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.

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.

Individuals exposed to chronic, severe, and/or inescapable stress may adopt dissociation as a coping mechanism to alleviate suffering. In dissociation, individuals report losing connection to their bodies, reality, memories, and more. Dissociative experiences are hallmark symptoms of psychiatric disorders such as Post-Traumatic Stress Disorders (PTSD) and Dissociative Identity Disorder (DID), which have a high comorbidity with personality disorders. Maladaptive personality patterns can be thought of as chronic patterns of behavior that are resistant to change, which often are heavily present in brain systems that focus on habitual learning. However, the interactions between dissociative experiences and action-learning mechanisms are still poorly understood. In this project, we review the history of dissociation and action-learning research to synthesize a model of how dissociative mechanisms may interact with action-learning mechanisms as a cause for the development of pathological behavioral patterns and even multiple personalities. We propose employing the PRISMA method to select relevant literature from PubMed or other medical databases systematically and conduct a comprehensive review across the spectrum of dissociative disorders. By utilizing the Dissociative Experiences Scale (DES) scores as a measure method, we aim to identify action-learning brain region changes and explore how these changes correlate with dissociative symptoms; thus far, we’ve found that DID, dissociative disorders, and PTSD have the highest DES mean scores. Beyond this, our findings show that in these patients with different kinds of dissociative disorders, the hippocampus and amygdala are smaller and the volume of the palladium is typically larger. When combined with future findings and discoveries, the relationships between dissociative experiences and action-learning mechanisms will be better understood.

Mutations in phosphodiesterase 6 (PDE6) underlie photoreceptor degeneration through cyclic guanosine monophosphate (cGMP) accumulation, triggering a series of down-stream processes, which eventually kill photoreceptors. We hypothesize that knocking out inosine monophosphate dehydrogenase 1 (IMPDH1), the rate-limiting enzyme in de novo guanine synthesis, will rescue cell death caused by PDE6 mutations. Supporting evidence from a mouse mutant model (rd10) suggests that inhibiting IMPDH1 pharmacologically delays photoreceptor degeneration (Yang, 2020). Our procedure for this experiment is as follows. Fish heterozygous for impdh1a and pde6c mutations are mated to produce fish that are double homozygotes. Fish homozygous for mutations in both the cone-specific pde6c and the impdh1a genes are genotyped and embedded for histological analysis of the retina. Histology is examined on days 3,5, and 7 post-fertilization (dpf) for cone degeneration. To date, we have genotyped our two mutant lines. Normally, pde6c^-/- fish have severe cone photoreceptor degeneration at 5 dpf and impdh1a^-/- fish show no signs of photoreceptor degeneration even as adults. If degeneration is rescued, the double knockout larvae should retain similar photoreceptor nuclei counts to wildtype fish at all time points. Demonstrating that IMPDH1 inhibition rescues PDE6 deficiency would provide proof-of-concept for the therapeutic potential of IMPDH1 targeted inhibition for the treatment of photoreceptor degeneration due to cGMP imbalance.

Individuals exposed to chronic, severe, and/or inescapable stress may adopt dissociation as a coping mechanism to alleviate suffering. In dissociation, individuals report losing connection to their bodies, reality, memories, etc. Dissociative experiences are hallmark symptoms of psychiatric disorders such as Post-Traumatic Stress Disorders (PTSD) and Dissociative Identity Disorder (DID), which has high comorbidity with personality disorders. Maladaptive personality patterns can be thought of as chronic patterns of behavior that are resistant to change. Brain systems are known to underlie these sorts of habitual learning. The interactions between dissociative experiences and action-learning mechanisms are still poorly understood. In this project, we review the history of dissociation and action-learning research and synthesize a model of how dissociative mechanisms may interact with action-learning mechanisms to develop pathological behavioral patterns and even multiple personalities. We propose employing the PRISMA method to select relevant literature from PubMed or other medical databases systematically and conduct a comprehensive review across the spectrum of dissociative disorders. By utilizing the Dissociative Experiences Scale (DES) scores as a measure method, we aim to identify action-learning brain region activity (BOLD signal) and volume changes and explore how these changes correlate with dissociative symptoms; and we’ve found that DID, Dissociative Disorders, and PTSD has the highest DES mean scores. Beyond this, our findings show that in these patients with different kinds of dissociative disorders, for the patients with different kinds of dissociative disorders, their Hippocampus and Amygdala are smaller while their Pallidum Volumes in their brains become typically larger. Despite this relationship having elementary processes, combining with future findings and discoveries, the relationships between dissociative experiences and action-learning mechanisms will be better understood.

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.

Every year, substance abuse, mental disorders, and psychotic behavior become more and more severe, especially in the local communities of Seattle. Our research explores the interconnection between psychology and the utilization of modern computer vision and emotion recognition tools to analyze human semantics/behavioral patterns in order to comprehend the underlying dynamics that lead to these behaviors and ultimately, spearhead efforts for prevention. As a computer science researcher, I employ advanced machine learning algorithms built upon open source programs to track and interpret gestures, facial expressions, and body language in video data. By filtering the data through a database and comparing emotions through statistical analysis in similar individuals, I am able to uncover nuanced patterns in behavior and emotion that a human researcher would otherwise not notice. While the study is ongoing, our current data illustrates correlations between specific gestures, facial expressions, and emotional states in hallucinogenic use. Though these individuals exhibit typical behavior of substance use, they have different backgrounds and contexts that lead to unique obscure changes in emotion and behavior, and our program allows us to identify and analyze these transformations that current medical knowledge overlooks. These findings hold promising implications for informing future research directions and intervention strategies across multiple domains, from understanding human behavior in social interactions to enhancing human-computer interfaces.

The causative agent of malaria, Plasmodium spp., generated 608,000 deaths worldwide in 2022 according to the World Health Organization and disproportionately threatens endemic areas of Africa. Plasmodium sporozoites infect the host by entering the bloodstream through the skin following bites by female Anopheles mosquitoes. From there, sporozoites migrate to the liver and infect hepatocytes. A single sporozoite-infected hepatocyte is capable of producing thousands of merozoites, which go on to enter the bloodstream. Complete elimination of infected hepatocytes is necessary to achieve sterile protection. In order to observe adaptive and innate immune cell localization towards infected hepatocytes, we applied fluorescence microscopy on livers in a BALB/c rodent model of malaria. Naïve unvaccinated mice were infected with sporozoites of Plasmodium yoelii, a rodent malaria parasite. Two important cell populations are recruited to infected hepatocytes. The first are tissue resident memory CD8+ T cells (Trm), which are crucial in pre-erythrocytic protection. The second are Kupffer cells, which are specialized liver macrophages. To measure these adaptive and innate cell populations, respectively, we applied fluorescently-labeled antibodies to mark the parasite as well as Trms and Kupffer cells. After staining the collected liver tissue and imaging with a widefield fluorescent microscope, we visualized recruitment and measured immune cell proximity quantitatively within a region of interest of the area surrounding infected hepatocytes using microscopy imaging analysis software. This method will be used to test the hypothesis that Trms and Kupffer cells are induced following sporozoite challenge in the rodent malaria model.

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.

As our world progresses through technological advancements, much of our planet regresses as an effect of climate change, highlighting a need for underutilized resources to be brought to the forefront of industry. One avenue for transforming abundant resources into useful chemicals for generating sources like fuel is the catalytic upgrading of biomass derived molecules. However, catalysts traditionally used for these reactions are not stable to contaminants in biomass mixtures, such as water or organic acids. For biomass derived molecules to serve as precursors for biofuel and other related energy sources, more stable and efficient catalysts are needed. Our group has recently shown that a bifunctional acid–base MOF with co-localized acidic and basic sites outperforms a MOF with randomly dispersed acid–base sites for the aldol condensation reaction. To further demonstrate the importance of having the acid and base groups co-localized, I synthesized and tested three control frameworks for comparison: (1) a framework with no functionality, (2) a framework with only acidic sites, and (3) a framework with only basic sites. I then tested stability and recyclability of the bifunctional acid–base frameworks by conducting recycling experiments. I resubjected the same sample to reaction conditions for a total of 5 cycles. After each cycle, I used 1H NMR to quantify the conversion of starting material to ensure that there were no changes in catalytic activity. Lastly, I used powder X-ray diffraction (PXRD) to ensure that the catalysts maintained their crystalline structure after 5 cycles. Here I show that metal–organic frameworks (MOFs), a class of porous crystalline solids, can be used as efficient and recyclable catalysts for the aldol condensation, an important reaction for biomass conversion. Overall, this work illustrates the stability and reusability of metal organic frameworks as catalysts and thus their potential for utility in biomass upgrading reactions.

Pembrolizumab (brand name KEYTRUDA), is a monoclonal antibody therapy classified as an immune checkpoint inhibitor, a type of immunotherapy that works by facilitating the detection of cancer cells by T cells. Specifically, it blocks the PD-1 pathway that cancer cells use to suppress and evade the immune system. With neoadjuvant-adjuvant treatment, patients receive systemic therapy both before and after the surgical resection of their tumor(s). There is limited research evaluating the association between tumor responses (changes in tumor measurements) and survival time with neoadjuvant anti-PD-1 treatment. In this study, I analyzed the association between tumor measurements and event-free and overall survival in a clinical trial of patients receiving neoadjuvant-adjuvant anti-PD1-therapy. Event-free and overall survival were estimated using the Kaplan-Meier method, and associations with RECIST tumor size were evaluated using martingale residual plots and Cox proportional hazards regression models. In this study, I found significant associations between event-free survival and baseline tumor burden and changes (quantitative and categorized) in tumor size between baseline and the end of neoadjuvant therapy. Increases in tumor size were associated with a lower 2-year event-free survival. Larger values of baseline tumor burden were significantly associated with event-free survival but were not significantly associated with overall survival. The findings from this study may serve to better inform clinicians on making prognoses for patients on anti-PD-1 therapy and indicate a need for more research to be done on associations between tumor size and overall survival outcomes.

Vocabulary acquisition in children involves many cognitive processes, with semantic descriptions playing a potentially crucial role in word learning. Broader literature points to a positive impact of metacognitive strategies early in children’s learning. Additionally, studies have highlighted semantic descriptors in facilitating word acquisition. However, there is a lack of literature regarding the direct correlation between children's productions of semantic descriptions and success in word learning, which is the current focus. We examined the number of semantic descriptions produced by children alongside their corresponding word-learning performance to determine whether a relationship exists. We analyzed data from 33 participants ages 2.7 - 6.7 years (mean = 4.6 years, SD = 1.2) with an average Expressive Vocabulary Test-3 standard score of 120. Our team coded a total of 165 word-learning assessments from videos of participants engaging in a storybook listening activity where participants were exposed to novel words paired with objects, assessing their receptive and expressive word learning. Participants were asked to look at the objects, imitate the novel words in real-time, and both point to and label the associated objects after a delay. We recorded the number of times children made semantic descriptions (ex. “The gek is spiky”), total correct identifications (receptive performance), and total phonemes correctly imitated and labeled (expressive performance). For analysis, we tested the correlation between semantic descriptions and both receptive and expressive word learning scores. I hypothesize that a positive correlation between these scores will indicate that children who produce semantic descriptions find more success in word learning. I anticipate that our study will contribute to a better understanding of how semantic descriptions play a role in receptive and expressive word learning outcomes. Also, study findings could serve as a foundation for future research on how parents and educators might better support children’s vocabulary acquisition.

Panãra, an Indigenous language native to Brazil, is currently the focus of Dr. Myriam Lapierre, Sunkulp Ananthanarayan, Ella De Falco, and Jessamine Jeter as some of the only linguists to document and conduct a comprehensive study on this language. Our research focuses on streamlining the process of organizing and analyzing field data – specifically in the context of Panãra, though generally applicable to other Indigenous and/or under-researched languages  – for use in future research by Dr. Lapierre and other scholars in the field of linguistics as it applies to Indigenous and minoritized languages. We have digitized the data from the field journals of Dr. Lapierre and the graduate students working with her, and our current focus is on the analysis of verb and sentence construction, via this digitized data, to organize grammatical paradigms into efficient and accessible indexes. We are also compiling and organizing PDF, image, sound, video, and experimental data for use on the California Language Archive (CLA) with a similar focus on efficiency and accessibility. The completion of this research entails the more complex understanding and organization of Panãra sentence and word structure for use in future research, both by Dr. Lapierre and by other scholars, as well as for usage in a Panãra dictionary. Our expected results also involve the creation and organization of the CLA page dedicated to Panãra, with a transparent structure making this data available to a wider audience of both linguists and non-linguists interested in learning more about the language.

Advances in language models have made diverse applications in social and health sciences possible. With many models emerging daily, it is important to understand general principles behind how language models represent text data. The study aims to investigate the effects of text manipulation on the numerical representation of meaning, or embeddings, through language models. The research is focused on numerous text manipulations (ex. changing direction of sentiment, sentence incompleteness, object of reference, intensity of statement). The research employs SentenceTransformer for embedding generation and UMAP for the visualization of semantic shifts. A comprehensive analysis of over 50 sentence manipulations provides a preliminary basis for understanding the nuances of semantic space organization. The core hypothesis suggests that incomplete and intensity based modifications lead to greater shifts compared to negative and referencing modifications. This outcome is expected to be substantiated through measures of embedding displacement from original text, and generalized through statistical validation, with tests accounting for multiple comparisons. This research is positioned to scale towards publishable results, aiming to systematically quantify the effects of semantic modifications across a larger dataset. The anticipated contributions of this work are twofold. It offers insights into the organization of semantic space as influenced by sentence modification, providing implications for the development of more nuanced NLP (Natural Language Processing) applications. And crucially, it lays a foundational basis for understanding how large language models (LLMs) process psychological statements and terms, an area of increasing importance as these models become more integrated into applications involving psychological analysis. Overall, the outcomes of this research are poised to deepen the understanding of how semantic alterations impact sentence embeddings, with potential applications in enhancing NLP models' interpretability in processing complex linguistic constructs.

Cardiopulmonary bypass (CPB) is required for most cardiac surgeries. More importantly, CPB is used during heart surgeries to circulate blood out of the patient's body for surgeons to operate on the heart under optimal conditions without blood obstructing their view. However, CPB has been shown to induce systemic inflammation which can lead to complications including multiorgan dysfunction. Lack of understanding, specifically not enough knowledge of the molecular mechanisms of post-CPB inflammation has been a major obstacle to improve treatment methods. To better understand these mechanisms, we performed mRNA and Assay for Transposase-Accessible Chromatin (ATAC) sequencing on total circulating leukocytes from neonatal patients undergoing CPB. Prior data identified myeloid cells, particularly monocytes, as the major cell type driving transcriptional responses to CPB. Furthermore, Interleukin-8 (IL-8) and Tuman Necrosis Factor alpha (TNF-α) were inflammatory cytokines found to be robustly upregulated in leukocytes in patients. To further explore these findings, we performed in-vitro experiments of running THP-1 human monocytic cells to CPB-like conditions, including artificial surfaces, high shear stress, and cooling/rewarming. These experiments were collected and studied at times post shear allowing us to study and contrast how the blood is affected and recovers from CPB. Additionally, we performed drug treatment experiments with egtazic acid (EGTA) to see how calcium signaling may benefit post-CPB inflammatory response. Observing the opening and closing of chromatin of the sheared and the static blood has shown positive correlation that IL-8 and potentially IL-2 contribute to patient inflammation. We hypothesize that specifically these regions, IL-8 and IL-2, are the areas to determine where the root cause and solution are to post-CPB complications. Finally, further analysis with Topologically Associating Domains (TAD) was shown to increase chromatin density and activation in post-CPB samples in IL-8 and IL-2 genomic regions. We hope this research can reduce complications with patients going through CPB.

Most research on health and food choice is conducted with samples of college students with low racial and socioeconomic (SES) diversity. The University of Washington, Tacoma (UWT) has a uniquely heterogeneous student body, composed of various ages, SES, and races, but the aspect of non-traditionality that interested us was our large population of commuting students. The economic hypothesis for overnutrition highlights the health disparity created by the inverse relationship between food price and diet quality. Yet, in this population, we do not see a significant difference in body composition across income (F (3, 315) = 1.137, p = 0.334). However, there is a significant negative correlation between perceived stress and household income (r = -0.119, p < 0.05). Typically, time scarcity drives convenient food choices and consumption of sugar-sweetened beverages (SSB), often associated with adverse health indicators. In this project, I asked if longer commute times (zip codes farther away from campus) contribute to economic choices (money spent on gas, less for food) and time scarcity. I hypothesize that individuals with zip codes farther from campus (longer commute time) will show greater implicit preferences for SSBs and be more likely to select SSBs in a laboratory study. An independent sample t-test showed no significant relationship between commute time and SSB selection, t (318) = 0.875, p = 0.382. Again, a chi-square test showed no significant association between SSB selection and SES category 𝝌² (4, n = 318) = 2.505, p = 0.644. There is a modest inverse correlation between SES and implicit wanting for SSBs, r = -0.099, n = 291, p < 0.10. Addressing SSB consumption from a unique perspective accounting for external and personal factors with diverse sample populations is crucial to addressing the personal responsibility narrative in the psychology of eating.

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.

Over the past few years, patients have been identified with debilitating phenotypes due to mutations in MSTO1, a nuclear gene. These patients often have distal muscle loss and weakness leaving patients incapable of walking but to date there is no known treatment. One barrier to progress is that virtually nothing is known about MSTO1 function, making the development of therapeutics for these patients extremely challenging. The goal of this project is to use an unbiased approach to discover functions of MSTO1. To do this, I will find genetic interactors utilizing yeast to perform an unbiased screen. Yeast DML1 is the homolog to MSTO1 and is required to keep the yeast cells alive. This screen will identify genes in the yeast genome that support survival of cells lacking DML1 when the gene is overexpressed. We utilize an auxin-degron system that targets DML1 for degradation when the yeast are grown with auxin. To find genes from the yeast genome that keep the cells alive when DML1 is degraded, I express random fragments of genomic DNA. Those genes must, therefore, be linked to DML1 function in some way, thus providing insight into what MSTO1 does, how it works, and how to help MSTO1 defective patients. I have obtained hundreds of yeast colonies that survive without DML1 when other genes are overexpressed. Currently, I am extracting these overexpressed DNAs to determine the gene(s). This work is an essential step toward fully understanding MSTO1 function in cells and we plan to characterize these connections in yeast and human cells.

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.

Family businesses are some of the most important economic contributors in the United States, accounting for approximately 64% of the U.S. GDP. The family business model, which refers to any business with two or more family members on the board or in ownership, is a crucial and enduring part of business in the Seattle area and abroad. Historians have often pointed out that the family business model seems to be the base model for business and has thus been present since the beginning of organized business, often in the form of farms, merchant companies, banks, and other small businesses. Despite its prevalence, the family business model is far from perfect because of its numerous commonly encountered limitations. One of the limitations family businesses face is the challenge of succession, as only about 30% are able to succeed from the first generation to the second. Other limitations relate to growth, sustainability, and qualification problems. This study, conducted as a literature review, uses a combination of peer-reviewed articles and popular sources (chosen based on criteria of relevancy and prominence) as quantitative data to examine the consensus of family businesses in Seattle and the solutions that have been proposed to address these limitations. Interviews with family business owners in the Seattle area were also conducted to provide qualitative data and to highlight specific opinions. The economic and historical implications of Seattle family business are also discussed. This research aims to provide insight into otherwise costly financial, succession, and leadership difficulties in order to ensure that the family business model is an enduring contributor to the Seattle economy. Having the proper knowledge on how to approach these difficulties and reconcile with their seemingly conflicting nature can help family businesses in the Seattle area thrive while working through complicated business situations.

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.
 

Dravet Syndrome (DS) is a severe form of childhood onset epilepsy occurring in about 1 out of 16,000 births. The disease is characterized by treatment-resistant seizures, ataxia (or loss of muscle coordination), developmental delay, cognitive impairment, and increased rate of premature mortality mostly due to sudden unexpected death in epilepsy (SUDEP). DS is predominantly caused by a heterozygous loss-of-function mutation in the SCN1A gene, which codes for the pore-forming alpha subunit of the NaV1.1 voltage-gated sodium channel. Our lab has previously shown that selectively introducing these mutations into neurons expressing the neurotransmitter GABA, specifically GABAergic interneurons of the forebrain, is sufficient to cause DS phenotypes in mice. In this study, we investigated whether an SCN1A gene replacement therapy precisely targeted to this interneuronal population can rescue epilepsy and SUDEP. Our lab, in collaboration with the Allen Institute, has developed a novel dual SCN1A-intein-AAV with forebrain GABAergic interneuron targeting capability using a Dlx56-based enhancer. Mice treated with this vector at postnatal day (P) 0 via intracerebroventricular injection were monitored for spontaneous mortality up to P70 and tested for susceptibility to thermally induced seizures. All untreated mice (n=31/31) died by postnatal week 6. In addition, 86.5% (n=13/15) of them exhibited thermally induced myoclonic seizures (MCS) and 100% (n=15/15) of them showed generalized tonic clonic seizures (GTCS). In striking contrast, none of the treated mice died (n=9/9, p=3.3e-14, Fisher’s exact test) nor exhibited MCS (n=0/9, p=7.1e-4, Fisher’s exact test) or GTCS (n=0/9, p=1.1e-5, Fisher’s exact test). These findings suggest that precision therapy targeting the very site of disease etiology can completely protect against epilepsy and related mortality in DS.

Advances in language models have opened up endless applications in the social and health sciences. A key to fulfilling this promise is the development of rigorous practices for gathering data used for model training. This research project reports the development of standardized protocols for building databases for self-reported psychological questionnaires that can be used to fine-tune language models. These questionnaires cover a spectrum from childhood experience to altered states of consciousness and beyond. We systematically review the literature on appropriate database-building strategies, use combined data collection techniques, and instill specific criteria into our collection process to help facilitate the research’s computational pipelines on evaluating the relationship between semantics and psychological factor membership. Using a 2D semantic map of the PsycTests database as a reference, we can further evaluate the effectiveness of our protocols by developing quantitative measures to assess comprehensiveness and objectivity in our database building. Our initial explorations involve measuring data variance and density of data distribution. This research provides a general toolkit for building text databases for appropriate and effective model training purposes across various disciplines.

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.

This study seeks to explore the perspectives of Latine students at the University of Washington (UW) regarding racial representation within the institution. Do Latine students see their experiences and identities represented and reflected in university life? How do Latine students experience and perceive Latine representation (or lack thereof) in terms of the composition of faculty, student body, and community spaces at UW? This research project aims to uncover the realities, challenges, and promise of support and community on campus. Through interviews with Latine students, faculty, and staff, this inquiry will describe how students find support at UW and navigate their academic environment. To attain a comprehensive understanding, the research utilizes a combination of primary and secondary sources, incorporating interviews with Latine students, staff, and faculty at the UW to capture personalized and nuanced perspectives. By examining the lived experiences and perspectives of individuals directly affected, the study aims to thoroughly examine the complex dynamics at play. Exploring the lived experiences of Latine students, the study will contribute to the discourse on racial representation in academia and its impact on student well-being and academic success. The findings will inform discussions on how institutions can foster an inclusive environment that recognizes and supports the diverse backgrounds of all students. This research project has emerged from ongoing conversation and collaboration with the Washington State Commission on Hispanic Affairs members. This research project will inform the community report that the Commission is preparing.

