Many microorganisms that are crucial to the human body and environment need to use highly controlled electron transfer processes to catalyze challenging chemistry under a variety of oxygen levels. The under-studied anaerobic ubiquinone-8(UQ-8) biosynthesis pathway, found across multiple bacterial classes, uses unprecedented oxidation chemistry with proteins containing [4Fe-4S] clusters. Understanding the electron flow and mechanism of control in this pathway is key to understanding microbial adaptation to anoxic conditions. Two recently identified proteins, UbiU and UbiV, catalyze the oxygen-free hydroxylation in UQ-8 synthesis. Preliminary in vivo evidence shows the following highly conserved redox-active amino acids, Tyrosine 177,181 in UbiU and Tyrosine 281 and Tryoptophan 282 in UbiV are necessary to complete the reaction. I hypothesize that these amino acids facilitate electron transport from the active site to an external electron acceptor. UbiU/NHis-UbiV heterodimers containing Y177F, Y181F, Y281F, and W282F were expressed in E. coli and purified using his-tag affinity chromatography, then analyzed via size-exclusion chromatography to evaluate the impact of the mutations on structure. The mutations have had a variety of impacts on the oligomeric state implying some level of disruption to the dimer-interface, however, the majority of protein remains in dimerized form. Spectroscopic characterization of these mutants via EPR and UV-Vis is consistent with the identification of the metallocofactors as [4Fe-4S] clusters, although site occupancy is consistently lower than for the wild type. In vitro protein assays test observed catalysis of octaprenyl phenyl(OPP) to UQ-8 to illuminate the mutations impact on activity. Structural data gathered thus far forms a foundation for future work with radical-trap synthetic amino acids and further activity assays.

Age-related macular degeneration (AMD), a multifactorial eye disease, is distinguished by drusen formation and thickening of Bruch’s membrane. Early onset macular drusen (EOMD) is a rare inherited retinal degeneration with clinical similarity to AMD. EOMD results from genetic variants that cause decreased protein expression levels of complement factor H (CFH) and factor H-like protein 1 (FHL-1). The precise mechanism of drusen formation is unknown, although there are multiple lines of evidence that complement dysregulation and inflammation play a major role. RPE cells derived from EOMD patient induced pluripotent stem cells (iPSCs) can serve as in vitro models for understanding the effects of altered local complement. The complement system is a cascade of proteins and reactions that modulate inflammatory responses for the removal of pathogens. Specific components, such as C3a, could be involved in inflammatory responses that contribute to drusen formation and AMD. The purpose of this project is to observe how increased C3a impacts inflammatory cytokine secretion in EOMD RPE cells. iPSCs were generated from peripheral blood mononuclear cells collected from two patients in an EOMD family and differentiated into RPE cells. Western blot analysis was performed on EOMD and control RPE cells to quantify C3a, CFH, and FHL-1 levels to determine baseline expression levels. Control and EOMD RPE were treated with C3a, and inflammatory cytokine (IL-6 and IL-8) secretion was measured by ELISA. Decreased CFH/FHL-1 secretion and increased local C3a were observed in EOMD RPE. Preliminary data indicate that increased C3a levels may alter cytokine secretion by RPE, indicating that increased complement may play a role in local inflammatory responses that contribute to the pathophysiology of EOMD and AMD.

My field of research holds significant promise for advancing our understanding of the intricate interplay between immune cells and hormonal regulation, with broader implications for both basic science and clinical applications. In this study, I am advancing in vitro models crucial for toxicology and fertility research, specifically addressing the understudied role of resident macrophages within the testis niche. The research question aims to explore the avenues of generating M2 testicular macrophages in vitro from peripheral blood mononuclear cells (PBMCs). M2 macrophages are anti-inflammatory and are associated with wound healing and repair, unlike pro-inflammatory M1 macrophages. I hypothesize that adding macrophage colony-stimulating factor (M-CSF) combined with exposure to testosterone-rich conditioned media from a primary testis cell culture will induce the polarization of monocytes towards the M2 phenotype. The methodology involves the in vitro culture of primary PBMCs obtained from male Sprague-Dawley rats, with assessments based on surface marker expression (CD68 and CD163) and the evaluation of pro-inflammatory interleukin-6 and anti-inflammatory (interleukin-10) cytokine gene expression. M-CSF growth factor is added to monocytes to induce change to macrophages. The conditioned media for macrophages will be generated from primary neonatal rat testis cells cultured with 500 mIU/mL luteinizing hormone (LH). The media contains a higher LH concentration than in vivo, which helps produce a relevant testosterone concentration in the macrophage in vitro culture. RNA for RT-qPCR (reverse transcription–quantitative PCR) is extracted. Cells are fixed for ICC immunocytochemistry of markers (CD68/163). The implications of this research are substantial, ranging from the ability to study inflammation mechanisms in vitro to achieving a more accurate representation of the testicular hormonal environment. Furthermore, the study sheds light on the intracrine function of immune cells, emphasizing their capacity to generate sex steroids and derivatives that mediate intracrine, autocrine, and paracrine effects.

Substitution reactions are frequently utilized in organic chemistry due to their capacity to enable the interconversion of functional groups among a wide array of molecules to generate a variety of new distinct compounds. Our research focused on optimizing and designing a general reaction procedure between acid chlorides and alcohols. Benzoyl chloride and 1-pentanol were used as our model. High yields (92 – 97%) were achieved relatively quickly (2 h) when the acid chloride was added in excess. Lower temperatures (0oC) and gradual addition of the acid chloride to the reaction mixture also increased yields. Future studies will focus on the versatility of these reaction parameters on electron-donating, withdrawing, and sterically hindered acid chlorides.

With the global roll-out of dolutegravir-based antiretroviral therapy (DTG-ART) for people living with HIV, emergence of DTG-resistance is of concern. People who inject drugs (PWID) are one of the key populations most vulnerable to HIV. Data on DTG-resistance, especially among key populations and in "real-world" settings are limited. To address this knowledge gap, we performed a longitudinal cohort study of PWID living with HIV in Kenya on DTG-ART to determine the prevalence of virologic failure and DTG resistance. We enrolled PWID living with HIV who had been taking DTG for ≥six months at eight clinical sites. Plasma was collected at enrollment and every six months for 24 months and plasma HIV RNA was measured. HIV genotyping for resistance was performed on any viremic (HIV RNA >200c/mL) specimens using PacBio sequencing. At each study visit, ~15-20% of the 250 enrolled participants had viremia; however, the participants with viremia at each visit were not the same. Pre-DTG genotypes were available for 61/250 participants. I compared the rates of viremia among those with vs without pre-DTG resistance to DTG-ART and found that pre-DTG resistance was not associated with virologic failure on DTG-ART. Interestingly, while 65/250 (26%) participants experienced intermittent viremia, which could potentially result in selective pressure for DTG-resistance, resistance to DTG by month-12 was rare in this cohort. One participant had detectable DTG-resistance at month-6, with the mutation G118R detected in 1/100 (1%) viral templates sequenced. Genotyping of the month-18 and -24 viremic plasmas is in-progress; however, given the frequency of DTG-resistance detected by month-12 we anticipate that DTG-resistance will still be rare in this cohort by month-24. These findings provide new data on the frequency of virologic failure and DTG-resistance among a key population living with HIV and may help inform clinical management of PWID living with HIV in resource-limited settings. 

Bacterial metabolic engineering holds great promise for applications in medicinal, industrial, and climate technologies. A key element of metabolic engineering is the integration of non-native genes and pathways into microorganisms. However, the current state of technology is inefficient and time-intensive. Large cargo sizes of above 2-4 kilobases (kb) reduce integration efficiency, preventing entire metabolic pathways from being integrated into an organism at once. To maintain large heterologous genes and pathways in an organism’s genome, a seamless method for genomic integrations is necessary. A recent breakthrough in genetic engineering uses transposase enzymes and clustered regularly interspaced short palindromic repeat (CRISPR) machinery for more efficient and generalizable genomic integrations. Guided by RNA elements, this genomic integration system improves target site specificity and selection, as well as multiplexing capability (the direct insertion of genes at multiple genomic sites simultaneously). This system is expected to handle cargo insertions of around 10kb, meaning entire metabolic pathways can be implemented into a genome. My research aims to utilize this tool to demonstrate metabolic pathway integrations in non-model organisms and multiplexed knockouts for improved organism engineering. I plan to insert a fluorescent protein in 3 different industrially relevant organisms to demonstrate the generalizability of this genetic engineering toolkit. Additionally, I intend to establish multiplexing capability in multiple organisms by integrating the same genetic cargo at multiple sites using an array of guide RNAs, and determined results using polymerase chain reaction, gel electrophoresis, and DNA sequencing. Finally, using analytical methods such as liquid chromatography-mass spectrometry, I will measure the metabolic effects from integration of complete pathways. I will present the results of ongoing progress for all of the outlined tasks. Overall, my research on CRISPR RNA-guided transposases will enable the targeted, efficient integration of novel genes and pathways in bacteria, leading to significant advancements in therapeutics, biomanufacturing, and sustainable chemical conversion.

Traditional methods of sampling for respiratory illnesses can be uncomfortable and possibly act as a deterrent for children and adults. The CandyCollect is a lollipop-inspired device developed to aid in the testing for respiratory infections. Fabricated by a computer numerically controlled (CNC) mill, the device contains a plasma-treated microfluidic channel that collects pathogens from saliva; the addition of strawberry-flavored isomalt candy on the head of the stick aids in the resemblance, feel, and taste of a traditional lollipop. In previous remote human subjects studies, approved by the Institutional Review Board (IRB), we demonstrated the ability of CandyCollects to detect commensal bacteria, Streptococcus mutans and Staphylococcus aureus, in healthy adults using qPCR and detect infections in adults displaying symptoms of respiratory infections. From these and IRB-exempt device improvement studies, we aimed to shorten the dissolve time of the candy to make it comparable to the sampling time of nasal and oral swabs. In order to investigate the usability and accuracy of the CandyCollect for children, our team launched the Parent-Child Dyad Study. The IRB-approved study recruited parents with children displaying symptoms of respiratory illness via online forums. The 40 eligible dyads, consisting of children aged 5-15 and their parents, received a kit including a nasal swab, two mouth swabs, and three CandyCollects. After using the CandyCollects, the children and parents completed their respective surveys asking them about their comfort and experience with the different testing methods. As with all remote sampling methods, limitations included potential biases towards nasal and/or mouth swabs. However, the CandyCollect is no more susceptible than currently employed methods. User feedback data demonstrates children preferring the CandyCollect over mouth and nasal swabs, reporting better taste and comfort. The parent survey results also show preference for the CandyCollect. Here we will present the results of their user feedback.

The war in Ukraine has resulted in a high number of refugees fleeing to nearby countries. The literature on the economic effects followed by such migration is very limited. In particular, the effects of the influx of refugees on the labor markets of host countries are broadly researched. The purpose of this study is to analyze such effects in the context of Poland and Ukrainian refugees. This study investigates the effects of labor supply shocks caused by refugees on Poland’s labor market outcomes. Analysis was conducted using data on Ukrainian refugee migration within Poland, and the labor market factors such as wages and employment. The findings of this research help to have a clearer understanding of the expected effects on labor markets in similar refugee situations as Poland. Recognizing these effects can help countries be more prepared when facing labor market supply shocks which is beneficial for both the host country and the refugees.

Chronic motor deficits are one of the most debilitating symptoms experienced by individuals with spinal cord injury (SCI). Use-dependent physical rehabilitation is the current standard of treatment after chronic injuries, but typically leads to marginal recovery of motor function, creating a need for interventions that target chronic motor damage. Our laboratory developed a neuromodulatory intervention that utilized targeted delivery of quipazine, a broad-spectrum serotonergic agonist, to improve motor function in a rat SCI model. Chronically-injured rats received physical rehabilitation combined with intraspinal delivery of quipazine. Our results show after a severe SCI, delivery of quipazine caudal to the lesion promoted substantial and long-lasting recovery, compared to physical rehabilitation alone, as assessed through changes in forelimb-motor performance. In the present study, we will use electrophysiology to assess changes in corticomuscular connectivity via motor-evoked potentials (MEPs) between motor-cortical areas in the brain and forelimb muscles. MEPs will be recorded in wrist flexors, wrist extensors, and triceps through chronically-implanted wires, and are elicited by electrical stimuli delivered to the motor cortex (via microwires in the rostral and caudal forelimb areas). An increase in MEP amplitude is indicative of strengthening corticomuscular connections. MEPs will be assessed before, during, and after a therapy period consisting of physical rehabilitation and delivery of quipazine. Additionally, MEPs will be recorded before the cervical contusion SCI to acquire pre-injury baselines. Weekly changes in MEP amplitudes, relative to pre-injury levels, will be compiled and compared to changes in motor performance. We hypothesize quipazine will increase motoneuron excitability and firing caudal to the lesion, which will strengthen corticomuscular connections between the motor cortex and forelimb muscles that were weakened by the cervical SCI. We expect increases in MEP amplitude will be correlated to behavioral improvements. Our experiments will establish a high-sensitivity metric for quantifying the electrophysiological mechanisms behind quipazine-driven motor repair.

The miR-9 family of microRNAs, known for its remarkable conservation across species, exerts significant influence over neural proliferation, differentiation, and maturation processes. However, the specific role of individual miR-9 family members is not widely known. Previous work in the Cherry Lab shows that loss of miR-9-2 in mice disrupts brain vascular development. Furthermore, previous studies have implicated the miR-9 family as important regulators of neural progenitor proliferation. Thus, I assessed the proliferative properties of brain progenitor cells and vascular development in miR-9-2 mutant and control mice from early to mid-neural development to test the hypothesis that miR-9-2 is a significant regulator of progenitor proliferation and vasculogenesis in the developing brain. To assess neural progenitor cell proliferation and vascular development, I performed immunohistochemistry and confocal microscopy to label and visualize vascular and progenitor cell populations. Images were quantified using ImageJ and AngioTool. I found that primary neural progenitor proliferation does not appear to be altered in the forebrains of E12.5 miR-9-2 mutants, while intermediate progenitor cell proliferation is increased in E12.5 mutants. However, by E16.5, both neural progenitors and intermediate progenitors display increased proliferation in miR-9-2 mutants relative to controls. The vascular vessel analyses showed no significant changes in the overall organization of the vascular network in either the E12.5 or E16.5 miR-9-2 mutants. Further work will reveal the role of miR-9-2 in regulating brain vascular functional integrity during development that may alter brain homeostasis when dysregulated and potentially serve as therapeutic targets.

As deep learning vision models become more prevalent, understanding the adversarial risk associated with them is important for maintaining safety and security. A common adversarial approach, evasion attacks, involve adding perturbations to the input data until it is correctly classified by humans but misclassified by machine learning models. Previous methods for physical-world evasion attacks include placing stickers, projecting artificial light sources, and casting shadows to mask the target object. The use of shadows, a naturally occurring phenomenon, is likely to remain undetected by people, and is therefore the focus of this project. Past shadow-based evasion attacks restrict the shadow design to more inconspicuous shapes, like triangles and other simple polygons. By designing a sculpture that can detract attention from the shadows it casts, this project aims to determine whether more complex shapes can be more successful at masking the target object. To compare the effectiveness of the shapes under the black-box setting, we use the same task as previous shadow-based evasion attacks, traffic sign classification, with the LISA and GTSRB datasets. To test the attack method in a simulated environment, I use SketchUp to create various sculpture designs that cast the selected 2D shapes. A model of the sculpture is then tested in a real-world setting, evaluating both general and scheduled attacks in indoor and outdoor environments. Because previous shadow-based evasion attacks are more effective when using polygons with more sides, we expect that complex shapes will result in a higher attack success rate.

The latest Eocene Florissant Formation (deposited ~34 million years ago) contains a rich flora and fauna that has received much study by paleobotanists since the 19th century. However, several questions about the ecology and evolution of biota are outstanding and much material remains to be studied. Using observations from a high-definition compound microscope, dichotomous keys, and published literature, I seek to directly analyze and identify an unidentified fossil of a latest Eocene angiosperm, gain a comprehensive view of their surrounding habitat, and contribute to a better understanding of plant-pollinator relationships in the Florissant region. The fossilized angiosperm flower I am studying was collected by Judge Junius Henderson from lacustrine deposits of the Florissant Formation (in modern day Teller County, Colorado). It is a compression fossil with perfectly preserved petals and anthers, providing a rare opportunity for detailed analysis of its anatomy. The rock additionally contains the abdominal region of an insect, which I will attempt to place taxonomically to draw inferences about its ecological role in the Florissant ecosystem. My preliminary studies suggest that the fossil flower belongs to the extinct species Phenanthera petalifera (family unknown)- originally described by Theodore Cockerell in the early 20th century- due to matching dimensions, spatulate appendages, and two-lobed stamens exerted beyond the calyx. The insect is harder to place due to incomplete preservation, but anatomy suggests Aeschneta larvata, a bee fly (family bombyliidae), or a similar insect in order Diptera; I will explore the prominence of these possibilities. Documenting the diversity of plants and potential pollinators in ancient ecosystems existing during past warm climates is crucial for understanding how plant-pollinator relationships might change as anthropogenic warming causes shifts and losses in plant-pollinator niches.

Gastrointestinal symptoms are a common comorbidity of autism spectrum disorder (ASD), and individuals with the disorder tend to have a distinct gut microbial community composition and circulating metabolomes. My work in the Rajakovich Group focuses on a gut-derived metabolite, 4-ethylphenolsulfate (4-EPS), found in higher abundance in ASD mouse models and children with ASD. 4-Ethylphenol (4-EP), its precursor, is produced by gut microbiota before host-mediated sulfation, but the microbial biosynthetic pathway is unknown. A proposed metabolic pathway suggests the microbial stepwise conversion of plant-derived complex polysaccharides to 4-EP. My project goal is to identify a gut microbial enzyme responsible for the first step of this proposed pathway: a hydroxycinnamoyl esterase. I used literature searches and bioinformatics tools to identify characterized bacterial cinnamoyl esterases and candidate enzymes. I designed plasmids for two candidate enzymes (both from E. faecium, known to colonize the gut) and one characterized esterase (from L. plantarum). Currently, I am working on expressing the proteins in E. coli cells and purifying them by affinity chromatography. Once purified, I will assess the enzymes for their anticipated cinnamoyl esterase activity by incubating them with dietary hydroxycinnamic acid esters and detecting products with high-performance liquid chromatography (HPLC) and UV/Vis spectroscopy. Since the candidate enzymes are homologs of confirmed esterases and have conserved catalytic motifs, I hypothesize that they will have hydrolytic activity. If correct, I will see consumption of the substrate (no detection) and detect the anticipated products. Positive results from these assays would complement ongoing work by the lab to identify other E. faecium enzymes in this proposed pathway. Though it is debated if 4-EPS is causal to the disorder or simply a biomarker, elucidating its biosynthetic pathway and studying the biochemistry of gut microbes will contribute to detangling the gut’s role in ASD.

Human-induced pluripotent stem cells can be differentiated into many neuronal cell types, including astrocytes. Astrocytes are a critical brain cell, generally called glia, that interact and communicate with neurons. Their dysfunction is apparent in Alzheimer’s disease (AD), but how these processes contribute to AD development is not well understood. I created and refined an astrocyte differentiation protocol from hiPSCs to understand astrocyte dysfunction in AD. The induction protocol starts at neural progenitor cells (NPCs) already differentiated from hiPSCs. I used astrocyte-specific cell surface markers, CD44 and CD184 to purify astrocyte progenitors from this population, and then matured the cells by culturing them for 28 more days in Astrocyte-specific media. To analyze the purity of the astrocyte cultures and success of the induction, I firstly ran a glutamate uptake assay via a colorimetric glutamate assay kit. Secondly, via RT-qPCR I tested for an upregulation of astrocyte genes GFAP, ALDH1L1, P1TX1, EEAT1 as cells differentiated from NPCs to mature astrocytes. At the same time I tested if there is downregulation of NPC genes Nestin, Sox2, and Pax6. I stained for astrocyte markers such as GLAST, S100b, and GFAP via immunocytochemistry (ICC) to confirm the expression of astrocyte relevant proteins. Following the validation of the astrocyte differentiation protocol, I tested activation of the astrocytes using conditioned media from familial AD (FAD) neuronal cultures, differentiated from hiPSCs that have the FAD Swedish mutation, and represent AD-mimicking conditions. Next, I tested astrocyte activation in comparison to 2 groups: a negative control with regular media treatment, and a positive control with a known inflammatory cytokine such as IL-1β or LPS. Activation of astrocytes were analyzed via a cytokine ELISA kit and through ICC. This project helps elucidate in what ways astrocytes interact with disease progression of FAD, and how their activity is differentially triggered in FAD.

In the US, there is an average of 69,500 Traumatic Brain Injury (TBI) related deaths, 223,135 TBI-related hospitalizations, 326,600 inpatient stays, and 801,700 Emergency Department visits per year. The Centers for Disease Control report the annual cost of treating non-fatal TBIs to be over $40B. Currently, there is no pharmacological treatment for TBI, and 138 clinical treatment trials were completed since 2004 with a 100% failure rate. A rigorous screening model in vitro is needed to increase the probability of successful clinical trials. TBI is complex with many possible modalities of injury. The primary insult to brain tissue may result from compression or shear stress and strain, followed by swelling that compounds into the secondary insult. The cascade of TBI causes additional neuronal death and dysfunction to complicate injury and treatment further. The range of unknown potential injury to the brain during a TBI makes a single TBI model too simplistic to represent the full extent of injury accurately. I have developed a set of living-tissue organotypic whole hemisphere (OWH) brain slice models to mimic compressive damage with a whole slice and novel partial slice compression. The models simulate mild, moderate, and major TBI representing primary and secondary insult inflammation and cytotoxicity propagation across multiple brain regions. Future work will model shear strain damage and the neurochemical response to injury. This set of robust models will be used to screen treatments for TBI before in vivo and clinical trials to study how the compounds affect damaged tissues at a cellular and molecular level.

Diabetic Cardiomyopathy (DCM) is a cardiovascular complication developed from diabetes mellitus, causing a dilation of cardiac ventricle tissue, ultimately impairing systolic function. Although this condition affects 1.1% of the population and nearly 17% of all diagnosed diabetics, mortality rates are exceeding large, with almost 1 in 3 developing death or heart failure after less than a decade. Therefore, effective therapeutics are required to mitigate this prevailing epidemic. Chloride Intracellular Channels (CLICs) are a family of ion channel proteins, permeable to chlorides, which maintain specific cytoplasmic ion concentrations to regulate necessary homeostatic conditions for cellular function. Previous research from our laboratory demonstrates that the absence of CLIC4, a member of the CLIC family and a mitochondrial-associated membrane ion channel in cardiomyocytes, prevents the alteration of sarcomere integrity and beat rate upon high glucose exposure, which is highly prevalent in DCM. Additional research suggests CLIC4 regulates sarcoplasmic reticulum (SR) mitochondrial calcium signaling in cardiomyocytes, and the absence of CLIC4 prevents the occurrence of diabetic cardiomyopathy. However, the mechanism of CLIC4-mediated cardiac dysfunction is still relatively unknown. Previous investigation demonstrates that dysregulation of Ryanodine Receptor 2 (RyR2) function in the SR of cardiomyocytes, due to its oxidation, could augment cardiac dysfunction upon diabetes via modulating calcium levels. This experiment illustrates that pharmacologically blocking CLIC4 reduces oxidative stress in cardiomyocytes, which we measured via staining of cardiomyocytes with DCFDA. Additionally, we found the association of CLIC4 with RyR2 through immuno-pulldown experiments. We anticipate that CLIC4 regulates the oxidative status of RyR2 and modulates its activity in diabetic cardiomyocytes.

The COVID-19 pandemic disrupted learning for students across the U.S., leading to a sharp decline in academic performance nationwide. Learning losses from the pandemic pose dire consequences on students’ future financial and social wellbeing as well as the health of the labor market as a whole. Policymakers have recognized the necessity of educational interventions such as high-dosage tutoring that can accelerate learning to make up for this gap, dedicating $122 Billion in funds for Elementary and Secondary School Relief (ESSER) as part of the American Rescue Plan Act of 2021. The State of Ohio utilized ESSER funds by launching its Statewide Mathematics and Literacy Tutoring Grant, through which college students in teacher training programs are paid to tutor school students in small groups. I am analyzing the impacts of this Grant on educational achievement of Ohio’s students to determine whether it has been sufficient to overcome pandemic-induced learning losses. I hypothesize that schools that have received tutoring through Grant partnerships experience significantly higher growth in student achievement than those that do not. I utilize data from Ohio School Report Cards from 2013 to 2023, published by the Ohio Department of Education and Workforce, to conduct a difference-in-differences analysis with propensity score matching. The findings of this study will enable critical analysis of educational policy efforts and their differential impacts on students of different backgrounds. Particularly, the study will provide insight into the efficacy and cost-efficiency of tutoring by “paraprofessional” teachers such as the college students who will receive payment through the Grant, which is not as well studied as tutoring by professional teachers. Finally, it will explore the feasibility of adapting reactionary educational interventions to programs that can help students in the long term.

The human proteome consists of tens of thousands of proteins produced from sequences translated from the human genome. Further, each of these proteins can be modified post-translationally to create an even larger set of unique proteoforms. With such a massive catalog, a tool that could accurately and inexpensively fingerprint proteins with single-molecule resolution in real-time would have a transformative impact on biology, medicine, and healthcare. To develop such an approach, we are utilizing nanopore sensor technology. Nanopores function by electrically-examining proteins at the molecular scale. As a protein molecule passes through the nanopore—a minuscule orifice in a thin membrane—it modifies the ionic current. Each protein induces a unique alteration in the current, producing a distinctive signal pattern, or 'squiggle'. These squiggles effectively act as molecular fingerprints, potentially enabling us to identify and classify different proteins based on their specific current changes as they traverse the nanopore. In this project, we are tasked with building a machine learning model to classify proteins based on their squiggle templates when passed through a nanopore. We found that a classification model based on a standard Convolutional Neural Network (CNN) performed well on simulated data of eight synthetic protein designs, but failed to generalize properly to experimental test data. In contrast, a 1-Nearest Neighbor model significantly outperformed the neural network architecture on the synthetic protein test data. We plan to assess this model's performance on fingerprinting the human proteome through a simulated dataset, with the ultimate goal of sharing our findings with other labs that specialize in developing precision medicine, targeted drugs, and technologies for understanding protein structure, function, and interaction.

Cervical spinal cord injury (SCI) can severely limit motor functions of the arms and hands. With very few available and effective therapy options, SCI results in reduced independence and quality of life. Electrical stimulation of the spinal cord is a promising therapeutic method that improves motor function in individuals with a spinal cord injury beyond what can be achieved by spontaneous recovery. However, this improvement has primarily been measured by manually scoring motor-based tasks and it remains unclear how these functional improvements are represented in the control of muscle activity. In this study, we conducted differential, intramuscular electromyography (EMG) recordings in rats while they performed a forelimb reach and grasp task. These recordings targeted the tricep brachii, wrist extensors and digit flexors. Trials highlighted the initial, intermediate, and final stages of an eight-week therapeutic window during which the rats received targeted, activity-dependent spinal stimulation (TADSS). TADSS is based on the principles of spike-timing dependent plasticity to enhance the electrical activity of spared motor pathways. The stimulation protocol delivers intraspinal microstimulation in synchronization with functionally related motor movements. I hypothesized that rats with a unilateral, cervical contusion of the spinal cord receiving TADSS will exhibit changes in EMG patterns throughout therapy with improved muscle strength and coordination of activity across muscles. This would suggest that TADSS can improve the strength of signals traveling through the injured spinal cord to the muscles. Results also measure functional recovery using an objective method rather than subjective behavioral scoring addressing a methodology problem in the field. Future directions will be directed towards differentiating the precise mechanisms of motor improvement as an objective method of recovery analysis.

Thousand-and-one amino acid kinase 2 (TAOK2) is an autism-associated serine-threonine kinase that has been shown to be important for several aspects of neurodevelopment, including axon elongation, dendritic branching, and spine formation. TAOK2α is localized to the endoplasmic reticulum (ER) and mediates the tethering of the ER to the microtubule cytoskeleton. Interestingly, it is found in specific subdomains within the ER membrane, however, the identity and function of these distinct ER subdomains remain unknown. Further, during mitosis, TAOK2α is found at the points of contact between ER and mitotic spindles including mitotic spindle poles or centrosomes. While it is clear that TAOK2 plays an important role in regulating ER dynamics during cell division, the molecular mechanisms mediating these functions and specific localization of TAOK2 are yet to be determined. To better understand the molecular function of TAOK2, I performed an immunoprecipitation (IP) mass spectrometry in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs) and identified 31 potential interactors of TAOK2α. These interactors are implicated in several important cellular processes such as mitosis, RNA splicing, transcription and translation, as well as lipid metabolism. I will further shortlist the interactors by validating the interaction through immunocytochemistry. I will examine changes in cell cycle in wildtype and TAOK2 knockout NPCs through live cell confocal microscopy. Additionally, given that some of the interactors regulate lipid homeostasis, I performed lipidomics to study how the absence of TAOK2 affects lipid metabolism. Together, these experiments will reveal fundamental insights on TAOK2 and the unique link between dysfunction in organelles and autism.

