Previous studies have found that jellyfish benefit from warming temperatures and eutrophication, resulting in large jellyfish blooms worldwide. However, the impact of warming ocean temperatures on the cross jellyfish, Mitrocoma cellularia, which are common in the Pacific Northwest, has been relatively unexplored. This study tests the hypothesis that warmer water temperatures would increase M. cellularia growth. A total of 36 individuals were collected from the UW Friday Harbor Laboratories Dock, San Juan Island in September 2023. They were observed in individual jars without water flow, and equally distributed across four separate temperature-controlled baths at 13°C, 16°C, 18°C, and 20°C. Over the 96-hour exposure period, they were fed excess live zooplankton collected before each feeding and had daily water replacements. Surface area was measured with ImageJ, mortality, and overall condition after the acclimation period (initial), day two (mid), and day four (final). A growth rate polynomial regression characterized the final measurements of normal condition jellyfish with a maximum closest to 16°C, resulting in an R2 =0.24 and p-value <0.05. At 20°C, shriveling and mortality increased. While 20°C decreased M. cellularia growth, our results support previous studies that jellyfish are resilient to impacts of climate change within the range of near-future prediction for the Pacific Northwest. Further investigations of the adaptability of M. cellularia to changing temperatures is necessary to understand the future outcomes of their ecology. Examination of this species can inform the state of a jellyfish ecosystem’s adaptability to climate change, which will allow further studies to create solutions to combat changing environments for ocean habitats.

Zooplankton are vital to the marine food web, supplying nutrients and energy from primary producers to secondary consumers. During Diel Vertical Migration (DVM), zooplankton travel between depth and the surface during day and night to capitalize on food and avoid predation. This study investigated diel differences in zooplankton community composition at two locations, one exposed and one protected, in the San Juan Channel, WA over four days in September 2023. Zooplankton were collected using net tows from surface waters at both sites during day and night times. Samples were analyzed using a stereoscope and different taxonomic groups were counted. Copepods were the most abundant zooplankton taxa at both locations, with mean abundances up to 1000 individuals per cubic meter. At the exposed site, there was a significantly higher (p<0.05) abundance of zooplankton at night versus during the day. The exposed site had significantly higher diversity than the protected site at night (p<0.05). At both locations, species richness was significantly higher (p<0.05) at night compared to day. The exposed location also had significantly higher richness (p<0.05) compared to the protected location during the day. Our results indicate that zooplankton abundance and diversity in surface waters of the San Juan Channel are controlled by DVM, and differences in locations perhaps due to exposure to different flow regimes. This study reinforces the flexibility of zooplankton community composition and emphasizes the importance of understanding factors that influence changes in the base of the marine food web.

Nearly 70% of older adults hospitalized in an intensive care unit (ICU) experience delirium, a risk factor for long-term cognitive impairment that persists beyond discharge. The severity of critical illness, coupled with the 24-hour care provided in the ICU, is associated with significant disruptions to sleep and the circadian rhythm. These circadian rhythm disturbances, which affect up to 80% of ICU patients, may decrease the efficacy and benefits of interventions to improve cognitive function. Few intervention studies have been conducted testing circadian-based approaches to optimize timing of interventions to prevent cognitive decline in older ICU survivors. The study aims are: 1) to assess the feasibility, adherence, tolerability of morning or afternoon sessions of a computerized cognitive training intervention, and 2) to explore the role of individual chronotype on intervention usability and acceptability in older ICU survivors. Participants are randomized to one of three arms: morning computerized cognitive training sessions, afternoon computerized cognitive training sessions, or usual inpatient care. Participants assigned to the intervention groups complete daily 30-minute cognitive training sessions for up to 7 days or until hospital discharge. Wearable sensors monitor circadian rhythm patterns (via continuous body temperature and activity/sleep), and participants answer a questionnaire to determine their individual chronotype (“morning” versus “evening” circadian preference). Upon study completion, participants provide quantitative and/or open-ended feedback via surveys. We hypothesize that participants whose assigned intervention timing aligns most closely with their individual chronotype will demonstrate higher intervention adherence and will report higher tolerability and acceptability. Data collection is ongoing; results will investigate the potential of circadian-based and chronotherapeutic interventions to mitigate cognitive impairment in older ICU survivors. Additional research is needed to develop personalized interventions that integrate individual circadian rhythm and chronotherapy as targets to accelerate cognitive recovery throughout critical illness.

Climate change is increasing glacial melt worldwide, causing freshening events in marine ecosystems that rapidly decrease salinity. In the Salish Sea, summer low salinity events occur regularly from the Fraser River meltwater. This negatively impacts many organisms including sea urchins, which are resilient to other climate change impacts like marine heatwaves and reduced food availability. Previous studies found that low salinity impacts tube foot mobility and function in green sea urchins (Strongylocentrotus droebachiensis). We replicated the Salish Sea freshening events with a treatment of 20 PSU saltwater (control 30 PSU) to investigate the impacts on red sea urchin (Mesocentrotus fransiscanus) coordination and spine movement. This study implemented new techniques to quantify urchin motility to determine the negative effects that low salinity had on sea urchins over 96 hours. We quantified spine movement using image analysis to track individual spines of urchins in low and regular salinities. We also measured righting time, which is an indicator of urchin coordination. We found that urchins exposed to low salinity had significantly longer righting times and less spine movement overall. The low salinity treatment spine movement and righting time were highly correlated (p < 0.01), but not in the ambient salinity tanks (p > 0.01). We found that lower salinity waters have the potential to reduce urchin coordination and movement, which may impact urchin populations and kelp forests in the changing climate. Thus, there may be a lessened impact on the kelp forests needed to maintain ocean health.

Air pollution is a key component to understanding the Public Health of populations globally, with Diesel Exhaust Particles (DEP) being a significant contributor to traffic-related air pollution. Exposure to DEPs varies across populations and is therefore crucial to understanding the continual impacts of traffic-related air pollution on the public. Prior research has indicated that the formation of Amyloid-𝛽 (A-𝛽) plaques and activation of the  nucleotide-binding domain, leucine-rich–containing family, pyrin domain–containing-3 (NLRP3) inflammasome is linked with the development of Alzheimer’s disease (AD) later in life. AD is a form of progressive disease that impairs memory and other cognitive functions and impacts the lives of tens of millions of people globally. This study aims to confirm the linkage between exposure to DEP and memory impairment through NLRP3 inflammasome activation, utilizing an animal model to investigate a potential increase in AD later in life. We exposed male and female low-density lipoprotein receptor knockout (LDLR KO) mice chronically to inhaled DEP or filtered air as a control for 18 weeks. We then utilized the Object Location Memory (OLM) and Object Recognition Memory (ORM) behavioral tests to investigate the immediate impact of multi-week DEP exposure on short-term memory, another indicator in AD progression. Afterward, we sacrificed the mice and harvested a variety of tissues, including the brain. I conducted Immunohistochemistry (IHC) on cryosections of the exposed and non-exposed brain to assess DEP-induced AD-like brain architectural changes and to quantify the impact of DEP exposure in activating the NLRP3 inflammasome, ultimately leading to neurotoxicity, and to the development and progression of AD. Confirming the association between diesel exhaust and the NLRP3 pathway provides a potential therapeutic target in populations at an elevated risk for AD.

Parkinson’s disease (PD), the second most common neurodegenerative disorder, is characterized by Lewy bodies, pathogenic protein aggregates that include alpha-synuclein oligomers. The missense mutation p.G192R in the RAB39B gene was recently found to cause X-linked dominant PD. Loss of function mutations in RAB39B are associated with X-linked intellectual disability and autism spectrum disorder. RAB39B is a member of the human Rab GTPase family which plays a role in early autophagosome formation and is implicated in intracellular vesicular trafficking. This project investigates how defects in endolysosomal trafficking caused by the p.G192R mutation in RAB39B gene leads to parkinsonism and neurodegeneration. Because RAB39B is highly conserved, we developed a Drosophila model as human RAB39B and Drosophila RAB39 share 75% similarity in amino acid sequence, including 100% identity at p.G192 and flanking amino acids. Using CRISPR/Cas9 genome editing, we created a RAB39G196R Drosophila model that we are currently characterizing for possible neurodegenerative phenotypes. We are examining locomotor deficits and lifespan in RAB39G196R mutant flies compared to isogenic controls, as well as protein aggregation by Western blot. Complementary to the Drosophila model, we developed a human neuronal model by generating induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells (PBMC) of an affected male and similar age unaffected male family member kindred with X-linked PD due to the p.G192R mutation. We are investigating endolysosomal trafficking defects in neurons differentiated from iPSCs using antibodies specific for early and late endosomes and lysosomes. We are also examining whether insoluble ubiquitinated protein aggregates and oligomerizes alpha-synuclein are present in RAB39BG192R neurons compared to control neurons. Understanding mechanisms underlying the pathogenesis of X-linked Parkinson’s disease will elucidate the development of PD and potential novel therapeutic targets.

A product we consume daily, such as honey, may contain heavy metals like copper (Cu). Copper can get into our environment and food from urban sources such as tires, roofing materials, and generators. We therefore expect food products from more urbanized areas to show a higher concentration of copper. To test this hypothesis we evaluated copper levels in raw honey from different regions with different levels of urbanization. The honeys we tested were divided into three different categories according to their source: rural, suburban, and urban. The samples were digested by reflux with HNO₃ and H₂O₂ then it was diluted and filtered in preparation for analysis by Atomic Absorption Spectroscopy. The results suggest that the honey with the highest concentration of Cu was from an urban area, and the honey from a rural setting had the least amount of Cu. A one-way ANOVA analysis confirmed a statistically significant difference in the copper levels in raw honey from the regions (p < 0.01). The concentration of Cu in the samples of honey we analyzed ranged from 0.2 ug/g to 0.4 ug/g which is well within the recommended upper limit of 300 ug/g. Since bees collect pollen and honey from plants within roughly one mile of their hive, evaluation of the levels of copper and other metals in honey can provide a snapshot of the background levels of exposure in that area.

Acorn barnacles (Balanus glandula) are among the most common species found in the Northern Pacific Ocean, inhabiting rocky surfaces across intertidal zones. These barnacles’ distribution is attributed to various factors, including surface exposure, spatial competition, and predation. The size and abundance of barnacles may serve as an indicator of the primary abiotic and biotic processes that influence barnacle populations in highly dynamic intertidal systems. This study tests our hypothesis that higher abundance and smaller-sized barnacles will be observed at higher tide elevations, while lower abundance and larger-sized barnacles will be observed at lower intertidal elevations on the shore. In September 2023, at Friday Harbor, (San Juan Island, WA) we photographed 10 quadrats (24x24cm) at low (0m), mid (1m), and high (2m) elevations. We observed barnacle distributions at two sites along the San Juan Channel. Barnacle abundance and size were measured with ImageJ. We calculated the mean and median barnacle size at each elevation and location. Small barnacles (0-1.5mm) were predominant in the high elevations, whereas large barnacles (>3mm) dominated the lower elevations. Our results are associated with a combination of abiotic and biotic factors. Abiotic factors include greater desiccation risks in the high intertidal elevation. Biotic factors involve food availability, with larger barnacles having greater access to the nutrients coming from the ocean, along with spatial competition, where higher abundance may lead to increased competition, thereby reducing available resources for each individual. Differences between sites may be attributed to diverse characteristics unique to each location.

Cells' ability to efficiently replicate their genomes is essential for regulating chromosomal division and maintaining chromosome integrity.  Defects in any of these cellular processes may cause genomic instability, potentially leading to cancer.  The Chaos3 allele in the yeast Saccharomyces cerevisiae is a single base pair change causing an amino acid substitution in the Mcm4 protein.  Mcm4, a component of the replicative helicase, is recruited to replication origins to unwind double stranded DNA and initiate replication.  Chaos3 is in a region of MCM4 that is highly conserved across eukaryotes; while mutations in conserved regions are generally non-viable, Chaos3 is a viable allele that causes genomic instability, leading to elevated cancer rates in mice.  In S. cerevisiae, Chaos3 decreases early firing of the autonomously replicating sequences (ARS) where DNA replication begins.  Chaos3 does not affect all early firing ARSs in the genome; rather, a large proportion of origins near centromeres, thereby delaying replication of those centromeres.  Essential for chromosome segregation, the centromere is the location where spindle fibers attach to pull apart sister chromatids during cell division.  I hypothesize that this delay in centromere replication results in chromosomal instability, including the loss of a chromosome.  I am using CRISPR guided cutting directed by a customizable guide RNA to replace centromeric adjacent ARS510, that has decreased firing levels in Chaos3, with unaffected, early firing ARS305, to see if firing levels in the mutants are affected based on ARS chromosome location (i.e., proximity to a centromere) or ARS sequence.  If replacing ARS510 with ARS305 restores early origin firing in this region this will confirm the Chaos3 mutation affects specific ARS sequences rather than ARS location on the chromosome.  Furthermore, if centromere replication delays are the cause of genomic instability in Chaos3, this ARS replacement should rescue chromosome loss.

Benthic foraminifera are single-celled organisms that are a useful proxy of environmental conditions. They can provide insights into water quality, sediment composition, and ecological changes. In the past, urban bays of Puget Sound developed chemical toxicity in sediments surpassing acceptable state limits. Recent mitigation efforts have brought most chemicals within limits. However, foraminifera health parameters continue to show signs of poor environmental conditions including increased test dissolution and decreased species richness and density. Studies on individual embayments are necessary to understand local variations and utilize foraminifera in an effective monitoring program. In this study, we investigated how the percentage of dissolved foraminifera varies based on distance from shore in Elliot Bay, Seattle. We obtained grab samples through the Washington Department of Ecology collected in 2021 from multiple sites in Elliot Bay. We processed the samples and picked up to 300 foraminifera from each sample then calculated the percentage of dissolved Elphedilla hannai, the most common calcareous species in Elliot Bay. Additionally, we reviewed foraminiferal densities, species richness, and diversity for distance from shore. We found that the percentage of dissolved Elphedilla hannai increased closer to shore and with decreased depth. These results suggest a spatial influence on the health of foraminifera.  As Elliot Bay is a major maritime hub, its shorelines are heavily industrialized, and areas both shallower and closer to shore may be experiencing higher levels of anthropogenic activities. This study highlights potential water quality gradients in urbanized embayments such as Elliot Bay, contributing to our overarching aim of understanding interactions between foraminiferal health and environmental factors in urbanized embayments.

On February 24, 2022, Russia began its full-scale invasion of Ukraine. Washington state was already the home of over 42,000 Ukrainian immigrants, and since the invasion, upwards of 22,000 Ukrainian refugees have arrived. Refugees face significant challenges due to obstacles stemming from the trauma of war, displacement, resettlement, and the lack of access to essential health and social services. The Nashi Immigrants Health Board is a non-profit, community-based organization founded by public health professionals. Nashi partners with the Ukrainian community via health promotion, education, and advocacy programs and provides culturally and linguistically appropriate public and mental health services. Nashi’s warm-line was created as a caller line for Ukrainian-speaking communities, primarily refugees fleeing Ukraine to provide psychosocial support and connection to community resources. The purpose of this study is to examine the data collected during warm-line calls to identify the greatest needs and streamline resources for the community. Warm-line operators collect anonymous information such as age, zip code, primary language, the purpose of the call, and action taken are recorded. Caller data are entered into a database with specific categories and analyzed for trends and patterns of needs, which will help Nashi refine the pathways to interventions and resource allocation. We hypothesize the callers will be mainly calling about needs such as housing, health insurance, and job opportunities. We expect the navigators to provide emotional support in addition to resources, even if callers are not expecting or requesting it. The findings would help Nashi inform the Office of Refugee and Immigrant Assistance (ORIA) for future programming and quality improvement interventions. The study results are not inclusive of every need in the Ukrainian refugee population. Ongoing efforts of resource allocation would continue to evolve based on the changing needs of the Ukrainian community.

Protists are single-celled eukaryotic plankton that are abundant and diverse in the surface ocean. Many of these protist species are motile often through the use of flagella or cilia. The gene expression of protists is closely synchronized with the daily cycle of light (diel), particularly through the activity of photosynthesis-related genes. However, there has been little investigation of which motility-related genes are expressed in open-ocean protists, among which species, and whether motility-related gene expression is also coupled with the diel cycle. This study aims to investigate the hypotheses that motility-related genes are highly expressed in protist communities, particularly among mixotrophs, and that their expression is synchronized with daytime light. To investigate motility-related gene expression of open-ocean protists throughout the diel cycle, triplicate eukaryotic metatranscriptomes, within the 0.2 – 100 μm size fraction, were collected from 15-m depth approximately every four hours for three days at 158 °W, 41.6 °N, located in the North Pacific Ocean. We annotated protein families (Pfams) present in the metatranscriptomes with Gene Ontology (GO) terms. Pfams were selected based on GO terms related to motility, such as flagella, motility, and cilia. This approach resulted in the examination of the expressions of 21 motility-related Pfams.

Parkinson's Disease (PD) is a progressive neurodegenerative disease characterized by slowness or stiffness of movement and cognitive impairment. PD is characterized neuropathologically by Lewy Body (LB) aggregates that include lipids, proteins and oligomerized alpha-synuclein. Mutations in the gene glucosidase, beta acid 1 (GBA), are not only the most common genetic risk factor for PD but also accelerate the progression of the disease. We hypothesize that mutations in GBA may mediate faster spread of pathogenic protein aggregation from neuron to neuron. Our previous work has implicated GBA in extracellular vesicle (EV) regulation, suggesting a non-cell autonomous mechanism for GBA accelerating propagation of LBs. To test this hypothesis, we are first exploring how GBA influences EV biogenesis in neurons and astrocytes by examining endolysosomal trafficking in GBA mutated neurons and astrocytes, as well as controls, differentiated from human induced pluripotent stem cells (iPSCs). Our initial results indicate that neurons heterozygous for a GBA null mutation have impaired endolysosomal trafficking with enlarged early endosomes and lysosomes, while astrocytes heterozygous for GBA null do not have impaired early trafficking. These results suggest that GBA mutations differently affect different cell types in the brain and improve our understanding of how GBA influences the spread of LB pathology. I image the iPSC derived neurons and astrocytes using a confocal microscope, for endolysosomal markers and distributions. The goal of this work is to identify novel therapeutic targets for slowing PD progression. 

Neurons, the fundamental cellular units of the human brain and nervous system, are crucial to transmitting signals throughout the human body. In human anatomy, anything that obstructs the communication between neurons could lead to neurodegeneration, decline in function, disorders, and diseases. Alzheimer’s disease (AD), which affects more than 6 million people across the nation as of 2023, is one such disorder. An extensive array of research has been done investigating the underlying cause of the neurodegeneration that occurs in AD. One such theory of neuronal dysfunction, the amyloid hypothesis, points to an accumulation of a protein called beta-amyloid that is present in the brain but in some people accumulates in excess and disrupts neuronal signaling. This ultimately leads to neurodegeneration and cognitive decline. I take part in conducting the AHEAD study, a Phase 2 clinical trial, which is currently underway investigating this theory and a new drug called lecanemab. The drug is designed to remove beta-amyloid from the brain and prevent further neurodegeneration in individuals who have accumulations of amyloid and are at risk of developing AD. This is one of the first preventive clinical trials for Alzheimer's. In this review, I have explored findings from Phase 1 of the AHEAD study and described the screening process for participants for the Phase 2 trial. I have also explored the science behind beta-amyloid, Alzheimer’s disease, and treatment with lecanemab. I expected a large population to pass the screening process, but the statistics show otherwise. I dive into why this is in this project.

Plants are generally unable to move reasonable distances as single adult organisms. This lack of mobility necessitates robust pathways that allow for response to environmental stimuli which can cause changes in the plant’s morphology to adapt to their changing environment. One such trait is flowering, and it is crucial for plant survival because it allows for plants to reproduce. The vast majority of agricultural plants are flowering plants, and robust growth and reproduction of these plants is especially important for the growing human population. This experiment aims to understand the interaction between an Arabidopsis thaliana nitrogen response gene named NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1), and an Arabidopsis gene which controls flowering called FLOWERING LOCUS T (FT). NIGT1 is known to modulate plant flowering despite being a nitrogen response gene. Here, I used a Dual-Luciferase Reporter System to test whether NIGT1 proteins directly interact with the FT promoter to regulate FT gene expression. In this system, the FT promoter is used to drive expression of Firefly Luciferase rather than FT. Separately, the NIGT1 gene coding region will be highly expressed under a constitutive 35S promoter. It will also be fused to the transactivation domain of the viral protein VP16 which converts transcriptional repression into transcriptional activation, as NIGT1 is known to be a transcriptional repressor. The VP16 transactivation domain will be repeated as four tandem repeats, forming the construct called VP64. The gene constructs of interest will be inserted into Nicotiana benthamiana using agrobacterium infiltration, then the leaf material from N. benthamiana will be used for the Luciferase assay. I hypothesize that the binding of NIGT-VP64 to the FT promoter will cause increased in Firefly Luciferase production compared to the absence of NIGT1-VP64. Higher amounts of Firefly Luciferase will result in greater luminescence, which we will quantify with a luminometer.