When students describe physics, they often associate this science with facts, formulae, and objectivity. Unfortunately, all too often, STEM classes completely overlook cultural influence and when it is discussed, it is described as a historical and static phenomenon. This can block students from connecting physics to their own experiences. In our research, we asked students to reflect on their sense of the nature of physics and how their own experiences influence their perception. We used a phenomenological qualitative analysis to investigate 51 students’ ideas across five introductory physics classes at a two year college. Using an emergent theming analysis, we coded students’ written descriptions of physics and how their background shaped their ideas. Students described their own familial, cultural, and professional backgrounds, as well as their instructors’ identities and teaching methods, as impacting their perspective of subjectivity and objectivity in physics. By making space in class to compare and contrast physics culture with students’ own experiences, we hope to show students that their individual background is key to shaping their learning and improving the often inequitable field of physics.

There is currently a lack of tractable data on what was published in England in the early 20th century. However, this information exists in printed volumes of The English Catalogue of Books, which have been digitized through the HathiTrust digital library. The English Catalogue of Books, released in the UK by the trade publication Publishers’ Circular, provides a yearly record of books published from the mid-19th to the early 20th century. Each catalog has been converted to plain text automatically through optical character recognition (OCR). Our aim was to parse this plain text into user-friendly data on books published each year in the UK. However, the OCR-generated text often contained errors and inconsistencies that prevented the effective extraction of data on books listed in the catalogs. Thus, we aimed to gauge the accuracy of existing methods for parsing the catalogs and to tailor processes for gathering data from catalogs published between 1908 to 1922. By writing regular expressions to capture, split, and match the patterns of bibliographic entries, we were able to improve the accuracy of processes for extracting data. Our solutions increased the number of publications for which information was accurately being captured by on average 28%, and we were able to record information on over 21,500 books that previously had not been captured. We also created a summary dataset from the catalogs with information on the overall output of the publishing industry during these years. By analyzing and visualizing this publishing data, we were able to show that fiction was the most frequently published genre during the period. We anticipate this project to be the foundation of more work towards efficiently parsing The English Catalogue of Books in order to offer insights into the British publishing industry in the 19th and 20th centuries.

Within STEM, physics ranks among the least aligned with the US population regarding racial and gender representation. This not only has the potential to hinder new discoveries and innovations, it also highlights a lack of equitable opportunities for individuals. In an effort to identify ways in which teaching practices may contribute to this problem, our research explores correlations between active learning strategies and growth in students’ conceptual understanding. The data analyzed are from a pre/post survey in a two-year college calculus-based introductory university physics class with a primarily Vietnamese, Black, and white population. We present topics including force and free-fall that show either substantial or limited improvement in student learning gains. We compare data across several demographics, and relate corresponding learning activities. We provide recommendations to improve both learning outcomes and instructional methods, with the aim of increasing opportunities for all identities to complete degrees and pursue career goals.

Alzheimer’s Disease (AD) is a progressive brain disorder that debilitates memory, learning, and decision-making. Early-stage AD represents the initial phase where individuals are still able to function independently, but with increasing age, their condition steadily progresses to dementia and loss of independence. Because a significant number of the aging population is affected by AD, understanding the neuroinflammatory processes would help develop more effective strategies for treatment. Examining markers such as MCP-1 and TNF-alpha, known to be associated with inflammatory response, will help identify the modulatory processes that lead to mild cognitive impairment associated with early-stage AD. Subsequently, higher levels of inflammation markers within the brain leads to mild cognitive impairment. This research study involved 40 C57BL/6 mice, 20 males and 20 females (21 months old), retro-orbitally infected with 80 µL of neurotrophic AAV-AD vector or AAV-Sham for a duration of 2 months before humane euthanasia. Brains were collected, and specific regions were examined by immunohistochemistry (IHC) and digital imaging to assess the expression levels and distribution of the inflammation markers. Preliminary observations showed that hippocampal regions of the brain from mice with early-stage AD had higher staining intensity for MCP-1and TNF-alpha compared to respective areas in Sham mice, suggesting increased inflammation is a very early lesion that develops in the presence of AD pathogenic components that might be controlled by anti-inflammatory drugs. The preliminary data suggests that the characteristics of AD manifest in part due to the neuroinflammatory response of brain factors that change with onset AD.

In recent years, the United States has seen an increasing number of opioid overdoses, causing many research studies to focus on opioid drugs of abuse. However, we still lack a fundamental understanding of the opioid receptor that these drugs bind to. The mu-opioid receptor (MOR) is involved in both the pain-relieving and euphoric effects of opioid drugs. The Ventral Tegmental Area (VTA), known to be a major source of dopamine, contains a significant amount of inhibitory gamma-aminobutyric acid (GABA) neurons that express MORs. Previous research has shown that activity at the MOR in the VTA is rewarding and that dopamine projections from the VTA to the Nucleus Accumbens (NAc) are activated to reinforce behavior. However, whether the expression of MORs on GABA neurons in the VTA is important for influencing VTA to NAc dopamine activity during reward seeking behavior is unclear. To investigate the role of the MORs in reward seeking behaviors, I knocked out MORs in the VTA and used dLight, a fluorescent dopamine sensor, to measure dopaminergic release from synapses in the NAc during Operant and Pavlovian conditioning tasks in the absence of these receptors. Pavlovian conditioning utilizes chambers in which a house light turns on and a sucrose pellet is delivered via food hopper to food-restricted mice. In the operant conditioning task, mice must learn to complete a nose poke in order to receive the sucrose pellet reward. These tasks allow me to gain a more complete understanding of how the absence of MORs in the VTA changes behavior and dopamine activity during reward-seeking. This research furthers our understanding of how the MOR affects natural reward and motivated behaviors and is crucial in helping us understand how opioids of abuse alter existing brain circuitry to cause opioid use disorder.

Kelp forests are hotspots for productivity and biodiversity in marine ecosystems. Currently along the West Coast, many kelp forests face significant threats due to climate change. Several studies have looked at the effects of ocean warming on kelp, but less is known about the effects of ocean acidification (OA), and how OA and warming in conjunction impact kelp. With climate change continuing to worsen, it is crucial to understand how these drivers may contribute to kelp’s decline. We examined the effects of warming and acidification, both separately and concurrently, on bull kelp (Nereocystis luetkeana) from two populations in Puget Sound, WA. Bull kelp, the primary canopy-forming kelp species in Puget Sound, has a heteromorphic life history with macroscopic (sporophyte) and microscopic (gametophyte) stages. Little is known regarding how the microscopic stages will be impacted by multiple stressors in Puget Sound. This study aims to better characterize the effects of warming and OA on Puget Sound bull kelp throughout its microscopic life stages. We exposed kelp gametophytes from two genetically distinct populations to elevated levels of temperature and pCO2 in laboratory conditions for five weeks, monitoring their survival, development, and reproductive success from spore settlement to the juvenile sporophyte stage. Our collection sites differed in the overall temperature, urbanization level, and state of the kelp forests. Previous studies have shown declines in reproductive metrics when subjected to thermal stress, and an increased thermal tolerance when subjected to acidic conditions, which is what we expect to find within our experiment. Understanding local adaptability is critical in predicting future population responses to climate change. The potential range shifts or local extinctions that could occur because of these stressors will need to be understood to plan for conservation, restoration, and recovery of healthy kelp forests.

Antarctic blue whales (Balaenoptera musculus intermedia) are the largest animal on Earth, but much of their life history remains a mystery, including mating behavior, gestation periods, and early development. Antarctic blue whales were hunted excessively throughout the 20th century and are currently listed as endangered due to this exploitation. More than 340,000 blue whales were killed which led to an immense amount of data regarding the length, sex, and reproductive status of individuals. Using this data, compiled by the International Whaling Commission, I will build a model of Antarctic blue whale fetal growth and calf development. I will fit this model to the fetal and calf catch data to predict fetal and calf lengths in each month of the year. This model will result in predictions of the time of year that Antarctic blue whale calves are born and weaned as well as their growth rates. Determining the trends of fetal and calf growth in Antarctic blue whales contributes to the knowledge of reproductive behavior and growth trajectories. This is especially important for Antarctic blue whales, where no breeding areas have been identified. Understanding when calves are born and weaned can be combined with other data, such as satellite tracking, to provide insight into breeding areas.

The kidney is composed of thousands of filtration units called nephrons. Within each nephron lies a tuft of capillaries, the glomerulus, that filters from the blood through a filtration barrier. Over time this filtration barrier thickens, ultimately causing decreased blood filtration. A main marker of this age-related degradation are telomeres which comprise the ends of chromosomes and protect the coding DNA from degradation. If telomeres become too short, the coding region of DNA will begin to degrade. To combat this, telomere shortening signals for cells to enter a state of permanent cell cycle arrest, senescence, which prevents replication of cells with degraded DNA. Accurately quantifying telomere length will enable the development of correlations between cell lineage and structural changes within the kidney. I hypothesize that Expansion Microscopy (ExM) and quantitative-Fluorescent In-Situ Hybridization (Q-FISH) will allow me to determine the relationship between physiological changes in the filtration barrier and single-cell telomere length. ExM enables a superresolution cellular view by embedding a tissue sample in a swellable hydrogel, achieving four-fold isotropic expansion. This technique confers greater resolution of Q-FISH signal versus traditional confocal microscopy. To determine telomere length, I developed custom analysis scripts to quantify Q-FISH signal brightness. Preliminary results indicate an increased brightness of younger mice compared to their aged counterparts. Additionally, to receive a base-pair output I compared the Q-FISH signal to the signal of a DNA region of known length, Major Satellites, determining young telomeres to have an average base-pair length of 30 kb. I am validating these results in collaboration with the Miller Lab using next-generation sequencing techniques. Future work includes concurrent application of general physiology stains to identify and measure the glomerular filtration barrier physiology. Results from this method will allow for a wealth of information regarding the relationship of single-cell telomere length and glomerular structural health.

Plants recognize herbivore-associated molecular patterns (HAMPs) during herbivory that activates signaling to induce immune defenses. Caterpillar oral secretions contain Inceptin 11 (In11) which is a HAMP recognized by legumes such cowpea via Inceptin Receptor (INR). Thus, In11 and INR are a model system to study proteins involved in HAMP induced defenses, including Kunitz trypsin inhibitors (KTIs). It is known that KTIs are serine protease inhibitors with anti-herbivore activity; however, the precise role of In11 induced KTIs and the effect of cysteine content variation in cowpea KTIs remains unknown. Here, we show that selective removal of cysteines has a negative effect on KTI function in cowpea experiencing herbivory from the fall armyworm (Spodoptera frugiperda). We found that cowpea KTIs act as antiherbivore proteins against the fall armyworm when expressed in Nicotiana benthamiana, as we saw reduced weight gain on larvae feeding on leaves expressing wildtype KTI. Furthermore, we found that KTI function was negatively affected by the removal of cysteines, and larvae fed leaves expressing any of the mutant gained more weight than those feeding on wildtype. We hypothesize that these findings are due to reduced protein stability because we did not detect mutant KTIs in frass samples by westernblot. Understanding KTI protein structure and how it influences protein function is important for designing and selecting antiherbivore proteins to be used for plant defense in agriculture.

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.

Leigh Syndrome (LS) is a neurodegenerative disease due to the dysfunction of mitochondria. It usually begins in infancy and its incidence is around 1 in 40,000 individuals. Children with LS experience a progressive decline in their cognitive and motor functions often accompanied by severe treatment-resistant epileptic seizures. Mutations in Ndufs4, the gene that encodes a subunit of mitochondrial complex have been linked to LS. Mice carrying Ndufs4 recapitulate several key characteristic clinical manifestations of LS. Using these mouse models, our lab has demonstrated that GABAergic interneurons play an important role in the pathophysiology of LS. Mice with Ndufs4 knockouts (KO) restricted to GABAergic neurons located across all brain regions exhibit seizures. However, seizures in epilepsy patients and animal models typically originate from forebrain structures. Therefore, in this project, we examined whether the inactivation of Ndufs4 in GABAergic neurons of the forebrain alone is sufficient to cause seizures in mice. Homozygotes floxed Ndfus4 mice were crossed with Dlx56Cre+ or Gly2TCre+ mice to KO the gene specifically in interneurons of the forebrain or brainstem. We hypothesized that only mice with KO in the former region will exhibit seizures. Conditional KO mice from these two lines were tested for thermal seizure susceptibility. Surprisingly, both Dlx56creKO and Gly2TCre KO mice exhibited thermally induced myoclonic and generalized tonic clinic seizures. These findings indicate that GABAergic interneurons regions outside of the forebrain are critically involved in the pathogenesis of epilepsy in LS.

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. 

Epigenetic factors, including histone marks, change the patterns of gene expression without altering the DNA sequence. Variations in such marks are known to account for the ability of stem cells to differentiate into various cell types, but a preliminary experiment conducted by a former member of the Vaughan Group, Dr. Marcus Woodworth, has revealed that even in a phenotypically homogeneous, terminally differentiated cell population, the presence of H3K27me3, a repressive histone mark, varies on the HOXC gene of human retinal pigment epithelium (RPE1) cells at single-cell, single-loci level. My role is to evaluate the two possible origins of such heterogeneity: inheritance (histone mark varies due to events that happened during differentiation, or the random drift after differentiation, and the variations are kept within each lineage of cells), and multiple mark co-repression (one histone mark varies, but summing its effect with another histone mark that perform a similar function lead to the observed functional homogeneity), and to validate that such pattern exists among a broader range of genes. To achieve these ends, I profile selected histone marks (H3K27me3 and H3K9me3) on genes that experience different types of regulations during differentiation (HOXC, GAPDH and SIX6), using imaging-based methods, including the time-lapse imaging of live cells to map out lineages, and expansion microscopy (ExM) to capture fluorescently labeled histone marks at single-loci level. If the hypothesized origins are true, a significant difference in the number of histone mark clusters around the genes of interest would be observed between cells of different lineages, and complementary variation patterns would be observed between H3K27me3 and H3K9me3. The study reveals the nuances of histone mark dynamics on the single-cell, single-loci level, and optimizes an imaging-based method that has the potential for multiplexing at high spatial resolution, thereby providing a powerful tool for further studies on epigenetics.

Music interventions are gaining attention due to the evidence they improve health and cognition in elders. In the US, there is an increasing number of Mandarin-speaking elders whose cultural background affects their aging experience. After English and Spanish, Chinese is the third most spoken language in the US. Three and a half million households in the U.S speak Mandarin or Cantonese. However, there is little information regarding specific music choices or culturally-tailored music interventions for Mandarin-speaking elders to improve their health and aging experience. The purpose of this study was to gain insights into Mandarin-speaking elders’ views of aging, ageism, and the relationship between music and health. We conducted a qualitative study that involved interviewing Mandarin-speaking elders in Mandarin. The interview consisted of questions related to their cultural perspectives on aging, experience with ageism in the US, and the impact of music on their health. The participants selected music to play during the interview and discussed what the music meant to them and their thoughts on how music affects their health. Four interviews in Mandarin have been conducted to date. Initial findings reveal that filial piety and respect are recurring cultural themes that influence participants’ perspective and experience of aging. Internal ageism was identified in one of the interviews while the participant discussed their experience with ageism. Participants expressed that music benefits their health by providing emotional support and outlet, motivation, reminiscence of the past, brain activity, and stimulation through physical movement such as dance. The findings increase our understanding about the role of culture in the aging experience and music’s role in enhancing health for Mandarin-speaking elders. Future studies can use this information to develop music-based interventions tailored for Mandarin-speaking elders to improve their health.

Compassion fatigue, also known as secondary traumatic stress or vicarious trauma, is a condition characterized by emotional and physical exhaustion, often experienced by individuals who provide care, support, or assistance to people who are suffering or traumatized. This phenomenon commonly affects professionals in helping and caregiving roles such as healthcare workers, social workers, counselors, and first responders as they’re constantly exposed to secondary traumas. This study investigates five domains of worker well-being of social services employees at a local Homeless Services Agency in King County. Seventy-five social workers and case managers were invited to participate in the online, anonymous survey that contains the National Institute for Occupational Safety and Health (NIOSH) Worker Well-being Questionnaire. This questionnaire consists of sixty-eight questions related to work evaluation and experience, workplace policies and culture, workplace physical environment and safety climate, health status, and home, community, and society. We hypothesize that those who have been employed at the Compass Housing Alliance for more than 2 years will exhibit higher compassion fatigue through their survey responses. The insights gathered will aid in understanding the working environment on service employees’ well-being. Results will offer areas to support workers and hopefully serve to mitigate the potential development of compassion fatigue among staff members.

In recent years, organizations have debated whether elements of “white supremacy culture”, including a sense of urgency, may create inequitable environments for people of color. We aimed to empirically investigate whether cultures of urgency in professional settings undermine the recruitment of racially minoritized groups. Undergraduate participants (N = 219) read job advertisements for two jobs: one where urgency culture is highly valued (e.g., “swiftly reset priorities at any given time”) and one with less sense of urgency (e.g., “adjust priorities based on capability”; order counterbalanced). Participants then reported how likely they would be to apply to each job. We hypothesized that individuals from racially minoritized groups will be more likely to apply to lower-urgency jobs over high-urgency jobs. The results show that most participants preferred lower-urgency jobs. However, countering our hypothesis, individuals from racially minoritized groups held more positive attitudes towards high-urgency jobs (e.g., how well they think they'd perform in the job) when compared to white participants. This finding casts doubt on the proposed elements of "white supremacy culture". It urges for more empirical research on how different racially minoritized groups may perceive these elements in work settings. Furthermore, our sample consists mainly of Asian Americans, which does not speak for the experiences of other racially minoritized groups. Our future research will focus on diversifying samples collected.

H3K9me3 heterochromatin regulates gene silencing and plays key roles in genome stability and cellular identity. During cell reprogramming, H3K9me3 has been shown to block transcription factor binding and changes to cell identity. Recently, enhancer of rudimentary homolog (ERH) was identified as a master regulator of H3K9me3 and a repressor of reprogramming in humans. However, the roles that specific ERH protein amino acids play in its function remain unknown. We hypothesize that elucidating the role of ERH and identifying pivotal amino acids will enhance our understanding of its molecular mechanisms. We are targeting amino acids which are evolutionarily conserved as these are more likely to be important for ERH function. We have shown that the ERH knockdown phenotype of low proliferation and decreased H3K9me3 can be rescued by exogenously expressing a wild-type copy of ERH. Our approach has involved generating mutant variants of ERH, introducing them into cells where the endogenous ERH is depleted and then assessing whether they rescue the phenotype. To efficiently assess many amino acid substitutions in the ERH protein simultaneously we are developing a multiplexed alanine scanning approach with Nanopore readout in a functional screen. In this approach, multiple ERH mutants will be simultaneously introduced and integrated into the genomes of a population of cells with the endogenous ERH depleted. Mutant forms of ERH which do not rescue the proliferation phenotype are expected to decrease in abundance over subsequent proliferation. The ratio of exogenous ERH sequences will be assessed upon initial introduction and after 2 weeks by targeted long read DNA sequencing. Identifying which amino acids are important for ERH function will allow us to design further experiments, investigating their role in localization, protein-protein interactions and H3K9me3 regulation. Understanding the regulation of H3K9me3 heterochromatin will be essential to improve cell reprogramming, enabling autologous transplantation and regenerative therapies.

As the percentage of individuals facing homelessness rises, many organizations working closely with unhoused populations aim to secure consistent housing and essential resources for those who lack this necessity. There are roughly 14,000 individuals facing homelessness in the greater Seattle area. Previous studies have shown positive correlations between employee well-being and job performance. Our research aims to investigate worker well-being among staff members who are currently employed at the Compass Housing Alliance, an organization working closely with unhoused populations to provide both housing and access to other essential needs. This research utilizes the National Institute for Occupational Safety and Health (NIOSH) worker well-being survey. We collected data on five factors that influence the perceptions of 75 staff members on their overall well-being including workplace safety, mental wellness, leadership support, coping strategies and job satisfaction. Expected results from our survey indicate that staff members' perceptions significantly impact their overall well-being. Collecting data using quantitative methods enables us to gain a deeper understanding of these current perceptions in order to utilize relevant resource implementation in areas where gaps are identified to support the needs of staff and improve their well-being.

Glomeruli are the basic filtration unit of the kidney. The current understanding of its physiology is limited by the partial or 2D analysis of its structural components. The Vaughan Group uses optical super-resolution microscopy in combination with advanced chemical labeling techniques and powerful data analysis approaches to perform high-resolution 3D reconstruction of the whole mouse glomeruli. Overall, the work has the potential to provide a novel understanding of the glomerular structures and how they are altered in aged and diseased conditions. The labeling of the overall morphology of the glomeruli is achieved by chemically labeling the distribution of abundant macromolecules (carbohydrates, amine, and DNA) using Fluorescence Labeling of Abundant Reactive Entities (FLARE). Though we could visualize the general physiology of the sample with FLARE, incorporating specific targeting of molecules with FLARE is still challenging. My role is to optimize the FLARE protocol to add the capability of labeling the distribution of specific molecules using immunolabeling. The most challenging part is that all the fluorophores labeled prior to FLARE will be bleached out by the strong oxidation step while labeling carbohydrates. I am focusing on exploring possible workarounds to incorporate immunostaining with FLARE. The only way to bypass the bleaching fluorophores is to label dyes after the FLARE. However, the FLARE involves the gelation part, and the gel makes antibodies which are linked to fluorophores hard to get into the sample. So, instead of using regular secondary antibodies, I use biotin and then link to the streptavidin dye, which is smaller in size and easier to enter the sample. With this optimization working, we could incorporate whatever target of interest with high resolution on top of three general stains provided by FLARE, giving us an extra degree of information for our 3D reconstructions of glomeruli.

Individual eating behaviors, and the motivations behind food choices, impact a person’s overall health and wellbeing. While cognition plays a significant role in food decision-making, processes outside of conscious awareness like high levels of perfectionism (cognitive rigidity) can influence a person's eating habits. On the other hand, these choices are impacted by emotional processes, as a person’s interoception sensitivity levels and experience of interpersonal stress impact food intake. The notions of cognitive rigidity and interpersonal stress contributing to changes in eating habits are contrary to the current discourse of personal accountability surrounding food choice and diet. The personal accountability narrative emphasizes each person’s individual responsibility in deciding what to consume, the quantity, and quality of the food. In contrast to the idea that each person is responsible for their health, analysis of surrounding factors that contribute to the decision-making process yields a more accurate understanding of health and well-being. Therefore, I aim to explore the relationship between interoceptive processes, interpersonal stress, and cognitive rigidity to explain food decision-making and diet quality. To examine this relationship, I am recruiting a sample of college students from psychology courses at the University of Washington Tacoma campus. Participants will complete an online self-report questionnaire assessing interoception, perfectionism, mood, interpersonal stress levels, and eating habits. I hypothesize that interpersonal stress and cognitive rigidity adversely impact interoceptive sensitivity, ultimately worsening participants' diet quality. Understanding the relationship between interoceptive sensitivity, interpersonal stress, and cognitive rigidity and their impact on well-being can help inform future health interventions guiding improving dietary consumption.