Capillary microfluidics capitalize on surface tension effects encoded in microchannel geometry and chemistry to transfer liquids without external instruments, making them a user-friendly technology for point-of-care tests. For most applications, hydrophilic surfaces (contact angle < 90˚) are necessary to induce surface tension driven flow. Currently, this is achieved with vacuum plasma chambers that alter surface chemistry. Unfortunately, the hydrophilic properties made with plasma processing are temporary and unstable. Alternatively, an inherently stable hydrophilic 3D-printing resin containing polyethylene glycol diacrylate (PEGDA) and acrylic acid (AA) was recently developed for capillary microfluidics. However, this hydrophilic resin has not been thoroughly validated for inexpensive (<$300) liquid crystal display (LCD) printers. Our objective is to optimize and validate 3D-printing parameters including exposure time, UV power, layer thickness, and lift/retract speed using this hydrophilic PEGDA-AA resin with three LCD 3D printers (AnyCubic Photon Mono X 6K, AnyCubic Photon Mono M5s Pro, and Phrozen Sonic Mini 8K). Validation includes measuring hydrophilic properties as well as the dimensional fidelity of the printed channels compared to the design specifications. Our proof-of-concept prints on the Mono X 6K printer had average contact angle measurements of 42.8° ± 8.77. The percent differences between designed and printed channel lengths, widths, and depths were 31.5 ± 0.23%, 28.9 ± 3.41%, and 2.40 ± 13.9% respectively. By optimizing the print parameters of cost-effective 3D printers with the inherently stable hydrophilic resin, we enable capillary microfluidic technologies for users in low income/resource settings who may not have access to vacuum plasma chambers. Future work will explore additional resin modifications to encourage applications like spatial patterning of hydrophilicity and protein immobilization in microchips. [1]V. Karamzadeh, A. S. Kashani, M. Shen, and D. Juncker, “Digital Manufacturing of Functional Ready‐to‐Use Microfluidic Systems,” Advanced Materials, vol. 35, no. 47

The Monte Carlo Physarum Machine (MCPM) is a modeling program constructed similarly to the more traditional Monte Carlo Markov Chain. The program is modeled after the Physarum slime mold, an organism which seeks out nutrients to absorb and consume. When applied to matter distribution in the universe, MCPM is designed to seek out the largest density objects, primarily in the form of galaxies and galactic clusters. Given previous applications of the program, I wanted to know whether it could be put into further use to produce accurate predictions of the current structure of matter in the universe. We call these large structures of matter that make up the universe Large Scale Structures (LSS). To determine the accuracy for LSS environment predictions via MCPM, I am cross comparing the results from the Value Added Catalog (VAC), obtained using MCPM, with the results from the most recent Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) catalog. The VAC, which was the first catalog of matter dense galaxies obtained using MCPM, and MaNGA both possess matter density data that I have compared to determine if the same galactic structures were documented. The step that I am currently working on is seeing if I can replicate the VAC results with data compiled in the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) catalog. I am currently still working with and sorting through the data from HETDEX to produce the most accurate results. If I can determine with certainty MCPM produces the same results as other methods, its use as a primary data modeling process in cosmology would establish a concrete method for mapping the cosmos with unprecedented accuracy and reliability. Continued work with MCPM will allow for further advancements in its modeling and mapping procedures and push the boundaries of cosmological modeling and prediction.

Sound symbolism is a phenomenon wherein the phonetic forms of certain words iconically represent attributes of the objects, qualities, or events they describe. This study focuses on the sound-meaning link in Panãra animal names, using vocabulary from field notes collected in the Panãra community by Dr. Lapierre the summers of 2015-19 and by Dr. Lapierre and PhD students Ananthanarayan, De Falco, and Jeter the summer of 2023. The Panãra vowel system has a combination of features not present in some more widely studied languages such as English, namely, a back, unrounded series, contrastive length, and contrastive nasality. Using this extensive inventory, I assess strength of size sound symbolism created by nasality, height, vowel length, and backness, as well as the interactions between multiple features. I organize Panãra names for different animals and find the average weight of that species. I calculate the percentage of vowels that have a certain feature in a word and assess the correlation between this percentage and the weight of the species denoted using a regression model. Previous research has shown that front and high vowels are associated with smaller sizes and back and low vowels with larger sizes. I predict that the phonetically central and mid series will be associated with sizes intermediate to the peripheral series. Alongside providing observations from an under-documented language regarding its sound symbolism, findings from this study will help guide the continued lexicographic and field research inquiries into the Panãra language.

B-cell lymphoma-extra large (Bcl-xl) is a mitochondrial transmembrane protein that acts as an anti-apoptotic protein by sequestering the apoptosis-inducing proteins Bim, Bak, and Bad. This prevents the release of cytochrome c from the mitochondria, preventing activation of apoptosis pathways. Higher levels of Bcl-xl expression are commonly found in cancer cells. This contributes to the prevention of apoptosis in cancer cells, allowing them to proliferate uncontrollably. Bcl-xl is an incredibly important target for cancer therapeutics. A Bcl-xl binder would inhibit the interaction between Bcl-xl and apoptosis inducing proteins, allowing cancer cells to undergo apoptosis. In my research, I am using deep learning methods to design cyclic peptides that bind to Bcl-xl. To design the binders, I used RFDiffusion - a generative diffusion model - to produce thousands of cyclic peptide binder scaffolds bound to Bcl-xl. I then used a sequence-based deep learning tool to generate multiple sequences for each backbone design. The resulting binders were computationally validated with the highly accurate, machine-learning-based structure prediction tools AlphaFold and RoseTTAFold. Of the 40000 generated cyclic peptides, 2052 were predicted to bind to Bcl-xl based on standard metrics. Along with their excellent metrics, these designs show a high structural similarity and binding location to the known Bcl-xl binders Bim, Bak, and Bad. The designs were clustered by backbone into 350 unique clusters. We synthesized the top designs and identified which peptides display binding to Bcl-xl through a Homogeneous Time-Resolved Fluorescence (HTRF) assay. A successful Bcl-xl binder has the potential to serve as the basis for an effective and affordable cancer therapy.

Plainfin midshipman (Porichthys notatus) are seasonally reproducing teleost fish found along the Pacific Coast of North America. During the non-reproductive months (December-February), midshipman live offshore in deep waters. Between March and July, they migrate to the intertidal zone to reproduce. During the reproductive period, dominant (type I) males build and defend nests and hum to attract female mates. Unlike most vertebrates, courtship (humming to attract mates) and parental care (egg cleaning, nest defense) are both conducted only by type I males. These males therefore face energetic and temporal trade-offs between courtship to parental care within a single reproductive season. Our research investigates the neural mechanisms underlying the transition from courtship to paternal care in type I males during the reproductive period. We propose that this behavioral shift is regulated by steroid hormones (i.e. testosterone and estrogen) and neuropeptides (i.e. galanin). We are measuring hormone levels in blood and brain of midshipman fish across various conditions of courtship and parental care. We show the relationship between changes in steroid and neuropeptide levels in both blood and brain and changes in courtship and parental care behavior in type I males. Understanding these mechanisms in midshipman fish is crucial, as the steroid and neuropeptide pathways that regulate social behaviors share similar pathways across vertebrates. Therefore, studying this in teleost fish can provide valuable insights into the broader regulatory mechanisms of reproductive life-stage transitions in vertebrates.

Phytoliths are silica bodies inside and around plant cell which hold crucial evolutionary insights into the grass family, Poaceae. This study focuses on phytolith morphology within the PACMAD group, consisting of the Poaceae subfamilies Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae. By examining over 1,500 phytoliths across 114 extant species within these subfamilies, we aim to identify patterns in the distribution and abundance of specific phytolith morphologies, so-called morphotypes. This analysis could help deepen our understanding of both phytolith morphotypes as potential indicators of evolutionary relationships within grasses. We can also use these patterns to determine the taxonomic affinities of fossil phytoliths, which allows us to trace the evolutionary history of grasses in the fossil record. Additionally, we focus on the evolution of C4 photosynthesis, a key adaptation in grasses to dry and hot climates; specifically, how we can use phytolith morphology as an indicator for this evolutionary trait in the fossil record. Through comparative analyses within and beyond the PACMAD clade, we aim to compare phytoliths from modern C3 and C4 grasses to gain a better understanding of the differences between phytoliths from grasses with the two photosynthetic pathways and apply it to fossil phytoliths to better understand when C4 grasses evolved and spread. Furthermore, we emphasize the significance of this research in the context of climate change. By linking phytolith morphotypes to the climatic preferences of extant grasses and applying this information to the fossil record, we can trace past climatic shifts and patterns, learning how grasses adapted to environmental changes. Our preliminary results so far show that there are distinct patterns in phytolith morphology across PACMADs, although, at the genus and species level, there is an overlap in morphological traits that we hope to address with increased data.

The University of Washington Neonatal Intensive Care Unit (NICU) Extremely Preterm (EP) program aims to provide outstanding care to EP infants born at 22 0/7-24 6/7 weeks’ gestation. The objective of this study is to assess the feasibility of night telerounds in a level IV academic NICU for EP neonates to enhance the support for teams caring for EP patients. This was a retrospective cohort study. Through review and analysis of electronic medical records, the EP database, and telemedicine records from July 2022 to June 2023, the frequency and duration of telerounds during the night shift (8-11pm) were examined. Comparisons of EP outcomes were made between two epochs: 6 months pre- and 6 months post-telerounds implementation. Descriptive statistics, chi square and independent samples t-test were used to compare EP outcomes between epochs. There were a total of 195 telerounds encounters, with improvements noted in network connectivity over time (fewer dropped calls lasting <20 sec). In the pre-implementation period, 9 (36%) of EPs were transferred for subspecialty/surgical care, mortality before 36 weeks’ postmenstrual age (PMA) was 14 (56%) and median length of stay (LOS) for survivors to discharge was 182 days (SD 72). Post-implementation, 10 (50%) EPs were transferred with mortality before 36 weeks’ PMA of 7 (35%) and median LOS for survivors to discharge was 139 days (SD 24). In conclusion, there was a reduction in neonatal mortality before 36 weeks’ postmenstrual age and a trend towards decreased length of stay during the post-implementation period. The findings suggest that night telerounds are feasible in supporting bedside NICU teams caring for critically ill EP neonates and may facilitate care advancement. Additional chart review is in progress to characterize orders entered during night rounds in order to evaluate the impact of this intervention.

African immigrants are highly disproportionately affected by Human Immunodeficiency Virus (HIV) compared to US-born individuals in the U.S.. In King County, HIV stigma is a significant barrier to HIV testing among African immigrant communities. Our study aims to partner with communities to confront the HIV epidemic among the African immigrant population in King County by decreasing HIV stigma that prevents individuals from utilizing HIV testing. In this formative study, we have partnered with three African community organizations, Ethiopian Health Board, Eritrean Health Board, and the Congolese United Foundation, to deliver community-based HIV testing via health fairs at faith-based organizations and adapt and pilot an existing HIV stigma reduction intervention (Project FAITHH). We are working with faith-based organizations to address religious/moral beliefs that may foster negative social labels towards and further stigmatize people living with HIV. Data collected at health fairs hosted in churches serving each of these communities include HIV stigma scales, perceived barriers faced by individuals and community members that impact HIV testing, and demographics including country of origin, gender, religious affiliation, and primary language(s). Additionally, we have adapted an 8-module, faith-based stigma reduction intervention for these communities, aimed to address inequities in HIV testing perpetuated through HIV stigma, misinformation, and lack of awareness among intersecting, religious identities. The intervention includes activities to explore and address the sources of stigma around HIV in African immigrant communities, as well as information about HIV, including HIV epidemiology in King County. Anticipated findings regarding HIV stigma of participants before and after the intervention will inform our implementation of Project FAITHH among a more diverse group of African immigrant communities in King County. This work furthers the impact of community-based interventions designed to address the disparities in HIV in King County.

Tuberculosis is the leading cause of infectious disease death globally, but understanding of the host factors that contribute to immune control are incompletely understood. Mtb-infected macrophages, the primary host cell defense cell and replicative niche of Mycobacterium tuberculosis (Mtb), become lipid-laden, or "foamy," which promotes Mtb growth. Toll-interacting protein (TOLLIP) is a tuberculosis-resistant protein that metabolizes lipids in other cell types. Our study objective was to determine whether TOLLIP was responsible for preventing lipid accumulation and impairing host defense in macrophages. I harvested alveolar macrophages of B6 and Tollip^-/- mice via bronchoalveolar lavage and measured lipid accumulation, cell death, and cytokine production. Macrophages were incubated with the Mtb cell wall lipid mycolic acid and labeled with a fluorescent neutral lipid stain to measure intracellular lipid content. Mycolic acid was also instilled intratracheally into the lungs of mice and lipid content in lung-resident macrophages was measured using flow cytometry. Since lipid accumulation can induce cell death, cellular apoptosis and necrosis were measured via Annexin V and membrane permeability staining. Cytokine responses were determined via enzyme-linked immunosorbent assay (ELISA), and data was gathered through a standard curve. Statistical significance was determined using a two-sided t-test, with a threshold p-value of less than 0.05. Mycolic acid-stimulated Tollip^-/- macrophages developed increased lipid accumulation and cell death in a dose-dependent fashion. Tollip^-/- alveolar macrophages selectively accumulated more lipids than B6 mice (mean B6 0.45%, mean Tollip^-/- 0.68%). Tollip^-/- macrophages secreted increased cytokines (mean B6 131pg/mLvs Tollip^-/- 233 pg/mL, p=0.05) after mycolic acid stimulation. We conclude that Tollip^-/- macrophages accumulate excess lipids and produce more cytokines, which may contribute to its role in Mtb host defense in macrophages. These results suggest that excess cytokine production leads to worsened defense mechanisms and increased lipid production induces macrophage immune response. 

While research on burnout has focused specifically on service-oriented roles (e.g., healthcare), recent trends indicate a growing prevalence of burnout in academic settings. Burnout syndrome (BS) is a set of psychological symptoms arising from interplay of chronic occupational stress and individual factors. These symptoms often manifest as emotional exhaustion, depersonalization, and diminished professional satisfaction. Academic burnout has become a concern due to its association with poor academic performance, dropout rates and mental health symptoms (e.g., depression & anxiety). This study employed a pre-and post-design, assessing burnout before and after a burnout management workshop. An online survey via Qualtrics gathered data from community college students in the Pacific Northwest (N = 28, primarily women (78%), aged 16-20 (63%), including dual enrolled high school students. The survey employed a revised Purdue Burnout Questionnaire and collected demographic information. The burnout management workshop, facilitated by two psychology faculty members, addressed burnout facets and various management techniques. We hypothesized that participating students would show improvement after attending the workshop. Initial analysis revealed a reduction in total burnout scores before and after the workshop. Despite a noteworthy decrease, the change did not reach statistical significance. This nonsignificant trend suggests a positive direction, and further qualitative data, scheduled for collection in Spring 2024. Understanding and addressing academic burnout is crucial as it directly correlates with students' academic performance and mental health. By examining burnout in the college setting, we hope to contribute valuable insights that can inform policies and interventions to create a more supportive academic environment. 

Active galactic nuclei (AGNs) are galaxies that consist of a supermassive black hole at the center. Quasars are a type of AGN, which are up to thousands of times more luminous than entire galaxies due to the active accretion of gas onto the supermassive black hole. When active accretion shuts off, a quasar could change into a more normal galaxy. According to standard theory, such significant changes in accretion processes are predicted to occur over timescales of 10,000 to 100,000 years. However, recent studies have discovered a new and unusual type of quasars that undergo dramatic change on timescales of decades to years, contrary to predicted timescales. These objects are dubbed “changing-look quasars” (CLQs). To better understand the physical processes behind CLQs, more CLQ spectra must be identified and examined to perform further statistical analyses. This study analyzes on the order of 102 quasar spectra from the Sloan Digital Sky Survey (SDSS). For each object analyzed, we first assess whether the SDSS spectroscopic pipeline got the classification and redshift correct. In multi-epoch spectra, we then identify spectral features that change over time to distinguish CLQs from regular quasars with relatively constant accretion. This is done by looking at changes in velocity widths of emission lines in at least one of the common quasar emission lines. By producing a larger statistical sample of new CLQs, this study can reveal new information about accretion changes in AGNs, improve our understanding of accretion physics near supermassive black holes, and potentially challenge the standard theory of accretion.

In the 20th century, the discovery and widespread use of antibiotics became humanity's primary weapon against pathogenic bacteria. Overuse of antibiotics has unfortunately given rise to antimicrobial resistance, weakening us in this evolutionary arms race. Proteolysis-targeting chimeras (PROTACs) have been proposed as a strategy for development of novel therapeutics. By tagging target proteins with ubiquitin, targeted protein degradation (TPD) can occur via a eukaryote's own molecular machinery. Due to prokaryotes lack of ubiquitin, research has shifted to the development of PROTAC-like molecules to achieve proteolysis and cell death in bacteria, called BacPROTACs. However, to eventually experiment with these small molecules and see their mechanism of TPD, off-target effects, and changes in host and bacterial proteomes, we must be able to profile the degradation of proteins in an unbiased manner. Proteomics and mass spectrometry can identify and measure thousands of proteins simultaneously, enabling systems-level and mechanistic understanding of these novel therapeutics. In order to ensure reliability, reproducibility, and overall accuracy in analyzing a cell’s proteome, an optimized proteomics workflow is imperative. Our lab sought to understand the downstream impacts of different sample preparation protocols, differing in the material used to capture precipitated protein. Here, I present an evaluation of three proteomic sample preparation methods used on triplicates of reduced and alkylated aliquots of human cell lysate: "SP3" (single-pot solid-phase sample preparation), uses magnetic carboxylate beads as a substrate for protein aggregation; "SP4", omits a capture substrate in favor of centrifugation; and "S-Trap/S-Tip," captures protein on a borosilicate glass fibers filters. Following a Trypsin and LysC digest and desalting, samples will be run on an Orbitrap Eclipse mass spectrometer. Analysis and subsequent optimization with more complex human samples will ensure the selection of a protocol providing the highest proteomic coverage for further research.

Land plants have evolved the ability to uptake silicon from the soil and deposit it as silica-based structures called phytoliths in their tissues. Phytoliths are hypothesized to play a variety of roles in plants including contributing to structural support, defense against abiotic stressors such as drought, and herbivore deterrence. Grasses (Family Poaceae) in particular are known for their high silica concentrations of up to 40% of dry mass. We are investigating whether or not high silica concentrations are more common in grassland species and are associated with C4 photosynthesis. This directly tests the “C4-grazer hypothesis,” which states that, compared to other species, C4 grasses (i.e., those with adaptations allowing more efficient photosynthesis under hot and dry conditions relative to the ancestral C3 photosynthesis) have evolved increased silica accumulation as a response to ungulate herbivory in grassland environments. Using material from herbariums across the world, we have prepared 482 grass leaf samples for analysis. Our samples derive from approximately 200 species from all 12 subfamilies of Poaceae. These samples are analyzed using a portable X-ray fluorescence spectrometer to measure silicon concentration, which serves as a proxy for accumulated silica. To do so, we have established a custom calibration and protocol for measurements. Preliminary results show that high silica concentrations have evolved in a range of grasses, including species occupying both open grasslands and shady forest habitats, and both C3 and C4. This suggests that the mechanisms and influences on silica accumulation may depend not only on photosynthetic pathway and herbivory pressure, but may also depend on other evolutionary and environmental factors. Overall, this research will improve our understanding of how grasses adapt to stressors that will worsen under climate change, and how grasses might contribute to global carbon-silicon cycling.

Spinal cord injury (SCI) is a prevalent human trauma that greatly reduces an affected individual’s quality of life. Natural healing post-SCI results in glial and fibrotic scarring, which are common bodily reactions to central nervous system (CNS) injury, but components within these scars unfortunately inhibit axonal regeneration and the sprouting of injured neurons. Interestingly, mammals of the genus Acomys have evolved mechanisms to overcome these deficits and regenerate CNS cells to full functionality post-SCI. Since adult mammalian neurons do have an intrinsic capacity to regenerate, we reasoned that neuron-extrinsic factors are the likely culprit for failed cell regeneration in SCI patients. Thus, the overall aim of our project is to characterize neuron-extrinsic factors such as immune cells and alterations in extracellular matrix (ECM) molecules that give the species Acomys cahirinus their regenerative capacity. We hypothesized that Acomys will exhibit greater axonal regeneration and less fibrotic scarring than the common mouse model, Mus musculus, after SCI. To study this, we produced a clinically relevant contusion SCI in both Mus and Acomys. We then examined major inflammatory cells known to be activated post-SCI. Standard immunohistochemistry targeting IBA1 (a microglia marker) and GFAP (an astrocyte marker) was used to detect: 1) microglia, the first-responders to injury in the CNS and 2) astrocytes, a major component of the glial scar. My analysis showed that more microglia, but less astrocytes, were activated in Acomys than Mus. This suggested that after SCI, Acomys activated less astrocytes but recruited more reparative immune cells compared to Mus. Next, we will examine the distribution of fibroblasts and collagen, important ECM components that compose fibrotic scars, in post-SCI Acomys and Mus tissue. Understanding how neuron-extrinsic factors respond to SCI in Acomys will help us further identify and define cellular targets for the development of novel therapeutics to treat human SCI.

Hypoxic-ischemic encephalopathy (HIE), resulting from loss of oxygen and blood flow to the brain, remains a leading cause of death and disability in infants with no cure. Following the onset of HIE, inflammation and oxidative stress can drive ongoing injury in the newborn brain. Microglial and neuronal cell populations are promising therapeutic targets. However, drug delivery to the brain and into disease-mediating cells remains a challenge. Our prior work has demonstrated the ability of poly(ethylene glycol)-poly(lactic-co-glycolic acid) (PEG-PLGA) nanotherapeutics to overcome biological barriers in the brain. PLGA-PEG nanoparticles formulated with polysorbate 80 (P80) can further localize to microglia and neurons after systemic administration. We aimed to develop PLGA-PEG nanoparticles for cell-specific delivery of N-acetylcysteine (NAC), an anti-inflammatory agent, in neonatal hypoxia-ischemia (HI). We first varied formulation parameters to optimize a NAC-loaded PLGA-PEG/P80 nanoparticle platform. PLGA-PEG composition and surface-active agent concentration tuned particle size distribution, surface charge, and encapsulation efficiency characterized by dynamic light scattering and high-performance liquid chromatography. Leveraging an ex vivo rat brain slice model of neonatal HI, we investigated cellular uptake of fluorescently labeled nanoparticles. We observed particle localization in microglia and neurons, demonstrating cell-targeting ability following topical application to brain tissue. This work informs optimal particle design for delivering a therapeutically relevant dose of NAC, which is currently limited in clinical application due to unfavorable pharmacokinetic properties. Future experiments could apply the NAC nanoparticle platform using in vivo models to evaluate therapeutic potential for newborns with HIE.

The COVID-19 pandemic has reshaped our social dynamics, leading to a decline in in-person interactions across American society. This shift has raised concerns about increased loneliness and diminished social connections, with significant ramifications for mental health. College students, in particular, are likely to feel the impact of reduced social interaction, given its centrality to academic and campus life.The aim of our study is to determine the relationship between the amount of time University of Washington undergraduates spend interacting with others while feeling socially connected and their perceived levels of anxiety. Our cross-sectional study used an anonymous online survey to measure hours spent socializing per week, and self-perceived anxiety levels amongst 18–24-year-old undergraduate students. We will collect data through convenience sampling in February 2024 distributing our survey via social media and direct outreach. We will conduct our analysis including prevalence ratios, descriptive statistics and qualitative content analysis. We hypothesize that UW undergraduate students spend 35 hours a week interacting with others and that low social interaction would be correlated with high self-perceived anxiety levels, adjusting for >4 roommates and >40 hours spent working per week.Our findings could hold potential significance for public health initiatives aimed at addressing population-level mental well-being, reducing anxiety, and enhancing access to effective mental health care interventions.

Tissues like the meniscus, a wedge-shaped pad of connective tissue found in the knee, are fibrous and have complex architecture that regenerates poorly and undergoes active mechanical stimulation which modifies cell signaling and tissue health. In vitro models are beneficial for characterizing these interactions as they create a controlled environment where single variables can be altered. We previously used the J1 Mechanoculture bioreactor to apply strain on a fibrous polymer scaffold laden with primary meniscal cells and observed nonsignificant variances between testing groups with mock injury vs. no injury. Applied strain was modeled after physiological strain levels, ~10%. Based on the minimal changes in cell behavior observed in mock injury samples, it is likely that the mock injuries in conjunction with the applied strain did not induce comparable plastic deformation to that experienced post injury within the native meniscus. We hypothesize that increasing strain and applied force to achieve plastic deformation within the electrospun samples will create a fibrotic and apoptotic response like that in vivo. Ongoing work is analyzing how the bioreactor will interact with unaligned electrospun polymer samples with no cells present. This will demonstrate the optimal parameters to instigate a significant material response. By inducing significant changes to scaffold material properties and underlying structure, it is more likely cells with demonstrate fibrotic and apoptotic responses in vitro mimicking immediate cell reactions to meniscal injuries in vivo. This response will be assessed by assaying for fibrosis through αSMA activation and apoptosis by caspase-3 activation. On the conclusion of this study, we expect that greater applied stress and associated strain will cause more plastic deformation within the polymer scaffold. This can be applied to an in vitro meniscus injury model to better understand the response of primary meniscal cells to stress in an environment with disrupted mechanics.

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

Undergraduate students experience high levels of stress, with approximately 75 to 80% of college students reporting moderate stress and 10 to 12% reporting severe stress. Cross-sectional research has shown that students drink more heavily and frequently on days they experience a greater number of life stressors. In our cross-sectional study, we investigated the association between the amount of self-perceived stress undergraduate students (aged 18-24) at the UW-Seattle Campus have and the amount of alcohol they consumed during a week in the Winter 2024 Academic Quarter. Study participants reported perceived stress (how often they felt overwhelmed by situations in their lives), by responding to 10 prompts from the Perceived Stress Scale (PSS), using a 0 (Never) to 4 (Very often) scale. Study participants also reported the number of servings of alcohol (as defined by the National Institute of Health) they consumed during that week. From these responses, we calculated prevalence ratios and compared alcohol usage between participants who had high perceived stress versus low perceived stress. We hypothesized that UW undergraduate students with high perceived stress would consume 25% more alcohol than their peers with low perceived stress, during a one week period. Our study showed that the prevalence of high alcohol consumption was 1.3 (CI: 0.5, 3.5) times as high among those with high perceived stress compared to those without. These results indicate no significant association between our exposure and outcome, in part due to our small sample size (N=78). We believe that further research is needed, with a larger sample size, to better understand the true association between perceived stress and alcohol consumption on our campus.

The tumor microenvironment (TME) is a complex network of cells surrounding the tumor including blood vessels and immune cells, such as dendritic cells (DCs) and natural killer (NK) cells. DCs play a key role in driving anti-tumor immune responses against cancer. We recently discovered that NK cells control immunotherapy responses through their production of a cytokine called FMS-like tyrosine kinase 3 ligand (Flt3L), which supports DC function. However, the mechanisms regulating NK cell production of Flt3L in the tumor remain unknown. Preliminary work from our lab has suggested that hypoxia, a common feature of solid tumors marked by reduced oxygen levels, diminishes Flt3L production by NK cells. We hypothesize that spatial localization of NK cells within the hypoxic and normoxic TME differentially shapes the NK cell – DC axis. Two mouse melanoma tumors, highly hypoxic YUMM1.G1 and minimally hypoxic YUMM1.7, were grown in XCR1-venus mice (genetically modified to visualize DCs). 1.5 hr prior to tumor taking, I injected mice with the hypoxia marker pimonidazole, a compound which covalently binds to thiol groups in proteins and amino acids under hypoxic conditions. I am using a multiplex immunofluorescence panel to study NK cell (anti-NKp46), DC (anti-Venus), blood vessels (anti-CD31) and hypoxia (anti-pimonidazole) localization in the TME. By mapping the TME, I aim to uncover the spatial distribution of hypoxia and its impact on the abundance and distribution of NK cells and DCs. I hypothesize less colocalization of NKs and DCs in hypoxic regions compared to normoxic regions due to reduced NK cell function. My research seeks to explore the interplay between hypoxia and immune cell localization, potentially showing hypoxia to be a tumor-intrinsic regulator that shapes the NK cell-DC axis. Overall, this will improve our understanding of immune cell behavior within the TME, and predict new therapeutic treatments to improve patient outcome.

The gut microbiome regulates the gut-brain axis, impacting metabolic and neurological health. Dysbiosis in the gut microbiome through a wide range of environmental neurotoxins can negatively influence microbial imbalance or dysfunction, leading to various health effects as well as gastrointestinal and neurological disorders, such as autism. In this study, I explore the potential of microbial metabolites to ameliorate social deficits induced by environmental neurotoxins. While the mechanisms underlying these prospective rescue effects remain elusive, our high-throughput behavioral analysis in larval zebrafish offers a platform to uncover the therapeutic potential of specific microbial metabolites. Using this analysis system, I screened larval zebrafish treated with the environmental toxin chlorpyrifos to induce a social deficit; from this, the larvae were screened with microbial metabolites that have been observed to have beneficial effects on mental health. Sodium butyrate and butyric acid are two short-chain fatty acid metabolites that were observed to have a significant rescue effect on the social behavior of larval zebrafish. Warranting further investigation into the precise mechanism underlying this rescue effect, these findings point to a potential therapeutic strategy for butyrate derivatives in addressing neurobehavioral abnormalities associated with environmental stressors.

The technology industry has developed rapidly since the last decade of the 20th century. It has provided a large amount of job positions for cities. However, when society was getting back to the pre-pandemic condition in 2022, the tech industry announced layoffs. More than 188,568 workers were unemployed in the United States. My research focuses on the indirect effect of mass tech layoffs. The indirect effect is the employment changes of other companies in the same community as the firm that announced the layoffs. In other words, the indirect effect measures the impact on the locals. The research topic is to analyze the short-term effect of technology industry layoffs in 2022, focusing on the indirect effect on the labor market. I measured the relationship between every sector’s employment, except the technology sector, and tech layoffs in this city using fixed effects models. After layoffs, numerous unemployed people are looking for jobs. Many people have to find other jobs to support their family or themselves. They are more likely to look for jobs in the same city because it is the easiest way to overcome adversity. Therefore, employment in other companies will increase. The anticipated result is that the correlation is positive, meaning when layoffs happen, employment in other non-tech industries will increase.