One of the most common types of vaccines used today are subunit vaccines. Subunit vaccines consist of an antigen that triggers the adaptive immune system to create antibodies but also require a separately added adjuvant, which is a substance that induces longer-term immunity by stimulating the immune system to pay attention to the antigen. Current adjuvants are non-specific - often things like oil-water emulsions that irritate the immune system and cause inflammation in unknown ways to draw attention to the antigen. This project aims to create a more specific adjuvant by directly stimulating B cells. In order for B cells to replicate antibodies, they need a primary signal from the antigen and a secondary signal that certain ligands on T-cells can initiate. We decided to investigate whether CD40Ligand (CD40L), an immune protein present on T cells that works to signal B cells to either replicate or create antibodies, could be used to achieve this goal. The idea behind the project is to co-display CD40L with antigen on the nanoparticle in hopes of creating a more specific adjuvant. We designed 10 different versions of this nanoparticle, where we tested two versions of CD40L, the placement of CD40L, and the linker length between CD40L and the nanoparticle surface. Our preliminary results also show that our cages retain their ability to bind both antibodies and CD40 as well as activate NFkB transcription - a proxy for B cell activation. We expect CD40L-displaying nanoparticles will promote B-cell proliferation to a greater extent than the nanoparticle vaccine displaying only hemagglutinin (flu) antigen accompanied with an adjuvant like Addavax. Ultimately, we hope to examine how co-display of CD40L with antigen will change the quality of immune response and memory in-vivo in comparison to currently used vaccine adjuvants, and begin testing in-vivo in the coming quarters.

An important part of addiction recovery is degrading high value associations between drug cues and the drugs themselves. Dopamine plays a crucial role in learning, and is specifically implicated in the prefrontal cortex (PFC) and reversal learning - learning to update and change behavior when it is no longer being rewarded. Past studies have reported elevations in dopamine during contingency reversal, but the timescale of how activity of PFC dopamine neurons maps to reversal learning remains unclear. Here we investigated the activity of PFC dopamine during reversal learning in a longitudinal fiber photometry study, recording dopamine signal on a timescale of seconds. Mice were trained on a reversal learning task where they initially learned that two of four presented odors precipitated a sucrose reward in 85% of the trials while the remaining two odors precipitated the reward for only 15% of the trials. Once the learning was stable, reward probability flipped for two odors (one 85% odor and one 15% odor) and the mice had to update their behavior to the new odor/reward structure. Fiber photometry recordings were conducted during pre-reversal, reversal, and post-reversal stages of the study. Our data replicate findings demonstrating elevated dopamine release during the reversal period, centered around the 15-85 cue. Analysis of the relationship between the dopamine signal and behavior also revealed significant cue, reward prediction error, and 15-85 reversal coding in the majority of animals, suggesting a multi-faceted role for dopamine in the PFC. Given this, dopamine in the PFC may play an important mediating role in the enhancement of associations between drugs and drug cues, but does not play a clear role in contingency degradation.

Early-Stage Alzheimer’s Disease (ESAD) is characterized by the development of beta-amyloid aggregates (Aβ42) and phosphorylated tau (pTau) leading to mild cognitive decline and variable personality changes. Because specific diagnostic criteria have not yet been established for ESAD at middle age, there is no way of knowing who might be susceptible and who might be resilient to more severe neuropathology and dementia in later years. The geroscience concept assumes pathways associated with aging are also associated with age-related diseases including ESAD. Therefore, a simple skin biopsy procedure shown to predict resilience to aging in middle-aged mice should be able to predict resilience to ESAD in middle-aged mice. An adeno-associated-viral (AAV) vector system carrying pathogenic components of AD, Aβ42, and pTau, was used to induce ESAD in 23-month-old C57BL/6 mice. Before receiving the AAV vector, 2 mm ear punch biopsies were performed, and the rate of closure was measured over 3 weeks. The study ended when mice were 26 months of age, and the closure rate for each mouse was calculated and correlated with behavioral and neuropathological features of EASD. Preliminary observations will help address the question of whether the healing rate of a simple skin wound can predict susceptibility to the burden of AAV-mediated ESAD. It is expected increases in physical resilience will be associated with increased wound closure, and thus, mice with increased wound closure will have greater resilience to the onset of ESAD neuropathology. This could have highly impactful implications for the early treatment of ESAD in human patients thus preventing the irreversible and fatal progression of dementia associated with late-stage AD. In addition, DNA from skin biopsy cores could be used to obtain DNA methylation signatures for determining biological age thus providing an enriched, translationally relevant data set.
 

Rare Intracranial Tumors (RIT) are a heterogeneous group with unmet medical needs. Although infrequent in individuals, RIT affect millions of people who lack effective disease monitoring and treatment. Frequent chromosome gains and losses are common in cancer, leading to the upregulation of oncogenes and downregulation of tumor-suppressor genes, respectively. Somatic Copy Number Variations (CNVs) affect a greater fraction of the genome than single nucleotide polymorphisms (SNPs) and have been correlated to drug resistance and tumor progression, highlighting a potential prognostic value. Cell-free circulating tumor DNA (ctDNA), which are DNA fragments released by necrotic or apoptotic tumor cells can act as a noninvasive cancer biomarker, offering a potential alternative to invasive tissue biopsies. In the present work, we aim to establish the somatic CNV signature of tumor and matched ctDNA to identify non-invasive tumor-related CNVs that may serve as biomarkers for use in liquid biopsy. We performed Whole Exome Sequencing (WES) in gDNA isolated from tumor tissue and matching ctDNA of 15 patients with RITs (pituitary tumor (n=9), craniopharyngioma (n=2), and meningioma (n=4). Raw reads were assessed for quality (Trimmomatic, FastQC), following alignment against human reference genome GRCh38 (BWA). Aligned reads were sorted and subject to duplicate removal using Picard. CNV profiles will be generated using CNVkit tool. Data analysis and visualization will be performed using R and python. The most promising aspects of liquid biopsy in cancer applications are cancer screening and early diagnosis because they can lead to better survival results and less disease burden. At the end of this work, we hope to identify the CNV signatures shared between tumor tissue and ctDNA, provide novel insights into the pathophysiology of these RITs and ultimately, suggest promising biomarker candidates for liquid biopsy.

It is well documented that pet cats develop age-related diseases similar to humans with chronic age-related diseases, including Alzheimer’s disease (AD). Since pet cats live in the same environment as their owners and by extension are subjected to the same environmental stressors, older pet cats are an excellent mammalian model to study therapeutic targets to slow or reverse brain aging. However, aging within the brains of pet cats is not well characterized, partly because valid reagents have not been identified. This study was designed to test several human-specific antibody reagents that identify non-neuronal cells, aging pathways, and Aβ amyloid and phosphorylated tau (pTau) seen at autopsy in brains from patients with AD. Archived brain samples, collected from pet cats at autopsy, were graciously provided by the veterinary pathology departments at University of California Davis campus and University of Pennsylvania. Immunohistochemistry staining was done to detect: 1) Microglia, a non-neuronal inflammatory reactive cell type, using an IBA1-specific marker; 2) An inflammatory pathway using an MCP-specific marker; 3) Amyloid plaques using E610, an Aβ42-specific marker; and 4) pTau fibrillary tangles using AT8, a pTau-specific marker. A digital imaging software program was used to generate a heat map to visualize staining and quantify results. It was found that brain samples from older pet cats had increased inflammation as determined by high staining intensity of microglia and MCP1. Brains from several cats showed evidence of amyloid plaques and pTau tangles. These observations suggest that the human-based reagents tested can identify analogous cell types, pathways, and pathogenic components of AD in brains from pet cats. These prototype reagents can now be used to begin the task of characterizing neuropathology in deceased pet cats donated to the Cat Alzheimer’s disease Program at the University of Washington.

The use of opioid drugs for pain management in postoperative settings has been widespread since the 1860s. However, the risk factor for developing an opioid use disorder (OUD) has increased substantially with its continued use, with addiction rates of more than 10% for those taking opioids. An obstacle to abstinence in opioid addiction are the adverse side effects that occur during cessation of drug use once dependence has formed, including nausea, anxiety, vomiting, and depression. The Nucleus Accumbens (NAc) is part of the mesocorticolimbic reward pathway. Decades of pharmacological studies demonstrate that nearly all abused drugs evoke dopamine release within the NAc, thus altering innate systems for how reward is processed. The activity of NAc neurons is strongly regulated by efferent excitatory input from numerous brain regions. The paraventricular thalamus (PVT) a relatively understudied brain region, regulates behavioral responses to reward and aversive stimuli as well as to drugs of abuse such as morphine. Our preliminary data demonstrate that the activity of these projections is highly regulated by the Cannabinoid 1 Receptor (CB1), which mediates the primary psychoactive effect of cannabis. This is particularly relevant on account of recent clinical findings demonstrating that activation of CB1 can ameliorate the aversive effects of opiate withdrawal. Using fiber photometry (which uses fluorescence emission of the calcium sensitive fluorophore, GCaMP, as a proxy measurement for neural activity), I have shown that this circuit is activated by aversive stimuli and inhibited by rewarding stimuli. Furthermore, treatment with morphine can attenuate the pain-induced activation of this circuit. However, whether cannabinoids can influence this circuit's activity to reduce withdrawal symptoms remains untested. Our research will contribute to our understanding of the neurophysiological basis for opiate withdrawal and how cannabinoids could represent a novel class of therapeutics for the treatment of opiate use disorder.

Alzheimer's disease (AD) is a neurodegenerative age-related disease characterized by the presence of amyloid-beta aggregates and hyperphosphorylated tau tangles. It has been well documented that cognitive decline and changes in age-related pathways are associated with disease progression. Mitochondria play an important role in degradation of amyloid protein through a mitochondrial protein-mediated quality control system. This pathway can break down with increasing age and lead to the overwhelming presence of amyloid, disrupting normal mitochondrial activity. This damage leads to the formation of more Aβ plaques and neuroinflammation, contributing to the pathogenesis of AD. Mitochondrial regulators may be potential therapeutic drug targets but models are needed to help identify and characterize them. In this regard, an Adeno-Associated-Viral (AAV) vector was used to induce AD protein expression in the brains of old mice. 40 Male and 40 Females mice aged 24 months were infected with either the AAV-AD or AAV-SHAM vector and given 3 months for expression of the proteins to build. Mice were euthanized and brain tissue collected into formalin, with the hippocampus cut into slides for immunohistochemistry (IHC). Data generated from these mice has shown trends in decreased synaptic integrity, increased inflammation and DNA damage associated with expression of the vector proteins. Utilizing the same model, this experiment aims to understand how expression of the AAV-AD proteins may be associated with known roles of mitochondria and characterized pathways in the early stages of AD. IHC was performed using antibodies specific for PITRM1, a mitochondria protein degradation regulator, and PINK1, responsible for mitochondrial-mediated cell death (mitophagy). Imaging software “ImageJ” will be used for quantitative analysis of the stains. This study will help clarify an association between varying levels of AD protein expression and mitochondrial regulation, providing valuable information for enhancing therapies aimed at preventing the progression of early stage AD.

Resilience in Alzheimer's Disease (AD) is defined by the difference between a person's expected and actual rate of cognitive decline given the severity of their disease. However, the mechanisms behind resilience are still unclear and I wanted to see if the anatomy of the brain over the course of AD could offer any clues. To accomplish this, cognitive tests and brain scans were obtained from patient data taken at Harborview Medical Center. Brain tissue atrophy in regions of interest were defined and combined into two measures. The first--biological subtypes--is whether the disease primarily affected the limbic regions or the cortical regions, while the second is left-right asymmetry. I found that resilience correlated with biological subtypes but not asymmetry. This suggests a way for us to predict resilience to better personalize treatment and eventually find ways to increase resilience.

Alzheimer's Disease (AD) is incredibly complex such that development of neuropathology and cognitive impairement is driven by multiple pathways. Therefore, targeting these pathways simultaneously, could provide a more effective treatment for AD compared to any single drug. Rapamycin, acarbose, and phenylbutyrate each have independent but overlapping effects on multiple pathways involved in cellular respones to pathogenic beta amyloid such as inflammation, glucose homeostasis, synaptic integrity, autophagy, and DNA damage. To test the safety and effectiveness of a cocktail of these three drugs, a proof of concept experiment was undertaken in transgenic mice carrying mutations for genes associated with early onset AD (5xFAD). These mice express neuronal amyloid plaques, a major feature of AD neuropathlogy. Transgenic and wild type mice were given either a control feed or feed containing the drug cocktail starting at 4 months of age and continued until 12 months of age. Medicated transgenic mice showed significantly less cognitive impairement in a spatial navigation learning task and reduced amyloid plaque levels in the hippocampal brain region compared to untreated transgenic mice. Immunohistochemistry will be used to identify specific biomarkers for inflammation, synaptic integrity, glucose homeostasis, autophagy, and DNA damage in the hippocampus of treated and untreated transgenic mice. Observation from this study will suggest the need to conduct additional preclincial experiments testing this specfic drug combination for a successful approach to treat Alzheimer's Disease. 

Addiction is characterized by the compulsive use of substances despite adverse consequences, a process closely linked to dopamine-induced changes in the Nucleus Accumbens (NAc) and its role as the brain's "reward center." The NAc integrates information from various brain regions, including the Paraventricular Thalamus (PVT), to produce motivated behaviors. Recent studies have identified the PVT, especially its anterior segment (aPVT), as a critical hub in addiction neurocircuitry, but findings have been inconsistent, likely due to the PVT's heterogeneity and the specific neurochemical and anatomical properties of its connections to the NAc. Prior research has shown that aPVT neurons, identifiable by neurotensin expression, send excitatory projections to the NAc, which are modulated by endogenous cannabinoids (eCBs). These interactions suggest a complex regulatory mechanism. Preliminary experiments used techniques including transsynaptic viral tracing and in vivo calcium imaging, to study the activity dynamics of NAc neurons, particularly those expressing Proenkephalin (PENK) and receiving aPVT inputs, during reward-seeking tasks. I propose to extend these findings by employing a multidisciplinary approach that combines experimental neuroscience with sophisticated computational analysis. By applying dimensionality reduction techniques, clustering algorithms, and machine learning models to neural and behavioral data, I aim to map the functional connectivity within the NAc and elucidate the roles of specific neuronal ensembles in reward-seeking behavior. This comprehensive analysis will not only clarify the neurobiological underpinnings of addiction but also contribute to the development of targeted therapies for addiction and related disorders, leveraging the unique intersection of computational neuroscience and behavioral analysis.

The composition of metropolitan governance has many effects on land use decisions, budget allocations, housing development, transportation planning, and racial, economic, and social equity in urban areas. However, there has been little academic inquiry into the effect of regional governance structure on transportation accessibility. This paper seeks to examine statistical linkages between regional governance fragmentation and trends toward and away from greater transportation accessibility in metropolitan areas. I perform a comparative statistical analysis of 47 of the 50 largest Metropolitan Statistical Areas, examining census data from 2002 to 2022 and transit accessibility data from the University of Minnesota Accessibility Observatory from 2014 to 2021 to examine this relationship. The causal factor I investigate is metropolitan governance fragmentation, which I capture through a Governance Fragmentation Index (GFI). The dependent variable, transportation accessibility, is captured through an Accessibility Gap Index, which categorizes transportation access through accessibility levels throughout each Metropolitan Statistical Area, utilizing data from the Accessibility Observatory from 2014 to 2021. My analysis controls for potential confounding variables, such as geographic area, population size, poverty levels, and region. I expect to find that lower levels of governance fragmentation in a Metropolitan Statistical Area will be associated with greater gains in transportation accessibility. Whether or not a significant relationship is identified, the research conducted will contribute to literature and ongoing research surrounding metropolitan governance and transportation accessibility.

Neuroscience research relies heavily on cell counting to assess brain injury and evaluate neuroprotective treatments. While manual methods (i.e. hand counting) have been used traditionally, automated programs offer the potential for standardized and error-free data analysis. In the context of studying hypoxic-ischemic encephalopathy (HIE), a prevalent brain injury in infants, we aimed to assess the accuracy of an automated cell counting program in an in vitro slice culture brain injury model of injury and treatment. Code templates from ImageJ/Fiji were taken and modified using ChatGPT, and other snippets were used and modified from online forums like GitHub. The program searches through folders/subfolders for images, converts them into a binary image based on fluorescence threshold data (used to stain cell nuclei), applies the ImageJ function “watershed” that breaks larger groups into smaller groups, runs the “analyze particles” function which outputs a total cell count based on the size and circularity of the cells, and then saves the final image. Fluorescence threshold, cellular size, and circularity values were determined before data collection by adjusting the values to best fit the final image of a random slice. The settings were then kept consistent within studies. Preliminary results show the program’s high accuracy and precision, with consistent results across caffeine and Azithromycin treatments in our in vitro injury model. Despite yielding higher counts than manual methods, the program remained consistent across models. Validating this automated method represents a significant advancement in research methodology. These programs offer standardized data collection, error elimination, and faster analysis compared to manual counting, potentially saving time and resources for labs. Current limitations in our research involve differentiating between healthy and dead or dying cells, which would be an important future step for automated cell counting.

The fallopian tube function is central to several pathophysiological processes from facilitating fertilization to initiating ovarian cancer. However, existing models to study these functions are limited in relevance to the human condition due to the available conventional cell sources and culture systems. Many make use of mouse models that do not naturally develop pathologies such as ovarian cancer and lack the ability to replicate human genetic variation. Others use traditional 2D culture systems that have been shown to be poor in maintaining fallopian tube epithelium (FTE) secretory and ciliated function. Here, we propose to develop a novel in vitro model of FTE that is easy to manipulate and better mimics the in vivo environment through use of induced pluripotent stem cells (iPSC) as a cell source and a scaffold-based microfluidic culture system. We have modified an existing protocol and found that 3D culture allows for generation of organoids expressing FTE markers faster and at a higher rate. Additionally, I have developed a prototype device with a lumen and assessed cell viability and behavior of seeded immortalized FTE to establish the device. Further work can be done to elucidate drivers in FTE maturation through assessing primary FTE function in the device, and incorporation of iPSC-derived FTE cells into the device for studies on functional maturation.

The use of deepfake technology to produce pornographic content (deepfake pornography) is a form of sexual exploitation and violence of those most vulnerable to sexual harassment in our society: women and girls. Deepfake pornography, sometimes called synthetic pornography, refers to the process of manipulating an image by adding sexually explicit content. A 2019 study conducted by Deeptrace Labs found that 96% of deepfake technology is used to create non-consensual pornography targeting women and girls. As technology develops, US privacy laws fail to keep pace, leaving online predators unchecked. While there is no federal regulation on the use of deepfake technology, in the past few years, nine states including California, Texas, and New York have passed laws governing their use. The most substantial of which is California's AB 602, passed in January of 2023, which banned the distribution of pornographic deepfake images and videos made without consent and which may result in the defendant paying up to $150,000 in statutory damages. This literature review examines the rise of deepfake pornography used against women and girls, and the impact it has on its victims. It also compares how regulators in the US and certain other jurisdictions are addressing this issue. This review brings awareness to the growing online predatory activity facilitated through deepfake technology and the need for swift action to address this crisis on a nationwide scale.

While environmental writing is nothing novel, environmental journalism as a beat and research area is relatively recent. The available literature on the field provides insight into the challenges environmental reporters face and what their environmental backgrounds in the field are, but little research details how they respond to challenges and why they originally chose the beat. This research examines how environmental journalists respond to the challenges they face, what values they attribute to the beat, and why they chose to write about the environment. My hypotheses are that these reporters have had influential experiences in nature; they see their work as a form of social activism; and they rely on their social connections as a form of support. For my sample, I first used random systematic sampling, followed by purposive sampling to reach targeted demographics, such as gender and race. I conduct semi-structured, in-depth interviews to collect my data, with a goal of at least 15 interviews or until saturation. So far, I have conducted five interviews that average around 45 to 60 minutes each. Most of them grew up as outdoorsy people, all of them see their work as important, and most find that talking to someone about challenges they encounter is helpful. Through more interviews, I hope to begin recognizing strong trends in responses to compare to my hypotheses. In addition to filling the gaps in the literature on environmental journalism, this research provides these reporters with a chance to talk about their experiences and challenges. Additionally, building on this beat as a research area could help provide data to create a meaningful support network for environmental reporters. As climate change intensifies and more people feel its effects, it’s imperative that these journalists feel supported enough to continue highlighting climate solutions and inequities to advocate for climate action.

Within the mainstream misogynistic and homophobic narrative of Chinese society, radical feminists and lesbians face significant challenges. But the issues each of these groups face and their communities are separate and seldom intersect. This project addresses this gap between lesbian and feminist communities while aiming to comprehend how individuals within them perceive themselves and each other. It also explores the possibilities for solidarity and greater communication between the lesbian community and the radical feminist community in China. Through interviews with Chinese radical feminists, lesbians, and lesbian feminists, this project aims to bridge the divides between Chinese lesbians and radical feminists and to facilitate discussions about negotiating different aspects of one’s identity.Both lesbians and radical feminists are engaged in reconstructing intimate relationships. With the current rise of feminism in China, lesbians are reevaluating gender roles in intimate relationships. At the same time, some radical feminists are exploring lesbian feminist ideas, such as gender separatism. This project draws on theories from the second wave of the feminist movement in the U.S and queer theories to highlight important conversations in contemporary China with the goal of stimulating discussions on envisioning intimate relations beyond the framework of a heteropatriarchal society. Preliminary analyses of interviews conducted in winter 2023 show that many radical feminists and lesbians have struggled to assert their identities and find belonging in a community. Additionally, the lack of platforms and offline spaces for gender and sexuality communities leads to the isolation of individuals. The project to be presented will offer a more detailed interpretation on the reasons behind such isolation and miscommunication between the two groups. On a broader level, this project aims to offer a perspective on how we can understand the relations between people and power dynamics in this current world.