In the 20th century ethnographic works that much of what is known about the day-to-day lives and culture of historical Coast Salishan peoples, tribal informants noted that there were often associations made with certain professions and those who specialized in them, particularly when it came to personality. Though intending to reflect upon an earlier and bygone age, Coast Salishan tribes are still modern peoples, and these informants were discussing a still-living culture. My research focuses upon establishing continuity between the professions and personalities described in Coast Salishan ethnographic works with members of modern Southern Coast Salishan communities who specialize in those same traditional practices. For determining the general perception of certain professions and their associated personality traits, I consult a selection of ethnographic works concerning Coast Salishan peoples that provide information by and the perspectives of tribal informants. To note both the continuation of older perspectives and newer developments, I interview tribal Elders and other tribal community members who are either adjacent to traditional practices or do such work themselves. My questions center around the perspectives of the interviewee on persons who participated in these practices when the interviewee was young, alongside any major or otherwise notable shifts in personal characteristics they have noticed over the course of their lives. Through the combination of examining prior works and my own original research, I present a society and culture that has been forced to endure massive changes but has nevertheless persisted well into the modern day.

In my research, I explore the role of children in Late Bronze Age Mycenaean society (ca. 1600-1100 BCE) by focusing on the relationships, socioeconomic and religious roles, gender dynamics, and burial practices of and for children, as well as ideas surrounding adolescence and the representation of children in Mycenaean art. Children hold a unique role in society, and it is important to understand the roles and perceptions of children. In doing so, we gain a better understanding of the experience of childhood as well as the culture as a whole. I begin by defining Mycenaean views on childhood, providing a framework to contextualize the discussion. This project is a synthesis of previously published data, incorporating the Linear B tablets, sites, excavations, and art from Late Bronze Age Mycenae, explored in this paper through comparative analysis. I utilize a similar approach when discussing the burial practices for children, focusing on burial architecture and style and archaeological reports on specific sites, such as Ayia Sotira and Mycenae. By studying the roles and lives of children, we gain insight into generational dynamics, family structure, gender roles, and domestic dynamics, which all contribute significantly to understanding the cultural structure of a society. Through the specifics of material culture, social spaces, and practices involving or surrounding children, I look to develop a larger picture of the experience and significance of children in Mycenaean society, in effort to give context and perspective for existing and future research surrounding Mycenaean culture.

The Disability Inclusive Development Initiative (DIDI) is a project that brings together students and faculty from various fields to promote the human rights of persons with disabilities. Our current project builds upon the findings of a 2020 Memorandum of Understanding (MoU) between the International Disability Alliance (IDA) and the United Nations High Commissioner for Refugees (UNHCR). We are conducting a comparative analysis of asylum procedures in Uganda and Colombia, specifically examining how these procedures consider the rights of persons with disabilities. Our goal is to ensure that refugees and asylum-seekers with disabilities have access to fair and accommodating processes. We are also looking into the challenges faced by persons with disabilities during the asylum process and how governments are addressing these challenges. To achieve these aims, we are conducting a comprehensive literature review, including primary legal research, using resources from the University of Washington libraries. Additionally, we are consulting with experts working in this field. Our team is dedicated to producing a report for the United Nations High Commissioner for Refugees, which will outline our findings, highlight effective practices, and offer recommendations for future actions.

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.

Affordable housing has recently emerged as a central focus of many policymakers’ agendas, especially in big cities, and they have implemented a variety of reforms to address this. In Seattle, the Mandatory Housing Affordability (MHA) program was rolled out in 2017, and then implemented citywide in 2019. The MHA created zones within the city, with new developments in MHA zones required to either build a certain number of rent-restricted affordable housing units for low-income people, or pay into a fund for affordable housing. Studies have shown mixed impacts of programs like the MHA on the housing supply; research about the impacts of such programs on housing and especially rent prices, however, is limited. Additionally, there is evidence that the effects of such policies are heterogeneous, varying by location and other factors. In this paper, I test for changes in rent and housing prices in Seattle overall using a difference-in-differences analysis. I also test for spatial variation within Seattle in these rent and housing prices by comparing MHA zones with non-MHA zones. The implications of these results will be important in addressing the next steps in housing policy. Since the MHA was a novel program in the inclusionary housing policy space, analyzing its effectiveness is crucial to determining how future policies should be shaped.

Implicit bias, rooted in unconscious attitudes, fuels discrimination based on race, gender, or sexual orientation, disproportionately impacting marginalized groups. Despite the development of interventions addressing provider awareness of implicit bias, the advancement of clinical education through technology has been slow. In the UnBIASED research project, we investigated the usability of ConverSense, a personalized communication assessment tool to raise healthcare providers' awareness of bias in their communication with patients. This web-based tool measures social dimensions such as warmth, interactivity, engagement, and assertiveness from recorded patient-provider visits, and visualizes these patterns through graphs and embedded clips. In this study, we (PT, NE) examined whether ConverSense meets usability standards through heuristic evaluations conducted by design experts. Six healthcare technology experts participated in the evaluation of ConverSense using Nielsen's 10 usability heuristics. Experts documented usability issues for each heuristic and rated their severity on a scale from 0 (not a problem) to 4 (catastrophic problem). Through our analysis, we (PT, NE) identified three cross-cutting themes: 1) Poor design, where experts noted the absence of undo or delete buttons, making navigation challenging, and the distracting color scheme on graphs; 2) Data visualization issues, with experts expressing difficulty interpreting charts and uncertainty about what is considered ideal or good communication. One expert said “It's unclear what is considered ideal/good…for each gauge chart, high interactivity, engagement, and warmth I would assume are ideal/good. But how the charts are displayed in the system I cannot know for certain”; 3) Ambiguity in information presentation, where experts sought more definitions for measured social dimensions and recommended training links to help them identify personal actions they can take to improve their communication. This study underscores the value of incorporating expert feedback and addressing usability issues to improve tools like ConverSense to address implicit bias and promote equitable patient-provider interactions.

In the United States, education has historically been utilized as a vehicle of cultural assimilation. What that looks like, and its goals, has varied across time and region. Initially starting as the dominant white, anglo-saxon, protestant culture violently and brutally oppressing and subsuming the cultures of all others (including Black Americans, Indigenous peoples, and immigrants of a variety of backgrounds), and in current times moving towards a co-existence state in which multiculturalism and cultural pluralism is championed. It has yet to be determined as to whether the education system has caught up to societal shifts and what it means in terms of racially and culturally non-dominant student experiences. The primary question is how has assimilation-based educational practices impacted culturally non-dominant students in K-12 public schools? I conducted a qualitative synthesis across federated search databases evaluating common themes of resiliency and success, risk factors and failures, and avenues of potential change. I included qualitative peer-reviewed studies from the year 2000 or later, that focused on K-12 public schools in the United States, and that focused on culturally non-dominant students. Preliminary findings include language barriers being insufficiently addressed, culturally insensitive and irrelevant curriculum, lack of acknowledgement on the cultural perception of the value of education within teaching pedagogues, black/white racial paradigms of diversity and achievement gap, insufficient modeling of Americanness that reflects all students and an accurate history of the United States, and gaps with data aggregation and the resulting need for further research. Implications and future directions include key data disaggregation in research and school-based data collection, a reconsideration of what constitutes “standard” curriculum, and teacher education focused on humanistic and equitable principles.

The recent decline in the body size of sockeye salmon (Oncorhynchus nerka) returning to Bristol Bay, Alaska has been associated with increased competition within the marine environment as these populations have increased in abundance. As an anadromous species, different populations of sockeye salmon return to freshwater environments, occupying streams of varying sizes to which they have evolved habitat-specific adaptations to local habitat conditions. In particular, fish spawning in small streams are substantially smaller than ecotypes that spawn in the deep water of rivers and lakes where sexual selection promotes large body sizes. We hypothesized that density-dependent marine growth in sockeye salmon would be most intense for large-bodied spawning ecotypes, compared to small-bodied populations where there is less evolutionary pressure to achieve large body size. Using general linear mixed-effects models, I compared the effect of run size on growth rates in sockeye salmon from a range of streams of different sizes. My preliminary results suggest that ecotypes spawning in large water bodies (stream mouth >5m wide, rivers, and beach spawners) show stronger density-dependent marine growth than ecotypes spawning in small streams (stream mouth <5m wide). These results demonstrate that evolutionary selection for spawning success as adults affects the development programs of juvenile salmon while in the ocean.

One outcome of strong intraspecific interactions is the top-down regulation of juveniles by older individuals in a population, resulting in cohort dominance. Due to their distinct spawning patterns and high variability in juvenile recruitment, many species of fish experience these interactions. Arctic char (Salvelinus alpinus) is a commercially and ecologically important species native to Alaska whose intraspecific interactions are only vaguely understood. The goal of this study was to assess the evidence for suppression of recruitment by older individuals that both compete with and cannibalize younger individuals in a population. I used Arctic char fork length data from Little Togiak River, Alaska, between 1972-2023 to construct annual size distributions. I conducted a wavelet analysis for periodicity to determine whether there was distinct cyclicity in the size distribution of individuals in the population, as would be expected by a population regulated by a dominant cohort. The analysis suggests periods of 10-15 years, the natural life span of Arctic char, where a new cohort arises from a successful recruitment event and suppresses subsequent generations through competition and cannibalism. Improving the understanding of top-down intraspecific regulation in Arctic char can help inform fisheries policy and provide additional insight into Alaskan ecosystem functions.

This global change study examines the multiple-stressor impacts of heat and plastic leachates on a symbiotic clonal cnidarian, the aggregating anemone, Anthopleura elegantissima. Marine heatwaves and ocean plastics are two forms of anthropogenic pollution that are increasing and predicted to rise in future ocean conditions. In Puget Sound, intertidal marine organisms are most at risk of exposure to these combined stressors. In summer, low tides at noon leave intertidal organisms in stagnant warming water or fully exposed to desiccation. Marine heatwaves, like the one that occurred in June 2021, caused water temperatures to spike along Puget Sound coasts. Concurrently, road run-off and sewage likely expose intertidal organisms to higher concentrations of plastic leachates. Leachates are derived from machine-washed polyester clothing microplastics, polyvinyl chloride sewage pipes, and non-source point pollution that is swept through watersheds toward the coasts. Plastic pollution in the form of leachates is understudied in coastal ecosystems, compared to thermal stress. Plastic-derived leachates are the complex cocktail of chemicals that leach from plastics into the environment and are considered pollutants of emerging concern. We do not fully understand the impacts they have on the physiology of marine organisms, and even fewer studies address their impacts in the context of marine heatwaves. We will test physiological and photophysiological responses of aggregating anemones to thermal stress and plastic leachates, separately and combined. We will develop respirometry and light response curves for each of the treatment conditions and a control. We hypothesize that the cnidarian host will show increased metabolic activity indicating stress under both types of pollution, and that photosynthetic efficiency in the algal symbiont will increase with leachate exposure. We hope to use the results of this study to better understand how anemones and other cnidarians like corals are affected by the threats of plastic pollution and global warming.

The lithium isotopic composition of metasomatized rocks preserves a history of fluid movement that may be related to large subduction zone earthquakes. High pressure and temperature conditions within subduction zones cause the dehydration of hydrous minerals, and the resulting fluid can raise the pore pressure and trigger slip along the plate interface. The role of fluid movement in subduction zone processes can be better understood by constraining the duration of these events. These relatively fast and periodic fluid increases are recorded by chemical diffusion between the fluid and rock. Fluid containing lithium within a subduction zone can drive the diffusion of lithium into the surrounding rock. Lithium has two stable isotopes that diffuse at different rates, ⁶Li diffusing faster than ⁷Li, creating spatial heterogeneity in the isotopic composition of the reacted rock. Metamorphic rocks from the Western Alps have a reacted rind structure where fluid interaction occurred within an extinct subduction zone. The period of this interaction was examined using lithium isotopes. I prepared these samples for isotopic analysis, first weighing rock powders, then digesting them in acid, and finally separating the lithium with cation exchange columns. Lithium isotopes were measured on a multi-collector inductively coupled mass spectrometer. The spatial distribution of lithium isotopes along the profile from the reaction rind to the unreacted core, together with a thermodynamic model of Li diffusion through the rock, constrain the duration of the fluid interaction and provide insight into the role of fluid in catalyzing slip along the plate interface. I expect the duration of this fluid contact to be short, consistent with pulsed fluid movement within subduction zones. Modern subduction zones, including the Cascadia Subduction Zone that underlies Seattle, pose seismic hazards that can be better understood by examining the relationship between fluid movement and slip in extinct subduction zones.

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.

Over 38 million Americans have diabetes, with 90% of diabetic Americans having Type 2 Diabetes. Diabetes causes an increased risk of complications, including diabetic kidney disease (DKD), a disease that affects kidney filtration. This occurs in the glomerulus, a specialized capillary network of single-layered endothelial cells on one side and podocytes on the other, and their extracellular matrix (ECM). Injury, reduced function, or changes in the ECM of either of these cells cause abnormal filtration and kidney disease. Preliminary data from our group suggests that ECM remodeling driven by endothelial cells is a key feature in DKD in both our mouse model and in humans. Additional preliminary data from our lab indicates that two metalloproteases involved in ECM remodeling, ADAMTS6 and ADAMTS9, are increased in endothelial cells in diabetes via elevated lipids. My hypothesis is that very-low-density lipoprotein (VLDL), a lipid often increased in diabetes, induces increased endothelial cell ADAMTS6 and ADAMTS9 expression, contributing to remodeling the ECM and altering the filtration capacity of the glomeruli. To investigate this, isolated endothelial cells from non-diabetic mice were stimulated with varying VLDL concentrations, alone or with elevated glucose, to simulate diabetes. Following the stimulation, I isolated the RNA from these cells and measured the mRNA expression of Adamts9 and Adamts6 using real-time PCR. To test if endothelial cells isolated from mice with diabetes would respond differently, similar experiments are being carried out in cells isolated from diabetic mice. Western blots are used to verify the altered protein expression I observe. I am utilizing already acquired kidney sections from mice with diabetes with different lipid levels and determining the glomerular endothelial cell ADAMTS9 and ADAMTS6 expression by immunohistochemistry. Results from these experiments will help us understand the mechanisms through which endothelial cells respond to diabetes and thus contribute to DKD.

People with diabetes have an increased risk of developing cardiovascular disease (CVD). Hyperglycemia is the hallmark of diabetes, but diabetic dyslipidemia with increased circulating lipid levels is also present, which is believed to contribute to the augmented CVD seen in diabetes. The Cluster of Differentiation 36 (Cd36) receptor mediates fatty acid and lipoprotein uptake in macrophages. Lipid-loaded macrophages are a key feature of atherosclerosis, the underlying CVD pathology. Preliminary data suggest that monocytes (macrophage precursors) are lipid-loaded via increased Cd36. However, it is unclear what drives the increased Cd36 expression in diabetes. Reduction in blood glucose, but not lipid levels, in diabetic mice reduced monocyte cell surface Cd36 expression. Based on these preliminary data, I hypothesize that hyperglycemia induces increased Cd36 mRna expression in monocytes in diabetes. To address whether glucose or lipids increase monocyte Cd36 mRna expression, I will isolate monocytes from the bone marrow of non-diabetic mice and stimulate them ex vivo. To address if hyperglycemia alters Cd36 expression, I will stimulate monocytes with 4 glucose conditions: 5.6 mM, 15 mM, 30.6 mM D-glucose, and an osmotic control of 5.6 mM D-glucose and 25 mM L-glucose. The 5.6 mM represents non-diabetic blood glucose conditions. To address if dyslipidemia alters monocyte Cd36 expression, I will use the same 4 glucose conditions in conjunction with 50 µg/mL of VLDL, a triglyceride-rich lipoprotein that is elevated in diabetic dyslipidemia. Following a 24-hour stimulation, I will isolate monocyte RNA and use qPCR to determine the amount of Cd36 mRna. If elevated glucose induces an increase in Cd36 expression, this suggests that hyperglycemia stimulates increased Cd36 expression in monocytes in diabetes. However, if the presence of VLDL is required to observe an increase in Cd36 mRna, this indicates that dyslipidemia is needed for increased monocyte Cd36 mRna expression. Results from this study will help us understand the relationship between lipids and hyperglycemia in the context of diabetes-induced monocyte lipid loading.

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.

Coccidioidomycosis, also known as Valley Fever (VF) is caused by the fungus Coccidioides. Pigtail macaques (PTMs) bred at the Washington National Primate Research Center (WaNPRC) in Mesa, AZ are naturally infected with Coccidioides and are similar to humans in their physiology, symptoms, and immune responses. Populations with a weakened immune system, notably older individuals, are at risk for severe complications from infection. Additionally, there is evidence that males have a higher incidence of VF than females in endemic areas. I characterized the immune responses in a PTM model across age and sex to better understand how VF affects the immune response of these populations. Forty-two PTMs (2.25-19.24 years, 3.66-18.29 kg, 37 female, 5 male) at the WaNPRC were sampled for blood. The frequencies of immune cell subsets in whole blood were characterized by flow cytometry and compared for significant differences based on age and sex. I analyzed sex-based differences with Brown-Forsythe and Welch ANOVA t-tests and found no statistically significant differences. For age-based differences, we used a simple linear regression to analyze differences by age in immune cell subsets. We found that old PTMs (10.07-19.24 years) have higher activation of CD8+ T cells, myeloid dendritic cells, intermediate monocytes, and higher frequency of γΔ T cells and CD4+ γΔ T cells than young PTMs (2.25-9.69 years). Young PTMs have a higher frequency of CD45+ granulocytes, PD-1 High CD8+ T cells, plasmacytoid dendritic cells, and NK cells. By correlating older PTMs with higher immune cell activation, and younger PTMs with higher immune cell frequency, we have a better understanding of how a vaccine or treatment could be developed to support older individuals, who are at greater risk of severe infection.

Damage to the spinal cord causes one of the most debilitating injuries to the human body. The challenge of promoting the regeneration of this dense network of neurons and glia after spinal cord injury has been seen as insurmountable. However, new techniques emerging from the field of regenerative medicine have illustrated the possibility of encouraging the body to repair these injuries on its own. In the Wills Lab, we study the model organism Xenopus tropicalis, or the Western clawed frog, which has the ability to regenerate its spinal cord and associated tissue following amputation. My project focuses on how X. tropicalis uses the developmental morphogen Sonic Hedgehog (Shh) to re-establish the dorsal-ventral (DV) patterning of the spinal cord during regeneration. I have used cyclopamine, a Shh inhibitor, and SAG, an agonist, in order to perturb Shh signaling during regeneration. I then monitored the effect on DV patterning via immunohistochemical labeling of dorsal and ventral markers. Work so far has shown that Shh signaling is in fact necessary to the establishment of proper DV domains in the regenerate spinal cord. However, my research has also hinted that this specification is complex. Shh appears to have a more proliferative role early on, with patterning effects coming later. In addition, there appears to be an interaction between Shh and other signals that specify anterior-posterior polarity. Overall, my research so far has generated new evidence for how developmental signals are repurposed in the context of regeneration. 

People living with untreated HIV have a compromised immune system, which increases the risk for enhanced inflammation and disease severity in those co-infected with SARS-CoV-2. This emphasizes the importance of understanding the underlying mechanisms during immunosuppression that impact SARS-CoV-2 pathogenesis and disease outcomes. Since the microbiome plays an important role in immunity, microbial dysbiosis during HIV infection could contribute to prolonged SARS-CoV-2 pathogenesis. Microbial dysbiosis can be determined through the loss of diversity and changes to the composition of the microbiome. There is an established link between the increase in HIV disease progression and gastrointestinal microbial dysbiosis, however, the understanding of HIV-induced microbial dysbiosis during COVID-19 progression is unknown. In this project, we will investigate the gastrointestinal microbiome diversity and composition during SIV infection, to serve as a basis for understanding this undefined association. Utilizing the SIV macaque model for AIDS, we will test the hypothesis that the microbiome diversity and composition during SIV infection will be dissimilar between different gastrointestinal areas (stool, rectal swabs). Seven female rhesus macaques were intravaginally infected with SIVmac251. Rectal swabs and stool samples from the macaques were collected at baseline: 17~34 weeks post-SIV infection, and 7 days pre-SARS-CoV-2 infection. We extracted genomic DNA using a QIAgen PowerFecal Pro DNA kit and sequenced the ribosomal RNA after 16s amplification. We use the bioinformatics platform, QIIME2, to analyze the sequencing data. I am probing the data for relative microbial abundance, and diversity of microbial communities through metrics of richness, evenness, and specific indexes. Preliminary findings report that during SIV infection, the overall diversity of the gut microbiome is similar in stool and rectal swabs, and the microbiota composition is different between them. The results from these studies will then be used to understand the role of SIV-induced microbial dysbiosis on SARS-CoV-2 virological and disease outcomes.
 

Corepressors are proteins recruited by partner proteins to negatively influence the transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and while we understand a lot about how TPL works, many mysteries still remain. My project aims to identify other proteins that work with TPL to form a transcriptional repression complex at a single-engineered promoter site. First, we created a synthetic repressor called dCas9-TPL that binds and represses the transcription of the RUBY reporter. The RUBY reporter is a visual marker designed to express throughout the entire plant, turning the green plant a bright purple. Our engineered RUBY line also carries two guide RNA binding sites in its promoter with sequences not found anywhere else in the Arabidopsis genome. This allows dCas9-TPL to bind to and repress this synthetic gene and not affect the transcription of other genes. Many of these plants have morphological phenotypes, and visual screening of the repressed RUBY line showed the plants turn a faint whitish-pink instead of bright purple, signifying that the repression by TPL is working. I have screened mutagenized populations of 40,000 individuals from the validated repressed RUBY plant strains using the Ethyl methanesulfonate (EMS) protocol, which creates new point mutations. I identified 257 individuals from 129 mutagenized families with bright purple organs, which signifies that the RUBY reporter is no longer repressing due to a putative TPL interactor being mutated. I will then proceed to form complementation groups and subsequent DNA sequencing to map the mutations. By identifying regulators of corepressor function in plant biology through downstream whole genome sequencing, I hope to learn principles that can inform cellular engineering across many organisms and better understand why certain mutations associated with transcriptional repression cause developmental defects or diseases like cancer in humans.

3D measurements made with digital tools are increasingly useful for studying morphology, but methods that capture sub-millimetric detail are rarely portable, inexpensive, or usable on live animals. These issues are especially troublesome when studying bird bills, which are often small, complex, and delicate to handle. I strove to develop a method that could cheaply, accurately, and quickly generate models of live hummingbird bills in the field. Using photogrammetry, I scanned Burke Museum specimens of several hummingbird species modifying aspects such as light, number of cameras, and number of photographs, to determine the ideal conditions for generating bill models. After developing a methodology, I scanned Green Hermit (Phaethornis guy) specimens from the Burke to establish the efficacy of the system in determining sexual dimorphisms in bill curvature and bill surface area. I then applied the methodology developed in the museum at a replicated setup in the San Juan Islands to study live Rufous Hummingbirds (Selasphorus rufus). This system is capable of quickly capturing and posterior rendering high-resolution 3D models, is field-amenable, allows color analyses, is adaptable to subjects of a variety of sizes, and is easy to update. In hummingbirds, fine-scale details like sharpness, curvature, and minute variations in bill-tip shape can have large behavioral implications. They can tell us more about how bills are used for feeding, fighting, and preening. However, bill tips are delicate, and fine details are difficult to preserve and easily lost in museum specimens due to wear and tear. A complete picture of bill morphology requires individuals that cover a wider range of life history than those commonly available in a museum collection. The 3D imaging of these traits in the field represents a powerful new way to learn about bird bills and other fine-scale features in live animals.