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

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

The majority of people with Alzheimer’s dementia confirmed at autopsy are found to have one or more additional brain pathologies. To address this, we have developed a harmonized brain pathology score (BPS) across autopsy cohots that incorporates multiple forms of postmortem neuropathology. We sought to explore the genetic architecture of BPS using a systems-biology approach to further understanding of mixed pathology. We ran genome-wide association studies (GWAS) of BPS using HRC imputed data from European ancestry participants in each cohort separately, adjusting for age at death, sex, and population substructure. We performed meta-analysis using METAL. We performed gene-wide analysis using the GWAS results which we then integrated into the human protein-protein interaction (PPI) data using a dense module searching (DMS) method to identify network hub genes for BPS. We interrogated the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) dataset on the middle temporal gyrus to determine which cell types both hub genes were expressed in and how they differed across donors with higher degrees of AD pathology. The sample size consisted of 1,848 brain donors where 63% were females and mean age at death was 89.3. The quantile-quantile plot and genomic inflation (λ=1.005) for GWAS meta-analyses showed no bias. Apart from significant SNPs around the APOE region, we identified two candidate loci a) (Chr 9: rs1332179; MAF=0.1; P_meta=8.7×10-8) and b) (Chr 17: rs11078196; MAF=0.34; P_meta=1.9×10-7). The PPI network analysis identified VCP and IQCB1 as hub genes. While both hub genes were expressed broadly across cell types, IQCB1 was specifically higher with higher degrees of AD pathology in Microglia and VCP was lower with higher degrees of AD pathology in several neuronal populations in the SEA-AD dataset. Further functional enrichment analyses of these candidate loci are needed to determine whether these novel loci may identify targets for interventions to ameliorate AD.

Impairments in memory formation are commonly observed during aging, even in the absence of disease-related neuropathology. However, we currently lack a comprehensive animal model of normative aging. Monkeys have a keen ability to remember pictures they have seen before, and this memory can be quantified through the tracking of eye movements. Previous research from the Buffalo Lab has shown that monkeys, like humans, show distinct patterns of eye movements when they first view an image, compared to when they view it during a second presentation. To investigate whether these behaviors are impacted in normative aging, I analyzed data from 6 young Macaca mulatta (4 female, 2 male, aged 7.5 ± 2.1 years) and 3 aged (female, aged 21.3 ± 2.5 years). In each block of trials, monkeys were shown 12-16 complex full-screen images on a computer monitor for 5-7 seconds of cumulative looking-time. If the monkey looked away from the screen, the picture remained on screen, but this time was not counted towards the cumulative looking requirement. Each behavioral session contained 5 blocks of trials, for a total of 60-80 unique images, each shown twice per session. I quantified attention as the total time the picture was onscreen compared to the required cumulative looking time, creating a ratio (or percent overage) for both novel and repeat images. Thus, the more time the monkey spent looking away from the image, the larger the ratio, representing less attention to the image. The data suggest that aged monkeys exhibit less attention to repeated images compared to novel images and less attention to repeated images than young monkeys. These differences in viewing behavior for repeated images may be indicative of age-related changes in memory processes, and this metric has the potential to better inform mechanisms of normative aging.

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

Alpine areas are host to diverse plant communities that support ecosystems with their structure and floral resources and existing through specialized adaptations to harsh high-elevation conditions. An ongoing question in these plant communities is whether composition is shaped by stochastic processes (e.g., dispersal limitations) or by deterministic processes (e.g., climate) and if those processes select for common phylogenetic clades across space. This study evaluates the drivers of dissimilarity in vascular plant communities of alpine areas of 32 peaks in the Cascade Mountain Range of Washington State and the effects of incorporating phylogenetic relatedness to these conclusions. Observing an average of 54 species per peak, an inventory of 315 vascular total plant taxa were compiled to construct a phylogenetic tree relating each taxa to one another. We used multivariate techniques to quantify the phylogenetic and taxonomic differences between alpine plant communities and to relate those differences to each peak’s climate, geology, and topography. Our models indicate that each peak’s elevation, geologic parent material, and precipitation seasonality had the largest role in shaping alpine plant communities relative to the baseline effects of distance between peaks. Despite phylogeny contributing to lower overall dissimilarity, it conforms to the same trends between peaks and does not change the relationships to space, geology, and climate seen in taxonomic distance at the mountain-range scale. These results support the existence of deterministic spatial patterns of geology and climate driving community composition but fail to explain any evolutionary processes influencing colonization and survival in alpine environments.

Influenza is a deadly virus that remains a worldwide problem despite vaccinations, modern medicine, and public awareness. After infection, antiviral drugs are the primary treatment option. One common antiviral strategy is to prevent viral entry by targeting the hemagglutinin protein (HA) which sits on the surface of the virus. There are currently 18 known subtypes of HA, resulting in the efficacy of many antiviral drugs being limited. The goal of this project is to computationally design disulfide-closed cyclic peptides that target conserved binding regions on HA and test for broad spectrum activity against multiple HA subtypes. To start, I used RFdiffusion to generate peptides that are docked against the H1 subtype of HA. Then I used ProteinMPNN to optimize the amino acid sequence of the peptides. Afterwards, I used a custom written program named Protein Transform to take the peptides and dock them on the different HA subtypes. I then ran a custom program that uses RoseTTAFold2 (RF2) to predict the root mean square error (rmsd) between the target binding spot and the spot RF2 believes the peptide will stay and score the interface predicted align error (ipae), which is a confidence metric for the binding interaction. Next, I ran a Rosetta program to calculate the interaction energy (ddG) between the protein-peptide complex. The designs were then filtered based on ipae, rmsd, and ddG scores using our lab’s standard filtering thresholds. Our lab then used yeast surface display screening to test the peptides and measure the binding affinity (KD) against the H1 subtype. Then we verified the hits using surface plasmon resonance. We anticipate to see KD values in the range of 10 to 1000 nM. Identifying a lead compound with broad spectrum HA binding is an important step to creating a drug to treat any strain of Influenza.

We looked at the effect of age on location discrimination and reversal learning in horses. In location discrimination the animal learns to select a reinforced location and ignore other unreinforced locations. In reversal learning, the reinforced and unreinforced locations are switched. Research with humans and animals has found that while age has no effect on initial learning, older animals show impaired reversal learning since this task requires greater cognitive flexibility. Based on this information, we predicted that older horses would learn the location discrimination as quickly as younger horses, but would show impaired reversal learning due to age-related cognitive decline. We recruited 27 horses aged 5-27 years from Overlake Farm in Bellevue. All horses learned to discriminate between two locations, approaching a location that had a pan with food more quickly than a location with an empty pan. We then examined reversal learning by switching the location of the pan with food and the empty pan. As predicted, compared to younger horses (aged 5-17 years), older horses (aged 18-27 years) learned the location discrimination task as quickly as younger horses, but showed impaired reversal learning, primarily as a result of their inability to inhibit previously reinforced approach responses. Horses showed signs of frustration and aggression during reversal trials, so we conducted a systematic analysis of anticipation and frustration behaviors for 15 horses that participated in 2023. We predicted that they would show positive food anticipation behaviors when approaching reinforced locations, and frustration behaviors when approaching previously but no longer reinforced locations during reversal trials. This research is the first to explore the behavioral indicators related to cognitive processes involved in reversal learning, and these tests of cognitive flexibility serve as a potential use for future diagnoses of cognitive decline in older humans and animals.

Recent findings suggest that decreased chromatin acetylation leads to neurodegenerative diseases including Alzheimer's Disease (AD). Histone acetylation alters chromatin structure which regulates gene expression. One of the key proteins involved in this genetic modification is KAT5 (TIP60) acetylase. The Young Lab recently demonstrated that increased chromatin acetylation leads to the expression of genes involved in cognition and neuronal maturation. KAT5 is known to interact with the intracellular region of the Amyloid Precursor Protein (APP), which is a main player in the development of Alzheimer’s Disease (AD). In wild-type cells, the KAT5 protein is believed to be released from the membrane and translocated to the nucleus where it leads to increased chromatin acetylation and gene expression. Recent hypothesis suggest that an amyloidogenic cleavage of APP, either due to mutations or in AD conditions, prevents KAT5 nuclear translocation. To address this question, we will perform the following three experiments using human brain tissue and human induced pluripotent stem cell-derived neurons (hiPSC-Ns): 1. Immunohistochemistry for KAT5 on control and AD brains to see if we can detect a reduction in nuclear KAT5 localization in AD. 2. Immunocytochemistry on hiPSC-derived neurons harboring a familial AD (fAD) mutation in APP (Swedish mutation-K670N/M671L) as well as in neurons derived from cells that are deficient in APP (APP KO). 3. RNA-sequencing to determine differential gene expression between cells with fAD mutations and those that are deficient in APP, with a focus on genes regulated by KAT5. We expect to see aberrant KAT5 localization and gene expression in cells and tissues with AD and fAD mutations. Since treatments targeting the deposition of beta-amyloid led to many unsuccessful medical trials, we anticipate this study will demonstrate the importance of the absence of KAT5 signaling during early development of AD and devise new strategies for treatments.

In plant physiology, germination is a crucial process through which a seed transforms into a seedling. Physiological dormancy is a natural state in seeds where germination is internally inhibited until specific biochemical changes occur, ensuring that favorable conditions for plant development are met. To promote germination in Thalictrum occidentale, Western Meadow-Rue, I used Gibberellic Acid (GA) to break the physiological dormancy of the seeds. The SER-UW Native Plant Nursery had not successfully germinated Thalictrum occidentale but wished to grow and distribute this species to ecological restoration sites and the public, which motivated my investigation. GA has been used to successfully germinate other species in this genus as it is an essential plant hormone required for breaking seed dormancy and promoting germination. 900 seeds were divided into three groups, seeds received GA treatments applied either before or after 54 days of cold stratification in peat moss, alongside a control group. These were then sown in greenhouse flats. GA washes involved imbibition for 24 hours in 1000 ppm GA. This experiment was repeated in a growth chamber, placing seeds on blotter paper in petri dishes to more easily detect germination and to compare 6- vs. 10-week stratification periods. Seeds treated with GA before stratification produced higher and earlier germination rates in both greenhouse and growth chamber settings than other treatment groups. These findings support the hypothesis that applying GA treatments to Thalictrum occidentale seeds breaks their physiological dormancy and promotes germination. This study addresses limited research on this species’ physiological dormancy, offering insights into GA’s role in promoting germination. Additionally, it encourages further investigation into factors such as GA concentration and growing media selection to optimize germination outcomes. By deepening our understanding of Thalictrum occidentale’s germination process, this research contributes to plant physiology and ecological restoration efforts.

Gaming is a well-defined experience of play, but it has not been thoroughly explored in media studies. Although methods to preserve games focus on console games or emulation, they lack focus on preserving the gaming experience as a whole, especially the context of play. Preserving the user’s engagement with a game beyond playing the game itself is limited because many of these experiences occur outside of the game world. Cultural institutions such as libraries, museums, and archives cannot preserve every game and gameplay experience due to time and financial constraints. Scholars have suggested using player-generated content such as walkthroughs and let’s plays as a preservation solution. These videos are already available online, making it unnecessary for cultural heritage institutions to create them from scratch. The question is: how can we use player-generated gameplay content to assist in the preservation of games? To answer this, a content analysis was conducted. 31 YouTube channels were randomly sampled, with 10 videos from each channel. The aim of this study is to gain a better understanding of online gaming communities and ludic activities and their implications for future frameworks of knowledge organization. With gameplay content on YouTube growing rapidly, it is important to conduct this research before the rate of new content becomes too overwhelming to keep up with.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects various cognitive functions. Progressive neurodegeneration and disruption of normal brain function can arise due to accumulation of neurofibrillary tangles (tau) in neurons within the entorhinal cortex and hippocampus, driven by a burden, or buildup of amyloid beta (ABeta) plaques. Motivating the present work, those who have experienced traumatic brain injury (TBI) have an elevated risk of developing AD. Our previous study found that low-intensity focused ultrasound (LIFU) reduced the ABeta burden, in a mouse model of AD. Additionally, studies have shown that enhanced activation of cholinergic pathways (therapeutically, by the drug Idazoxan) may be required for improved ABeta clearance and, subsequently, reduce tau accumulation. We therefore sought to test that LIFU (alone or with Idazoxan) can improve brain function after TBI, using a 3XTG AD mouse model expressing both ABeta and tau. After induction of a controlled cortical impact (CCI), we applied treatment to four cohorts of 3XTG AD mice while testing their visual-spatial working memory via a weekly T-maze alternation test. Treatment conditions consisted of: LIFU alone; Idazoxan alone; LIFU + Idazoxan; and CCI only (sham) for four weeks post-injury, whereafter the animals’ brain tissue was collected for protein quantification. I specifically carried out a number of the aseptic (minimal contamination), survival surgeries to create a mouse model of TBI, administered LIFU and Idazoxan treatment, and performed computational analysis of protein burden and behavioral testing results. We observed that AD mice treated with LIFU performed significantly better in the T-maze alternation test at 4 weeks post-injury, despite no change in their ABeta burden as well as significant increase in the phosphorylated-tau/total tau burden. The finding of this study challenges prevailing theories of Alzheimer’s intervention, which largely focus on reducing ABeta burden as a means of reducing tau burden.

An unexplained phenomenon in physics is the significant imbalance of matter and antimatter in the universe. The violation of the Charge-Parity (CP) symmetry is a known source of this imbalance. However, the observed instances of this violation are not enough to explain the magnitude of the imbalance observed in the universe. In this research, I am looking for additional sources of CP violation using tau leptons, heavier cousins of the electrons. I examine the decay of a Z boson, one of the weak force carriers, to tau leptons in search of CP violation. Of interest is a quantity called Psi, a probability distribution related to the polarization of the Z boson. The distribution’s general shape is sinusoidal, and CP violation manifests itself through horizontal shifts in Psi. The taus decay extremely quickly inside the detector and I calculate Psi from their visible decay products. Previous research formulated a calculation of Psi in one decay channel (hadhad) which I have replicated. My research shows it is also possible to calculate Psi for a different channel (lephad) which is easier to study at the Large Hadron Collider. I used simulated events to calculate Psi and study its dependencies with ideal detector simulation. Ongoing work on this project involves performing analysis with more realistic simulations accounting for a realistic detector, and preparing for the measurement with real data from the ATLAS detector. If Charge-Parity symmetry is found to be violated, it would be striking evidence for new physics beyond the Standard Model and a significant milestone in explaining the imbalance of matter and antimatter.

Alzheimer's Disease (AD) is clinically characterized as a predominantly amnestic (memory impairment) syndrome at presentation that progresses to affect other cognitive domains. AD is pathologically defined by the presence of amyloid plaques and neurofibrillary tangles of hyperphosphorylated tau (pTau) in stereotypical brain regions. AD shows clinical and pathological diversity, including non-amnestic subtypes, severity of tau pathology across brain regions, and co-pathologies such as aggregates of hyper-phosphorylated transactive response DNA-binding protein 43 (pTDP-43). This study aims to examine the association between pTau and pTDP-43 using new highly quantitative approaches. By examining the combined pathology, we hope to identify patterns of pTau related to pTDP-43 across the different clinical and pathologic subtypes. The University of Washington Alzheimer's Disease Research Center clinical core autopsy cohort was characterized and subdivided into amnestic and non-amnestic syndrome subtypes. The subjects were analyzed to identify the prevalence of pTDP-43 and its correlation to the subject's cognitive data and patterns of progression. This analysis was used to select a subset of 29 cases with non-amnestic dementia and a matched subset with an amnestic subtype for more in-depth neuropathological and molecular profiling of several brain regions. Using the HALO platform, I generated quantitative measures of pTau in the frontal, temporal, and parietal cortex, as well as the hippocampus. The integration of these findings aims to understand how pTDP-43 pathology influences tau distribution based on clinical presentation These results will allow us to select a small set of cases for further work that will include using NanoString GeoMx Digital Spatial Profiling to identify potential pathways relevant to the association between pTDP-43 and pTau severity concerning mechanisms of clinical and pathologic heterogeneity in AD. These insights will allow for further research of these pathways to determine their biological relevance and ways to mitigate their effects.

Renal Cell Carcinoma (RCC) is one of the seven most frequent malignant cancers in the United States and is incurable for most patients when metastatic. One potential new treatment for RCC is T-cell immunotherapy, which has proved effective for treating certain blood cancers. To study T-cell interaction with RCC cells, I am utilizing a microphysiological system to model RCC, known as RCC-on-a-chip, which comprises spheroids of RCC cells embedded in a 3D collagen extracellular matrix (ECM). From these studies, I have observed that T cells are better able to infiltrate the collagen matrix at lower collagen concentrations (1.75 mg/mL) than at higher collagen concentrations (2.5 mg/mL). The higher collagen concentration reflects the dense tumor ECM in vivo. This led to my hypothesis that there is a subset of T cells that exhibit enhanced collagen invasion. The approach to test this hypothesis involves 1) Retrieving T cells that have infiltrated the collagen matrix in the chip; 2) Injecting the T cells that have infiltrated the collagen matrix once before into another chip to compare their migration capabilities to unselected T cells; and 3) Quantifying T-cell invasion utilizing novel custom ImageJ/FIJI macros I have written to automate the extraction of data from confocal Z-stack images taken of the chip system. If successful, I aim to retrieve enough of these infiltration-enriched T cells to conduct single-cell RNA sequencing to analyze the transcriptomic profiles of the T cells that are superior infiltrators. The knowledge gained could lead to advanced therapeutic T-cell products with the enhanced ability of targeting solid tumors. These studies demonstrate how use of the RCC-on-a-chip model can facilitate the investigation of T-cell immunotherapy for RCC.

The HIV-1 gag polyprotein consists of the core structural proteins of the virus. During the late stages of viral replication, gag assembles beneath the plasma membrane into a curved immature hexagonal lattice. This process is primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains which form a six-helix bundle with the assistance of the naturally occurring small molecule inositol hexakisphosphate (IP₆). Following budding of the immature virion, the HIV-1 protease cleaves the gag domains and CA protein assembles into a mature conical capsid, the protective shell of the virus. Disruption of CA assembly has been shown to inhibit viral replication and in turn has led to the development of the novel antiretroviral drug lenacapavir. While lenacapavir can bind mature capsid cores, the exact mode in which this drug impacts viral assembly and specifically interacts with immature CA remains unclear. My project aims to investigate the effect of lenacapavir and chemically and structurally related analogues of this drug, which have been designed and synthesized by a collaborator, on immature CA assembly in vitro. For this study I optimized the expression and purification of a gag construct that spans the CA to NC domains with an additional N-terminal Serine residue (s-CANC). I transformed E. coli cells with a plasmid containing the s-CANC construct and then overexpressed the protein. I optimized the purification protocol involving gel filtration, ion exchange and immobilized metal affinity chromatography. The purified s-CANC was then used to perform assembly assays using IP₆ in the absence and presence of lenacapavir and the analogues. The formation of immature capsid cores was confirmed via negative staining electron microscopy. Insights from these studies aim to provide a better understanding of how lenacapavir impacts the assembly of immature CA in addition to aiding the development of new capsid targeting antiretroviral drugs.

Current research on substance use suggests a positive correlation between emotion dysregulation and cannabis misuse or cannabis use disorders (CUD). This study aims to identify which specific facets of emotion dysregulation increase CUD symptom severity. While previous studies using the Difficulties in Emotion Regulation Scale (DERS) have linked overall composite scores of emotion dysregulation to CUD, there is a gap in the understanding of how individual DERS subscales relate to CUD, which limits our ability to develop targeted interventions. Young adults (N=68, Mage=23.7 years, SD=3.05, 54.4% female, 63.2% White) who reported using cannabis 2-3x/week or more in the past month completed measures of emotion dysregulation (DERS) and CUD (Cannabis Use Disorder Identification Test; CUDIT). To test associations between the 6 DERS subscales and CUDIT total score, we will first conduct bivariate correlations. If significant associations are found, we will conduct a multiple linear regression model to test which subscales best predict CUDIT total score. We hypothesize a moderate-to-strong correlation between the DERS and CUDIT scores, with Nonacceptance and Impulse control demonstrating stronger correlations. We also hypothesize that Nonacceptance and Impulse control subscales will most strongly predict CUDIT total scores. Results from the present study could help identify which of the emotion dysregulation subtypes should be targeted in future prevention and intervention efforts for young adults. If these findings are supported, additional efforts may want to teach skills to increase acceptance of emotional responses and improve impulse control. The proposed study is an important step in the treatment of cannabis misuse and CUDs as we will be able to narrow our aim toward isolated treatments to improve the livelihood of those involved.

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

Falls are a leading cause of injury, disability, and death in older adults. One common but understudied risk factor for falls includes knee instability (KI), defined as the loss of postural support across the knee during weight bearing, which is more common in older adults with knee osteoarthritis (KOA). The goals of our project are to (1) evaluate the feasibility of using a new thigh worn accelerometer device called Move4 to measure movement-evoked pain and (2) explore the association between movement-evoked pain and KI in older adults with KOA. Move4 uses sensing technology to trigger a brief survey (called an Ecological Momentary Assessment [EMA]) on a participant’s study phone asking them to rate their pain after a bout of physical activity (e.g., 15 minutes of walking) or inactivity (e.g., 30 minutes of sitting). EMAs are also collected at random times in the day (morning, early and late afternoon, and evening) over a 1-week period to assess pain level, mood, and incidence of KI. Feasibility is established if >80% of participants wear the Move4 device for 6-7 days and complete >70% of the triggered EMAs over a 1-week period. Multilevel statistical modeling is used to examine movement-evoked pain and KI occurrence and examine physical activity patterns before and after KI. The findings of this study may establish a novel method to measure movement-evoked pain in daily life that can overcome challenges of recall bias and improve estimates of KI incidence through real-time data capture. This research has the potential to improve our understanding of a prevalent symptom that increases risk of falling and limits physical functioning in a rapidly growing population of older adults with KOA.

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

Burnout is high among community mental health providers (CMHPs) and is important to remediate due to its associations with poor provider well-being and worse quality care. CMHPs’ clinical supervisors are well-positioned to address burnout, though little is known about whether supervisors implement burnout strategies that are perceived to be helpful by CMHPs. Thus, the purpose of this project is to investigate at what rates strategies identified as helpful by CMHPs are currently used by supervisors. Given the exploratory nature of this project, there were no a priori hypotheses. This mixed-methods study was conducted as part of an ongoing Washington state-funded evidence-based treatment (EBT) initiative called CBT+ which trains CMHPs serving youths in cognitive behavioral therapy (CBT) for depression, anxiety, trauma and behavior disorders (Dorsey et al., 2016). Participants (N=197) were CMHPs that participated in the 2022-2023 CBT+ training cohort and were predominantly masters-level, White, and identified as women. CMHPs were asked in a survey “How could your supervisor or agency help reduce your burnout?” and indicated whether or not (yes/no) each strategy was currently used by their supervisor/agency. Burnout solutions were coded inductively using thematic analysis by two independent coders who met weekly to resolve discrepancies. Chi-square goodness of fit tests and confidence intervals were used to examine and compare the rates of use for the solutions endorsed by at least 10% of CMHPs: Time off (endorsed by 26.9%), General self-care (16.2%), Supervision sessions (12.7%), Flexible work arrangement (12.2%), Check-ins (12.2%), Manageable caseload (11.2%), Morale/team building (11.2%), and Engaged supervisor (10.7%). Study findings can help mental health agencies and supervisors focus efforts on ways to implement strategies that are less often used to reduce CMHP burnout, and ultimately increase the quality of mental health care for youths.

Many ecologically and economically important coastal invertebrates that live on the seafloor (eg. mussels, oysters, crabs, sea stars) have distinct larval stages that live up in the water column – collectively categorized as meroplankton. Meroplankton may face different environmental conditions than their adult forms that live on the seafloor. Moreover, planktonic larval stages are often more vulnerable to changes in oceanographic conditions than their adult counterparts. A variety of climate-related abiotic stressors (low pH due to ocean acidification, high temperature, low salinity) have been shown to negatively affect a variety of important life processes such as swimming ability, metabolism, growth, and survival in laboratory settings. However, owing to the logistical constraints of measuring oceanographic conditions and plankton abundance in the same time and place, it remains largely unknown which oceanographic variables affect the abundances of different meroplankton taxa in their natural habitat. To identify the oceanographic variables that primarily drive patterns of meroplankton abundance, we collected a two-year time series of oceanographic data (temperature, salinity, pH, dissolved oxygen, turbidity, current velocity) using the Friday Harbor Labs Ocean Observatory (FHLOO), the Salish Sea’s only multi-instrument remote sensing network. We simultaneously collected a two-year time series of plankton abundance for 20 different taxa of meroplankton by performing regular plankton tows at the FHLOO. Here, we focus on the oceanographic drivers of barnacle larvae (nauplii) abundance, as they metamorphose into important fouling organisms that slow boats by attaching themselves to the hulls, but also form ecologically important habitat for other organisms by attaching to rocky shores. We show several transient high temperature, low salinity events caused by freshwater pulses due to seasonal snowmelt into the Fraser River, which outputs into the Salish Sea north of the FHLOO in British Columbia. These hot, low salinity events coincide with spikes in the relative abundance of barnacle nauplii, suggesting that temperature and salinity drive barnacle nauplius abundance in the Salish Sea. Overall, we show the importance of collecting collocated oceanographic and plankton abundance datasets to uncover the climate-change related stressors that drive meroplankton abundance in ecologically important coastal habitats.

The 2021 Heat Dome represented a historic climate event for the Pacific Northwest, resulting in 159 excess deaths in Washington State alone. Within this region, public health departments and other government agencies regularly warn the communities they serve about upcoming extreme weather events such as extreme heat, to encourage people to take preventive actions that protect their health. Social media and online communications are some of the media commonly used to disseminate these advisory messages. From June 2023 to September 2023, we captured social media and web communications about extreme heat shared via city and county-wide government sources in Multnomah County, OR, King County, WA, Spokane County, WA, and Ada County, ID. Sources included Facebook, Twitter, Instagram, and official agency websites. We then used qualitative content analysis methods to assess the types of messages that were published, as well as differences across jurisdictions, message timing, and the frequency of reposting/sharing the same content, across organizations in the same jurisdiction. Entries were coded using NVivo qualitative analysis software. Some notable themes found in this content review included risk communication (e.g., identifying highly vulnerable populations); heat-related health symptoms and interventions for heat exhaustion and stroke; promoting formal and informal cooling centers, and communicating through languages other than English. Preliminary findings across Multnomah County, King County and Ada County indicate that Multnomah County’s messages frequently targeted high-risk populations through messages that promoted free transportation to/from cooling centers and by posting in four or more languages. These findings can be used to determine the feasibility of using social media and website communications to assess the implementation of public health extreme heat messaging on a large scale. Future research should explore the effectiveness of these communications in prompting behavioral changes and in reaching vulnerable subpopulations with targeted recommendations.

In recent years, organizations have increasingly expressed support for efforts to promote diversity, equity, and inclusion (DEI). Some of these efforts are informed by research on how to promote DEI, but much of this research on how to communicate and promote DEI in organizations fails to account for qualities of the communicator, that is, the diversity specialists charged with operationalizing and implementing DEI sentiments to improve organizational equity and inclusion. Critically, communicators bring their own social identities (e.g., gender, race) and experiences (e.g., status, power) to their work. This proposal aims to better understand how DEI personnel in the public sector experience their roles, understand their jobs and their ability to effect change, as well as consider how their personal identities interact with their work. We are conducting semi-structured interviews with DEI management personnel across cities in Pacific Northwest states (Washington, Oregon, Idaho, and Alaska). Participants will be asked about their perceptions of their job responsibilities as well as their backgrounds and identity. We will be coding interview responses to examine the pressures that individuals feel in their jobs, constraints they experience in how they can advocate for DEI as a function of their social identities, how they conceptualize and communicate the importance of DEI. By better understanding the daily experiences of implementing DEI practices in organizations, this proposal aims to improve our understanding of efforts to improve DEI in public organizations.

As part of the National Science Foundation funded Washington Resurvey of Pierids (WARP) project in the Buckley lab, I am conducting a comparison between the temperature dependent growth rates of Pieris rapae caterpillars collected 25 years ago and this past summer. Pieris rapae, the cabbage white butterfly, is a recently introduced, abundant, and invasive crop pest across North America that is active in the warm spring and summer months (May to September) with 4-5 generations each year. This species has been previously studied as a model for insect thermophysiology, as ectotherms and insects in particular rely on permissive thermal environmental conditions for many core life processes. Our goal is to investigate if evolution has occurred in these caterpillars over more than 100 generations to take advantage of their new, warmer thermal environment compared to a historical baseline. We hypothesize that the temperature sensitivity of relative growth rates (RGRs) has shifted due to increasing temperatures during their season of activity, and predict that contemporary caterpillars grow faster at high temperatures than their historical counterparts did. We caught female butterflies in the Seattle area and reared their caterpillar offspring in a standardized thermal environment (10-30॰C). We then measured short term (2-24hr) RGRs by exposing caterpillars in their 4th developmental stage to 5 different temperature conditions in sequence (11-35॰C), observing their mass after each treatment. I am performing an analysis of variance (ANOVA) test of the data using two covariates of interest, temperature and time period (current or historical), to test for differences within each temperature treatment across time. Understanding how insects, especially pollinators, are evolving in response to climate change is vitally important to building accurate models for future population ranges and densities, as without this evolutionary and mechanistic knowledge, our predictions will be unreliable.