The largest scale structure in the universe creates a cosmic web. Nodes of the web are connected by mega-parsec scale filaments of warm gas, galaxies, and cold dark matter. Cosmic filaments are typically assumed to form and cool uniformly in many cosmological models. Recent works suggest that the internal structure, particularly with regard to the cooling mechanism, may be more complex. Gas clouds larger than a characteristic length appear to shatter as they cool below 106 K, fragmenting into smaller cloudlets. Other factors may also contribute to a more turbulent and irregular structure. The behavior of these filaments has implications for many of the issues at the forefront of astronomy. Cold dense clouds could create Lyman limit systems in the early universe, restricting the the distance that ionizing photons can travel. Further, the structure of these filaments may influence the mass of dark matter and constraints on cosmological models. To study these systems, I am simulating the formation of a single cosmic filament using a cosmological hydrodynamics code. Together with my mentor, I derived functions for the initial displacement and velocities of the particles from theory to create the desired collapse of matter into a filament. I then run the simulations with these initial conditions on a supercomputer, enabling simulations with tens of millions of particles. The simulations have mass resolutions that have not been previously achieved, allowing us to better understand the internal behavior. Preliminary findings indicate that there is indeed a complicated structure within the filaments.

Eelgrass (Zostera marina) is a marine flowering plant that provides important ecological, environmental, and economic services in the Puget Sound. Z. marina reproduces both asexually and sexually; however, the cellular regulation behind each mode of reproduction is poorly understood. Establishing Z. marina’s regulation behind sexual reproduction will improve predictions of Z. marina’s resilience to anthropogenic pressures. FLOWERING LOCUS (FT) is a highly conserved gene that promotes floral development in flowering plants and is well-characterized in the model organism A. thaliana. As a marine flowering plant, we hypothesized that a homologous, functionall FT exists within Z. marina. We identified 13 candidate Z. marina FT homologs (ZmFT), and from analysis of relative flowering time, 5 homologs of interest emerged: 2 that promote flowering, 2 that inhibit flowering, and 1 that has striking sequence conservation to A. thaliana FT, yet has no observable impact on flowering. To determine how intracellular distinctions alter the function of these respective Z. marina FT homologs, I am currently investigating putative protein-protein interactions of the ZmFT homologs with components of the A. thaliana floral activating complex, such floral promoting transcription factors, and scaffold proteins . I can characterize these protein-protein interactions using Yeast Two-Hybrid assays (Y2H) and BiFC fluorescent microscopy In which protein-protein interactions between ZmFT and A.thaliana floral complex proteins yields either yeast strains with conferred prototrophy, in Y2H, or a fluorescent signal, in BiFC. From my Y2H and BiFC work, I will characterize interactions of the ZmFT homolog proteins, with known components of the A. thaliana flowering pathway. The results of this study will help define how Z. marina regulates flowering onset and sexual reproduction. 

Tuberculosis remains a global public health threat due to the rising number of multi- and extensively drug resistant strains of the causative pathogen Mycobacterium tuberculosis. Development of novel drugs and an understanding of their resistance mechanisms is urgently needed. Aminothiazoles (AmT) are potent molecules with killing activity against M. tuberculosis; these compounds act as copper ionophores and target a key enzyme (enolase) by displacing its Mg²⁺ co-factor, a substance required for its activity, with Cu²⁺ imported by the compounds. Spontaneous mutations in an essential protein export system (the Esx 3 Type VII secretion system) confers resistance to AmTs. My research focuses on understanding how mutations in the secretion system cause AmT resistance. We hypothesize that copper imported by AmTs could disrupt other metallo-proteins including EccA3, a key ATPase of the of the Esx-3 secretion system that hydrolyzes ATP into ADP and inorganic phosphate, and that resistance mutations (e.g. E237K) reduce Mg²⁺ co-factor displacement by Cu²⁺. To test this hypothesis, I expressed wild-type (WT) EccA3 and mutant EccA3 [E237K] proteins in Escherichia coli BL21(DE3) expression strain and purified the proteins via Ni-NTA His-tag chromatography. Subsequently, I measured the activity of the purified EccA3 (WT) and EccA3 [E237K] proteins via an ATPase assay based on colorimetric detection of free inorganic phosphate released by ATP hydrolysis. I aim to understand whether copper inhibits EccA3 activity through this assay, anticipating that copper reduces EccA3 (WT) ATPase activity while EccA3 [E237K] ATPase activity is unaffected. Thus, my work will provide an avenue for understanding AmT resistance in M. tuberculosis.

Major Histocompatibility Class I (MHC) Molecules serve as a window into the cell, whereby T-cells can use their T-cell receptor to recognize foreign peptides presented on the MHC of a cell and induce apoptosis. Unfortunately, for diseases such as cancer, cancerous mutations may only be a single residue different from the native protein, resulting in similar mutant and wild-type peptide-MHCs. This small difference often results in negative selection of T-cell receptors that recognize mutant peptide-MHCs, leading to an absence of T-cells that can target cancer cells. This issue motivated us to use de novo protein design to generate binders with a high level of specificity between mutant and native peptide-MHCs. Using deep learning based protein design methods such as RFdiffusion and ProteinMPNN, we have generated promising in silico designs against a range of target peptides and MHC alleles. After selecting our top designs, we tested them using yeast surface display against our target MHC molecules with peptides loaded from KRas, PIK3CA, MAGE, and TP53 mutants. We observed binding events to all targets; some designs also had specificity to their respective mutant peptide-MHC over the wild-type peptide-MHC. After further work we have shown that the same design scaffold can bind to multiple peptide-MHC targets after slight redesign, similar to native T-cell receptors, holding promise that we could easily and quickly repurpose these scaffolds for new targets. Following these results we will incorporate our binders into T-cells as chimeric receptors and test for the ability of our binders to activate T-cell signaling and cell killing. This method of targeting peptide-MHC molecules is promising as a novel and rapid way to target cancer.

Toll-like receptor 4 (TLR4) is an immune protein which binds lipopolysaccharide (LPS) present on the outer membrane of Gram-negative bacteria and activates the innate immune response. In mice, an mRNA splice variant composed of only the extracellular domain of TLR4 was shown to encode a soluble product (sTLR4) capable of inhibiting inflammatory response to LPS. sTLR4 has been recovered from human saliva and demonstrated to dampen the production of pro-inflammatory cytokines by macrophages. Prior work showed that TLR4 was also present in endometrial glands, uterine tube epithelia and endocervical glands. However, there are no published studies exploring the presence or role of sTLR4 in lower genital tract secretions. We tested primary female genital epithelial cells’ supernatants as well as human endocervical cytobrush and vaginal swab samples for the presence of sTLR4 by using a chemiluminescent immunoassay. We found sTLR4 in cervicovaginal secretions, with increased concentration of sTLR4 present in participants with endocervical ectopy and in those sampled during the proliferative phase of the menstrual cycle. Supernatants from endocervical cell lines possessed higher levels of sTLR4 than those derived from ectocervical or vaginal cells. sTLR4 concentration was not correlated with the presence of bacterial vaginosis, age, the concentration of common vaginal Gram-negative bacteria or with genetic variation in the TLR4 locus. By western blotting, we demonstrated that sTLR4 is composed of a ~100 kDa polypeptide, corresponding to the entire TLR4 ectodomain. In a reporter monocytic cell line, we showed dose-dependent inhibition of the LPS/Interferon-regulatory factor (IRF) pathway when LPS was preincubated with endocervical cells’ supernatants. These results point to an unappreciated form of innate immune regulation in the cervicovaginal niche, which could potentially open new avenues for understanding inflammatory disorders such as cervicitis and pelvic inflammatory disease.

Biofilm is a community of bacteria enclosed in an extracellular polymeric substance (EPS) attached to a surface. Inside the biofilm, bacteria can collaborate to increase their survival. The EPS also protects bacteria from drug penetration, leading to increased antibiotic resistance. Therefore, biofilm formation is often linked with chronic bacterial infections. Pseudomonas aeruginosa is an opportunistic pathogen that often causes chronic lung infections in cystic fibrosis patients. It is also a common model for studying biofilm formation. The initial step for biofilm formation is bacteria attaching to and sensing a surface. Upon surface contact, P. aeruginosa may produce cyclic adenosine monophosphate (cAMP), which is a universal second messenger that regulates cellular functions in both eukaryotes and prokaryotes. In P. aeruginosa, cAMP is synthesized by two adenylate cyclases, CyaA & CyaB, and degraded by a cAMP phosphodiesterase, CpdA. cAMP is a key regulator for P. aeruginosa virulence by upregulating the production of the type III secretion system, the type II secretion system, and the type IV pili. However, recent observations in our lab suggest that cAMP may also contribute to the homeostasis of the cell envelope. To investigate this phenomenon, I used microscopy to characterize the cell morphology of strains with different cAMP levels and found that increased cAMP levels lead to longer cells. I also found that high cAMP strains are more sensitive to êžµ-lactam antibiotics specifically, while low cAMP strains become more resistant. Ongoing work includes characterizing the genetic factors that connect cAMP and êžµ-lactam sensitivity, as well as using microscopy to determine changes in cell envelop induced by cAMP. Overall, this work reveals an important role of cAMP in bacterial physiology and provides insight into the complex relationship between virulence and antimicrobial resistance.

Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an opportunistic pathogen of wounds, cornea, and the Cystic Fibrosis lung. P. aeruginosa is also a model organism for the study of bacterial biofilm formation. Biofilms are multicellular communities that form from bacterial growth concomitant with the production of extracellular polymeric substances (EPS). EPS includes polymers such as polysaccharides, DNA, and proteins; these polymers provide structure and protection to the biofilm cells. Proteomics experiments by the Parsek Lab and others have demonstrated that a notable component of the biofilm matrix are the secreted proteases. Secreted proteases have defined roles in virulence and nutrient acquisition, but their role in the biofilm matrix of P. aeruginosa has not been explored. I hypothesize that these secreted proteases recycle nutrients, remove cell waste, and protect cells from host immunity. To test my hypothesis, I generated a mutant strain of P. aeruginosa that lacks the six major secreted proteases. While we see that loss of the proteases does not impact planktonic growth, preliminary data suggests that loss of proteolytic activity results in moderately increased biofilm formation. Using a general proteolysis assay relying on casein hydrolysis, I have determined the relative contribution of each of the six proteases to the total proteolytic capacity of P. aeruginosa in planktonic growth. I will further test the impact of the proteases on biofilm growth in different growth environments, including under flow conditions and in artificial sputum medium. I will also assess which proteases contribute the most to proteolysis during biofilm growth. My work fits into a growing body of literature that suggests that the biofilm matrix is not an inert scaffold, but is instead a dynamic and active network.

The retina is a unique neuronal structure in the eye that facilitates vision. Many diseases cause the death of retinal cells and this can lead to blindness. Frogs and fish have retinal stem cells that can repair the retina after retinal cell death; these stem cells are concentrated in a region called the ciliary marginal zone (CMZ). It was thought that humans lack these cells; however, we have discovered a region of the retina that has some features of the CMZ. We call this the Late Proliferative Zone (LPZ). One of my research goals was to determine whether the LPZ in humans also contains retinal stem cells that could be harnessed to repair the injured retinae. To start, I measured the area of small cuttings of fetal retinal tissue grown in culture, called retinospheres (RSs), over time and identified a window from 250-325 days gestation in which the LPZ of the human retina continues to grow after the rest of the retina is quiescent. This result shows that the cells of the LPZ can make new retinal cells much later than we thought, supporting the idea that these are retinal stem cells. My second goal was to find factors that can stimulate the growth of these cells. I tested several factors known to be important for the stem cells in frogs and fish. I found the effects of these factors on the types of neurons made by the LPZ. In sum, investigating different ways to manipulate the LPZ provides the field with insight into what is needed to regenerate cell types lost in blinding diseases.

The Boomplaas cave is located in the Cango Valley in South Africa and has been the site of many recent archaeological inquiries. The cave contains archaeological deposits spanning the Middle to Late Stone Age. Cave environments, like Boomplaas Cave, are ideal for the preservation of sediment deposits and can tell us about past environments and changes in human occupation patterns over time. Archaeologists can use the magnetic susceptibility of sediments as an indicator of human occupation intensity and climatic changes. Activities such as burning increase the magnetic susceptibility of soil, and warmer climates will result in higher magnetic susceptibility of soil compared to colder climates. We used an Bartington MS2 meter to measure the magnetic susceptibility of 44 sediment samples collected from the cave to infer climatic changes and occupational patterns over time. Our results show clear periods of more intensive human occupation. With this information, we can provide a more comprehensive understanding of variation in the intensity of hominin occupation within this region of South Africa.

 The Amazon rainforest is one of the most biodiverse regions on this planet and home to thousands of species of butterflies. Our pilot study aimed to investigate correlations between vegetation diversity and temperature and butterfly species richness in the Madre de Dios region of southeastern Peru. This study was conducted across three sites of differing plant diversity, including a monoculture orchard, a mixed orchard, and a rainforest. We hypothesized that there would be a strong positive correlation between species richness and vegetation diversity, resulting in high species richness in the rainforest. We also predicted that each species would only be found within one site, as most butterflies rely on specific plant species for reproductive purposes. Finally, we hypothesized that the hottest times of day would have the least amount of butterfly activity. By attracting butterflies with baited banana leaves, we were able to record an array of species during multiple, daily 45 minute observational sessions. After classifying photographs of butterflies during our sessions to morphospecies and averaging species richness, we found that the sites with higher vegetation diversity had a wider range of species. Most species demonstrated specialist behavior, found only in one site. Out of 26 morphological species, only three were observed at more than one site. Limitations in our sample size made any data surrounding behavior across a temperature gradient inconclusive. By critiquing this pilot study and analyzing its small set of data, we suggest protocols for future research on butterfly species richness and activity.

Going into an academic career is a path frequently chosen by archaeology graduate students after their graduation. Job listing websites often serve as the first place for these students when seeking academic positions. It's crucial to understand the expectations of institutions, given the limited number of available positions and the abundance of candidates. This study examines tenure-track job advertisements over the past decade to gain insights into the academic job market for archaeologists. Using data from the community-edited Academic Jobs Wiki for Archaeology, we examine the evolution of the academic job market over time. We studied the text of 449 job ads posted from 2013-2023. Our analysis focuses on shifts in archaeological topics and methods requested in job ads. We investigate whether the burden on applicants has changed over time: do institutions request more information and documents from applicants at the initial stages of application, compared to a decade ago? We also examine whether there is an increasing trend in job advertisements highlighting diversity and inclusivity, thereby encouraging a broader range of applicants. Additionally, we assess the influence of socio-political factors on the changing focus of research topics in the field.
Our data analysis indicates an uptrend in the complexity of application requirements and a more pronounced emphasis on diversity and inclusivity in job advertisements. This research aims to assist current and future archaeology students and graduates in better understanding the job market and the requirements of employers, thereby aiding them in effectively preparing for their applications for positions in archaeology.
 

General anesthesia (GA) is administered as a sedative in nearly 60,000 surgeries daily in the United States. Yet, there is a very limited understanding about how GA impacts brain activity, leading to induced loss of consciousness and pain sensation. Preliminary work in the Heshmati lab has highlighted key subcortical structures that are engaged during anesthesia, but it remains unclear how activity in these regions and across the brain regulates awareness or pain sensation as anesthesia is induced (“induction”), maintained at a steady state (“maintenance”) and removed (“emergence”), as is done during surgeries. My work aims to identify the neural circuits that regulate the loss of consciousness and pain sensation during GA by recording local field potentials (LFP) from mice as they undergo volatile anesthetic isoflurane (ISO). During LFP recordings, I will insert small electrodes into highlighted regions of interest, to capture low-frequency extracellular voltage signals generated by the synchronized activity of nearby neural populations during the three periods of interest: induction, maintenance, and emergence from isoflurane GA. I will analyze the amplitude fluctuations and frequency patterns to identify synchronized oscillations within subregions and assess the level of synchrony, or coherence, across different regions. Given previous findings on the shared and opposed involvement of subcortical regions in pain and anesthesia, I expect to observe coherence among some of the regions, such as the amygdala and hypothalamus, but potentially anti-correlation within specific subsections, such as central vs. basolateral amygdala. Through these experiments, I will be able to monitor the effects of isoflurane anesthesia through a temporally-defined electrophysiological lens, capturing real-time activation dynamics of large neural populations across induction and recovery from anesthesia. Thus, my research aims to further develop our understanding of the brain under GA, by providing novel insight into the neural circuits regulating wakefulness and pain during surgical procedures.

Lipotoxicity in cells occurs when lipids in biological tissue accrete to a toxic level. This toxic buildup is associated with obesity and type 2 diabetes, two of the leading causes of death around the world. Various studies have induced obesity in mice through a diet consisting of high levels of saturated fats. Some of these studies also investigated the effects Adefovir Dipivoxil, an antiviral and inhibitor of mitochondrial DNA replication, had on these obese mice. My research investigates fibroblasts that have been grown in a high-lipid environment and how Adefovir Dipivoxil affects these cells. We hypothesized that administering Adefovir to these cells would halt apoptosis and prevent further progression of lipotoxicity by stabilizing levels of triacylglycerol synthesis. To test this, I induced lipotoxicity in the cells using palmitic acid, a saturated fatty acid. Next, I treated the cells with Adefovir Dipivoxil. To measure the efficacy of the drug, I used a staining kit to measure the ratio of live to dead cells before and after administering the drug. Furthermore, I used a dye-based assay to measure the intracellular triglyceride levels before and after treatment. In addition to treating fibroblasts with palmitic acid, I treated a new set of fibroblasts with oleic acid, an unsaturated fatty acid, to determine how Adefovir acts on these cells. Data from this research will contribute to further understanding the mechanism of lipotoxicity on various cells, as well as the role that mediators of mitochondrial function like Adefovir Dipivoxil could play in treating lipotoxicity. On a broader scale, we hope that this research will provide insight into future treatments for obesity and type 2 diabetes.

Alzheimer's Disease (AD) impacts over 6 million people in the U.S, but there are currently no fully effective treatments. Ageing is the biggest risk factor for AD and is associated with cellular changes called senescence. Cellular senescence describes a natural process in cells, leading to cell cycle arrest and metabolic changes due to insults from aging/disease processes. Factors contributing to senescence include DNA damage, and others. A risk factor in neurodegeneration is the ageing of microglia- our brain's immune cells that maintain a healthy brain. Senescent microglia express a senescence associated secretory phenotype- a combination of inflammatory proteins released into their environment- that enhances neurodegenerative processes. My project investigates the relationship between microglial senescence and AD by comparing the levels of senescence markers in AD brains, healthy young brains, and aged brains. I hypothesized that AD brains will contain the greatest amount of senescence markers, followed by aged brains, then healthy young brains. I performed immunohistochemistry for p16Ink4a and gammaH2AX (two robust senescence markers) on 10 human individuals (5 male/5 female per cohort) who donated their brain post-mortem. p16Ink4a is involved in cell cycle regulation and gammaH2AX signals DNA damage. The brain samples were also stained with Iba-1 to identify microglia. A confocal microscope imaged the samples and data was analyzed using the IMARIS software and ImageJ. Senescence markers were quantified in each cohort and localized in microglia or non-microglia cells. I expect to see the greatest amount of p16Ink4a and gammaH2AX in AD brains (specifically AD microglia), with the least amount in healthy young brains. I also expect co-localization of gammaH2AX and p16Ink4a in my samples. Understanding the relationship between microglial senescence and AD pathology could aid in finding methods to target cellular senescence. Slowing down this process could be a usefull tool in decreasing the progression of AD.

Dopamine (DA) producing neurons of the ventral tegmental area (VTA) in the midbrain regulate reward association learning and motivation. These DA neurons are modulated by neuropeptides and can be separated into distinct subpopulations based on differential gene expression, regulation of activity, and projection patterns. But how these different patterns are established and contribute to distinct functions of DA subpopulations remain poorly understood. One potential key component for these neuropeptides is the transient receptor potential canonical (TRPC) channels. Specifically, we identified the gene encoding TRPC type 6 channel (Trpc6) as having enriched expression in the VTA DA neurons. To determine whether Trpc6 is differentially expressed in VTA DA subpopulations, I utilized the quantitative, multiplexed in situ hybridization methods. Using wild-type mice, I probed for the expression of tyrosine hydroxylase (Th), a marker of all DA neurons, and Trpc6 as well as markers of two subpopulations, corticotropin releasing hormone receptor 1 (Crhr1) and cholecystokinin (Cck). The analysis showed that Trpc6 expression is significantly higher in the Crhr1 subpopulation, of 81%, than in the Cck subpopulation, of 66%. Because neuropeptides like neurotensin increase calcium concentration in DA neurons, we hypothesized that TRPC6 contributes to these neuropeptide-evoked calcium signals. To investigate the role of TRPC6 in DA signaling, I used a viral-based CRISPR/Cas9 approach to induce selective mutagenesis of TRPC6 in specific DA subpopulations. Then, I assessed the calcium responses of subpopulations to neurotensin by measuring the amplitude and neurotensin-evoked oscillations using acute brain slices. We expect the calcium responses to decrease more in the Crhr1 subpopulation than in the Cck subpopulation compared to the control as the Crhr1 population has higher Trpc6 expression. By elucidating the role of TRPC6, we hope to contribute to discovering pharmacological interventions for diseases caused by dopaminergic system dysfunctions such as Parkinson’s disease and substance use disorders.