Rhabdomyosarcoma (RMS) is a devastating soft tissue sarcoma most commonly affecting children. The components in the RAS-PI3K-MAPK signaling pathway are frequently mutated in RMS and are being studied as a critical target for treatment. A MEK1/2 inhibitor, trametinib, has shown clinical efficacy singly or in combination with other drugs in improving survival outcomes of patients with cancer types harboring mutations in the MAPK pathway. In addition, vincristine is a common chemotherapeutic drug used to treat RMS, but its efficacy has been limited due to RMS cells developing resistance. The study aims to determine whether combined treatment of vincristine and trametinib could more significantly inhibit RMS cancer growth compared to treatment with each drug alone. For this study, a clonal zebrafish line bearing RMS tumors labeled with a fluorescent protein was first treated with a range of trametinib concentrations to find the appropriate dosage for optimal effectivity yet minimal toxicity. Then, RMS-bearing zebrafish received two doses of trametinib, vincristine, or a combination of both through intraperitoneal injections (IP). Finally, we collected tumors from each treatment group to assess treatment-induced changes in gene expression by quantitative RT-PCR and changes in tumor cell proliferation and cell death by immunohistochemical stains. The changes in tumor volumes were determined by quantifying the intensity of tumor fluorescence in the ImageJ software. Preliminary findings showed that zebrafish tumors treated with the combination of vincristine and trametinib significantly inhibited tumor growth compared to the other with each agent alone. Thus, the results of this in vivo study on zebrafish may introduce a drug dosage combination with translational potential in creating a new treatment composed of lower doses of each drug while increasing potency against chemotherapy-resistant tumors and lessening side effects in patients. The end results will translate into improved survival outcomes and well-being of RMS patients.

Alzheimer’s disease and related dementias (ADRD) are neurological disorders that affect cognitive function, including impaired memory, thinking, and reasoning, primarily in older adults (OA). Cultural and linguistic differences can pose additional challenges. The experience of ADRD differs between patients from diverse backgrounds, and language barriers can create additional challenges when communicating with healthcare professionals. Our overall objective is to improve healthcare processes for persons with ADRD and limited English proficiency (LEP) in the United States. In this phase of a larger qualitative study, we are seeking to understand the experiences of older adults experiencing dementia whose primary language is Chinese and their family members. To understand the experiences of this population, we are conducting semi-structured interviews with OA with LEP and ADRD and their family members. I am performing qualitative data analysis along with three other team members. Data gathered from these interviews is transcribed and coded using a codebook developed using the inductive method. In this poster, I present key themes that are emerging in our preliminary analysis. There are significant barriers in patient-provider interactions between healthcare providers, OA with ADRD, and their family members, in the context of LEP. A complex dynamic is formed as providers seek to convey information to the OA and family members who play different roles in an OA’s life, including but not limited to acting as interpreters. OAs struggle to adjust to their progressive symptoms as they lose autonomy over time while navigating life with ADRD. Language barriers, lack of understanding of cognitive decline, and denial can also exacerbate problems. By identifying challenges experienced in patient-provider communication in the context of ADRD and LEP, we hope to work with healthcare providers to equip them with a better understanding of how to serve this demographic.

Data visualizations are critical to understanding large, complex datasets. For example, visualizations help us detect missing and erroneous data values, identify potential relationships between data variables, and review the output of machine learning models. That being said, customized visualizations can be difficult to create, because they require the use of specialized toolkits such as ggplot2, Vega-Lite, or D3. In this research, we study how people use a browser-based toolkit called D3 to program custom visualizations, with the long-term goal of creating AI-assistants to help people code in D3. However, to train rigorous AI models, we need a large input corpus of D3 examples that is accurate and reliable. In this presentation, we share our progress towards building this training corpus. First, we mined hundreds of real-world examples from the web. Then, we analyzed these examples to understand how visualization users take complex D3 programs and break them down into easily understandable parts, which we call components. Currently, we are investigating how these different components can be remixed and reused to create D3 visualizations for datasets that a model may not have encountered before. Future research will involve collecting more examples to grow our corpus, and training AI to use the corpus to generate documentation and relevant examples to help new visualization users better understand D3.

China’s rise and growing presence in the Indo-Pacific region is a major source of concern for the United States. To meet this challenge, President Biden’s administration has envisioned an Indo-Pacific Strategy aimed at keeping that vast region “free, open, prosperous, secure, and resilient” in conjunction with its allies and partners. This Task Force assesses the effectiveness of this strategy from the perspective of China as well as that of Australia, India, Japan and South Korea. It also examines the workings of this strategy from the standpoint of ASEAN and EU/NATO and that of such important world regions as the Middle East, Africa and the Pacific Islands. What can and must the U.S. do to maintain and enhance its ties to existing allies and partners and line up additional prospects to advance its Indo-Pacific strategy.

Sporadic inclusion body myositis (sIBM) is an acquired progressive inflammatory muscle disease. It is most commonly seen in individuals over 50 years old and affects more men than women. Symptom onset is generally gradual and characterized by progressive muscle weakness and atrophy. Weakness often starts in the quadriceps and finger flexors but can affect other muscles in the arms and legs as the disease progresses. Difficulty swallowing also can be present. The disease remains challenging to diagnose due to its non-uniform presentation. There is currently no cure or standard treatment for sIBM as it is unresponsive to corticosteroids and immunosuppressive drugs. In this study, we investigated the prevalence of and associations between different features considered in the diagnosis of sIBM. We reviewed the electronic medical records of adult patients diagnosed with sIBM using ICD-10 codes at the University of Washington Medical Center from 2003 to 2023. Data was collected including creatine kinase (CK) levels, presence of the anti-cytosolic 5′-nucleotidase 1A (NT5c1A) antibody, pulmonary function testing, presence of dysphagia, muscle strength testing, muscle biopsy findings, electromyography (EMG)/nerve conduction studies, and magnetic resonance imaging (MRI). Statistical analyses were performed to identify the presence of sIBM phenotypes and correlations between them. This study confirms the heterogenous presentation of sIBM and highlights the associated diagnostic challenges this presents. Understanding both typical and atypical presentations is key to preventing delayed diagnosis and misdiagnosis commonly seen in this patient population. Timely diagnosis allows for more tailored management of disease-related symptoms and can help to eliminate the unnecessary administration of ineffective medication and invasive testing. In addition, further characterization of sIBM phenotypes may lead to improvements in both current diagnostic criteria and considerations for clinical trial outcome measures.

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.

Signaling of fibroblast growth factor receptors (FGFR) is critical for the development of vascular cell types. FGFR exists as two alternative splice variants: the b and c isoforms. Previous experiments have shown that activation of the c isoform leads to arterial endothelial cell development and inhibition of the c isoform is critical to perivascular development. These results were found using a c isoform-specific computationally designed protein. The goal of my project is to replicate these isoform specific results in an endogenous context. Our hypothesis is that induced pluripotent stem cells (IPSCs) overexpressing the b isoform will develop into pericytes and IPSCs overexpressing the c isoform will develop into arterial endothelial cells. I used the Gibson assembly method to create b/c isoform overexpression plasmids that can be inserted into the AAVS safe harbor site and used bacterial transformation to increase the amount of DNA. I am using stable transfection to create IPSC overexpression cell lines and adapting a previously verified 14-day protocol for creating endothelial cells from IPSCs to monitor each cell line’s differentiation. I am performing assays such as qPCRs, Western Blots, and immunofluorescence to quantify perivascular and endothelial markers in the cell lineages. Our findings should agree with our isoform specific hypothesis. In future experiments, we plan to engraft the overexpression cell lines into immunodeficient mice and assay how varying ratios of the two cell types affect their regenerative potential in vivo.

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.

T cells rely on cytokines for cell communication and regulating effector function to respond to infections and cancer. Cytokines are sensed by T cells when bound to surface receptors, activating common second messengers that modulate cell differentiation and distinct cell activity. Second messengers allow T cells to mount controlled and effective immune responses; extracellular signal-regulated kinase (ERK) is phosphorylated (pERK) primarily downstream of antigen-T cell receptor engagement to drive proliferation, differentiation, and survival; signal transducer and activator of transcription (STAT) proteins consist of polyfunctional transcription factors phosphorylated (pSTAT) downstream of cytokine signaling, inducing gene expression to regulate cell activity. Different cytokines give rise to distinct responses by activating the same set of second messengers, raising an unresolved question: how can T cells distinguish between different cytokines and mount distinct functional responses? My project aims to investigate the hypothesis that T cells encode information about cytokine identity and magnitude by activating and translating unique combinations of second messengers into distinct gene expression programs. I will stimulate splenocytes with interleukin (IL)-2, IL-7, IL-15, and IL-21 and measure pSTAT and pERK levels using flow cytometry. To analyze differential gene expression, I will analyze an unpublished single-cell RNA sequencing dataset to determine the effects of different cytokines on CD8+ T cell gene expression programs using single-cell sequencing analysis packages. Previously, I found T cells use combinatorial second messenger activity through differential activation of STAT3 and STAT5 in response to IL-2 and IL-21, and expect cells to upregulate effector and memory genes respectively. I expect IL-7 and IL-15 to differentially activate STAT5, respectively upregulating cell survival and memory response genes while both promoting memory cell proliferation. By elucidating relationships between cytokines, second messengers, and gene expression, we can further our understanding of T cell differentiation mechanisms to inform potential therapeutic targets to combat disease.

By 2050, it is predicted that over half of the global population will be over the age of 65. Therefore, it is of the utmost importance that we study the impacts of aging on human health and well-being. One major obstacle researchers face in seeking to understand human health relates to the extensive number of newly discovered biological systems that exist and interact in every individual at various levels and timescales. Furthermore, many well-known age-related neurodegenerative diseases are thought to begin years to decades before any clinically relevant symptoms are present. The current study attempts to address some of these challenges by examining the interaction of cognition with immune function, inflammation, gene expression, and the microbiome. This research will allow us to begin unpacking the complex interactions of these numerous biological factors and their impact on natural aging and age-related neurodegenerative diseases. To accomplish these goals, our project has created and implemented a novel high-throughput cognitive testing system to assess a range of cognitive abilities including, but not limited to, attention, memory, and object recognition, on two species of well-known non-human primates (NHPs). At numerous time points, we concurrently collected and analyzed blood, fecal, and cerebrospinal fluid to characterize each animal's health profile. With our collection of data sets, we anticipate that older NHPs will display higher levels of neuroinflammation and decreased immune function. We hope to find correlations between these factors and other variables with genes that are known to be related to a host of neurodegenerative diseases including Alzheimer's Disease (AD), Alzheimer’s Disease-Related Dementia (ADRD), and Parkinson’s Disease, among others. Results from this ongoing project will unravel mechanisms associated with age-related neurodegenerative diseases, allowing for earlier detection; this early detection is regarded as the most effective approach for preventing and treating such diseases.

Pain is the number one reason why patients seek medical treatment, yet current pain therapeutics such as opioids have limited efficacy and produce harmful side effects. This has produced a critical need for the development of novel therapeutics for the treatment of acute and chronic pain. Cannabidiol (CBD) shows promise as an analgesic, but the mechanism of action is not well understood as it interacts with several receptors such as cannabinoid receptors CB1 and CB2 and noxious nociceptors TRPA1 and TRPV1. I am investigating how CBD acts on the nervous system to disrupt nociception (pain perception) utilizing the Danio rerio model system and human embryonic kidney cell line 293T (HEK 293T). I use behavioral assays with genetic knockout models to interrogate the molecular mechanism of CBD-mediated analgesia and ratiometric Fura-2 calcium imaging of HEK 293T cells that express TRPA1 or TRPV1 to further elucidate their responses to combinations of CBD, heat, and allyl isothiocynate (AITC, a TRPA1 agonist). My preliminary results indicate that CBD is pronociceptive at low concentrations (10uM) and analgesic at high concentrations (20uM). Recent experiments suggest that CBD’s pronociceptive properties occur via TRPA1 activation, and that this sensitization attenuates CBD-mediated analgesia. I anticipate each CBD receptor knockout will alter CBD-mediated analgesia, with CB1 and CB2 null animals experiencing deficits, while CBD-evoked analgesia may be potentiated in TRPA1 and TRPV1 null animals. I anticipate observing heightened intracellular calcium concentrations when HEK293T cells expressing TRPA1 are perfused with CBD, and increased responses to AITC when cells are perfused with CBD. Importantly, this project creates a platform for the investigation and characterization of minor cannabinoids and other potential therapeutics, using behavioral phenotype based screening to aid in the development of novel, non-opioid analgesics that can revolutionize pain treatment.

Many transgender and gender diverse (TGD) people desire gender-affirming hormone treatment (GAHT) to alleviate discomfort due to the misalignment of one’s gender identity with their secondary sex characteristics, though little is known about its effects on the body. One area of interest that may be affected by GAHT is the gut microbiota (GM). GM and the sex hormones (estrogen, testosterone, and progesterone) have been shown to interact bidirectionally, referred to as the “gut microsexome.” At puberty, the commensal microbiota of males and females diverge due to circulating sex hormones. This difference is hypothesized to contribute to sexual dimorphism of disease prevalence between cisgender males and females, although little research on the effect of GAHT in the TGD population exists. Alteration of the gut microbiota, or dysbiosis, also has many adverse effects that overlap those of testosterone GAHT (THT) such as acne, weight gain, and hypercholesterolemia. Dysbiosis has also been shown to lead to intestinal and systemic inflammation by disrupting immune function. More information on the effects of THT on the gut microbiota is necessary to counsel transmasculine clients effectively. In this study, we injected mice born of the female sex biweekly with testosterone enanthate dissolved in sesame oil versus sesame oil alone. We profiled GM of mice throughout treatment using 16S rRNA sequencing and measured markers of inflammation in serum to assess the effect of THT on both the population of GM and intestinal and systemic inflammation. We expect that the mice receiving THT will have differentially abundant gut microbiota and increased concentration of inflammatory markers compared to controls. The findings of this study will serve as a basis for further studies exploring additional analysis of the gut microbiota and inflammation in both transmasculine and transfeminine people receiving GAHT.

Chemical communication is the oldest and most widespread form of communication across the tree of life, and markedly present among lizards. However, the drivers of chemical profile variations in this group remain for the most part uninvestigated. In South American lizards of the Tropiduridae family, semiochemicals are produced by epidermal gland organs called α-glands, exclusively found on the ventral side of male individuals of at least 40 species from four genera. The chemicals produced by these glands are hypothesized to interact with their environments in different ways since chemical species are naturally reactive and tend towards their lowest energetic state. Thus, the intrinsic properties of a semiochemical impact its survival and efficacy for communication. Given the diverse ecology and broad geographical distribution of tropidurids, we investigated whether variation in the chemical composition of α-gland secretions correlates with temperature, humidity, and habitat openness. We performed liquid chromatography-mass spectrometry (LCMS) to obtain the metabolomes of three different sample types. We sampled male skin containing the α-glands, undifferentiated male skin, and female skin. Environmental and chemical property data were extracted from online databases, literature, and field observations. Preliminary tests were done by making Venn diagrams comparing the metabolomes of each sample type. These revealed differences in metabolite compositions, notably between males and females as well as between glandular and undifferentiated skin. From the metabolomes of α-glands, we expect to see chemical species with properties that confer greater survival given the specificities of the environment. For example, given a lizard from a hot and humid environment, we expect the metabolome of the α-glands to contain higher molecular weight species with less functional group complexity. Understanding how environmental parameters drive the chemical composition of α-glands is expected to provide a deeper understanding of the evolutionary history of chemical signaling in terrestrial vertebrates.

Colorectal Cancer (CRC) incidence is rapidly rising in patients younger than fifty with no prior family history. Recent research has revealed that very low frequency somatic mutations accumulate in normal tissue with aging. Many of these mutations occur in common cancer genes and are positively selected, producing clonal expansions, that might be linked to cancer risk. I hypothesize that the normal colon of patients with early onset CRC might carry clonal expansions driven by mutations in CRC genes, which could be detected with ultra deep duplex sequencing. Duplex sequencing is an error correction method that improves sequencing accuracy through double stranded molecular tagging. I used duplex sequencing to perform ultra deep sequencing (~3000x) of the main driver genes of colorectal cancer (CRC) which includes: BRAF, APC, FBXW7, KRAS, PIK3CA, SMAD4, and TP53. First, I performed adjustments of gene probes by increasing or decreasing the proportion of each probe in each gene pool to achieve comparable depth of sequencing across genes. Then, I sequenced normal colon tissue of two patients with and without CRC. Preliminary data showed deleterious mutations in tumor suppressor genes: APC, FBXW7, and TP53, which occurred at higher frequency in the patients with cancer. The next steps of this research involve analyzing the normal colon from a larger cohort of patients with and without CRC. Our results have demonstrated that clonal expansions are visible in early onset CRC with these sequencing methods, and I anticipate that I will identify more clonal expansions in patients with early onset CRC than in those without CRC. In conclusion, duplex sequencing allows for the detection of cancer driver mutations in normal tissue, allowing the discovery of early somatic events in CRC and offering potential for early CRC detection, prevention, and prediction.

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.

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.

Teachers play an integral part in a child's development as they are responsible for educating youth. Since COVID-19, schools are reporting rising rates of teacher burnout (52%) and students exhibiting problematic behaviors (e.g., disruptions [59%], disrespectful [52%], rowdiness [49%]). Disruptive classroom behaviors hinder the ability of teachers to adequately implement curriculum which results in a variety of disciplinary actions administered. My research analyzes the correlation between elementary school teachers' burnout rate and disciplinary actions taken. My data comes from a larger study that examined the implementation of a preventative social-emotional behavioral program in nine different schools. Teachers completed an online survey distributed in the middle of the academic year, including a measure on burnout, and the district provided systematically obtained disciplinary records (i.e., September to December) upon completion of the study. Preliminary analysis is ongoing to examine the relationship between teacher burnout and disciplinary actions recorded. This can be a first step towards improving teachers' professional well-being and creating a more prosocial classroom environment for student growth.

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.

Mind-wandering, characterized by the inward direction of attention towards thoughts, represents a widespread cognitive phenomenon that can disrupt task-related attention. Evidence indicates that the frequency of mind-wandering increases during sustained attention tasks, and previous research has proposed several hypotheses, such as resource-depletion, control-failure, and resource-control hypothesis, to explain the increases as well as the declines in task performance from their perspective. This study first aims to investigate the impact of incorporating a strategy of break on the frequency of mind-wandering during a Sustained Attention to Response Task (SART). It seeks to determine whether a break strategy can mitigate the frequency of mind-wandering and to identify which of the aforementioned hypotheses best fit the experiment outcome. Specifically, it examines whether a rest break or a task-switching intervention can reduce the frequency of mind-wandering, comparing these effects to a no-break condition. Forty students from the University of Washington will participate in a four-part experiment that includes two 480-trial SART tasks, an intervening break condition (rest break, task-switch, or no break), and a concluding questionnaire. Mind-wandering will be measured through thought-probe methodology, and task performance will be assessed using error rates and response times. Additionally, subjective workload and fatigue level will be assessed using NASA Task Load Index (NASA-TLX) questionnaire. Based on the three existing hypotheses and behavioral data, the second aim of the study is to construct three cognitive architecture ACT-R models, and by comparing different models to reflect potential mechanisms of the role of breaks in mind-wandering.

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.

Cancer is characterized by uncontrolled cell proliferation, and its potential to affect almost anyone as they age poses a significant threat. Extracellular vesicles (EVs) are lipid-bilayer membrane-enclosed structures that cancer cells produce and use for intercellular communication. EVs are typically loaded with a variety of proteins, nucleic acids, and other cargo that can be delivered to recipient cells. Tumor-derived EVs aid in the progression of various cancers by enhancing malignant cell survival, proliferation, and invasion. Working with our graduate mentor, we conducted an 866 chemical screen and found kinase inhibitors that altered EV production by cancer cells via luminescence assay. From the hits, we chose to study kinases from the JNK and p38 MAPK pathways, which both promote cancer progression. Reactive oxygen species (ROS), which damage cells through oxidative stress, can activate both of these pathways. Based on this, we proposed the question: what role do ROS play in EV biogenesis and cancer development in living organisms? To answer this question, our research utilizes Drosophila melanogaster, an ideal in vivo model due to its vast genetic toolbox and brief generation times. We used Drosophila with the Ras^V12, scrib^-/- tumor model to study EV biogenesis, and crossed them with flies that have knocked down homologs of JNK and p38 MAPK. We then selected specific progenies and dissected the imaginal discs and placed them in media to allow for EV biogenesis, and quantification was done by live imaging EV production from tumor discs, fluorescence assays, and qPCR. Our preliminary results show that imaginal discs from Ras^V12, scrib^-/- flies produce a large amount of EVs. We anticipate that in organisms, both JNK and p38 MAPK knockdowns will lead to a decrease in EV production. Future work could be done to implement our findings in humans to potentially develop novel cancer therapeutics.

Mentoring is an effective way to improve diversity and retention in STEM fields. The UW Psychology Undergraduate Mentoring Program (PUMP) matches psychology students from underrepresented groups with mentors, including undergraduates, graduate students, faculty, and alumni. Matches are made based on a combination of career interests and personal identities. In this study, we aim to understand predictors of mentees’ success in the program, defined by feelings of belonging, academic preparedness, and satisfaction with the mentoring relationship. These predictors include meeting characteristics and match characteristics. We hypothesized that in-person meetings, more frequent meetings, and greater similarities between mentors and mentees would be linked with greater success. 32 out of 168 mentees completed our survey on Qualtrics in Spring 2023. We measured meeting frequency (“How often did you meet with your mentor during [quarter]?”), format (“In what modality did you meet with your mentor? In-person, video/phone calls, texting, email”), match characteristics (e.g., whether the mentor and mentee shared similar demographics such as BIPOC, first-generation, or gender; how far apart they were in their class levels), belonging (e.g., “I know other people in the psychology major”), preparedness (e.g., “I feel prepared to pursue the psychology major at UW”), and satisfaction (e.g., “My mentor and I have had a successful mentoring relationship”). We will conduct correlations and multiple regression analyses to test the prediction that in-person meetings, more frequent meetings, and greater similarity between mentors and mentees will be linked with higher feelings of belonging, preparedness for the major, and satisfaction with the mentoring relationship. We hope to demonstrate that controllable variables such as these can improve program outcomes. Identifying the most effective program strategies, like in-person meetings or demographics-based matching, can aid mentees in our program and may also guide the development of new mentoring programs in other departments.

Neuropsychiatric disorders, such as major depressive disorder, pose a difficult challenge for healthcare providers. Treatments for such disorders vary in efficacy and come with detrimental costs. Historically, preclinical animal models have failed to incorporate the nuances of volitional human social behavior. This project used chronic social defeat stress in which mice experienced bouts of antagonistic encounters to induce depression-like behaviors in male and female mice, this was followed by self-administered social interactions within an experimental chamber in which lever presses were reinforced by social contact. The goal is to develop preclinical animal models that can be assessed to identify neural mechanisms responsible for stress-induced social motivation. Male and female mice will train to self-administer social interaction with a sex and age-matched housing partner over the course of ten 12-trial sessions. Next, experimental male and female mice will be subjected to both social and witness defeat (observation of social defeat) sessions followed by social self-administration. Before and after the 10-day social stress sessions, we will test social reward seeking via non-reinforced self-administration of social reward followed by a progressive ratio test. Brain tissue will be collected and prepared for immunohistochemistry and whole-brain clearing. Social defeat decreased social reward seeking behaviors in male mice. Witness defeat did not alter social reward seeking in males but increased seeking behavior in female mice. Social stress can be used to discern differences in social motivation in male and female mice as a result of stress-induced factors. There is potential in using whole-brain activity mapping to identify brain structures activated during social reward following social stress. We hope to build a technical tool for the field that can encompass whole-brain activity responsible for social stress responses by utilizing nuclear localization and retrograde tracing.