Cannabis is the most commonly used drug of abuse used by approximately 2.5% of the world's population. Tetrahydrocannabinol (THC) is the major psychoactive component of cannabis. Cannabidiol (CBD) on the other hand is a pharmacologically active component of cannabis that is not psychoactive. THC is metabolized via cytochrome P450 enzyme-mediated oxidation to 11-hydroxy-THC (11-OH-THC) and subsequently to 11-carboxy-THC (11-COOH-THC). 11-COOH-THC then undergoes glucuronidation to form an acyl glucuronide (AG), 11-nor-9-carboxy-Δ9-tetrahydrocannabinol glucuronide (11-COOH-THC-Glucuronide). CBD is also metabolized via an analogous pathway to THC, where CBD is oxidized to 7-hydroxy cannabidiol (7-OH-CBD) and then subsequently to 7-COOH-CBD and ultimately glucuronidated to form the AG 7-COOH-CBD-Glucuronide. The THC and CBD AGs are important because they circulate at high concentrations in biological samples. Thus, identifying the enzymes responsible for the formation of cannabinoid AGs is important for understanding inter-individual variability and disease effects of cannabinoid exposures and pharmacological effects. Glucuronidation is governed by UDP-glucuronosyltransferases (UGTs). The goal of this study is to identify and characterize the UGTs that form THC and CBD AGs, to define in what organs these glucuronides are formed, and to determine whether disease states may alter 11-COOH-THC and 7-COOH-CBD glucuronidation. To accomplish this I incubated human liver microsomes (HLMs) and recombinant UGTs with 11-COOH-THC (5 µM) or 7-COOH-CBD (5 µM). The incubations were done at pH 7.4, 37℃ for 5 (THC-COOH) or 45 (7-COOH-CBD) minutes. Formation of the THC and CBD AGs was detected in HLMs and with UGT1A1, UGT1A3, UGT1A7, UGT1A8, UGT1A9, and UGT2B7. UGT2B4 and UGT2B17 were specific to THC AG formation and UGT1A10 was specific to CBD AG formation. Kinetic assessments such as intrinsic clearance measurements and inhibition assays will further the understanding of the importance of the specific UGT isoforms responsible for cannabinoid acyl glucuronide formation in vivo.

Various anti-cancer therapeutics, known as microtubule targeting agents (MTAs), target the microtubule, a tube-like structure that is a major component of cell mechanisms including mitosis and maintenance of the cell shape. MTAs selectively bind to tubulin — the building block of microtubule —, disrupting microtubule dynamics and inducing cell death. Despite their known impact on antitumor activity, the precise mechanism by which MTAs promote cell death remains unclear. To understand the efficacy of ST-401 (an MTA drug) as a tumor suppressor, I conduct various assays including drug treatment and Western blot to compare the expression of specific proteins in response to the drug treatments. These assays contribute to understanding cellular processes, molecular interactions, and the effects of various treatments or conditions on cells. Currently, I am being trained to conduct an experiment called XFe Seahorse analyzer. I’m carrying out this experiment to assess how the laboratory-discovered drug affects the mitochondrial function in various cancer cell lines. This experiment aims to determine whether the compound down-regulates mitochondrial function, leading to cell death. I’m leading a project to test a specific fission (cell splitting) protein, DRP1, and how its protein level responds to treatment with ST-401 in two GBM cell lines (resistant and sensitive) and one Colon cancer cell line. DRP1 regulates mitochondrial fission to maintain healthy mitochondrial function. Recently, I found an increase in mitochondrial fission 24 hours after ST-401 treatment in the sensitive GBM cell line, so I’ll further examine DRP1 expression by drug treatment and Western blot to understand these results and see whether ST-401 recruits DRP1, resulting in promotion of mitochondrial division. After DRP1 project, I will expand the project to asses the combination drugtreatment where we combine FDA-approved cancer drug and ST-401 to reflect real-world scenarios, aiming to ensure clinical relevance and safety by studying potential drug interactions.

Introductory biology classes are often a stepping stone for students in various STEM majors, as prerequisites or major requirements. For this reason, it is vital that these courses properly prepare students for life beyond their classes, through the ability to apply the knowledge they are gaining to the real world. Because textbooks are often used as preparatory assignments or as the content on which a course is grounded, we decided to focus on this type of circular tool, in order to evaluate the level of humanization in introductory biology courses. We set out to find out the degree to which six popular and prominent introductory biology textbooks humanize science, by positioning the content in a social context. We did this by developing our definition of humanization, and based on this, a continuum of humanization. We then developed a rubric for coding the extent of humanization, with the lowest being scarce humanization and highest being content that centers justice. We also coded topics of biology, from ethics to the environment. The team went through page-by-page and line-by-line to apply the rubric to all six textbooks, including the text as well as questions. In terms of the questions, we found that out of 9262, only 236 questions were humanizing. For the text, out of 9670 pages, there were 1352 humanizing passages. Overall, we found the inclusion of humanizing content to be rare across the six textbooks analyzed, and humanization by inclusion of justice to be particularly rare. We end by giving suggestions to educators, a main one being to pose justice-centered problems to students - a “problem-posing” model of science education.

Industrial chemical separation processes, such as distillation, drying, and evaporation, consume 10-15% of the world’s annual energy production. Membranes, which act as a selective barrier to separate compounds, are substantially more energy efficient than traditional chemical separation methods that require heat. Inorganic membranes are inherently suitable for many separation processes because they are chemically and thermally stable; however, ceramic membranes are mechanically fragile and costly to produce, which limits their usefulness. Commercial polymeric membranes are economical compared to inorganic membranes but degrade in harsh organic solvents and high-temperature environments. To reduce the cost of chemical separations, methods to improve the chemical and thermal stability of polymeric membranes are needed. Vapor phase infiltration (VPI), a gas-phase synthesizing technique, is one possible strategy for improving membranes, consisting of sorption, diffusion, and entrapment of vapor-phase inorganic reactants within organic polymers. The infiltration of inorganics through VPI has been shown to enhance the properties of polymeric membranes by producing cost-effective, chemically stable, and temperature-tolerant hybrid membranes. However, the change in mechanical properties when converting polymeric membranes to hybrid membranes is generally not well understood, and this understanding is crucial for maximizing the lifetime and durability of organic-inorganic membranes. In this study, polyethersulfone (PES) membranes are subjected to trimethylaluminum and water under various VPI process conditions in a custom-built reactor. Thermogravimetric analysis is utilized to quantify the extent of inorganic infiltration by measuring the aluminum oxide loading within PES membranes. The mechanical properties of these hybrid membranes after VPI are characterized for their tensile stress, modulus, and maximum pressure through dynamic mechanical analysis and burst pressure testing. Ongoing research to establish the physical properties of organic membranes with inorganic nanostructures is discussed. These results help optimize the trade-off between membrane stability and mechanical properties, which may allow many industrial chemical operations to become more sustainable.

Access to basic healthcare is not just a fundamental human right. It’s an urgent need that many people in Southern Ethiopia's rural communities are struggling to meet. This lack of healthcare access leads to high mortality rates among infants, children, and mothers. To address this pressing issue, an extension of clinics and health education has been proposed for the rural areas of Ethiopia, which would significantly reduce these mortality rates and increase life expectancy. The goal of our research proposal is to advocate and expand healthcare services and education across rural Southern Ethiopia, with a focus on drastically reducing mortality rates and improving life expectancy. Our research strategy involves a dual approach. Firstly, we plan to conduct a comprehensive survey to highlight the lack of primary healthcare access. This survey will include questionnaires and direct interviews with key stakeholders, including community leaders, healthcare workers, and residents from these rural communities. We aim to map out the health infrastructure, gauge the availability of medical professionals, and assess community health awareness. This data will guide us to identify critical gaps in healthcare service provision. Secondly, to understand the causes of high maternal and child mortality rates, we will review medical records and engage in discussions with healthcare providers and community members to understand the specific health challenges faced and the barriers to accessing care. Our analysis will focus on important factors such as the distance to medical facilities and the presence of healthcare personnel. By collaborating with local authorities and communities, we plan to develop targeted health education programs.Our project seeks to bridge the healthcare access gap in Ethiopia's rural areas, aiming for a holistic improvement in public health outcomes. This research represents an informed effort to make healthcare accessible to everyone, particularly those in underserved rural communities.
 

Polychlorinated biphenyls (PCBs) are a group of widespread persistent organic pollutants that pose a substantial health risk to humans and wildlife, made up of 2 phenyl rings and 1 to 10 chlorine groups. Previous bioremediation efforts targeting PCBs have shown promise, particularly in aerobic bacteria expressing the biphenyl degradation pathway (bph gene cluster). However, the efficiency of this pathway is greatly decreased with higher degrees of chlorination. Therefore, a critical step for more effective bioremediation of PCBs is the removal of chlorine atoms, which can be catalyzed by dehalogenase enzymes. These dehalogenase enzymes are often oxygen-sensitive, making them difficult to implement in aerobic settings (such as wastewater). Also, their activity varies greatly depending on the number and position of chlorines, where the degradation of highly chlorinated PCBs is often less efficient. We hypothesized we could computationally redesign a naturally-occuring non-oxygen-sensitive dehalogenase, NpRdhA, to have a greater binding efficiency for more highly chlorinated PCBs with different chlorine positions. We used LigandMPNN to generate mutated NpRdhA sequences and analyzed the theoretical energy scores of the resulting NpRdhA-PCB complexes using Rosetta. We aim to experimentally validate the best scoring protein designs by expressing the dehalogenase proteins in E. coli, exposing the E. coli to a range of PCB congeners, and quantifying the dechlorination efficiency for each congener. Eventual application of this research in wastewater could expand the range of conditions under which PCB degradation is possible, as well as increase the range of PCBs able to be degraded.

Are we happier when we experience more comfortable weather, or do we prefer seasons that provide increased social opportunities? Current studies have shown improvement in mood due to warmer, more tolerable climates or spending more quality time with loved ones. There is a gap in the relation of these two factors combined towards an individual's mood. We hypothesized change in relationship between mood and social activity throughout fall and winter. After our second survey period, we will review and organize data points based on temperatures and climates, time in and out of school sessions for students, levels of socialness, and those who changed their answers after reflecting on the social aspects of the questions. In this study, we surveyed 260 Washington State residents aged 18-64 (M = 24.46, SD = 10.03), 56% from Eastern Washington and 44% from Western in the fall prior to the holiday season (September-November 2023) and again in winter (January-February 2024) to measure changes in mood changes. Both surveys, administered through Qualtrics, asked participants about weather types experienced during each season, followed by a Brief Mood Introspection Scale (BMIS) regarding their last two weeks and the Self-Assessment Manikin (SAM) scale of weather tolerance (0°F-104°F). Participants then were asked about socialness during each season and potential seasonal affective diagnoses. We had two target populations: participants under 23 and those who are students and those who are not students or are 23 or older. We expect students to favor periods not in school regardless of socialness, as opposed to those who are not students, who we expect to favor the times they spend with those they care about over periods of isolation as they tend to have more defined schedules.

Type 2 diabetes (T2D) is among the most common and costly chronic diseases in the United States. Nearly 10% of Americans have T2D and a further 34% have prediabetes. The brain has increasing emerged as a promising target for the treatment of T2D. For example, our group has demonstrated in rodent models of T2D, that remission of diabetic hyperglycemia lasting for weeks or months can be induced by a single intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1). Injection of FGF1 into the brain induces sustained activation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling pathway. ERK signaling is most highly induced in tanycytes which are specialized ependymo-glial cells that line the 3rd ventricle and are implicated in the central control of energy and glucose homeostasis. However, whether MAPK/ERK activation in tanycytes is required for sustained glucose lowering to occur in response to icv FGF1 is unknown. To begin testing of the hypothesis that activation of the MAPK/ERK pathway in tanycytes is necessary for sustained diabetic remission induced by FGF1, we proposed to inhibit the activation of MAPK/ERK pathway specifically in tanycytes by microinjection of a mouse MAPK shRNA silencing adenovirus into the 3rd ventricle 1 week prior to injecting FGF1. In preliminary studies in wild-type mice, I have shown that the ability of FGF1 to induce MAPK/ERK activation is blocked by prior injection of the MAPK shRNA silencing adenovirus. I will now take C57Bl/6J mice placed on high-fat diet to induce diabetic hyperglycemia and determine if pretreatment with the MAPK shRNA silencing adenovirus blocks the ability of icv FGF1 to induce diabetes remission. I predict that successful completion of this study will deepen our understanding of the pathogenesis of T2D, bringing us closer towards a treatment for this devastating disease.

Seattle airport communities are communities that are located near and underneath flight paths headed to and from Seattle airports– the largest of these airports being Seattle-Tacoma International Airport. Communities located on these flight paths are exposed to ultrafine pollution particles from aircraft emissions, negatively impacting air quality in these areas. This research project aims to investigate the dispersion of aircraft pollution from Seattle-Tacoma International Airport and how it’s associated with communities’ health outcomes. By using an air quality dispersion modeling system (AERMOD), I can track how air pollution from aircrafts spreads based on atmospheric conditions such as rain and wind patterns. With AERMOD and public databases of health disparities, my project produces overlayed geospatial data that combines aircraft emissions and health disparity factors to study how aircraft emissions correlates with the health of vulnerable communities. My expected results are the communities that are the most impacted by aircraft emissions, as modeled by AERMOD, will have worsened health outcomes in a range of categories once compared to communities located outside of the Sea-Tac Airport flight path. These results could serve to notify affected residents of their level of exposure from aircraft emissions and how it may be impacting their health, improving residents’ agency over their health. Additionally, these results could inform policy and regulation of aircraft emissions standards.

Eutrophication fuels toxic algal blooms that can harm biodiversity and human health. Phosphate is often the limiting nutrient in freshwater ecosystems and, when in excess, causes eutrophication. Our study compares urban lakes prone to algal blooms to rural lakes with fewer anthropogenic sources of pollution to better correlate nutrient dynamics of pacific northwest lakes to population density. We collected sediment and water samples from two lakes in the Seattle area and two lakes in a more remote setting, then measured phosphate uptake and release over time using ion chromatography. To determine the potential for the sediments to uptake phosphate, we placed air-dried sediment samples into a phosphate solution and measured the concentration over time. We also put the sediment in distilled water and measured the phosphate released from the sediment over a 24 hour time period. These two data sets allow us to quantify the capacity of sediment to store and release phosphate into the surrounding environment. Our research shows sediments from urban lakes release more phosphate and have a reduced ability to uptake nutrients from the water. This suggests that the lake will continue to eutrophy whereas the lakes more removed from human activity have a better ability to mitigate excess phosphates. This model for assessing the ability of sediment to store phosphate allows prediction of future eutrophication events.

Traumatic brain injury (TBI) is recognized as a risk factor for neurodegenerative diseases, but the underlying mechanisms remain unclear. This study aimed to investigate how localized brain injury alters pathologic protein aggregation associated with neurodegenerative disease, focusing on hyperphosphorylated tau (p-tau) and beta-amyloid deposition in brain parenchyma adjacent to chronic contusion. Using brain donors from the University of Washington Brain Repository, cases with a diagnosis of chronic contusion were identified. Beta-amyloid and p-tau deposition were assessed in sections adjacent to the contusion and in contralateral sections without contusion (internal control). Manual counting and HALO imaging software were utilized to quantify the highest density of neuritic plaques/neurofibrillary tangles and overall deposition of abnormal protein in grey matter, respectively. Statistical analyses were performed to compare deposition in contusion versus control sections. Preliminary data was collected in 9 cases, predominantly male with a median age of 79 years. Neurofibrillary tangles were significantly higher in sections with contusion compared to internal controls (p=0.0188), with a similar trend observed for neuritic plaques (p=0.0723). HALO software analysis confirmed increased deposition of both proteins in the contusion compared to control sections (p=0.0391 for both p-tau and beta-amyloid). These findings support that TBI may modulate neurodegeneration by increasing p-tau and beta-amyloid deposition and underscores the importance of further research into the relationship between TBI and neurodegenerative diseases. Next, I will expand our cohort with more cases from the last few years and plan to compare brain contusion in mid-life to contusion occurring after the age of 65. In addition to assessing abnormal protein deposition, I will also examine the neuroinflammatory response. I expect to find greater levels of neuroinflammation as well as increased tau and beta-amyloid aggregation in the older age group as the neuroinflammatory response becomes prolonged during aging.

The #MeToo movement in 2017, which represents a global call to action against sexual harassment and assault, has encouraged corporations to prioritize gender equality and diversity. This phenomenon has likewise led to an increase in the literature on gender equality and diversity. Focusing on the fashion industry, specifically Victoria’s Secret, this study examines the changes and impact of workplace code of conduct policies as a result of the #MeToo movement. Victoria’s Secret, known for its popular lingerie products and a corporate culture dominated by sex, exemplifies the fashion-industry-wide challenge of addressing gender disparities and misconduct. Guided by feminist ethics, which prioritizes values of care as ethical practice, this research focuses on Victoria’s Secret’s activities and changes in response to the #MeToo allegations from 2020 to now, and aims to understand how gender equality-focused social movements influence corporate culture and behavior. A qualitative thematic analysis investigates Victoria’s Secret’s strategic changes, including transformations in its flagship show, modifications to policies regarding sexual harassment of employees including models hired, and some critiques and reactions from the audience to these policy changes. This study seeks to provide a critical analysis of whether the actions of Victoria’s Secret align or deviate from the broader objectives of the #MeToo movement. Findings from this research have the potential to contribute to understanding the impacts of social movements in influencing fashion corporate conduct and the aims of corporate social responsibility.

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

Hydrogels are soft materials with high water content that are widely used as scaffolds to interface with the central nervous system (CNS). Spinal cord trauma leads to destruction of a highly organized cytoarchitecture that carries information up and down the spinal column. Experimental therapeutic efforts aim to create scaffolds with aligned topography to support anisotropic regeneration. Current methods are typically complex and make it difficult to introduce specific topography into 3D hydrogels. Here we examined a simple and reproducible system that resulted in consistently aligned fibrils within 3D matrices using thermally gelling biomimetic polymers compatible with neuronal cells. A collagen type I (Col)-based hydrogel system was used in combination with other native extracellular matrix proteins: laminin I (LN) and hyaluronic acid (HA). It was found that all three types consistently formed gels at 37°C. Aspiration and ejection were used to produce hydrogels containing aligned fibrils. Scanning electron microscopy (SEM) images confirmed successful alignment in all gel types, and the size of fibers were consistent with reported values for collagen (~250 nm in diameter). We found that embryonic spinal cord neurons survive and produce processes aligned to collagen fibrils after 14 days in vitro. Next, we investigated the functionality of aligned and un-aligned Col hydrogels implanted acutely after a contusion type spinal cord injury to the thoracic spinal cord at T7/T8. Within all implants, we found pan neuronal-positive fibrils and that the aligned hydrogels supported neurite growth along the parallel direction of the implanted hydrogels. Our data indicate that thermally gelling biomimetic polymers can produce aligned matrices by a method of aspiration and ejection. The material composition and process of aligning hydrogels outlined here presents a novel platform for regenerative therapies for the CNS that is compatible with the survival of neuronal cells in vitro and in vivo.

Including undergraduate peer facilitators (UPFs) in lectures is often done to support students in large and often challenging introductory science courses. Our team increased UPF involvement by creating BIOL113, an undergraduate-led companion course to BIOL180, the largest biology course at the University of Washington. This study is a part of a larger project that assessed the overall experience of both UPFs and students, and this particular work focuses on the latter. We examined how BIOL113 enhanced students' learning and academic success in Introductory Biology. By incorporting quantitative and qualitative data, we compared the performance of students who received UPF support in this companion class with those who did not. Quantitative data included grades, exam scores, and course completion rates, while qualitative data encompassed students' perceptions of peer facilitation though blast surveys. We found that undergraduate-led programs play a unique role in improving students' learning and including UPFs promoted peer-to-peer interaction and student engagement. Additionally, UPFs serve as relatable role models, providing mentorship and practical guidance. Moreover, programs like BIOL113 have a rare opportunity to disproportionately support students from minoritized groups. Understanding the impact of BIOL113 on students' success can inform instructional strategies, with potential expansion of such programs across the University. 

 COVID-19 is an infectious viral disease that is caused by the SARS-CoV-2 virus entering host cells through surface spike proteins that bind to surface ACE-2 receptors. Some anti-SARS-CoV-2 antibodies allow SARS-CoV-2 to also have antibody-mediated entry (AME) into immune cells, independent of the ACE-2 receptor. Instead, they often enter via Fcγ receptors. This phenomenon has been correlated with cytokine release syndrome, which occurs when the immune system has a highly inflammatory response to infection and is implicated in severe COVD-19 cases. It has also been shown that other antibodies have demonstrated inhibition of SARS-CoV-2 entry. During binding and viral fusion, all three receptor binding domains (RBD) of the spike protein fold to an upward conformation, which is necessary for binding. Inhibitory anti-SARS-CoV-2 antibodies can impede this process through competitive binding as well as mechanisms such as premature cleavage of the RBD or stabilizing a three-down conformation. We hypothesize that inhibitory antibodies can stop AME from occurring to varying degrees of effectiveness based on inhibitory mechanisms and avidity to the spike protein. To understand the dynamic between AME and inhibitory antibodies, we tested the infection levels of monocytes by SARS-CoV-2 pseudo-virus in the presence of antibodies shown to induce AME combined with varying concentrations of inhibitory anti-SARS-CoV-2 antibodies that have different mechanisms of affecting the spike RBD conformation. ELISA-based assays were also run to quantify antibody avidity to the spike protein. Analysis suggests that high concentrations of multiple neutralizing antibodies inhibit AME and that conformationally inhibiting antibodies are more effective at inhibiting AME than strongly activating ones. Studies of this type can aid in continued development of safe vaccines and therapeutics, as well as help understand how antibodies affect SARS-CoV-2 spike conformational regulation and therefore viral entry.

Many individuals living in refugee camps have limited access to soap. Ready access to soap gives refugees the ability to maintain their own hygiene. Proper hygiene helps to reduce the spread of diseases through proper sanitation, thereby increasing life expectancy–especially among young children and mothers. The goal of this research is to empower individuals living in refugee camps by giving them the ability to make their own soap. To achieve this goal, I first, identified methods for making soap with resources accessible to refugees, such as oils, sodium hydroxide, and protective gear like gloves to ensure their safety during the process. Second, I created and led two workshops to teach leaders within refugee camps how to make soap with these resources. I conducted pre- and post-workshop focus group questioning with 30 refugees to assess their beliefs, attitudes, and experiences with using soap and making their own soap. The results of the pre-workshop focus group with women living in refugee camps revealed that soap is important for their daily lives, particularly for those working in the farming field. They reported that having more access to soap would significantly contribute to an enhanced sense of self and promote a healthier community. Post-workshop focus group responses revealed that participants expressed positive feelings about learning to make their soap, and many expressed interest in experimenting with ingredients like milk or rose flowers for added fragrance. Participants also reported that they plan to test their handmade soap, and if satisfied with its quality and feel, intend to sell it in the local market. Empowering refugees to make their own soap has the potential to provide them with greater agency over their health, dignity, and self-sufficiency. It could also potentially create opportunities for income generation, which could significantly improve their lives.

A keystone bacterium involved in the pathogenesis of chronic periodontitis, commonly known as gum disease, is Porphyromonas gingivalis. Two well-studied wild-type strains, 33277 and 381 have nearly identical genomes, however, they possess different immunostimulatory capacities. Experiments in our lab have compared the interbacterial interactions of these two strains, with a focus on outer membrane vesicles (OMVs) as mediators via abundance and cargo. We have characterized differences in the abundance of OMVs between the two strains, with 381 producing more. Through a peptide degradation assay, we have determined that 381 OMVs also exhibit more protease activity than the 33277 strain. Through biofilm assays, we observed a difference in biofilm morphology, in which 381 formed a dense biofilm aggregating in columnar structures, while 33277 formed an evenly distributed biofilm. Finally, by performing protein isolation and analysis through SDS-PAGE, 381 OMVs displayed a reduction in a specific band, compared to 33277 OMVs. Our ongoing work is to optimize an outer membrane protein isolation protocol to identify the differentially loaded protein in 33277 OMVs, and any other differences in protein composition between 33277 and 381. In our work to compare 33277 and 381 wild type strains, we can further understand the mechanism behind their difference in virulence and how this contributes to pathogenicity of P. gingivalis.
 

Respiratory viruses are a major cause of mortality and morbidity in vulnerable populations. Together, Respiratory syncytial virus (RSV) and Human metapneumovirus (HMPV), are responsible for over ⅓ of serious viral respiratory infections in hematopoietic stem cell transplant (HCT) recipients. Currently, no treatments are available for RSV or HMPV in immunocompromised adults. While monoclonal antibodies (mAbs) show promise as a treatment, challenges arise, including limited efficacy when administered post-infection. Our goal was to enhance the therapeutic efficacy of a newly discovered cross-neutralizing human mAb to RSV and HMPV. We aimed to investigate whether modifying the Fc domain of the antibody could increase its binding to Fcγ receptors (FcγRs) found on different types of immune cells. Activation of FcγRs initiates important cell processes such as clearance of virus-infected cells, also known as Antibody-dependent cellular cytotoxicity (ADCC). This modification potentially makes the antibody a more effective treatment option for RSV and HMPV infections. To do this we looked at the binding kinetics and affinity of modified antibodies to human FcγRIIIa, FcγRIIa and FcγRIIb receptors using Bio-Layer Inferometry (BLI). Our data indicate that certain amino acid modifications or afucosylation of the Fc region can increase the antibody’s binding affinity to different human FcγRs. Since hamsters are an important preclinical model used to determine RSV and HMPV drug efficacy, it was important to examine the binding affinity of our human antibody to hamster FcγR’s. Our data indicate that the wild-type Fc region does bind to the homologous hamster receptors. Moreover, certain modifications in the Fc region led to increased binding to hamster FcγR’s. Together, these data indicate that modifications in the Fc region of human antibodies can increase their binding affinity to both human and hamster FcγRs. This increase in binding affinity could translate to enhanced potency in the preclinical hamster model and in humans.

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

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

In vitro cell culture models allow scientists to directly study mammalian cells outside of living subjects. The drawback is that it is challenging to reproduce physiological complexity in vitro, showing a clear need for more complex models. Our goal is to use microfluidics and 3D printed devices to produce culture models which mimic certain physiological conditions, and are thus more physiological relevant representations of how cells function in vivo. We achieve this through modeling and printing millimeter wide devices, and flowing cells embedded in a hydrogel scaffold to generate three dimensional regions Using these design principles, I developed and tested a model focused on mimicking the conditions of human vasculature. Vascular endothelial cells (ECs) experience constant shear stress due to blood flow and an oscillating hydraulic pressure due to the pumping action of the heart. These forces change both the structure and function of endothelium. My goal was to develop a model capable of being cultured under these continuous stress conditions for a period of at least 3 days. In order to do this, we needed to create a channel lined with endothelial cells that was capable of being perfused through. I accomplished this by utilizing open microfluidic hydrogel patterning to generate a region with endothelial cells surrounded by a collagen region with human fibroblast cells. I was able to create a closed channel composed of ECs capable of being perfused via syringe pump. This model will advance our understanding of how mechanical stresses impact cell functionality and vasculogenesis.

Mitosis is the fundamental biological process that ensures equal separation of genetic material during cell division. Microtubules and their associated structures in the mitotic spindle execute this partitioning by carefully aligning and separating duplicated chromosomes. Despite intrinsically variable growth rates across microtubules and stochastic assembly and disassembly phases, chromosome-bound microtubules exhibit highly coordinated behavior that drive mitosis. The basis for this high degree of synchronization is currently unknown. Previously, we used a novel dual laser trap assay to show that microtubule pairs growing in vitro are coordinated by mechanical coupling (Leeds et al. 2023). A simple model incorporating both force-dependent pausing and growth speed heterogeneity explains the measured coordination of microtubule pairs. Our findings illustrate how microtubule growth may be synchronized during mitosis and provide a basis for modeling multiple microtubules in a bundle. In this project, we expand on the techniques we used with the dual optical laser setup and combine them with a cutting laser to induce disassembly in our microtubules. Studying the coordination of shortening microtubules encompasses a broader spectrum of microtubule dynamics and sheds light on other aspects of microtubule regulatory mechanisms. We can then extend our model to include the degree by which mechanical coupling can coordinate microtubules in disassembly in addition to growth. Bundles of multiple microtubules are in mixed states of shortening and growth while executing the coordinated motion necessary to drive mitosis, so understanding how mechanical coupling affects disassembling microtubules gives insight into the complete picture of the mechanisms behind their synchronous motion essential for life.