The Campanian stage of the Cretaceous (~84–72 million years [Ma]) was the zenith of dinosaur diversity. Western North America is highly fossiliferous and preserves Campanian-age rock units throughout the Western Interior Basin. Most studies that investigated dinosaur diversity from this interval used data obtained from macrosites (e.g., skeletons), whereas few have investigated vertebrate microfossil sites. Vertebrate microfossil sites are a rich source of data on biodiversity (e.g., taxon richness, relative abundance) and how it changes through time. The Judith River Formation of north-central Montana is rich in vertebrate microfossil sites, preserving 4 million years of the Campanian (~79–74 Ma). Here we aim to observe patterns of dinosaur diversity in the Judith River Formation by quantifying dinosaur taxon richness and relative abundances based on dinosaur teeth from two stratigraphically and temporally separated microfossil sites. These sites are the lower Makela-French 1 (~77 Ma) and the upper Clamfetti (~75 Ma). Presently, we have 300 specimens out of a planned 400. We hypothesize that changes in diversity and abudance occurred between these two sites. Our preliminary results reveal a change in dinosaur diversity between Makela-French 1 and Clamfetti. Hadrosaurs and ceratopsians are present and relatively abundance at both sites, whereas ankylosaurs decrease in abundance from Makela-French 1 to Clamfetti. Small herbivores like pachycephalosaurs and hypsilophodonts are rare at both sites. Theropods show similar patterns to the herbivore’s trends. Tyrannosaurs and dromaeosaurs are common at both sites, whereas troodontids are absent from Makela-French 1. These preliminary findings reflect diversity patterns that are not easily observable solely through the collection of dinosaur macrofossils. Our continued collection of fossils from Makela-French 1, Clamfetti, and additional sites will increase our sample size and provide better fine-scale resolution of dinosaur diversity patterns during this crucial interval in their evolution.

Patients with Human Immunodeficiency Virus (HIV) are known to have increased risk of cardiovascular complications. High Density Lipoprotein (HDL) is a circulating lipoprotein responsible for removing lipids, such as cholesterol, from the blood and returning them to the liver, and is known to have a large impact on cardiovascular health. HDL is also known to have a protective effect on endothelial cells, which line the blood vessel walls, and it normally stimulates nitric oxide to cause an anti-inflammatory response. However, little is known about whether HDL from HIV patients has unique effects on the function of endothelial cells. I hypothesize that HIV-positive patients have increased inflammation due to impairment of HDL’s protective anti-inflammatory function. To test this, I am determining whether there is an increase in pro-inflammatory cytokines in plasma from HIV-positive patients compared to control patients, using enzyme-linked immunosorbent assays. I am also testing the hypothesis that HDL from HIV patients has a more pro-inflammatory effect on endothelial cells. I am culturing human microvascular endothelial cells (HMEC) and treating them with HDL from HIV-positive and non-HIV patients, along with appropriate control stimuli, followed by in-cell Western assays to measure activation of NFkB protein, a master pro-inflammatory regulator. I am using the same methods to measure activation of Akt, an intracellular signaling protein that can activate the production of nitric oxide via the enzymatic activity of endothelial nitric oxide synthase. I anticipate that HDL from HIV patients will cause increased activation of NFkB and decreased activation of Akt, which could explain, at least in part, the increased inflammation and cardiovascular issues in HIV patients. This research will begin to reveal possible mechanisms by which dysfunctional HDL may contribute to cardiovascular risks in HIV patients, and such findings could ultimately identify novel targets for therapeutic intervention.

The four letters in DNA (ATGC) construct the basis of life as we know it. Unnatural base pairing xenonucleic acids (ubp XNAs) are synthetic nucleic acids that can be used orthogonally to the 4-letter code. XNAs have the potential to revolutionize a myriad of biotechnologies, but commercial sources of XNA nucleotides are limited and expensive. Here, we fill one step of an enzymatic cascade required to sustainably produce XNA nucleotides. Nucleoside phosphorylases (NPs) are enzymes that catalyze the reversible phosphorolysis of nucleosides to their base and sugar components. We purified and assayed promiscuous NPs from two thermophiles, Geobacillus thermoglucosidasius (GtNP) and Thermus thermophilus (TtNP). Using a combination of mass spectrometry and fluorescence assays, we show that these phosphorylases have activity on a subset of three XNA substrates (B, Sⁿ, and P). This enzymatic pathway allows us to synthesize non-standard nucleotides in a cost-efficient manner and provides a crucial tool for the biosynthesis of XNAs.

When a cell undergoes stress conditions, such as oxidation or aging, an increase in protein instability can occur and prevent proper cell functions. Small Heat Shock Proteins (sHSPs) are molecular chaperones that work to maintain a healthy proteome by associating with misfolded “client” proteins to delay aggregation under such conditions. HSPB5, a human sHSP, is ubiquitously expressed throughout the body. HSPB5’s disease mutant, R120G, is a defective chaperone associated with cataracts and desmin-related myopathy. It is still unknown how this mutation is detrimental despite many years of research. My research aims to understand how this mutation retunes the electrostatic properties of HSPB5, affecting its chaperone activity. Residue R120 is part of an electrostatic network that helps create an important structural feature in the folded region of HSPB5, the alpha-crystallin domain (ACD). In the unmutated (WT) protein, the ACD surface is overall positively charged. Substitution of the positive R120 to glycine alters both ACD’s structure and electrostatics. I generated two mutants, R120K (retaining positive charge) and R120D (switching to negative charge) to investigate how R120 plays a role in ACD’s conformation. Using a negatively-charged molecule, ATP, as an “electrostatic” probe in 2D NMR, I observed differences between its binding affinity to my R120 variants. I found that only R120K ACD behaves similar to WT ACD, suggesting a possible correlation between charge potential and ACD’s interactions with ATP. Currently, I am investigating if charge potential affects chaperone activity through aggregation assays with a client protein, human γD-crystallin, found in the lens and implicated in cataracts. I predict that WT and R120K, with similar electrostatic properties, will have similar chaperone activity. R120G and R120D, prevalently in an “active” state, will have higher chaperone activity. Understanding how such mutations affect HSPB5’s conformations and chaperone activity is a step forward in understanding sHSPs’ chaperone mechanism.

Following the COVID-19 pandemic in March 2020, mental health has become a prominent issue in the lives of many as reports of depression, anxiety, and other psychological distress increase. However, due to the sudden and drastic decline in collective mental health, resources including access to therapy and other treatments have been highly in demand. This has caused a shortage with facilities that offer psychiatric and psychological care being overbooked and unavailable. Using a dataset that observed mental health during the COVID-19 pandemic in US households, we utilized a hierarchical Bayesian model to analyze the reported rates of those who took prescription medication for their mental health within the last four weeks for 51 different locations (50 US states including Washington D.C.) across 12 time periods (from August 2020 to March 2021). We used the rstan package in R to implement this model using Markov Chain Monte Carlo (MCMC) methods. Our model applies a partial-pooled model that allows data from different US states to inform others in the case that there are not a sufficient amount of data points or high variance. In our analysis, we were able to conclude that Bayesian modeling is useful for removing noise from data, as when we analyzed the prescription usage rates per state for fewer time periods, our model was able to correct for uncertainty in the given data and give a more accurate reflection of the true rates. The model did not influence the results as significantly when using data across all given time periods. Despite these findings, our hierarchical Bayesian model did correct for the reported variation between the different average rates across the different US states by helping distinguish between signal and noise in the data. Our analysis provides an alternative approach to statistics that allows for analyses tonot only utilize current data, but also considers prior information to create a more informed posterior conclusion.

Glutamine synthetase (GS) is a highly regulated enzyme critical for converting glutamate to glutamine and associated with ammonia assimilation. Dysregulation in the GS interconversion process can lead to hyperammonemia, potentially resulting in death or brain damage. GS is conserved across prokaryotes and eukaryotes. Among enzymes, glutamine synthetase has the ability to polymerize but the functional characteristics of its self-assembling filaments remain unknown. This study aims to elucidate the occurrence of filament formation in GS and its effects on enzyme activity. We hypothesized that filaments might influence the association of GS substrates or allosterically regulate the enzyme. I purified GS from Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Helicobacter pylori using Ni-column and size exclusion chromatography (SEC). The focus was primarily on Pseudomonas GS, examining it under various buffer conditions (Mg²⁺, Co²⁺) through negative staining. Under magnesium conditions (10 mM), dodecamer strcture of GS was observed and filaments was induced under cobalt conditions (10 mM). To investigate the structural mechanism of filament formation further, we utilized cryogenic electron microscopy (Cryo-EM) to create a model of the GS filament interface and identifying involved residues. Additionally, I am conducting mutagenesis on key residues of Pseudomonas GS to disrupt filament formation. This research holds significant implications for metabolic engineering, as understanding the structure and role of filament formation in GS could lead to new therapeutic targets in metabolism.

Fifth Harmony’s BOSS music video, which showcases female empowering choreography, has been viewed 267 million times. The choreographer behind it, Sean Bankhead, said in an interview the higher you go the bigger the budget and the bigger the ego of the artist that you are working with. He went on to say about how when he was working with Missy Elliot, she would challenge him to pull things out of him that he didn’t know he had and he was told "start fresh tomorrow you can do better.” As hard as it is to break into this industry, choreographers continuously mention being extremely proud of sharing their work with millions of people. From the outside, it seems like music video choreographers have so much freedom in artistic choices like style of the piece and movement influences, but how much do choreographers truly get to create the exact choreography that they want? The exploration of music video choreography is really important because music videos are a way for the dance artform to be shared widely, but in scenarios like the one above, commercial popularity influences the creation of a choreography. Bankhead also mentioned that in music videos, he incorporates a snippet of choreography that even non-dancers can do, and these are usually the pieces that go viral. How do Los Angeles dance industry choreographers strike a balance between their own artistic vision and commercial pressures to create viral videos to become successful in the LA music video scene? My research seeks to answer this question through analysis of YouTube interviews, close reading of popular dance music videos, and interviews with choreographers.

Recently there has been interest in two possible sources of mass in the outer solar system. First, observations of recently discovered remote outer solar system objects have suggested the presence of a ninth planet. Different numerical simulations have suggested either a less massive (1.5-3 Earth masses) planet with a semimajor axis of 250-500 AU from the Sun (the Earth orbits at 1 AU), or a more massive (5-15 Earth masses) planet at 400-800 AU. Second, data from the New Horizons spacecraft has suggested that there may be an additional roughly circular belt of objects, similar to the Kuiper Belt, beyond 60 AU. This raises the question of whether this belt would be compatible with some or all of the proposed forms of planet 9. To answer this question, I ran a series of orbital dynamics simulations with randomly generated test particles representing the proposed second Kuiper Belt, and different masses and orbital parameters for planet 9. By looking at how planet 9 changed the orbits of the test particles over the period of the simulation, I concluded that although planet 9 would not significantly affect objects orbiting at 60-100 AU, in the most extreme cases, it would significantly broaden the distribution of orbital inclinations of objects beyond 100 AU. Astronomical deep and wide surveys conducted over the next few years have the potential to detect both planet 9, and objects beyond the Kuiper Belt. If second Kuiper Belt objects are discovered, these objects having a wider-than-expected range or orbital inclinations would point to gravitational disturbances, such as those caused by planet 9. Alternatively, if planet 9 is discovered, these simulations suggest that a second Kuiper Belt would need to be more inclined than has been so far assumed.

Skin cancer is the most common cancer in the United States, with 5.5 million annual cases. It is strongly associated with ultraviolet (UV) radiation that generates many mutations. There is thus a need to investigate what mutations drive skin cancer. The CDKN2A gene encodes the p16 tumor suppressor protein, and silencing of the CDKN2A gene plays a key role in cancer progression. Our previous mouse study showed that chronic UV irradiation to mouse skin induced mutations at the mouse Cdkn2a/p16 promoter. However, the impact of the mutations at this promoter on cancer progression remained unclear. We hypothesized that these UV-induced mutations at the Cdkn2a/p16 promoter may inhibit the binding of transcription factors, thereby suppressing the expression of the p16 tumor suppressor and leading to cancer development. The mutations at the Cdkn2a/p16 promoter were found in the DNA sequence that was similar to the ETS transcription factor binding motif. Also, it has been shown that ETS2 is expressed in the skin. Thus, we tested whether mouse ETS2 binds to the mouse Cdkn2a/p16 promoter by measuring light signals from luciferase that is expressed under the control of the promoter. Overexpression of mouse ETS2 resulted in higher light signals than no overexpression control, indicating that ETS2 binds to the mouse Cdkn2a/p16 promoter. We also tested mutated promoters that carry the UV-induced mutations. With overexpression of mouse ETS2, the mutated Cdkn2a/p16 promoter showed lower light signals than wild-type promoter, implying that the mutation at the promoter inhibits the binding of ETS2 transcription factor to the promoter. Although further investigations are needed, these results suggest that UV-induced mutations affect the binding of transcription factors. This study highlights the importance of investigating promoter mutations that may contribute to cancer progression.

Atherosclerosis is characterized by the accumulation of lipids, inflammatory cells, and fibrous tissue in arterial walls, forming plaques. Plaque accumulation can lead to stenosis and potentially severe outcomes such as myocardial infarction or stroke. The gut microbiome, including Collinsella aerofaciens, is believed to play a role in the prevention or development of atherosclerosis. Gut bacteria can directly influence systemic inflammation, a factor correlated with the pathogenesis of atherosclerosis, and produce metabolites that alter the disease course. This study explores the potential link between C. aerofaciens and atherosclerosis by investigating the abundance of C. aerofaciens in the gut microbiome of individuals with and without atherosclerosis. We collected 179 stool samples from participants at the Kisumu District Hospital HIV Clinic in Kenya and conducted a comprehensive analysis of their gut microbiomes. 100 participants had carotid ultrasonography, categorized as showing atherosclerosis with visible plaque or intima medial thickness ≥ 0.7 mm. We employed bacterial 16S ribosomal RNA gene sequencing to characterize the stool microbial composition and noted that the relative abundance of C. aerofaciens was 2.6-fold less in participants with atherosclerosis (p=0.006). To validate these findings, I employed a Quantitative Polymerase Chain Reaction with a cloned plasmid control for targeted quantification of C. aerofaciens. We found 6.9-fold more C. aerofaciens copies per total 16S in Kenyan adults without atherosclerosis versus with (p=0.020). This suggests a potential protective or mitigating role for this bacterium in cardiovascular health. Future work could include assessing changes in C. aerofaciens abundance over time and its association with cardiovascular disease progression. Additionally, in vitro or preclinical studies could reveal the specific mechanisms by which C. aerofaciens influences atherosclerosis development and progression. This research contributes to our understanding of the intricate interplay between the gut microbiome and atherosclerosis, offering insights that may inform future therapeutic strategies and personalized interventions for cardiovascular diseases.

The effects of the fungal pathogen Swiss needle cast (SNC) on its host species, Douglas-fir, and its timber harvest repercussions have been researched. However, more research is needed regarding the effects of SNC on understory species and, consequently, browsing ungulate species. This study analyzes the effects of various thinning methods on SNC and SNC’s influence on understory species richness, diversity, and cover. The goal is to articulate a clear dynamic of SNC in Sitka spruce and Douglas-fir - western hemlock zones to provide insights for guiding forest management. I will analyze the Olympic Natural Resource Center’s pre and post-treatment data from Siuslaw National Forest with statistical analyses to articulate patterns in SNC presence, thinning, and understory change. The early, mid, and late seral/thinned treatments vary in density and by species replanted. I expect that thinning will decrease SNC abundance and increase understory species richness. Additionally, I predict that the stands replanted with red alder and conifers will see a higher abundance of understory due to red alder’s nitrogen-fixing ability. The enhanced understanding of SNC and thinning’s interplay aims to educate current and future forest managers about ecologically responsible management.

Small heat shock proteins (sHSP) are a family of molecular chaperones whose function is to delay the harmful aggregation of other proteins. Protein aggregation is associated with neurological disorders such as Alzheimer's disease and Parkinson's disease. In many tissues, multiple sHSPs are coexpressed and tend to assemble into hetero-oligomers. Hetero-oligomers are complexes of two or more different protein species. The extent and mechanism by which these hetero-oligomeric complexes form is yet to be fully understood. The goal of my discovery-driven research is to assess how the properties of sHSP hetero-oligomers differ from the properties of homo-oligomers. In my project, I focus on three sHSPs that are highly expressed in muscle: HSPB1, HSPB5, and HSPB6. Each of these proteins exhibit different behavior when on their own. HSPB1 and HSPB5 form a distribution of large homo-oligomers, whereas HSPB6 forms a small homo-dimer. One of the most characteristic properties of the small heat shock proteins is formation of oligomers that span different sizes. Thus I am primarily determining the sizes and composition of the sHSP hetero-oligomers. I performed a comprehensive study to characterize the sizes of the hetero-oligomers using three complementary methods: analytical size exclusion chromatography, mass photometry, and native gel electrophoresis. I have found that HSPB6 is able to readily incorporate into hetero-oligomers as the concentration of the other sHSP is increased, and that the complexes are formed in a distribution of intermediate sizes. I am currently working on assessing the ability of the hetero-oligomers to act as molecular chaperones by aggregation assays. I predict the hetero-oligomers will delay protein aggregation more efficiently than HSPB6 on its own. The findings of my project give insight into why sHSPs are coexpressed and form hetero-oligomers in cells. Understanding these hetero-oligomers sheds light into the complex pathways of sHSP function. 

The stratigraphic integrity of stone artefacts found in Australia’s earliest archaeological site, Madjedbebe in northern Australia, has been questioned due to the potential impact of termites burrowing through the deposits. Studies have claimed that the 65,000-year date of early human settlement in Madjebebe is invalid due to biodisturbance - in particular, termite disruption, which causes vertical and horizontal displacement of artefacts. Here we analyse the chemical composition of the archaeological sediments and termite mound sediments to investigate the claim that bioturbation processes have impacted the dating of the Madjebebe site. We used a micro-X-Ray Flouresence instrument to analyse the elemental composition of micromorphology samples from the Madjedbebe. Our prediction is that there are distinctive, non-overlapping chemical fingerprints for termite sediments and the archaeological sediments, suggesting minimal termite activity in the archaeologial deposits. The results will provide new information on the validity of the stratigraphic integrity of deposits in Madjebebe, clarifying its significance for debates about the movement of modern humans out of Africa.

During times of increased hospital capacity, unconventional areas (what we have termed “non-standard clinical spaces” such as converted conference rooms, hallways etc.) may be activated for inpatient activities. Studies regarding issues with Emergency Department boarding while awaiting an inpatient bed have been well documented, but the same practices in inpatient spaces have not been well studied. Qualitative semi-structured interviews were conducted between February-April 2023 at a large urban, public hospital to understand how patients experience these spaces. Any adult English-speaking patient admitted to the hospital for at least two days who was physically located in a non-standard clinical space (hallway beds, PACU beds, former Emergency Department bays converted to inpatient spaces) upon approach for interview was eligible to participate. Eight participants ranging in age from 20-70, across diverse demographics were interviewed for the study. Three themes were identified from the interviews: overall experience, unspoken messaging, and impact to care. Poor patient experience was affected by noise related to crowding in their space and a lack of barriers from noise, lack of privacy from close quarters with others, lack of reliable bathroom access, loss of control over their environment, and inability to gain the attention of nursing staff (though, interestingly, this was not universal as some mentioned that they were in closer proximity to their nurses and able to receive more direct interaction). They described perceiving unspoken messaging about being selected for a nonstandard clinical space. Most commented on the kindness and understanding of the nursing staff and did not necessarily perceive a significant impact to their overall care. When these types of spaces are considered for use for inpatient boarding, patient privacy, control, and access should be prioritized. Transparency and communication about the situational context may help mitigate negative effects of these spaces.