In the rapidly evolving landscape of remote work, the challenges associated with recalling important information from meetings and missing meetings have increased. One potential solution is to use large language models (LLMs) to summarize meetings to help participants catch up after meetings are over. To have a better understanding of this topic, we systematically reviewed 17 existing commercial tools and research prototypes for LLM-generated meeting summaries. The results show that existing solutions fell short of supporting users to verify and validate the comprehensiveness and accuracy of the generated summary, hindering users from trusting the summary. To address this, the project aims to design and build a more trustworthy LLM-generated meeting summary tool. Specifically, we propose that LLM-generated summary should progressively display relevant meeting information based on the importance of the information and the user’s goals, and include trustworthiness cues to aid users in making accurate trust judgments of the summary. Our preliminary interviews and a literature review showed that users are more hesitant to trust the AI summary when the information is consequential, such as when they missed the meeting or specific action items. While trustworthiness cues such as quotes or links to raw transcripts could increase users’ trust, irrelevant and redundant information erodes people’s trust. To further validate these observations, we will conduct a formative interview study. We will show participants mid-fidelity prototypes exemplifying the key design decisions and elicit their feedback on appropriate trustworthiness cues, desired ways to indicate their goals and intentions, and expectations on the importance of different portions of a summary. These empirically supported insights will inform the final design of a trustworthy LLM-generated meeting summary tool, which we plan to implement and evaluate in the next step.

Quantum computers represent data through qubits, as opposed to bits in classical computers. These qubits can be implemented using various physical systems, including trapped ions where they are represented by the internal energy levels of individual ions confined within electromagnetic fields. Trapped ions are an attractive choice for qubit implementation since this system has the potential to meet all the DiVincenzo criteria, which are a set of requirements needed to build a mainstream quantum computer. To facilitate the development of mega-qubit (MQb) trapped-ion quantum technologies, the Scalable Quantum Research Lab is conducting extensive research on the persistent issue of collisions with background gas molecules, an error immune to the standard quantum error correcting codes. My research focused on answering the question, 'Can error rates be controlled through trap design?'. To answer this question, there are 3 parameters to determine: (1) trap height: vertical location of the ions from the surface trap; (2) trap depth: how strong the trap is (i.e., how stable is the trapping potential); and (3) trap anharmonicities: the coefficients associated with polynomial potential. These anharmonic potentials can accelerate ions after collisions, thereby increasing collision errors. These results were found using Particle-in-Cells simulations and computational analysis for error minimization. Optimizing the trap design allowed greater control over the collision error rate for a long ion-chain trap. In short, finding a way to control anharmonicity and trap depth using trap geometric optimization can reduce the additional measured errors in the bigger experiments. The results presented are a model of trapped ion and graphs showing relationship between different trap paramters and the three variables mentioned above. 

The T3 Watershed Experiment Upland Silviculture Study explores innovative approaches to managing forests in the Olympic Experimental State Forest (OESF) managed by Washington state DNR. This model study is an addendum to the T3 study exploring different treatments to enhance ecological heterogeneity through the implementation of variable-density plantings in the context of marigold growth. Variable-density planting increases heterogeneity by adding a variety of clumped areas across a unit which has the potential to enhance biodiversity and habitat, improve ecological resiliency, increase carbon sequestration, and optimize tree growth. We chose marigolds to act as a model specie for conifers due to its short life cycle, ease of use, and ability to growth tall and straight. Our team planted marigolds using three treatment groupings including small clump, large hex clump, and regular spacing (control)— implemented in six boxes within a controlled greenhouse environment. In Autumn 2024, volunteers and I collected comprehensive data on various growth metrics. Later, I measured the biomass of leaves, stems, reproductive shoots, and total biomass to determine biomass variations. I analyzed the effects of treatment on the stem straightness/sway, mortality, biomass of different tissues, and social class proportions. This research contributes to the broader understanding of how variable-density plantings influence vegetation dynamics, providing valuable insights for silviculture practices. The findings aim to inform future land management strategies by providing data that supports the hypothesis that variable density planting may provide numerous benefits without decreasing timber harvests.

Kathak is a classical dance form which originated in Uttar Pradesh, North India. Kathak loosely translates to “story-teller,” and has become a symbol of Indian culture and national identity. Additionally, this dance form is very physically demanding, with skills that challenge the biomechanics of human anatomy. Therefore, the purpose of this research is to explore the cultural context of Kathak, as well as examine Kathak from a medical perspective. Specifically, I sought to examine the injuries which are common to Kathak dancers, particularly focusing on the risk factors, prevalence, and mechanisms of these injuries. The methods to investigate this research question were primarily through literature review. Kathak dancers experience injuries in the lower extremities due to high rates of twisting, jumping, and stomping in the dance form. These repetitive and compressive motions may lead to hyperpronated feet, flattened arches, and extreme dorsiflexion and plantarflexion. These foot injuries overall produce a lack of alignment in the dancer’s anatomy and can decrease proprioceptive orientation and neuromuscular function and control of the lower extremities. The outcome of this research has the potential to bridge the gap between dance and medicine. Education is powerful for dancers so that they can be aware of high-risk injuries and perform exercises as preventative efforts. Preventative efforts may include reducing static stretches and instead incorporating more dynamic stretches into their daily warm-up routine. Additionally, dancers should be empowered to take initiative of their health and seek professional guidance when necessary, and dance schools should play an active role in encouraging this.

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.

Mice missing NADH: Ubiquinone Oxidoreductase Fe-S Protein 4 (NDUFS4) are a model of Leigh Syndrome, a mitochondrial disease. NDUFS4 KO mice show reduced lifespan and high levels of acetylation of mitochondrial proteins. The anti-diabetic acarbose increases survival in NDUFS4 knockout mice and reduces mitochondrial protein acetylation, as deduced by reduced acetylation of SOD2 on Lysine 68. SIRT3 is a NAD+/- dependent deacetylase that deacetylates mitochondrial proteins. We sought to determine whether acarbose reduces acetylation in NDUFS4 mice via SIRT3. NDUFS4 and SIRT3 double KO mice were fed acarbose and dissected at 35 days of age. Brain samples were collected and analyzed via western blot. We determined the levels of acetyl K68 SOD2, total SOD2, and actin for each sample. Our results show that acarbose reduces acetylation in knockout NDUFS4 regardless of the presence of SIRT3. Acarbose reshapes the intestinal microbiome and the production of short-chain fatty acids in NDUFS4 KO mice. We are currently devising in vitro experiments to determine whether short-chain fatty acids can reduce mitochondrial protein acetylation in NDUFS4 knockout cells. This research investigates if short-chain fatty acids are responsible for acetylation of mitochondrial proteins. The results can be significant because the acetylation of mitochondrial proteins can prevent diseases from being as deadly by extending lifespan. The work completed during this research is hopeful to be applied to a human model, in which this model can be used to treat mitochondrial diseases.

Autism spectrum disorder (ASD) is defined as a complex developmental condition involving persistent challenges with social communication, restricted interests, and repetitive behavior. The development of autism spectrum disorder (ASD) has been associated with altered brain development in infants with high familial likelihood for developing the disorder. Some of the same subcortical regions associated with altered brain development in ASD are also associated with sleep problems, including the hippocampus. Healthy sleep is an integral contributor to brain development during childhood and there is increasing evidence that chronic sleep loss can lead to neuronal loss and impaired functioning. Additionally, the multi-site, NIH-funded Infant Brain Imaging Study (IBIS) has previously reported sleep problems are associated with hippocampal alterations in infants who developed ASD. However, the relationship between sleep problems and altered brain development in autistic school-age children is not well understood, even though clinically significant sleep problems affect 75-80% of this population. Based on prior findings from the IBIS network, this project will examine the relationship between hippocampal volume and sleep problems in 137 school-age children with high familial likelihood of ASD (HL-ASD), no diagnosis of ASD (HL- noASD) and low familial likelihood of developing ASD (LL). Our prior findings suggest there will be differences across the three school aged groups in hippocampal volume, sleep duration, and sleep quality. We also expect that hippocampal volume in the HL-ASD children is differentially affected by sleep quality and sleep duration compared to the HL-noASD and LL children. Understanding the connections between sleep patterns and autism will help steer future research endeavors examining a largely understudied but significant issue. Additionally, this project will provide new insights into the negative consequences associated with chronic sleep loss in autistic children, affecting both their daily functioning and their quality of life.

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. 

PARP inhibitors are a revolutionary precision cancer therapy that inhibits PARP function and causes synthetic lethality in cells with homologous recombination deficiency (HRD) such as cells with BRCA1/2 loss. As such, BRCA1 presence plays a key role in PARP inhibitor sensitivity, providing a basis to predict treatment response based on BRCA1 expression in patient tumors. In addition to protein loss mutations, hypermethylation of BRCA1 gene may also result in the loss of BRCA1 expression, and subsequent HRD and potential PARP inhibitor sensitivity. The NRG-GY005 clinical trial focuses on the development of a clinically useful predictor of PARP inhibitor sensitivity/resistance to spare toxicities for patients unlikely to derive benefit. I will first characterize BRCA1 expression in randomized and blinded tumor samples as a biomarker for response to PARP inhibitors in patients. I will then relate BRCA1 protein expression to methylation status of BRCA1. Combining these two aims will describe BRCA1 function/presence in tumors, and better define overall homologous recombination deficiency to optimize patient-specific treatment between PARP inhibitors or other precision therapies. I conducted immunohistochemistry (IHC), a targeted staining with antibody MS110, towards BRCA1 to identify protein presence in tumor tissue and have compiled and analyzed droplet digital PCR (ddPCR), IHC, and clinical treatment reports. I am currently working through Aim 1 by performing IHC staining on tissues from the first phase of the NRG-GY005 clinical trial and will continue investigating whether a lack of BRCA1 expression is associated with cancer cells that are responsive to therapies. In combining IHC and ddPCR assays, we can compare BRCA1 presence with methylation to analyze tumor cases without BRCA1 expression and contribute toward identifying biomarkers to inform patient-specific treatment for individuals with recurrent ovarian cancer. I anticipate that cases lacking BRCA1 expression have an increased likelihood of hypermethylation in the tumor, causing loss of BRCA1.

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.

Convection in porous media within an inclined layer is relevant to a wide range of geophysical and engineering applications, e.g., in understanding large-scale convection in a geothermal reservoir. Previous work found that stable stationary localized convective structures are present at moderate Rayleigh numbers and a sufficiently large inclination angle when the boundary conditions are symmetric with respect to the layer midplane. In this project, I study the dynamics of traveling localized structures in inclined porous medium convection in the presence of asymmetric temperature boundary conditions. I conducted direct numerical simulations (DNS) of the fluid equations and found that one- and two-pulse structures exhibit a quadratic relationship between the travel speed of the structure and the symmetry breaking control parameter in the boundary conditions, while three- to five-pulse domain-filling structures display a linear relationship. With further simulations and increasing domain size, we discovered that, for sufficiently strong symmetry breaking, adjacent pulses repel each other while traveling and so tend to spread out, eventually becoming equidistant in the finite domain. The repulsion is sensitive to the travel speed (and thus to the asymmetric boundary conditions) and the domain size. I show that these interactions are associated with the spatial eigenvalues of the base flow that are responsible for the leading and trailing tails of the 1D along-slope temperature profile of the localized structures. These eigenvalues are complex implying that the tails oscillate while decaying exponentially. We employ the computed spatial eigenvalues to predict the tail profiles of traveling pulses and show that these successfully match observations from DNS. This comprehensive analysis enhances our understanding of the stability and bifurcations in the dynamics of traveling localized structures in inclined porous medium convection, offering valuable insights for geophysical and engineering applications.

The Poolos Lab has made significant progress in elucidating the regulation of tau phosphorylation in the brain and its relationship to both Alzheimer’s disease (AD) and temporal lobe epilepsy (TLE). However, conflicting data exists in the field regarding whether patients with epilepsy exhibit increased or decreased tau phosphorylation and expression compared to health controls. From our preliminary findings using mass spectrometry, we hypothesize that tau undergoes dephosphorylation at several amino acid sites in TLE, as opposed to the hyperphosphorylation observed in AD. To validate this hypothesis, I conducted western blots to separate sample proteins based on their molecular weight via gel electrophoresis. Western blotting has increased sensitivity compared to mass spectrometry in measuring protein phosphorylation levels. I assessed changes in tau expression and phosphorylation using phospho specific antibodies that quantify site specific tau phosphorylation levels. These samples are derived from hippocampal tissues obtained from a chemo-convulsant rat model of TLE, which mimics the chronic seizures experienced by human patients, and compared to age-matched naive controls. Densitometry is employed to quantify the relative amount of phosphorylated tau, and a two-tailed t-test statistical analysis confirms significant changes in tau phosphorylation and expression between tissues from chronically epileptic animals and control subjects. Additionally, I plan to conduct western blots on human tissue from TLE patients to generalize our findings from animal models, deepening our understanding of tau dysregulation in epilepsy. Given the increased risk of premature death and adverse effects on physical and mental health experienced by epilepsy patients, our research holds significant implications for the well-being of epileptic patients and their loved ones. By identifying alterations in tau phosphorylation, we aim to develop a biomarker of epilepsy in cerebral spinal fluid and the blood, thereby advancing diagnostic tests and potential treatments for epilepsy.

Dilated cardiomyopathy (DCM), a heart muscle disease characterized by ventricular enlargement and disorganized sarcomeres, stands as a leading cause of heart failure in young adults. Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) can be used to study diseases with genetic components such as DCM which can be caused by mutations in structural components of the sarcomere. Missense mutations in the myosin heavy chain 7 gene (MYH7), encoding for the myosin heavy chain beta isoform (β-MHC), are the third most common genetic cause of DCM. However, the mechanism by which MYH7 variants lead to sarcomere disarray is poorly understood. In this study, I developed a novel assay to interrogate sarcomere incorporation and turnover dynamics in hiPSC-CMs. CRISPR/Cas9 genome editing was used to knock-in mEos, a green-to-red photoconvertible fluorescent protein, into the endogenous MYH7 locus of hiPSCs to visualize sarcomeric β-MHC incorporation and turnover. Upon differentiation of transduced hiPSCs, MYH7-mEos fusion protein is expressed and integrated in the sarcomeres of hiPSC-CMs. Pre-photoconversion, these cells exhibit green fluorescent sarcomere striations, transitioning to red fluorescence upon UV irradiation. Tracking green signal recovery (incorporation) and red signal depletion (turnover) over time post-photoconversion allows for quantification of sarcomere kinetics in these hiPSC-CMs. Through preliminary experimentation, I revealed a steady state fluorescence recovery and depletion of 40% in wildtype MYH7-mEos hiPSC-CMs. Future work is aimed towards using this novel strategy to analyze sarcomere dynamics of pathogenic hiPSC-CMs, thus allowing for the discovery of how and which of these rates differ across various MYH7 variants. I hypothesize that in hiPSC-CMs derived from a DCM patient expressing the MYH7 E848G variant, decreased incorporation or increased turnover rates may contribute to sarcomere disarray leading to a disturbance in sarcomere homeostasis among patients with this disease.

Apolipoprotein E (APOE) is a polymorphic gene with 3 main alleles: APOE2, APOE3, APOE4.The APOE4 allele is the greatest genetic risk factor of late-onset Alzheimer’s disease (AD). Carriage of the APOE4 allele results in increased amyloid-β (Aβ) accumulation, aggregation, and deposition in the brain compared to other genotypes, thus contributing to AD pathogenesis. Preeclampsia (PE) is a pregnancy-specific disorder associated with maternal and perinatal mortality. PE has also been linked to protein misfolding pathology, characterized by the accumulation of misfolded proteins (including Aβ) in the placenta, urine, and blood. Due to the similarities with AD pathology, we investigated the relationship between APOE4 and the development of PE-symptomatology in a transgenic mouse model carrying human APOE. To assess this relationship, we induced a PE-like syndrome in APOE3 +/+ and APOE4 +/+ pregnant females on gestational day 13.5 using the Reduced Uteroplacental Perfusion Pressure (RUPP) procedure (n=5-6/group). Sham procedures were performed on the same number of females in each group as controls. On gestational day 17.5, differences in blood pressure, proteinuria, kidney integrity, placental efficiency, placental morphology, and fetal weights in response to RUPP were assessed and compared between APOE3 and APOE4 mice. Our results show that RUPP induced significant kidney damage in APOE4 mice (p=0.014), while APOE3 mice maintained normal kidney morphology. Moreover, RUPP was associated with a significant reduction in placental efficiency in both groups, but only APOE4 fetuses developed fetal growth restriction (FGR, p=0.045). APOE3 was also associated with mild changes in placental morphology, but APOE4 was not. Blood pressure or proteinuria did not vary in response to RUPP in either genotype. Our findings suggest that APOE4 confers an increased susceptibility to kidney damage and FGR in response to RUPP compared to APOE3. Further investigation is needed to determine the molecular basis of these genotype-dependent effects.

The drug resistance in tuberculosis (TB) is a rising concern for the diagnosis and treatment of the disease. Being able to detect the presence of drug resistance accurately and rapidly in the patient strain is essential for improving individual treatment outcomes and reducing further transmission of resistant strains, which are more costly and difficult to treat than drug-susceptible strains. However, the current methods come in short in point-of-care (POC) settings, due to problems such as long processing time, high complexity, and necessity for specialized personnel/equipment. Oligonucleotide ligation assay (OLA) provides a high sensitivity and specificity against TB drug resistance, and here, I have developed a novel lateral flow test (LFT) device that incorporates OLA into it, which have shown comparable specificity and sensitivity against traditional protocol of OLA in lab setting followed by LFT. Moreover, the simplicity of the design enables further incorporation of other techniques such as isothermal DNA amplification, for a compact, one-step TB drug resistance diagnostic device for low-resource environment. 

Staphylococcus aureus is an important human pathogen that has increasingly developed resistance to antibiotics and antimicrobials. It is important to understand how genetic mutations influence antibiotic resistance to anticipate how the organism is able to evolve and combat emerging resistance. My project aims to fully characterize the impact of variants in the norA gene, which is associated with efflux-mediated resistance. The Salipante lab has developed a system for precision genome engineering in S. aureus by constructing a vector that is able to conduct recombineering while suppressing DNA repair, and a separate vector for killing unmodified bacteria using programmed CRISPR/Cas9. Using this system, I will construct a library of genetic mutations in the S. aureus genome that will encompass all possible single mutations in norA and to subsequently test the fitness costs of those mutations in the presence and absence of antibiotics.We will recombineer into S. aureus randomly mutagenized oligonucleotides that encode a silent mutation that renders transgenic bacteria immune to targeted CRISPR/Cas9 cutting. After killing off unmodified bacteria, the transformed population will be composed entirely of different mutants, so that with a large population size, we can statistically ensure that all possible random mutations are represented. We will analyze the gene sequence from the initial population, after the population has expanded in the absence of drugs, and after exposure to different concentrations of drugs, to compare the relative representation of each specific mutation. Changes that are detrimental under a condition will be underrepresented relative to the starting population, while those that are beneficial will be overrepresented. Mutations that are lethal will not be recovered in the first place. Our project has the potential to fully and comprehensively address clinically important questions regarding antibiotic resistance evolution in this gene.

The effective treatment of individuals with HIV relies on maintaining therapeutic drug concentrations, necessitating accurate measurement of antiretroviral (ARV) drug levels. Current methods, such as liquid chromatography tandem mass spectrometry (LC-MS/MS), are limited by cost and accessibility. Our research addresses this gap by developing the INTEGRase activITY (INTEGRITY) assay for measuring integrase strand transfer inhibitors (INSTIs), a leading class of ARV drugs. This 2-step assay quantifies INSTIs using a DNA strand transfer reaction and quantitative polymerase chain reaction (qPCR). The presence of INSTI drugs disrupts the strand transfer reaction, inhibiting full-length target DNA formation, which is then measured through real-time qPCR. My work focused on optimizing the limit of detection of INTEGRITY by altering the strand transfer reaction conditions and protocol. Specifically, I conducted experiments altering INSTI drug concentrations and optimizing pre-incubation times of integrase with the drug to enhance the LOD. I observed that preliminary incubation of integrase and INSTI drugs for 5 minutes at 37 degrees Celsius improved the LOD of INTEGRITY by an order of magnitude. The simplicity of the INTEGRITY assay, utilizing standard laboratory equipment, holds immense promise for broadening access to routine clinic-based ARV drug level monitoring. This advancement has the potential to significantly enhance HIV care on a global scale by offering a cost-effective and accessible solution for monitoring therapeutic drug concentrations.

Snow is an essential resource, especially in the Pacific Northwest, where it provides clean drinking water, irrigation water, and helps prevent wildfires. Despite the importance of the snowpacks in the Pacific Northwest, the composition of snow is not well documented. The ion concentrations in snow can indicate where the snow came from. I have created a dataset of the concentrations of anions found in snow throughout Washington State. Snow samples were collected primarily throughout the Cascade Mountain Range by volunteers using sterilized plastic containers. Samples were melted and then analyzed using ion chromatography to quantify the anions in each sample. Samples were found to contain concentrations of fluoride, chloride, nitrate, bromide, phosphate, nitrite, and sulfate. These anions have previously been found to be present in glaciers, clouds, and freshly fallen snow. Cataloging these anions provides an important baseline from which to observe how human and natural impacts, including climate change, are affecting the snow in the Pacific Northwest.

Angiogenesis, or the formation of new blood vessels, is crucial for normal bodily function but is especially important in diseases that cause blood vessel breakdown such as diabetic vasculopathy. Angiogenesis is regulated by activation of the Tie2 receptors in endothelial cells, which have two main ligands: angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2). Ang1 binding has been shown to stabilize blood vessels and inhibit vascular leakage, while Ang2 antagonizes these effects. We have previously shown that a computationally designed Tie2 super-agonist which presents eight copies of the Ang1 F-domain strongly activates Ang1-like signaling in human umbilical vascular endothelial cells (HUVECs). In this project, we hope to assess the Tie2 super-agonist’s ability to rescue diabetes induced blood vessel defects in a diabetic blood vessel organoid (BVO) model. To model diabetic conditions, a three-dimensional blood vessel organoid model has been cultured in a high glucose media along with inflammatory cytokines associated with the diabetic phenotype. Western blotting and immunofluorescence staining will be used to assess the relative quantities and localization of proteins involved in vascular stability and inflammations upon treatment with the Tie2 super-agonist. Vascular degeneration is a very harmful condition associated with many prevalent diseases including diabetes, so the Tie2 super-agonist could potentially be a new therapeutic drug candidate for treating blood vessel dysfunction in patients with these conditions in the future.

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.