The nervous system is composed of two major cell types, neurons and glia. While previously regarded as passive support cells for neurons, glia’s active roles in nervous system development and function have recently gained appreciation. Glia have elaborate cell shapes across which they asymmetrically localize neuron-regulatory proteins. Thus, to fully understand glial roles in nervous system dynamics, we must determine how glial morphology and polarity are regulated. To investigate this, we use the amphid sheath (AMsh) glia of Caenorhabditis elegans. AMsh glia exhibit apical-basal polarity, with apical-protein-marked membranes contacting neurons at the cell’s anterior, and basal membranes extending posteriorly toward the cell body. A striking feature of the apical membrane is a discrete projection within the anterior glial process, which we term the Glial Apical Boundary or “GAB”. We find that the GAB localizes many glial cues which regulate neuronal properties. Upon comparing GABs of different apical proteins expressed by a single cell, we discovered they all overlayed. However, GABs of bilateral glia can be out of register, suggesting that the GAB is independently localized on a cell-to-cell basis. Because AMsh glia derive from neuroepithelial progenitors, we then asked if mechanistic regulation of the GAB is analogous to that of epithelial apical domains. Surprisingly, canonical epithelial polarity regulators PAR-3 and PAR-6 do not localize to AMsh apical membranes. Furthermore, junctional markers AJM-1 and DLG-1, which demarcate epithelial apical-basal domains, are absent either from the GAB or from the cell altogether. RNAi knockdown of these and other polarity genes does not impact GAB integrity or morphology. Thus, the GAB is a novel polarity feature of AMsh glia not governed by canonical apical-basal polarity mechanisms. Our current work focuses on elucidating how the GAB develops and is maintained, with overall importance to understanding how glia localize regulatory proteins in health and disease.

Gravitational waves (GWs) are ripples in spacetime propagating outward from a source at the speed of light. Compact astrophysical objects such as rapidly spinning neutron stars that have miniscule “mountains” on their surfaces are expected to produce continuous gravitational waves (CWs) that are persistent in time. Detecting CWs would be revolutionary, providing new information about the properties of neutron stars. The expected CW signal is mimicked by background noise from some environmental and instrumental sources, so detecting them using the Laser Interferometer Gravitational Wave Observatory (LIGO) is a challenge. We can improve the detector sensitivity by mitigating the instrumental noise. In this project, my goal is to identify how individual frequencies of instrumental noise change in response to changes in components of the detector. Given a known change in a detector component, I analyze how the noise artifacts change around the time of the component change. Averaging over time and taking the ratio of the spectrum after the change to the spectrum before the change reveals changes in individual frequencies, which I can identify and monitor for changes day-by-day. Results of this study highlight correlations between the reduction in particular frequencies of noise and particular changes in detector components. In this ongoing investigation, I find that several combs of equally spaced frequencies are significantly and persistently reduced in magnitude on the same day as an electric bias flip on the test mass at the end of a detector arm, so the electric components of test masses seem to contribute some noise. By identifying another source of instrumental noise, this study helps scientists more clearly distinguish between noise and astrophysical signals, increasing the sensitivity of LIGO to CWs.

Mount Rainier National Park (MORA), also known by several indigenous names including Tahoma, has over a hundred alpine wetlands, each playing an essential role in the ecosystems’ hydrology and providing habitat to several species (National Park Service, 2023). Due to a changing climate, wetlands and their surrounding ecosystems are at risk, potentially threatening these critical habitats and species that rely on them. This research aims to quantify surface water and land cover changes to ten National Park Service designated high priority wetlands and their surrounding areas over a 39-year period. Landsat satellite imagery was used in a spectral mixture analysis to examine the wetness and change in fractional cover of trees and meadow vegetation of the surrounding habitat. The analysis indicates that within a 500-meter buffer of the wetlands, meadow vegetation is decreasing and tree cover is increasing. In addition, surface water area is increasing in wetlands at higher elevations, and decreasing in wetlands at lower elevations. Wetlands in Mount Rainier National Park are experiencing significant shifts in surface water across the elevation gradient, as well as changes in their surrounding habitats. This research provides park stewards with critical information on changing wetland ecosystems to make informed decisions when managing these habitats moving forward.

At 1:44 PM EST on March 11th of 2020, Trump tweeted that he would be “addressing the nation” at 9 PM EST that same day. This oval office address was a statement on COVID-19 and what the pandemic meant for America. This research is a rhetorical analysis of Trump’s public address on that day. His speech, already given in a time of uncertainty, led to widespread panic amongst consumers, with U.S. stocks falling the next day by almost 10%, in their worst day since the 1987 crash. News outlets and economists reported that the uncertainty that came along with the pandemic was only worsened because of Trump’s fear stoking and the atmosphere of uncertainty this speech created. What were people reading in the speech that could have pushed them towards this economic behavior? Conducting a rhetorical analysis of the speech through an innovation on the textual-intertextual method, this paper analyzes Trump’s speech and what people and the Trump administration said in response. In the first part of the paper, close textual analysis allows us to have an in-depth, microscopic understanding of the speech itself. In the second part of the thesis, we examine intertextual evidence of the speech’s extrinsic effect. Reading secondary sources that explicitly mention the primary text, including those produced by audiences hailed by the text as well as by Trump and his proxies, we can understand its broader reception especially as it relates to investor behavior and consumer attitudes. This study finds that Trump’s lack of key information, sparse emphasis on international cooperation, and contradictory rhetoric towards public officials all help explain the economic uncertainty that resulted from this speech. Studying the relationship between rhetoric and the economy through this research has implications on presidential rhetoric, unsuccessful early pandemic communication and the factors influencing stock price volatility.

Pulmonary Arterial Hypertension (PAH) is a deadly vascular disease, affecting the blood vessels of the lungs rather than the systemic circulation, with no existing cure. PAH is characterized by pulmonary arterial smooth muscle cell (PASMC) hypertrophy and hyperplasia, which increases resistance to blood flow within the pulmonary arteries and leads to rapid symptom progression and death from right heart failure over several years. We hypothesize that defects in PASMC differentiation and alignment may contribute to PAH. Prior work has shown that micropatterned scaffolds encourage vascular SMC alignment and differentiation towards a contractile phenotype. To test whether these responses differ in patients with PAH, we designed a micropatterned collagen scaffold atop a glass coverslip. Scaffoldings were imprinted with either alternating 10-µm wide x 10-µm deep microchannels or left unpatterned. Explanted PASMCs from patients with PAH or failed donors (controls) were cultured on patterned versus unpatterned constructs and alignment, protein expression, and cellular morphology were compared across conditions. I evaluated 3 PAH and 3 control subjects and have collected preliminary data for each condition (control versus PAH), with three technical replicates each. Through these preliminary studies, I have demonstrated success of my model with consistent alignment observed on patterned substrates. Excitingly, PASMCs from patients with PAH expressed significantly decreased levels of the contractile protein, Calponin, when compared with control cells, including after responding to cues that promote alignment and contractility. This suggests that PAH PASMCs remain in an inappropriately synthetic or proliferative state. Subsequent testing will include assessment of calcium signaling in response to contractile stimuli and transcriptomic evaluation of cellular responses to micropatterning. This work will enhance understanding of whether SMC abnormalities contribute to disease initiation and progression in PAH and will contribute to the broader effort of developing more complex models of pulmonary vascular disease.

There is a strong need for rapid and inexpensive tests for monitoring human immunodeficiency virus (HIV) drugs to prevent treatment failure. The REverse TranscrIptase Chain Termination (RESTRICT) Assay provides fast and inexpensive measurement of HIV reverse transcriptase (RT) inhibitors by measuring the extent of DNA synthesis with the HIV RT enzyme in the presence of a patient’s blood. RESTRICT uses an intercalating dye, PicoGreen, to provide fluorescence as a function of the amount of DNA synthesized. However, PicoGreen interrupts DNA synthesis and binds to any double-stranded DNA (dsDNA) present in the sample including background DNA in blood samples, precluding real-time measurements and potentially decreasing the accuracy of results. This project uses RESTRICT in conjunction with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) complexes and reporters to accurately measure RESTRICT results in real-time. Fluorescence is produced by reporters which are made up of a quencher and a fluorophore. When the CRISPR complex detects a specific complementary sequence formed from the single-stranded DNA (ssDNA) template, the Cas enzyme is activated and cleaves the fluorescent reporter. Once cleaved, the fluorophore is released from the quencher thus generating fluorescence. Because the CRISPR complex binds only to specific segments of DNA produced by RESTRICT, we can obtain more specific results without interference from background DNA. In addition, CRISPR complexes and reporters do not interfere with DNA synthesis and can be added at the same time as other RESTRICT reagents, enabling real-time monitoring of RESTRICT reactions. Using a portable fluorescence reader (T8-ISO, Axxin Pty Ltd.), positive control reactions containing RT enzyme provided at least 5X more fluorescence than negative controls without RT. Future work will focus on measuring clinically relevant levels of HIV drugs in aqueous buffers using RESTRICT with CRISPR readout.

Knee meniscus tears are common musculoskeletal injuries that have difficulty healing on their own and usually require surgery. Surgical interventions and other available treatments such as allografts often fail to restore the function of damaged tissue resulting in the need to develop effective therapies. To do so, it is necessary to develop models that further investigate mechanisms of regeneration in the meniscus. A major component of the meniscus is the extracellular matrix (ECM), which contains various proteins that provide structural and biochemical support and chemical and mechanical cues to the cells. Its mechanical properties are known to affect crucial regeneration processes such as growth, proliferation, and differentiation. To model the mechanical environment of the meniscus, our lab utilized a pentanoate-functionalized hyaluronic acid (PHA) hydrogel system and cultured meniscal fibrochondrocytes (MFC), the cells responsible for regulating the biomechanical properties of the knee meniscus. Our lab has previously shown modulating the degrees of substitution (DOS) of the reactive-ene groups in the hydrogel controlled compressive moduli and preliminary data indicated possible control of viscous responses. Expanding from this, I predict that tunable viscoelastic properties can be created by using the system above with crosslinked and un-crosslinked HA. Ideally this scaffold will mimic the viscoelasticity properties of native menisci ECM. I aim to build upon previous research by considering creep and stress relaxation responses (time dependent increases in strain or decrease in stress respectively) which are crucial to preventing cellular confinement and encouraging regeneration. By using mixed ratios of crosslinked and un-crosslinked HA in the hydrogel system to control ECM viscoelastic properties, we predict that we will be able to control MFC behaviors such as morphology. Ultimately, the knowledge of viscoelastic properties’ impact on MFC behavior will contribute to the development of regenerative therapies for meniscal tears.

Perineuronal nets are extracellular matrix structures comprised of chondroitin and dermatan sulfate-glycosaminoglycans (CS/DS-GAGs). Histological imaging of brain PNNs is achieved using Wisteria floribunda agglutinin (WFA) labeling of PNN CS/DS-GAGs, while composition can be determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Although these methods are used to determine PNN CS/DS-GAG abundance and composition, it’s unknown whether brain fixation or processing influence these outcomes. We first explored whether tissue processing, using cryosectioning (CRYO) or paraffin embedding (PE), influence PNN analyses. Ten mice were perfused with PBS and post-fixed in 4% paraformaldehyde (PFA). Brains were cut sagittal, and one hemisphere was prepared as floating tissues (CRYO) and the second hemisphere was processed as direct mounted tissues (PE). Histochemical analyses show a 78.9% reduction in hippocampal WFA+ PNNs in the PE processed hemisphere compared to CRYO processed side. LC-MS/MS analysis of hippocampal CS/DS isomers also showed differences between each method. In a second cohort of mice, we determined that fixative (4% PFA vs 10% formalin) did not influence hippocampal WFA or CS/DS isomers between groups, suggesting tissue processing (not fixative) influences PNN analyses. We then explored whether we could correct for these CS/DS baseline differences. By comparing CS/DS isomers isolated from CRYO vs PE processed tissues within each mouse, we discovered reproducible correction factors for each isomer. Adjusting the CRYO group using these factors normalizes baseline compositional differences between CRYO and PF groups. To determine translational relevance, we compared hippocampal CS/DS isomers between three CRYO vs PE prepared non-human primate (M. nemestrina) tissues and observe similar baseline CS/DS differences. Adjusting the CRYO prepared group using corrections factors normalizes the baseline composition. These results provide strong, translational evidence that tissue processing greatly influences both PNN glycan histology and composition analyses, and that corrections must be made to account for baseline differences before comparing groups.

Hypoxic ischemia (HI), the loss of blood and oxygen to the brain, is a common cause of neurological impairment and mortality. Astrocytes are one cell type that responds to acute trauma like HI and modulate the vascular-brain interface via their role in maintaining the blood-brain barrier (BBB). Therefore, astrocytes can be a potential therapeutic target; however, to screen methods to target astrocytes, there is still more to be discovered about astrocyte behavior in response to different stimuli. Towards this goal, this project aims to (1) create a robust and detailed characterization of cultured astrocytes over time, (2) evaluate astrocyte changes to different culturing conditions, and (3) measure the uptake of polymer nanoparticles, commonly used as drug delivery systems, on stimuli exposed astrocytes. My results show that after isolation, astrocytes are initially evenly distributed and form snowflake clusters, collectively assuming a star-shaped morphology. Over time, individual astrocytes move away from clusters and independently adopt the characteristic star shape. This suggests a dynamic process wherein astrocytes exhibit both collective and individual behaviors, contributing to the intricate architecture of astrocyte growth. Additionally, changes in the ratio of glial cells were observed. While microglia decreased in number and became less branched over time, oligodendrocyte populations remained relatively stable over time. Neurons that were initially sparse in the population decreased rapidly over time. Current studies involve the application of polymer nanoparticles to oxygen-glucose deprivation (OGD)-exposed cells immediately after OGD to evaluate uptake via imaging co-localization of particles with cells; OGD exposure induces HI injury in vitro. I have confirmed astrocyte response to OGD by analyzing cell morphology using imaging and cell viability assessments. These studies will establish an in vitro astrocyte model of HI and enable future studies incorporating additional BBB cells and other therapeutic platforms.

Burnout presents a significant challenge for mental health clinicians, affecting not only their well-being and turnover rate but also the quality of care provided to clients. Moreover, studies have shown that clinicians working in community settings face more burnout compared to those in private practice. Among the factors that have been implicated in clinicians’ burnout are the level of education, limited experience and training opportunities, individual variables, and demographic factors. In this study, I examined how clinicians’ reported competencies in core cognitive behavioral therapy (CBT) skills for treating anxiety, depression, trauma, and behavioral concerns are associated with their experiences of burnout. I further evaluated whether the relationship between competencies in core CBT+ skills and experiences of burnout is moderated by CBT+ training. The study draws on a diverse sample of 200+ community mental health clinicians who took part in Washington State’s CBT+ training initiative. I employed t-test and multiple regression models to analyze the data. Based on these analyses, there are anticipated insights of uncovering clinician experiences in how clinicians’ level of CBT skills and professional training experiences intersect with burnout. Findings are expected to inform targeted interventions aimed at reducing burnout and enhancing clinician retention across the workforce.

Tooth decay is a public health challenge that disproportionately impacts Indigenous populations. The main risk factor for pediatric tooth decay is added sugar intake. This study was part of a community-based clinical trial aimed at reducing sugared fruit drink intake among Yup’ik Alaska Native children by introducing families to sugar-free fruit drinks, and sought to collect caregiver feedback on various components of the intervention. Our team administered a 14-item semi-structured interview script to caregivers during their 6-month and 12-month study visits. I inductively analyzed the data, classified the data into categories, and further organized these categories into domains: opinions about sugar-free Kool-Aid (SFKA), accessing SFKA, and thoughts about the SFKA program among the intervention arm. This feedback will be used to redesign the intervention for the delayed-treatment control group, which is currently receiving a modified version of the intervention. The long-term goal is to develop a sustainable, scalable intervention that can help reduce sugar intake in Alaska Native communities.
 

Spasticity is an increase in muscle tone (hypertonus) and abnormal muscle stiffness that impedes functional activity. Oftentimes observed among individuals with chronic neurological conditions such as traumatic brain or spinal cord injury (SCI), spasticity develops as a result of damage to the central nervous system (CNS). This damage disrupts the balance of supraspinal inhibitory and excitatory inputs to the spinal cord, which can lead to the loss of inhibitory inputs and hyperexcitation of the spinal reflex arc. The aim of this project is to develop an electrical stimulation protocol that regulates imbalances of supraspinal input and the spinal reflex in order to potentially alleviate spasticity caused by traumatic neural injury in patients. The hyperexcitation associated with spasticity is measured using the Hoffman-reflex (H-reflex). Previous studies have revealed that electrical stimulation of the rat motor cortex can modulate long-term spinal excitability. In this study, behaving noninjured Long Evans rats are implanted with cortical implants to induce stimulation to the motor cortex, grounding electrodes to filter environmental noise, cuff electrodes to evoke the H-reflex, and EMG electrodes to record the H-reflex response. The H-reflex is assessed by stimulating a cuff electrode surrounding the median nerve and measuring the consequent activity of EMG electrodes that are implanted into the flexor, extensor, and tricep muscles before and after electrical stimulation of the motor cortex. Our preliminary results indicate that different frequencies of cortical stimulation can modulate the H-reflex, suggesting that our novel cortical stimulation protocol may reduce spasticity and promote restoration of motor function. In future studies, I plan to assess the efficacy of cortical stimulation for improving spinal excitability in spastic animals following chronic SCI.

Retinoic acid-inducible gene (RIG-I) receptors (RLRs) are pathogen recognition receptors (PRRs) that play a major role in innate immune defense against RNA virus infection. RLR RIG-I and melanoma differentiation-associated protein 5 (MDA5) interact with viral RNA ligands in the cytoplasm via their N-terminal caspase recruitment domains (CARDS) to modulate antiviral immunity during an infection. Activated RLRs then signal through mitochondrial antiviral-signaling protein (MAVS) to stimulate the production of type 1 interferon (IFN). IFN upregulates transcription of interferon stimulated genes (ISGs) which encode proteins implicated in inducing an antiviral state to eliminate invading viruses.
Herein, we continue the evaluation of RLRs and their subsequent signaling partners in response to viral infection. To this aim, we utilize West Nile Virus (WNV), a neurotropic virus belonging to the Flaviviridae RNA virus family and commonly used to model positive sense RNA viruses and their role in RLR induced immunity. Two strains of WNV, WNV Madagascar (WNV MAD) which is attenuated in mice and WNV Texas (WNV TX) which is virulent in mice are used. The results demonstrated that the RLRs, specifically RIG-I, are significant contributors to the difference in virulence of pathogenic WNV TX and the non-pathogenic WNV MAD strains. Replication kinetics in knockout immunocompetent cell lines demonstrate that primarily RIG-I signaling through MAVS, not other RLRs (MDA5), restrict viral replication of WNV MAD but WNV TX in cell culture models. We also show the role of RIG-I and its restriction of WNV MAD intracellular viral protein accumulation. The specific mechanism of the restriction of WNV by RLR signaling is further elucidated, specifically the role of IFN in our cell culture model. Further studies will allow for the development of small molecule inhibitors or treatments that may aid in the prevention of severe disease caused by positive sense viral pathogens.

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

As the climate changes, we are beginning to see the impacts on a global scale. In order to understand how our landscapes will change with future warming, we can look back to see how landscapes were impacted by past warm, variable climates. This project looks to understand how climate variability in the Middle Miocene is expressed in terrestrial sedimentary records. Using X-ray fluorescence (XRF) analysis, we created a high-resolution elemental geochemical profile of sediment samples from Clarkia, ID (~16 Ma). From XRF, elemental concentrations for a host of elements, including Ca, Fe, K, Mn, Sr, Ti, Zn, and Zr, were calculated. Some elements, notably Ca, showed long-term trends but also sections of shorter-term cyclic variability. It is possible that this variability reflects changes in basin weathering rates of Ca-bearing minerals as a function of climate change occurring on timescales of tens to hundreds of thousands of years. Alternatively, Ca concentrations may reflect changes to precipitation of Ca-bearing minerals within the ancient lake, responding to algal productivity. These hypotheses are tested using X-ray diffraction (XRD) to identify minerals and their crystalline structures as well as characterizing the elemental trends from an additional site, Clarkia’s P-40. Understanding the depositional history of the Clarkia lakebeds aids our understanding in how climate impacts Miocene landscapes.

It is well documented that women are predisposed to various musculoskeletal injuries, including hip labrum, Anterior Cruciate Ligament (ACL), and meniscus tears. Literature has detailed the regenerative potential of human mesenchymal stromal cells (hMSCs), and clinical trials have confirmed their medicinal application within tissue repair and healing, particularly in the musculoskeletal system. hMSCs are commonly used in the field of tissue engineering due to their immunomodulatory capabilities, differentiation capacity, and autograft availability. Across the lifespan, cells in male and female bodies experience varying levels of estrogen exposure, which elicits different responses. During in vitro cell culture, cells are typically exposed to sources of exogenous estrogens, including phenol red and fetal bovine serum (FBS). Although these additives are commonplace in the practice of cell culture, little research has been done to understand the impact of these additives on hMSCs in in vitro cultures, especially among female hMSCs. To investigate these cellular responses, we studied the impact of these estrogen-mimetic media components on cell proliferation and metabolism in vitro for hMSCs derived from male and female donors. Specifically, we investigated phenol red, which is shown to behave as an estrogen, and FBS, which naturally contains 17β-estradiol (E2). We hypothesized that estrogen-mimetic compounds would be associated with an increase in cellular proliferation and metabolism in a sex-dependent manner. These results clarify the response patterns of male and female hMSCs due to exogenous estrogen exposure, improving our sex-specific understanding of their potency for in vitro studies and regenerative medicine applications.

BK channels are potassium channels activated in response to depolarization and elevated intracellular calcium ion levels. It has been observed that BK channels form clusters in cells, but the mechanism for clustering has not been characterized. This project attempts to discover important components that lead to BK channel clustering using super-resolution microscopy, proximity ligation assay, and Fluorescence Recovery After Photobleaching (FRAP) experiments. One possible mechanism relates to denser regions in the plasma membrane of PtdIns(4,5)P₂ as a possible lipid raft, hypothesized to localize proteins. We used tsA-201 cells to express BK channels (α subunit). In FRAP experiments, BK channels were tagged with a green fluorescent protein (GFP). To modify the levels of PtdIns(4,5)P₂, we co-expressed PIP5Kγ, the enzyme that catalyzes the synthesis of PtdIns4P to PtdIns(4,5)P₂. Expression of PIP5Kγ is known to increase PtdIns(4,5)P₂ levels by 30%. In our analysis, we assumed that large, bright fluorescent dots in live cells correspond to BK clusters. We found that co-expression of PIP5Kγ with BK decreases cluster size by 43% in super-resolution experiments and increases the number of puncta (BK clusters) by 41% in PLA experiments. FRAP experiments on a PIP2 biosensor, PH-PLCδ1-GFP, showed reduced fluorescence recovery speed when PIP5Kγ was co-expressed. Future FRAP experiments observing BK channels will allow us to determine if membrane components, such as PtdIns(4,5)P₂, influence the integrity and mobility of BK clusters and if the addition of these lipids is sufficient to induce additional cluster formation. 

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

Long-term neonatal intensive care unit (NICU) hospitalizations are emotionally and financially stressful for families. While family presence at the bedside and active involvement in their baby’s care have been linked to healthier outcomes, many families are unable to visit regularly. As technology continues to advance, live-streaming video platforms have been utilized in many NICUs to address the limitations of in-person presence. As the parents are able to continuously connect with their baby virtually, this allows for increased bonding with the newborn and engagement with the patient care team. The extended family and friends can interact with the infant as well. The objective of this study was to describe the utilization of the Seattle Children’s Hospital (SCH) NICU virtual visit program and its effectiveness in maintaining or increasing caregiver and patient bonding during the infant’s hospitalization. This was done through a program evaluation using mixed methodology with a parent survey and interviews. Parents and caregivers of NICU patients who used the virtual visits at least once during a patient's hospital stay were recruited using phone calls and text messages with the link to the survey. The virtual visit call frequency, time, and number of visitors were reviewed. The results showed that from July 2021 to December 2023, there were 348 virtual visits since July 2021, most of them lasting over 20 minutes (median 23.5, IQR range 3, 68.5). Most participants used the program one to two times (range min 1, max 69). Many of the calls occurred between 7 am - 7 pm with one to two attendees. In conclusion, the virtual visits program was utilized frequently and the timing of the virtual visits overlapped with the availability of the primary healthcare team which may have supported active involvement in care. The parent surveys and interviews about the program’s impact are in progress.

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

Down syndrome (DS), a chromosomal condition that affects 1 in 700 babies in the United States, is associated with intellectual disability and delays in motor development. Early intervention can support motor and social development and participation in children with DS. While both Partial Body Weight Support (PBWS) systems and enriched play environments have been shown to enhance development and participation in children with DS, few studies have looked at these interventions in combination. The purpose of this study was to explore the benefits of a PBWS harness system within an enriched play environment on the mobility and social exploration of infants with DS. Our team hypothesized that PWBS would lead to a greater percentage of time engaged in both mobility and social behaviors during play. We conducted a multi-site clinical trial with 15 pre-walking infants with DS. The infants and their caregivers participated in 30-minute play sessions within an enriched 9’x9’ indoor play area with standardized toys 3 times a week for 6 weeks. Children used a PBWS harness for 3 of the 6 weeks, with harness/no harness order randomized for each participant. All play sessions were recorded and a subset of 6 participants’ data were analyzed using an adapted version of the CASPER-III coding scheme. Results showed that on average, infants showed a 5.28% increase in motor activity when using the PBWS harness compared to a 4.11% increase in motor activity when not using the harness. Additionally, when using the harness, infants on average showed an 8.99% increase in social activity whereas they showed a 0.07% decrease in social activity without the harness. These results show promise in facilitating greater access to mobility and exploration opportunities for children with DS using low-tech interventions such as PWBS in enriched play environments.

Social connection is fundamental to human well-being, encompassing mental and physical health, and overall quality of life. The importance of forging deep, meaningful relationships is a key focus within relationship sciences. Evidence from 140 studies highlights the significant impact of loneliness on health, equating its risk to that of severe health behaviors and conditions, such as heavy smoking. This underscores the essential role of close relationships in maintaining health. The process of building these relationships, according to relationship sciences, involves mutual disclosure and perceived responsiveness. While extensively studied in individual interactions and laboratory settings, group dynamics remain less explored. Functional Analytic Psychotherapy (FAP), a treatment developed at the University of Washington that is practiced by clinicians worldwide, indicates that relationships strengthen when vulnerable disclosures are met with validating and compassionate responses. The principles of FAP, distilled into the concepts of Awareness, Courage, and Love (ACL) are now being disseminated to the general public through the ACL relational model. A randomized-controlled pilot study with 10 participants evaluated the impact of a three-week ACL group intervention on depression in a clinically depressed sample, using the Montgomery–Åsberg Depression Rating Scale for assessment. The intervention, focusing on exercises in self-disclosure, reflection, and compassionate response, demonstrated promising results. Participants showed significant reductions in depression symptoms and increased self-compassion compared to a control group engaging in self-guided, personally meaningful activities. This study indicates the potential of ACL group interventions in enhancing self-compassion and alleviating depressive symptoms, highlighting the importance of supportive group dynamics in mental health improvement. The findings advocate for the integration of relationship-focused practices in mental health interventions, emphasizing the value of vulnerability and mutual support in fostering psychological well-being.

Seattle is known to be infested with invasive rodents such as the Norway rat or the roof rat; both of which are considered public health nuisances, causing damage to the built environment, carrying zoonotic diseases, and causing overall mental unrest as a communal species. This project collected community-level data using two urban rodent survey (URS) methodologies: The Centers for Disease Control (CDC) URS methodology, which focuses on identifying causative conditions for rodents, and a newer method, Indexing, which focuses on active rodent surveillance. We surveyed census tracts spanning the University of Washington Seattle campus, UDistrict, and Ravenna neighborhoods using both URS methodologies. We then assessed the effectiveness and efficiency of both methods in determining the severity of rodent infestation within these communities. The data collected was used to inform a URS classroom model for ENVH 442, Zoonotic Diseases and their Control, offered by the Department of Environmental and Occupational Health and Safety at the University of Washington Seattle. In addition, this project was shared with the Public Health Seattle & King County Rodent Control Program, to help inform their work on active rodent surveillance in the city of Seattle.

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

About 400 million to one billion years after the Big Bang, radiation from the earliest light sources began to ionize the neutral hydrogen gas that filled much of the universe. Data from this era, which is known as the Epoch of Reionization (EoR), provides constraints on our models of structure formation and evolution of the early universe. One of the instruments currently being commissioned for this purpose is the Hydrogen Epoch of Reionization Array (HERA). Located in South Africa, HERA is a radio telescope that uses a large array of antennas to study the large-scale structures of the universe during the EoR. My work has been focused on validating the instrument while it is being built by analyzing systematics present in the data as well as calibration solutions. Most recently, I've been focused on validating the HERA data processing pipeline. One of the major challenges with studying the EoR is that the radiation from this era is extremely faint in comparison to foreground radiation from other sources in the sky. In order to isolate the EoR signal, the radiation from other sources on the sky must be subtracted from the total signal. Calibration solutions, which give solutions to an equation for correcting instrumental effects, are one of the key pieces in this process. HERA is backed by an international collaboration that has built a bespoke data processing pipeline; by comparing the plots of the calibration solutions, I've been able to help validate that the results from the HERA pipeline hold up against results from the Fast Holographic Deconvolution (FHD) pipeline, a well-established, open source pipeline for processing radio interferometric data. This furthers our confidence in our results while ensuring any potential issues are addressed before the telescope is fully completed.

Music box, invented in the 18th century, has been reimagined by the design industry as an interactive and assembly-friendly toy product. This innovation serves as a seamless integration of a nostalgic object with the demands of contemporary life experience. However, such "packaged in box" products face significant customization limitations from the user's perspective, including fixed music options and predetermined model parts. Given the burgeoning resources in digital modeling and rapid prototyping, the product design process is poised to advance into the computational fabrication era. Our interdisciplinary student team has been re-envisioning the structure and functionality of our music box through programming, Computer-Aided Design, and 3D printing. Specifically, our team developed the three parts to construct the music box: a digitally constructed spinner, where its 3D model was transformed from MIDI file, allowing for a wide range of musical expression; an adaptable mechanical connection structure for spinners of various sizes; and an innovative mechanism that triggers keyboard notes without direct spinner contact, maintaining sound quality and reducing wear out plastic parts. These designs enable customizable features, easy part replacement, and solve sound and durability issues associated with plastic components. With the goal of creating a customizable product in mind, each member of our team contributed to and took responsibility for the components in which they specialized. The purpose that our music box serves does not stagnate as a mere music playback machine; rather, its functionality expands across various aspects. Our innovation is not only ideal for those who wish to integrate artistic perspectives with functional machine prototyping and customize their songs , but also boosts creativity for individuals and institutions, enabling further projects that could benefit early education and future engineering workshops.