Vaccines have successfully reduced global infectious disease burden, but there is room to improve vaccination technologies. Because many pathogens infect at mucosal sites, a goal of new vaccines is to promote strong mucosal and systemic antibody and T-cell responses. Integrated fiber microneedle devices (iFMN) are a novel oral vaccination method that may achieve this goal. These devices are patches with a polymer backfill matrix and multiple >1 mm pyramidal needles that penetrate immune cell-rich mucosal tissue in the mouth, inducing immune responses at draining lymph nodes. To test the hypothesis that priming with iFMN delivery of a DNA vaccine increases mucosal and systemic antibody responses after systemic booster immunization with the same vaccine, male rhesus macaques (n=6) were primed with an iFMN delivery of a DNA vaccine encoding Influenza A Virus (IAV) Nucleoprotein (NP) at weeks (0) and (6). The macaques then received a single boost of the same NP DNA vaccine at week (12) using the proven delivery modality of Gene Gun epidermal delivery (GG). Mucosal secretions (including bronchoalveolar lavage, saliva, and nasal/tracheal swabs) and serum were collected 2-4 weeks before and after each immunization. I conducted enzyme-linked immunosorbent assays (ELISAs) to quantify antigen-specific IgG and IgA binding antibody at each timepoint. To characterize the priming effect of iFMN oral delivery on systemic and mucosal antibody responses, I compared these animals’ responses to macaques (n=8) previously immunized with a single GG dose of the same NP DNA vaccine. The iFMN-primed animals had robust post-GG boost NP-specific IgG responses in serum but these responses were not significantly higher than for macaques boosted solely with GG DNA. These results demonstrate that iFMN delivery did not effectively prime for robust systemic and mucosal antibody responses. Additional experiments will be done to confirm these findings.

The Cretaceous-Paleogene (K-Pg) mass extinction (66.052 Ma) is one of the most important events in mammalian evolution as it was the catalyst for mammals to diversify and fill the ecological holes left by the extinction of the non-avian dinosaurs. This extinction event impacted all groups of mammals, including the multituberculates, one of the longest-lived and most successful clades of Mesozoic and early Cenozoic mammals. The Constenius vertebrate fossil locality is in the lowermost Tullock Member of the Fort Union Formation in Garfield County, northeastern Montana, deposited within the first 28,000 years after the K-Pg mass extinction (66.052-66.028 Ma). Constenius is a very rich but understudied fossil locality that provides a snapshot of the immediate aftermath of the mass extinction. In this study, we used qualitative descriptions partnered with linear measurements to identify 44 lower fourth premolars (p4s) to the lowest possible multituberculate taxon. We recognize three genera of multituberculates from Constenius: Cimexomys, Mesodma, and Stygimys. The presence of these multituberculates supports the previous assignment of Constenius to the Pu1 interval zone of the Puercan North American Land Mammal Age (early Paleocene, 66.052-65.820 Ma). Further work on this project will include expanding the dataset to include other multituberculate dental specimens, such as upper premolars, and conducting a geometric morphometric analysis with the lower fourth premolar specimens to further confirm taxonomic identifications.

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental condition characterized by differences in attention, focus, and emotional regulation. We investigate the relationship between parent temperament, including negative affect, and emotional socialization in ADHD parent-child dyads (parents and their children with ADHD).  Temperament refers to innate behavioral traits shaping one’s personality. Individuals with ADHD are known to experience higher rates of temperamental negative affect. Negative affect is a temperament factor that includes significant aversion from feelings like sadness. Emotional socialization refers to response methods of emotion regulation and can be categorized as supportive and unsupportive. Our study is impactful because ADHD has high heritability rates, yet there is little research on parental ADHD symptoms and associated temperament differences’ effect on ADHD families. We hypothesize that parents who report more ADHD symptoms and/or higher levels of temperamental negative affect use less supportive emotional socialization strategies and more unsupportive strategies when interacting with their children with ADHD. To test this hypothesis, I assist with administration of parent self-report measures and assess negative talk during laboratory-based, video-recorded parent-child interactions. Parents complete the self-report Adult Temperament Questionnaire (ATQ), which evaluates negative affect frequency. We measure negative talk by coding frequency of verbal disapproval of the child’s behavior/ attributes during parent-child interactions, where I instruct parents to perform standardized tasks with their children and code parental verbalizations into categories like negative talk using the Dyadic Parent-Child Interaction Coding System (DPICS). I then use bivariate correlation analysis to determine the likelihood that the two variables occur together and are linked. Through our anticipated findings, we hope to better inform care for children with ADHD and provide more resources for ADHD parent-child dyads. We want to identify emotional state-based targets to use in parental interventions to better support emotional regulation strategies in ADHD families.

Phosphoribosyl Pyrophosphate Synthetase (PRPS1) is an enzyme in the nucleotide biosynthesis pathway that makes a molecule necessary for de novo nucleotide synthesis. It is known that PRPS1 protein hexamers can stack into linear filaments in the presence of ADP and phosphate. When these filaments are broken, catalytic activity is lost, and it is hypothesized that enzyme inhibition is lost as well. Mutations in PRPS1 lead to a wide spectrum of diseases in humans. In addition, changes in cell regulation of the enzyme have been linked to cancer. Motivated by research that connects PRPS1 phosphorylation to increased cancer proliferation, my project investigates the effects of phosphorylation on PRPS1 structure, enzyme activity, and inhibition properties. I have transformed plasmid DNA containing the PRPS1 phosphomimetic mutations S47E, S103D, and S308E into E. coli strains BL21 and pLysS. I then grew overnight bacterial cultures and induced protein expression using IPTG. After verifying protein expression with gel electrophoresis, I purified the protein from bacteria using nickel resin affinity and size exclusion chromatography. Having made and purified protein mutations that mimic phosphorylation, I conducted a negative stain screen to analyze filament formation trends. This has yielded preliminary findings that S47E and S103D phosphorylation mutations of PRPS1 break enzyme filament formation. Variation in filament formation between mutations points to the importance of phosphorylation location and its potential impact on enzyme activity and inhibition. To assess the catalysis of the phosphomimetic mutations in PRPS1, I will conduct biochemical assays which measure the activity and inhibition of the enzyme. Through these ongoing experiments we will learn how phosphorylation modifies PRPS assembly and activity and the implications of PRPS1 dysregulation in cancer proliferation.

Transportation between the Endoplasmic Reticulum (ER) and Golgi is the first step of the secretory pathway, essential for correctly localizing intracellular proteins. USO1 is a long tethering protein between the ER and Golgi. USO1 acts as the first contact between transport vesicles and the Golgi initiating the transport process. Deletion of USO1 is lethal. YPT1 is a GTPase that is needed to recruit USO1 to these membranes. It is believed that physical interaction between YPT1 and USO1 is required for this transport function. Using AlphaFold2 predictions, we identified potential binding sites of YPT1 on USO1. If those sites are mutated, how would it affect the cell? I mutated sites proposed to bind to YPT1 on USO1 by Alphafold2 in order to break this interaction. Using yeast, I plan to determine if these mutation sites break the physical interaction. The resulting mutants cannot grow at elevated temperature. Further experiments will test how important these sites are in the overall process of protein secretion.

TAR DNA binding protein 43 (TDP-43) is an RNA/DNA binding protein that forms pathological aggregates in most amyotrophic lateral sclerosis (ALS) and half of frontotemporal lobar degeneration (FTLD) cases. Knockout of TDP-43 in animal models leads to neurodegeneration and motor deficits, but overexpression of wildtype TDP43 leads to the same events; therefore, TDP43 protein homeostasis is critical to prevent ALS/FTLD. To achieve this homeostasis, TDP-43 autoregulates its own mRNA splicing, resulting in multiple TDP-43 isoforms, some of which go through non-sense mediated decay to regulate overall TDP43 levels. However, other isoforms encode unique proteins with differing C-termini, leading to variable cellular localization. It is unknown if these alternative, protein-coding isoforms are predominantly associated with ALS/FTLD or if aging changes the frequency of these isoforms. To determine how TDP43 overexpression yields these different isoforms and interacts with aging and ALS-like symptoms, we created a novel approach to overexpress human TDP43 via Adeno-Associated Virus (AAV) delivered through retro-orbital injection, leading to ALS-like motor deficits. Surprisingly, when tested in older and younger mice, we found the older mice were paradoxically protected from severe motor deficits and mortality. To determine if tardbp alternative splicing is linked to ALS-like symptoms and aging, I designed and validated primers and protocols to measure the nine tardbp mRNA isoforms in mice via quantitative real-time polymerase chain reaction (qRT-PCR). I have started to determine if hTDP43 overexpression leads to differential splicing compared to mice injected with a sham AAV in these old and young mice. Once this is done, we will clone the most interesting differentially spliced isoform in an AAV and inject that AAV and a full-length TDP43 AAV into mice to see if the spliceform causes increased toxicity, manifesting in worsening motor deficits and mortality.

Old (> 4 million years ago) ice drilled at the Allan Hills, Antarctica, can help us understand how Earth’s atmosphere has changed in the past. The bubbles trap bits of the atmosphere when they form, which can be analyzed to see what the climate was like. However, the preservation of this old ice depends on ice flow dynamics, possibly including localized shearing (one side of the ice is getting pulled faster than the other), that are difficult to observe. Bubbles in the ice become elongated when the ice around them deforms from strain. Over time, surface tension processes tend to restore bubbles to spherical. Thus, they can indicate the directions of recent or ongoing strain in the ice. We analyze thin/thick section images taken from four samples of Allan Hills ice. The images include information on grain size (size of individual ice crystals) and bubble size, shape, and distribution. We use the Segment Every Grain (SEG) model, a Python package based on the Segment Anything Model developed by Meta, to automatically calculate the sizes and shapes of bubbles in an image. We validate this method by comparing the values it returns with those obtained using another segmenting software, ImageJ, and manually calculated measurements. We can see if automated calculations are reliable enough to use regularly. So far, the SEG model has analyzed one image and it has made mostly correct bubble identification. The data shows that most bubbles are either elongated and small area, or round and large area. It is expected that the SEG and ImageJ models are close to humans in accuracy. The bubble orientations that we measure show the predominant directions of strain in the ice. Future work will use these data along with models of bubble elongation to estimate the strain rates at the Allan Hills.

Mycobacterium abscessus are non-motile bacilli that cause soft-tissue and pulmonary infections, commonly in healthcare settings or patients with cystic fibrosis. Though it is considered an opportunistic pathogen, its many virulence factors signal its potential for evolution into a true pathogen. Upon infection, the bacilli are internalized by macrophages, forming granulomas to contain the infection. Macrophages can harbor bacilli during infection stages and induce drug resistance by expelling toxins through ABC transporters. Treatment is often challenging as M. abscessus is intrinsically resistant to many antibiotics. Current treatment uses a combination of two or more intravenous drugs and one or more oral antibiotics over several months. Treatment success is challenged by patient adherence and may also be impacted by drug efflux by macrophage ABC transporters. Transporters identify certain drugs as toxic to the body and try to flush them out of the cell. Since Mycobacteria infect macrophages, these channels pose a significant disadvantage to treatment since the cell will actively efflux the drug, preventing the drug's intracellular concentration from increasing to an effective level against the bacilli inside. Certain drugs are known to inhibit ABC transporters, and the addition of these inhibitors in treatment could increase bacteriocidal activity and reduce the development of drug tolerance. First, we will determine the drug's minimum inhibitory concentrations to each inhibitor to see if there is an intrinsic activity on M. abscessus. Next, we will use the Human THP-1 cell line infect with Mycobacterium abscessus and treat with known ABC transport inhibitors in concert with a current therapeutic drug, Clarithromycin. They will then be plated at various time points to determine the colony-forming units. If efflux by macrophage transporters reduces the efficacy of Clarithromycin, bacteriocidal activity will increase between the combination therapy and the clarithromycin-only treatment. These results may improve the current treatment regimens for M. abscessus.

Alzheimer's Disease (AD) is a relentless neurodegenerative condition for which there is presently no known cure. Latino and Hispanic individuals are at a higher risk of developing Alzheimer's Disease or related dementia (ADRD). By 2060, the number of Latino people living with dementia (PLWD) is expected to increase by 832%. With an uptake in PLWD, there will be an increase in the number of Latino families caring for PLWD. Latino families face unique barriers in accessing support and care, which can increase their vulnerability to adverse health outcomes. This study identifies the structural obstacles hindering the use of supportive services among Latino caregivers of PLWD. The seven-week intervention provided fifteen family caregivers from across the nation with information on how to manage the behavior of those with memory loss, including crying, arguing, refusal of care, and irregular sleep patterns. The program also teaches family caregivers how they can better care for themselves. Each week, the caregivers received one video to watch at their convenience. After reviewing the module, caregivers were asked to complete a survey to identify the effectiveness and usability of the intervention. Once the intervention was completed, participants were interviewed and asked a series of questions regarding the intervention and how it could be improved to provide better access to Latino caregivers caring for PLWD. Preliminary data indicates that Latino caregivers, balancing multiple responsibilities while caring for family members with dementia, often face challenges in maintaining consistent attendance at supportive service appointments due to unpredictable schedules. Overall, we aim to improve the quality of life for both the person with memory loss and their family caregivers through the use of a tailored online program that provides support and empowers caregivers in the Latino community.

The COVID-19 pandemic has created an overwhelming shift to using technology to connect with others. Coinciding with a growing mental health crisis among youth, mental health therapy has been largely moved to digital spaces. Three years later, providers are having to choose if they will provide their services through in person, remote, or hybrid interventions. My initial hypothesis is that there will be access barriers for youth of certain demographics when utilizing digital interventions. I conducted a systematic literature review to look at the effectiveness of the use of digital mental health therapy services among adolescents using PubMed, PsychInfo, and UW Libraries databases. The journals assess barriers and facilitators of digital mental health services for youth. Articles are found through systematic searches using combinations of the MeSH terms ‘digital mental health’, ‘adolescents’, ‘accessibility’ and ‘depression’. The demographics of the adolescents are compared with their preferences for digital therapy. Preliminary results indicate that youth who identify as lower income, rural residents, or BIPOC will face greater barriers to accessing mental healthcare and may benefit from continuing digital therapy. This synthesis of peer reviewed journals will prove to be useful in helping providers move forward with their practice in a way that aligns with their client’s needs.

Skin is a densely innervated sensory organ that protects us every day from environmental trauma. As a barrier organ, skin is susceptible to frequent damage that must be promptly and properly healed to prevent infection and restore sensory function. Our lab uses adult zebrafish as a model to study skin injury and repair. Adult zebrafish skin is similar in composition to human skin and transparent, lending itself to high-resolution microscopy. Previous experiments in our lab revealed that dynamic, skin-resident immune cells known as Langerhans cells (LCs) rapidly engulf cellular and axonal debris after injury in the zebrafish skin. Calcium signaling regulates phagocytosis and cell motility in other immune cells, but the role of calcium signaling in LCs is unstudied. Through skin explant assays, various injury paradigms, and confocal fluorescence microscopy, I have established a model for monitoring calcium signaling in LCs. I found that LCs exhibit rapid, transient calcium flashes under homeostatic conditions. However, upon engulfment of large cellular debris generated by precise laser-ablation of skin cells, LCs exhibit an atypical sustained calcium signal lasting an hour on average. To test the requirement of calcium during engulfment by LCs, I treated skin with the drug Thapsigargin to perturb calcium flux. I confirmed that Thapsigargin increases intracellular calcium in LCs and keeps intracellular calcium concentrations elevated for hours after drug addition. During Thapsigargin treatment, I showed that LCs formed phagocytic cups around cellular debris but engulfed fewer laser-ablated corpses compared to controls. Thapsigargin-treated LCs also experienced normal migration to a wound site. My results indicate that calcium flux regulates LC engulfment of large debris, but not through migration. Identifying the molecular mechanisms underlying LC motility and debris removal is ultimately relevant to understanding skin repair and disease states in which the wound healing response is attenuated, such as in chronic wounds.

Escherichia coli (E. coli) abundance is commonly used to indicate water quality and environmental health. The pH of water has been shown to affect the survival of E. coli. Possession Sound is an estuary that faces a wide range of pH (around 7.5-9.0) throughout the year due to alkaline salt water from Puget Sound mixing with acidic fresh water from the Snohomish River. Primary production, organism respiration, nutrient runoff, carbon emissions, and currents also affect pH levels. This study aims to analyze the relationship between pH and E. coli abundance in an estuarine environment. PH and E. coli data was collected from 2018 to 2023 by myself and other Ocean Research College Academy students. PH data was collected with a YSI EXO2 Sonde. E. coli data was collected using a Niskin bottle to obtain water samples which were then transferred to Petri dishes for growing and counting E. coli. My preliminary analysis shows that Possession Sound’s average pH range is around 7.5-8.5, with pH being higher in spring and summer than in fall and winter. Early analysis using Spearman’s Rank Correlation suggests that pH and E. coli have a weak, inverse relationship. There is minimal research on the relationship between pH and E. coli in a marine setting, so my study helps to provide insight into the relationship between E. coli and pH in a unique estuary.

Vulcanized rubber, the main component of tires, is prized for its chemical durability and thermal stability. These properties, however, make disposal difficult and contribute to the increasing problem of polymer waste. To broaden the applications of end-of-life tires, we developed a method to chemically upcycle polybutadiene, a primary component of vulcanized rubber, via selenium-mediated allylic amination. We hypothesized that functionalizing the backbone of crosslinked polybutadiene with sulfonamide groups—without breaking their double bonds—would result in favorable thermal properties, creating a new life for the crosslinked polybutadiene. We used infrared spectroscopy and scanning electron microscopy with energy dispersive X-ray spectroscopy to confirm the aminated crosslinked polybutadiene’s molecular structure and differential scanning calorimetry and thermogravimetric analysis to measure its changes in thermal properties. Our research has future implications for the reduction of tire waste and reprocessing of other end-of-life crosslinked polymers.

Solar energy is a promising form of renewable energy that will play a major role in reducing carbon emissions. Perovskite-based solar cells have attracted significant attention due to their high power conversion efficiency (PCE), which reached 26.1% this year, surpassing commercial silicon’s (23.3%). High PCE, low cost of materials, and ability to be solution processed make perovskite solar cells a prime candidate to replace silicon. However, efficiencies are still below the theoretical limit and these materials suffer from limited operational stability. To tackle these problems, scientists have focused on minimizing active layer and interfacial defects which act as barriers for charge extraction in a solar cell, lowering the device efficiencies. Defects also electronically dope the perovskite layer, changing the recombination kinetics in the sample. The goal of this project is to quantify how the electronic doping and defect concentration of the perovskite sample is affected by surface passivation treatements via fluence dependent photoluminescence (PL) and time resolved photoluminescence (TRPL) spectroscopy. By solving the kinetic equations at the basis of charge recombination, we can extract the rate constants that correspond to different charge recombination pathways. We pioneer a global fitting analysis to simultaneously fit TRPL and PL measurements for robust determination of these kinetic constants that are subsequently used to determine the doping density of films before and after passivation. We show that the electronic doping density is higher than previously reported in literature, and that this doping is reduced with a surface passivation treatment. We collaborate with the University of Arizona to correlate our measured electronic doping density to electrochemically measured defect densities on the same samples. This work will provide an implementable tool to quantitatively assess electronic doping and defect density values for various perovskite compositions which will be useful for optimizing future solar cell devices.

Hydrostatic pressure can be used to tune the electronic properties of atomically thin layered materials by decreasing the interlayer spacing, thereby enhancing the strength of interlayer interactions. In moiré systems, pressure can be used to create flat bands in samples with twist angles away from the usual ‘magic angle’. Twisted trilayer graphene (tTLG) has a Dirac band superimposed atop a flat band. These two bands can hybridize in a finite displacement field making it possible to further tune the flat band. The flat band is host to a variety of flavor-polarized correlated states, which may be an important ingredient in generating the exotic superconducting phases seen in tTLG. Although pressure could provide a new avenue for tuning these correlated states, a high-pressure study has not previously been performed on tTLG owing to the challenges of applying pressure to layered 2D materials: limited sample space, difficulty mounting the sample, and challenges in establishing electrical contacts. In this talk, I will discuss advances we have made in addressing these issues via a custom printed circuit board (PCB). The PCB provides a sturdy platform for mounting samples, and has gold pads to enable wire bonding. I will also discuss ongoing high-pressure electrical transport measurements of tTLG nanodevices. This work could elucidate further the origin of the unusual superconducting phase seen in tTLG, and provide a blueprint for future high-pressure studies of 2D materials.

Cannabidiol (CBD), a non-psychoactive cannabinoid compound found in cannabis, has been reported to attenuate morphine tolerance and can potentially be used as an alternative to opioids in treating chronic pain. Previous work has established connections between morphine tolerance and Reactive Oxygen Species (ROS) production through JNK-mediated Peroxiredoxin 6 (PRDX6) activation. Excess ROS production promotes desensitization of opioid receptors, which in turn leads to opioid tolerance. CBD administration is associated with decreasing pain-related Reactive Oxygen Species (ROS) production, and it was hypothesized that CBD directly interacts with JNK, blocking JNK’s activities. This project aims to investigate the connections between CBD administration and ROS production to determine CBD’s effects on JNK-mediated ROS production. To quantify ROS production through fluorescence imaging, I will transfect wild-type HEK 293 cells with oROS, a genetically encoded sensor, which fluoresces proportionally to ROS production. Coverslips of HEK 293 cells expressing oROS are treated with buffer (control) and CBD before administration of Tumor Necrosis Factor alpha (TNFα), a known activator for JNK released during pain states. After imaging with oROS, I will quantify ROS production and compare this between groups with and without CBD pretreatment to determine CBD’s activity on inhibiting JNK-mediated pro-inflammatory pathways. I predict that relative to the control, cells treated with CBD will have significantly less ROS production. If the results are consistent with this prediction, CBD could be a potentially promising co-treatment with opioids in managing chronic pain as it can potentially attenuate opioids' side effects like tolerance. 