Continuous gravitational waves (CW) from sources such as a non-axisymmetric spinning neutron star have not yet been detected. If CW from neutron stars exist, the weak signals could be hidden within noise. The search for CW signals is impeded by the presence of narrow spectral artifacts (lines) caused by instrumentation or the environment at the Laser Interferometer Gravitational Wave Observatory (LIGO). Better identification of line noise would make a detection more likely, and a detection has the potential to expand our current knowledge of neutron stars. A non-machine learning (non-ML) line finding algorithm is currently used on a daily basis at the LIGO Hanford and Livingston Observatories. A different approach to line finding utilizes a machine learning (ML) algorithm. My research uses both the ML and non-ML line finding methods, comparing the accuracy and efficiency of these two methods applied to various data sets. Expected results are that the non-ML method is currently more accurate and efficient from a computing resources perspective, but that the ML approach has the potential for high accuracy and adaptability, and will eventually be more efficient in human hours. The impact of my research is to implement more accurate and efficient line finding algorithms. This work is important because automated line finders at LIGO Hanford and LIGO Livingston save researchers hundreds of hours of work and could be set up to alert researchers on changes in noise behaviors.

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.

In response to acute genotoxic stress, such as chemoradiation therapy, stem cells undergo temporary cell cycle arrest at the G1/S phase transition. This state, called quiescence, is reversible once stress-free conditions allow reentry into the cell cycle. We have previously identified the underlying mechanism behind quiescence in Drosophila Germline Stem Cells (GSCs) and human-induced pluripotent stem cells (hiPSCs). Mitophagy, or autophagy of the mitochondria, is required to enter quiescence. Surprisingly, we have observed a reserve of cyclin E (CycE) associated with the outer mitochondrial membrane that’s present in normal GSCs and hiPSCs but is reduced in quiescent stem cells. The role of CycE in quiescence remains unclear. Previously we have shown that reduced levels of CycE via inhibition of mTOR have driven cells toward mitophagy-dependent quiescence. This reveals that mitophagy serves as an alternative mechanism of CycE inhibition in contrast to the typical p21-mediated inhibition. Additionally, Parkin, a ubiquitin ligase activated by a serine/threonine kinase PINK1, is a key protein involved in mitophagy required for quiescence, and it has been found that CycE is a degradation target of this protein complex. Our hypothesis is that CycE degradation is necessary for entry into quiescence. To test this we upregulated CycE with a deleted portion of its PEST domain, which is a target for ubiquitination, under UAS-GAL4 control and used the GSC spectrosome morphology to observe quiescence. We observed a six-fold reduction of quiescent GSCs with overexpressed CycE, and hence concluded that CycE degradation is necessary for entry into quiescence. Determining the mechanism of CycE in stem cell quiescence is critical to understanding how cancer stem cells can avoid chemoradiation therapy. This project allows us to characterize the role of CycE within mitophagy and strengthen our understanding of the mechanisms that govern the cell cycle and quiescence.

When a landslide impacts a river, it may form a dam that blocks the flow of water and builds up a lake. These lakes are prone to sudden outbursts, where they rapidly drain and catastrophically flood downstream areas. Recent UW research has estimated how susceptible rivers in the Oregon Coast Range are to landslide dam formation. However, where these outburst floods would be most dangerous for humans remains unknown. In this project, we ask in which Oregon Coast Range drainage basins are the flood risk and vulnerability the highest. In other words, where would a landslide dam cause the most harm? To answer this, we follow a GIS based methodology for computing flood risk for the Oregon Coast Range. We assess the magnitude of the flood risk in the study area. We define risk as the amount of people (or building footprints) that may be exposed to future flooding hazards. We will also be assessing flood vulnerability, which we calculate using population demographic data. Using these results, we will analyze flood risk and vulnerability in concert with the probability of landslide dam flooding to determine which areas should be highlighted for further detailed study and possible mitigation planning.
 

Prior research has shown that parent spatial language use predicts child spatial language use, and as a result, a child’s spatial ability. In our current study, we seek to identify factors that influence differences in both parent and child spatial language use. Using a picture book called “Flashlight”, which contains no words, parents were instructed to read aloud to their children (N=75 dyads, range: 2-4 years). Parents created their own story based on the pictures. After the storybook task, the parent and child were given blocks to play with for 5 minutes. Both these tasks seek to examine what types of language are naturally produced between parents and children, such as spatial words, questions, and number words (e.g., “at”, “What animal is that?”, and “one”). The videos of these sessions were manually transcribed. Parents also completed a series of questionnaires on their beliefs about the utility of play and their child’s language, motor, and communication skills. We hypothesize that the more questions a parent poses, the more spatial language a child will produce. This study is multifaceted in that it examines total language used overall (tokens), different types of language, free play, and spatial abilities. Studying these aspects of communication and underlying factors that impact the type of language parents use can lead to a better understanding of children’s spatial development and the factors influencing it. For example, parents who believe that play offers children unique opportunities to learn spatial concepts might use more spatial language with their children during play, which could scaffold their child’s spatial development. By identifying these factors, we can develop ways to increase spatial language use between parents and children, thus facilitating spatial development.

Repetitive transcranial magnetic stimulation (rTMS) is a psychiatric treatment which has shown promise for experimental treatment of memory loss in Alzheimer’s Disease. rTMS uses a coil and electric current which is able to create a magnetic field that can depolarize neurons noninvasively and induce synchronized activity of large populations of neurons, ultimately inducing, lasting changes through synaptic plasticity. Alzheimer’s disease patients show disruptions in the Default Mode Network (DMN), a network of brain regions which is typically active at rest. The DMN has an important role in memory consolidation and is disrupted in Alzheimer's Disease. We hypothesize that strengthening the default mode network through rTMS applied to area left 8AV of the frontal cortex will create improvements in patient memory. To answer this question, we are performing a single-blind, single-arm, randomized cross-over trial of rTMS on early-stage Alzheimer's disease patients. Region 8AV is located by using MRI scans obtained before patients receive either the sham or experimental procedure. This region was chosen due to its connection to the default mode network and previous promising TMS research. Our primary outcome measure is the speed of forgetting, a new, reliable index of memory function obtained by fitting a computational model of episodic memory to behavioral data from an adaptive memory test. Due to the frequent use of rTMS in mood disorder treatment, we are using depression and anxiety scales to track possible mood improvements as a secondary outcome measure. MRI scans will also be analyzed to see if the experimental treatment caused any structural differences in patient brains. Should our hypothesis be correct, we expect to see improvements in memory or cessation of memory decline in patients. Successful treatment would provide a novel target for Alzheimer’s Disease treatment using rTMS, and additional evidence for the continued investigation of rTMS for Alzheimer’s Disease.

Beavers are widely considered to be ecosystem engineers because of the way they construct, modify, and maintain their dams, which in turn, alters the surrounding ecological system. Beaver dams can act as a natural filter and help clean pollution from streams and rivers. The dams also slow down the water flow in a creek or river and form ponds, which means less erosion and, in some cases, less flooding. In spring of 2023, a family of beavers began constructing a new dam along Piper’s Creek, an urban stream in Carkeek Park, Seattle. This recent arrival of beavers provides an opportunity to investigate the impact of beaver dams on water quality in Piper’s Creek. This study investigates the levels of phosphate and nitrate above and below the beaver dams as both ions are commonly implicated in eutrophication events. We took three water samples at each of nine sites along the creek, six upstream from the dam, as a baseline, and three downstream. Ion chromatography was used to measure the concentrations of ions, including phosphates and nitrates. Initial results suggest that nitrate levels may vary seasonally, perhaps due to the presence of salmon carcasses and decaying vegetation in late fall. Longitudinal studies of water quality in Piper's Creek can help elucidate both seasonal variation as well as the impact of the beaver population in this important urban stream.

Saccades are rapid eye movements that are essential for tasks like reading, and their accuracy is maintained through motor adaptation across life stages and in response to neural injuries of diseases. Our long-range goal is to identify the neural mechanisms of such saccade adaptation. While saccade adaptation has been intensively studied before, our understanding of the neurophysiological basis of this phenomenon is based largely on amplitude-decrease adaptation. However, the clinical relevance of amplitude-decrease adaptation is marginal at best, as overshooting saccades rarely occur in real life. Most erroneous saccades fall short of their target, necessitating an amplitude-increase adaptation. This is what we propose to investigate in this application. The challenge in studying amplitude-increase adaptation lies in the requirement of numerous saccades over extended periods to observe significant amplitude alterations. Our preliminary studies, conducted over daily sessions spanning more than a month, discovered a bimodal distribution of adapted saccades characterized by low and high gains, with gain defined as the ratio of saccade amplitude to the target step. Low-gain saccades surface initially, reaching peak velocity saturation leading to a gain increase saturation. Conversely, high-gain saccades emerged after extensive trials, characterized by their reduced velocities and prolonged durations, suggesting a novel adaptation mechanism through the fusion of consecutive saccade pairs. Our project aims to (1) characterize this newly found adaptation mechanism and (2) investigate the superior colliculus's (SC) role, which is pivotal in commanding saccade size, in generating both low and high-gain adapted saccades and the integration of saccade pairs. The overarching impact of this research lies in its potential to enhance our understanding of motor adaptation's role in recovering from motor deficits caused by neural damage. Understanding these changes may help refine the strategy of rehabilitation for patients with saccade dysmetrias, and perhaps motor hypometrias in general.

Brain-computer interfaces (BCI) are systems that allow direct control of machines or computers by decoding neural signals from the motor cortex, particularly the signals associated with movement intention. Existing BCI designs tend to combine signals from the premotor and primary motor cortices, treating them as a unified source for processing despite their functional and anatomical differences. Preliminary data indicates that different depths within these motor cortical areas perform different computations. Based on this data, my hypothesis is that shared computations are performed in the output layers of the premotor cortex and the input layers of the primary motor cortex. Addressing this hypothesis is difficult due to technological limitations. Many sensors used to measure neural activity in the motor cortex do not provide layer-specific information. To counteract this, my project leverages Neuropixel probes, which are high-density microelectrode arrays that record the activity of individual neurons (spiking activity) and groups of neurons (local field potentials). I developed a fixture capable of holding multiple Neuropixel sensors to simultaneously capture neural signals at known depths from the primary and premotor cortices. After determining the depth of each neuron by analyzing the local field potentials, we will compare spiking activity patterns across depths as a non-human primate learns a motor task. I expect to see similar patterns of spiking between the output layers of the premotor cortex as the input layers of the primary motor cortex. The analysis of this data will reveal how movement-related information is transmitted through motor cortical areas, which will inform the design of future BCIs.

Seattle's Black community faces significant challenges in banking and finance, including a lack of trust, limited access, and systemic barriers. While FinTech presents potential solutions, concerns persist regarding data privacy and cultural sensitivity. In response to these issues, I took on a central role in facilitating a research project that aimed to co-design an inclusive FinTech solution directly with Black communities in Seattle. To create a participatory design approach and host collaborative sessions with a Black community advisory board, my research group worked closely with community leaders and stakeholders. This involved organizing focus group sessions, where we explored three key questions: 1) What challenges do Black Americans face in banking and FinTech? 2) How can FinTech revolutionize their economic outlook? 3) How can community members co-design a culturally sensitive virtual AI assistant for mobile FinTech? Throughout these sessions, I played an active role in observing and leading discussions to ensure that community members had a meaningful voice in shaping the solution. I also analyzed the data collected from these sessions using inductive and deductive coding techniques to identify key insights and inform the process and steps for the next focus group. We anticipate developing a prototype solution designed by and for Black communities, prioritizing trust, accessibility, and empowerment. Preliminary findings suggest that community engagement and co-design processes are crucial for creating effective and culturally sensitive FinTech solutions. Additionally, fostering understanding and collaboration between Black communities, financial institutions, and FinTech developers is essential for paving the way towards a more equitable financial future for all stakeholders involved.

Treponema pallidum subspecies pallidum (T. pallidum) is growing in incidence in high-income countries like the United States and remains endemic and highly prevalent in low-income countries, primarily sub-Saharan Africa, and South America. Despite being treatable, syphilis is associated with significant fetal and perinatal mortality in low-income settings, due to congenital transmission of the infection. Improving our understanding of syphilis pathogenesis, immunology, and T. pallidum biology, could result in novel measures to curtail syphilis spread, including improved diagnostics, novel therapeutics, and a preventive vaccine. We are exploring the use of a chimeric antigen, composed of a scaffolding/carrier protein of T. pallidum and a series of protective epitopes from other T. pallidum antigens previously described and patented by our laboratory, to be used as a recombinant vaccine. The first step to using this protein as a vaccine scaffolding is determining the most immunogenic sequences of the protein to be used for replacement. Specifically, we used sera from 63 patients with syphilis at different stages, and sera longitudinally collected from rabbits infected with either the Nichols or SS14 isolates of T. pallidum, which represent the model strains for the two known clades of this pathogen. Recognized amino acid sequences were then mapped to the experimentally determined Tp17 structure. Reactive epitopes in both serum groups mapped predominantly to the α-helix preceding the Tp17 soluble β-barrel and to the loops of the barrel. We are currently using the same Enzyme-Linked Immunosorbent Assay (ELISA) to assess reactivity levels in control sera of naive human patients. These results identify sequences of the Tp17 antigen that could be replaced by protective epitopes. Our work provides the basis for future research on the use of this scaffolding to develop a syphilis vaccine able to confer protection from this this serious infection.

Lizards in the family Tropiduridae have ventral epidermal gland organs that are involved in chemical signaling and whose secretory mechanism is entirely unknown. This is because, like other epidermal generation glands, 'alpha-glands' lack a pore through which their secretion can be exerted. Chemical signaling is a valuable aspect of tropidurid lizards' social and ecological interactions, and some have been observed territorially scraping their alpha-glands against the substrate. This process has been hypothesized to facilitate the release of chemical signals via abrasion. To investigate this abrasion hypothesis, we analyzed 74 skin samples from 27 tropidurid species, using light microscopy and scanning electron microscopy (SEM). The SEM revealed incredible surface variability in epidermal glands, providing morphological insight. We found that the exposed glandular mass of each gland scale rests atop the oberhautchen layer of the skin's subjacent generation, which indicates that the secretion of chemicals involves exposing a mostly solid glandular material on the outside of the scales. Histological sectioning of gland scales revealed morphological consistency, indicating that the same secretory mechanism is shared across the tropidurid phylogeny. Imaging of histology samples also revealed that the shedding process which exposes the glandular material may be facilitated by the clear layer, found directly above the glandular mass during development. Characterization of morphological patterns in the formatted SEM images and comparison with histological data should provide evidence for or against taxon-specific or ecology-specific alpha-gland structures, and further support the idea of chemical secretion requiring epidermal exposal of glandular material. Investigations of the morphology and functional mechanism of this unique organ provide insight into the behavior and evolution of tropidurid lizards and shed light on factors influencing the evolution of chemical signaling in terrestrial organisms. 

Syphilis remains a serious global health concern, underscoring the need for better control strategies. If left untreated, the syphilis agent, Treponema pallidum subsp. pallidum (T. pallidum), can persist for decades due to its ability to evade the host immune response. Antigenic variation of the surface-exposed outer membrane protein TprK is believed to mediate persistence. TprK contains seven discrete variable (V) regions. TprK antigenic variation occurs via non-reciprocal gene conversion between the variable regions in the tprK expression site and 53 donor cassettes (DCs). We previously engineered a T. pallidum strain impaired of antigenic variation (SS14-DC^KO) by eliminating 51 of the 53 DCs. Rabbits infected with the DC^KO strain developed an attenuated infection phenotype with a reduced burden of T. pallidum cells compared to wild type (WT). Therefore, we hypothesized that if immunosuppressed rabbits are infected with SS14-DC^KO, the disease would undergo similar progression to rabbits infected with the WT strain. In this study, two rabbit groups (n=8) were either immunosuppressed with Depomedrol or untreated. Four rabbits in each group were infected intradermally with SS14-WT or SS14-DC^KO strain on clipped backs. Sera was isolated weekly to measure antibody titers using VDRL and TPPA. In addition, DNA was isolated from lesion biopsies to perform TprK profiling. Based on TprK profiling data, synthetic peptides for the most abundant V5, V6, and V7 variants were used to measure antibody reactivity by ELISA. Antibody titers measured by TPPA and VDRL were similar between immunosuppressed rabbits regardless of infecting strain. TprK profiling shows that the most abundant V sequence at the inoculum decreases over time in lesions as humoral reactivity to these peptides increases. Overall, this research demonstrates the role that TprK plays in the persistence of T. pallidum during syphilis infection and the need for novel control strategies.

Engineered heart tissues (EHTs) have emerged as a promising tool for cardiac disease modeling and drug screening, allowing for better study of cardiovascular diseases (CVDs). However, most current EHTs are composed of only a mixture of an extracellular matrix and heart muscle cells, called cardiomyocytes (CMs), without a vascular element. This prevents the study of the impacts of flow and the endothelium on cardiac function, and the role that endothelial cell (EC) dysfunction may play in cardiovascular disease. Endothelial function is closely related to cardiac homeostasis, as risk factors for CVD (smoking, obesity, diabetes, etc.) lead to an increase in pro-inflammatory cytokines, which can trigger EC dysfunction. Thus, this interaction is important to study further. The Zheng lab has developed a perfusable collagen-based EHT model, which incorporates a vascular element. The constructs form a lumen through utilization of needles and collagen, support CMs within the bulk collagen matrix, and the inner lumen of the tube can be endothelialized, serving as an effective in vitro model of cardiac vasculature. This project aims to identify healthy and unhealthy EC flow conditions within the EHTs, hypothesizing that physiologically relevant shear stress will lead to EC alignment and strong barrier properties. . We optimized the fabrication and culture process of the EHTs by fabricating a secondary dish for the EHT constructs while they are under perfusion, in order to avoid contamination risks. We then employed this model to look at EC retention and health at different flow rates, and examined the effects of altered shear stress on EC dysfunction. ECs perfused under physiological shear stress have shown markers of healthy barrier function and alignment. This project establishes a perfusable EHT model that allows us to interrogate EC function under perfusion and, in the future, assess the effect of endothelial dysfunction on cardiac dysfunction.

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.

The Pacific Northwest (PNW) saw an unprecedented heatwave between June 25 to July 3 of 2021, with temperatures reaching up to 15℃ above the climatological mean. Previous research has examined the impact of this event on plants in Western Washington and Oregon through observational studies, and has focused on the economic implications for poor crop turnout. We used remote sensing data to take a top-down approach and examined how all plants throughout the PNW fared during and after this historical heatwave. Solar induced fluorescence (SIF) and Near-Infrared Reflectance of vegetation (NIRv) are two remotely sensed products that have been used to estimate plant health and gross primary productivity (GPP). SIF is more closely connected to plant processes like photosynthesis but has a short record (2018-2021) compared to VIIRS NIRv (2012-2021). We compared the responses of SIF to NIRv and found that both vegetation indices increased in trees and woody savannas, but decreased in grasslands and crops. However, SIF showed more intense and geographically larger increases in areas covered by trees. We then compared these vegetation indices to in-situ flux tower measurements of carbon fluxes, which did not always agree with SIF during the heatwave in woody areas. This study shows how remote sensing can further our understanding of how extreme events impact plant health, which is increasingly important as heatwaves become more intense and frequent in the future.

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.

Drug use has been stigmatized for more than 140 years. This stigma has influenced public policy, school curriculum, and treatment for drug addiction. Additionally, the US has a historical pattern of shaming and excluding people who use drugs, which is especially concerning as opioid overdose death rates have risen every year. This research aims to analyze this historical, morally centered stigma and its effects on people who use drugs, while exploring the role of epigenetics (i.e., gene expression changes) in opioid addiction and opioid addiction treatment. This Literature Review examined textbooks, journal articles, blog posts, book sections, and government websites. This review analyzes historical timelines relating to societal stigma, public policy, and addiction treatment, as well as how the epigenetic mechanisms of opioids relate to those of popular opioid addiction treatments. This research indicates that how popular treatments alter the gene expression changes seen in opioid addiction is unclear due to a lack of research in this area. My analysis of historical timelines shows that the “maintenance” model of treatment, seen with methadone and buprenorphine today, was created approximately 50 years before discoveries that shaped the science of modern epigenetics. Thus, today’s leading treatments were incapable of considering the role of epigenetics in opioid addiction during their development because they were introduced before the science was fully developed. This research suggests a possibility for future use of precision medicine methods for gene editing, like CRISPR-Cas9, as a treatment modality for drug addiction. This analysis also points towards a role of epigenetics in psychiatric conditions like Borderline Personality Disorder and altering gene expression changes associated with successful psychotherapy treatment, suggesting a possibility of precision medicine in a mental health setting as well.

Elementary school educators are primary influences on children’s development by helping shape their behavior with peers and in the classroom. Employees in education are deferred to by their newer coworkers regarding student interactions and set precedents for students’ school environment. New and seasoned educators’ disciplinary practices greatly vary when addressing students exhibiting problematic behaviors which may differently affect student-instructor relationships. I use an existing dataset from a larger study testing the impact of a novel implementation strategy on the implementation of a universal social, emotional, and behavioral program in nine elementary schools from one district. Educator participants in this study completed a survey battery when starting and ending the school year and the district provided quarterly discipline records via a universal prevention program. The findings identify trends in student disciplinary actions between new (<5 yrs) and experienced (>5 yrs) instructors. Understanding the relationship between teacher tenure and the treatment of student misbehavior is crucial to demystifying the manifestation of poor student enrichment and hostile student-instructor relationships. These findings could suggest how differential disciplinary practices by educators based on their years of experience influence student learning.

Stimulator of Interferon Genes (STING) signaling contributes to tumor immunity. However, treatments targeting the STING pathway are limited by route of administration, insufficient STING activation, and off-target toxicity. We introduce poly-STING, a copolymerized, mannosylated variant of the diABZI STING agonist-3 known to activate the cGAS-STING signaling pathway, promoting the release of type-1 interferons and pro-inflammatory cytokines leading to tumor immunogenicity. The STING agonist-3 is a non-nucleotide molecule that activates the STING pathway, but it has poor solubility, which limits its usage in-vivo. The developed poly-STING platform improves the drug's solubility, is designed to target immune cells, and provides enzyme-triggered drug release upon delivery, which has been shown to induce improved therapeutic efficacy compared to the free drug. The Pun and Stayton labs seek to investigate modalities for optimization of the cGAS-STING pathway activation and characterize the mechanism of action. Specifically, my project will evaluate STING activation by observing macrophage repolarization from type M2, as the mannose from the poly-STING binds to the CD206 receptors on M2 macrophages. This activates the STING pathway, repolarizing the macrophage to pro-inflammatory type M1. To test effects in vitro, I will culture bone marrow-derived M2 macrophages with various formulations of poly-STING, and repolarization will be measured through flow cytometry and RT-qPCR to quantify expression of macrophage markers. We expect to find higher M1 activity in macrophages treated with poly-STING as opposed to the free drug. Next, I evaluate the therapeutic efficacy of the STING formulations through an in-vivo tumor reduction study using murine models of breast cancer and melanoma, expecting to find longer survival of mice treated with poly-STING. The culmination of this project will result in a polymer-based STING agonist delivery platform that solves the solubility and bioavailability issues associated with the STING-3 agonist, with enhanced efficacy and decreased toxicity after systemic administration.