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

Agricultural workers (AW) work on fields planting, maintaining, and harvesting food crops for the United States (US). Agriculture is one of the most hazardous occupations in the US. Some of the hazards that AW are exposed to daily are unsanitary work conditions, fall hazards, exposure to chemicals, pesticides, or other extreme conditions. Furthermore, only some states provide workers’ compensation benefits to AW. Workers’ compensation provides benefits to employees who suffer from a work-related injury and ensures that they receive compensation for health care and for lost wages while they recover. Legal epidemiology methods were used to develop coding questions to measure how 39 states across the US include or exclude AW in their workers’ compensation laws from January 1, 2001, to December 31, 2017. The legal text (law) was collected from WestLaw for each state to answer coding questions. We then coded each state depending on the inclusion of agricultural workers in the workers’ compensation laws. Thirty-nine states were included in the study, and they all had a state-level workers’ compensation law. States were coded into categories: “yes, all AW are included” (all AW are included in workers’ compensation benefits), “yes, some AW included” (some exemptions for certain AW like small employers), “optional for employers to include AW” (there are exclusions for AW but there’s options for employers to opt in), and “no, AW are excluded” (AW are explicitly excluded from workers’ compensation coverage). Ten states were coded as “yes, all AW included,” 15 states as “yes, some AW included,” eight as “optional”, and two states excluded AW from workers’ compensation coverage. This study demonstrates that not every state provides workers’ compensation benefits to AW despite it being a hazardous occupation in addition to them doing essential work that provides food for the US.

Bacteria face a variety of threats, including antagonistic killing by other bacteria in competition for space and resources. In response to this antagonism, many bacteria have evolved specific defense systems. One pertinent example is the Pseudomonas aeruginosa Response to Antagonism (PARA) in P. aeruginosa, which provides defense against various antagonists by activating a suite of genes, mediated by two-component pathway Gac/Rsm, in response to kin cell lysis. The Gac/Rsm machinery is conserved across the Pseudomonas genus, but its function in defense has not been studied outside of P. aeruginosa. Here, we investigate whether two divergent Pseudomonas species, P. putida (KT2440) and P. protegens (Pf-5), similarly use Gac/Rsm in defense. To do this, we performed competitive growth assays against an antagonistic competitor, Enterobacter cloacae, comparing Gac/Rsm deletion mutants against wild-type, and quantified relative survival as an indicator of competitive fitness. Preliminary data indicate that the deletion of the core Gac/Rsm gene gacS results in dramatically decreased competitive fitness for Pf-5, but not for KT2440. This indicates that Pf-5 uses the Gac/Rsm system in a similar manner to P. aeruginosa and that, while Gac/Rsm is conserved, it may differ in function between species. To identify additional specific genes involved in defense systems, we set up a genome-wide screen. The screen indicated that genes related to the flagellum and lipopolysaccharide biosynthesis may be involved in defense against antagonism, which was surprising because these well-characterized structures have never before been implicated in defense. Work is currently underway to validate these genes as true defense factors and determine the mechanism by which they confer survival. Our findings advance the understanding of defense systems among Pseudomonas species by shedding light on their conservation and complexity, thus providing a foundation for future work on defense systems across bacterial phyla.

In recent years, screen time has become an integral part of daily life for people of all ages, whether that be using social media, entertainment apps, or engaging in various online activities. However, many researchers worry that too much screen time may have negative impacts on one’s well-being, especially when it comes to adolescents and to young adults. This study analyzed the impacts of screen time on college students’ social well-being. The Social Model of Well-Being Scale (Keyes, 1998) was distributed online through Qualtrics. The survey also asked participants to report their average daily screen time and which category their most used application falls into (social media, entertainment, creativity, information and reading, etc.). We hypothesized that higher screen time would negatively impact college students’ social well-being. Participants were aged 18-64 and were students at a public 2-year college in the Pacific Northwest. Participants were recruited through voluntary sampling via recruitment posters around campus and through several psychology professors offering extra credit for participation in the survey. As data collection is still ongoing through the winter, the preliminary results (N = 166) revealed that the average social well-being score was 41.56 (SD = 7.28) with a range of 18-64, with higher scores indicating a greater sense of social well-being including social integration, acceptance, contribution, and cohesion. Cell phone use ranged from 30 minutes to 20 hours a day, with an average of 5.73 hours per day. 63% of the sample also reported social media as their most used application. Our findings will provide insight into the mental health of 2-year college students as it relates to screen time. This information may aid in the development of on-campus resources to decrease screen time and increase social well-being.      

Spinal cord injury (SCI) causes significant sensorimotor deficits that negatively impact autonomy and quality-of-life. In a previous study, we determined that optogenetic spinal stimulation significantly enhanced forelimb recovery, axonal growth, and angiogenesis compared to sham controls. However, we have yet to determine the synaptic changes associated with optogenetic stimulation after SCI. The current project addresses this important detail by quantifying the synaptic changes that occur with and without optogenetic spinal stimulation in rats with cervical SCI.To investigate this, rats received a moderate hemicontusion of the 4th cervical segment (C4) and a spinal injection of an optogenetic viral vector (AAV2-hSyn-ChR2-YFP) to express light-sensitive proteins in the ipsilateral sixth segment (C6). Four weeks later, rats received a second surgery to receive a blue uLED implanted over ipsilateral C6 for optogenetic or sham stimulation. Rats were trained and scored regularly on a variety of forelimb behavioral tasks throughout the course of the study, while the rats in the stimulated group received stimulation 1x/week for 6 weeks beginning on the 6th week post-injury. After perfusion, the cervical spinal cord was sectioned and underwent immunohistochemistry (IHC) staining to examine synaptic density around motoneurons caudal to the lesion site where stimulation or sham stimulation occurred. Synaptic quantification has been completed using FIJI software. Our initial results reveal increased synaptic density around the motoneurons of rats that received optogenetic spinal stimulation, suggesting an increase in synaptic plasticity and connectivity. This indicates that stimulation not only enhances axonal growth but also supports the formation of new connections with downstream neurons partially disconnected by the injury. This study provides insight into the circuitry-related changes involved in SCI recovery. Identifying specific mechanisms of how optogenetic stimulation improves recovery can guide the development of more effective stimulation paradigms and treatment strategies in order to optimize functional recovery for people with spinal cord injury

Chlorophyll, a green pigment found in plants, algae, and cyanobacteria, is responsible for catching light during photosynthesis and converts it to chemical energy that is vital for organisms to grow, reproduce, and survive. Preliminary work has shown that periodic ocean heat waves have impacted the concentration of chlorophyll measured in sediments of the Salish Sea. Bed sediments from the Salish Sea were analyzed using fluorescence. Specifically, I am analyzing the 2018 Puget Sound Ecological Monitoring Project Sediment Survey samples. Preliminary results for chlorophyll concentration ranged from 9.14x10^4 - 1.59x10^6 cfu with an average of 7.89x10^5 cfu. The outcomes of this project will be used to connect how climate-related factors may affect habitat health through monitoring chlorophyll a concentration in bed sediments. Future investigations will include connecting results to a time series of known warming anomalies in the Salish Sea.

 After someone suffers from a heart attack, heart tissue can become scarred. Scarred heart tissue cannot regenerate, leading to many dangerous outcomes, including dysrhythmia, chronic heart failure, and even sudden cardiac death. Therefore, there is a need in tissue engineering to create a “band-aid” that could functionally replace damaged heart tissue. Utilizing open microfluidic patterning techniques, we can generate suspended heart tissue that could reinforce and replace unviable heart tissue. Towards this aim, we designed an open microfluidic patterning removable rail that interfaces between two posts such that an open channel is formed around the posts. Combining human vein endothelial cells (HUVECs) and enzyme-degradable polyethylene glycol (PEG) hydrogel, we pattern the cell-gel solution through the open channel. After the hydrogel has gelled, the rail can then be removed from the posts, revealing a suspended tissue model, acting as the vasculature of the heart tissue. Then, a second patterning rail that has a larger open channel can be placed around the first generated suspended tissue. We will then pattern human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM) in fibrin (a physiologically relevant extracellular matrix of heart cells) such that the hiPSC-CM laden fibrin gel will completely encapsulate the first HUVEC laden PEG gel. Once the complete tissue is made, the construct can be treated with an enzyme that specifically degrades PEG, resulting in a hollow core within the hiPSC-CM gel, releasing the HUVECs into the newly formed cavity. The HUVECs can then localize around the walls, thus generating an endothelized vascular chamber. Overall, this platform models the inner walls and lumen of a blood vessel, thereby representing an endothelium. Eventually, to further this project, I intend to integrate this blood vessel within a thick, multilayered engineered heart tissue patch and test its efficiency in providing structural support and useful circulation.

Housing First (HF) is low-barrier, permanent supportive housing for individuals experiencing homelessness without the prerequisites of attaining abstinence. Past research shows that in-person harm reduction treatment for alcohol (HaRT-A) within HF facilities are preferred because they focus on client-centered goals and improving quality of life. Unfortunately, COVID-19 caused significant disruptions to in-person service provision, and although they requested remote alternatives, currently no services or best practices for HF residents exist. This ongoing project is adapting HaRT-A into a digital platform (eHaRT-A), which when completed, will be tested among HF residents with alcohol use disorder. Our project aims to examine barriers to technology use among HF residents through user-centered design (UCD) principles to improve the acceptability of eHaRT-A. Semi-structured interviews were conducted with HF residents (n=31) discussing technology literacy, viewpoints on technology use, and HaRT-A. Findings highlighted that only a few residents are comfortable enough to use technology on their own; thus, eHaRT-A will be better implemented as a “telehealth station” that is set up in a “somewhat common,” “but still private” environment. Some residents (n=10) were recruited as consultants on the Community Advisory Board (CAB) to provide ongoing input on the eHaRT-A platform. Over a one-year period, UCD interviews on low- and high-fidelity prototypes were conducted with the CAB to inform iterative changes made to the eHaRT-A platform. Within our team, I took this feedback and adjusted HTML and JavaScript code to reflect what is preferred. Feedback included a preference for a “whimsical” theme, presenting personalized feedback through line graphs to show change over time, and interpolating reported outcome measures (e.g., substance use frequency/related-consequences). These findings offer insight into best practices for implementing eHaRT-A within HF facilities. This project serves as a foundation for future eHaRT-A phases and provides the necessary tools to integrate digitized healthcare for underserved communities.

My research explores the metabolic flexibility and longevity of Rhodopseudomonas palustris (R. palustris). This alpha-proteobacterium has become a model organism for studying bacterial survival in non-growing states. R. palustris can endure long-term starvation in a growth-arrested state without forming dormant structures, prompting a comprehensive investigation of the molecular basis of growth-arrest and metabolic modes under these conditions. Recent studies have demonstrated that R. palustris can enter the growth-arrested state due to nutrient limitation but not energy limitation. R. palustris utilizes cyclic phosphorylation to generate ATP, allowing it to sustain viability for an extended period, even in the absence of nutrients including carbon and nitrogen. Earlier research examined the molecular response of R. palustris to growth arrest induced by carbon starvation under light and dark anaerobic conditions. Results indicated that light-incubated cells remained viable for months while dark-incubated cells exhibited a significant decrease in viability following growth arrest. The decline in viability was associated with ATP depletion, which underscores the critical role of ATP in R. palustris’s survival during growth arrest. To further investigate the versatile metabolism of R. palustris, we conducted anaerobic growth experiments using wild-type strain CGA009. We manipulated casamino acids concentrations in nitrogen-rich medium (PM) and nitrogen-free medium (NFM). Results revealed that R. palustris CGA009 utilizes casamino acids as both carbon and nitrogen sources. Our experiments also confirmed that R. palustris CGA009 can grow in the amino acid L-Leucine. Currently, we are researching the capacity of R. palustris CGA009 to utilize diverse carbon substrates through aerobic and anaerobic cultivation on Gelrite medium. Distinct growth patterns provided insights into specific concentrations of carbon substrates tolerated by R. palustris. This ongoing research aims to identify additional carbon substrates supporting R. palustris’s growth, with implications for harnessing its unique metabolic capabilities and expanding our understanding of R. palustris’s metabolic versatility.

Alzheimer's disease (AD) is the most common type of dementia with an estimated 1 in 85 people affected worldwide. It is characterized by accumulations of amyloid beta which result in difficulties with memory and other cognitive activities. While there are treatments that show promise, these are only effective in the preclinical phase of the disease where there are no symptoms, which take approximately 20 years to appear. Unfortunately, measuring amyloid beta directly is invasive and costly, so functional magnetic resonance imaging (fMRI) is used to detect changes in the brain caused by amyloid beta accumulation. Moreover, established techniques for using fMRI for detecting AD show limited success. Therefore, the goal of my project is to generate biomarkers of the earliest neural communication changes associated with AD to allow the application of treatment when it is most effective. This will be done through the use of a graph diffusion autoregressive (GDAR) model, recently developed in my lab. The GDAR model is capable of estimating dynamic changes of neural communication, but has only been applied to electrical recordings. I have demonstrated its validity for fMRI data using a healthy control group through analyzing the model’s prediction capabilities and test-retest consistency, which are both strong. Furthermore, I correlated the GDAR model’s outputs with the primary method in the field, functional connectivity analysis, showing only loose correlation and the potential for biomarkers that are novel from what is currently known. Currently, I am applying the model to AD patients, and anticipate its outputs to contrast those of healthy patients through the use of unsupervised clustering techniques. This would allow the model’s outputs to be used as biomarkers for AD and improve the feasibility of its treatment and prevention.

The term “nature”, as a concept, is incredibly vague and abstract. There is no single definition that fits how all people interpret nature. The disagreement over what qualifies as "nature" is evident; for instance, some may regard a small patch of grass in a bustling city as nature, while others would completely disagree. Many researchers have attempted to understand differences in what is and is not included in individuals' definitions of nature. This includes, but is not limited to, whether or not humans, and our human-influenced environments (e.g., parks or farms) may be considered nature. Questions also arise about which natural elements—such as bodies of water, vegetation, weather, and animals—are encompassed in different definitions of nature. Ideas relating to vastness, degrees of wildness, and type of landscape have also been considered. Gaining a better understanding of how people define nature is imperative for interpreting nature-related measurement scales, understanding how peoples’ experiences influence their nature-related thinking, shaping legislation and policy, and guiding environmental management. This poster conducts a review of literature exploring individuals’ definitions of nature. It aims to examine similarities and differences amongst existing frameworks, synthesizing and offering a comprehensive catalog of different definitions. This review provides the basis for planned research exploring how demographics (e.g., ethnicity, culture, political affiliation, urban/rural residency, age, gender, religion/spirituality, etc.) shape individuals’ definitions of nature.

The Manduca sexta hawkmoth, a proficient pollinator, employs its antennae to efficiently navigate its surroundings. With their antennas highly developed olfactory sense as well as their wide range of odor recognition using their sensory receptor cells, moth antennae are an ideal candidate for developing reliable biosensors. In contrast, commonly used artificial sensors are inefficient and inaccurate in chemical detection. Furthermore, their manufacture is challenging due to their inconvenient design for the user. To evaluate the antenna's effectiveness as a biosensor model, we assessed neural activity in the moth antenna by means of an electroantennogram (EAG). To do this, we attached the removed antenna to a circuit to amplify and measure voltage variations across the antennal nerves during odor stimulation. We then placed the circuit into a wind tunnel and administered a selection of odorants over a determined cycle of durations ranging from 0.2, to 10 seconds. The odorants included a floral mixture from Datura flowers and a certain compound in the mixture (linalool) known to be attractive to moths, as well as volatile organic chemicals (VOCs) replicating both healthy and COVID breath. Our findings show strong initial spikes of electrical activity in the receptor cells correlating to odorant release​, favoring the shorter durations and both the floral mixture and linalool. Prolonged exposure (5 and 10 second durations) to odorants caused continuous increased activity in the antennae, with a more pronounced response observed in the COVID VOCs and linalool. These results demonstrate that moth antennas are a suitable model for the construction of highly accurate and efficient biosensors, and support the feasibility of implementing them in devices aimed at detecting and identifying substances of interest. Future work will explore additional COVID-associated compounds and apply data to an algorithm for machine learning software to enhance capabilities for disease diagnosis.

This study explores how experiences with mental health issues affect stigma and outlook on life. An experience with mental health issues can have an enormous impact on a person's functioning and wellbeing. Stigma and bias against mental health can hinder help-seeking behaviors and increase distrust in professional treatment. One's attitude toward life, such as how optimistic a person is, can significantly mediate a mental health experience. I explored the following questions: (1) How do experiences with mental health issues relate to a person's stigma against mental health topics? (2) How do experiences with mental health issues relate to a person's outlook on life? (3) Is there a difference in the significance in the different forms of or lack of an experience relate to stigma and outlook? Surveys were collected digitally through an undergraduate campus, poster on the same campus, and multiple social media campaigns. 242 participants (M_AGE = 27.4, SD_AGE = 16.6) completed the Satisfaction with Life Scale, Revised Life Orientation Test, Stigma Scale for Receiving Psychological Help, Self-Stigma of Seeking Help Scale - Revised, and investigator written assessment of mental health experiences. All measures were reliable. There were significant correlations between experience, stigma, and outlook. Multiple linear regression analysis revealed experience significantly predicted the variance in stigma (R² = .03, R²_ADJUSTED = .02, F (2, 239) = 3.67, p < .05) and the variance in outlook (R² = .11, R²_ADJUSTED = .098, F (2, 239) = 14.04, p < .001). Experience of someone close with mental health issues significantly predicted outlook (Beta = .14, p = .05). These findings suggest that sharing experience and promoting optimism would improve wellbeing and foster positive attitudes. 

Robotic ultrasound (RUS) is a branch of medical robotics and is defined as the synergistic combination of a robotic arm and ultrasound imaging in medical interventions. The long-term research goal of our team resides in human-robot cooperation with semi-automated robotic imaging, and we seek to develop a deployable robotic ultrasound system that can monitor blood flow towards the brain and inform emergency responders of the efficacy of compressions in real time Cardiopulmonary Resuscitation (CPR). We hypothesize that implementing an intuitive feedback interface with meaningfully linked audio-visual cues will allow first responders to correct deficiencies in CPR technique. My primary study goal is to investigate how various cues affect human perception, as well as how the interface design of a feedback app improves CPR performance. To better understand the context of the device and the users, I have gathered background information about CPR procedure and technology from academic sources and personal interviews. My work has included learning about user interface coding frameworks, analyzing the design process and using this knowledge to create multiple adaptive designs with different types of cues (e.g. sounds, color, animations, text). I have utilized an Arduino microcontroller to communicate information to an app via Bluetooth, as well as the React Native coding framework, which allows me to create interactive user interfaces. The next phase of my research will involve performing experiments with potential users to find dominant cues and efficiently combine them in order to develop the most successful design.The future of this project will provide data about human perception of audio-visual cues in the context of app design which will be useful for future technical projects that use feedback to communicate with a user.

The modification of tRNA plays a significant role in the efficiency and accuracy of translation during protein synthesis. A modification that plays a direct role in reading cognate codons of mRNA in E. coli is the 5-oxyacetic acid methyl ester (mcmo5) modification. This modification occurs on the uracil base at position 34 (U34). The biosynthetic pathway of this modification is initiated via a hydroxylation reaction. Previous in vivo studies demonstrate the enzyme TrhP, tRNA hydroxylation protein, performs this hydroxylation reaction in anaerobic conditions. No in vitro work has been done to study this enzyme and its mechanistic function. TrhP is known to coordinate an iron-sulfur cluster, a metallic cofactor known to contribute to a variety of critical cellular processes, however, the necessity of an iron-sulfur cluster for a hydroxylation reaction is unique to this newly discovered protein family. The goal of this research project is to spectroscopically characterize TrhP’s iron-sulfur cluster to understand the importance of the FeS cluster. Site-directed mutagenesis is utilized to study the coordination of the iron-sulfur cluster. Changes to iron-sulfur cluster coordination are monitored via UVVIS, electron paramagnetic resonance (EPR), and colorimetric assays. These experiments determine how the loss of cysteine, a known iron-sulfur cluster ligand, impacts the iron-sulfur cluster coordination. Coordination of a [2Fe2S] cluster by 4 conserved cysteines is expected, and UVVIS data agrees with that hypothesis. Colorimetric assays show the cysteine to alanine mutants contain less iron than wild-type TrhP, indicating each cysteine has a significant role in cluster binding. Learning more about the specific coordination will establish the site of cluster-binding within TrhP and shed light on the cluster’s role in TrhP’s stability, geometry, and redox properties which all contribute to the enzyme’s modification activity.

A century-old building is currently being renovated in the Green Lake neighborhood. Hubbard’s Corner is an adaptive reuse project attempting to reduce its carbon footprint by replacing conventional building materials with novel, low-impact materials such as concrete-free “C-crete”, hempwool insulation, cross-laminated timber, and reused structural steel. This building project is the first instance of real implementation of some of these novel materials. The manufacturing of two building materials, cement and steel, are responsible for over 10% of global greenhouse gas emissions. The purpose of this study is to use Life Cycle Assessment to analyze the impacts and possible benefits of using novel, low-carbon building materials. We will use environmental life cycle assessment (LCA) to evaluate environmental impacts of manufacturing these novel materials. We will then estimate the difference in environmental impacts between the novel materials and functionally equivalent conventional materials and expect the results to be significantly lower. By analyzing the materials through an LCA framework, we will be able to compare the relative impact of the different design decisions on this project and help understand the relative significance of choosing these materials.

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

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

Organs-on-a-chip (OOAC) are biomimetic structures that replicate the physiological environments of human organs. OOACs are growing in popularity as they provide control of parameters including shear stress, concentration gradient, and biological interactions between cells and biofluids; they can be used in pharmacokinetic, physiological, and toxicological studies. The Kelly-Yeung lab works with kidney OOACs to study toxicology and pharmacokinetics. An important component of the chips is the hydrogel that provides a tubular scaffold and biological substrate for the kidney cells. The hydrogel mixture typically consists of decellularized kidney matrix, Collagen I (Col-I), and two types of cell culture media (PTEC and 199x). The matrix mimics the kidney microenvironment, the Col-I is a stabilizer and tissue regeneration agent, and the two cell culture media are used to mimic the extracellular fluids. More matrix in the hydrogel is ideal since it will better mimic a kidney. However, the matrix by itself is not structurally stable, hence the need for a stabilizing agent. The goal of this project is to maximize the ratio of matrix to Col-I while maintaining a stable hydrogel. In order to determine the optimal ratio, stiffness testing of the hydrogels will be performed via AFM (atomic force microscopy) and a Parallel Plate Rheometer to find out how much matrix can be used before the stiffness of the hydrogel composition is compromised. At this stage, we have started testing the collagen hydrogel with the rheometer to gain base measurements before adding the kidney matrix. We aim to incorporate the kidney matrix, achieving measurements closely mirroring those obtained with the collagen hydrogel alone, while supporting healthy cell growth. Creating a more accurate OOAC based on optimized kidney extracellular matrices will help improve the models and recapitulate the effects of drugs, toxins, and diseases on human kidneys more precisely.

Alzheimer’s disease (AD) is the most common cause of dementia in the aging population, characterized pathologically by the presence of amyloid plaques and tau neurofibrillary tangles in the brain. However, AD often coexists with other pathologies contributing to dementia, such as hyperphosphorylated aggregates of the protein TDP-43. TDP-43 induces a dementia syndrome similar to AD and the combination of AD and TDP-43 is associated with accelerated cognitive decline, greater brain atrophy, and increased AD pathologic burden. AD and TDP-43 pathology are definitively diagnosed post-mortem upon neuropathologic examination but there is a great need to be able to identify these pathologies in living patients using biomarkers. Currently there are accepted biomarkers for AD, including measures of amyloid beta and hyperphosphorylated tau proteins in cerebrospinal fluid (CSF), but there are no biomarkers for TDP-43. Leveraging the reliability of CSF in detecting pathologic proteins, we hypothesize that measurable hallmarks of underlying TDP-43 pathology also exist in CSF. We tested four groups of brain donors (n=36 per group) defined by presence or absence of AD and TDP-43 pathology at autopsy: healthy controls, AD only (amyloid plaques and tau tangles), TDP-43 only, and AD+TDP-43. Post-mortem CSF samples are analyzed for TDP-43, hyperphosphorylated tau (pTau-181), and the brain injury marker glial fibrillary acidic protein (GFAP) using the Quanterix SR-XTM Biomarker Detection System. Because these assays are intended for ante-mortem samples, the first aim of the study was to determine optimal sample preparation for post-mortem samples, followed by the second aim to determine if there are concentration differences between proteins in CSF across groups. Successful identification of reliable TDP-43 biomarkers in living patients would improve neurodegenerative disease diagnostics, enabling accurate underlying pathology diagnosis and facilitating tracking disease progression and treatment response as therapies for AD, TDP-43, and other causes of dementia emerge.

Heschl’s gyrus (HG) is a region of the brain containing the primary auditory cortex. The extent of folding within the HG shows high morphological variability across individuals. Interestingly, increased HG folding is more likely to be found in expert than amateur musicians, suggesting a possible role of auditory experience in shaping HG gyrification. In my research, I examined HG folding in blind individuals—another population with extensive auditory experience. I hypothesized that, if experience alters HG structure, then individuals with early-onset blindness might have increased HG gyrification compared to those with late-onset blindness or those who are sighted. I analyzed T1-weighted images collected from previous MRI studies at the University of Washington, University of Pennsylvania, and Oxford University. The combined dataset included 6 anophthalmia (individuals born without eyes), 48 early blind, 18 late blind, and 28 sighted control participants. I created hand-drawn HG regions of interest for each participant in both hemispheres and measured HG gyrification in two ways: 1) by visually categorizing the extent of HG folding (single, partial, or complete duplication), and 2) by obtaining continuous metrics (gyrification index and curvedness index) using FreeSurfer. A chi-squared test revealed that the degree of HG folding was not different across the four groups. A linear mixed-effects model (controlling for the effects of age, hemisphere, and scan location), similarly showed no effects of group on the gyrification index or the curvedness index. To conclude, my findings show that blindness does not affect HG gyrification. The results challenge the idea that auditory experience alters HG structure and offer important insights into previous findings in professional musicians. Our results suggest that the prevalence of duplicated HG in musicians may be the result of individuals with larger processing capacity within the auditory cortex being more likely to take up music as a profession.

As cloud computing and artificial intelligence continue to evolve, data centers increasingly rely on a variety of accelerators to enhance performance. Field Programmable Gate Arrays (FPGAs), known for their exceptional speed and flexibility, are emerging as a viable alternative to conventional processors such as CPUs, GPUs, and ASICs. Despite their potential, a key challenge in cloud-based FPGA deployment is efficient multi-tenancy, particularly due to the nascent stage of this technology in cloud environments. This study addresses this challenge by focusing on the emerging Disaggregated FPGA Architecture, which conceptualizes FPGAs as independent compute nodes. This approach facilitates smoother integration into data centers and offers a solution to prevalent integration challenges. The importance of this study lies in its potential to revolutionize the deployment and scalability of FPGAs in cloud environments, thereby significantly enhancing data center performance and efficiency. This not only contributes to the field of cloud computing by advancing FPGA integration strategies but also sets a new benchmark in resource optimization and scalability for cloud infrastructures. To underscore the effectiveness of Disaggregated FPGA architectures, the research first advocates for their strategic advantages in cloud settings. Following this, a detailed test plan is presented, comparing Disaggregated FPGA architectures with existing cloud FPGA frameworks. This comparison aims to validate the feasibility and scalability of the proposed architecture. Through this research, we contribute a novel perspective to FPGA deployment in cloud computing, offering a potential paradigm shift in data center technology and paving the way for more efficient, scalable, and adaptable cloud infrastructures.

Polycystic Ovary Syndrome (PCOS) is the most prevalent reproductive condition in pre-menopausal women, impacting around 5-10% of women in the U.S., despite being underdiagnosed. Previous research has linked a higher free androgen index with cardiovascular risk factors in women with various forms of ovarian dysfunction. Given that elevated androgen levels are a criterion for PCOS diagnosis, understanding the potential association between total testosterone and cardiometabolic risk factors in women with PCOS, specifically, is crucial. This cross-sectional study investigates the relationship between total testosterone levels and cardiometabolic risk factors among women diagnosed with PCOS. Limited research exists on endocrine and cardiometabolic health in PCOS patients, prompting our inquiry. Data for this study was extracted from women with PCOS who attended the University of Washington Endocrinology Clinical and Diabetes Institute. Blood samples underwent analysis for biomarkers including total testosterone, glucose metabolism, and lipid levels. Linear models, both adjusted and unadjusted, were applied to assess correlations between total testosterone levels and the aforementioned biomarkers. Insights into the impact of total testosterone on insulin resistance and lipid levels could offer better insights into how women with PCOS can better manage their health. Preliminary findings indicate a limited correlation between total testosterone and cardiometabolic risk factors, contradicting previous studies. Further analysis, including controlling for factors such as oral contraceptive use, will be done to bring greater clarity to these results. This study aims to bridge gaps in our understanding of the mechanisms by which PCOS can affect the health of women. It also seeks to address the underfunding and underrecognition of research in diseases that primarily affect women. Future research in this domain must be done to investigate biomolecular pathways on how testosterone could potentially affect cardiometabolic health.