The peptide neurotensin (NTS) has been known as a regulator of dopamine neuron activity and its system, which modulates numerous functions in the brain. Although ample research has now demonstrated that NTS in Ventral Tegmental Area (VTA) increases dopamine release in some regions, much remains unknown about the endogenous sources of NTS in the VTA and the impact of physiological NTS release. Recent NTS mapping data from the Soden lab demonstrated that there is a NTS projection from Periaqueductal Gray (PAG) to the VTA and also to hindbrain regions including the ventral medulla. This project investigates the effect of this interconnection between these three regions on the dopamine system. Utilizing advanced techniques in circuit mapping, mice will be injected in the VTA and the ventral medulla with fluorescent Retrobeads or a retrograde virus (rAAV2 anti mcherry or GFP), which are taken up by synaptic terminals and migrate up the axon retrogradely to label cell bodies, one color assigned for each region. Following euthanasia, mice brains will undergo immunohistochemistry such as histology and in-situ RNA staining. Then, data will be collected using imaging microscopes for results and further analysis. If NTS neurons in the PAG have green and red expressions, this will indicate that the same population of neurons send axons to both downstream regions, compared to PAG NTS neurons with only one color, indicating the presence of two separate neuron populations. Experiments on retrograde mapping of NTS inputs will contribute to building onto our current knowledge about VTA-PAG-ventral medulla circuit and effects on dopamine neurons following their interplay. In the end, our goal is to establish a novel understanding of endogenous NTS signaling mechanisms, mediation of complex reward processes, and treatment targets with experimental outcomes, giving rise to the development of therapeutic interventions towards addiction and related psychiatric disorders.

2023 was the Year of Open Science, part of a national push requiring public accessibility to the products of federally funded research. The Infant Brain Imaging Study (IBIS) Network is one such federally funded multi-site research network collecting neuroimaging data to study early brain development in infants with Down Syndrome. Data from the IBIS will be part of the INCLUDE Data Coordinating Center (DCC), a National Institutes of Health (NIH) managed open database intended to accelerate Down Syndrome research through sharable data. Understanding attitudes towards data sharing is important to ensure public trust in scientific research, and though much research exists assessing attitudes towards public sharing of genomic data, there is a lack of knowledge regarding attitudes towards public sharing of neuroimaging data. To combat this gap, I helped develop the CARDS-DS (Capturing Attitudes towards Research and Data Sharing in Down Syndrome) questionnaire, a novel parent-report measure to understand the perspectives of families participating in longitudinal Down Syndrome neuroimaging research. Currently, I am interviewing families enrolled in Down Syndrome neuroimaging research to get their feedback on the effectiveness of the questions asked in the CARDS-DS, a method called cognitive interviewing. Following this pilot study, CARDS-DS will be implemented throughout the IBIS Network. As such, CARDS-DS queries parent attitudes towards aspects of research participation that are particularly relevant to the INCLUDE DCC goals, namely: attitudes towards sharing of a child’s neuroimaging, genomic, and behavioral data, perspectives on data privacy, preferences for return of research results, and attitudes towards ongoing engagement with research teams throughout a longitudinal project. The anticipated data will reveal how attitudes may differ between parents from different sociodemographic or educational backgrounds, how attitudes may differ between the sharing of neuroimaging versus genomic data, whether attitudes are associated with study retention, and how attitudes may change over the course of longitudinal participation.

Over the last two decades, the threat of climate change has inspired significant research in the Salish Sea. Understanding trends and correlations between water temperature, dissolved oxygen (DO), and chlorophyll levels can help us understand how climate change and other anthropogenic activity has already affected the Salish Sea. My reseach focuses on seasonal and annual trends of water temperature, DO, and chlorophyll levels between 2019 and 2023 in Possession Sound, located in Everett, Washington. This longterm data-stream is generated by the Ocean Research College Academy, collected autonomously every 15 minutes by a pair of EXO sondes that are moored at Mount Baker Terminal and Everett Marina. My goal is to understand the relationship between water temperature, DO, and chlorophyll seasonally and historical trends over multiple years in Possession Sound. Preliminary figures and outside research have shown fairly consistent seasonal cycles for temperature and chlorophyll. DO trends are not as clear and data suggest significant variation is occurring within a short time frame. Future reseach may include comparing river discharge data to water chemistry data, however a more comprehensive understanding of specific inputs to the Snohomish River system is needed to draw solid conclusions about the affects of climate change.

Saltwater estuaries can experience high turbidity levels due to river input and tidal influences. Turbidity is a measure of inorganic and organic particles suspended in the water column. Reduced light penetration due to higher turbidity levels can contribute to decreased levels of primary production and the introduction of harmful pathogens to the environment. Understanding the relationship between river discharge, tides and turbidity levels could lead to a better understanding of the causes of turbidity in estuaries such as Possession Sound, WA. I hypothesize that higher current velocity contributes to higher turbidity levels. I analyzed data from a moored Acoustic Doppler Current Profiler (ADCP) and a Conductivity, Temperature, Depth (CTD) sensor located in the Everett Marina. ADCP and turbidity data were collected every 15 minutes, 24 hours a day, from 2017 to 2021. Preliminary results suggest that higher current velocity correlates to higher turbidity levels. Future research looks to discover how river discharge, tides and seasonal variance play into turbidity spikes.

Amidst the Black Spring of 2020, I found much of my exposure to and understanding of Black interiority and experience, Black history, institutional racism, police brutality, and other topics at hand to be coming from the young, Black, femme content creators I encountered on TikTok rather than my public-school education. Meeting at the intersection of Black and performance studies, communication, education, and sociology, this research seeks to answer the questions of how social media, specifically TikTok, serves as a site of informal education and how the digital performances of young, Black, femme content creators serve to shape this education. To address these questions, I examined the TikTok profiles of five content creators fitting the above qualifications with follower counts in the millions and varying niches across a three-month period. Attending to these archives through the lenses of norms and aesthetics, I’ve come to find that, among other observations, young, Black, femme content creators are educating the general public both intentionally and unintentionally on a plethora of topics, but consistently with a significant emphasis placed on joy. In a political landscape where Black history and truth are under attacked within the traditional education system, we must begin to recognize and create space for the immense value of informal education that occurs outside of the classroom and the performances that make it possible.

Pollutant removal in soils, for example through bioremediation, has long been touted as a potential solution to anthropogenically induced climate change impacts by improving soil health. Yet, these efforts are not often implemented at large-scales, and when they are, pollutant run-off and greenhouse gas (GHG) emissions outpace existing attempts. As atmospheric GHGs continue to rise outside of the safe operating space, it becomes crucial to search for avenues that offset them. Soils have huge potential to store carbon long-term, but when soils are polluted, it impacts their carbon storage capacity. It is clear we are in dire need of sustainable solutions that remove soil pollutants, increase soil carbon storage, and promote a healthy soil community. The physiological pathways that exist in plants, bacteria, and fungi are often interlinked, and evidence shows that certain interactions can ultimately lead to the storage of carbon in soils. Therefore, we hypothesize that the delivery of synergistic bacteria, fungi, and biochar via hydrogel beads will promote plant and soil communities’ ability to increase soil nutrients for plant uptake while removing pollutants and facilitating carbon storage. Preliminary data from our study, in which we applied mixed fungal-bacterial-char hydrogel beads to polluted soils growing Sorghum bicolor or Helianthus anuus, demonstrated that our novel biotechnology has potential to decrease heavy metal concentrations and toxic compounds. Additionally, we have begun analyzing the carbon storage potential through Loss on Ignition methodology, which provides measures of soil organic and inorganic carbon. Preliminary measurements show that soils that received hydrogels with an encased fungal-microbial-char consortia also increase soil carbon. These studies will not only inform the efficacy of hydrogel-delivered biofertilizers in terms of plant growth and productivity, but will also build a foundation for future research into how to promote soil health to mitigate the negative impacts of climate change.

Understanding human mobility based on location data from smartphones and other digital accessories has become a fundamental part of urban and environmental planning in cities. Through collection of these geo-traces, it has become possible for the scientific community and policy-makers to model citizens’ daily mobility patterns. Because of privacy issues, collection of location based data is rare, sparse and infrequent. To this end generative mobility models are used to create synthetic data. Because this data can be used in big decisions such as resource allocation and planning, if the data is skewed towards privileged groups, existing social and structural inequities can be exacerbated. Therefore, a critical concern that arises is the extent to which such synthetic data is fair and inclusive. Our goal is to create tools that measure whether socioeconomic conditions and geographical location affect individual and group trajectory predictions made by generative models. Using Gravity, Deep Gravity, and other models to generate mobility flow dataframes, we layered census data onto the flow dataframes by census tract to analyze the high income areas against lower income areas. We used this analysis to establish and implement a set of fairness metrics for mobility datasets and models in a python package that’s distribution could identify skewed modality data and hopefully influence other researchers to measure fairness in their generative models.

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

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

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

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

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

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

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

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

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

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

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

In this project, I explore the settler colonial dynamics that shape Wilderness Therapy, a for-profit carceral institution that has come under scrutiny for allegations of abuse despite their mission of curing “troubled teens” through the healing benefits of the outdoors. Specifically, I investigate the relationship of Wilderness Therapy to Indigenous land dispossession, violent cure-based medical models, and power and privilege within incarcerated communities. As someone who has been to Wilderness Therapy, I am interested in exploring the web of entanglements among carceral institutions, and how my experience and research can dismantle the carceral state and prioritize equitable reparations. My research takes the form of a novel written in a hybrid structure that braids fiction and nonfiction sections. The fiction part of my novel follows a student through her journey at Desert Destinies, a made-up Wilderness Therapy Center based on the average statistics of my research. The thesis of the nonfiction work postulates that Wilderness Therapy perpetuates slow colonial violence, meaning violence that replicates colonial structures and takes place in hidden ways over such a long period of time that it is invisibilized and naturalized. My research has taken many different forms and has been guided by various methodological approaches, including ethnographic research; close readings of archival documents, including my own journals from my time incarcerated; bibliographic research in the fields of Indigenous Studies, Settler Colonial Studies, and the Environmental Humanities; and creative writing. Through this project, I hope to imagine a decolonial future beyond the carceral state in which we address the slow violence inflicted by society on a personal and community level.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The hallmark neuropathological finding of Parkinson’s Disease (PD) is the presence of intraneuronal protein aggregates, consisting of aggregated proteins and misfolded forms of alpha-synuclein. These intraneuronal protein aggregates, known as Lewy bodies, are implicated in many neurodegenerative diseases. Lewy pathology spread in a PD brain correlates with clinical disease progression. Glucosidase, beta, acid (GBA) gene mutations, the strongest genetic risk factor for PD, is also associated with accelerated disease progression and altered extracellular vesicles (EVs). EVs play a crucial role in intercellular communication and delivery of bioactive cargos throughout the central nervous system (CNS). I use a human neuronal cell culture model derived from induced pluripotent stem cells (iPSCs) to examine how GBA mutations alter EV composition, and investigate whether EVs truly act as a vehicle for the seeding of Lewy pathology in other cells, potentially accelerating the propagation of Lewy pathology throughout the CNS. To isolate and purify EVs from the conditioned media of neurons, I use centrifugation and size exclusion chromatography. I visualize and quantify the EV’s size and concentration using a ZetaView nanoparticle analyzer. I perform Western Blot Analysis for candidate cargo proteins within EVs, including alpha-synuclein, ubiquitinated proteins, and EV intrinsic proteins (CD-63 & CD-81). I isolate EVs from the media of GBA PD or WT control neurons expressing alpha-synuclein-GFP fusion protein and apply these EVs to GBA PD or WT neurons. I anticipate that EVs secreted by GBA versus control neurons will contain increased alpha-synuclein protein levels and that increased cell death, endolysosomal trafficking defects, and aggregation of endogenous alpha-synuclein will be associated with the uptake of GBA EVs by recipient neurons. This work will provide evidence supporting the role of GBA in influencing Lewy pathology propagation via EVs, which could elucidate a novel therapeutic mechanism that could be targeted to slow the progression of neurodegeneration.

Lck is a lymphocyte specific tyrosine kinase involved in T cell activation in response to T cell receptor (TCR) mediated signaling. T cell activation is essential for the adaptive immune response, as it results in the proliferation of T cells after the detection of a peptide presented on a Major Histocompatibility Complex (MHC) and the production of cytokines necessary for immune response coordination. Lck activity is dependent on its global conformation, which is dynamically regulated via phosphorylation on its activation loop and C-terminus tail. Upon TCR engagement, active Lck phosphorylates the CD3ζ chains of the TCR complex, transducing the intracellular signaling events that activates T cells. Because Lck activity is dependent on its global conformation, we sought to map the conformational changes in Lck upon TCR simulation, as well as identify cysteine-reactive fragments that target and stabilize Lck in its conformational extremes. Lck has few endogenous cysteines, so we performed a yeast-growth-based deep mutational scan (DMS) of Lck–in which we utilized Lck’s toxicity to yeast to calculate the activity scores of ~5,000 Lck mutants–and identified 109 solvent-exposed, wild-type-like cysteine mutants of Lck. Expressing these wild-type-like cysteine mutants in T cells, and utilizing competition-based mass spectrometry, we can quantify changes in electrophilic reactivity of the cysteine side chains in the wild-type-like cysteine mutants upon T cell receptor (TCR) stimulation. Thus far, I have identified six wild-type-like cysteine mutants of Lck that are quantifiable using mass spectrometry and exhibit reactivity to our set of cysteine-reactive fragments, some of which show differential reactivity upon TCR simulation and fragment selectivity. Currently, I am using these mutants to map the dynamics of a hyperactive mutant of Lck. These quantifications provide insight into changes in the conformational flexibility of Lck, accessibility of the mutated residue sites, and intramolecular protein-protein interactions of Lck upon TCR stimulation.
 

Budding yeast cultures grown in limited sulfate conditions are overtaken by cells with an inverted triplication of the gene SUL1, which encodes for a sulfate transporter. The extra copies of the sulfate transporter provide a selective advantage because these cells outcompete other yeast cells for the limiting resource. To explain the mechanism behind this type of amplification the Brewer and Dunham Labs proposed a model (Origin Dependent Inverted Repeat Amplification or ODIRA), which requires both a DNA replication origin and inverted repeats flanking SUL1. ODIRA starts with a DNA replication error involving replication fork regression that leads to an extrachromosomal DNA intermediate. This intermediate then replicates and recombines into the genome, producing the observed amplification. Because similar triplications are observed in the human genome, including in human disorders, the mechanism of ODIRA offers insights into human genome evolution and disease. While the yeast research is consistent with ODIRA, we still do not know which proteins are responsible for the process. I am testing whether the genes RAD5 and RAD54 — involved in fork regression and strand switching, respectively — are involved in ODIRA. To do so, I am measuring the ODIRA frequency in strains with each gene deleted compared to a wild-type control. If either gene deletion leads to a statistically significant change in ODIRA frequency compared to the wild-type strain, I can conclude this gene is involved in ODIRA. To measure ODIRA frequency, I grow the deletion strains under selection for DNA recombination events and use whole chromosome gel electrophoresis and Southern blotting to detect ODIRA events. Preliminary data analysis suggests that there is a reduction in ODIRA events when either RAD5 or RAD54 is deleted, indicating that these genes are likely needed for ODIRA. These results may provide insight into how inverted triplications may arise.

On June 29, 2023, the United States Supreme Court ruled that using affirmative action in college admissions is unconstitutional in the case, Students for Fair Admissions, Inc. v. President and Fellows of Harvard College. This research analyzes arguments presented by both parties to reveal the effects of this policy removal on the future of underrepresented minority students applying to college. I analyze Harvard’s admission statistics through regression models cultivated by each party’s expert witness to identify the lack of true diversity in Harvard’s admission process. The statistical findings the experts present highlight the use of the Asian American experience to justify the removal of affirmative action measures in higher education. Additionally, I conduct a complex legal analysis of prior Supreme Court cases through the lens of reparation jurisprudence to expose the lucrative, and performative, system of affirmative action in higher education. The Court’s decision to remove affirmative action requires universities to develop a new form of admission criteria that aids underrepresented minority students in the college admission process. Statistical evidence provided by the Department of Education and economist, Richard D. Kahlenberg, points to a new form of affirmative action that considers varying intersectional factors to develop a complex method of class-based affirmative action. Such studies identify the benefits of looking at various demographic factors contributing to an applicant’s experience to cultivate a diverse class of students that goes deeper than race.

Myotonic dystrophy type 1 (DM1) is a genetic disease that causes many serious health conditions in a variety of tissues including skeletal muscle stiffening and cardiac conduction disorders. This disease affects 1 in 2,300 people worldwide and is the most common form of muscular dystrophy. DM1 is caused by a CTG repeat expansion, which in lay terms means that in a gene, there's a sequence of 10 CTG DNA bases. However, in a specific part of the gene responsible for making messenger RNA (mRNA), the number of CTG repeats increases significantly. This unusual mRNA sequence is linked to the development of the disease. This mutated mRNA (messenger RNA) disables the splicing regulator muscle-blind-like 1 (MBNL1) gene and ultimately causes disease. It does this by sequestering and limiting the MBNL1s critical role in splicing mRNA (figure 1). In my proposed research project, I am focusing on cardiac function when testing adeno-associated viral vector (AAV)-mediated systemic delivery of the MBNL1 gene to increase MBNL1 protein expression in muscle. The lab found that body-wide delivery of AAV vectors with CK8-intron-MBNL1, which expressed MBNL1 only in striated muscle, was toxic in the hearts of mice and caused death (figure 2). Over the last few months, my mentor Matt Karolak and I have learned together methods such as echocardiography and tissue histological techniques to determine whether it is possible to prevent MBNL1 protein production and its damaging effects in the heart while still expressing MBNL1 protein in skeletal muscle for therapeutic disease benefits.

What is personal space? It describes the “invisible bubble” immediately around an individual, where intrusion by others may feel uncomfortable or even threatening. Despite personal space being important for determining the size and dynamics of large groups and how animals behave, it is unknown how animals generate and maintain their sense of personal space. I explore this question using Drosophila flies, a powerful model system for studying behavior. Individual flies communicate via a large set of behaviors (e.g. kicking, flicking the wings, flying, and running) that can shape group interactions. Between pairs of flies, there is a rich repertoire of interactions that cause them to either move away (e.g. appendage touching) or move closer (e.g.courtship behaviors). To capture these behaviors, I use high resolution cameras running at 150 fps to collect videos of flies interacting in a circular arena and deep-learning software for annotating body parts (SLEAP). I use this data to track the poses of multiple flies throughout time and quantify appendage touching behaviors in addition to an estimate of each fly’s personal space. Using optogenetics, I model a situation in which a wild-type fly responds and adapts to being surrounded by other flies that crowd tightly. One expected outcome is that the wild-type fly will increase appendage touching in response to the space around itself shrinking. My goal is to determine exactly how the dynamics of such inter-fly interactions form a sense of personal space for each fly. My work will uncover the patterns of interactions that develop personal space and how these patterns scale out to larger social networks.

The European Union's (EU) New Pact on Migration and Asylum demonstrates the EU’s securitizing behavior towards migration. Current discussion surrounding the measures prevalent within the New Pact is primarily focused on the EU’s severity towards managing migration flows. While there has been a consensus on the inherent flaws of these extreme measures, previous research has taken the rationale behind the EU’s decisions for granted. The lack of clarification on the EU’s logic leads to a failure to explain why the EU continues to push this New Pact despite both the flaws present within it and the opposition to the pact by African nations directly affected by it. To illustrate the EU’s reasoning, I utilize discourse analysis of semantic structures and the use of metaphors in seven speeches made by key European Commission members on the New Pact. This process finds and measures the salience of the Commission members' ideations of an EU “home” that needs to be defended from threats to collective identity. These findings are supplemented by content analysis of European Newspapers to find underlying economic and political factors that also explain the EU’s stubbornness on the New Pact. The content analysis of articles will demonstrate why ontological insecurity has emerged as a problem now. My findings indicate that the European Commission members' refusal to adjust the New Pact is caused by a break in the psychological anchors that make people feel secure. Specifically, Commission members have been found to feel ontologically insecure when governing migration. They demonstrate the belief that migration flows are a threat to the EU’s collective identity and the idea of an EU “home.” To prevent a supposed deterioration of the EU “home” harsh policies such as the New Pact are passed to stem supposedly threatening migration flows.

