) machine learning to classify interactions during social trials. Once the trials were completed, brain tissue from regions associated with reward and social neural circuitry was collected and investigated using transcriptomic methods. Our data found sexually divergent social adaptations and gene expression following chronic pain. Future experiments will further delineate these sex-specific adaptations following a traumatic injury. This research can inform social intervention as an adjunct or alternative treatment to pharmacological pain intervention and its comorbidities.

In nature, Per-Arnt-Sim (PAS) domains comprise a sensor that undergoes conformational changes upon signal recognition which either activates or deactivates an effector domain. Natural PAS domains detect environmental cues, such as oxygen, light, and small ligands; however, they do not sense phosphorylation, a key post-translational modification. Here, we present a designed de novo phosphorylation-inducible heterodimer that serves as a sensor domain. This system toggles between association and dissociation states in response to phosphorylation and dephosphorylation events. To engineer reversible association and dissociation, we designed phosphorylated peptides and their corresponding binders. Starting from a library of previously designed peptide-binder complexes, mutations were introduced into the peptide sidechains, replacing selected residues with phosphorylated tyrosine, serine, or threonine. Next, we ran iterative cycles of LigandMPNN-FastRelax to generate binder sequence candidates. Finally, we used AlphaFold2 and Chai1 to predict the folded structures of our input sequences and selected those that were predicted with high confidence. For experimental validation, the designed proteins will be overexpressed in Escherichia coli and purified using affinity and size exclusion chromatography. Phosphorylation-dependent binding specificity and affinity will be assessed through enzyme-linked immunosorbent assays (ELISA), surface plasmon resonance (SPR), and fluorescence polarization (FP). Subsequently, we will fuse these sensor domain designs to a collection of previously designed hinge proteins—which can bind/release an effector protein—to produce de novo PAS domains, thereby linking the sensing event to downstream functional responses. This adaptable system offers broad applications in biomaterials and synthetic biology, including the development of responsive scaffolds for biosensors and synthetic protein motors with controlled conformational cycles. 

Estrogen plays a key role in metabolic regulation including fat distribution and glucose homeostasis. Less understood are the differences of estrogen metabolism in different fat depots, and the conversion mechanisms that underlie the effects we see between two prominent isoforms of estrogen, Estradiol (E2) and Estrone (E1). E2 dominates during reproductive years, shifting to an increase in E1 post-menopause. These hormonal changes contribute to a switch in fat storage from subcutaneous to visceral depots, elevating the risk of metabolic diseases. My research investigates how differences in estrogen metabolism, mediated by cytochrome P450 aromatase (CYP19A1) and 17β-hydroxysteroid dehydrogenase (HSD17B1), influence glucose uptake in inguinal (IWAT) and epididymal (EWAT) white adipose tissue. Using ex vivo explants from C57BL6/J male and female mice, I treated IWAT and EWAT with E1, E2, an agonist of CYP19A1, and an HSD17B1 inhibitor. Glucose uptake was measured at baseline, after 24 hours, following insulin stimulation. Additionally, I performed RT-qPCR to quantify depot-specific expression of CYP19A1, HSD17B1, and related metabolic genes. Preliminary results show that IWAT exhibits higher baseline expression of CYP19A1 than EWAT correlating with IWAT also demonstrating greater insulin-stimulated glucose consumption. E1 treatment decreased glucose uptake in both depots, while E2 had minimal effect in IWAT. Most interestingly, E1 and the forskolin + HSD17B1 inhibitor combination significantly decreased glucose consumption. This suggests depot-specific metabolic adaptations driven by differences in estrogen metabolism. The differences between IWAT and EWAT in estrogen-mediated glucose regulation offers new opportunities to better understand the metabolic impact of E1 and E2 in estrogen metabolism and glucose uptake. Understanding these mechanisms could inform strategies for targeting adipose tissue to mitigate impacts of insulin resistance and obesity, especially for postmenopausal women. My contributions include conducting tissue treatments, measuring glucose uptake, and analyzing gene expression data.

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

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

The aorta is the largest blood vessel in the body and is responsible for transporting blood to our organs and extremities. A type A aortic dissection (TAAD) is a tear in the inner and middle layers of the ascending aorta. Given the significant and traumatic nature of such an event, the mortality rate is a major concern as some literature cites up to a 2% increase in mortality rate per hour of an individual suffering from TAAD. Genetic aortopathy, which is an umbrella of genetic diseases, significantly increases the risk of catastrophic aortic events such as TAAD. Patients with genetic aortopathy have been found to have an increased risk of aortic dissections which has already proven to be deadly. However, there is very little research that has been done to show the effect of genetic aortopathy on the short-term outcomes of patients who have undergone surgical repair of TAAD. Our goal is to identify whether differences in outcomes between patients with and without genetic aortopathy truly exist. The dataset we are using is localized to treatment at the UW Medical Center, and contains genetic testing on TAAD patients – something very few centers have previously done. To date, we have completed the database entry of the patients relevant to the study and are beginning the statistical analysis phase which is executed with R programming. The results of this study concern both patients and physicians interested in postoperative outcomes. But, to the patient, this is perhaps the most pressing question moving forward. What is the risk of needing a repeat surgery? What effect does this have on my life expectancy? These are all common yet largely unanswered questions which we provide clarity on.

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

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

In the face of global climate change, there is growing interest in growing seaweed and sinking it to depths to remove carbon dioxide. However, quantifying the carbon sequestration potential of such ventures is challenging. One key consideration is that rising seawater temperatures may increase the rate of kelp decomposition, thereby reducing the export of carbon-containing tissue to the seafloor. To assess whether blades of the bull kelp Nereocystis luetkeana decompose more rapidly in warmer water, twelve 35 mm-diameter tissue disks were allowed to decay at 10-12 °C (ambient temperature treatment) and another 12 tissue disks were allowed to decay at 17-19 °C (elevated temperature treatment). After 7 days, the mean change in disk mass for the ambient temperature treatment was compared to the mean change in mass for the elevated temperature treatment. Samples at elevated temperatures were visibly flimsier and more diaphanous, which was correlated with a significantly greater decrease in weight. In tandem with other studies, this finding suggests that brown algae may decompose more rapidly at elevated temperatures, which has important implications for how to maximize future macroalgal carbon sequestration as ocean temperatures rise.

Hydrogels with tunable stiffnesses are a versatile method to study the interactions of human cells in vitro. These systems recreate human extracellular matrix (ECM) and capture the stiffness changes associated with a variety of biological processes and diseases, like cancer and cirrhosis. Photoresponsive chemistries allow light to be used to modulate the stiffness in these materials with high resolution. However, when creating more complex patterned gels with photomasks, bulk property analysis cannot capture the variation. To circumvent this and measure the stiffness of these complex gels, I performed rheology and fluorescence recovery after photobleaching (FRAP) to establish a correlation between diffusivity and stiffness in flood-illuminated gels. By finding and using the correlation, I am able to calculate the stiffness of the more complex patterned gels based off of their FRAP-derived diffusivity measurements. This method allows for better fine tuning of gels for use as a platform to study human cell growth through a range of stiffening events in multiple different parts of the body.

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

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