As we receive spatial and temporal information, our brain develops sequential patterns to store events, giving us the ability to learn and store relationships. For learning and memory, these rapidly-encoded sequences are reactivated as “replay” sequences after experiencing the original trajectory, as often observed in the hippocampus. This brings up the question: what biological mechanisms enable us to build, encode, and trigger these relationships and replays? The goal of this project is to model sequential replay in spiking neural networks to explore and understand various biological mechanisms that produce the acquisition of such sequences. We are using NEST Simulator, a spiking neural network simulator software, to model large-scale neural networks. Then, we explore how changing dynamics such as non-random structure of the network and interactions between excitatory and inhibitory cells can contribute to sequence generation, as well as the salience and speed of such sequences. We have observed the significance of interplay between particular parameters, such as the widths of spatial Gaussian distributions for neuron connection strengths, by analyzing generated spiking raster plots. Recent work has also suggested an important role of long-term potentiation of intrinsic excitability in sequential replays, which we are integrating with the aforementioned dynamics by building a unique synapse model within the simulation software. This is a novel method to introduce excitability in a network, which is important to determine how changing excitability through potentiation, rather than plasticity, facilitates network formation and propagation. This research is significant because it highlights the components of neural networks that could be crucial to quickly generating and maintaining sequences for learning and memory, therefore helping us understand the brain’s mechanisms for storing spatiotemporal relationships.

HIV is characterized by a chronic state of inflammation that may lead to the development of cardiomyopathy, a condition where the heart muscle cannot effectively pump blood. The purpose of this report is to explore the relationship between HIV and the phenotypic expression of hypertrophic cardiomyopathy (HCM). In this patient case study, I analyze the possibility of HIV-related changes in heart structure affecting HCM’s development into heart failure, as well as an increased risk of surgical complications. I examined a 43-year-old female HIV patient who showed symptoms of heart failure and was diagnosed with HCM. She went through various surgical procedures that were complicated by post-pericardiotomy syndrome, an inflammatory response to cardiac surgery. I used the patients' hospital vitals and procedures, as well as current HIV and HCM literature to propose the possible relationship between HCM phenotype and HIV, as well as the role that inflammatory properties play between HIV and the probability of post-surgery complications. HCM phenotype may vary among patients due to its interactions with gender, genetics, and the environment, and can result in heart failure. In this patient, it is possible that there is an increase in severity in HCM phenotype due to the inflammatory factors associated with HIV, further contributing to the development of both heart failure and complications in surgery. The case of this patient illustrates how further research needs to evaluate the specific molecular mechanisms in HIV that could be impacting the expression of HCM, as well as the further development of post-pericardiotomy syndrome.

Local Group galaxies are the closest ones we can study in detail to decipher the processes that shape the universe around us. An interesting property of these galaxies is their star formation history (SFH), which provides a fossil record of when stars were formed in a galaxy. The process by which this occurs is a complex interplay between the gas, the interstellar medium (ISM), and the energy from newly formed stars. By pairing SFH measurements with data on the galaxy’s gas content, we can investigate the timescales on which young massive stars affect the structure of the surrounding gas in the (ISM) as well as its ability to form more stars. Furthermore, since star formation is closely linked to the properties of the gas in a galaxy, such as metallicity and extinction, the SFH also probes these properties. By utilizing resolved stellar photometry from the Hubble Space Telescope (HST), I measured the SFH for four Local Group galaxies (IC10, IC1613, WLM, and NGC 6822) that already have detailed imaging of their gas content from radio observations. First I measured the colors and brightnesses of resolved stars in each galaxy from the HST imaging. Next, I generated and processed a set of artificial stars using the same photometry pipeline as the real observations to provide statistical measures of our data quality. With the processed artificial stars and the original photometry, I then fitted a series of model Hess diagrams for a range of ages and metallicities to obtain each galaxy’s SFH. These measurements allow us to pair this SFH with other observational data. For example, we can map star formation and compare it with observations such as supernovae locations, and we can explore links between the star formation and the ISM as measured through emission from neutral and ionized hydrogen.

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

People are more likely to stigmatise the mental health of an out-group compared to an in-group member. People are also more likely to distribute resources toward in-group than out-group members. The present study applies these findings to understand how likely a person is to appraise another’s mental health experiences as legitimate and share mental health resources with them based on identified social groups. Participants recruited from the University of Washington Psychology Department subject pool were randomly assigned to one of four different conditions. They read a vignette about a hypothetical individual with or without a specified diagnosis of OCD who attends the University of Washington or Washington State University. The participants reported their legitimacy appraisal of the outlined mental health challenges and their willingness to share mental health resources with the target. I hypothesise that participants who read a description of an individual from Washington State University without a specified diagnosis will rate the individual’s mental health condition as less legitimate. I also hypothesise participants who read about an individual from Washington State University without a specified diagnosis will be less likely to share mental health resources with them. The findings of this study will help shed light on the type of stigma surrounding mental health and resource sharing from the perspective of social groups. In turn, the findings can help the public recognise more acute mental health biases they may hold and thus work towards dismantling them. This can foster the growth of a more empathetic and united community.

Graph workloads are challenging for query optimizers in databases because of query features like larger sizes, frequent joins, and fewer filters. Traditional methods see large errors on queries with more joins, while machine learning methods tend to be complex and slower. We propose a framework to improve estimators by using graph colorings to make compact summaries of a data graph, storing important information about node relations. By modelling cardinality estimation as a subgraph matching problem, we can make use of this summary information and traverse the lifted graph to estimate the number of query graph matches. Additionally, we explore optimizations such as node summation and sampling to enable estimation even for larger queries. After evaluating various designs using this framework, we find improvements up to 100x to cardinality estimation accuracies compared to other recent methods while still maintaining efficient runtimes and memory usage. We discovered that quasi-stable colors, where nodes of one color have similar connections to other colors, result in these improved results when used to build the summary. These findings help improve graph database performance and offer a new application for graph theory.

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

Examining environmental exposures during pregnancy and their impacts on fetal and child development is vital for maternal and child health. As researchers, we have a responsibility to return these individual environmental results to participants. DERBI (Digital Exposure Report-Back Interface) is an online tool to specifically return environmental exposure results. This study examines: Are there distinguishable demographic-based patterns in those who logged in to open their results versus those who did not? What demographics are we missing in getting participants their results? PATHWAYS GAPPS is an NIH-funded study that examines environmental exposures and child outcomes in Seattle and Yakima, Washington. DERBI provided personalized biomonitoring results for environmental chemicals after over a decade of participation in research. Three hundred ninety-three participants across the Seattle (N=194) and Yakima (N=199) sites were sent an access code for their child’s return of results. I compiled demographic data on socioeconomic factors, such as race and maternal education. Within each site, I analyzed the demographics on which participants had opened their child’s return of results and those who did not open them. I then calculated and rounded percentages over the opening status for each site. At the point of data collection, mothers had five months to log in and open their results. I observed that mothers with less education were less likely to open their results, and fewer non-Hispanic Black mothers opened their results, suggesting that education and self-identified race are key factors in determining who is likely to access their results. The manner we present the return of results to participants and provide additional resources to process and take action on the results also matters. Future directions include conducting qualitative interviews and focus groups to hear first-hand from participants about barriers in accessing results and what resources would increase inclusivity and likelihood of opening their results.

The mammalian brain contains neurons and glia in equal numbers. Glia contribute to proper neuronal communication by removing unnecessary synapses via a process known as pruning. Pruning plays a critical role in brain development, learning, and memory. How do neurons communicate which synapses must be pruned by glia? One way is through cell surface exposure of the lipid phosphatidylserine (PS) which serves as an “eat me” signal to glia. In other contexts, like apoptosis, flippases and scramblase enzymes regulate PS exposure. Flippases are membrane transporters that restrict exposure of lipids like PS on the extracellular leaflet, while scramblases translocate lipids bidirectionally, thereby promoting PS exposure. We don’t know if these molecules also regulate PS exposure during glial pruning. The Singhvi Lab previously established conservation of glial pruning in C. elegans. This optically transparent model contains a stereotyped nervous system, making it ideal for studying in vivo pruning with single-cell resolution. We focus on a single neuron-glia pair, AFD-AMsh, and use widefield fluorescence microscopy and posthoc image analysis to quantify the number of neuron fragments pruned by glia. We previously found that mutants lacking the flippase TAT-1/ATP8A have more pruning, suggesting a novel inhibitory role for this protein. Here, I examine several candidate scramblases: SCRM-1/PLSCR1, ATG-9/ATG9, CED-8/XKR8, and ANOH-1/TMEM16F. I conduct genetic crosses to put mutants for these scramblases in a fluorescent background to visualize pruning and use the described methods to characterize any pruning defects. Specifically, I expect that relevant scramblase mutants will have less pruning, as the “eat me” signal is not properly exposed. Dysregulation of pruning contributes to neurodegenerative disorders like Alzheimer’s. Similarly, flippase and scramblase mutations are linked to human brain dysfunction. Thus, studying the role of these enzymes in pruning offers novel insight into human brain health and disease. 

The mechanisms underlying the development of neurodegenerative diseases such as Alzheimer's Disease (AD) are not well understood. The characteristic accumulation of pathological protein plaques and tangles has led AD research to focus primarily on abnormal protein function and metabolism contributing to the pathology. Tau is one such protein that forms toxic aggregates in those with AD and various other neurodegenerative diseases. Our lab researches the mechanisms of tau toxicity using the nematode C. elegans. Recent research has implicated improper lipid metabolism as another potential contributor to neurodegeneration. Mutations in a gene known as gba-3, which is critical for lipid metabolism, are risk factors for the development of Parkinson’s Disease (PD), but little is known about the relationship between gba-3 mutations and tau toxicity in AD models. My research project will investigate the role of gba-3 in a C. elegans model of tau toxicity. I have crossed strains with various mutations in the gba-3 gene into two strains with tau toxicity. I will perform motor performance assays, measure the accumulation lipids, quantify the amount of tau, and measure oxidative stress to investigate whether gba-3 mutations modulate tau toxicity. Preliminary results suggest some gba-3 mutations slightly rescue some tau models but not others, but further investigation is needed to validate these findings. Ultimately, this project will provide further insight into the complex mechanisms underlying neurodegenerative diseases such as AD and may guide future development of treatments targeting lipid metabolism.

This poster describes a qualitative study highlighting the intersection of ethnic identity and Christian faith in shaping South Asian college students’ perceptions of LGBTQ+ individuals. Current sociopolitical climates toward LGBTQ+ individuals in South Asian countries tend to be hostile, and even South Asian communities within the United States can reflect similar beliefs. Zaidi (2014) found that shame in the South Asian community was in conflict with a desire to express one’s queer identity among South Asian youths (Zaidi, 2014). Moreover, environmental factors such as the religious setting might contribute to varying perspectives regarding LGBTQ+ individuals; in the current study, we highlight faith-based higher education institutions (i.e., Christian university) as an institution that can shape views regarding LBTBQ+ folks and their experiences. We conducted 6 semi-structured interviews with South Asian college students enrolled in a Christian university located in the Pacific Northwest region of the U.S. Our three-member research team transcribed the interviews, coded the transcriptions, and placed the codes in themes according to Braun and Clarke’s (2006) guidelines for Thematic Analysis. The four themes that we identified include support for LGBTQ+ people on campus, Christian messaging around LGBTQ+ identity, South Asian communities, and participant’s own attitudes. These major themes also included subthemes, some of which are campus advocacy and protests influenced participant’s beliefs, feelings of an internal struggle, attitudes of South Asian communities, and individual affirming attitudes. Broadly, we found that the participants viewed their own South Asian communities as generally silent or passive in LGBTQ+ dialogues, and that their Christian campus promoted both helpful and unhelpful conversations about the topic. We will present some implications for practice in higher education around fostering an inclusive space for LGTBQ+ individuals, especially as they pertain to intentional integration of culture-specific (e.g., South Asian) and religious (e.g., Christian) perspectives.

Spinal cord injury (SCI) causes physical disability and chronic pain, but there can also be psychological issues like depression and/or anxiety. Clinically, the estimated rates of depression among the SCI population are from 11% to 37%, according to UW Medicine. In rodents, after SCI, both males and females demonstrated anxiety-like behavior, and female mice became more anxious while male rats became more hypersensitive to thermal stimuli. These findings highlight the complexity of the systematic changes after SCI, all of which may impact the quality of life and limit functional recovery. We have found a sex difference in the effectiveness of electrical stimulation in promoting functional recovery after cervical SCI. In our experiment, females show robust functional improvements with activity-dependent spinal stimulation. The current study aims to investigate the role of affective behaviors (depression and anxiety) and pain after SCI on functional recovery in male and female rats. Before injury, all rats will undergo baseline assessments to establish behavioral norms, which involve training and evaluations designed to measure motor ability, emotional state, and sensitivity to various stimulations. Three weeks after SCI, rats will be assessed with the same battery of tests and then start daily treatment of drugs that can modulate emotional states and relieve pain, including a mixed serotonin and norepinephrine reuptake inhibitor, duloxetine (or no drug control), for five weeks. Behavioral assays will be repeated at the end of the treatment period, and tissue will be collected for histological analysis. I will primarily be responsible for conducting and analyzing an assay of anxiety-like behaviors, the open field test, and the assay of depression-like behaviors, the sucrose splash test. We expect to understand better the relationship between affective responses and motor function post-SCI, and the potential therapeutic benefits of antidepressant treatments, and particularly identify sex differences that may limit recovery.

We have observed that conventional respiratory pathogen sampling methods, such as pharyngeal swabs, elicit unpleasant experiences for both adults and children. Particularly for pediatric patients, having a non-invasive, enjoyable sampling approach is crucial to facilitate prompt diagnosis and treatment. In prior research, we introduced a novel saliva sampling device, the CandyCollect. This lollipop-inspired device, with its isomalt candy coating, is specially produced and surface-treated for capturing pathogens from saliva, providing a pleasant sampling experience to child patients. Clinical studies approved by multiple Institutional Review Boards (IRB) revealed an average candy dissolving time for CandyCollect (with a mass of 0.90g~1.10g) of 3.51 minutes, with a minimum of 1.25 minutes. To compete with original sampling methods which take up to 10 seconds, it is desirable for CandyCollect to have a shorter sampling time around 15–20 seconds. Therefore, this study aims to decrease the dissolving time by introducing a new CandyCollect recipe and design. For the new candy recipe, we replaced isomalt with a mix of glucose and sucrose. Additionally, baking soda (sodium bicarbonate) was added to increase the candy’s contact area with the tongue. An ongoing experiment will assess if baking soda affects PCR results for pathogen samples, and this modified recipe will be employed in a new clinical study. Concurrently, we have modified the CandyCollect design by placing the candy on the same side as the spiral, with a small candy reservoir beneath the spiral to decrease the mass to 0.06g-0.1g. To validate the efficiency of this new design, we plan to conduct another clinical study recruiting 30 younger participants and obtaining feedback about the new design. This collaborative study will provide valuable insights towards achieving a faster dissolving time, ultimately enhancing the viability of CandyCollect as an improved and more efficient replacement for conventional sampling methods.

The HIV-1 capsid is a conical lattice comprised of over 1500 monomeric capsid proteins (CA) that acts as a protective casing for the viral genome. Assembly of the capsid core is driven by the small negatively charged molecule, inositol phosphate (IP6), which interacts with positively charged CA residues. The ability to inhibit viral replication through the disruption of CA assembly has been demonstrated by the novel capsid binding antiretroviral, lenacapavir. Antiretroviral research is also being done on “clickable” compounds which should covalently interact with CA through a Sulfur (VI) Fluoride Exchange (SuFEx) reaction. Our lab has received lenacapavir analogues as well as compounds that potentially interact with CA via a SuFEx reaction (SuFEx compounds). My aim is to assess the impact of lenacapavir and the synthesized analogues on CA assembly, in addition to validating the ability of 15 promising SuFEx compounds to covalently bind CA. In preparation, I transformed E. coli cells with a plasmid containing the HIV-1 CA sequence and induced expression using IPTG. The cells were then pelleted, lysed and the protein purified utilizing gel filtration, anion- and cation-exchange chromatography. Assembly of the purified CA was induced in vitro by the addition of IP6 in both the absence and presence of lenacapavir and the analogues. Relative to lenacapavir, two analogues promoted assembly to a greater extent, while one performed on par and three enhanced assembly to a lesser extent. These analogues will be further studied to determine antiviral activity. Samples of CA in the presence of the SuFEx compounds have also been prepared and sent for mass spectrometry analysis. It will then be determined which of the SuFEx compounds bind CA covalently in vitro and may aid in the development of new capsid targeting antiretrovirals.
 

Discoid lupus erythematosus (DLE) is the most common subtype of chronic cutaneous lupus erythematosus (CLE) that may present with or without systemic lupus erythematosus (SLE). Treatment for DLE remains limited, as there are no medications specifically approved to treat DLE. Deucravacitinib (DEUC), an oral, selective, allosteric tyrosine kinase 2 (TYK2) inhibitor, is currently being studied for adults with moderate-to-severe discoid and/or subacute CLE. This case report aimed to communicate a case of refractory DLE successfully treated with DEUC. Clinical data concerning the patient’s course of treatment was abstracted and a literature review on DEUC and the current treatment methods for DLE was conducted. This case report of the patient’s successful treatment of their DLE with DEUC was subsequently written. A 65-year-old female with a longstanding history of systemic lupus erythematosus presented with prominent discoid lesions involving the nose, cheeks, and mid upper cutaneous lip. Having tried topical medications, multiple courses of systemic steroids were attempted, but the patient flared shortly after the tapers. Despite the patient experiencing some improvement on mycophenolate mofetil and prednisone, the decision to switch to DEUC was made due to the patient developing multiple infections while on the former regimen. Three months after starting DEUC, the patient returned with their skin completely clear. A better understanding of the molecular pathogenesis of CLE is informing the development of more targeted therapeutic strategies. TYK2 and Janus Kinases (JAKs) both mediate the signaling of cytokines, some of which play a role in the pathogenesis of SLE. DEUC binds to TYK2 at the regulatory domain, which is unique to its respective kinase unlike conventional JAK inhibitors that bind to the active domain conserved across all JAKs. DEUC offers more targeted inhibition with a potentially improved safety profile compared to conventional JAK inhibitors.

For this research, I am developing an algorithm for reconstructing particle trajectories using data from the proposed MATHUSLA (Massive Timing Hodoscope for Ultra Stable Neutral Particles) detector at CERN’s (the European Council for Nuclear Research) Large Hadron Collider. The MATHUSLA detector is specifically designed to capture LLPs (Long-Lived Particles), a class of theoretical neutral high-energy particles that are undetectable by current CERN detectors due to their large decay times, potentially emitted during particle collisions using a series of tracking layers. My objective is to identify potential LLP candidates using the data collected by these highly precise trackers. The algorithm I developed determines the most probable particle trajectories that occurred corresponding to the data collected by the trackers. The algorithm has demonstrated a path detection accuracy exceeding 90% in sample point clouds with reasonably high efficiency. Future work includes examining how to take into account and accurately detect the non-linear paths frequently taken by real-world particles, in addition to better fitting the algorithm to the more realistic and cluttered data expected from the detector. The study of LLPs is a fast growing subfield in particle physics; finally detecting and analyzing them could play a massive role in taking the field beyond the Standard Model.

Traumatic brain injury (TBI) is one of the most prominent environmental risk factors for neurodegenerative disease, including Alzheimer’s disease (AD) and chronic traumatic encephalopathy (CTE). Both AD and CTE are characterized by the accumulation of abnormal phosphorylated tau (p-tau) protein in neurons in the brain in addition to other pathologies. In CTE in particular, the p-tau deposition occurs around the vasculature at the sulcal depths of the brain. Inhibitory neurons are the brakes of neuronal circuits in the brain and many previous studies using animal models have revealed a deficit or loss of inhibitory neurons after TBI. Some inhibitory neurons even have a special role in monitoring the vasculature of the brain, where the p-tau accumulates in CTE. However, no one has evaluated whether these inhibitory neurons are affected by p-tau pathology after human TBI. Here, I evaluate whether p-tau pathology accumulates in inhibitory neurons in ten cases of CTE and ten cases of brain contusion that have associated p-tau pathology compared to a positive control group (ten cases of AD without any history of head injury). Double-staining immunohistochemistry labeled with different colored chromagens is performed using three different inhibitory neuron markers (parvalbumin (PV), somatostatin (SOM) and TAC1R) combined with an antibody for the abnormal phosphorylated tau protein. Using the Halo image analysis system, the colocalization module is used to determine if p-tau accumulates in inhibitory neuron subtypes. These results will be confirmed with immunofluorescence and 3D confocal microscopy. I anticipate that inhibitory neurons, especially ones associated with vasculature (TAC1R+) will be affected by p-tau pathology in contusion and CTE cases, but not in positive controls. This project will give further insight into possible mechanisms of circuit and neuronal dysfunction that may occur after head injury and have therapeutic implications.

Computational protein design has successfully designed nanoparticle cages that self-assemble and effectively deliver encapsulated therapeutics to cells. These nanoparticle cages are readily taken up by the cell via receptor-mediated endocytosis. Despite the promise of these cages, one of the greatest challenges that remain is the successful endosomal escape of the encapsulated biologics and their precise delivery to the cytosol. To address this, we have engineered a high throughput complementation assay, based on split green fluorescent protein (GFP) construct, that helps screen and quantify cytoplasmic delivery of therapeutics through fluorescence intensity. Split-GFP is a protein complementation assay in which the normally monomeric GFP is made of two fragments: the larger non-fluorescent beta barrel and a 15 amino acid (a.a) peptide. When these two components unite, the GFP fluoresces. In this project, I created a stable HeLa cell line expressing the beta barrel of split GFP using lentiviral transduction under antibiotic selection. The cell line has been further validated, through transient transfection of the complementary 15 a.a peptide to test the assay performance. I propose to test endosomal escape, through introduction of endolytic peptides (EEPs) into model proteins, which force early endosomal membrane fusion and destabilization. Future research will explore adapted designs of nanoparticle cages, incorporating the EEPs and the split-GFP complementary strand in the HeLa cell line, to quantify the endosomal escape of our designs. The outlook of this project has transformative implications for targeted therapeutic delivery. By creating a screening assay that can quantify targeted delivery into cytosol, we can expedite refinement of protein designs for therapeutic delivery, thus accelerating the timeline for developing novel protein-based therapeutics.

Down syndrome (DS, trisomy 21) is the most common chromosomal condition, affecting 1 in 700 live births. In addition to neurodevelopmental issues, people with DS also have an increased susceptibility to infections such as influenza and COVID. Altered immune function is one likely driver. Additionally, non-immune factors may also contribute. For example, upregulation of TMPRSS2, an enzyme that promotes cellular entry of SARS-COV2 encoded on chromosome 21, may predispose people with DS to severe SARS-CoV2 infection. This project builds on recent data from the Khor lab that suggests a link between DS and susceptibility to malarial infection. P. vivax is a parasite that causes malaria and is endemic across wide regions, from South America to South Asia. P. vivax enters cells through a protein called Duffy which is a chemokine receptor on the surface of red blood cells (RBCs). Recent profiling of whole blood from patients with DS showed dysregulation of many genes. Geneset enrichment analyses identified heme metabolism as the second most affected pathway. Within these heme metabolism genes, ACKR1, the gene encoding Duffy, was particularly and disproportionately upregulated. This suggests that people with DS may express higher levels of the Duffy protein on their RBCs, which in turn may predispose to P. vivax infection. This project seeks to better understand and validate how Duffy expression is dysregulated in people with DS. The goal of the project is to quantify the level of Duffy present in the RBC’s of patients with and without DS. If validated, the next step will be to test the susceptibility of these cells to malaria. This may point to a need for altered clinical management of malaria in people with DS and inform further studies looking at the mechanistic differences in RBC biology in people with DS.

There is a growing emphasis on providing "equitable" mental health care, and yet ‘equity’ is seldom defined clearly. Publicly-funded community mental health clinics’ (CMHCs) clinicians often serve clients from minoritized and underrepresented backgrounds, and thus may regularly observe and address equity issues, making their perspectives invaluable. This qualitative study explores CMHC clinicians’ perspectives of equity in their clinical practice. Our data was obtained from an online cognitive-behavioral therapy (CBT) training initiative in Washington State targeting CMHC clinicians serving youth. Participating clinicians (N = 245) received nine consultation sessions from CBT experts over a six-month period and completed pre-training and post-consultation surveys. In the pre-training survey, we asked clinicians to define equity and list resources they would want access to that can improve their consideration of equity in their practice. Descriptive statistics summarized clinician demographics. Using thematic analysis, clinicians’ open-ended responses were coded to identify emerging themes. Clinicians were predominantly female (74.7%), White (58.8%), had a master’s level training (90.2%), and a mean age of 34.2 years (SD = 9.3). After coding clinicians’ definitions of equity, ‘accommodation’ (i.e., tailoring services to clients) was the most endorsed theme (38.8%, n = 95), followed by ‘equality’ (i.e., treating clients the same; 19.6%, n = 48) and ‘fairness’ (i.e., treating clients with justness, 17.6%, n = 43). When asked about resources that could improve their considerations of equity, clinicians’ responses most frequently included diversity, equity, and inclusion (DEI) trainings, expanding reach to more diverse populations, equity-focused supervision, and financial aid (e.g., gas cards, food pantry). While CMHC clinicians’ perceptions of equity included common themes, their understanding may at times conflate equity and equality. These findings highlight the importance of increasing access to DEI-focused trainings and supervision along with other resources to assist CMHC clinicians in delivering equitable care.

The cerebellum, which accounts for 10% of human brain volume, contains approximately 80% of all brain neurons and has long been understudied relative to the cerebral cortex. During development, the cerebellar ventricular zone (VZ) is a transient progenitor zone which generates all cerebellar GABAergic (inhibitory) neurons. This includes Purkinje cells (PCs) and PAX2+ interneuronal progenitors (PIPs). While the mouse cerebellar VZ has been relatively well characterized, there is limited knowledge about its human counterpart. In this study, we investigated organization of progenitors and birth of neurons derived from the human cerebellar VZ, uncovering several notable features. Specifically, I conducted image analysis in conjunction with immunohistology (IHC) assays to (1) identify different cell types and marker gene expression across developmental stages and (2) quantify proliferative cells at different stages of development. We found that a substantial number of PCs are generated during embryonic development, particularly within the first 50 post-conception days, within a compact two-week timeframe. This occurs well before the onset of cerebral neurogenesis, with interneuronal differentiation commencing during early fetal development. Neuronal differentiation predominantly occurs from the inner and outer subventricular zones (SVZ), zones which are completely absent in the mouse developing cerebellum, with the initial wave of differentiation occurring from the outer SVZ. Significantly, relative to mice, we observed variations in migratory patterns and the quantity of PC plates, including a subset of PCs that retain the expression of cell cycle genes several weeks after these cells leave progenitor zones. This work extends our knowledge of human-specific birth and organization of progenitors and neurons originating from the ventricular zone and cellular and molecular differences in ventricular zone progenitors, Purkinje cells, and PIPs across different developmental ages.
 

The acceleration of antimicrobial resistance (AMR) in pathogens and commensal organisms is an emerging global health crisis due to the overuse and misuse of antimicrobial drugs. In addition, it is unknown how other factors such as a changing climate may impact AMR. We utilized wastewater surveillance to investigate if the diversity of antimicrobial resistant genes (ARGs) in influent wastewater is associated with rainfall. We utilized our workflow for the detection of specific ARGs in the greater Seattle area, contributing to AMR stewardship efforts. I conducted qPCR, PCR, and nanopore sequencing of CTX-M genes, an antimicrobial resistance gene, extracted from influent wastewater from wastewater treatments plants servicing the Seattle area. The purpose of this approach is to assess diversity of AMR gene alleles with high accuracy to contribute to the surveillance of AMR genes in populations. I hypothesize that higher rainfall—typically occurring from October to March—leads to a lower diversity of AMR genes due to increased dilution and decreased potential for horizontal gene transfer between organisms. During the dry season—April to September—I hypothesize we will find more unique alleles of AMR genes. In this poster, I will present the results of my statistical analyses investigating the relationships between ARG abundance, ARG diversity, and rainfall The utility of contextualizing the diversity of targeted antimicrobial resistance genes can inform clinical practices that benefit the health of populations.

One of the current challenges with evidence based practices (EBP) is addressing social risk factors (SRF) in conjunction with mental health therapies. SRFs are adverse social conditions which impact the physical and mental health of an individual, group, or community. Addressing SRFs in low-resource settings increases access to and engagement in EBPs by reducing immediate threats presented by SRFs. Training in EBPs does not typically include how to address SRFs. To understand possible ways to address SRFs in EBPs, we examine whether counselors delivering EBPs in a low-to-middle income country are addressing SRFs and how the strategies impact the implementation and delivery of an EBP. This study builds on the parent study, “The Building and Sustaining Interventions for Children (BASIC)”, which examines the implementation and sustainment of an adapted version of Trauma-Focused Cognitive Behavioral Therapy, called Pamoja Tunaweza (PT) implemented by lay counselors in Kenya.To examine strategies used to address SRFs in PT, twelve PT counselors from the BASIC study participated in semi-structured interviews with trained interviewers. We conducted an inductive thematic analysis to identify codes and themes derived directly from the interview data. We identified and organized segments of the interviews into codes which were further categorized into themes. Themes include types of strategies counselors used to address SRFs as well as their impact within the context of PT. We report the frequencies of the codes and themes as they relate to their impact. Preliminary results indicate that when counselors reported using strategies to address SRFs, such as referring guardians to resources and collaborating with school administration, counselors saw increases in child self-esteem and PT attendance. Understanding how addressing SRFs impact mental health and implementation outcomes can help inform training of counselors to effectively improve use and engagement of PT and other EBPs.