This digital humanities capstone project builds upon my senior thesis “An Analysis of Western Perspectives on the Khmer Republic, 1970-2023”. The thesis examined Western scholarly works related to the escalating events that enabled the Khmer Rouge’s rise in Cambodia, revealing biases in how the events leading up to the Cambodian Genocide were portrayed. This research demonstrated that the roots of the Cambodian genocide stretched back years before the Khmer Rouge came to power, fueled by political instability and civil war. Through an interactive digital timeline, this project synthesizes primary and secondary sources across media reports, government records, and academic analysis, to name a few, to visually display the narratives and divergences in Western scholar’s perspectives. My main research question has changed from the start of this project, today resulting in: How can a digital timeline effectively showcase the divergences in Western scholars’ portrayal of events during the Lon Nol Era, that preceded the Cambodian Genocide? Over the past two semesters, I have been building a website to illustrate the history leading up to the Khmer Rouge regime. The website features an interactive timeline and globe, based on latitude and longitude points. It features three interlinking sections tracking: 1) Scholarly Works, 2) Surrounding World Events, and 3) The Lon Nol Era and Cambodian Genocide. By revealing biases and gaps through a visual model, it can reveal blind spots or skewed narratives. It can also track interconnections, and observe how scholarly interpretations evolved to provide context for the escalating political instability to demonstrate the Khmer Rouge’s rise in power. By uniquely challenging oversimplified narratives, this project can provide a more contextual understanding of how Western perspectives shaped understanding of the Cambodian Genocide.

PIONEER is a rare-pion decay experiment, which aims to test Lepton Flavor Universality (LFU), a consequence of the Standard Model (SM) of particle physics. The SM is very successful but is known to be incomplete as it cannot describe gravity, dark matter, and other observed phenomena. PIONEER will test LFU by measuring the relative frequency of the two primary decays of a subatomic particle known as a pion. The ratio of the rates of pion decay to muon and pion decay to electron is predicted extremely precisely by the SM and is sensitive to physics beyond the SM. Therefore, this ratio is extremely important to measure. Muons quickly decay to electrons, so the final product of both decays is an electron, but their energies can distinguish the decay path. Thus, this measurement requires an extremely sensitive calorimeter to measure the energies of the resulting electrons. One candidate for this calorimeter is a large array of LYSO crystals. LYSO is a fast, dense, high-light-yield scintillator whose intrinsic properties suggest it would be a natural candidate for the experiment. Despite its advantages, a large, LYSO-based calorimeter has never been developed. We wish to measure certain properties of large LYSO crystals, such as energy resolution and uniformity, to determine if they meet the requirements necessary for use in the PIONEER calorimeter. Bench tests conducted thus far have displayed impressive single-crystal resolution and uniformity at low energies when crystals are wrapped in a well-fitted specular reflector. Energy resolution tests were conducted on an array of 10 LYSO crystals, using 17.6 MeV gamma rays produced by the Van der Graff accelerator at the Center for Experimental Nuclear Physics and Astrophysics (CENPA) here at UW. LYSO crystal performance and energy resolution have been shown in preliminary tests to be within the specifications for the PIONEER calorimeter.

Photoreceptor cells in the retina use several opsin proteins to detect light and confer visual information. Mutations to genes encoding opsins are associated with varying degrees of color blindness and retinal degeneration. In a previous mouse model for color blindness the retina degenerated, with a significant reduction of healthy cones by 3 months (Ma, et al., 2022, Human Gene Therapy). I am characterizing a new mouse line that was gene edited to lack both blue and green sensitive cone opsins, making it a double knock out. We fix and embed the eyes before freezing them, and then I stain frozen eye sections with fluorescent antibodies.  Using a high-resolution microscope, I am able to examine retina health and cone populations. I am comparing knockout animals with a wild type strain of normal mice and a retinal degeneration strain processed in the same way. I confirmed the absence of both blue and green cone opsin in the knockout mice, and despite being a model for color blindness, the mice maintain a healthy population of ospin-less cones for at least one year. However, at one year the knockout mice have approximately 30% fewer cones in their retinas than normal mice. The populations of dying cells and immune response cells in the knockout retinas match those seen in the wild type retinas, and are significantly lower than the populations seen in the degeneration model. This suggests that the retina is not in an active state of degeneration for at least one year. This model will be useful for future development of cone opsin gene therapies, and can serve as a model for color blindness. It also has implications for the health of cones without the cone opsin protein.

Androgen deprivation therapy (ADT), the pharmacologic reduction of testosterone (T), is a critical treatment for prostate cancer patients, improving cancer-related outcomes but markedly increasing the risk of cardiovascular disease development. Our recent findings suggest that patients with prostate cancer subjected to ADT have increased hypothalamic gliosis (the activation of astrocytes and microglia), a hallmark of central nervous system injury. Similarly, castrated mice fed a high-fat, high-sucrose with added cholesterol diet (HFHS) develop hypothalamic astrogliosis and atherosclerosis, which can be prevented through T replacement at the onset of castration. In this experiment, we tested whether established astrogliosis in hypogonadal mice can be reversed by restoring healthy T levels. Using a gonadotropin-releasing hormone antagonist (acyline) as ADT, we treated 3 groups of HFHS-fed C57Bl/6 wild-type mice with: 1) vehicle, 2) acyline for 4 weeks, and 3) acyline for 4 weeks followed by a 4 week period of reversal to vehicle. Hypothalamic brain sections were used for immunohistochemistry analysis to quantify levels of glial fibrillary acidic protein (GFAP) expression, a marker for astrogliosis, and neurokinin B (NKB) expression, a marker for reproductive function. As anticipated, ADT resulted in a significant reduction in testes weight and NKB expression, serving as surrogate measurements of low T production. ADT also induced a significant increase in hypothalamic GFAP expression, confirming that gliosis is exacerbated in hypogonadal conditions. Following the discontinuation of ADT, testes weight and hypothalamic NKB expression rebounded to normal levels, however, hypothalamic astrogliosis remained significantly elevated. Together these data suggest that once astrogliosis is established, the restoration of T via 1 month of ADT cessation is insufficient to reverse it. This finding is a critical step forward in clarifying the pathways between androgen signaling and cardiometabolic regulation, and raises an important clinical concern given the high incidence of morbidity and mortality associated with ADT.

Stress-related physiological and social factors can have a direct impact on cancer biology and patient outcomes. Exposure to a stressor can lead to downstream activation of signaling pathways that can impact cancer-related processes. Compared to older and younger patients with cancer, adolescents and young adults (AYAs) have had less improvement in clinical outcomes and report high levels of psychosocial distress. The goal of this study is to examine the feasibility and acceptability of a multimethod triangulation protocol collecting stress biomarkers along with subjective patient reported outcomes among AYAs with cancer. Eligible participants are 12-24 years old within six months of initial cancer diagnosis and undergoing treatment at Seattle Children's Hospital. Once enrolled, participants wear a sensor measuring autonomic nervous system activity [quantified as heart rate variability (HRV)] while completing validated patient reported outcome (PRO) surveys assessing psychosocial symptoms and participating in a qualitative interview querying the same domains. Interviews are recorded using Microsoft Office Dictation services. I listen to the audio files and go over the transcribed document making corrections and highlighting key quotations. Additionally, at the time of a participant's planned clinical blood dram, 5mL of blood is collected to measure a social genomics stress biomarker called the conserved transcriptional response to adversity (CTRA). We expect to find greater than 70% feasibility and 80% acceptability in this study. Feasibility is defined as the percentage of participants who complete all (100%) study procedures; acceptability is defined as the percentage of participants who agree that similar patients could complete the study. Results from this pilot study will inform future longitudinal investigations and the development of targeted biopsychosocial interventions for AYAs with cancer. 

Currently, over 6.6 million Americans use walking canes, rollators, and forearm crutches. However, little work has been done to improve the practicality of mobility aids for users. Prior work on modifying these mobility devices has centered around sensing and monitoring user interactions with their mobility device, without changes to the core structure of the devices. Our project aims to explore a set of mobility aid modifications including aesthetics, comfort, and ergonomics. We conducted over 15 qualitative interviews with mobility aid users using phenomenological interviewing strategies to understand user preferences and experiences better and gain feedback on possible adjustments to mobility devices. After qualitative analysis and creating codes based on patterns observed in the interviews analyzed, we identified and compiled unique experiences amongst mobility aid users into a codebook. We then sought to address these observations using fabrication methods such as 3D printing, laser-cutting, and soldering to modify existing mobility devices and develop prototyping materials. Subsequently, we conducted a follow-up design workshop to have users develop modifications and accessory ideas using the tools and templates we provided. Some modifications considered included interactivity stickers, physical feedback mechanisms, and improved mobility aid tip designs. Ultimately, we gained feedback for modifications in future mobility aids research and produced guidelines from our experiences working with mobility devices that can improve community input in accessibility aid research. This work also contributed valuable insights into approaching mobility aid improvements from a Human-Computer Interaction perspective.

Gun violence is a prevalent and rising issue in the United States. However, limited research assesses the connection between gun prevalence and public health outcomes. Previous research indicates healthcare professionals are hesitant to have a role in addressing the rising gun violence statistics. Another previously drawn implication is that gun violence is associated with worse behavioral and physical health. These findings led us to pursue our research. This project aims to acquire quantitative insights into the relationship between neighborhood-level gun prevalence and violence and neighborhood-level utilization of primary healthcare. Within the context of this study, neighborhood gun prevalence and violence are defined as instances of violence encompassing firearm-related fatalities or the mean quantity of firearms within households. We define utilization of primary healthcare as a composite of a variety of healthcare variables, including, but not limited to, the percentage of dental check-ups, the percentage of the population with established primary care providers, health indicator screenings, and vaccination rates. We are using data from the Seattle & King County Public Health Database to examine the association between our variables of interest at the neighborhood level. We will conduct a linear regression model to statistically examine the correlation between the utilization of primary health care and neighborhood gun violence statistics. We anticipate that the findings of this study will elucidate a discernible correlation between indicators of primary care access and firearm-related violence at the neighborhood level in the Puget Sound region. We intend to employ this data to aid local public health officials in understanding and addressing the correlation between healthcare disparities and gun violence. Subsequently, this information can serve as a foundation for their efforts in formulating population-level legislation aimed at mitigating healthcare disparities to alleviate firearm violence at the neighborhood level.

Alzheimer's disease (AD), the most common form of dementia, is characterized by the improper cleavage of amyloid precursor protein by a complex containing presenilin 1 (PSEN1) or presenilin 2 (PSEN2). Notably, PSEN1 and PSEN2 are strong genetic risk factors for heritable AD. However, 95% of AD cases currently have no known genetic cause. Recent work from the Valdmanis lab found PSEN2 isoform variations at the RNA level in sporadic AD. One such variation was the detection of differential 3'UTR lengths on the PSEN2 transcript. The 3'UTR is an important regulatory region that controls transcript maturation, stability, and abundance and is subject to environmental regulation. The length of this regulatory region is determined by RNA processing machinery during polyadenylation, and differences in this post-transcriptional process lead to differences in the 3'UTR length known as alternative polyadenylation (APA). APA may represent a functional mechanism by which PSEN2 regulation differs in AD. The goal of these studies is to understand the impact of PSEN2 APA on neuronal function. We hypothesize that the length of the 3'UTR on PSEN2 transcript aligns with phenotypic changes associated with AD. To test this hypothesis, we are cloning PSEN2 with short and long 3'UTRs to test the functional differences of PSEN2 APA in vitro. Our goal is to introduce the short and long PSEN2 3'UTR constructs in the cells, specifically, microglia, the brain's immune cells, which are heavily implicated in AD pathology. Then, we will visualize the subcellular location of these transcripts and test for altered amyloid beta processing, which is a pathological hallmark of AD. We anticipate detecting differences in regulation and subcellular localization between the short and long PSEN2 3'UTR transcripts. Elucidating the functional relevance of the short and long 3'UTR of the PSEN2 transcript will further our understanding of APA in AD.

Respiratory viruses are a major cause of mortality and morbidity in vulnerable populations. Together, Respiratory syncytial virus (RSV) and Human metapneumovirus (HMPV), are responsible for over â…“ of serious viral respiratory infections in hematopoietic stem cell transplant (HCT) recipients. Currently, no treatments are available for RSV or HMPV in immunocompromised adults. While monoclonal antibodies (mAbs) show promise as a treatment, challenges arise, including limited efficacy when administered post-infection. Our goal was to enhance the therapeutic efficacy of a newly discovered cross-neutralizing human mAb to RSV and HMPV. We aimed to investigate whether modifying the Fc domain of the antibody could increase its binding to Fcγ receptors (FcγRs) found on different types of immune cells. Activation of FcγRs initiates important cell processes such as clearance of virus-infected cells, also known as Antibody-dependent cellular cytotoxicity (ADCC). This modification potentially makes the antibody a more effective treatment option for RSV and HMPV infections. To do this we looked at the binding kinetics and affinity of modified antibodies to human FcγRIIIa, FcγRIIa and FcγRIIb receptors using Bio-Layer Inferometry (BLI). Our data indicate that certain amino acid modifications or afucosylation of the Fc region can increase the antibody’s binding affinity to different human FcγRs. Since hamsters are an important preclinical model used to determine RSV and HMPV drug efficacy, it was important to examine the binding affinity of our human antibody to hamster FcγR’s. Our data indicate that the wild-type Fc region does bind to the homologous hamster receptors. Moreover, certain modifications in the Fc region led to increased binding to hamster FcγR’s. Together, these data indicate that modifications in the Fc region of human antibodies can increase their binding affinity to both human and hamster FcγRs. This increase in binding affinity could translate to enhanced potency in the preclinical hamster model and in humans.

Chronic kidney disease of unknown etiology (CKDu) is a pervasive condition not prompted by diabetes or hypertension but instead by environmental stimuli and occupational associated risks. Often detected only in advanced stages, CKDu necessitates interventions such as dialysis and kidney transplant, significantly burdening healthcare systems globally and disproportionally affecting rural populations. Ochratoxin-A (OTA), an abundant, ubiquitous, natural contaminant found in food products and is among the postulated risk factors for (CKDu). While animal studies indicate dysregulation of mitochondrial dynamics and production of superoxides via redox cycling as potential mechanisms of OTA-associated nephrotoxicity, its exposure risk in humans and kidney health remain poorly understood. This study investigates the biological pathways that contribute to the toxicity of OTA in the proximal tubule, leading to CKDu. Luminescence-based imaging approach evaluated the occurrence of OTA-induced oxidative stress in human proximal tubular epithelial cells (PTEC) by detecting cytoplasmic reactive oxygen species (ROS). Preliminary mRNA transcriptomic analysis has indicated the down-regulation of glutathione pathways, a major antioxidant pathway removing cellular oxygen. I probed OTA-treated PTECs with a reduced glutathione detection reagent, ThiolTracker Violet, to investigate the cell’s response capability for oxidative stress and detoxify xenobiotics. To verify oxidative stress mediated by OTA in live cells, CellROX Green Reagent probe treated PTECs were brought under confocal microscopy to visualize mitochondrial phenotype. The results of this investigation seek to reveal the metabolic response to OTA cytotoxicity in the human kidney and elucidate its role in CKDu progression to address diagnostic challenges and confront unmet medical needs.

Most eukaryotes use histones to package the genome. However, many animals package their sperm genomes using specialized DNA-binding proteins called protamines, which package DNA in sperm more tightly to fit inside the sperm head. Based on the transcriptional silencing role of protamines, we hypothesize that protamines can suppress meiotic drivers, which kill other sperm to bias their own transmission. Previously, we found that one protamine gene, Mst77F, is required to suppress meiotic drivers on the Y-chromosome in Drosophila melanogaster. Since drive is generally deleterious for the transmission of autosomal alleles (due to lower male fertility for example) theory predicts that multiple suppressors of drive will arise in populations; Mst77F may represent just one such suppressor. We hypothesized that multiple natural variants in distinct genetic loci interact with and impact meiotic drive in Drosophila melanogaster. To identify these natural variants, I crossed wildtype flies to knock out flies and generate hemizygous Mst77F flies carrying genetic backgrounds from four different populations. I measured the fertility and drive strength by crossing a single hemizygous male from each cross to five wild type females. In all cases, I found that the sex ratio was skewed to favor male offspring, indicating they all carry X-linked targets. However, I did not identify any dominant genetic variation associated with the drive strength, indicating Mst77F might be the major suppressor of this drive. I am conducting reciprocal crosses to determine whether Y chromosomes from different populations carry the same strength of drive. In the future, I will extend my analyses to other genetic backgrounds. My study contributes to a better understanding of the pervasive effects of meiotic drive in natural populations and unexpected functions of protamines.

Joubert syndrome (JS) is a rare, congenital neurodevelopmental condition diagnosed by the appearance of the “molar tooth sign” on axial brain magnetic imaging (MRI). Patients typically display hypotonia, abnormal eye movements, and ataxia. Substantial progress has been made on identifying the genetic causes of JS, which typically displays recessive inheritance. Nonetheless, the cause still cannot be identified in ~27% of our cohort of JS-affected families and the contribution of causal variants that impact RNA splicing remains unknown. Canonical splice variants impact RNA splicing by disrupting the splice site directly, whereas noncanonical splice variants affect it through alternative mechanisms, which must be validated by RNA analysis. Our goal is to evaluate the role of noncanonical splice variants in the pathogenesis of JS. We previously identified genetic causes in 582 of 714 families with JS. To identify additional causes, we used SpliceAI, a deep learning-based tool to identify variants with predicted splicing effects (SpliceAI score >0.5) for functional validation. We extracted RNA from patient cell lines then used polymerase chain reaction (PCR) and evaluated amplicons using gel electrophoresis and Sanger sequencing. Five families with candidate noncanonical splice variants that may confirm their genetic cause provided skin biopsies for further splice analysis. We confirmed the pathogenicity of three of these variants by demonstrating abnormal splicing in JS genes, AHI1 and MKS1, bringing the total contribution of aberrant splicing up to 77/714 families. The final two variants did not render conclusive results after 10+ attempts of PCR-based assays and may therefore be candidates for other methods of investigation such as mini-gene assays or long-read sequencing. By extrapolation from our data in JS, splice variants may contribute ≥11% to the genetic causes of conditions. A precise genetic diagnosis informs prognosis, avoids unnecessary work-up, guides monitoring for associated complications, and opens the door to gene-specific treatments.

Preterm birth is one of the leading causes of infant morbidity and mortality worldwide, with a strong association between the degree of prematurity and the likelihood of death or neurodevelopmental impairment. Intracranial hemorrhage (ICH) is one of the most common neurological injuries for extremely preterm infants (born less than 28 weeks’ gestation). During the last trimester of pregnancy, neurons and glial cells develop in the germinal matrix requiring vast amounts of vascular support. In preterm infants, disturbances to blood and hydrostatic pressure are thought to rupture the immature vessels of the germinal matrix, leading to the bleeding in and around the ventricles. ICH is rated on a scale of I to IV, with severe ICH being grade III-IV. Mortality associated with ICH ranges from 30-60 percent, increasing with ICH severity, and survivors have an increased risk of cerebral palsy, seizures, and neurodevelopmental delay. From 2018-2020 the University of Washington (UW) neonatal intensive care unit (NICU) implemented an ICH Prevention Bundle, which focused on minimizing blood pressure disturbances during the first 72 hours after birth in infants born extremely premature, and appeared to result in a decrease in severe ICH. This study will evaluate the incidence rate of ICH at the UW NICU over a ten-year period. In a retrospective analysis of the UW NICU’s admissions, we will investigate extremely preterm infants born during the time periods of December 2013-September 2016 versus January 2017-December 2023 and record the incidence of ICH. Our primary outcomes will be ICH, by grades I-IV, as well as ICH complications such as posthemorrhagic ventricular dilatation with and without need for intervention, and death before discharge. We hypothesize that with improved prevention methods, such as the implementation of the ICH Prevention Bundle, we will see an associated long-term decrease in the incidence rate of ICH.

Half of the earth's photosynthetic activity occurs in the ocean. However, marine ecosystems generally have lower rates of carbon sequestration when compared to terrestrial ones. This is an opportunity to enable large scale carbon sequestration. The waters of the open ocean are nutrient deficient and can have low primary productivity. Supplying the limiting nutrients can theoretically enable rapid growth of photosynthetic cells but this growth must be contained or it will be lost to the ocean. By preparing these missing nutrients in hydrogels with efficient photosynthetic consortia, the growth process and inputs can be contained and the biomass harvested. The Winkler Lab is using this method to develope biological systems for carbon sequestration. I am researching the efficiency of microalgae and cyanobacteria consortia in seawater with native microbes. I aim to form cultures of photosynthetic marine microbes by inoculating hydrogels containing chlorella sp. in seawater samples. The objective is to optimize squestration with naturally occurring microbial consortia. Through multiple trials I have identified a mix of microbes and macroalgae cultured from the Puget Sound that exhibits rapid biomass production. Data is collected via microscopy, imaging and by measuring chemical oxygen demand and chlorophyll content. My aim is to compare this wild microbial mix to the Winkler lab's established mixes of cyanobacteria and microalgae and determine which is more effective in fixing carbon. Expected results will demonstrate this wild culture more efficient in low nutrient environments than the lab culture. Success in this project could help refine commercializable methods to remove atmospheric carbon dioxide and fight climate change. 