Elevated concentrations of CO2 in classrooms are a persistent issue facing colleges because of both its ability to reduce academic performance by impairing cognitive function and as an indicator of the increased risk of airborne disease transmission in the classroom. The COVID-19 pandemic applied pressure on most colleges to upgrade ventilation systems including North Seattle College (NSC). Preliminary data collected pre-pandemic found that NSC classrooms’ CO2 concentrations exceeded public health recommendations. We resumed our study post-pandemic now that classrooms have returned to regular occupancy levels. We created updated ventilation efficiency curves by placing Aranet4 carbon dioxide detectors in classrooms with multiple classes under varying occupancy levels. We collected daily attendance of classrooms during each of the courses and their corresponding carbon dioxide levels. We were then able to produce a ventilation efficiency curve to contrast our preliminary data and offer a basis for further study. Initial findings suggest that NSC classrooms exceeding an occupancy of 30 people will surpass 1000 ppm, thereby reaching CO2 levels that impair cognitive functions. This is a sufficient improvement from preliminary studies which found that under previous ventilation conditions, classrooms’ occupancy was limited to 22 people. Continued monitoring of CO2 levels in academic spaces is crucial. With the growing popularity of remote teaching, and online learning becoming more accessible for students, one must wonder if our homes can meet the same standards we hold our classrooms to.

Fluoride is an important element for dental health as it helps to strengthen tooth enamel. Insufficient fluoride intake can lead to weakened teeth that are more susceptible to cavities, leading to further dental issues. On the other hand, dental fluorosis is a condition that causes white or brown speckling of the teeth due to overexposure to fluoride during the development of permanent teeth. For most people, a large portion of their fluoride intake is through water, but water from different sources is expected to contain different amounts of fluoride. Many Americans consume tap water, but bottled water is a popular choice. In fact, US consumers buy about 50 billion water bottles each year which equates to 13 bottles per person monthly. This mass consumption of bottled water raises important questions: 1) Is bottled water a sufficient source of fluoride? 2) How does it compare to tap water? To answer these questions, we collected tap water samples from six cities in the Puget Sound area, along with samples from six popular brands of bottled water. We then used ion chromatography to determine fluoride concentrations in each sample. We found the levels of fluoride in our six municipal sources averaged 0.702 +/- 0.031 mg/L as advertised, however, the levels within the different bottled water brands averaged +/- 0.282 0.307 mg/L, and none met the CDC recommended levels of 0.7 mg/L. The findings of our research are important for keeping consumers well informed about the possible risks or advantages associated with their preferred source of water and for upholding public trust.
 

Test anxiety is a prevalent issue among K-16 students, with approximately 20-40% reporting its adverse effects. This pilot study assessed the preliminary efficacy of a Short Mindfulness Activity to Reduce Test Stress (SMARTS) recording in mitigating test anxiety, indicated by heart rate (HR) physiological markers. Our research team’s undergraduate students assembled a student advisory panel to receive feedback on existing mindfulness recordings and narrow down the most effective traits of each one. From the feedback, we designed a 7-minute mindfulness recording to be administered to University of Washington Bothell Introductory Biology students before an exam. Using a randomized controlled trial design, 29 students were randomly assigned to the mindfulness recording group (n = 15) and to the control group (n = 14). The intervention group was exposed to the SMARTS recording before an exam while the control group studied in the hallway. We found that listening to the SMARTS recording reduced the increase in heart rate due to the exam by an average of 8 beats per minute. Additionally, 56% of participants expressed intentions to continue using the recording before future exams, suggesting its perceived efficacy in alleviating test anxiety. This research suggests promising implications for integrating mindfulness interventions into educational settings to support students in managing test anxiety. Further study is warranted to evaluate the intervention’s efficacy in a fully powered trial. In addition, we will explore heart rate variability to provide insight into the role of parasympathetic activity in stress management.

Methicillin resistant Staphylococcus aureus (MRSA) is an antibiotic resistant pathogen that causes severe illness and thousands of deaths each year in the US. It spreads within the community through improper hand hygiene and is often found in hospitals and on public transport surfaces. This poses a danger to the public, specifically to vulnerable populations such as the elderly and immunocompromised. This study in Seattle, Washington compares the prevalence of the antibiotic-resistant MRSA bacterium on public transport surfaces both proximate and distant to Harborview Hospital. Swabs from bus stops and pedestrian call buttons were collected outside of Harborview Hospital and urban areas of Capitol Hill, a Seattle neighborhood approximately one mile away from any major hospitals. The swabs were streaked onto Tryptic Soy Agar plates, gram stained, and streaked on Mannitol Salt agar plates;catalase and coagulase tests were run to help further confirm the presence of Staphylococcus aureus. The resulting colonies were then screened for antibiotic resistance using the Kirby Bauer Disk Diffusion method. One instance of potential MRSA was isolated from a crosswalk button in Capitol Hill. A higher MRSA prevalence on surfaces close to hospitals could establish a link between the spread of pathogenic bacteria from hospitals to Seattle's city surfaces but was not found in this study. These results suggest that the spread of MRSA in Seattle may have more to do with foot traffic and public transportation usage. However, the presence of MRSA on urban surfaces puts sensitive populations at risk regardless of its source. Practicing good hand hygiene can help curb the spread of MRSA in the community.

The potential cognitive benefits of mindfulness meditation, such as its effects on memory processes, are gaining increasing attention. The growing interest in mindfulness meditation as a technique to improve cognitive functions, particularly long-term memory, motivates this investigation. The purpose of this study is to determine how mindfulness meditation affects the individual’s rate of forgetting in long-term memory as practice days increase. Using a computational model of episodic memory fitted to data obtained from an adaptive memory test, the study is able to monitor and predict the rate of forgetting for each individual and acquire a deeper understanding of how mindfulness meditation influences individual differences in memory retention and retrieval. The study will recruit thirty healthy participants through the Psychology Subject Pool of the University of Washington. The participants will be randomly assigned to either a group that practices mindfulness meditation or a control group that engages in podcast listening. For six days, participants will complete online memory tasks before and after each mindfulness meditation session or podcast listening session, while their performance data will be analyzed to model the rate of forgetting. To assess the principal effects of mindfulness meditation on the rate of forgetting, statistical analyses, such as linear mixed models, will be employed. We hypothesized that participants who participate in mindfulness meditation will have a lower rate of forgetting than those in the control group who engage in podcast listening after six days. Moreover, the study also hypothesizes that participants engaging in mindfulness meditation will demonstrate a decreasing rate of forgetting as the number of practice days increases. The finding of this study may inform interventions using mindfulness to enhance memory retention, benefiting those with age-related cognitive decline or stress-related memory challenges. It contributes to understanding the potential of mindfulness in cognitive function and memory-related disorders.

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.

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.

Seriously ill hospitalized patients and their families experience elevated stress, anxiety, and depression, resulting from factors like the complexity of serious illness, fragmented medical care, and transitions across settings. They struggle to navigate treatment options, make difficult decisions, and express their values and goals to their clinicians. In addition to communication challenges between patients and clinicians, poor communication among healthcare team members exacerbates the stress associated with serious illness. The aim of this study was to continue work from previous Facilitating Communication Studies to gain knowledge from bedside nurses' experiences with collaborative communication (CC) between patients and families and their healthcare team, and to elicit ideas from nurses about what might improve CC within the hospital system. We defined CC as patients and families being active participants with their healthcare team working towards shared goals of care. We recruited and interviewed 15 bedside nurses from ICU and acute care units at Harborview Medical Center. Following each interview, we input each participant's audio-recorded content into a matrix table, created summaries of each transcript, and synthesized content across transcripts to distill major themes. Nurses reported that breakdowns in CC most often occur when multiple clinicians are involved, during transitions of care, and during the discharge process, resulting in confusion and distress for the patient, family, and bedside nurse. Suggested solutions to overcome these barriers include (1) promoting in-person interactions by rounding as an interprofessional team, (2) inviting bedside nurses to goals of care meetings, (3) implementing a CC training program for clinicians to standardize the CC approach among team members, and (4) empowering patients and families to initiate CC by educating them about their role in their healthcare. These suggestions should be implemented in a future Facilitating Communication Study to reduce distress for seriously ill patients, their families, and their healthcare team. 

Why does human rights law fall short in protecting people from human rights abuses made by governments acting in the name of self-sovereignty? In this project, I analyze these questions in the context of human rights abuses, such as extrajudicial killings, false imprisonments, rapes committed by law enforcement officers, and forced disappearances in Panjab, India. To do so, I use official reports from non-governmental organizations, an original interview I conducted with a survivor of Operation Blue Star, which was an attack on one of the holiest shrines for Sikhs, process-tracing, and human rights legal analysis. After developing the political and legal framework, I present my research in the form of three narrative case studies. I argue that the acts orchestrated by the Indian government and the tactics they employed to eradicate Sikhs constitute genocide under human rights law. Nonetheless, Sikhs struggle in gaining recognition due to extreme efforts by the Indian Government to cover-up and malign the names of Sikhs through their own governmental groups, and an international political environment that discourages foreign governments from condemning Indian government actions. With the research conducted in this project, links between other human rights violation in India can be found. The lack of accountability of the Indian government in multiple cases can be uncovered, which will prove how even with the existence of human rights law, governments have the most power.

The UN Truth Commission tasked with accounting for El Salvador’s armed conflict described it as a war in which “nobody won” (“nadie ganaba”). Between 1980 and 1992, the small Central American country was devastated by a civil war that claimed the lives of more than 70,000 and exposed its people to gross human rights violations committed, overwhelmingly, at the hands of state security forces. This project asks how the armed conflict in El Salvador existed within a broader ecosystem of right-wing state terror by examining one particularly crucial relationship: that between El Salvador and Argentina in the period immediately before the outbreak of war (1978-1980). I argue that the military regimes in El Salvador and Argentina took on a consultatory relationship during the late 1970s in which Argentina passed its “successful” model of repression onto key Salvadoran military officials. As El Salvador barreled toward war in late 1979 and early 1980, those very same Salvadoran officials came to occupy the highest positions of power, paving the way for an urban war campaign that looked eerily like Argentina’s “dirty war.” By pairing archival research conducted at the Historical Archive of the Chancellery (Archivo Histórico de la Cancillería) in Buenos Aires with existing scholarship on Argentine involvement in Central America, I trace the rise of Argentine influence in El Salvador from a few well-placed offers of aid to the minds of four of El Salvador’s top-ranking wartime officials. In doing so, I look beyond the Cold War in Latin America as a phenomenon imposed from above by the United States and instead interrogate the middle layer, in which Latin American states, driven by politics, culture, and their own will to survive, reproduced the Cold War along more local and regional lines.

American Samoa’s unique relationship with the U.S. today escalated throughout the 19th century and reached its official turning point when it became a U.S. territory in 1900. This archipelago comprises the eastern islands of the greater Samoan islands within the South Pacific, approximately 2,500 miles southwest of the U.S. state of Hawai’i. This study examines and analyzes the imperial history of the United States and participating actors attempting to dismantle Samoan cultural practices in food, labor, and politics. The U.S. also tries to associate a false narrative of primitiveness and ignorance with the Indigenous Samoan people. However, I will analyze white travelers' accounts and documentaries about American Samoa to chronicle Americans’ perspectives on the imperial project in American Samoa by reading against the grain. I will analyze the actions of the Samoans filmed and discussed to put forward an alternative reading of this history, highlighting their use of cultural resistance tactics to defy American imperialism. I will also use evidence from my and my family’s history in American Samoa to continue to bring an Indigenous perspective to this history and show the importance of Pacific Islanders' historical experiences in academia. With this project, I will share the importance of studying imperial histories between the U.S. and the Pacific and, ultimately, bringing an indigenous perspective to the histories that Western ideas have silenced. The preliminary results I hope to get from this study, is to contribute a literary source to academia for a history that is only transmitted through oral trdaitions. I also hope to raise awareness about the need for the study of Pacific Islander history within the academy, which is not currently offered at 4-year institutions in the U.S. today.

Exclusionary zoning laws — which limit population densities and land uses in specific neighborhoods — are a typical feature of American municipal land use regulation. An extensive body of evidence links traffic-related air pollutant (TRAP) exposure to adverse health effects. Using zoning data and a model of TRAP levels in cities across the Seattle metropolitan area, I hypothesize that TRAP exposure will be greater on average in zones where higher-density housing is an allowed use, and lower on average in zones reserved for lower-density housing. I used the software package QGIS to spatially join zoning and air pollution data and used the software package R to perform correlation analyses between zone types (classified by maximum population density) and three common TRAPs (NO₂, black carbon, and ultra-fine particles.) This research highlights the public health implications of normative policy regimes like exclusionary zoning. These results can assist elected officials and planners in pursuing a more geographically distributive approach to increasing housing supply in the Seattle area, in order to minimize the TRAP exposure burden – and associated adverse health effects – faced by residents.

The adaptor protein MAVS plays an essential role in the immune system's antiviral defenses. Upon sensing viral RNA in the cytosol, RIG-I-like receptors trigger MAVS to form a signalosome with other proteins and induce interferon (IFN) expression. Recent datasets have identified three regions in the MAVS protein that might bind to RNA. However, the functions underlying these RNA-binding regions (RBRs 1, 2, 3) are still not understood. In this study, we aim to identify the differential functions of these RBRs on regulating MAVS interactions. I tested the ability of FLAG-tagged MAVS constructs with different RBR deletions to induce IFNB1 when overexpressed in MAVS knockout (KO) 293T cells. Different combinatorial deletions of these RBR regions lead to differential levels of IFN induction; deletion of RBR2 abolishes IFN expression, while constructs with additional deletions of RBRs 1 or 3 slightly restores IFN expression. We then investigated where the RBRs perform their regulatory role in the MAVS signaling pathway. We hypothesized that RBRs may be involved in MAVS-TRAF binding or MAVS ubiquitination, both of which would induce differing levels of IFN expression if disrupted. I used immunoprecipitation to find that the RBR2-deleted construct abrogated MAVS-TRAF binding, while any constructs with RBR1 deleted showed increased MAVS-TRAF binding, consistent with their restoration of IFNB1 expression. I will also use immunoprecipitation to measure the influence of RBRs on HA-tagged degradative K48 or activating ubiquitin K63. If the constructs interact with these ubiquitin mechanisms, we expect HA pulldowns from RBR1 deletions to show increased MAVS-K63 binding and/or the RBR2-deletion to increase MAVS-K48 binding. This study provides analysis of key regulatory regions that control the downstream IFN production and antiviral defense through MAVS, which could expose therapeutic targets for either treating viral infection or reducing the effects of abnormal IFN production such as in autoimmune disorders.

Bacterial CRISPR immune systems defend against foreign genetic material, such as bacteriophage viruses. CRISPR systems are classified into six types with diverse protein components and mechanisms of interference. Among these, our research investigates the function of CRISPR-Cas13 systems, which uniquely target RNA rather than DNA. To overcome immunity, bacteriophages have evolved anti-CRISPR mechanisms that are designed to inhibit specific CRISPR types, restoring infection and proliferation of the viral invader. We recently discovered a novel anti-CRISPR mechanism, in which a noncoding RNA provides inhibition of CRISPR-Cas13 function. The central questions surrounding this RNA anti-CRISPR (rnAcr) are how it associates with CRISPR-Cas13 in order to inhibit its function, as well as the boundaries of its length and anticipated mechanism of inhibition. rnAcr is predicted to have three vital stem loops, which have been experimentally deleted and structurally disrupted by performing site directed mutagenesis to mutate select regions of nucleotides in each stem’s structure. We did this in order to determine if the stem loops’ structures were necessary for rnAcr’s anti-CRISPR function. We found that these were all essential for its function, which gives rise to the hypothesis that its structure is interacting with the bacterial host’s CRISPR-Cas13 system to effectuate its inhibitory mechanism. In order to test anti-CRISPR function, we conjugated a target and nontarget plasmid, in which the target plasmid would be recognized by Cas13, and cellular RNA would be cleaved, leaving no growth if no anti-CRISPR mechanism is present. We have shown that rnAcr is sufficient for anti-CRISPR function, allowing for tolerance of these target plasmids and cellular growth. rnAcr suggests a novel anti-CRISPR mechanism, as until now, the majority of reported anti-CRISPRs have been composed of small proteins produced during phage infection, suggesting rnAcr’s significant implications when considering new players in the host-bacteriophage evolutionary competition.

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.

Mitochondrial calcium is essential for energy metabolism and cell survival. Deranged mitochondrial calcium leads to pathological remodeling of the heart. Little is known regarding the regulation and roles of mitochondrial calcium in cardiomyocyte growth. Mitochondrial calcium uniporter (MCU) is a major channel for mitochondrial calcium uptake. Germline knockout of MCU on the inbred C57BL/6 background is lethal. However, αMHC-Cre-driven MCU deletion in the heart just before birth yields viable offspring with normal heart function. In this study, we will use human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) to study the regulation and roles of MCU in cardiomyocyte growth. First, the expression of MCU in iPSCs and iPSC-CMs at different stages of their differentiation and maturation process will be determined at mRNA and protein levels. Then, we will delete MCU gene in undifferentiated iPSCs and follow a protocol to differentiate them into beating cardiomyocytes. The iPSC-CMs will be monitored for their morphological changes, cardiac troponin T expression, and electric pacing-induced calcium transients and cell contraction. The proliferation of iPSC-CMs will also be evaluated by using BrdU staining and molecular markers. This study will demonstrate how MCU expression changes during the differentiation and maturation of iPSC-CMs and whether it plays a role in cardiomyocyte growth.

The synthesis of key organic molecules often requires toxic, expensive, non-reusable reduction agents and extreme conditions. In recent years, electrochemistry has emerged as a sustainable alternative to standard methods, but this approach is often hindered by high energy barriers for electron transfer to the substrate. Electrocatalysts address this challenge by shuttling charge between the electrode and dissolved substrates, accessing lower transfer barriers, and reducing the overall energy needed. Current electrocatalysts, however, cannot stabilize reactive intermediates, which often leads to harmful side reactions and degradation of the electrode. We hypothesize that redox-active supramolecular cages can address this limitation by both shuttling charge and providing unique microenvironments capable of stabilizing intermediates. Previously, we synthesized two tetrahedral supramolecular cages that incorporate redox-active perylene diimide (PDI) and pyromellitic diimide (PMDI) motifs. Using cyclic voltammetry, we then showed that both cages can lower the voltages required for the electroreduction of vicinal dihalides to alkenes, indicating electrocatalysis. To better understand these results, I used density-functional theory (DFT) calculations to obtain computer models of the PDI and PMDI cages. These DFT-optimized structures revealed significant differences in charge density between redox centers due to electron-donating functional groups, which may explain why the PMDI cage lowered the substrate reduction voltages more than the PDI cage. With these models, I have also studied the shape and volume of the cages’ internal cavities, thereby providing information about substrate compatibility. I am conducting additional DFT analysis to understand how modifications to the ligand motifs may alter the electrocatalytic behavior. By continuing to investigate supramolecular cages for reductive electrocatalysis, I aim to contribute to the development of low-waste synthetic strategies for the production of alkenes and other commercially significant organic compounds.

The catalytic ability of an industrial heterogeneous catalyst is determined by the interactions between the active sites, which are often transition metals, and the support. Insights into the interplay between the active sites and support during catalysis are difficult to gain because of the inherent complexity of heterogeneous surfaces. Alternatively, molecular catalysts are well-defined, and can be studied by a range of spectroscopic characterization techniques. To model multi-active site dynamics on a molecular scale, the Velian group has developed a system involving a cobalt selenide cluster with amido phosphine ligands that are used to tether transition metals that act as catalytically active sites onto the cluster surface. My project is probing the tri-metalated clusters’ (M₃Co₆Se₈L₆; M = Cr, Mn, Fe, Co, Cu, Zn; L = PPh₂N^-Tol, Ph = phenyl, Tol = 4-tolyl) ability to catalyze intramolecular carbon-hydrogen (C-H) amination. Previous work has shown that these clusters are remarkable catalysts for carbodiimide formation, but we have yet to compare reactivity among the tri-metalated clusters. I probed the transformation of aliphatic azides to pyrrolidines, a class of 5-membered-N-heterocycles with. This study seeks to understand how the reactivity of the clusters change as edge metal identity changes, and the role of the three active sites during catalysis. A substrate scope has shown how the steric and electronic profile of the azide affects the capability of the clusters for this reaction. This research provides insights into metal-support interactions that are important for heterogeneous catalysis. Development of next generation catalysts that can perform complex transformations benefits from the information these studies provide.

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.

A key neuromodulatory system involved in anxiety disorders is the locus coeruleus noradrenergic system (LC-NE), which projects broadly throughout the central nervous system. The LC is stress responsive and tonic activation of the LC and its projections to the BLA is anxiogenic. Previously, the Bruchas Lab has used two-photon calcium imaging to show that a powerful stressor (predator odor) increased synchronous activity of LC neurons. They also found that mimicking this predator odor evoked activity with optogenetics altered the activity of individual neurons downstream in the BLA in a β-adrenergic receptor (β-AR) dependent manner. Although these data support the LC's involvement in promoting aversion and increasing anxiety-like behavior, the specific neurotransmitter, neuronal cell types, and receptors responsible for these effects remain unidentified. Therefore in hopes of identifying these specific signaling molecules and neuronal cell types and receptors, I first used fiber photometry and a novel biosensor (GRABNE2m) to detect norepinephrine (NE) release in the BLA while mice were exposed to a predator odor. I found that predator odor produced robust increases in NE release in the BLA compared to control odor (n=5, 3 male, 2 female) Further, we found that optogenetic activation of terminals from the LC to the BLA produced very similar levels of NE release compared to what was evoked by predator odor. To determine the cell type and receptor that is sensing this stress-induced NE release, I used a CRISPR/SaCas9 virus, developed in collaboration with Dr. Larry Zweifel’s lab, to knock-down β2-adrenergic receptors (β2-ARs) in glutamatergic BLA neurons to test their causal role in stress-induced anxiety-like behavior. CRISPR knockdown of β2-ARs in the BLA blocked several stress-induced anxiety-like behaviors (n=4, 4 female). By understanding the circuit-based mechanisms of how stress-induced anxiety is regulated, researchers could identify potential targets for therapeutic treatments of anxiety disorders.

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 mental health of family caregivers who care for elders who have passed is often dismissed by healthcare providers and society because of the age of their family members. When an older adult dies, their death is seen as expected and as the natural ending to having lived their life. However, there is still a tremendous grieving process that family members, friends, and caregivers experience with the death of a loved one. After losing a loved one, family caregivers report experiencing higher rates of depression, anxiety, and ambiguous grief. Additionally, many family caregivers find that medical help decreases drastically after the death, thus creating a sense of isolation. Current studies tend to explore one aspect of the experience of caregiver loss. Furthermore, much of these findings are based on data that is homogeneous in race and social status with an overwhelming majority being white and middle class. No existing studies have attempted to untangle the complexity of emotions that come with family caregiving. This systematic literature review starts to fill these gaps by answering the question: What are the psychological impacts experienced by family caregivers following the loss of an elderly loved one they provided care for? The databases used to identify the articles include PubMed, Web of Science, and PsycINFO. Approximately 15 articles have been identified that meet the inclusion criteria. The preliminary findings are themes of support changing before and after death, relationship with caregiving, relationship with family members cared for, psychological adversities (anxiety, depression, and loneliness), and religion as a way to find peace. These findings will help family caregivers see trends in their experience, helping with the loneliness that comes while grieving. It will also be a starting point to show healthcare workers what to look for when determining whether the grieving process is chronic.