Marine inhabitants of the benthic zone play a large role in the health of an ecosystem. They regulate the water quality, removing debris and pollutants and sit at the base of the food pyramid. This zone is also where nutrients cycle through the environment, which inhabitants rely on to sustain themselves. Many factors can contribute to an ecosystem's health, including the particle grain size (PSA) and total organic carbon content (TOC) of sediment of the benthic zone. The grain size indicates the energy of an environment. A finer grain size indicates a low energy environment meaning less water movement or disturbance while a coarse grain size indicates a high energy environment with strong water movement. TOC measures the amount of carbon and other organic materials in an area. Too much organic material leads to nutrient overload and toxicity, causing the benthic species to die off. The purpose of this study is to determine if there is a change of sediment characteristics in PSA and TOC over time and how possible change effects the environment. This is done by long-term analysis of 50 locations within the Puget Sound on a yearly basis. To analyze the grain size, I used a Beckman-Coulter laser diffractometer to generate a histogram of grain sizes. To measure TOC, I dried and then burned sediment samples from each sample site using a Thermolyne furnace. Total content was measured by the mass recorded throughout steps. We expect to see a correlation between grain size and TOC, with more organic content in areas with a higher energy in our results. I will complete Statistical analysis of processed samples and create a GIS map of the spatial pattern of sediment quality and benthic health. All data contributes to future decisions made to best monitor our changing aquatic environments.

Multiple Sclerosis (MS) is a chronic central nervous system (CNS) disease in which the immune system attacks the myelin surrounding nerve cells, resulting in decreased communication between the brain and the rest of the body, and severe physical and neurological defects. Gut metabolites produced by gut microbiota play a significant role in maintaining host immune homeostasis, and research has shown that short-chain fatty acids (SCFAs) have therapeutic potential. When tested in the mouse model of MS, experimental autoimmune encephalomyelitis (EAE), delivering butyrate-conjugated block copolymer micelles to the distal gut ameliorated EAE progression by increasing the amount of regulatory T cells and cytokines, and strengthening intestinal barrier functions. For prolonged SCFA delivery to the distal gut, a SCFA-conjugated hybrid lipid-polymer nanopolymer carrier is required. A nanoparticle is required because butyrate has a strong odor/taste and requires many pills per day to have significant suspension. To synthesize this nanoparticle, we optimized the nanogenerator to determine its effects on size and charge. This included modulating the total flow rate, flow rate ratio, input concentration ratio (lipid:polymer). We hypothesize that larger size, smaller surface area-to-volume ratio, and anionic surface charge will prolong retention and time in the distal GI. Once the nanoparticle is optimized, the potential of SCFA-conjugated nanocarriers to ameliorate EAE progression will be measured by comparing EAE mice and healthy controls, using the same outcome measures. This will allow us to select which polymer-conjugated SCFAs to incorporate into the optimized nanocarriers. We believe the SCFAs will inhibit proinflammatory macrophage activation, induce anti-inflammatory Treg cells, and promote demyelination and axonal degeneration to reduce the effects of MS in mice. In humans, delivering these nanoparticles as a drug will serve as a much more efficient means of treating MS when compared to the current treatment procedures.

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

Ewing sarcoma (EwS) is the second most common bone cancer in children and young adults, which also arises in soft tissue, characterized by the fusion of FET and ETS genes, with EWS::FLI1 being the most common fusion protein. Menin, a protein encoded by the MEN1 gene, is a scaffolding protein that can activate or repress transcription depending on its binding partners. Menin plays an oncogenic role in EwS, but the precise mechanism remains to be elucidated. To investigate the role of menin in tumorigenesis, we first examined whether menin directly modulates the protein and transcript levels of the driver of EwS, EWS::FLI1. We generated whole cell extracts from MEN1-knockout (KO) and control cell lines and used western blotting to determine the EWS::FLI1 protein levels. These results showed that the loss of menin led to an increase in EWS::FLI1 for some of the MEN1-KO cell lines. RNA was purified from the MEN1-KO and control cell lines to assess the levels of EWS::FLI1 mRNA by RT-qPCR to determine if menin modulates EWS::FLI1 transcript levels. We are currently examining menin’s role in modulating essential histone modifications, specifically H3K4me3 at promoters and H3K27Ac at enhancers since menin modulates the activity of histone-modifying enzymes. We generated nuclear extracts under high salt conditions to extract histones from chromatin in MEN1-KO and control cell lines. To assess the success of the fractionation of the nuclear and cytoplasmic proteins, we conducted a western blot analysis to confirm the histones were extracted exclusively in the nuclear fraction. The levels of H3K4me3 were lower in some MEN1-KO cell lines, suggesting menin may have a role in epigenetic regulation in EwS. By understanding menin’s role in modulating EWS::FLI1 levels and global histone modifications, we may identify potential drug targets for future cancer treatments.

 Alzheimer’s Disease (AD) has well-known brain alterations such as Tau protein build-up, beta-amyloid plaques, and neuronal cell death, yet the role of the brain’s microvasculature on the progression of this neurological condition has not been fully uncovered. My research examines changes in the microvasculature density, length, and function during normal aging using a well-established aging model in Brown Norway rats. This study contributes to the pantheon of previous microvascular research and forwards the field toward understanding AD development from another perspective. My hypothesis is that the density and length of these microvasculature are decreased in areas associated with learning and memory (i.e., the hippocampus and parietal cortex) before the development of AD symptoms and worsen as the disease progresses. To test this hypothesis, first in normal aging, 3 experimental groups of Brown Norway rats are employed: (n=6) young rats at 5-6 months, (n=6) middle-aged rats at 15 months, and (n=6) old rats at 20-24 months. Sagittal slices of the right hemisphere were fluorescently marked for their microvasculature, astrocytes, and cellular nuclei. The ImageJ analytical program was used to compartmentalize the areas of the dentate gyrus, CA1, CA2, and CA3 along with the parietal cortex into 900 x 900-pixel boxes for examination. The preliminary results show that the density of microvasculature within the 3 age groups were consistent while the distribution of the vessel lengths had more variability. The two leading postulates are increased tortuosity with increased age and/or rarefaction, where the microvasculature experience shortening with increased age. Further analysis is needed to examine this distribution among the 3 age groups.

Cell co-culture systems are used to study intracellular interactions by culturing distinct cell-type populations within a shared environment. This in vitro method is more representative of the highly complex and diverse processes that occur in organisms, allowing accurate insight into mechanisms of cell signaling pathways, disease, drug interactions, etc. Existing designs can be two- or three-dimensional, with or without cell-cell contact, and use systems like microfluidics, solid supports, or transwells to control contact. Methods that physically partition individual cell-type populations often allow soluble factor transmission by using permeable material or flooding the compartments so the solvent is shared. However, this is less representative of the human body, where physical partitions do not divide different cell types. Thus, there is a need for a co-culture system with a partition allowing initial separation, that can later be removed to allow interaction without a physical barrier. We are developing this system by utilizing open microfluidic gel patterning techniques to test if a removable partition can be formed with enzyme-degradable polyethylene glycol (PEG). I first use computer-aided design to engineer a rail scaffold outlining two compartments, and fabricate these devices using 3D printing. I pipette PEG into an inlet in the rail, flowing along the scaffold channel due to spontaneous capillary flow and patterning the insert. The PEG polymerizes to form the insert with two distinct cell chambers on the well’s bottom surface, and the cells are seeded into their corresponding compartments. After the cell culture period is complete, sortase (SrtA) is added to completely degrade the PEG insert, allowing the cell populations to interact. We expect the PEG inserts to polymerize similarly to agarose, and leave no residue in the well once degraded. Future work will include utilization of this device for experiments using functionalized beads to monitor soluble factor signaling in co-cultures.

Neurogenic bladder is a common condition associated with traumatic spinal cord injuries (SCIs), which results in inhibited detrusor function, bladder-sphincter dyssynergia, and scarring of the bladder walls and muscle. Care for neurogenic bladder is aimed at reducing abnormally high pressures, which left untreated lead to hypertrophy and tissue fibrosis of the bladder wall, as well as upper urinary tract complications. Current treatments target the neurotransmitter release of acetylcholine, utilizing anticholinergic drugs to counter the overactive bladder. However, these drugs can have negative/deleterious side effects, and have broad symptoms influencing unintended targets around the body. Targeted chemodenervation that uses Botulinum toxin (Botox) to interfere with nerve conduction is often reserved as a second line of defense to treat neurogenic bladder. Unfortunately, this late provision concedes irreversible damage to the detrusor muscle. We hypothesize that administering early chemodenervation can prevent the development of neurogenic bladder, improve bladder compliance post SCI, and increase the overall quality of life of SCI affected patients. Using a rat model, the Khaing lab administers a controlled contusion injury to the T8/T9 vertebrae, simulating a spinal cord injury in humans. The recovery of the rats is tracked with behavioral observations, cystometry data collection, and histological stains. My team and I are working to determine the effective therapeutic time post SCI for Botox injections, and the optimal doses for treatment. Our results thus far support that acute chemodenervation with Botox reduces bladder overactivity, and bladder wall thickness.

Therapeutic Drug Monitoring (TDM) serves a critical role in optimizing the effectiveness and safety of dapivirine (DPV) vaginal rings as an HIV prevention tool, ultimately leading to improved health outcomes for individuals at risk of HIV infection. Liquid chromatography-tandem mass spectrometry (LC/MS) is a commonly used method for HIV TDM, however, its limited availability leads to delayed results, high cost, and limited utility in clinical practice. The REverse TRanscrIptase Termination (RESTRICT) assay is a rapid and inexpensive test for TDM. DPV has low solubility in aqueous solutions due to its hydrophobic properties. Organic solvents like isopropyl alcohol (IPA), acetonitrile (ACN), and dimethylsulfoxide (DMSO) are typically used for extracting DPV from returned vaginal rings. However, organic solvents often interfere with the performance of enzymatic assays like RESTRICT. In this study, we investigated the compatibility of organic solvents used for DPV extraction with the RESTRICT assays. We tested mixtures of IPA, ACN, and DMSO at varying concentrations of solvent in water. After performing a preliminary experiment with 25%, 50%, and 75% concentrations of IPA in water using RESTRICT, we found similar fluorescence readouts between the different concentrations indicating that IPA and RESTRICT are compatible. The solvent that results in the smallest decrease in signal intensity compared to solvent-free assays will be selected. In the future, we will extract DPV from new and returned vaginal rings and measure drug levels using the RESTRICT assay benchmarking against a conventional laboratory technique like Raman spectrometry. This work represents a first step towards developing a user-friendly test for measuring DPV levels at the point of need.

The backsplash galaxies of the Milky Way are galaxies that have once entered the virial radius of the Milky Way but reside outside of which today. As a backsplash galaxy enters the Milky Way, its gravitational interaction with the Milky Way causes its star forming material to be stripped away and causes it to appear to be more diffused and older. The evolution and properties of a backsplash galaxy depend significantly on the properties of its dark matter halo as it makes up the majority of its mass. In my research, I use cosmological simulations of Cold Dark Matter (CDM) and Self-Interacting Dark Matter (SIDM) of Near-Milky Way halos done by my mentors and their colleagues to identify and analyze the properties of backsplash halos during their evolution and compare the results across the two dark matter models. Significant differences between the results from the CDM and the SIDM models are anticipated, with the major difference caused by the interactions between the SIDM particles allowing the exchange of energy and momentum between particles, causing the energy to transfer between regions of the halo, resulting in altered density profiles which influences the tidal evolution history. After the analysis of both models are completed, the results can be compared and matched to observational data of the candidates of backsplash galaxies of the Milky Way, and conclude in each model’s ability to make accurate predictions. This research contributes to the ongoing investigation of the properties of dark matter particles and the analysis of the evolution of backsplash galaxies.

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

Smartphone use among adolescents has dramatically increased in the past decade, with adolescents allocating more time inside on their screens and less time outside in nature. Given these shifts in behaviors, there has been a rise in concerns about the impact of smartphones on adolescents’ mental health. Studies on nature exposure have found that spending time in nature promotes human well-being; however, a limited body of research exists exploring how smartphone use impacts our ability to experience these physical and psychological benefits of nature exposure. To address this gap in the literature, we conducted a between-subjects experiment with college students at the University of Washington (N ~ 40) randomly allocated to one of two conditions to spend 20 minutes in nature: a smartphone condition and a no-smartphone condition. Participants self-reported on positive and negative affect and rumination before and after their experience in nature. After completing these scales, participants reported on their experience of Presence, a state of being in which the mind is highly aware but without active thought, by self-reporting on a recently validated 14-point scale and writing about it for further analysis using an interaction pattern approach. I anticipated that participants who feel more attached to their smartphones spend more time using them in nature and, in turn, are less likely to experience the emotional benefits of nature. If the findings reflect this, future research should explore how smartphones impact adolescents’ mental health and the extent to which smartphone-free time spent outside in nature can improve their well-being.

TBC1(Tre2/Bub2/Cdc16) Domain-Containing Kinase (TBCK) is a pseudokinase with proposed involvement in the endocytic pathway. Kinases are proteins that can post-translationally modify other proteins through the addition of inorganic phosphate from ATP to serine/threonine/tyrosine residues. TBCK, being a pseudokinase, lacks critical residues that allow ATP binding and, therefore, cannot catabolize ATP. Pseudokinases, while catalytically inactive, have been shown to have protein scaffolding properties as well as modulate the activity of other kinases. Whether pseudokinase TBCK plays a role in any of those functions has yet to be discovered. Via the TBC1 domain, TBCK interacts with Rab proteins, a class of membrane-binding proteins involved in multiple cellular pathways that coordinate intracellular vesicle transport with GTP active and GDP inactive states. TBCK functions as a Rab GAP(GTP-hydrolysis activating protein), hydrolyzing Rab bound GTP and leaving an inactive GDP-bound Rab. Mutations in TBCK have been found to be clinically associated with a rare neurological disorder, TBCK syndrome, characterized by delayed development, intellectual disorder, and hypotonia. The interactors and Rab substrates of TBCK are under researched and still poorly understood; we aim to illuminate those interactions through immunoprecipitation (IP) and mass spectrometry. Early attempts at this goal involved co-transfection of various Rab protein targets with TBCK WT and TBCK R511H (a TBC1 inactive mutant) in HEK 293T cells and subsequent co-IP, enriching for TBCK and interacting Rab proteins. These preliminary results, in combination with live imaging and immunofluorescence of TBCK and its mutants with Rab proteins and other membrane markers, proved inconclusive. Therefore, we are now performing crosslinking immunoprecipitation mass spectrometry to allow the identification weakly interacting protein complexes through mass spectrometry. These experiments will provide insight into the fundamental biology underlying TBCK’s role in neurodevelopment and how its dysfunction contributes to disease states.

Cellular retinoic acid binding proteins (CRABP) are soluble proteins that play an important role in binding to retinoids, primarily all-trans-retinoic acid (atRA). RA isomers and their metabolites play a vital role in embryonic development and the central nervous system. CRABP binding regulates retinoid signaling. Retinoid binding affinity to CRABP is described by the equilibrium dissociation constant K_d. CRABP1 interacts with atRA metabolizing enzymes, where relative concentrations of atRA and CRABP1 determine the rate of atRA metabolism. Therefore, measurements of the accurate K_d for endogenous retinoids to CRABP1 are an important aspect of understanding retinoid signaling during development. My goal was to determine the binding affinities of various endogenous retinoids to CRABP1, using a modern fluorescence spectrometric assay and lower CRABP1 concentrations compared to historical methods. The Norris equation was fit to the data to determine the K_d from the decrease of peak tryptophan fluorescence as retinoid bound to CRABP1. The calculated K_d was <1 nM for atRA, 3-10 nM for 4-oxo-atRA, 50-100 nM for 9-cis RA, and near 1 uM for 4-oxo-13-cis and 13-cis RA. When the K_d is much lower than CRABP1 concentration, binding of the retinoid to CRABP1 results in depletion of the retinoid in solution and hence an overestimation of the K_d value. As this work uses lower CRABP1 concentrations than previous studies, the predicted K_d estimates for retinoids that tightly bind to CRABP1 would be lower and more accurate. This is supported by the data. While the K_d of atRA is similar to its endogenous concentration in human plasma, the K_d of the other retinoids tested are much higher than their concentrations, suggesting that small fractions of these retinoids are bound to CRABP1 in vivo. Knowing these K_d values may give insight into how altered CRABP1 concentrations impact development through their modulation of RA concentration.

As computing continues to evolve, there are few fields with more extensive and revolutionary prospects than quantum computing. Advanced quantum technologies have the potential to see into a world that classical computing cannot, enabling more advanced encryption methods, precision atomic interaction modeling, and molecular simulations for pharmaceutical drug research. Students should be exposed to modern quantum technologies, but providing students with hands-on experience is challenging at the undergraduate level. Our project aims to remove that barrier. Ion traps are the fundamental mechanisms for information storage in trapped ion quantum computers, so we designed and built a scaled-up version of one of these traps for use in a classroom setting. Our trap, a linear quadrupole trap, is based around 4 conductive electrodes that utilize alternating current (AC) to confine charged particles to a linear trapping axis, bounded on either end by 2 direct current (DC) rods. The trap features a 3-D printed polylactic acid (PLA) base and lid with a locking mechanism to prevent undesired air movement within the trapping region. We implemented a high-voltage lower DC plate in combination with a grounded upper plate to emulate an infinite parallel plate capacitor when the distance between the two is minimized and the plate area is maximized, allowing for additional vertical manipulation of the particles. To guarantee student safety, all high-voltage components remain covered while trapping, and each conductive element has undergone distance and breakdown voltage calculations to ensure that no electrical arcing can occur. As a result, undergraduate students in the lab are able to manipulate different aspects of the electric field geometry to observe micromotion, Coulomb Crystals, secular frequencies, and determine the charge-to-mass ratios of different charged particles such as lycopodium moss spores (25µm) or polyethylene microspheres (50µm).

The expected launch of the Nancy Grace Roman Space Telescope (Roman), a next-generation space-based infrared observatory, will soon allow us to observe fields in minutes that would previously have taken months to cover. As such, it will advance our knowledge of galactic structure and evolution at a rapid rate. To better leverage the influx of science that will come out of the launch and commissioning of Roman, we are developing a pipeline that simulates observational images taken by Roman and then performs photometry on the images. As a first step, we are testing methods for recovering dwarf galaxies from photometry catalogs that contain both a dwarf and a surrounding stellar halo. In order to produce mock Roman observations, we use the Space Telescope Science Institute's Space Telescope Image Product Simulator (STScI-STIPS) software tools, which are able to add background galaxies, realistic background levels, and noise along with source catalogs to produce simulated images. Our early testing uses input catalogs designed to simulate typical dwarf galaxy characteristics added to stellar catalogs generated from numerical simulations that mimic the nearby spiral galaxy M81. The ultimate goal of this pipeline software is to determine the observational strategy to resolve structures in extended stellar halos of nearby galaxies. Such measurements would allow us to distinguish between formation and evolution scenarios for these halos. This work is part of the Roman Infrared Nearby Galaxies Survey (RINGS), a large Roman Wide-Field Science (WFS) program funded by NASA under grant 80NSSC24K0084.

The poster highlights our study of shared pantry operators in Washington State. Shared pantries are generally small, unattended, open-access food-sharing areas that operate on a "take what you need, leave what you can" concept, supplied by donations from members of the local community. Professor Emily Hovis and I developed and deployed an operator survey to examine the differences between pantry operational structures. This research was prompted by a pattern we noticed during previous fieldwork: many pantries located at private residences were no longer active. I was involved in developing the survey, analyzing the data, and creating the poster. Over 300 current or former share pantry operators were contacted to participate in an online survey focused on operator demographics and operations. We received 62 survey responses in Autumn 2023. The majority of survey respondents (95.2%) identified their pantry is located outdoors, open 24/7, and accepts community drop-off food donations. More than half of the pantries are operated by individuals. Most of the organizations or groups operating the pantries were churches, schools, university groups, neighbors, and advocacy services. The majority (87%) of the pantries do not have a fridge/freezer section. More than half of the operators visit the pantry site more than four times a week. Only half of the respondents indicated that they provided guidelines on appropriate/safe donations. This study not only emphasizes the critical role of shared pantries in community solidarity but also raises an important future research question: How could the development and implementation of standardized guidelines and support systems impact the sustainability and effectiveness of shared pantries, particularly in enhancing community participation, donation quality, and pantry longevity?

Naive B-cells in a primary follicle upon antigen exposure, start to proliferate and form a germinal center (GC) that also has other cells such as T-cell subsets, histiocytes, and follicular dendritic cells. The proliferating GC cells or centroblasts mainly occupy the 'dark zone' of the GC. Centroblasts further differentiate into centrocytes that are predominantly seen in the 'light zone' of the GC, and some of the selected 'centrocytes' further differentiate into memory B-cells or plasma cells. We set out to identify ideal markers to distinguish centroblasts and centrocytes and investigate them as biomarkers of disease classification, grading, and subtyping of GC B-cell lymphomas. We interrogated publicly available in-situ mRNA expression data from reactive lymph nodes using GeoMx Digital Spatial Profiler (PMID: 33083730), single-cell transcriptomic data from reactive lymph nodes and follicular lymphoma (FL) grade 1-2 and grade 3A (PMID: 35687817). Several markers were selected for single-antibody immunohistochemistry and multiplex-immunohistochemistry experiments. We focused on AID, CXCR4, Ki67, and PHH3 as markers for centroblasts and CD40 as a marker for centrocytes and tested them on tissue microarrays (TMA) with cores of 15 low-grade FL, eight high-grade FL, and 14 diffuse large B-cell lymphomas (DLBCL; 8 GCB type & 4 non-GCB). After analyzing the expression of the biomarkers on HALOlink with algorithms developed in the laboratory, we observed a significantly higher proportion of cells in high-grade FL expressing AID and Ki67 than in low-grade FL. The other markers showed no statistically significant difference in the percentage of cells expressed between high-grade FL and low-grade FL. Evaluating the proportion of cells expressing AID would help in objectively grading FL samples, but the impact of AID-assisted grading of FL on patient outcomes must be further evaluated.

Age-related macular degeneration (AMD) is an acquired degeneration of the retina characterized by the presence of lipid-rich deposits, or drusen, underneath the retinal pigment epithelium (RPE). Development of drusen has been linked to degradation of extracellular matrices and aberrant RPE lipid metabolism. Mutations in tissue inhibitor of metalloproteinase 3 (TIMP3), involved in extracellular matrix (ECM) degradation, have been associated with Sorsby Fundus Dystrophy (SFD), an autosomal dominant inherited disease phenotypically similar to AMD. SFD and AMD share clinical features, such as the presence of drusen, geographic atrophy, and choroidal neovascularization. The aim of this project is to evaluate the hypothesis that increased ECM degradation results in reprograming of SFD RPE metabolism towards increased branched chain amino acid (BCAA) oxidation, resulting in lipid synthesis and deposition. We found that SFD induced pluripotent stem cells (iPSC)-RPE have increased apolipoprotein E deposits, and may have increased lipid metabolism. SFD RPE were found to have decreased levels of FABP7, a lipid binding protein that regulates lipid metabolism by increasing fatty acid oxidation, by proteomics and confirmed by Western blot. SFD RPE cells show increased BCAA consumption and upregulated expression of branched chain amino acid transaminase 1 (BCAT1), an enzyme that catalyzes the animation of BCAAs. Control RPE were treated with BCAT1 inhibitors, BCATc Inhibitor 2 and gabapentin. Treatment of RPE with 50 µM of BCATc Inhibitor 2 resulted in a greater than two-fold decrease in BCAA consumption at 48 hours, indicating effective inhibition of BCAT1. Results from this study will help determine whether enhanced BCAA oxidation results in activation of increased lipid synthesis and lipid deposits in SFD iPSC RPE.

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

 Thousand and one amino acid kinase 1 (TAOK1) is a serine/threonine kinase expressed abundantly in neurons in the mammalian brain. Mutations in TAOK1 are closely associated with both autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD). Studies have shown that TAOK1 is a component of the Hippo pathway, which modulates cell proliferation, apoptosis, and differentiation. Loss of TAOK1 in mice causes decreased neuronal migration and defects in dendritic development, however, mechanisms that lead to neuropathology in patients with TAOK1 mutations are not known. We focused our investigation on a patient mutation in TAOK1, S111F, which clinically manifests as intellectual disability, developmental delay, and macrocephaly. We used induced pluripotent stem cell (iPSC) derived 3D cortical brain organoids with heterozygous and homozygous S111F mutation as a model system in order to examine phenotypical changes in early brain development. We also grew 2D cultures of neural progenitor cells (NPCs), and I used Fiji image analyses to track proliferation rates, which were significantly increased in the mutant cells compared to isogenic control. Western blots were used to observe the phosphorylation states of proteins in the Hippo pathway between wild-type and mutation-carrying cell lines. These experiments show that TAOK1 kinase-dead mutation led to shut down of the Hippo pathway, as evidenced by nuclear accumulation of Yap-Taz proteins. In a parallel research direction, the Yadav lab is interested in solving the structure of TAOK1 membrane binding region. To this end, I am using E. coli bacteria to purify TAOK1 protein using a bacterial expression vector, and after protein purification, the purified protein will be used in biochemical and structural studies. These studies will provide mechanistic insight into TAOK1 biology and how patient mutations in TAOK1 contribute to neurodevelopmental disorders.

Geoparsing, the task of assigning coordinates to locations extracted from text, enables us to better understand how places change over time through historical documents. The task has seen many advancements with the growth of neural machine learning methods, but these models require large amounts of training data. In the history domain, many geoparsing corpora are from newspaper collections because of the availability of labeled data. However, not all historical research benefits from rich data availability, so we seek to understand and improve existing geoparsing methods for small corpora. In this project, I focus on the Svoboda Diaries, a collection of personal diaries written by British steamship purser Joseph Svoboda during the late 19th century in Ottoman Iraq. How do geoparsing methods perform in the Svoboda Diaries, a small historical text corpus written primarily in English, but also including text in Arabic, Italian, and French? We develop a map-based generate-and-rank approach with clustering of context words surrounding each location in the text. The location data is retrieved from two knowledge bases: GeoNames, a gazetteer with over 25 million geographical names, and Wikidata, a free and collaboratively edited database. We first extract the locations from the text using a natural language processing method called named entity recognition. Since modern location names may differ from historical spellings, we then generate alternate names for each identified location through translation and hand-crafted Romanization rules, such as “Basra” for “Basreh”, and query knowledge bases to retrieve coordinate data associated with these names. We find that our method to augment transliterated Arabic names with alternate names helps with gazetteer lookups, suggesting potential for augmenting data in other small corpora tasks. Our research with the Svoboda Diaries expands on existing geoparsing methods and can apply to other digital humanities projects facing the small corpora challenge.

Plant root signaling is a complex process. An important growth hormone that is hypothesized to regulate this complexity is Auxin; this hormone is known to oscillate in a region of the root that initiates lateral root development. Auxin oscillations are established by auxin exporters called PIN proteins. However, the regulatory mechanism that determines PIN expression and distribution is unknown. In this project, we built an agent-based model in order to characterize expected auxin dynamics and investigate hypothesized PIN regulatory signaling cascades. In the model, each cell is an individual agent that follows a given rule set. Cells independently calculate their growth and the amount their circulatory components change as the root develops. I analyzed previous models and extracted parameters to determine the necessary spatial and circulatory conditions that initiate our model. I constructed the circulation module to calculate the concentration of circulating components and updates information stored in circulation data structures to track how the values have changed after each round simulation. I also implemented the input and output modules for initialization and results export respectively. The model is implemented in Python and was built following test-driven development to ensure all class functions and modules are tested using pre-defined conditions. Preliminary simulation results revealed an oscillatory change in auxin concentration. This agent-based model provides a means to explore the auxin circulation dynamics and interrogate the viability of hypothesized mechanisms that regulate the lateral root development by applying different rule sets.

Adipose tissue, also known as body fat, is vital in storing energy. It is composed of adipocytes and present in different depots. In this study we focused on omental (OM) adipose tissue, which is found between organs near the stomach, and subcutaneous (SC) adipose tissue, which is found under the skin. Functional differences have been observed among adipose depots. SC adipose tissue is responsible for insulation while OM adipose tissue has endocrine functions. OM adipocytes have been observed to be smaller and more variable in size compared to SC adipocytes in individuals with obesity. I hypothesized that the size of both OM and SC adipocytes is associated with increasing BMI. I tested this hypothesis using SC and OM adipose tissue biopsies collected during elective surgeries from metabolically healthy participants (20 females, 11 males) with a range of ages (25-65 years) and BMIs (21-56). Afterwards, the tissues were fixed and stained with H&E. I drew 2-5 squares per slide and counted the number of adipocytes within each square. The size difference between OM and SC adipocytes was tested using a Wilcoxon signed-rank test and a significant difference (p=0.004) was observed. A correlation between BMI and the size of OM (p = 0.008) or SC (p = 0.009) adipocytes was detected with weighted linear regressions. Sex was not observed to be a significant covariate. These findings expand on prior data by including lean individuals, and patients with obesity who are otherwise metabolically healthy. The results show there is a clear difference in the size of adipocytes. The adipocyte size in both depots correlated with BMI. This data shows that progressive obesity and adipose tissue enlargement is due to the enlargement of the adipocytes rather than an increase in the number of adipocytes in both OM and SC depots.