The use of pesticides in the Pacific Northwest is essential in the process of safeguarding public health, most notably by mitigating pests, protecting our food supply, and aiding in distribution to supermarkets, restaurants, and our homes. However, long-term exposure to pesticides can result in illness for those handling the substances as well as their families. Prior research has shown that current pesticide application methods play a role in accelerating illness. Newer methods, such as aerial drone spraying and “smart” sprayers, involve the use of emerging technologies that are poised to change the landscape of the agricultural industry and health outcomes of farmworkers. Under the supervision of the Pacific Northwest Agricultural Health and Safety (PNASH) Center, my project will be assessing thoughts regarding adoption of these technologies. Through the creation of an electronic REDCap survey, I will be obtaining a variety of responses from agricultural workers, farm decisionmakers, and others involved in the application of pesticides on farms. Once the survey is deployed, I will analyze responses both quantitatively and qualitatively using Dedoose and R statistical methods, respectively. From these responses, I will work with the PNASH team to evaluate the adoption of current and emerging pesticide technologies among Northwest fruit growers, as well as their impacts on occupational health and safety. Through this project, I hope to collect a wide range of perspectives and thoughts regarding the implementation of new pesticide application technologies, particularly unique opinion points (positive and negative) I did not otherwise consider in my initial research with the PNASH Center. The main objective of my research project is to capture the attitudes of the pesticide application technologies to inform policy, regulations, and decision-making regarding their uses.

According to the World Health Organization, Alzheimer’s Disease (AD) is the most common form of dementia – a major and growing cause of disability and dependency among older people globally. The Seattle AD Brain Cell Atlas (SEA-AD) project is a collaboration between the University of Washington (UW) and the Allen Institute for Brain Science (AIBS) aimed at discovering early vulnerable cell types in AD. In SEA-AD, we hope to further our understanding of the etiology and early progression of AD to ultimately identify targets for effective therapeutic intervention. Eighty-four participant brain donors with a postmortem interval less than 12 hours from the UW AD Research Center (12/84) and Kaiser Adult Changes in Thought (72/84) studies were included in the SEA-AD cohort. At the time of procurement, one hemisphere was frozen in super-cooled isopentane for transcriptomic analysis at AIBS; the contralateral hemisphere was fixed in 10% neutral buffered formalin for neuropathologic assessment at UW. The middle temporal gyrus, medial entorhinal cortex, and hippocampus were sampled, processed, embedded in paraffin, and sectioned for  immunohistochemical (IHC) studies. Seven antibodies, including duplexed stains, targeting amyloid b (6e10) and microglia (IBA1), pTau (AT8) and pTDP-43 (1D3), monoplexed a-synuclein (LB509), astrocytes (GFAP), neurons (NeuN), and triplexed histochemical stain: hematoxylin, eosin, and Luxol fast blue were deployed to assess the neuropathology associated with the presence and progression of AD and related neuropathologic changes. The data obtained from the quantitative assessment of the IHC staining is integrated with the transcriptomic data generated by the Allen Institute to enhance our understanding of the cellular vulnerabilities and associated molecular processes of AD. Public access to this neuropathological data through the SEA-AD resource potentiates research efforts to understand and identify the mechanisms of AD progression.

I aim to determine if intestinal fatty acid binding protein (I-FABP) is an accurate biomarker to assess the health of Kenyan children. I-FABP is an intracellular protein whose levels rapidly elevate after intestinal damage by various illnesses. Here I will correlate I-FABP levels to pediatric health status by analyzing I-FABP concentrations in plasma from hospitalized vs healthy children in 2 Kenyan pediatric cohorts for which we have concurrent clinical and symptom data. I used R&D Quantikine Human I-FABP ELISA kits to quantify I-FABP in plasma from <5-year-old children collected at hospital discharge (n=1024) and 2-year-old healthy children (n=109). I have completed ELISAs for the hospitalized children and am currently conducting the I-FABP ELISAs for the healthy children. Median I-FABP concentration from the hospitalized children is 1380 pg/mL (IQR: 920-2027 pg/mL). Published data suggests median I-FABP levels are typically <900 in healthy children, indicating that I-FABP levels may be elevated in hospitalized vs healthy children. However, the published data from healthy children is not from a Kenyan cohort and is from an older age group, thus it is important to compare our data from hospitalized children to healthy children with similar demographics. To minimize I-FABP concentration differences due to age, I will restrict the data from the hospitalized cohort to samples from children with a median age of 2 years (range: 1-3 years) to compare to the data I am currently generating from the 2-year-old healthy children in our cohort. I expect significantly elevated I-FABP concentrations in the hospitalized children in comparison to the healthy children. I will also analyze the data according to reported intestinal diseases like diarrhea. This work will help show whether I-FABP can be used as an accurate biomarker to indicate gut health of Kenyan children after hospitalization, which can inform and guide treatment of these individuals.

The heart is one of the most mechanically active organs in the body. In a mechanism known as the “Bainbridge Reflex”, the heart rate accelerates in response to the mechanical stretch induced by the increase in venous return. The cardiac pacemaker controls heart rate, and while stretch-activated channels have been identified in cardiac tissue, their molecular identity remains unknown. We hypothesize that PIEZO channels are the molecular determinant of the stretch-dependent heart rate acceleration responsible for the Bainbridge reflex. Using quantitative polymerase chain reaction (qPCR), we assessed the presence of Piezo1 and Piezo2 transcripts in the pacemaker, atrium, and ventricle of the mouse heart. Our findings revealed that both Piezo1 and Piezo2 are present in the three regions with significantly higher expression in the pacemaker and atria. Combining immunohystochemistry, tissue clearing, and super-resolution microscopy, we analyzed the distribution of Piezo1 and Piezo2 in mouse pacemaker explants. Our results show that Piezo2 is uniformly expressed in the pacemaker and surrounding atrial tissue, whereas Piezo1 exhibits higher expression levels outside the pacemaker. These results were further confirmed at the single-cell level, with immunostaining of Piezo1 and Piezo2 in isolated pacemaker cells (HCN4+) and transitional cells (HCN4-). We observed similar expression levels of Piezo2 in both cell types and increased Piezo1 expression in transitional cells. In addition, we observed distinct localization patterns for Piezo1 and Piezo2 at the subcellular level. Piezo1 predominantly localizes to the sarcolemma, while Piezo2 exhibits a striated distribution that colocalizes alternately with both the Z- and the M- line of the sarcomere. Given this pattern, half of the Piezo2 bands colocalize with the RyR. These results set the starting point to evaluate the functional role of PIEZO channels in the cardiac pacemaker.

Global Positioning Systems (GPS) technology plays a pivotal role in ensuring the safe and efficient navigation of drones by providing near real-time tracking of location and speed. The precision and reliability of GPS receivers are crucial for effective planning, sensing, and control applications in various domains. As Unmanned Aerial Vehicles (UAVs) continue to rise in demand and predominantly rely on GPS, minimizing the uncertainty in GPS performance becomes imperative. UAVs utilize the cost-effective nature of Micro-electromechanical Systems (MEMS) GPS receivers. This study identifies and analyzes GPS errors, specifically within consumer-grade MEMS receivers. The MEMS receivers are preferred for their low cost, low power, and low weight, making them ideal for integration into UAVs. Our methods include a series of controlled experiments in urban and semi-urban environments, encompassing varying weather conditions such as sunny and cloudy days. Static experiments evaluate GPS signal accuracy under stationary conditions, while dynamic experiments monitor GPS performance during drone flights. Our preliminary findings have shown a range of inaccuracies in GPS signal measurements. Horizontal signal accuracy varied from +/-1 to +/-14 meters, while vertical signal accuracy ranged from +/-3 to +/-12 meters. These results underscore the significance of further investigation to enhance GPS reliability, particularly in scenarios critical for UAV operations. In ongoing research, we are conducting more testing in other geographical locations and weather conditions to ensure the robustness of our conclusion. Additionally, we are developing environment-specific error detection algorithms utilizing the sensor fusion approach. Merging data from multiple sensors can reduce the uncertainty of an object's location, helping us when the GPS technology is not fully reliable. Our research contributes to advancing GPS technology capabilities, particularly for UAVs where accurate localization is important.

The Riemann Hypothesis is an important unsolved problem in mathematics under number theory, concerning the distribution of prime numbers. It can be characterized as finding precise bounds on the partial sums of the classical M\"obius function. The M\"obius function is a technical tool that generalizes the inclusion-exclusion principal in discrete math and combinatorics. Due to the difficulty of the Riemann Hypothesis, it is common to analyze a modification of the underlying structure. This project analyzes the M\"obius function defined on the partially ordered set of triangular numbers (of the form 1, 3, 6, 10...) under the divisibility relation. My mentor and I made conjectures on the asymptotic behavior of the M\"obius and Mertens functions on the basis of experimental data. We first introduce the growth of partial sums of the triangular M\"obius function and analyze how the growth is different from the classical M\"obius function, and then analyze the partial sums of its absolute values, and how it is similar to the asymptotic in the classical case. I then created Hasse diagrams of this structure, this is a method to visualize a partially ordered set (poset). This also serves as a basis for the zeta and M\"obius matrices. Looking specifically into the poset defined by $(\mathbb{N}, \leq_{\mathcal T})$, or triangular numbers under divisibility, and applying the M\"obius function to it, we were able to create our desired matrices. Using Python libraries I created visualizations for further analysis, and was able to project previously mentioned patterns. Through which we are able to introduce two more novel conjectures bounding $\mu_{\mathcal T}(n)$ and the sums of $\frac{\mu_{\mathcal T}(i)}{i}$. We conclude the project with divisibility patterns in the Appendix.

Adolescents increasingly use digital technology. However, there might be variability in how important adolescents perceive their interactions with media and technology 1) to bridge online and offline experiences, 2) to go outside one’s identity or offline environment and 3) for social connection. This study aims to validate the Spanish version of the Adolescent Digital Technology Interactions and Importance Scale (ADTI), originally developed for US adolescents, with a sample of Peruvian adolescents. In addition, we investigated developmental and gender differences in these subscales. A total of 1,425 Peruvian adolescents (10 - 17 years, Mage = 13.2; 52% female) completed the ADTI remotely via Qualtrics in April 2020, a few weeks after adolescents had started remote schooling. I ran descriptive statistics and linear regressions to test for age and gender differences. Factor 1 (bridging online and offline experiences) was the highest ranked M = 15.1 (5), followed by Factor 2 (going outside one’s identity or offline environment), M = 14.2 (4.6). Factor 3 (social connection) was the lowest ranked M = 12.6 (4.5). Age was significantly correlated with Factor 1 and Factor 3 indicating that older adolescents endorsed higher levels of importance of technology for bridging online and offline environments as well as social connection. There was no significant age difference for Factor 2. We investigated gender differences. Girls had significantly higher levels for Factor 1 compared to boys Mgirls = 15.4 (4.7); Mboys = 14.7 (5.2) and for Factor 3 Mgirls = 13.4 (4.6); Mboys = 11.9 (4.3). There were no significant gender differences for Factor 2. This work can lead to better understanding of the role that technology plays in the lives of adolescents, and to implementation of safer practices in media and technology.

Biological tissues are a group of cells that have similar structure and that function together as a unit. In between these cells is the extracellular matrix (ECM), which provides structural support for resident cells. The makeup of the ECM consists of fibrous proteins, such as collagen, that are interlocked and cross-linked, following a nonlinear stress/strain curve and is considered viscoelastic. The dominant mechanism behind this response is the presence of largely elastic, spring-like straightening/uncrimping of fibrils. This can be thought of like applying a force to springs in parallel. Overall, this mechanism allows the ECM fibrils to align and elongate significantly under small loads, thereby aligning the cells. This, in turn, affects the overall tissue structure and its mechanical properties. We have developed a method for patterning a cell-infused collagen mixture as a three-dimensional tissue, and subsequently stretching it, in order to observe how the cells develop in a strained environment. Specifically, we have engineered two devices that fit within a 6-well plate: the tissue is patterned on the first device, and then transferred to the second for stretching. During each phase, the suspended tissue is incubated for a period of time in order to facilitate cell development and hydrogel gelling. Once the tissue has been stretched for a certain period of time, it is then removed from the device and imaged. Our modular design designates strain as an known and adjustable value, allowing us to relate it to the internal stresses of the tissue via Hooke's Law. We are able to identify the quantitative conditions that promote tissue alignment and maturation within the suspended tissue.

Adolescence is a critical stage of development, a time in which social relations are pivotal to feelings of connectedness, belongingness, and wellbeing. Amidst the rise in usage of widespread social media platforms, adolescents have begun to seek out online-only friendships (OOFs), prompting our lab to explore the prevalence and quality of these social connections. We first gathered data from adolescents (n = 5756, ages 10-18) in Peru in 2020, during the COVID-19 lockdown. In 2023, we repeated and refined our prior analyses after gathering data from adolescents in Bolivia (n = 1071) and Uruguay (n = 647). We administered a Qualtrics survey asking participants to self-report on the number and perceived quality of OOFs and IPFs (in-person friendships), using the Network of Relationships Inventory (Furman and Buhmester, 1985). I served as a Research Assistant (RA) for the interACT Lab. I reviewed the literature on online friendships, performed data cleanup, and assisted on statistical analyses of our data. Given the lack of prior research on the topic, our lab sought to explore the quality of online friendships in order to provide a foundation for future investigations. Currently, our lab is analyzing the quality of IPFs vs. OOFs on the basis of self-reported levels of support, closeness, trust, and similar-interests. 79.8% of adolescents in our sample have OOFs. In addition, preliminary findings indicate that IPFs have more negative qualities than OOFs, and that OOFs have more negative qualities than IPFs . This work is important because not only does it examine adolescent technology usage in regard to social connectivity, but it also presents findings from the Global South, which is often underrepresented in psychology research. Our findings provide an understanding of the benefits and downsides of engaging in online-only friendships for adolescents in South America, a region that is too often underrepresented in psychology research.

The interplay between physical environments, particularly indoor spaces, and psychological well-being is an emergent research area with significant practical implications. Despite acknowledging the positive effects of clean and luminous spaces, robust methodologies to evaluate such environments objectively are scarce. This study addresses the challenge by proposing to estimate an environment's influence on well-being from a single photograph. Support Vector Machines, a type of machine learning algorithm particularly effective for pattern recognition tasks by finding the optimal hyperplane that best separates data points of different classes, are employed to analyze specific features like messiness and brightness, which have been empirically linked to comfort and mood. This analysis is part of a broader set of variables our comprehensive model assesses, aiming to provide a nuanced environmental quality assessment tool. The aim is to quantify this analysis into a suitability score that reflects an indoor space's potential to enhance well-being, based on the model’s confidence. Our model is trained on a diverse and ethically sourced dataset, including anonymized student contributions and internet images, preparing it to offer refined classifications. The ultimate objective is to inform non-clinical, preliminary evaluations of environmental quality and suggest enhancements for spaces used in daily life.

Segmentation is an imaging technique commonly used to isolate an object of interest, such as an organ, from the background, or other objects in the image. When analyzing the shape of an anatomical structure, segmentation of that structure is often the first step in analysis. Precise anatomical segmentations are often created manually by subject experts, which is time-consuming, does not scale well, and can be prone to error since it is subjective. In this project, we aim to develop a machine-learning model to expedite whole-body surface segmentation from fetal mouse scans as part of an automated pipeline to detect asymmetry and abnormality in the facial region. The International Mouse Phenotyping Consortium (IMPC) has generated a large repository of three-dimensional (3D) imaging data from mouse embryos, providing a rich resource for investigating phenotype/genotype interactions. To generate segmentations required for training and validation of our deep learning model, the full body surface was manually segmented in 91 baseline scans from the IMPC’s Knockout Mouse Phenotyping Program (KOMP2) dataset. I trained a UNet with transformers (UNETR), on these segmentations that is able to estimate surface segmentations from new micro-CT mice images with an accuracy of 0.9. I am currently developing a fetal mouse full-body segmentation application powered by our deep learning model, SurfaceExtract, that will be made publicly available as an extension to the open-source image analysis platform, 3D Slicer. SurfaceExtract will be used by our lab to quickly and accurately generate segmentations of fetal mice as part of our lab’s automated facial asymmetry phenotyping pipeline.

Climate change caused by CO2 emissions creates a need for greater energy efficiency, as energy production produces CO2. One area of improvement is in chemical separations, which consume roughly half of all industrial energy use. Most of these processes could be made ten times more efficient by switching from energy-intensive distillation and absorption processes to membrane separations. Mixed Matrix Membranes (MMMs) are a particularly promising option for use in gas separations. These MMMs incorporate Metal Organic Framework (MOF) crystallites within polymer membranes to balance the benefits of both. However, the parameters that determine the growth of some MOFs, like ZIF-8, are still unknown. Here, we explore the growth conditions of ZIF-8 to enable the production of these MMMs on an industrial scale. By exposing zinc oxide (ZnO) coated silicon wafers to 2-methylimidazole (HmIm) in a tube furnace, I measure ZIF-8 crystal formation at varying temperatures, temperature gradients, and anneal times. Crystal thickness is measured using ellipsometry to observe successful crystal formation. Using COMSOL software, we explore models of the HmIm concentration to determine what experimental variables could have the largest effect on ZnO to ZIF-8 conversion. Preliminary experimental results suggest a specific temperature profile is needed, as well as a required minimum anneal time for successful ZnO to ZIF-8 conversion. Furthermore, temperature gradients appear to impact HmIm concentration, which affects crystal growth. These findings may enable industrial-scale production methods for MMMs with ZIF-8, and may also prove useful when producing MMMs with other MOFs.

Trapped ion quantum computing (TIQC), with its large decoherence times and small operation times relative to other physical quantum computing architectures, has garnered significant attention in the public and private sectors. Planar Paul traps, which simultaneously utilize radio frequency and static voltages in a two-dimensional electrode array to spatially confine ions, are the primary candidates for trapping ions for TIQC due to their manufacturability and ability to shuttle ions between multiple trapping zones for quantum logic gates and memory storage. The growing relevance of this technology necessitates educating students about the advanced electrodynamics of ion trapping and ion shuttling. Therefore, I developed a macroscopic planar Paul trap which utilizes 50µm diameter proxy-ions along with high voltage (HV) alternating currents (AC) at 60 Hz and HV direct currents (DC). These are applied to a 5-rail electrode geometry to demonstrate ion shuttling and ion-group splitting along a linear trapping axis. The goal is to educate students on the electrodynamics of ion traps by allowing them to experiment with the tunable trapping parameters, such as AC voltage amplitudes, DC voltage magnitudes, and applied shuttling waveforms and observe the changes in the dynamics of the proxy-ions relative to theoretical predictions. I designed the trap by implementing the recommended relative electrode dimensions into COMSOL Multiphysics and optimizing the geometry by maximizing the pseudopotential confinement while simultaneously minimizing electrode surface area. Afterwards, I utilized an analytic model of a 5-rail planar Paul trap, along with the method of Lagrange multipliers, to optimize the voltage magnitude and waveform of the segmented electrodes for smooth, effective shuttling and ion-group splitting. I then integrated an HV relay circuit and the 5-rail electrode geometry onto printed circuit boards to allow for student-controlled ion shuttling via an Arduino microcontroller.

This research was designed to highlight the connections between the human evolutionary trait of loss aversion and implications for current marketing strategies through an analysis of consumer behavior. The objective of this research is to find which companies target human evolutionary traits in their marketing strategies, and if this is an effective strategy, by analyzing consumer purchase trends. This project focused on loss aversion, which originated as a field of behavioral economics through experiments designed to test human’s reactions to loss, change, and making decisions under uncertain circumstances, ultimately showing that not only do people value preventing equal losses over equal gains, but it’s nearly twice as important to prevent losses based on the emotional impact of the losses. Loss aversion can be used as a consumer behavior analysis method, as most consumers act under uncertain circumstances, weighing their need for a product against the money lost in the purchase. By analyzing the effects of loss aversion on modern day consumer behavior, companies can adapt to different scenarios, implementing marketing strategies using human evolutionary traits. This study compared the marketing trends of multiple large corporations and consumer purchase trends. The results of the study showed that the majority of companies used some type of loss aversion marketing strategy, and the ones that did employ this strategy were often financially better than companies that did not. This research has implications for a variety of companies aiming to expand their marketing strategies and increase their effectiveness. This information is also valuable for consumers, as this highlights subconscious decisions made during shopping, leading to more mindful consumers.

In quantum computing, computer engineers require a method to control the logical state of a quantum bit (qubit). Unlike its classical counterpart, a qubit’s logical state is not defined by a binary and discrete voltage. The QT3 lab is developing a quantum testbed with a defect in diamond known as the nitrogen-vacancy (NV) center. We present an on-diamond antenna that is optimized to manipulate the electron spin state of an NV center, which defines the qubit. Applying a radiofrequency magnetic field equal to the energy difference between the two spin states of our qubit, also known as resonant excitation, enables control of this state. The strength of this field directly correlates to the frequency at which this manipulation may occur. That frequency is known as the Rabi frequency. This is important as we want this frequency to be faster than the state can undergo decoherence, where state information is lost to the environment of the qubit. We have designed and simulated an antenna using finite element analysis software, which will supply our field and be fabricated on the diamond surface. For its geometry we realized a coplanar waveguide with a shorted end shaped around the NV center, which optimizes the field strength at the NV center, power reflections, and area consumption. Preliminary fabricated samples have been mounted, wirebonded, and characterized using a vector network analyzer, and have shown behavior that aligns with simulated results. We expect to have the antenna fabricated on our single NV center testbed sample and achieve a Rabi frequency on the order of 10’s of MHz. Once this sample is fully integrated into our cryogenic system, it will enable us to expand control to multiple nuclear spin qubits from a single NV center, as a quantum register. The testbed will be accessible to researchers and educators.