Vietnamese Amerasians are children of United States service members and Vietnamese women born during the Vietnam War. Many of these children grow up while experiencing various stressors in Vietnam, due to their biracial and inherently political identities. These challenges place them at a higher risk for developing a mental illness. There is limited research on the mental health challenges of Vietnamese Amerasians. I conducted a systematic literature review to examine the current mental health challenges of Vietnamese Amerasians. I identified nineteen relevant articles through a systematic search of APA PsycINFO, APA PsycArticles, and references of included articles.The inclusion criteria required studies to be conducted within Vietnam and the United States, include at least five Vietnamese Amerasians, and focus on mental health and related outcomes. Included articles are analyzed to find themes in the prevalence of mental health illnesses (such as PTSD, Depression, Suicidality, and Anxiety), mental health utilization, factors contributing to mental health illness, and protective factors. Preliminary findings identify high pre-migration expectations, frequency of thinking of ones’ American father, language barrier, experience of discrimination, witnessing traumatic events, acculturation stress, unaccompanied minor status, having multiple surrogate mothers, being African Amerasian, and family conflict as factors contributing to poor mental health outcomes for Vietnamese Amerasians. Family support has been identified as a protective factor. Due to the unique bi-racial identity of Vietnamese Amerasians, more research is needed to determine the applicability of these findings. In addition to informing future research, these findings aid clinicians in the relevant factors impacting Vietnamese Amerasian mental health.

The paradigm for manganese (Mn) cycling in the marine environment has shifted over the past two decades to include not only the +IV and +II oxidation states. It is now recognized that dissolved Mn(III) can also exist when stabilized by organic ligands. Mn is critical for sustaining life and influences the cycling of many other bioactive elements. Because of this, further research is needed for understanding how Mn cycles in the environment, both between physical and chemical phases. My project aimed to look at how Mn cycles between dissolved and particulate phases and its three environmentally relevant oxidation states along the salinity gradient of the Mississippi River delta and what role organic ligands play in mediating Mn transformations. I hypothesized that the salinity gradient would influence the availability of organic ligands, which would promote the oxidation of dissolved Mn(II) and particulate Mn oxides (MnOx), making the cycling of Mn during estuarine mixing more complex than previously understood. To test this, I collected water from the Mississippi River and the Gulf of Mexico to conduct a mixing experiment to model the salinity gradient. UV-Vis spectrophotometry was used to analyze particulate and dissolved Mn speciation as well as the characteristics of the organic matter present. Inductively coupled plasma-mass spectrometry was used in analyzing dissolved Mn and Mn flocculants. Preliminary results show increases of dissolved Mn during mixing, and potential loss of particulate MnOx. Combined, these suggest redox cycling of Mn during estuarine mixing impacts its solubility and ultimately transport to the Gulf of Mexico. This region experiences heavy nutrient loading that leads to seasonal hypoxia. Understanding the cycling and solubility of Mn is imperative because it has broader implications for redox processes and element cycling in the Northern Gulf of Mexico, especially during hypoxic events.

Marine heterotrophic bacteria play a pivotal role in microbial community dynamics. This study aims to understand interactions within the microbial community of the oligotrophic (nutrient-poor) equatorial Pacific, specifically investigating how heterotrophic bacteria respond to the growth of autotrophic picophytoplankton. This experiment attempts to provide a more faithful representation of in-situ conditions, overcoming previous difficulties in capturing the dynamic behavior of microbial communities in the field. A novel methodology utilizing continuous chemostats with natural communities in the field accomplishes this objective. Three growth chambers were employed, two as chemostat systems and one in batch culture mode. All three growth chambers contained the natural microbial community that passed through a 3 µm pore-size filter. Chemostat systems continuously received 0.2 µm-filtered seawater (without microbes) while an equivalent volume was removed from the growth chamber simultaneously. Dissolved inorganic nutrients required by autotrophs – silicate, phosphate, and nitrate – were added to one of the chemostat’s 0.2 µm filtered media reservoir. This methodology was compared to a traditional batch culture, where nutrients were added to the growth chamber once, at time-zero. Cultures followed a 16-hour on/8-hour off light/dark cycle using LEDs, simulating the equatorial Pacific day/night cycle. Community responses were measured by continuous optical density measurements (OD), with endpoint subsamples analyzed for microbial abundance and DNA content using flow cytometry. Distinct day/night responses were observed in all cases, with the nutrient-enriched chemostat showing the most pronounced response. Overall, the results provide new insight into the linkages between marine autotrophic and heterotrophic microbes, while demonstrating an effective new methodology for examining microbial community responses to added nutrients. Thus, this study not only advances our understanding of microbial community dynamics in the oligotrophic equatorial Pacific but also introduces a novel experimental method that can be applied across a diversity of marine and aquatic environments.

Nutrients and CO₂ are important oceanographic variables, as they provide information which can be used to understand phytoplankton abundance and processes such as the oceanic carbon cycle. Therefore, as climate change impacts ocean systems, it is increasingly important to measure how nutrient and CO₂ concentrations in the ocean change over time and space. This study measured pCO₂ (which takes into account temperature, total CO₂, salinity, and alkalinity of the water), nitrate, phosphate and silicate concentrations in the western equatorial Pacific (5S-5N along 167W) in January 2024. Over space, pCO₂ and nutrients were analyzed for correlation with physical processes, primarily upwelling, using sea surface temperature (SST) and mixed layer depth. To determine the relationship of pCO₂ and nutrient concentrations to the biomass of microorganisms, correlations with fluorescence and beam transmission were also analyzed over space. Over time, pCO₂ was compared to atmospheric CO₂ and El Nino Southern Oscillation (ENSO) state to determine correlations between temporal pCO₂ trends and atmospheric phenomena. pCO₂ surface concentrations in the western equatorial pacific were found to have increased from 1983 to 2024 at an average rate of 2.02 +/- 0.034 ppm/yr and had a positive correlation with increasing average atmospheric CO₂ (R = 0.71, p-value < 0001). Spatially, surface pCO₂ and the macronutrients nitrate, phosphate, and silicate in the upper 200 m showed similar patterns from 5S to 5N along 167W. The concentrations of nitrate and phosphate had a significant negative correlation to mixed layer depth (R = -0.4, p-value < 0.001) and nutrients and pCO₂ had a significant negative correlation to sea surface temperature (p-value < 0.001). They peaked from 0-2N due to upwelling and exhibited smaller secondary peaks around 3S and 3N, likely due to mixing caused by north and south subsurface countercurrents. These results reinforce the importance of physical oceanic and atmospheric processes as a control for nutrient and inorganic carbon cycles in the western equatorial Pacific.

Discipline and disciplining have been a set of processes wielded throughout history to order, control, and extract. These processes have served as efficient colonial tools and have been so intimately indicative of the way institutions wield and disseminate power that in 1976, French philosopher Michael Foucault theorized as a new form of power: disciplinary power. In my research, I explore the concept of discipline as it exists in the collegiate system, through the perspectives of Foucault's 'Discipline and Punish' and la Paperson’s 'A Third University is Possible,' while drawing inspiration from Niccolò Machiavelli's 'The Prince' to shape writing style. Rooted in the field of critical university studies and motivated by personal reflections, this project takes the form of a "how-to" guide for cultivating a docile body and aims to explore the limits and potentials of discipline within the context of STEM education at the University of Washington. As part of my methodological approach, I incorporate and analyze various university spaces’ contributions to the overall built environment and campus power structure(s). I ask what it takes for place to become space, or more simply put, how the various disciplinary bodies that inhabit space shape or alter its meaning, and vice versa. I present this project as part of an active effort to critique the colonially and penally adjacent power structures upon which many universities are built. While my research and reflections remain focused on the University of Washington, they may serve as a case study for most of modern Western academia. Through this work, I hope to advance the push towards decolonial and interdisciplinary futures within STEM and academia, at large.

The US education system is a tool used to push the dominant Anglo-American cultures among immigrants and other minoritized cultures within the United States. With their proximity to the US border and historical events, Mexicans living in the United States have faced subjugation and discrimination from the Texas Revolution to the anti-immigrant policies and rhetoric; these educational practices have targeted Mexicans for almost two centuries. This causes a conflict of cultural identity for Mexican youths living in the United States, as they grow up within multiple social spheres that consider them too American to be Mexican yet too Mexican to be American. This conflict of identity has caused multigenerational trauma and is only made worse by the discrimination from the media and the bias of the schools, as these students are forced to look elsewhere to discover their history, such as family or the community. My research study examines the value of ethnic studies and bilingual education practices and how they not only empower these students but gives them the motivation to succeed within an academic setting. This research is based on interviews that I have conducted with Mexican Americans who have experienced the education system during different years, ranging from the 60’s to the early 2000’s. Furthermore, I examine the autobiography of a prominent Mexican American scholar as I draw scholarship on ethnic studies and bilingual education, criticizing the current education system while offering solutions to address those critiques. Through the interviews I conducted, I found that the people who were most connected to their heritage and the Spanish language, not only experienced more success academically, but were also happier, indicating the need for ethnic and bilingual studies within the K-12 curricula.

A critical feature of autonomous cars is the ability to follow a road or predefined path. Classical methods often rely on extensive prior mapping with precise GPS positioning. These methods are labor intensive and struggle with changing, unstructured environments. Instead, machine learning (ML) models are trained to recognize paths and follow directions. In this work, we combine simulated and real-world data to train a neural network policy that controls an autonomous ground vehicle down a hallway, avoiding collisions. Training a ML road-following model consists of three steps: data collection and preprocessing, model training, and model evaluation. While all three steps pose challenges, collecting high-quality, real-world data can be expensive and dangerous in road environments. Because of this, simulator data is useful as it allows for data to be collected safely and inexpensively. Thus, we study how much the required amount of real-world data can be reduced to successfully train a road-following robot with the use of simulator data. So, we collected simulator data using AirSim to train a convolutional neural network that follows a path in simulation through live environment images. We then fine-tuned the model using real-world data collected from MuSHR cars through hallways of a building. Next, we test the fine-tuned model on the simulator to ensure limited degradation to the model solely trained from AirSim data. Finally, we deploy the model on a robotic car in a real-world environment and evaluate the model’s performance compared to the baseline model trained on real-world data. We demonstrate that we can successfully train a model in simulation (MSE <= 0.01radians), and we expect to show a comparable performance in reducing the number of collisions and minimizing trajectory differences between expert and learned controller from a model trained on simulator + less real-world data and a model trained solely on real-world data.

In this research project, we delved into the realm of gate-based quantum computation with a focus on qudit-based quantum computation. In the era of Noisy Intermediate-Scale Quantum (NISQ) computation, there are many avenues for physical implementations of qudits, such as trapped ions, superconducting circuits, and photonic systems. We primarily studied trapped ion qudit-based computation, investigating the notion of universality and how arbitrary gate operations can be simulated by experimentally realizable transformations in such systems. More quantitatively, we analyzed the fidelity under the assumptions of rotation angle errors in trapped ion implementations of quantum gates. We proved several lower bounds for various connectivity graph designs applicable to the 5-level calcium ion under this model of assumptions. Our techniques also generalize to physical systems with more than 5 levels. Currently, our attention is directed toward understanding the impact of entanglement on the aforementioned dynamics and studying the notion of universality for multi-qudit systems. A related question we are trying to answer is how qubit circuits can be converted into qudit circuits to reduce a well-defined notion of "circuit complexity".

Hypoxic-Ischemic Encephalopathy (HIE) resulting from a lack of blood and oxygen to the brain is the leading cause of mortality in term newborns. Extracellular vesicles (EVs) serve as critical transporters of biomolecules between cells, with evidence of alleviating inflammation in models after hypoxic ischemia (HI) injury. Therapeutic efficacy of EVs has only been evaluated in males because males are more susceptible to worse outcomes following HIE injury, yet knowledge about EVs and their behavior when administered to females is still needed. In this study, I aimed to address this knowledge gap by systematically comparing the efficacy of male and female neonatal brain-derived EVs (mEVs, fEVs, respectively) applied on male and female neonatal rat ex vivo brain slices. I first confirmed the purity of isolated EVs with protein assays and immunoblots, and utilized an ex vivo oxygen-glucose deprivation (OGD) model of HI injury, applying fEVs and mEVs to sex-matched OGD-exposed brain slices. I evaluated cell viability after 24h of EV exposure, and my results show that fEVs decrease inflammation and cytotoxicity in OGD models. When compared to previous results using mEV treatment, my results suggest that females have a more robust anti-inflammatory response system to injury. Ongoing work to better understand the therapeutic effect of EVs involves further observing morphological shifts in microglia through confocal imaging, as fEV application will likely result in microglia shifting towards anti-inflammatory phenotypes, similar to what was previously observed after mEV application. I am also quantifying expression levels of various inflammatory and reparative genes through reverse transcription quantitative polymerase chain reactions (RT-qPCR). Overall, I have demonstrated in these pilot studies that fEVs have a different therapeutic effect in OGD injury compared to mEVs. This research is intended to open up pathways for more personalized sex-based treatments for various injuries and therapeutics in the future. 

Multiple Particle Tracking (MPT) is a powerful technique for studying the behavior of microscopic particles, such as viruses and nanoparticles, by tracking individual displacement and movement. One application of MPT is to measure microstructural changes in the brain extracellular environment (ECM) in development and aging, and in response to disease onset and progression. MPT of nanoparticle probes results in the generation of thousands of individual nanoparticle trajectories, from which geometric features, diffusion coefficients, and viscosities can be extracted. The vast array of trajectories contained within our dataset presents a good opportunity for integration into deep learning models that contains self-supervised learning, equivariant graph neural network, and Equivariant transformer. However, to enable MPT data to be trainable and predictable by deep learning models, we need to curate the data to be readable and useable by these models. To enable this, I have created a database and developed a data architecture that would allow MPT data to be passed into Deep learning models that use various techniques such as transformers. I am currently working on utilizing the data architecture on a Deep Learning model that uses transformers and self-supervised learning to predict trajectories of MPT particles. From this model, my expected accuracy of prediction of the trajectories for the MPT data is around 85%. This can allow us to learn complex features directly from raw MPT trajectory data, improve our predictions, and extract biological insights. The python package with our data architecture, the various SQL scripts, and the model will be provided as an open-source resource, allowing other researchers to expand upon my code and apply their unique modifications based on their own data and trajectories.

Repeat thrombotic events have been associated with increased levels of Von Willebrand Factor (VWF) in patients prescribed dual antiplatelet therapies (DAPT), medications designed to prevent thrombosis. VWF is a protein that regulates platelet adhesion during hemostasis, allowing platelets to aggregate at sites of vascular injury. A microfluidic device containing a rigid block that simulates vascular injury and a flexible post to measure platelet contractile force through its displacement will be used to form shear-induced thrombi. I will determine how VWF affects platelet activation by testing whole blood samples and samples doped with DAPT (0.3 mM ASA and 10 μΜ 2-MeSAMP), 50 μg/ML VWF, or both VWF and DAPT. Platelet activation is measured through the area of platelet-plug, intracellular calcium levels, and platelet-plug contractile force. Preliminary experiments have shown that high VWF levels produced the largest platelet plugs whereas adding DAPT led to opposite effects. My results present that adding both VWF and DAPT to whole blood leads to similar platelet activation and larger platelet plug size as whole blood doped solely with VWF. The data obtained from this research can provide new insights into the improvement of therapeutic agents that aim to target VWF’s interaction with platelets and ultimately prevent repeat thrombotic events.

Heart disease takes an estimated 17.9 million lives each year, highlighting the pressing demand for cost-effective treatments. Melusin, a chaperone protein in the heart, holds potential as a target for heart failure therapeutics. Previous studies done in wild-type (WT) and melusin knockout (MelKO) mice discovered the absence of melusin was associated with a hypertrophic response indicative of heart failure. I plan to investigate the biomechanical role of melusin in humans using human-engineered heart tissues (EHTs) created from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) that lack melusin and their isogenic controls. EHTs are a 3D in vitro model of the human heart, ideal for studying the role of melusin in humans. I hypothesize that WT EHTs subjected to mechanical stress will outperform the MelKO EHTs. The EHTs are suspended between one flexible and one rigid silicone post. The EHT displaces the flexible post as it contracts, from which the displacement can be measured to calculate various auxotonic properties of the tissue. To induce mechanical stress on the tissues, I use a brace to restrict the movement of the flexible post. I am using histology to determine if there are any morphological differences between tissue types resulting from the brace. Thus far, I have cast WT and MelKO EHTs and completed twitch force measurements two and three weeks post-casting. Overall, I found the MelKO EHTs demonstrated lower contractile force than the WT EHTs. I plan to cast and collect more EHT data with and without braces in order to provide insight into the role of melusin in humans. Furthering our understanding of the heart’s mechanotransduction properties using EHTs is important in expanding our knowledge about the various pathologies of the heart. Ultimately, studying the pressure overload pathways involving melusin can lead to the development of future therapies for cardiovascular disease.

Heart disease is the leading cause of death in the United States. Due to the inability of cardiac tissue to self-heal, extreme cases necessitate heart transplants and most patients do not fully recover. A promising novel approach to create engineered heart tissue focuses on 3D extrusion-based bioprinting of stem cell-derived cardiomyocytes. Mature iPSC derived cardiomyocytes, the cells responsible for the contraction of the heart, do not proliferate. Therefore, the printed tissue construct must be created with the final desired cell-density de novo in order to mimic native cardiac tissue. Researchers need a viable method for extruding high cell-density bioinks to form functional constructs. In my research project, I am working  to generate 3D bioprinted cardiac tissues with high cell-density to measure both electrophysiological characteristics and contractile force output. The use of cell-only bioinks is atypical, and there is limited research in the literature documenting its properties. I measured the acute change in viability of NIH 3T3 cells extruded through a needle to investigate the effect of the needle’s hydrodynamic forces on the cells at high density. The data shows that cells extruded at high density maintain a high viability, and we observed strong structural cohesion in the extruded filaments. I optimized the extrusion parameters, needle diameter and flow rate, to create long-lasting filaments, and constructs remained intact over a 5 day observation period. However, we found they fail easily with agitation. Further work is needed to optimize bioink and conduct further studies using flexible posts to measure contractile force output and calcium imaging to determine the electrophysiological characteristics of our cardiac constructs. Quantifying these properties is critical to ensuring that constructs recapitulate the characteristics of native cardiac tissue. This research may aid in the development of engineered cardiac tissue for transplantation and drug discovery.

Although immunotherapy with T-cells is successful in treating non-solid cancers, targeting solid cancer tumors remains a challenge. Unlike T-cells, bacteria can colonize solid tumors and thrive in a hypoxic tumor microenvironment (TME). This means that bacteria could be used to treat solid tumors that T-cells cannot reach. I propose to develop new bacterial immunotherapies that can be used as an alternative treatment method to fight solid cancer tumors. Specifically, I aim to engineer E. coli that secretes therapeutic payloads upon sensing the TME. My research focused on comparing secretion efficiencies of signal peptides and secretion tags. Signal peptides are short sequences that transport cargoes, such as therapeutic proteins, to the periplasm. Similarly, secretion tags are small secreted proteins that can transport a partner cargo fused to them to the extracellular medium. From literature, I selected the signal peptide PelB and the secretion tag YebF. I compared their efficiencies in secreting the cargo human interleukin 2 (h-IL2), an immunostimulatory cytokine. To this end, I expressed h-IL2 with either the genes for the signal peptide or secretion tag fused to the N-terminus and a detection tag on the C-terminus, in an E. coli expression strain. I induced the expression of cargoes, after which I isolated the proteins that were secreted into the extracellular medium. I detected the proteins through quantitative Western blot analysis. I concluded from my experimental data that the cargoes were secreted at a higher concentration with YebF than with PelB. I plan to repeat this experiment with another secretion tag, OsmY. The next step is to use the secretion system with the highest secretion yield to secrete a variety of potential immunomodulatory cargoes. I plan to evaluate their effects on immune signaling and their ability to eliminate tumor cells.

Large language models (LMs) are prone to generate diverse factually incorrect statements, which are widely called hallucinations. Current approaches predominantly focus on coarse-grained automatic hallucination detection or editing, overlooking nuanced error levels. In this project, we propose a novel task—automatic fine-grained hallucination detection—and present a comprehensive taxonomy encompassing six hierarchically defined types of hallucination. To facilitate evaluation, we introduce a new benchmark that includes fine-grained human judgments on two LM outputs across various domains. To run this evaluation, I directly managed the collection of around 400 total human annotations which were analyzed to better understand the hallucinations present in LM outputs. My analysis using this benchmark reveals that ChatGPT and Llama2-Chat exhibit hallucinations in 60% and 75% of their outputs, respectively. A majority of these hallucinations fall into categories that have been underexplored in previous work. As an initial step to address this, I trained FAVA, a retrieval-augmented LM by carefully designing synthetic data generations to detect and correct fine-grained hallucinations. I set up the synthetic data generation pipeline to train FAVA which consists of prompting ChatGPT to noise a passage and insert errors one by one. The noisy passage is then post processed into our training erroneous input and edited output pairs. On our benchmark, our automatic and human evaluations show that FAVA significantly outperforms ChatGPT on fine-grained hallucination detection by a large margin though a large room for future improvement still exists. FAVA’s suggested edits also improve the factuality of LM-generated text, resulting in 5-10% FActScore improvements. These results further demonstrate the strong capabilities of FAVA in detecting factual errors in LM outputs.

Addressing bias in artificial intelligence (AI) and machine learning (ML) systems is crucial for ensuring fairness, transparency, and ethical integrity. This study introduces a pioneering interdisciplinary approach, blending advanced computational methods with social sciences insights to tackle the multifaceted nature of bias. Through a mixed methods strategy that combines quantitative and qualitative data, we scrutinize algorithmic outcomes and conduct different case studies of stakeholders—developers, users, and communities affected by AI/ML biases. Our initial findings indicate that bias transcends technical boundaries, manifesting as a complex socio-technical dilemma that demands both algorithmic adjustments and societal reforms. We highlight specific biases, such as gender and racial disparities in recruitment algorithms and facial recognition technologies, underscoring the critical need for our research. To address these biases, we propose adopting data enhancement techniques, fairness-focused learning algorithms, and promoting explainable AI practices. Inspired by influential figures like Joy Buolamwini, founder of the Algorithmic Justice League, and Cathy O'Neil, author of Weapons of Math Destruction, we emphasize the importance of inclusive datasets and critically examining opaque algorithms. Our future efforts concentrate on developing comprehensive guidelines to reduce AI/ML biases and exploring the broader societal impacts of establishing unbiased AI and ML systems. By cultivating more equitable and ethical AI and ML frameworks, our research aims to meet the diverse needs of global communities, setting a new standard for responsible AI development.

I investigate the influence of cultural and linguistic backgrounds on visual perception and semantic interpretation within computer vision. This study addresses the question: Are there significant variations in the semantic content described by vision-language datasets and models across different languages? Guided by the hypothesis that cultural and linguistic diversities lead to distinct semantic interpretations, I compare multilingual datasets against monolingual counterparts. I developed metrics such as scene graph complexity, embedding space width, and linguistic diversity to quantify semantic variations across languages in both human-annotated and model-generated image captions. The methodology involves using linguistic tools and translation techniques to ensure semantic consistency across languages. Our findings indicate that multilingual captions contain, on average, 21.8% more objects, 24.5% more relations, and 27.1% more attributes than monolingual ones. Furthermore, models trained on diverse linguistic content demonstrate improved generalizability across different linguistic datasets. This study contributes to the understanding of how language and culture impact visual perception in computer vision and advocates for more inclusive dataset compilation and model training strategies.

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

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

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

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

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

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.

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

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

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

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.

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.

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

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.

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.

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.

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

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

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.

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

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

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